Comparative study of sea ice dynamics simulations with a Maxwell elasto-brittle rheology and the elastic-viscous-plastic rheology in NEMO-LIM3

NASA Astrophysics Data System (ADS)

Raulier, Jonathan; Dansereau, Véronique; Fichefet, Thierry; Legat, Vincent; Weiss, Jérôme

2017-04-01

Sea ice is a highly dynamical environment characterized by a dense mesh of fractures or leads, constantly opening and closing over short time scales. This characteristic geomorphology is linked to the existence of linear kinematic features, which consist of quasi-linear patterns emerging from the observed strain rate field of sea ice. Standard rheologies used in most state-of-the-art sea ice models, like the well-known elastic-viscous-plastic rheology, are thought to misrepresent those linear kinematic features and the observed statistical distribution of deformation rates. Dedicated rheologies built to catch the processes known to be at the origin of the formation of leads are developed but still need evaluations on the global scale. One of them, based on a Maxwell elasto-brittle formulation, is being integrated in the NEMO-LIM3 global ocean-sea ice model (www.nemo-ocean.eu; www.elic.ucl.ac.be/lim). In the present study, we compare the results of the sea ice model LIM3 obtained with two different rheologies: the elastic-viscous-plastic rheology commonly used in LIM3 and a Maxwell elasto-brittle rheology. This comparison is focused on the statistical characteristics of the simulated deformation rate and on the ability of the model to reproduce the existence of leads within the ice pack. The impact of the lead representation on fluxes between ice, atmosphere and ocean is also assessed.

Estimating the Numerical Diapycnal Mixing in the GO5.0 Ocean Model

NASA Astrophysics Data System (ADS)

Megann, A.; Nurser, G.

2014-12-01

Constant-depth (or "z-coordinate") ocean models such as MOM4 and NEMO have become the de facto workhorse in climate applications, and have attained a mature stage in their development and are well understood. A generic shortcoming of this model type, however, is a tendency for the advection scheme to produce unphysical numerical diapycnal mixing, which in some cases may exceed the explicitly parameterised mixing based on observed physical processes, and this is likely to have effects on the long-timescale evolution of the simulated climate system. Despite this, few quantitative estimations have been made of the magnitude of the effective diapycnal diffusivity due to numerical mixing in these models. GO5.0 is the latest ocean model configuration developed jointly by the UK Met Office and the National Oceanography Centre (Megann et al, 2014), and forms part of the GC1 and GC2 climate models. It uses version 3.4 of the NEMO model, on the ORCA025 ¼° global tripolar grid. We describe various approaches to quantifying the numerical diapycnal mixing in this model, and present results from analysis of the GO5.0 model based on the isopycnal watermass analysis of Lee et al (2002) that indicate that numerical mixing does indeed form a significant component of the watermass transformation in the ocean interior.

The NeMO Explorer Web Site: Interactive Exploration of a Recent Submarine Eruption and Hydrothermal Vents, Axial Volcano, Juan de Fuca Ridge

NASA Astrophysics Data System (ADS)

Weiland, C.; Chadwick, W. W.; Embley, R. W.

2001-12-01

To help visualize the submarine volcanic landscape at NOAA's New Millennium Observatory (NeMO), we have created the NeMO Explorer web site: http://www.pmel.noaa.gov/vents/nemo/explorer.html. This web site takes visitors a mile down beneath the ocean surface to explore Axial Seamount, an active submarine volcano 300 miles off the Oregon coast. We use virtual reality to put visitors in a photorealistic 3-D model of the seafloor that lets them view hydrothermal vents and fresh lava flows as if they were really on the seafloor. At each of six virtual sites there is an animated tour and a 360o panorama in which users can view the volcanic landscape and see biological communities within a spatially accurate context. From the six sites there are hyperlinks to 50 video clips taken by a remotely operated vehicle. Each virtual site concentrates on a different topic, including the dynamics of the 1998 eruption at Axial volcano (Rumbleometer), high-temperature hydrothermal vents (CASM and ASHES), diffuse hydrothermal venting (Marker33), subsurface microbial blooms (The Pit), and the boundary between old and new lavas (Castle vent). In addition to exploring the region geographically, visitors can also explore the web site via geological concepts. The concepts gallery lets you quickly find information about mid-ocean ridges, hydrothermal vents, vent fauna, lava morphology, and more. Of particular interest is an animation of the January 1998 eruption, which shows the rapid inflation (by over 3 m) and draining of the sheet flow. For more info see Fox et al., Nature, v.412, p.727, 2001. This project was funded by NOAA's High Performance Computing and Communication (HPCC) and Vents Programs. Our goal is to present a representative portion of the vast collection of NOAA's multimedia imagery to the public in a way that is easy to use and understand. These data are particularly challenging to present because of their high data rates and low contextual information. The 3-D models create effective context and new video technology allows us to present good quality video at lower data rates. Related curriculum materials for middle- and high-school students are also available from the NeMO web site at http://www.pmel.noaa.gov/vents/nemo/education.html. >http://www.pmel.noaa.gov/vents/nemo/explorer.html

The Met Office Coupled Atmosphere/Land/Ocean/Sea-Ice Data Assimilation System

NASA Astrophysics Data System (ADS)

Lea, Daniel; Mirouze, Isabelle; Martin, Matthew; Hines, Adrian; Guiavarch, Catherine; Shelly, Ann

2014-05-01

The Met Office has developed a weakly-coupled data assimilation (DA) system using the global coupled model HADGEM3 (Hadley Centre Global Environment Model, version 3). This model combines the atmospheric model UM (Unified Model) at 60 km horizontal resolution on 85 vertical levels, the ocean model NEMO (Nucleus for European Modeling of the Ocean) at 25 km (at the equator) horizontal resolution on 75 vertical levels, and the sea-ice model CICE at the same resolution as NEMO. The atmosphere and the ocean/sea-ice fields are coupled every 1-hour using the OASIS coupler. The coupled model is corrected using two separate 6-hour window data assimilation systems: a 4D-Var for the atmosphere with associated soil moisture content nudging and snow analysis schemes on the one hand, and a 3D-Var FGAT for the ocean and sea-ice on the other hand. The background information in the DA systems comes from a previous 6-hour forecast of the coupled model. To show the impact of coupled DA, one-month experiments have been carried out, including 1) a full atmosphere/land/ocean/sea-ice coupled DA run, 2) an atmosphere-only run forced by OSTIA SSTs and sea-ice with atmosphere and land DA, and 3) an ocean-only run forced by atmospheric fields from run 2 with ocean and sea-ice DA. In addition, 5-day forecast runs, started twice a day, have been produced from initial conditions generated by either run 1 or a combination of runs 2 and 3. The different results have been compared to each other and, whenever possible, to other references such as the Met Office atmosphere and ocean operational analyses or the OSTIA data. These all show the coupled DA system functioning well. Evidence of imbalances and initialisation shocks has also been looked for.

Implementation of the NEMO model for estimating the spread of leakage from chemical munitions in the Baltic Sea - the first approach

NASA Astrophysics Data System (ADS)

Andrzejewski, Jan

2017-04-01

After the Second World War, during the Potsdam Conference a decision about demilitarization of Germany was made, and as a consequence, ammunition including chemical warfare agents (CWA) was dumped into the basins of the Baltic Sea. This type of weapon was stored in metal barrels that were under strong influence of electrochemical oxidation, also known as corrosion. Several tens years later, scientists were wondering what consequences for marine ecosystem could a leakage from this weapon bring. Although over 70 years passed since the Second World War, the influence of potential leakage of the CWA has not been properly estimated. Thus, the main goal of this work is to estimate dangerous area caused by potential leakage using the NEMO (Nucleus for European Modelling of the Ocean) ocean model. The NEMO ocean model is developed by the European Consortium including research institutes from France, England and Italy. The first step of this work is to implement the model for the area of the Baltic Sea. It requires generation of horizontal and vertical grid, bathymetry, atmospheric forces and lateral boundary conditions. Implemented model will have to be checked - it means it will have to pass a validation process. The Baltic Sea is one of the best measured sea in the World - as a consequence a lot of data are freely available for researchers. After validation and tuning up the model, implementation of passive tracer is planned. Passive tracer is the prognostic variable that could represent concentration of potential leakage and does not have influence on the density of the model. Based on distribution of the passive tracer, dangerous areas in the locations of dumpsites will be assessed. The research work was funded by the European Union (European Regional Development Fund) under the Interreg Baltic Sea Region Programme 2014-2020, project #R013 DAIMON (Decision Aid for Marine Munitions).

Estimating the numerical diapycnal mixing in an eddy-permitting ocean model

NASA Astrophysics Data System (ADS)

Megann, Alex

2018-01-01

Constant-depth (or "z-coordinate") ocean models such as MOM4 and NEMO have become the de facto workhorse in climate applications, having attained a mature stage in their development and are well understood. A generic shortcoming of this model type, however, is a tendency for the advection scheme to produce unphysical numerical diapycnal mixing, which in some cases may exceed the explicitly parameterised mixing based on observed physical processes, and this is likely to have effects on the long-timescale evolution of the simulated climate system. Despite this, few quantitative estimates have been made of the typical magnitude of the effective diapycnal diffusivity due to numerical mixing in these models. GO5.0 is a recent ocean model configuration developed jointly by the UK Met Office and the National Oceanography Centre. It forms the ocean component of the GC2 climate model, and is closely related to the ocean component of the UKESM1 Earth System Model, the UK's contribution to the CMIP6 model intercomparison. GO5.0 uses version 3.4 of the NEMO model, on the ORCA025 global tripolar grid. An approach to quantifying the numerical diapycnal mixing in this model, based on the isopycnal watermass analysis of Lee et al. (2002), is described, and the estimates thereby obtained of the effective diapycnal diffusivity in GO5.0 are compared with the values of the explicit diffusivity used by the model. It is shown that the effective mixing in this model configuration is up to an order of magnitude higher than the explicit mixing in much of the ocean interior, implying that mixing in the model below the mixed layer is largely dominated by numerical mixing. This is likely to have adverse consequences for the representation of heat uptake in climate models intended for decadal climate projections, and in particular is highly relevant to the interpretation of the CMIP6 class of climate models, many of which use constant-depth ocean models at ¼° resolution

Simulation of bombe radiocarbon transient in the Mediterranean Sea using a high-resolution regional model.

NASA Astrophysics Data System (ADS)

Ayache, Mohamed; Dutay, Jean-claude; Mouchet, Anne; Tisnérat-Laborde, Nadine; Houma-Bachari, Fouzia; Louanchi, Ferial; jean-baptiste, Philippe

2016-04-01

The radiocarbon isotope of carbon "14C", which a half-life of 5730 years, is continually formed naturally in the atmosphere by the neutron bombardment of 14N atoms. However, in the 1950s and early1960s, the atmospheric testing of thermonuclear weapons added a large amount of 14C into the atmosphere. The gradual infusion and spread of this "bomb" 14C through the oceans has provided a unique opportunity to gain insight into the specific rates characterizing the carbon cycle and ocean ventilations on such timescales. This numerical study provides, for the first time in the Mediterranean Sea, a simulation of the anthropogenic 14C invasion covers a 70-years period spanning the entire 14C generated by the bomb test, by using a high resolution regional model NEMO-MED12 (1/12° of horizontal resolution). This distribution and evolution of Δ14C of model is compared with recent high resolution 14C measurements obtained from surface water corals (Tisnérat-Laborde et al, 2013). In addition to providing constraints on the air-sea transfer of 14C, our work provides information on the thermohaline circulation and the ventilation of the deep waters to constrain the degree to which the NEMO-MED12 can reproduce correctly the main hydrographic features of the Mediterranean Sea circulation and its variations estimated from corals 14C time series measurements. This study is part of the work carried out to assess the robustness of the NEMO-MED12 model, which will be used to study the evolution of the climate and its effect on the biogeochemical cycles in the Mediterranean Sea, and to improve our ability to predict the future evolution of the Mediterranean Sea under the increasing anthropogenic pressure.

Transport and storage of anthropogenic C across the Greenland-Portugal OVIDE section: Observations vs NEMO-PISCES

NASA Astrophysics Data System (ADS)

Gehlen, M.; Racapé, V.; Zunino, P.; Lherminier, P.; Bopp, L.; Mercier, H.

2016-02-01

Authors: Racapé V., Zunino P., Lherminier P., Bopp L., Mercier, H. and Gehlen M. At present, the ocean takes up approximately one-third of total anthropogenic carbon dioxide emissions. The North Atlantic Ocean is a major sink region for anthropogenic carbon (CANT) and a major contributor to its storage and transport. While evidence is growing that storage and transport are variable on interannual to decadal timescales, their evolution in recent decades and in the future remains uncertain. The variability is thought to be controlled in large part by the intensity of the meridional overturning circulation (MOC), which is suggested to slow down over the 21st century. This study aims to investigate the relationship between CANT transport across the Greenland-Portugal OVIDE section and Cant storage in the North Atlantic basin, as well as their combined evolution over the past 40 years. It relies on the combination of a pluriannual data set and output from the global biogeochemical ocean general circulation model NEMO/PISCES at 1/2° spatial resolution forced by the atmospheric reanalysis DFS4.2. Based on an observation-model comparison, the CANT advective transport is largely underestimated by the model (5 times) compared to the data-based estimate. However, the vertical gradient of CANT in the water column is well reproduced by NEMO/PISCES, supporting the use of a novel indicator computed by Zunino et al. (2014) to express the variability of CANT transport (T°CANT). Following the approach by Zunino et al. (2014), the estimator, T°CANT, was first derived in the model from MOCσ and DELTA-CANT (the vertical gradient of CANT between the upper and the lower branch of MOCσ) averaged over the month of June. Next, the representativity of T°CANT derived from a single sampling event per year was evaluated against estimates computed from annual mean values of MOCσ and DELTA-CANT. After evaluation of the model skill over the period covered by observations, the model is used to extrapolate backward and forward in time. Here the approach was applied to the analyses of the interannual variability of CANT transport and storage over the past 40 years.

Isolating Tracers of Phytoplankton with Allometric Zooplankton (TOPAZ) from Modular Ocean Model (MOM5) to Couple it with a Global Ocean Model

NASA Astrophysics Data System (ADS)

Jung, H. C.; Moon, B. K.; Wie, J.; Park, H. S.; Kim, K. Y.; Lee, J.; Byun, Y. H.

2017-12-01

This research is motivated by a need to develop a new coupled ocean-biogeochemistry model, a key tool for climate projections. The Modular Ocean Model (MOM5) is a global ocean/ice model developed by the Geophysical Fluid Dynamics Laboratory (GFDL) in the US, and it incorporates Tracers of Phytoplankton with Allometric Zooplankton (TOPAZ), which simulates the marine biota associated with carbon cycles. We isolated TOPAZ from MOM5 into a stand-alone version (TOPAZ-SA), and had it receive initial data and ocean physical fields required. Then, its reliability was verified by comparing the simulation results from the TOPAZ-SA with the MOM5/TOPAZ. This stand-alone version of TOPAZ is to be coupled to the Nucleus for European Modelling of the Ocean (NEMO). Here we present the preliminary results. Acknowledgements This research was supported by the project "Research and Development for KMA Weather, Climate, and Earth system Services" (NIMS-2016-3100) of the National Institute of Meteorological Sciences/Korea Meteorological Administration.

Approximate Stokes Drift Profiles and their use in Ocean Modelling

NASA Astrophysics Data System (ADS)

Breivik, O.; Biblot, J.; Janssen, P. A. E. M.

2016-02-01

Deep-water approximations to the Stokes drift velocity profile are explored as alternatives to the monochromatic profile. The alternative profiles investigated rely on the same two quantities required for the monochromatic profile, viz the Stokes transport and the surface Stokes drift velocity. Comparisons with parametric spectra and profiles under wave spectra from the ERA-Interim reanalysis and buoy observations reveal much better agreement than the monochromatic profile even for complex sea states. That the profiles give a closer match and a more correct shear has implications for ocean circulation models since the Coriolis-Stokes force depends on the magnitude and direction of the Stokes drift profile and Langmuir turbulence parameterizations depend sensitively on the shear of the profile. The NEMO general circulation ocean model was recently extended to incorporate the Stokes-Coriolis force along with two other wave-related effects. I will show some results from the coupled atmosphere-wave-ocean ensemble forecast system of ECMWF where these wave effects are now included in the ocean model component.

The development of an advanced vertical discretisation scheme for a regional ocean model

NASA Astrophysics Data System (ADS)

Bruciaferri, Diego; Shapiro, Georgy; Wobus, Fred

2017-04-01

When designing an ocean model, the choice of the vertical coordinate system must be pursued very carefully (Griffies et al., 2000); especially in those regional areas where local multi-scale processes interact with large-scale oceanographic features. Three main vertical coordinates are usually used in ocean modelling, namely the geopotential, terrain-following and isopycnic, but each one presents its own limitations and strengths. In the last decades, much research has been spent to investigate and develop hybrid approaches able to combine the advantages of each vertical coordinate system but minimising their disadvantages. Here we propose the hybrid s-s-z vertical discretisation scheme, an advanced version of the approach used by Shapiro et al. (2013). In our new scheme, the vertical domain is divided into three zones: in the upper and middle zones use s-coordinates while the deeper zone uses z-levels. The s-s-z vertical grid is introduced into the NEMO (Nucleus for European Modelling of the Ocean) model code and we compare the model skill of our new vertical discretisation scheme with the NEMO vertical grid using z-levels with partial steps through a set of idealized numerical experiments for which analytical solutions or theoretical models exist. Modelling results demonstrate that the magnitude of spurious currents arising from the horizontal pressure gradient errors are of the same order (10 ^ -3 m/s ) both with z-partial steps or with s-s-z vertical grids for the conditions favourable for the geopotential grids ( horizontal initial density levels). For a number of more realistic conditions representing a general cyclonic circulation in the sea, the new discretisation scheme produces smaller spurious currents and hence is more accurate than the z-level approach. Moreover, the enhanced capability of the s-s-z scheme to reproduce dense water cascades as compared to the z-partial steps grid is shown. Finally, we show how the new s-s-z grid can be useful to improve lateral sub-grid-physics parametrisation in ocean model with s-levels. References: Griffies, S. M., Boning, C., Bryan, F. O., Chassignet, E. P., Gerdes, R., Hasumi, H., Hirst, A., Treguier, A.-M., and Webb, D., 2000. Developments in Ocean Climate Modelling, Ocean Modelling, 2, 123-192. Shapiro, G., Luneva, M., Pickering, J., and Storkey, D.: The effect of various vertical discretisation schemes and horizontal diffusion parameterisation on the performance of a 3-D ocean model: the Black Sea case study, Ocean Sci., 9, 377-390, doi:10.5194/os-9-377-2013, 2013.

Simulation-based performance analysis of EC-Earth 3.2.0 using Dimemas

NASA Astrophysics Data System (ADS)

Yepes Arbós, Xavier; César Acosta Cobos, Mario; Serradell Maronda, Kim; Sanchez Lorente, Alicia; Doblas Reyes, Francisco Javier

2017-04-01

Earth System Models (ESMs) are complex applications executed in supercomputing facilities due to their high demand on computing resources. However, not all these models perform a good resources usage and the energy efficiency can be well below a minimum acceptable. One example is EC-Earth, a global coupled climate model which integrates different component models to simulate the Earth system. The two main components used in this analysis are IFS as atmospheric model and NEMO as ocean model, both coupled via the OASIS3-MCT coupler. Preliminary results proved that EC-Earth does not have a good computational performance. For example, the scalability of this model using the T255L91 grid with 512 MPI processes for IFS and the ORCA1L75 grid with 128 MPI processes for NEMO achieves 40.3 of speedup. This means that the 81.2% of the resources are wasted. Therefore, it is necessary a performance analysis to find the bottlenecks of the model and thus, determine the most appropriate optimization techniques. Using traces of the model collected with profiling tools such as Extrae, Paraver and Dimemas, allow us to simulate the model behaviour on a configurable parallel platform and extrapolate the impact of hardware changes in the performance of EC-Earth. In this document we propose a state-of-art procedure which makes possible to evaluate the different characteristics of climate models in a very efficient way. Accordingly, the performance of EC-Earth in different scenarios, namely assuming an ideal machine, model sensitivity and limiting model due to coupling has been shown. By simulating these scenarios, we realized that each model has different characteristics. With the ideal machine, we have seen that there are some sources of inefficiency: about a 20.59% of the execution time is communication; and there are workload imbalances produced by data dependences both between IFS and NEMO and within each model. In addition, in the model sensitivity simulations, we have described the types of messages and detected data dependencies. In IFS, we have observed that latency affects the coupling between models due to a large amount of small communications, whereas bandwidth affects another region of the code with a few big messages. In NEMO, results show that the simulated latencies and bandwidths only affect slightly to its execution time. However, it has data dependencies solved inefficiently and workload imbalances. The last simulation performed to detect the slowest model due to coupling has revealed that IFS is slower than NEMO. Moreover, there is not enough bandwidth to transfer all the data in IFS, whereas in NEMO there is almost no contention. This study is useful to improve the computational efficiency of the model, adapt it to support ultra-high resolution (UHR) experiments and future exascale supercomputers, and help code developers to design new algorithms more machine-independent.

Scaling and stochastic cascade properties of NEMO oceanic simulations and their potential value for GCM evaluation and downscaling

NASA Astrophysics Data System (ADS)

Verrier, Sébastien; Crépon, Michel; Thiria, Sylvie

2014-09-01

Spectral scaling properties have already been evidenced on oceanic numerical simulations and have been subject to several interpretations. They can be used to evaluate classical turbulence theories that predict scaling with specific exponents and to evaluate the quality of GCM outputs from a statistical and multiscale point of view. However, a more complete framework based on multifractal cascades is able to generalize the classical but restrictive second-order spectral framework to other moment orders, providing an accurate description of probability distributions of the fields at multiple scales. The predictions of this formalism still needed systematic verification in oceanic GCM while they have been confirmed recently for their atmospheric counterparts by several papers. The present paper is devoted to a systematic analysis of several oceanic fields produced by the NEMO oceanic GCM. Attention is focused to regional, idealized configurations that permit to evaluate the NEMO engine core from a scaling point of view regardless of limitations involved by land masks. Based on classical multifractal analysis tools, multifractal properties were evidenced for several oceanic state variables (sea surface temperature and salinity, velocity components, etc.). While first-order structure functions estimated a different nonconservativity parameter H in two scaling ranges, the multiorder statistics of turbulent fluxes were scaling over almost the whole available scaling range. This multifractal scaling was then parameterized with the help of the universal multifractal framework, providing parameters that are coherent with existing empirical literature. Finally, we argue that the knowledge of these properties may be useful for oceanographers. The framework seems very well suited for the statistical evaluation of OGCM outputs. Moreover, it also provides practical solutions to simulate subpixel variability stochastically for GCM downscaling purposes. As an independent perspective, the existence of multifractal properties in oceanic flows seems also interesting for investigating scale dependencies in remote sensing inversion algorithms.

The Met Office Coupled Atmosphere/Land/Ocean/Sea-Ice Data Assimilation System

NASA Astrophysics Data System (ADS)

Lea, Daniel; Mirouze, Isabelle; King, Robert; Martin, Matthew; Hines, Adrian

2015-04-01

The Met Office has developed a weakly-coupled data assimilation (DA) system using the global coupled model HadGEM3 (Hadley Centre Global Environment Model, version 3). At present the analysis from separate ocean and atmosphere DA systems are combined to produced coupled forecasts. The aim of coupled DA is to produce a more consistent analysis for coupled forecasts which may lead to less initialisation shock and improved forecast performance. The HadGEM3 coupled model combines the atmospheric model UM (Unified Model) at 60 km horizontal resolution on 85 vertical levels, the ocean model NEMO (Nucleus for European Modelling of the Ocean) at 25 km (at the equator) horizontal resolution on 75 vertical levels, and the sea-ice model CICE at the same resolution as NEMO. The atmosphere and the ocean/sea-ice fields are coupled every 1-hour using the OASIS coupler. The coupled model is corrected using two separate 6-hour window data assimilation systems: a 4D-Var for the atmosphere with associated soil moisture content nudging and snow analysis schemes on the one hand, and a 3D-Var FGAT for the ocean and sea-ice on the other hand. The background information in the DA systems comes from a previous 6-hour forecast of the coupled model. To isolate the impact of the coupled DA, 13-month experiments have been carried out, including 1) a full atmosphere/land/ocean/sea-ice coupled DA run, 2) an atmosphere-only run forced by OSTIA SSTs and sea-ice with atmosphere and land DA, and 3) an ocean-only run forced by atmospheric fields from run 2 with ocean and sea-ice DA. In addition, 5-day and 10-day forecast runs, have been produced from initial conditions generated by either run 1 or a combination of runs 2 and 3. The different results have been compared to each other and, whenever possible, to other references such as the Met Office atmosphere and ocean operational analyses or the OSTIA SST data. The performance of the coupled DA is similar to the existing separate ocean and atmosphere DA systems. This is despite the fact that the assimilation error covariances have not yet been tuned for coupled DA. In addition, the coupled model also exhibits some biases which do not affect the uncoupled models. An example is precipitation and run off errors affecting the ocean salinity. This of course impacts the performance of the ocean data assimilation. This does, however, highlight a particular benefit of data assimilation in that it can help to identify short term model biases by using, for example, the differences between the observations and model background (innovations) and the mean increments. Coupled DA has the distinct advantage that this gives direct information about the coupled model short term biases. By identifying the biases and developing solutions this will improve the short range coupled forecasts, and may also improve the coupled model on climate timescales.

South Atlantic meridional transports from NEMO-based simulations and reanalyses

NASA Astrophysics Data System (ADS)

Mignac, Davi; Ferreira, David; Haines, Keith

2018-02-01

The meridional heat transport (MHT) of the South Atlantic plays a key role in the global heat budget: it is the only equatorward basin-scale ocean heat transport and it sets the northward direction of the global cross-equatorial transport. Its strength and variability, however, are not well known. The South Atlantic transports are evaluated for four state-of-the-art global ocean reanalyses (ORAs) and two free-running models (FRMs) in the period 1997-2010. All products employ the Nucleus for European Modelling of the Oceans (NEMO) model, and the ORAs share very similar configurations. Very few previous works have looked at ocean circulation patterns in reanalysis products, but here we show that the ORA basin interior transports are consistently improved by the assimilated in situ and satellite observations relative to the FRMs, especially in the Argo period. The ORAs also exhibit systematically higher meridional transports than the FRMs, which is in closer agreement with observational estimates at 35 and 11° S. However, the data assimilation impact on the meridional transports still greatly varies among the ORAs, leading to differences up to ˜ 8 Sv and 0.4 PW in the South Atlantic Meridional Overturning Circulation and the MHTs, respectively. We narrow this down to large inter-product discrepancies in the western boundary currents (WBCs) at both upper and deep levels explaining up to ˜ 85 % of the inter-product differences in MHT. We show that meridional velocity differences, rather than temperature differences, in the WBCs drive ˜ 83 % of this MHT spread. These findings show that the present ocean observation network and data assimilation schemes can be used to consistently constrain the South Atlantic interior circulation but not the overturning component, which is dominated by the narrow western boundary currents. This will likely limit the effectiveness of ORA products for climate or decadal prediction studies.

Evaluation of an operational ocean model configuration at 1/12° spatial resolution for the Indonesian seas (NEMO2.3/INDO12) - Part 1: Ocean physics

NASA Astrophysics Data System (ADS)

Tranchant, Benoît; Reffray, Guillaume; Greiner, Eric; Nugroho, Dwiyoga; Koch-Larrouy, Ariane; Gaspar, Philippe

2016-03-01

INDO12 is a 1/12° regional version of the NEMO physical ocean model covering the whole Indonesian EEZ (Exclusive Economic Zone). It has been developed and is now running every week in the framework of the INDESO (Infrastructure Development of Space Oceanography) project implemented by the Indonesian Ministry of Marine Affairs and Fisheries. The initial hydrographic conditions as well as open-boundary conditions are derived from the operational global ocean forecasting system at 1/4° operated by Mercator Océan. Atmospheric forcing fields (3-hourly ECMWF (European Centre for Medium-Range Weather Forecast) analyses) are used to force the regional model. INDO12 is also forced by tidal currents and elevations, and by the inverse barometer effect. The turbulent mixing induced by internal tides is taken into account through a specific parameterisation. In this study we evaluate the model skill through comparisons with various data sets including outputs of the parent model, climatologies, in situ temperature and salinity measurements, and satellite data. The biogeochemical model results assessment is presented in a companion paper (Gutknecht et al., 2015). The simulated and altimeter-derived Eddy Kinetic Energy fields display similar patterns and confirm that tides are a dominant forcing in the area. The volume transport of the Indonesian throughflow (ITF) is in good agreement with the INSTANT estimates while the transport through Luzon Strait is, on average, westward but probably too weak. Compared to satellite data, surface salinity and temperature fields display marked biases in the South China Sea. Significant water mass transformation occurs along the main routes of the ITF and compares well with observations. Vertical mixing is able to modify the South and North Pacific subtropical water-salinity maximum as seen in T-S diagrams. In spite of a few weaknesses, INDO12 proves to be able to provide a very realistic simulation of the ocean circulation and water mass transformation through the Indonesian Archipelago. Work is ongoing to reduce or eliminate the remaining problems in the second INDO12 version.

Idealised modelling of ocean circulation driven by conductive and hydrothermal fluxes at the seabed

NASA Astrophysics Data System (ADS)

Barnes, Jowan M.; Morales Maqueda, Miguel A.; Polton, Jeff A.; Megann, Alex P.

2018-02-01

Geothermal heating is increasingly recognised as an important factor affecting ocean circulation, with modelling studies suggesting that this heat source could lead to first-order changes in the formation rate of Antarctic Bottom Water, as well as a significant warming effect in the abyssal ocean. Where it has been represented in numerical models, however, the geothermal heat flux into the ocean is generally treated as an entirely conductive flux, despite an estimated one third of the global geothermal flux being introduced to the ocean via hydrothermal sources. A modelling study is presented which investigates the sensitivity of the geothermally forced circulation to the way heat is supplied to the abyssal ocean. An analytical two-dimensional model of the circulation is described, which demonstrates the effects of a volume flux through the ocean bed. A simulation using the NEMO numerical general circulation model in an idealised domain is then used to partition a heat flux between conductive and hydrothermal sources and explicitly test the sensitivity of the circulation to the formulation of the abyssal heat flux. Our simulations suggest that representing the hydrothermal flux as a mass exchange indeed changes the heat distribution in the abyssal ocean, increasing the advective heat transport from the abyss by up to 35% compared to conductive heat sources. Consequently, we suggest that the inclusion of hydrothermal fluxes can be an important addition to course-resolution ocean models.

The Role of the New Zealand Plateau in the Tasman Sea Circulation and Separation of the East Australian Current

NASA Astrophysics Data System (ADS)

Bull, Christopher Y. S.; Kiss, Andrew E.; van Sebille, Erik; Jourdain, Nicolas C.; England, Matthew H.

2018-02-01

The East Australian Current (EAC) plays a major role in regional climate, circulation, and ecosystems, but predicting future changes is hampered by limited understanding of the factors controlling EAC separation. While there has been speculation that the presence of New Zealand may be important for the EAC separation, the prevailing view is that the time-mean partial separation is set by the ocean's response to gradients in the wind stress curl. This study focuses on the role of New Zealand, and the associated adjacent bathymetry, in the partial separation of the EAC and ocean circulation in the Tasman Sea. Here utilizing an eddy-permitting ocean model (NEMO), we find that the complete removal of the New Zealand plateau leads to a smaller fraction of EAC transport heading east and more heading south, with the mean separation latitude shifting >100 km southward. To examine the underlying dynamics, we remove New Zealand with two linear models: the Sverdrup/Godfrey Island Rule and NEMO in linear mode. We find that linear processes and deep bathymetry play a major role in the mean Tasman Front position, whereas nonlinear processes are crucial for the extent of the EAC retroflection. Contrary to past work, we find that meridional gradients in the basin-wide wind stress curl are not the sole factor determining the latitude of EAC separation. We suggest that the Tasman Front location is set by either the maximum meridional gradient in the wind stress curl or the northern tip of New Zealand, whichever is furthest north.

An efficient climate model with water isotope physics: NEEMY

NASA Astrophysics Data System (ADS)

Hu, J.; Emile-Geay, J.

2015-12-01

This work describes the development of an isotope-enabled atmosphere-ocean global climate model, NEEMY. This is a model of intermediate complexity, which can run 100 model years in 30 hours using 33 CPUs. The atmospheric component is the SPEEDY-IER (Molteni et al. 2003; Dee et al. 2015a), which is a water isotope-enabled (with equilibrium and kinetic fractionation schemes in precipitation, evaporation and soil moisture) simplified atmospheric general circulation model, with T30 horizontal resolution and 8 vertical layers. The oceanic component is NEMO 3.4 (Madec 2008), a state-of-the-art oceanic model (~2° horizontal resolution and 31 vertical layers) with an oceanic isotope module (a passive tracer scheme). A 1000-year control run shows that NEEMY is stable and its energy is conserved. The mean state is comparable to that of CMIP3-era CGCMs, though much cheaper to run. Atmospheric teleconnections such as the NAO and PNA are simulated very well. NEEMY also simulates the oceanic meridional overturning circulation well. The tropical climate variability is weaker than observations, and the climatology exhibits a double ITCZ problem despite bias corrections. The standard deviation of the monthly mean Nino3.4 index is 0.61K, compared to 0.91K in observations (Reynolds et al. 2002). We document similarities and differences with a close cousin, SPEEDY-NEMO (Kucharski et al. 2015). With its fast speed and relatively complete physical processes, NEEMY is suitable for paleoclimate studies ; we will present some forced simulations of the past millennium and their use in forward-modeling climate proxies, via proxy system models (PSMs, Dee et al 2015b). References Dee, S., D. Noone, N. Buenning, J. Emile-Geay, and Y. Zhou, 2015a: SPEEDY-IER: A fast atmospheric GCM with water isotope physics. J. Geophys. Res. Atmos., 120: 73-91. doi:10.1002/2014JD022194. Dee, S. G., J. Emile-Geay, M. N. Evans, Allam, A., D. M. Thompson, and E. J. Steig, 2015b: PRYSM: an open-source framework for proxy system modeling, with applications to oxygen-isotope systems, J. Adv. Mod. Earth Sys., 07, doi:10.1002/2015MS000447. Kucharski et al., 2015: Atlantic forcing of Pacific decadal variability. Clim. Dyn., doi:10.1007/s00382-015-2705-z.

The CNRM-CM5.1 global climate model: description and basic evaluation

NASA Astrophysics Data System (ADS)

Voldoire, A.; Sanchez-Gomez, E.; Salas y Mélia, D.; Decharme, B.; Cassou, C.; Sénési, S.; Valcke, S.; Beau, I.; Alias, A.; Chevallier, M.; Déqué, M.; Deshayes, J.; Douville, H.; Fernandez, E.; Madec, G.; Maisonnave, E.; Moine, M.-P.; Planton, S.; Saint-Martin, D.; Szopa, S.; Tyteca, S.; Alkama, R.; Belamari, S.; Braun, A.; Coquart, L.; Chauvin, F.

2013-05-01

A new version of the general circulation model CNRM-CM has been developed jointly by CNRM-GAME (Centre National de Recherches Météorologiques—Groupe d'études de l'Atmosphère Météorologique) and Cerfacs (Centre Européen de Recherche et de Formation Avancée) in order to contribute to phase 5 of the Coupled Model Intercomparison Project (CMIP5). The purpose of the study is to describe its main features and to provide a preliminary assessment of its mean climatology. CNRM-CM5.1 includes the atmospheric model ARPEGE-Climat (v5.2), the ocean model NEMO (v3.2), the land surface scheme ISBA and the sea ice model GELATO (v5) coupled through the OASIS (v3) system. The main improvements since CMIP3 are the following. Horizontal resolution has been increased both in the atmosphere (from 2.8° to 1.4°) and in the ocean (from 2° to 1°). The dynamical core of the atmospheric component has been revised. A new radiation scheme has been introduced and the treatments of tropospheric and stratospheric aerosols have been improved. Particular care has been devoted to ensure mass/water conservation in the atmospheric component. The land surface scheme ISBA has been externalised from the atmospheric model through the SURFEX platform and includes new developments such as a parameterization of sub-grid hydrology, a new freezing scheme and a new bulk parameterisation for ocean surface fluxes. The ocean model is based on the state-of-the-art version of NEMO, which has greatly progressed since the OPA8.0 version used in the CMIP3 version of CNRM-CM. Finally, the coupling between the different components through OASIS has also received a particular attention to avoid energy loss and spurious drifts. These developments generally lead to a more realistic representation of the mean recent climate and to a reduction of drifts in a preindustrial integration. The large-scale dynamics is generally improved both in the atmosphere and in the ocean, and the bias in mean surface temperature is clearly reduced. However, some flaws remain such as significant precipitation and radiative biases in many regions, or a pronounced drift in three dimensional salinity.

Two-sided Ubiquitin Binding of NF-κB Essential Modulator (NEMO) Zinc Finger Unveiled by a Mutation Associated with Anhidrotic Ectodermal Dysplasia with Immunodeficiency Syndrome*

PubMed Central

Ngadjeua, Flora; Chiaravalli, Jeanne; Traincard, François; Raynal, Bertrand; Fontan, Elisabeth; Agou, Fabrice

2013-01-01

Hypomorphic mutations in the X-linked human NEMO gene result in various forms of anhidrotic ectodermal dysplasia with immunodeficiency. NEMO function is mediated by two distal ubiquitin binding domains located in the regulatory C-terminal domain of the protein: the coiled-coil 2-leucine zipper (CC2-LZ) domain and the zinc finger (ZF) domain. Here, we investigated the effect of the D406V mutation found in the NEMO ZF of an ectodermal dysplasia with immunodeficiency patients. This point mutation does not impair the folding of NEMO ZF or mono-ubiquitin binding but is sufficient to alter NEMO function, as NEMO-deficient fibroblasts and Jurkat T lymphocytes reconstituted with full-length D406V NEMO lead to partial and strong defects in NF-κB activation, respectively. To further characterize the ubiquitin binding properties of NEMO ZF, we employed di-ubiquitin (di-Ub) chains composed of several different linkages (Lys-48, Lys-63, and linear (Met-1-linked)). We showed that the pathogenic mutation preferentially impairs the interaction with Lys-63 and Met-1-linked di-Ub, which correlates with its ubiquitin binding defect in vivo. Furthermore, sedimentation velocity and gel filtration showed that NEMO ZF, like other NEMO related-ZFs, binds mono-Ub and di-Ub with distinct stoichiometries, indicating the presence of a new Ub site within the NEMO ZF. Extensive mutagenesis was then performed on NEMO ZF and characterization of mutants allowed the proposal of a structural model of NEMO ZF in interaction with a Lys-63 di-Ub chain. PMID:24100029

A weak AMOC in a cold climate: Causes and remedies for a bias in the low-resolution version of the UK Earth System Model

NASA Astrophysics Data System (ADS)

Kuhlbrodt, T.; Jones, C.

2016-02-01

The UK Earth System Model (UKESM) is currently being developed by the UK Met Office and the academic community in the UK. The low-resolution version of UKESM has got a nominal grid cell size of 150 km in the atmosphere (Unified Model [UM], N96) and 1° in the ocean (NEMO, ORCA1). In several preliminary test configurations of UKESM-N96-ORCA1, we find a significant cold bias in the northern hemisphere in comparison with HadGEM2 (N96-ORCA025, i.e. 0.25° resolution in the ocean). The sea surface is too cold by more than 2 K, and up to 6 K, in large parts of the North Atlantic and the northwest Pacific. In addition to the cold bias, the maximum AMOC transport (diagnosed below 500 m depth) decreases in all the configurations, displaying values between 11 and 14 Sv after 50 years run length. Transport at 26°N is even smaller and hence too weak in relation to observed values (approx. 18 Sv). The mixed layer is too deep within the North Atlantic Current and the Kuroshio, but too shallow north of these currents. The cold bias extends to a depth of several hundred metres. In the North Atlantic, it is accompanied by a freshening of up to 1.5 psu, compared to present-day climatology, along the path of the North Atlantic Current. A core problem appears to be the cessation of deep-water formation in the Labrador Sea. Remarkably, using earlier versions of NEMO and the UM, the AMOC is stable at around 16 or 17 Sv in the N96-ORCA1 configuration. We report on various strategies to reduce the cold bias and enhance the AMOC transport. Changing various parameters that affect the vertical mixing in NEMO has no significant effect. Modifying the bathymetry to deepen and widen the channels across the Greenland-Iceland-Scotland sill leads to a short-term improvement in AMOC transport, but only for about ten years. Strikingly, in a configuration with longer time steps for the atmosphere model we find a climate that is even colder, but has got a more vigorous maximum AMOC transport (14 Sv instead of 12 Sv). Conversely, if the isopycnal diffusivity is augmented by a factor of 1.5, we find a warming and an even weaker AMOC transport. This brings us to further strategies to modify the atmosphere-ocean fluxes of heat and freshwater.

The role of satellite directional wave spectra for the improvement of the ocean-waves coupling

NASA Astrophysics Data System (ADS)

Aouf, Lotfi; Hauser, Danièle; Chapron, Bertrand

2017-04-01

Swell waves are well captured by the Synthetic Aperture Radar (SAR) which provides the directional wave spectra for waves roughly larger than 200 m. Since the launch of sentinel-1A and 1B SAR directional wave spectra are available to improve the swell wave forecasting and the coupling processes at the air-sea interface. Moreover next year CFOSAT mission will provide directional wave spectra for waves with wavelengths comprised between 70 to 500 m. This study aims to evaluate the assimilation of SAR and synthetic CFOSAT wave spectra on the coupling between the wave model MFWAM and the ocean model NEMO. Three coupling processes as described in Breivik et al. (2014) of Stokes-Coriolis forcing, the ocean side stress and the turbulence injected by the wave breaking in the ocean mixed layer have been used. a coupling run is performed with and without assimilation of directional wave spectra. the impact of SAR wave data on key parameters such as surface sea temperature, currents and salinity is investigated. Particular attention is carried out for ocean areas with swell dominant wave climate.

Interactions between Arctic sea ice drift, concentration and thickness modeled by NEMO-LIM3 at different resolutions

NASA Astrophysics Data System (ADS)

Docquier, David; Massonnet, François; Raulier, Jonathan; Lecomte, Olivier; Fichefet, Thierry

2016-04-01

Sea ice concentration and thickness have substantially decreased in the Arctic since the beginning of the satellite era. As a result, mechanical strength has decreased allowing more fracturing and leading to increased sea ice drift. However, recent studies have highlighted that the interplay between sea ice thermodynamics and dynamics is poorly represented in contemporary global climate model (GCM) simulations. Thus, the considerable inter-model spread in terms of future sea ice extent projections could be reduced by better understanding the interactions between drift, concentration and thickness. This study focuses on the results coming from the global coupled ocean-sea ice model NEMO-LIM3 between 1979 and 2012. Three different simulations are forced by the Drakkar Forcing Set (DFS) 5.2 and run on the global tripolar ORCA grid at spatial resolutions of 0.25, 1° and 2°. The relation between modeled sea ice drift, concentration and thickness is further analyzed, compared to observations and discussed in the framework of the above-mentioned poor representation. It is proposed as a process-based metric for evaluating model performance. This study forms part of the EU Horizon 2020 PRIMAVERA project aiming at developing a new generation of advanced and well-evaluated high-resolution GCMs.

A comparative signaling cost analysis of Macro Mobility scheme in NEMO (MM-NEMO) with mobility management protocol

NASA Astrophysics Data System (ADS)

Islam, Shayla; Abdalla, Aisha H.; Habaebi, Mohamed H.; Latif, Suhaimi A.; Hassan, Wan H.; Hasan, Mohammad K.; Ramli, H. A. M.; Khalifa, Othman O.

2013-12-01

NEMO BSP is an upgraded addition to Mobile IPv6 (MIPv6). As MIPv6 and its enhancements (i.e. HMIPv6) possess some limitations like higher handoff latency, packet loss, NEMO BSP also faces all these shortcomings by inheritance. Network Mobility (NEMO) is involved to handle the movement of Mobile Router (MR) and it's Mobile Network Nodes (MNNs) during handoff. Hence it is essential to upgrade the performance of mobility management protocol to obtain continuous session connectivity with lower delay and packet loss in NEMO environment. The completion of handoff process in NEMO BSP usually takes longer period since MR needs to register its single primary care of address (CoA) with home network that may cause performance degradation of the applications running on Mobile Network Nodes. Moreover, when a change in point of attachment of the mobile network is accompanied by a sudden burst of signaling messages, "Signaling Storm" occurs which eventually results in temporary congestion, packet delays or even packet loss. This effect is particularly significant for wireless environment where a wireless link is not as steady as a wired link since bandwidth is relatively limited in wireless link. Hence, providing continuous Internet connection without any interruption through applying multihoming technique and route optimization mechanism in NEMO are becoming the center of attention to the current researchers. In this paper, we propose a handoff cost model to compare the signaling cost of MM-NEMO with NEMO Basic Support Protocol (NEMO BSP) and HMIPv6.The numerical results shows that the signaling cost for the MM-NEMO scheme is about 69.6 % less than the NEMO-BSP and HMIPv6.

A high resolution Adriatic-Ionian Sea circulation model for operational forecasting

NASA Astrophysics Data System (ADS)

Ciliberti, Stefania Angela; Pinardi, Nadia; Coppini, Giovanni; Oddo, Paolo; Vukicevic, Tomislava; Lecci, Rita; Verri, Giorgia; Kumkar, Yogesh; Creti', Sergio

2015-04-01

A new numerical regional ocean model for the Italian Seas, with focus on the Adriatic-Ionian basin, has been implemented within the framework of Technologies for Situational Sea Awareness (TESSA) Project. The Adriatic-Ionian regional model (AIREG) represents the core of the new Adriatic-Ionian Forecasting System (AIFS), maintained operational by CMCC since November 2014. The spatial domain covers the Adriatic and the Ionian Seas, extending eastward until the Peloponnesus until the Libyan coasts; it includes also the Tyrrhenian Sea and extends westward, including the Ligurian Sea, the Sardinia Sea and part of the Algerian basin. The model is based on the NEMO-OPA (Nucleus for European Modeling of the Ocean - Ocean PArallelise), version 3.4 (Madec et al. 2008). NEMO has been implemented for AIREG at 1/45° resolution model in horizontal using 121 vertical levels with partial steps. It solves the primitive equations using the time-splitting technique for solving explicitly the external gravity waves. The model is forced by momentum, water and heat fluxes interactively computed by bulk formulae using the 6h-0.25° horizontal-resolution operational analysis and forecast fields from the European Centre for Medium-Range Weather Forecast (ECMWF) (Tonani et al. 2008, Oddo et al. 2009). The atmospheric pressure effect is included as surface forcing for the model hydrodynamics. The evaporation is derived from the latent heat flux, while the precipitation is provided by the Climate Prediction Centre Merged Analysis of Precipitation (CMAP) data. Concerning the runoff contribution, the model considers the estimate of the inflow discharge of 75 rivers that flow into the Adriatic-Ionian basin, collected by using monthly means datasets. Because of its importance as freshwater input in the Adriatic basin, the Po River contribution is provided using daily average observations from ARPA Emilia Romagna observational network. AIREG is one-way nested into the Mediterranean Forecasting System (MFS, http://medforecast.bo.ingv.it/) using daily means fields computed from daily outputs of the 1/16° general circulation model. One-way nesting is done by a novel pre-processing tool for an on-the-fly computation of boundary datasets compatible with BDY module provided by NEMO. It imposes the interpolation constraint and correction as in Pinardi et al. (2003) on the total velocity, ensuring that the total volume transport across boundaries is preserved after the interpolation procedures. In order to compute the lateral open boundary conditions, the model applies the Flow Relaxation Scheme (Engerdhal, 1995) for temperature, salinity and velocities and the Flather's radiation condition (Flather, 1976) for the depth-mean transport. Concerning the forecasting production cycle, AIFS produces 9-days forecast every day, producing hourly and daily means of temperature, salinity, surface currents, heat flux, water flux and shortwave radiation fields. AIREG model performances have been verified by using statistics (root mean square errors and BIAS) with respect to observed data (ARGO and CDT datasets)

Open-Source Software for Modeling of Nanoelectronic Devices

NASA Technical Reports Server (NTRS)

Oyafuso, Fabiano; Hua, Hook; Tisdale, Edwin; Hart, Don

2004-01-01

The Nanoelectronic Modeling 3-D (NEMO 3-D) computer program has been upgraded to open-source status through elimination of license-restricted components. The present version functions equivalently to the version reported in "Software for Numerical Modeling of Nanoelectronic Devices" (NPO-30520), NASA Tech Briefs, Vol. 27, No. 11 (November 2003), page 37. To recapitulate: NEMO 3-D performs numerical modeling of the electronic transport and structural properties of a semiconductor device that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantum-mechanical behavior of the device resolved to the atomistic level of granularity. NEMO 3-D solves the applicable quantum matrix equation on a Beowulf-class cluster computer by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. A prior upgrade of NEMO 3-D incorporated a capability for a strain treatment, parameterized for bulk material properties of GaAs and InAs, for two tight-binding submodels. NEMO 3-D has been demonstrated in atomistic analyses of effects of disorder in alloys and, in particular, in bulk In(x)Ga(1-x)As and in In(0.6)Ga(0.4)As quantum dots.

Assessment of Global Forecast Ocean Assimilation Model (FOAM) using new satellite SST data

NASA Astrophysics Data System (ADS)

Ascione Kenov, Isabella; Sykes, Peter; Fiedler, Emma; McConnell, Niall; Ryan, Andrew; Maksymczuk, Jan

2016-04-01

There is an increased demand for accurate ocean weather information for applications in the field of marine safety and navigation, water quality, offshore commercial operations, monitoring of oil spills and pollutants, among others. The Met Office, UK, provides ocean forecasts to customers from governmental, commercial and ecological sectors using the Global Forecast Ocean Assimilation Model (FOAM), an operational modelling system which covers the global ocean and runs daily, using the NEMO (Nucleus for European Modelling of the Ocean) ocean model with horizontal resolution of 1/4° and 75 vertical levels. The system assimilates salinity and temperature profiles, sea surface temperature (SST), sea surface height (SSH), and sea ice concentration observations on a daily basis. In this study, the FOAM system is updated to assimilate Advanced Microwave Scanning Radiometer 2 (AMSR2) and the Spinning Enhanced Visible and Infrared Imager (SEVIRI) SST data. Model results from one month trials are assessed against observations using verification tools which provide a quantitative description of model performance and error, based on statistical metrics, including mean error, root mean square error (RMSE), correlation coefficient, and Taylor diagrams. A series of hindcast experiments is used to run the FOAM system with AMSR2 and SEVIRI SST data, using a control run for comparison. Results show that all trials perform well on the global ocean and that largest SST mean errors were found in the Southern hemisphere. The geographic distribution of the model error for SST and temperature profiles are discussed using statistical metrics evaluated over sub-regions of the global ocean.

Tests of oceanic stochastic parameterisation in a seasonal forecast system.

NASA Astrophysics Data System (ADS)

Cooper, Fenwick; Andrejczuk, Miroslaw; Juricke, Stephan; Zanna, Laure; Palmer, Tim

2015-04-01

Over seasonal time scales, our aim is to compare the relative impact of ocean initial condition and model uncertainty, upon the ocean forecast skill and reliability. Over seasonal timescales we compare four oceanic stochastic parameterisation schemes applied in a 1x1 degree ocean model (NEMO) with a fully coupled T159 atmosphere (ECMWF IFS). The relative impacts upon the ocean of the resulting eddy induced activity, wind forcing and typical initial condition perturbations are quantified. Following the historical success of stochastic parameterisation in the atmosphere, two of the parameterisations tested were multiplicitave in nature: A stochastic variation of the Gent-McWilliams scheme and a stochastic diffusion scheme. We also consider a surface flux parameterisation (similar to that introduced by Williams, 2012), and stochastic perturbation of the equation of state (similar to that introduced by Brankart, 2013). The amplitude of the stochastic term in the Williams (2012) scheme was set to the physically reasonable amplitude considered in that paper. The amplitude of the stochastic term in each of the other schemes was increased to the limits of model stability. As expected, variability was increased. Up to 1 month after initialisation, ensemble spread induced by stochastic parameterisation is greater than that induced by the atmosphere, whilst being smaller than the initial condition perturbations currently used at ECMWF. After 1 month, the wind forcing becomes the dominant source of model ocean variability, even at depth.

Scientific advances of the MyOcean projects underpinning the transition towards the Marine Copernicus service

NASA Astrophysics Data System (ADS)

Brasseur, Pierre

2015-04-01

The MyOcean projects supported by the European Commission period have been developed during the 2008-2015 period to build an operational service of ocean physical state and ecosystem information to intermediate and downstream users in the areas of marine safety, marine resources, marine and coastal environment and weather, climate and seasonal forecasting. The "core" information provided to users is obtained through the combination of satellite and in situ observations, eddy-resolving modelling of the global ocean and regional european seas, biochemistry, ecosystem and sea-ice modelling, and data assimilation for global to basin scale circulation. A comprehensive R&D plan was established in 2010 to ensure the collection and provision of information of best possible quality for daily estimates of the ocean state (real-time), its short-term evolution, and its history over the past (reanalyses). A service validation methodology was further developed to ensure proper scientific evaluation and routine monitoring of the accuracy of MyOcean products. In this presentation, we will present an overview of the main scientific advances achieved in MyOcean using the NEMO modelling platform, ensemble-based assimilation schemes, coupled circulation-ecosystem, sea-ice assimilative models and probabilistic methodologies for ensemble validation. We will further highlight the key areas that will require additional innovation effort to support the Marine Copernicus service evolution.

Ocean products delivered by the Mercator Ocean Service Department

NASA Astrophysics Data System (ADS)

Crosnier, L.; Durand, E.; Soulat, F.; Messal, F.; Buarque, S.; Toumazou, V.; Landes, V.; Drevillon, M.; Lellouche, J.

2008-12-01

The newly created Service Department at Mercator Ocean is now offering various services for academic and private ocean applications. Mercator Ocean runs operationally ocean forecast systems for the Global and North Atlantic Ocean. These systems are based on an ocean general circulation model NEMO as well as on data assimilation of sea level anomalies, sea surface temperature and temperature and salinity vertical profiles. Three dimensional ocean fields of temperature, salinity and currents are updated and available weekly, including analysis and 2 weeks forecast fields. The Mercator Ocean service department is now offering a wide range of ocean derived products. This presentation will display some of the various products delivered in the framework of academic and private ocean applications: " Monitoring of the ocean current at the surface and at depth in several geographical areas for offshore oil platform, for offshore satellite launch platform, for transatlantic sailing or rowing boat races. " Monitoring of ocean climate indicators (Coral bleaching...) for marine reserve survey; " Monitoring of upwelling systems for fisheries; " Monitoring of the ocean heat content for tropical cyclone monitoring. " Monitoring of the ocean temperature/salinity and currents to guide research vessels during scientific cruises. The Mercator Ocean products catalogue will grow wider in the coming years, especially in the framework of the European GMES MyOcean project (FP7).

Modelling Greenland icebergs

NASA Astrophysics Data System (ADS)

Marson, Juliana M.; Myers, Paul G.; Hu, Xianmin

2017-04-01

The Atlantic Meridional Overturning Circulation (AMOC) is well known for carrying heat from low to high latitudes, moderating local temperatures. Numerical studies have examined the AMOC's variability under the influence of freshwater input to subduction and deep convections sites. However, an important source of freshwater has often been overlooked or misrepresented: icebergs. While liquid runoff decreases the ocean salinity near the coast, icebergs are a gradual and remote source of freshwater - a difference that affects sea ice cover, temperature, and salinity distribution in ocean models. Icebergs originated from the Greenland ice sheet, in particular, can affect the subduction process in Labrador Sea by decreasing surface water density. Our study aims to evaluate the distribution of icebergs originated from Greenland and their contribution to freshwater input in the North Atlantic. To do that, we use an interactive iceberg module coupled with the Nucleus for European Modelling of the Ocean (NEMO v3.4), which will calve icebergs from Greenland according to rates established by Bamber et al. (2012). Details on the distribution and trajectory of icebergs within the model may also be of use for understanding potential navigation threats, as shipping increases in northern waters.

Influence of coupling on atmosphere, sea ice and ocean regional models in the Ross Sea sector, Antarctica

NASA Astrophysics Data System (ADS)

Jourdain, Nicolas C.; Mathiot, Pierre; Gallée, Hubert; Barnier, Bernard

2011-04-01

Air-sea ice-ocean interactions in the Ross Sea sector form dense waters that feed the global thermohaline circulation. In this paper, we develop the new limited-area ocean-sea ice-atmosphere coupled model TANGO to simulate the Ross Sea sector. TANGO is built up by coupling the atmospheric limited-area model MAR to a regional configuration of the ocean-sea ice model NEMO. A method is then developed to identify the mechanisms by which local coupling affects the simulations. TANGO is shown to simulate realistic sea ice properties and atmospheric surface temperatures. These skills are mostly related to the skills of the stand alone atmospheric and oceanic models used to build TANGO. Nonetheless, air temperatures over ocean and winter sea ice thickness are found to be slightly improved in coupled simulations as compared to standard stand alone ones. Local atmosphere ocean feedbacks over the open ocean are found to significantly influence ocean temperature and salinity. In a stand alone ocean configuration, the dry and cold air produces an ocean cooling through sensible and latent heat loss. In a coupled configuration, the atmosphere is in turn moistened and warmed by the ocean; sensible and latent heat loss is therefore reduced as compared to the stand alone simulations. The atmosphere is found to be less sensitive to local feedbacks than the ocean. Effects of local feedbacks are increased in the coastal area because of the presence of sea ice. It is suggested that slow heat conduction within sea ice could amplify the feedbacks. These local feedbacks result in less sea ice production in polynyas in coupled mode, with a subsequent reduction in deep water formation.

Nemo: an evolutionary and population genetics programming framework.

PubMed

Guillaume, Frédéric; Rougemont, Jacques

2006-10-15

Nemo is an individual-based, genetically explicit and stochastic population computer program for the simulation of population genetics and life-history trait evolution in a metapopulation context. It comes as both a C++ programming framework and an executable program file. Its object-oriented programming design gives it the flexibility and extensibility needed to implement a large variety of forward-time evolutionary models. It provides developers with abstract models allowing them to implement their own life-history traits and life-cycle events. Nemo offers a large panel of population models, from the Island model to lattice models with demographic or environmental stochasticity and a variety of already implemented traits (deleterious mutations, neutral markers and more), life-cycle events (mating, dispersal, aging, selection, etc.) and output operators for saving data and statistics. It runs on all major computer platforms including parallel computing environments. The source code, binaries and documentation are available under the GNU General Public License at http://nemo2.sourceforge.net.

Correcting Biases in a lower resolution global circulation model with data assimilation

NASA Astrophysics Data System (ADS)

Canter, Martin; Barth, Alexander

2016-04-01

With this work, we aim at developping a new method of bias correction using data assimilation. This method is based on the stochastic forcing of a model to correct bias. First, through a preliminary run, we estimate the bias of the model and its possible sources. Then, we establish a forcing term which is directly added inside the model's equations. We create an ensemble of runs and consider the forcing term as a control variable during the assimilation of observations. We then use this analysed forcing term to correct the bias of the model. Since the forcing is added inside the model, it acts as a source term, unlike external forcings such as wind. This procedure has been developed and successfully tested with a twin experiment on a Lorenz 95 model. It is currently being applied and tested on the sea ice ocean NEMO LIM model, which is used in the PredAntar project. NEMO LIM is a global and low resolution (2 degrees) coupled model (hydrodynamic model and sea ice model) with long time steps allowing simulations over several decades. Due to its low resolution, the model is subject to bias in area where strong currents are present. We aim at correcting this bias by using perturbed current fields from higher resolution models and randomly generated perturbations. The random perturbations need to be constrained in order to respect the physical properties of the ocean, and not create unwanted phenomena. To construct those random perturbations, we first create a random field with the Diva tool (Data-Interpolating Variational Analysis). Using a cost function, this tool penalizes abrupt variations in the field, while using a custom correlation length. It also decouples disconnected areas based on topography. Then, we filter the field to smoothen it and remove small scale variations. We use this field as a random stream function, and take its derivatives to get zonal and meridional velocity fields. We also constrain the stream function along the coasts in order not to have currents perpendicular to the coast. The randomly generated stochastic forcing are then directly injected into the NEMO LIM model's equations in order to force the model at each timestep, and not only during the assimilation step. Results from a twin experiment will be presented. This method is being applied to a real case, with observations on the sea surface height available from the mean dynamic topography of CNES (Centre national d'études spatiales). The model, the bias correction, and more extensive forcings, in particular with a three dimensional structure and a time-varying component, will also be presented.

Impact of the "Symmetric Instability of the Computational Kind" at mesoscale- and submesoscale-permitting resolutions

NASA Astrophysics Data System (ADS)

Ducousso, Nicolas; Le Sommer, J.; Molines, J.-M.; Bell, M.

2017-12-01

The energy- and enstrophy-conserving momentum advection scheme (EEN) used over the last 10 years in NEMO is subject to a spurious numerical instability. This instability, referred to as the Symmetric Instability of the Computational Kind (SICK), arises from a discrete imbalance between the two components of the vector-invariant form of momentum advection. The properties and the method for removing this instability have been documented by Hollingsworth et al. (1983), but the extent to which the SICK may interfere with processes of interest at mesoscale- and submesoscale-permitting resolutions is still unkown. In this paper, the impact of the SICK in realistic ocean model simulations is assessed by comparing model integrations with different versions of the EEN momentum advection scheme. Investigations are undertaken with a global mesoscale-permitting resolution (1/4 °) configuration and with a regional North Atlantic Ocean submesoscale-permitting resolution (1/60 °) configuration. At both resolutions, the instability is found to alter primarily the most energetic current systems, such as equatorial jets, western boundary currents and coherent vortices. The impact of the SICK is found to increase with model resolution with a noticeable impact at mesoscale-permitting resolution and a dramatic impact at submesoscale-permitting resolution. The SICK is shown to distort the normal functioning of current systems, by redirecting the slow energy transfer between balanced motions to a spurious energy transfer to internal inertia-gravity waves and to dissipation. Our results indicate that the SICK is likely to have significantly corrupted NEMO solutions (when run with the EEN scheme) at mesocale-permitting and finer resolutions over the last 10 years.

The COSMO-CLM 4.8 regional climate model coupled to regional ocean, land surface and global earth system models using OASIS3-MCT: description and performance

NASA Astrophysics Data System (ADS)

Will, Andreas; Akhtar, Naveed; Brauch, Jennifer; Breil, Marcus; Davin, Edouard; Ho-Hagemann, Ha T. M.; Maisonnave, Eric; Thürkow, Markus; Weiher, Stefan

2017-04-01

We developed a coupled regional climate system model based on the CCLM regional climate model. Within this model system, using OASIS3-MCT as a coupler, CCLM can be coupled to two land surface models (the Community Land Model (CLM) and VEG3D), the NEMO-MED12 regional ocean model for the Mediterranean Sea, two ocean models for the North and Baltic seas (NEMO-NORDIC and TRIMNP+CICE) and the MPI-ESM Earth system model.We first present the different model components and the unified OASIS3-MCT interface which handles all couplings in a consistent way, minimising the model source code modifications and defining the physical and numerical aspects of the couplings. We also address specific coupling issues like the handling of different domains, multiple usage of the MCT library and exchange of 3-D fields.We analyse and compare the computational performance of the different couplings based on real-case simulations over Europe. The usage of the LUCIA tool implemented in OASIS3-MCT enables the quantification of the contributions of the coupled components to the overall coupling cost. These individual contributions are (1) cost of the model(s) coupled, (2) direct cost of coupling including horizontal interpolation and communication between the components, (3) load imbalance, (4) cost of different usage of processors by CCLM in coupled and stand-alone mode and (5) residual cost including i.a. CCLM additional computations.Finally a procedure for finding an optimum processor configuration for each of the couplings was developed considering the time to solution, computing cost and parallel efficiency of the simulation. The optimum configurations are presented for sequential, concurrent and mixed (sequential+concurrent) coupling layouts. The procedure applied can be regarded as independent of the specific coupling layout and coupling details.We found that the direct cost of coupling, i.e. communications and horizontal interpolation, in OASIS3-MCT remains below 7 % of the CCLM stand-alone cost for all couplings investigated. This is in particular true for the exchange of 450 2-D fields between CCLM and MPI-ESM. We identified remaining limitations in the coupling strategies and discuss possible future improvements of the computational efficiency.

Modeling the interplay between sea ice formation and the oceanic mixed layer: Limitations of simple brine rejection parameterizations

NASA Astrophysics Data System (ADS)

Barthélemy, Antoine; Fichefet, Thierry; Goosse, Hugues; Madec, Gurvan

2015-02-01

The subtle interplay between sea ice formation and ocean vertical mixing is hardly represented in current large-scale models designed for climate studies. Convective mixing caused by the brine release when ice forms is likely to prevail in leads and thin ice areas, while it occurs in models at the much larger horizontal grid cell scale. Subgrid-scale parameterizations have hence been developed to mimic the effects of small-scale convection using a vertical distribution of the salt rejected by sea ice within the mixed layer, instead of releasing it in the top ocean layer. Such a brine rejection parameterization is included in the global ocean-sea ice model NEMO-LIM3. Impacts on the simulated mixed layers and ocean temperature and salinity profiles, along with feedbacks on the sea ice cover, are then investigated in both hemispheres. The changes are overall relatively weak, except for mixed layer depths, which are in general excessively reduced compared to observation-based estimates. While potential model biases prevent a definitive attribution of this vertical mixing underestimation to the brine rejection parameterization, it is unlikely that the latter can be applied in all conditions. In that case, salt rejections do not play any role in mixed layer deepening, which is unrealistic. Applying the parameterization only for low ice-ocean relative velocities improves model results, but introduces additional parameters that are not well constrained by observations.

Modelling the interplay between sea ice formation and the oceanic mixed layer: limitations of simple brine rejection parameterizations

NASA Astrophysics Data System (ADS)

Barthélemy, Antoine; Fichefet, Thierry; Goosse, Hugues; Madec, Gurvan

2015-04-01

The subtle interplay between sea ice formation and ocean vertical mixing is hardly represented in current large-scale models designed for climate studies. Convective mixing caused by the brine release when ice forms is likely to prevail in leads and thin ice areas, while it occurs in models at the much larger horizontal grid cell scale. Subgrid-scale parameterizations have hence been developed to mimic the effects of small-scale convection using a vertical distribution of the salt rejected by sea ice within the mixed layer, instead of releasing it in the top ocean layer. Such a brine rejection parameterization is included in the global ocean--sea ice model NEMO-LIM3. Impacts on the simulated mixed layers and ocean temperature and salinity profiles, along with feedbacks on the sea ice cover, are then investigated in both hemispheres. The changes are overall relatively weak, except for mixed layer depths, which are in general excessively reduced compared to observation-based estimates. While potential model biases prevent a definitive attribution of this vertical mixing underestimation to the brine rejection parameterization, it is unlikely that the latter can be applied in all conditions. In that case, salt rejections do not play any role in mixed layer deepening, which is unrealistic. Applying the parameterization only for low ice--ocean relative velocities improves model results, but introduces additional parameters that are not well constrained by observations.

Gene therapy decreases seizures in a model of Incontinentia pigmenti.

PubMed

Dogbevia, Godwin K; Töllner, Kathrin; Körbelin, Jakob; Bröer, Sonja; Ridder, Dirk A; Grasshoff, Hanna; Brandt, Claudia; Wenzel, Jan; Straub, Beate K; Trepel, Martin; Löscher, Wolfgang; Schwaninger, Markus

2017-07-01

Incontinentia pigmenti (IP) is a genetic disease leading to severe neurological symptoms, such as epileptic seizures, but no specific treatment is available. IP is caused by pathogenic variants that inactivate the Nemo gene. Replacing Nemo through gene therapy might provide therapeutic benefits. In a mouse model of IP, we administered a single intravenous dose of the adeno-associated virus (AAV) vector, AAV-BR1-CAG-NEMO, delivering the Nemo gene to the brain endothelium. Spontaneous epileptic seizures and the integrity of the blood-brain barrier (BBB) were monitored. The endothelium-targeted gene therapy improved the integrity of the BBB. In parallel, it reduced the incidence of seizures and delayed their occurrence. Neonate mice intravenously injected with the AAV-BR1-CAG-NEMO vector developed no hepatocellular carcinoma or other major adverse effects 11 months after vector injection, demonstrating that the vector has a favorable safety profile. The data show that the BBB is a target of antiepileptic treatment and, more specifically, provide evidence for the therapeutic benefit of a brain endothelial-targeted gene therapy in IP. Ann Neurol 2017;82:93-104. © 2017 American Neurological Association.

Modelling MIZ dynamics in a global model

NASA Astrophysics Data System (ADS)

Rynders, Stefanie; Aksenov, Yevgeny; Feltham, Daniel; Nurser, George; Naveira Garabato, Alberto

2016-04-01

Exposure of large, previously ice-covered areas of the Arctic Ocean to the wind and surface ocean waves results in the Arctic pack ice cover becoming more fragmented and mobile, with large regions of ice cover evolving into the Marginal Ice Zone (MIZ). The need for better climate predictions, along with growing economic activity in the Polar Oceans, necessitates climate and forecasting models that can simulate fragmented sea ice with a greater fidelity. Current models are not fully fit for the purpose, since they neither model surface ocean waves in the MIZ, nor account for the effect of floe fragmentation on drag, nor include sea ice rheology that represents both the now thinner pack ice and MIZ ice dynamics. All these processes affect the momentum transfer to the ocean. We present initial results from a global ocean model NEMO (Nucleus for European Modelling of the Ocean) coupled to the Los Alamos sea ice model CICE. The model setup implements a novel rheological formulation for sea ice dynamics, accounting for ice floe collisions, thus offering a seamless framework for pack ice and MIZ simulations. The effect of surface waves on ice motion is included through wave pressure and the turbulent kinetic energy of ice floes. In the multidecadal model integrations we examine MIZ and basin scale sea ice and oceanic responses to the changes in ice dynamics. We analyse model sensitivities and attribute them to key sea ice and ocean dynamical mechanisms. The results suggest that the effect of the new ice rheology is confined to the MIZ. However with the current increase in summer MIZ area, which is projected to continue and may become the dominant type of sea ice in the Arctic, we argue that the effects of the combined sea ice rheology will be noticeable in large areas of the Arctic Ocean, affecting sea ice and ocean. With this study we assert that to make more accurate sea ice predictions in the changing Arctic, models need to include MIZ dynamics and physics.

Evaluating the Impact of Changes in Oceanic Dissolved Oxygen on Marine Nitrous Oxide

NASA Astrophysics Data System (ADS)

Suntharalingam, Parvadha; Buitenhuis, Erik; Schmidtko, Sunke; Andrews, Oliver; LeQuere, Corinne

2013-04-01

Emissions of the greenhouse gas nitrous-oxide (N2O) from oceanic oxygen minimum zones (OMZs) in the Equatorial Pacific and Northwest Indian Ocean are believed to provide a significant portion of the global oceanic flux to the atmosphere. Mechanisms of marine N2O production and consumption in these regions display significant sensitivity to ambient oxygen, with high yields at low oxygen levels (O2 < 50 micromol/L), and N2O depletion via denitrification in anoxic zones. These OMZ regions display large gradients in sub-surface N2O, and high rates of N2O turnover that far exceed those observed in the open ocean. Recent studies have suggested that possible expansion of oceanic OMZs in a warming climate, could lead to significant changes in N2O emissions from these zones. In this analysis we employ a global ocean biogeochemistry model (NEMO-PlankTOM), which includes representation of the marine N2O cycle, to explore the impact of changes in dissolved oxygen on the ocean-atmosphere N2O flux. We focus on the period 1960-2000, and evaluate the impact of estimated changes in ocean oxygen from two alternative sources : (a) the observationally-based upper-ocean oxygen distributions and trends of Stramma et al. [2012]; (b) simulated oxygen distributions and temporal variations from a set of CMIP5 Earth System models. We will inter-compare the oceanic N2O estimates derived from these alternative scenarios of ocean de-oxygenation. We will also discuss the implications of our results for the ability to reliably predict changes in N2O emissions under potential expansion of oceanic OMZs, particularly in view of the recently noted discrepancies between observed and modeled trends in oceanic oxygen by Stramma et al. [2012].

Coupled ocean-shelf ecosystem modelling of northern North Atlantic

NASA Astrophysics Data System (ADS)

Harle, J.; Holt, J. T.; Butenschön, M.; Allen, J. I.

2016-02-01

The biogeochemistry and ecosystems of the open-ocean and shelf seas are intimately connected. For example Northwest European continental shelf receives a substantial fraction of its nutrients from the wider North Atlantic and exports carbon at depth, sequestering it from atmospheric exchange. In the EC FP7 EuroBasin project (Holt et al 2014) we have developed a 1/12 degree basin-scale NEMO-ERSEM model with specific features relevant to shelf seas (e.g. tides and advanced vertical mixing schemes). This model is eddy resolving in the open-ocean, and resolves barotropic scales on-shelf. We use this model to explore the interaction between finely resolved physical processes and the ecosystem. Here we focus on shelf-sea processes and the connection between the shelf seas and open-ocean, and compare results with a 1/4 degree (eddy permitting) model that does not include shelf sea processes. We find tidal mixing fronts and river plume are well represented in the 1/12 degree model. Using approaches developed for the NW Shelf (Holt et al 2012), we provide estimates of across-shelf break nutrient fluxes to the seas surrounding this basin, and relate these fluxes and their interannual variability to the physical processes driving ocean-shelf exchange. Holt, J., et al, 2012. Oceanic controls on the primary production of the northwest European continental shelf: model experiments under recent past conditions and a potential future scenario. Biogeosciences 9, 97-117. Holt, J., et al, 2014. Challenges in integrative approaches to modelling the marine ecosystems of the North Atlantic: Physics to Fish and Coasts to Ocean. Progress in Oceanography doi:10.1016/j.pocean.2014.04.024.

Computational nanoelectronics towards: design, analysis, synthesis, and fundamental limits

NASA Technical Reports Server (NTRS)

Klimeck, G.

2003-01-01

This seminar will review the development of a comprehensive nanoelectronic modeling tool (NEMO 1-D and NEMO 3-D) and its application to high-speed electronics (resonant tunneling diodes) and IR detectors and lasers (quantum dots and 1-D heterostructures).

Numerical Modeling of Nanoelectronic Devices

NASA Technical Reports Server (NTRS)

Klimeck, Gerhard; Oyafuso, Fabiano; Bowen, R. Chris; Boykin, Timothy

2003-01-01

Nanoelectronic Modeling 3-D (NEMO 3-D) is a computer program for numerical modeling of the electronic structure properties of a semiconductor device that is embodied in a crystal containing as many as 16 million atoms in an arbitrary configuration and that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantummechanical behavior of the device resolved to the atomistic level of granularity. The system of electrons in the device is represented by a sparse Hamiltonian matrix that contains hundreds of millions of terms. NEMO 3-D solves the matrix equation on a Beowulf-class cluster computer, by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. In a recent update of NEMO 3-D, a new strain treatment, parameterized for bulk material properties of GaAs and InAs, was developed for two tight-binding submodels. The utility of the NEMO 3-D was demonstrated in an atomistic analysis of the effects of disorder in alloys and, in particular, in bulk In(x)Ga(l-x)As and in In0.6Ga0.4As quantum dots.

Calibration of sea ice dynamic parameters in an ocean-sea ice model using an ensemble Kalman filter

NASA Astrophysics Data System (ADS)

Massonnet, F.; Goosse, H.; Fichefet, T.; Counillon, F.

2014-07-01

The choice of parameter values is crucial in the course of sea ice model development, since parameters largely affect the modeled mean sea ice state. Manual tuning of parameters will soon become impractical, as sea ice models will likely include more parameters to calibrate, leading to an exponential increase of the number of possible combinations to test. Objective and automatic methods for parameter calibration are thus progressively called on to replace the traditional heuristic, "trial-and-error" recipes. Here a method for calibration of parameters based on the ensemble Kalman filter is implemented, tested and validated in the ocean-sea ice model NEMO-LIM3. Three dynamic parameters are calibrated: the ice strength parameter P*, the ocean-sea ice drag parameter Cw, and the atmosphere-sea ice drag parameter Ca. In twin, perfect-model experiments, the default parameter values are retrieved within 1 year of simulation. Using 2007-2012 real sea ice drift data, the calibration of the ice strength parameter P* and the oceanic drag parameter Cw improves clearly the Arctic sea ice drift properties. It is found that the estimation of the atmospheric drag Ca is not necessary if P* and Cw are already estimated. The large reduction in the sea ice speed bias with calibrated parameters comes with a slight overestimation of the winter sea ice areal export through Fram Strait and a slight improvement in the sea ice thickness distribution. Overall, the estimation of parameters with the ensemble Kalman filter represents an encouraging alternative to manual tuning for ocean-sea ice models.

AMM15: a new high-resolution NEMO configuration for operational simulation of the European north-west shelf

NASA Astrophysics Data System (ADS)

Graham, Jennifer A.; O'Dea, Enda; Holt, Jason; Polton, Jeff; Hewitt, Helene T.; Furner, Rachel; Guihou, Karen; Brereton, Ashley; Arnold, Alex; Wakelin, Sarah; Castillo Sanchez, Juan Manuel; Mayorga Adame, C. Gabriela

2018-02-01

This paper describes the next-generation ocean forecast model for the European north-west shelf, which will become the basis of operational forecasts in 2018. This new system will provide a step change in resolution and therefore our ability to represent small-scale processes. The new model has a resolution of 1.5 km compared with a grid spacing of 7 km in the current operational system. AMM15 (Atlantic Margin Model, 1.5 km) is introduced as a new regional configuration of NEMO v3.6. Here we describe the technical details behind this configuration, with modifications appropriate for the new high-resolution domain. Results from a 30-year non-assimilative run using the AMM15 domain demonstrate the ability of this model to represent the mean state and variability of the region.

Overall, there is an improvement in the representation of the mean state across the region, suggesting similar improvements may be seen in the future operational system. However, the reduction in seasonal bias is greater off-shelf than on-shelf. In the North Sea, biases are largely unchanged. Since there has been no change to the vertical resolution or parameterization schemes, performance improvements are not expected in regions where stratification is dominated by vertical processes rather than advection. This highlights the fact that increased horizontal resolution will not lead to domain-wide improvements. Further work is needed to target bias reduction across the north-west shelf region.

Medicanes in an ocean-atmosphere coupled regional climate model

NASA Astrophysics Data System (ADS)

Akhtar, N.; Brauch, J.; Dobler, A.; Béranger, K.; Ahrens, B.

2014-03-01

So-called medicanes (Mediterranean hurricanes) are meso-scale, marine, and warm-core Mediterranean cyclones that exhibit some similarities to tropical cyclones. The strong cyclonic winds associated with medicanes threaten the highly populated coastal areas around the Mediterranean basin. To reduce the risk of casualties and overall negative impacts, it is important to improve the understanding of medicanes with the use of numerical models. In this study, we employ an atmospheric limited-area model (COSMO-CLM) coupled with a one-dimensional ocean model (1-D NEMO-MED12) to simulate medicanes. The aim of this study is to assess the robustness of the coupled model in simulating these extreme events. For this purpose, 11 historical medicane events are simulated using the atmosphere-only model, COSMO-CLM, and coupled model, with different setups (horizontal atmospheric grid-spacings of 0.44°, 0.22°, and 0.08°; with/without spectral nudging, and an ocean grid-spacing of 1/12°). The results show that at high-resolution, the coupled model is able to not only simulate most of medicane events but also improve the track length, core temperature, and wind speed of simulated medicanes compared to the atmosphere-only simulations. The results suggest that the coupled model is more proficient for systemic and detailed studies of historical medicane events, and that this model can be an effective tool for future projections.

Medicanes in an ocean-atmosphere coupled regional climate model

NASA Astrophysics Data System (ADS)

Akhtar, N.; Brauch, J.; Dobler, A.; Béranger, K.; Ahrens, B.

2014-08-01

So-called medicanes (Mediterranean hurricanes) are meso-scale, marine, and warm-core Mediterranean cyclones that exhibit some similarities to tropical cyclones. The strong cyclonic winds associated with medicanes threaten the highly populated coastal areas around the Mediterranean basin. To reduce the risk of casualties and overall negative impacts, it is important to improve the understanding of medicanes with the use of numerical models. In this study, we employ an atmospheric limited-area model (COSMO-CLM) coupled with a one-dimensional ocean model (1-D NEMO-MED12) to simulate medicanes. The aim of this study is to assess the robustness of the coupled model in simulating these extreme events. For this purpose, 11 historical medicane events are simulated using the atmosphere-only model, COSMO-CLM, and coupled model, with different setups (horizontal atmospheric grid spacings of 0.44, 0.22, and 0.08°; with/without spectral nudging, and an ocean grid spacing of 1/12°). The results show that at high resolution, the coupled model is able to not only simulate most of medicane events but also improve the track length, core temperature, and wind speed of simulated medicanes compared to the atmosphere-only simulations. The results suggest that the coupled model is more proficient for systemic and detailed studies of historical medicane events, and that this model can be an effective tool for future projections.

Death receptor-independent FADD signalling triggers hepatitis and hepatocellular carcinoma in mice with liver parenchymal cell-specific NEMO knockout.

PubMed

Ehlken, H; Krishna-Subramanian, S; Ochoa-Callejero, L; Kondylis, V; Nadi, N E; Straub, B K; Schirmacher, P; Walczak, H; Kollias, G; Pasparakis, M

2014-11-01

Hepatocellular carcinoma (HCC) usually develops in the context of chronic hepatitis triggered by viruses or toxic substances causing hepatocyte death, inflammation and compensatory proliferation of liver cells. Death receptors of the TNFR superfamily regulate cell death and inflammation and are implicated in liver disease and cancer. Liver parenchymal cell-specific ablation of NEMO/IKKγ, a subunit of the IκB kinase (IKK) complex that is essential for the activation of canonical NF-κB signalling, sensitized hepatocytes to apoptosis and caused the spontaneous development of chronic hepatitis and HCC in mice. Here we show that hepatitis and HCC development in NEMO(LPC-KO) mice is triggered by death receptor-independent FADD-mediated hepatocyte apoptosis. TNF deficiency in all cells or conditional LPC-specific ablation of TNFR1, Fas or TRAIL-R did not prevent hepatocyte apoptosis, hepatitis and HCC development in NEMO(LPC-KO) mice. To address potential functional redundancies between death receptors we generated and analysed NEMO(LPC-KO) mice with combined LPC-specific deficiency of TNFR1, Fas and TRAIL-R and found that also simultaneous lack of all three death receptors did not prevent hepatocyte apoptosis, chronic hepatitis and HCC development. However, LPC-specific combined deficiency in TNFR1, Fas and TRAIL-R protected the NEMO-deficient liver from LPS-induced liver failure, showing that different mechanisms trigger spontaneous and LPS-induced hepatocyte apoptosis in NEMO(LPC-KO) mice. In addition, NK cell depletion did not prevent liver damage and hepatitis. Moreover, NEMO(LPC-KO) mice crossed into a RAG-1-deficient genetic background-developed hepatitis and HCC. Collectively, these results show that the spontaneous development of hepatocyte apoptosis, chronic hepatitis and HCC in NEMO(LPC-KO) mice occurs independently of death receptor signalling, NK cells and B and T lymphocytes, arguing against an immunological trigger as the critical stimulus driving hepatocarcinogenesis in this model.

iMarNet: an ocean biogeochemistry model inter-comparison project within a common physical ocean modelling framework

NASA Astrophysics Data System (ADS)

Kwiatkowski, L.; Yool, A.; Allen, J. I.; Anderson, T. R.; Barciela, R.; Buitenhuis, E. T.; Butenschön, M.; Enright, C.; Halloran, P. R.; Le Quéré, C.; de Mora, L.; Racault, M.-F.; Sinha, B.; Totterdell, I. J.; Cox, P. M.

2014-07-01

Ocean biogeochemistry (OBGC) models span a wide range of complexities from highly simplified, nutrient-restoring schemes, through nutrient-phytoplankton-zooplankton-detritus (NPZD) models that crudely represent the marine biota, through to models that represent a broader trophic structure by grouping organisms as plankton functional types (PFT) based on their biogeochemical role (Dynamic Green Ocean Models; DGOM) and ecosystem models which group organisms by ecological function and trait. OBGC models are now integral components of Earth System Models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here, we present an inter-comparison of six OBGC models that were candidates for implementation within the next UK Earth System Model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the Nucleus for the European Modelling of the Ocean (NEMO) ocean general circulation model (GCM), and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform or underperform all other models across all metrics. Nonetheless, the simpler models that are easier to tune are broadly closer to observations across a number of fields, and thus offer a high-efficiency option for ESMs that prioritise high resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low resolution climate dynamics and high complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry-climate interactions.

iMarNet: an ocean biogeochemistry model intercomparison project within a common physical ocean modelling framework

NASA Astrophysics Data System (ADS)

Kwiatkowski, L.; Yool, A.; Allen, J. I.; Anderson, T. R.; Barciela, R.; Buitenhuis, E. T.; Butenschön, M.; Enright, C.; Halloran, P. R.; Le Quéré, C.; de Mora, L.; Racault, M.-F.; Sinha, B.; Totterdell, I. J.; Cox, P. M.

2014-12-01

Ocean biogeochemistry (OBGC) models span a wide variety of complexities, including highly simplified nutrient-restoring schemes, nutrient-phytoplankton-zooplankton-detritus (NPZD) models that crudely represent the marine biota, models that represent a broader trophic structure by grouping organisms as plankton functional types (PFTs) based on their biogeochemical role (dynamic green ocean models) and ecosystem models that group organisms by ecological function and trait. OBGC models are now integral components of Earth system models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here we present an intercomparison of six OBGC models that were candidates for implementation within the next UK Earth system model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the ocean general circulation model Nucleus for European Modelling of the Ocean (NEMO) and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform all other models across all metrics. Nonetheless, the simpler models are broadly closer to observations across a number of fields and thus offer a high-efficiency option for ESMs that prioritise high-resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low-resolution climate dynamics and high-complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry-climate interactions.

Effects of tides, vertical discretization schemes and runoff variability on a pan-Arctic Ocean simulation.

NASA Astrophysics Data System (ADS)

Luneva, Maria; Holt, Jason; Harle, James; Liu, Hedong

2013-04-01

The results of a recently developed NEMO-shelf pan-Arctic Ocean model coupled with LIM2 ice model are presented. This pan Arctic model has a hybrid s-z vertical discretization with terrain following coordinates on the shelf, condensing towards the bottom and surface boundary layer, and partial step z-coordinates in the abyss. This allows (a) processes near the surface to be resolved (b) Cascading (shelf convection), which contributes to the formation of halocline and deep dense water, to be well reproduced; and (c) minimize pressure gradient errors peculiar to terrain following coordinates. Horizontal grid and topography corresponds to global NEMO -ORCA 0.25 model (which uses a tripolar grid) with seamed slit between the western and eastern parts. In the Arctic basin this horizontal resolution corresponds to 15-10km with 5-7 km in the Canadian Archipelago. The model uses the General Length Scale vertical turbulent mixing scheme with (K- ɛ) closure and Kantha and Clayson type structural functions. Smagorinsky type Laplacian diffusivity and viscosity are employed for the description of a horizontal mixing. Vertical Piecewise Parabolic Method has been implemented with the aim to reduce an artificial vertical mixing. Boundary conditions are taken from the 5-days mean output of NOCS version of the global ORCA-025 model and OTPS/tpxo7 for 9 tidal harmonics . For freshwater runoff we employed two different forcings: a climatic one, used in global ORCA-0.25 model, and a recently available data base from Dai and Trenberth (Feb2011) 1948-2007, which takes in account inter-annual variability and includes 1200 river guages for the Arctic ocean coast. The simulations have been performed for two intervals: 1978-1988 and 1997-2007. The model adequately reproduces the main features of dynamics, tides and ice volume/concentration. The analysis shows that the main effects of tides occur at the ice-water interface and bottom boundary layers due to mesoscale Ekman pumping , generated by nonlinear shear tidal stresses, acting as a 'tidal winds' on the surfaces. Harmonic analysis shows, that at least five harmonics should be taken in account: three semidiurnal M2, S2, N2 and two diurnal K1 and O1. We present results from the following experiments: (a) with tidal forcing and without tidal forcing; (b) with climatic runoff and with Dai and Trenberth database. To examine the effects of summer ice openings on the formation of brine rejection and dense water cascades, additional idealised experiments have been performed: (c) for initial conditions of hydrographic fields and fluxes for 1978 with initial summer ice concentration of 2000; (d) opposite case of initial ocean conditions for 2000 and ice concentration of 1978. The comparisons with global ORCA-025 simulations and available data are discussed.

The Mediterranean interannual variability in MEDRYS, a Mediterranean Sea reanalysis over 1992-2013

NASA Astrophysics Data System (ADS)

Beuvier, Jonathan; Hamon, Mathieu; Lellouche, Jean-Michel; Greiner, Eric; Alias, Antoinette; Arsouze, Thomas; Benkiran, Mounir; Béranger, Karine; Drillet, Yann; Sevault, Florence; Somot, Samuel

2015-04-01

The French research community on the Mediterranean Sea and the French operational ocean forecasting center Mercator Océan are gathering their skills and expertises in physical oceanography, ocean modelling, atmospheric forcings and data assimilation, to carry out a MEDiterranean Sea ReanalYsiS (MEDRYS) at high resolution for the period 1992-2013. The reanalysis is used to have a realistic description of the ocean state over the recent decades and it will help to understand the long-term water cycle over the Mediterranean basin in terms of variability and trends, contributing thus to the HyMeX international program. The ocean model used is NEMOMED12 [Lebeaupin Brossier et al., 2011, Oc. Mod., 2012, Oc. Mod.; Beuvier et al., 2012a, JGR, 2012b, Mercator Newsl.], a Mediterranean configuration of NEMO [Madec and the NEMO Team, 2008], with a 1/12° (about 7 km) horizontal resolution and 75 vertical z-levels with partial steps. It is forced by the 3-hourly atmospheric fluxes coming from an ALADIN-Climate simulation at 12 km of resolution [Herrmann et al., 2011, NHESS], driven by the ERA-Interim atmospheric reanalysis. The exchanges with the Atlantic Ocean are performed through a buffer zone, with a damping on 3D theta-S and on sea level towards the ORA-S4 oceanic reanalysis [Balmaseda et al., 2012, QJRMS]. This model configuration is used to carry a 34-year free simulation over the period 1979-2013. This free simulation is the initial state of the reanalysis in October 1992. It is also used to compute anomalies from which the data assimilation scheme derives required characteristic covariances of the ocean model. MEDRYS1 uses the current Mercator Océan operational data assimilation system [Lellouche et al., 2013, Oc.Sci.]. It uses a reduced order Kalman filter with a 3D multivariate modal decomposition of the forecast error. A 3D-Var scheme corrects biases in temperature and salinity for the slowly evolving large-scale. In addition, some modifications dedicated to the Mediterranean area (more specific Post-Glacial-Rebound corrections, new model-equivalent for the Sea Level Anomaly for example) have been introduced. Temperature and salinity vertical profiles from the newly released CORA4 database, altimeter data and satellite SST and are jointly assimilated. Thus, the reanalysis benefits from the intensive observational field campaigns carried out during the HyMeX Special Observation Periods (SOPs) in fall 2012 and winter 2013 in the north-western Mediterranean Sea. We assess here the ability of a MEDRYS1 to reproduce the general circulation and the water masses in the Mediterranean Sea. We present the misfit between the reanalysis and the assimilated observations, as well as differences between the reanalysis and its twin free simulation. We show diagnostics on the surface circulation variability, heat and salt contents and deep water formation over the whole period of the reanalysis, with also a focus on the impact of the HyMeX data during the SOPs time period.

Downscaling Ocean Conditions: Initial Results using a Quasigeostrophic and Realistic Ocean Model

NASA Astrophysics Data System (ADS)

Katavouta, Anna; Thompson, Keith

2014-05-01

Previous theoretical work (Henshaw et al, 2003) has shown that the small-scale modes of variability of solutions of the unforced, incompressible Navier-Stokes equation, and Burgers' equation, can be reconstructed with surprisingly high accuracy from the time history of a few of the large-scale modes. Motivated by this theoretical work we first describe a straightforward method for assimilating information on the large scales in order to recover the small scale oceanic variability. The method is based on nudging in specific wavebands and frequencies and is similar to the so-called spectral nudging method that has been used successfully for atmospheric downscaling with limited area models (e.g. von Storch et al., 2000). The validity of the method is tested using a quasigestrophic model configured to simulate a double ocean gyre separated by an unstable mid-ocean jet. It is shown that important features of the ocean circulation including the position of the meandering mid-ocean jet and associated pinch-off eddies can indeed be recovered from the time history of a small number of large-scales modes. The benefit of assimilating additional time series of observations from a limited number of locations, that alone are too sparse to significantly improve the recovery of the small scales using traditional assimilation techniques, is also demonstrated using several twin experiments. The final part of the study outlines the application of the approach using a realistic high resolution (1/36 degree) model, based on the NEMO (Nucleus for European Modelling of the Ocean) modeling framework, configured for the Scotian Shelf of the east coast of Canada. The large scale conditions used in this application are obtained from the HYCOM (HYbrid Coordinate Ocean Model) + NCODA (Navy Coupled Ocean Data Assimilation) global 1/12 degree analysis product. Henshaw, W., Kreiss, H.-O., Ystrom, J., 2003. Numerical experiments on the interaction between the larger- and the small-scale motion of the Navier-Stokes equations. Multiscale Modeling and Simulation 1, 119-149. von Storch, H., Langenberg, H., Feser, F., 2000. A spectral nudging technique for dynamical downscaling purposes. Monthly Weather Review 128, 3664-3673.

Modeling Extra-Long Tsunami Propagation: Assessing Data, Model Accuracy and Forecast Implications

NASA Astrophysics Data System (ADS)

Titov, V. V.; Moore, C. W.; Rabinovich, A.

2017-12-01

Detecting and modeling tsunamis propagating tens of thousands of kilometers from the source is a formidable scientific challenge and seemingly satisfies only scientific curiosity. However, results of such analyses produce a valuable insight into the tsunami propagation dynamics, model accuracy and would provide important implications for tsunami forecast. The Mw = 9.3 megathrust earthquake of December 26, 2004 off the coast of Sumatra generated a tsunami that devastated Indian Ocean coastlines and spread into the Pacific and Atlantic oceans. The tsunami was recorded by a great number of coastal tide gauges, including those located in 15-25 thousand kilometers from the source area. To date, it is still the farthest instrumentally detected tsunami. The data from these instruments throughout the world oceans enabled to estimate various statistical parameters and energy decay of this event. High-resolution records of this tsunami from DARTs 32401 (offshore of northern Chile), 46405 and NeMO (both offshore of the US West Coast), combined with the mainland tide gauge measurements enabled us to examine far-field characteristics of the 2004 in the Pacific Ocean and to compare the results of global numerical simulations with the observations. Despite their small heights (less than 2 cm at deep-ocean locations), the records demonstrated consistent spatial and temporal structure. The numerical model described well the frequency content, amplitudes and general structure of the observed waves at deep-ocean and coastal gages. We present analysis of the measurements and comparison with model data to discuss implication for tsunami forecast accuracy. Model study for such extreme distances from the tsunami source and at extra-long times after the event is an attempt to find accuracy bounds for tsunami models and accuracy limitations of model use for forecast. We discuss results in application to tsunami model forecast and tsunami modeling in general.

The Mediterranean Forecasting System: recent developments

NASA Astrophysics Data System (ADS)

Tonani, Marina; Oddo, Paolo; Korres, Gerasimos; Clementi, Emanuela; Dobricic, Srdjan; Drudi, Massimiliano; Pistoia, Jenny; Guarnieri, Antonio; Romaniello, Vito; Girardi, Giacomo; Grandi, Alessandro; Bonaduce, Antonio; Pinardi, Nadia

2014-05-01

Recent developments of the Mediterranean Monitoring and Forecasting Centre of the EU-Copernicus marine service, the Mediterranean Forecasting System (MFS), are presented. MFS provides forecast, analysis and reanalysis for the physical and biogeochemical parameters of the Mediterranean Sea. The different components of the system are continuously updated in order to provide to the users the best available product. This work is focus on the physical component of the system. The physical core of MFS is composed by an ocean general circulation model (NEMO) coupled with a spectral wave model (Wave Watch-III). The NEMO model provides to WW-III surface currents and SST fields, while WW-III returns back to NEMO the neutral component of the surface drag coefficient. Satellite Sea Level Anomaly observations and in-situ T & S vertical profiles are assimilated into this system using a variational assimilation scheme based on 3DVAR (Dobricic, 2008) . Sensitive experiments have been performed in order to assess the impact of the assimilation of the latest available SLA missions, Altika and Cryosat together with the long term available mission of Jason2. The results show a significant improvement of the MFS skill due to the multi-mission along track assimilation. The primitive equations module has been recently upgraded with the introduction of the atmospheric pressure term and a new, explicit, numerical scheme has been adopted to solve the barotropic component of the equations of motion. The SLA satellite observations for data assimilation have been consequently modified in order to account for the new atmospheric pressure term introduced in the equations. This new system has been evaluated using tide gauge coastal buoys and the satellite along track data. The quality of the SSH has improved significantly while a minor impact has been observed on the other state variables (temperature, salinity and currents). Experiments with a higher resolution NWP (numerical weather prediction) forcing provided by the COSMO-MED system (provided by the Italian Meteorological Office), have been performed and a pre-operational 3-day forecast production system has been developed. The comparison between this system and the official one forced by the ECMWF NWP data will be discussed.

AlignNemo: a local network alignment method to integrate homology and topology.

PubMed

Ciriello, Giovanni; Mina, Marco; Guzzi, Pietro H; Cannataro, Mario; Guerra, Concettina

2012-01-01

Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.

Atmospheric and Oceanic Response to Southern Ocean Deep Convection Oscillations on Decadal to Centennial Time Scales in Climate Models

NASA Astrophysics Data System (ADS)

Martin, T.; Reintges, A.; Park, W.; Latif, M.

2014-12-01

Many current coupled global climate models simulate open ocean deep convection in the Southern Ocean as a recurring event with time scales ranging from a few years to centennial (de Lavergne et al., 2014, Nat. Clim. Ch.). The only observation of such event, however, was the occurrence of the Weddell Polynya in the mid-1970s, an open water area of 350 000 km2 within the Antarctic sea ice in three consecutive winters. Both the wide range of modeled frequency of occurrence and the absence of deep convection in the Weddell Sea highlights the lack of understanding concerning the phenomenon. Nevertheless, simulations indicate that atmospheric and oceanic responses to the cessation of deep convection in the Southern Ocean include a strengthening of the low-level atmospheric circulation over the Southern Ocean (increasing SAM index) and a reduction in the export of Antarctic Bottom Water (AABW), potentially masking the regional effects of global warming (Latif et al., 2013, J. Clim.; Martin et al., 2014, Deep Sea Res. II). It is thus of great importance to enhance our understanding of Southern Ocean deep convection and clarify the associated time scales. In two multi-millennial simulations with the Kiel Climate Model (KCM, ECHAM5 T31 atmosphere & NEMO-LIM2 ~2˚ ocean) we showed that the deep convection is driven by strong oceanic warming at mid-depth periodically overriding the stabilizing effects of precipitation and ice melt (Martin et al., 2013, Clim. Dyn.). Sea ice thickness also affects location and duration of the deep convection. A new control simulation, in which, amongst others, the atmosphere grid resolution is changed to T42 (~2.8˚), yields a faster deep convection flip-flop with a period of 80-100 years and a weaker but still significant global climate response similar to CMIP5 simulations. While model physics seem to affect the time scale and intensity of the phenomenon, the driving mechanism is a rather robust feature. Finally, we compare the atmospheric and oceanic responses among CMIP5 models. Since open ocean convection is the dominant mode of AABW formation in these models, the northward extent and strength of the AABW cell in the Atlantic correlates with the deep convection intensity but varies between models. Likewise, atmospheric response patterns outside the Southern Ocean region are not consistent among models.

Development of novel NEMO-binding domain mimetics for inhibiting IKK/NF-κB activation.

PubMed

Zhao, Jing; Zhang, Lei; Mu, Xiaodong; Doebelin, Christelle; Nguyen, William; Wallace, Callen; Reay, Daniel P; McGowan, Sara J; Corbo, Lana; Clemens, Paula R; Wilson, Gabriela Mustata; Watkins, Simon C; Solt, Laura A; Cameron, Michael D; Huard, Johnny; Niedernhofer, Laura J; Kamenecka, Theodore M; Robbins, Paul D

2018-06-11

Nuclear factor κB (NF-κB) is a transcription factor important for regulating innate and adaptive immunity, cellular proliferation, apoptosis, and senescence. Dysregulation of NF-κB and its upstream regulator IκB kinase (IKK) contributes to the pathogenesis of multiple inflammatory and degenerative diseases as well as cancer. An 11-amino acid peptide containing the NF-κB essential modulator (NEMO)-binding domain (NBD) derived from the C-terminus of β subunit of IKK, functions as a highly selective inhibitor of the IKK complex by disrupting the association of IKKβ and the IKKγ subunit NEMO. A structure-based pharmacophore model was developed to identify NBD mimetics by in silico screening. Two optimized lead NBD mimetics, SR12343 and SR12460, inhibited tumor necrosis factor α (TNF-α)- and lipopolysaccharide (LPS)-induced NF-κB activation by blocking the interaction between IKKβ and NEMO and suppressed LPS-induced acute pulmonary inflammation in mice. Chronic treatment of a mouse model of Duchenne muscular dystrophy (DMD) with SR12343 and SR12460 attenuated inflammatory infiltration, necrosis and muscle degeneration, demonstrating that these small-molecule NBD mimetics are potential therapeutics for inflammatory and degenerative diseases.

Disulfide-mediated stabilization of the IκB kinase binding domain of NF-κB essential modulator (NEMO).

PubMed

Zhou, Li; Yeo, Alan T; Ballarano, Carmine; Weber, Urs; Allen, Karen N; Gilmore, Thomas D; Whitty, Adrian

2014-12-23

Human NEMO (NF-κB essential modulator) is a 419 residue scaffolding protein that, together with catalytic subunits IKKα and IKKβ, forms the IκB kinase (IKK) complex, a key regulator of NF-κB pathway signaling. NEMO is an elongated homodimer comprising mostly α-helix. It has been shown that a NEMO fragment spanning residues 44-111, which contains the IKKα/β binding site, is structurally disordered in the absence of bound IKKβ. Herein we show that enforcing dimerization of NEMO1-120 or NEMO44-111 constructs through introduction of one or two interchain disulfide bonds, through oxidation of the native Cys54 residue and/or at position 107 through a Leu107Cys mutation, induces a stable α-helical coiled-coil structure that is preorganized to bind IKKβ with high affinity. Chemical and thermal denaturation studies showed that, in the context of a covalent dimer, the ordered structure was stabilized relative to the denatured state by up to 3 kcal/mol. A full-length NEMO-L107C protein formed covalent dimers upon treatment of mammalian cells with H2O2. Furthermore, NEMO-L107C bound endogenous IKKβ in A293T cells, reconstituted TNF-induced NF-κB signaling in NEMO-deficient cells, and interacted with TRAF6. Our results indicate that the IKKβ binding domain of NEMO possesses an ordered structure in the unbound state, provided that it is constrained within a dimer as is the case in the constitutively dimeric full-length NEMO protein. The stability of the NEMO coiled coil is maintained by strong interhelix interactions in the region centered on residue 54. The disulfide-linked constructs we describe herein may be useful for crystallization of NEMO's IKKβ binding domain in the absence of bound IKKβ, thereby facilitating the structural characterization of small-molecule inhibitors.

Impact of wave mixing on the sea ice cover

NASA Astrophysics Data System (ADS)

Rynders, Stefanie; Aksenov, Yevgeny; Madec, Gurvan; Nurser, George; Feltham, Daniel

2017-04-01

As information on surface waves in ice-covered regions becomes available in ice-ocean models, there is an opportunity to model wave-related processes more accurate. Breaking waves cause mixing of the upper water column and present mixing schemes in ocean models take this into account through surface roughness. A commonly used approach is to calculate surface roughness from significant wave height, parameterised from wind speed. We present results from simulations using modelled significant wave height instead, which accounts for the presence of sea ice and the effect of swell. The simulations use the NEMO ocean model coupled to the CICE sea ice model, with wave information from the ECWAM model of the European Centre for Medium-Range Weather Forecasts (ECMWF). The new waves-in-ice module allows waves to propagate in sea ice and attenuates waves according to multiple scattering and non-elastic losses. It is found that in the simulations with wave mixing the mixed layer depth (MLD) under ice cover is reduced, since the parameterisation from wind speed overestimates wave height in the ice-covered regions. The MLD change, in turn, affects sea ice concentration and ice thickness. In the Arctic, reduced MLD in winter translates into increased ice thicknesses overall, with higher increases in the Western Arctic and decreases along the Siberian coast. In summer, shallowing of the mixed layer results in more heat accumulating in the surface ocean, increasing ice melting. In the Southern Ocean the meridional gradient in ice thickness and concentration is increased. We argue that coupling waves with sea ice - ocean models can reduce negative biases in sea ice cover, affecting the distribution of nutrients and, thus, biological productivity and ecosystems. This coupling will become more important in the future, when wave heights in a large part of the Arctic are expected to increase due to sea ice retreat and a larger wave fetch. Therefore, wave mixing constitutes a possible positive feedback mechanism.

Mechanism Underlying IκB Kinase Activation Mediated by the Linear Ubiquitin Chain Assembly Complex

PubMed Central

Fujita, Hiroaki; Akita, Mariko; Kato, Ryuichi; Sasaki, Yoshiteru; Wakatsuki, Soichi

2014-01-01

The linear ubiquitin chain assembly complex (LUBAC) ligase, consisting of HOIL-1L, HOIP, and SHARPIN, specifically generates linear polyubiquitin chains. LUBAC-mediated linear polyubiquitination has been implicated in NF-κB activation. NEMO, a component of the IκB kinase (IKK) complex, is a substrate of LUBAC, but the precise molecular mechanism underlying linear chain-mediated NF-κB activation has not been fully elucidated. Here, we demonstrate that linearly polyubiquitinated NEMO activates IKK more potently than unanchored linear chains. In mutational analyses based on the crystal structure of the complex between the HOIP NZF1 and NEMO CC2-LZ domains, which are involved in the HOIP-NEMO interaction, NEMO mutations that impaired linear ubiquitin recognition activity and prevented recognition by LUBAC synergistically suppressed signal-induced NF-κB activation. HOIP NZF1 bound to NEMO and ubiquitin simultaneously, and HOIP NZF1 mutants defective in interaction with either NEMO or ubiquitin could not restore signal-induced NF-κB activation. Furthermore, linear chain-mediated activation of IKK2 involved homotypic interaction of the IKK2 kinase domain. Collectively, these results demonstrate that linear polyubiquitination of NEMO plays crucial roles in IKK activation and that this modification involves the HOIP NZF1 domain and recognition of NEMO-conjugated linear ubiquitin chains by NEMO on another IKK complex. PMID:24469399

Analysis of Nuclear Factor-κB (NF-κB) Essential Modulator (NEMO) Binding to Linear and Lysine-linked Ubiquitin Chains and Its Role in the Activation of NF-κB*

PubMed Central

Kensche, Tobias; Tokunaga, Fuminori; Ikeda, Fumiyo; Goto, Eiji; Iwai, Kazuhiro; Dikic, Ivan

2012-01-01

Nuclear factor-κB (NF-κB) essential modulator (NEMO), a component of the inhibitor of κB kinase (IKK) complex, controls NF-κB signaling by binding to ubiquitin chains. Structural studies of NEMO provided a rationale for the specific binding between the UBAN (ubiquitin binding in ABIN and NEMO) domain of NEMO and linear (Met-1-linked) di-ubiquitin chains. Full-length NEMO can also interact with Lys-11-, Lys-48-, and Lys-63-linked ubiquitin chains of varying length in cells. Here, we show that purified full-length NEMO binds preferentially to linear ubiquitin chains in competition with lysine-linked ubiquitin chains of defined length, including long Lys-63-linked deca-ubiquitins. Linear di-ubiquitins were sufficient to activate both the IKK complex in vitro and to trigger maximal NF-κB activation in cells. In TNFα-stimulated cells, NEMO chimeras engineered to bind exclusively to Lys-63-linked ubiquitin chains mediated partial NF-κB activation compared with cells expressing NEMO that binds to linear ubiquitin chains. We propose that NEMO functions as a high affinity receptor for linear ubiquitin chains and a low affinity receptor for long lysine-linked ubiquitin chains. This phenomenon could explain quantitatively distinct NF-κB activation patterns in response to numerous cell stimuli. PMID:22605335

The CONCEPTS Global Ice-Ocean Prediction System: Establishing an Environmental Prediction Capability in Canada

NASA Astrophysics Data System (ADS)

Pellerin, Pierre; Smith, Gregory; Testut, Charles-Emmanuel; Surcel Colan, Dorina; Roy, Francois; Reszka, Mateusz; Dupont, Frederic; Lemieux, Jean-Francois; Beaudoin, Christiane; He, Zhongjie; Belanger, Jean-Marc; Deacu, Daniel; Lu, Yimin; Buehner, Mark; Davidson, Fraser; Ritchie, Harold; Lu, Youyu; Drevillon, Marie; Tranchant, Benoit; Garric, Gilles

2015-04-01

Here we describe a new system implemented recently at the Canadian Meteorological Centre (CMC) entitled the Global Ice Ocean Prediction System (GIOPS). GIOPS provides ice and ocean analyses and 10 day forecasts daily at 00GMT on a global 1/4° resolution grid. GIOPS includes a full multivariate ocean data assimilation system that combines satellite observations of sea level anomaly and sea surface temperature (SST) together with in situ observations of temperature and salinity. In situ observations are obtained from a variety of sources including: the Argo network of autonomous profiling floats, moorings, ships of opportunity, marine mammals and research cruises. Ocean analyses are blended with sea ice analyses produced by the Global Ice Analysis System.. GIOPS has been developed as part of the Canadian Operational Network of Coupled Environmental PredicTion Systems (CONCEPTS) tri-departmental initiative between Environment Canada, Fisheries and Oceans Canada and National Defense. The development of GIOPS was made through a partnership with Mercator-Océan, a French operational oceanography group. Mercator-Océan provided the ocean data assimilation code and assistance with the system implementation. GIOPS has undergone a rigorous evaluation of the analysis, trial and forecast fields demonstrating its capacity to provide high-quality products in a robust and reliable framework. In particular, SST and ice concentration forecasts demonstrate a clear benefit with respect to persistence. These results support the use of GIOPS products within other CMC operational systems, and more generally, as part of a Government of Canada marine core service. Impact of a two-way coupling between the GEM atmospheric model and NEMO-CICE ocean-ice model will also be presented.

Dense water formation in the north-western Mediterranean area during HyMeX-SOP2 in 1/36° ocean simulations: Ocean-atmosphere coupling impact

NASA Astrophysics Data System (ADS)

Lebeaupin Brossier, Cindy; Léger, Fabien; Giordani, Hervé; Beuvier, Jonathan; Bouin, Marie-Noëlle; Ducrocq, Véronique; Fourrié, Nadia

2017-07-01

The north-western Mediterranean Sea is a key location for the thermohaline circulation of the basin. The area is characterized by intense air-sea exchanges favored by the succession of strong northerly and north-westerly wind situations (mistral and tramontane) in autumn and winter. Such meteorological conditions lead to significant evaporation and ocean heat loss that are well known as the main triggering factor for the Dense Water Formation (DWF) and winter deep convection episodes. During the HyMeX second field campaign (SOP2, 1 February to 15 March 2013), several platforms were deployed in the area in order to document the DWF and the ocean deep convection, as the air-sea interface conditions. This study investigates the role of the ocean-atmosphere coupling on DWF during winter 2012-2013. The coupled system, based on the NEMO-WMED36 ocean model (1/36° resolution) and the AROME-WMED atmospheric model (2.5 km resolution), was run during 2 months covering the SOP2 and is compared to an ocean-only simulation forced by AROME-WMED real-time forecasts and to observations collected in the north-western Mediterranean area during the HyMeX SOP2. The comparison shows small differences in terms of net heat, water, and momentum fluxes. On average, DWF is slightly sensitive to air-sea coupling. However, fine-scale ocean processes, such as shelf DWF and export or eddies and fronts at the rim of the convective patch, are significantly modified. The wind-current interactions constitute an efficient coupled process at fine scale, acting as a turbulence propagating vectors, producing large mixing and convection at the rim of the convective patch.

Noncanonical NF-κB Signaling Is Limited by Classical NF-κB Activity

PubMed Central

Gray, Carolyn M.; Remouchamps, Caroline; McCorkell, Kelly A.; Solt, Laura A.; Dejardin, Emmanuel; Orange, Jordan S.; May, Michael J.

2014-01-01

Precise regulation of nuclear factor κB (NF-κB) signaling is crucial for normal immune responses, and defective NF-κB activity underlies a range of immunodeficiencies. NF-κB is activated through two signaling cascades: the classical and noncanonical pathways. The classical pathway requires inhibitor of κB kinase β (IKKβ) and NF-κB essential modulator (NEMO), and hypomorphic mutations in the gene encoding NEMO (ikbkg) lead to inherited immunodeficiencies, collectively termed NEMO-ID. Noncanonical NF-κB activation requires NF-κB–inducing kinase (NIK) and IKKα, but not NEMO. We found that noncanonical NF-κB was basally active in peripheral blood mononuclear cells from NEMO-ID patients, and that noncanonical NF-κB signaling was similarly enhanced in cell lines lacking functional NEMO. NIK, which normally undergoes constitutive degradation, was aberrantly present in resting NEMO-deficient cells, and regulation of its abundance was rescued by reconstitution with full-length NEMO, but not a mutant NEMO protein unable to physically associate with IKKα or IKKβ. Binding of NEMO to IKKα was not required for ligand-dependent stabilization of NIK or noncanonical NF-κB signaling. Rather, an intact and functional IKK complex was essential to suppress basal NIK activity in unstimulated cells. Despite interacting with IKKα and IKKβ to form an IKK complex, NEMO mutants associated with immunodeficiency failed to rescue classical NF-κB signaling or reverse the accumulation of NIK. Together, these findings identify a crucial role for classical NF-κB activity in the suppression of basal noncanonical NF-κB signaling. PMID:24497610

Medicanes in an ocean-atmosphere coupled regional climate model

NASA Astrophysics Data System (ADS)

Akhtar, Naveed; Brauch, Jennifer; Ahrens, Bodo

2014-05-01

So-called medicanes (Mediterranean hurricanes) are meso-scale, marine and warm core Mediterranean cyclones which exhibit some similarities with tropical cyclones. The strong cyclonic winds associated with them are a potential thread for highly populated coastal areas around the Mediterranean basin. In this study we employ an atmospheric limited-area model (COSMO-CLM) coupled with a one-dimensional ocean model (NEMO-1d) to simulate medicanes. The goal of this study is to assess the robustness of the coupled model to simulate these extreme events. For this purpose 11 historical medicane events are simulated by the atmosphere-only and the coupled models using different set-ups (horizontal grid-spacings: 0.44o, 0.22o, 0.088o; with/with-out spectral nudging). The results show that at high resolution the coupled model is not only able to simulate all medicane events but also improves the simulated track length, warm core, and wind speed of simulated medicanes compared to atmosphere-only simulations. In most of the cases the medicanes trajectories and structures are better represented in coupled simulations compared to atmosphere-only simulations. We conclude that the coupled model is a suitable tool for systemic and detailed study of historical medicane events and also for future projections.

Data assimilation experiments using the diffusive back and forth nudging for the NEMO ocean model

NASA Astrophysics Data System (ADS)

Ruggiero, G. A.; Ourmières, Y.; Cosme, E.; Blum, J.; Auroux, D.; Verron, J.

2014-07-01

The Diffusive Back and Forth Nudging (DBFN) is an easy-to-implement iterative data assimilation method based on the well-known Nudging method. It consists in a sequence of forward and backward model integrations, within a given time window, both of them using a feedback term to the observations. Therefore in the DBFN, the Nudging asymptotic behavior is translated into an infinite number of iterations within a bounded time domain. In this method, the backward integration is carried out thanks to what is called backward model, which is basically the forward model with reversed time step sign. To maintain numeral stability the diffusion terms also have their sign reversed, giving a diffusive character to the algorithm. In this article the DBFN performance to control a primitive equation ocean model is investigated. In this kind of model non-resolved scales are modeled by diffusion operators which dissipate energy that cascade from large to small scales. Thus, in this article the DBFN approximations and their consequences on the data assimilation system set-up are analyzed. Our main result is that the DBFN may provide results which are comparable to those produced by a 4Dvar implementation with a much simpler implementation and a shorter CPU time for convergence.

Drosophila nemo is an essential gene involved in the regulation of programmed cell death.

PubMed

Mirkovic, Ivana; Charish, Kristi; Gorski, Sharon M; McKnight, Kristen; Verheyen, Esther M

2002-11-01

Nemo-like kinases define a novel family of serine/threonine kinases that are involved in integrating multiple signaling pathways. They are conserved regulators of Wnt/Wingless pathways, which may coordinate Wnt with TGFbeta-mediated signaling. Drosophila nemo was identified through its involvement in epithelial planar polarity, a process regulated by a non-canonical Wnt pathway. We have previously found that ectopic expression of Nemo using the Gal4-UAS system resulted in embryonic lethality associated with defects in patterning and head development. In this study we present our analyses of the phenotypes of germline clone-derived embryos. We observe lethality associated with head defects and reduction of programmed cell death and conclude that nmo is an essential gene. We also present data showing that nmo is involved in regulating apoptosis during eye development, based on both loss of function phenotypes and on genetic interactions with the pro-apoptotic gene reaper. Finally, we present genetic data from the adult wing that suggest the activity of ectopically expressed Nemo can be modulated by Jun N-terminal kinase (JNK) signaling. Such an observation supports the model that there is cross-talk between Wnt, TGFbeta and JNK signaling at multiple stages of development. Copyright 2002 Elsevier Science Ireland Ltd.

NF-κB Essential Modulator (NEMO) Is Critical for Thyroid Function.

PubMed

Reale, Carla; Iervolino, Anna; Scudiero, Ivan; Ferravante, Angela; D'Andrea, Luca Egildo; Mazzone, Pellegrino; Zotti, Tiziana; Leonardi, Antonio; Roberto, Luca; Zannini, Mariastella; de Cristofaro, Tiziana; Shanmugakonar, Muralitharan; Capasso, Giovambattista; Pasparakis, Manolis; Vito, Pasquale; Stilo, Romania

2016-03-11

The I-κB kinase (IKK) subunit NEMO/IKKγ (NEMO) is an adapter molecule that is critical for canonical activation of NF-κB, a pleiotropic transcription factor controlling immunity, differentiation, cell growth, tumorigenesis, and apoptosis. To explore the functional role of canonical NF-κB signaling in thyroid gland differentiation and function, we have generated a murine strain bearing a genetic deletion of the NEMO locus in thyroid. Here we show that thyrocyte-specific NEMO knock-out mice gradually develop hypothyroidism after birth, which leads to reduced body weight and shortened life span. Histological and molecular analysis indicate that absence of NEMO in thyrocytes results in a dramatic loss of the thyroid gland cellularity, associated with down-regulation of thyroid differentiation markers and ongoing apoptosis. Thus, NEMO-dependent signaling is essential for normal thyroid physiology. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Nor-ursodeoxycholic acid reverses hepatocyte-specific nemo-dependent steatohepatitis.

PubMed

Beraza, Naiara; Ofner-Ziegenfuss, Lisa; Ehedego, Haksier; Boekschoten, Mark; Bischoff, Stephan C; Mueller, Michael; Trauner, Michael; Trautwein, Christian

2011-03-01

Hepatocyte-specific NEMO/NF-κB deleted mice (NEMO(Δhepa)) develop spontaneous non-alcoholic steatohepatitis (NASH). Free fatty acids and bile acids promote DR5 expression. TRAIL/NK cell-mediated activation of TRAIL-R2/DR5 plays an important role during acute injury in NEMO(Δhepa) mice. To inhibit the progression of NASH in the absence of hepatocyte-NEMO/NF-kB signaling. NEMOf/f and NEMO(Δhepa) mice were fed with a low-fat diet, and with two anticholestatic diets; UDCA and NorUDCA. The impact of these treatments on the progression of NASH was evaluated. We show that high expression of DR5 in livers from NEMO(Δhepa) mice is accompanied by an abundant presence of bile acids (BAs), misregulation of BA transporters and significant alteration of lipid metabolism-related genes. Additionally, mice lacking NEMO in hepatocytes spontaneously showed ductular response at young age. Unexpectedly, feeding of NEMO(Δhepa) mice with low-fat diet failed to improve chronic liver injury. Conversely, anti-cholestatic treatment with nor-ursodeoxycholic acid (NorUDCA), but not with ursodeoxycholic acid (UDCA), led to a significant attenuation of liver damage in NEMO(Δhepa) mice. The strong therapeutic effect of NorUDCA relied on a significant downregulation of LXR-dependent lipogenesis and the normalisation of BA metabolism through mechanisms involving cross-talk between Cyp7a1 and SHP. This was associated with the significant improvement of liver histology, NEMO(Δhepa)/NorUDCA-treated mice showed lower apoptosis and reduced CyclinD1 expression, indicating attenuation of the compensatory proliferative response to hepatocellular damage. Finally, fibrosis and ductular reaction markers were significantly reduced in NorUDCA-treated NEMO(Δhepa) mice. Overall, our work demonstrates the contribution of bile acids metabolism to the progression of NASH in the absence of hepatocyte-NF-kB through mechanisms involving DR5-apoptosis, inflammation and fibrosis. Our work suggests a potential therapeutic effect of NorUDCA in attenuating the progression of NASH.

Estimation of the uncertainty of a climate model using an ensemble simulation

NASA Astrophysics Data System (ADS)

Barth, A.; Mathiot, P.; Goosse, H.

2012-04-01

The atmospheric forcings play an important role in the study of the ocean and sea-ice dynamics of the Southern Ocean. Error in the atmospheric forcings will inevitably result in uncertain model results. The sensitivity of the model results to errors in the atmospheric forcings are studied with ensemble simulations using multivariate perturbations of the atmospheric forcing fields. The numerical ocean model used is the NEMO-LIM in a global configuration with an horizontal resolution of 2°. NCEP reanalyses are used to provide air temperature and wind data to force the ocean model over the last 50 years. A climatological mean is used to prescribe relative humidity, cloud cover and precipitation. In a first step, the model results is compared with OSTIA SST and OSI SAF sea ice concentration of the southern hemisphere. The seasonal behavior of the RMS difference and bias in SST and ice concentration is highlighted as well as the regions with relatively high RMS errors and biases such as the Antarctic Circumpolar Current and near the ice-edge. Ensemble simulations are performed to statistically characterize the model error due to uncertainties in the atmospheric forcings. Such information is a crucial element for future data assimilation experiments. Ensemble simulations are performed with perturbed air temperature and wind forcings. A Fourier decomposition of the NCEP wind vectors and air temperature for 2007 is used to generate ensemble perturbations. The perturbations are scaled such that the resulting ensemble spread matches approximately the RMS differences between the satellite SST and sea ice concentration. The ensemble spread and covariance are analyzed for the minimum and maximum sea ice extent. It is shown that errors in the atmospheric forcings can extend to several hundred meters in depth near the Antarctic Circumpolar Current.

Recent assimilation developments of FOAM the Met Office ocean forecast system

NASA Astrophysics Data System (ADS)

Lea, Daniel; Martin, Matthew; Waters, Jennifer; Mirouze, Isabelle; While, James; King, Robert

2015-04-01

FOAM is the Met Office's operational ocean forecasting system. This system comprises a range of models from a 1/4 degree resolution global to 1/12 degree resolution regional models and shelf seas models at 7 km resolution. The system is made up of the ocean model NEMO (Nucleus for European Modeling of the Ocean), the Los Alomos sea ice model CICE and the NEMOVAR assimilation run in 3D-VAR FGAT mode. Work is ongoing to transition to both a higher resolution global ocean model at 1/12 degrees and to run FOAM in coupled models. The FOAM system generally performs well. One area of concern however is the performance in the tropics where spurious oscillations and excessive vertical velocity gradients are found after assimilation. NEMOVAR includes a balance operator which in the extra-tropics uses geostrophic balance to produce velocity increments which balance the density increments applied. In the tropics, however, the main balance is between the pressure gradients produced by the density gradient and the applied wind stress. A scheme is presented which aims to maintain this balance when increments are applied. Another issue in FOAM is that there are sometimes persistent temperature and salinity errors which are not effectively corrected by the assimilation. The standard NEMOVAR has a single correlation length scale based on the local Rossby radius. This means that observations in the extra tropics have influence on the model only on short length-scales. In order to maximise the information extracted from the observations and to correct large scale model biases a multiple correlation length-scale scheme has been developed. This includes a larger length scale which spreads observation information further. Various refinements of the scheme are also explored including reducing the longer length scale component at the edge of the sea ice and in areas with high potential vorticity gradients. A related scheme which varies the correlation length scale in the shelf seas is also described.

Particle transport model sensitivity on wave-induced processes

NASA Astrophysics Data System (ADS)

Staneva, Joanna; Ricker, Marcel; Krüger, Oliver; Breivik, Oyvind; Stanev, Emil; Schrum, Corinna

2017-04-01

Different effects of wind waves on the hydrodynamics in the North Sea are investigated using a coupled wave (WAM) and circulation (NEMO) model system. The terms accounting for the wave-current interaction are: the Stokes-Coriolis force, the sea-state dependent momentum and energy flux. The role of the different Stokes drift parameterizations is investigated using a particle-drift model. Those particles can be considered as simple representations of either oil fractions, or fish larvae. In the ocean circulation models the momentum flux from the atmosphere, which is related to the wind speed, is passed directly to the ocean and this is controlled by the drag coefficient. However, in the real ocean, the waves play also the role of a reservoir for momentum and energy because different amounts of the momentum flux from the atmosphere is taken up by the waves. In the coupled model system the momentum transferred into the ocean model is estimated as the fraction of the total flux that goes directly to the currents plus the momentum lost from wave dissipation. Additionally, we demonstrate that the wave-induced Stokes-Coriolis force leads to a deflection of the current. During the extreme events the Stokes velocity is comparable in magnitude to the current velocity. The resulting wave-induced drift is crucial for the transport of particles in the upper ocean. The performed sensitivity analyses demonstrate that the model skill depends on the chosen processes. The results are validated using surface drifters, ADCP, HF radar data and other in-situ measurements in different regions of the North Sea with a focus on the coastal areas. The using of a coupled model system reveals that the newly introduced wave effects are important for the drift-model performance, especially during extremes. Those effects cannot be neglected by search and rescue, oil-spill, transport of biological material, or larva drift modelling.

Benchmarking the mesoscale variability in global ocean eddy-permitting numerical systems

NASA Astrophysics Data System (ADS)

Cipollone, Andrea; Masina, Simona; Storto, Andrea; Iovino, Doroteaciro

2017-10-01

The role of data assimilation procedures on representing ocean mesoscale variability is assessed by applying eddy statistics to a state-of-the-art global ocean reanalysis (C-GLORS), a free global ocean simulation (performed with the NEMO system) and an observation-based dataset (ARMOR3D) used as an independent benchmark. Numerical results are computed on a 1/4 ∘ horizontal grid (ORCA025) and share the same resolution with ARMOR3D dataset. This "eddy-permitting" resolution is sufficient to allow ocean eddies to form. Further to assessing the eddy statistics from three different datasets, a global three-dimensional eddy detection system is implemented in order to bypass the need of regional-dependent definition of thresholds, typical of commonly adopted eddy detection algorithms. It thus provides full three-dimensional eddy statistics segmenting vertical profiles from local rotational velocities. This criterion is crucial for discerning real eddies from transient surface noise that inevitably affects any two-dimensional algorithm. Data assimilation enhances and corrects mesoscale variability on a wide range of features that cannot be well reproduced otherwise. The free simulation fairly reproduces eddies emerging from western boundary currents and deep baroclinic instabilities, while underestimates shallower vortexes that populate the full basin. The ocean reanalysis recovers most of the missing turbulence, shown by satellite products , that is not generated by the model itself and consistently projects surface variability deep into the water column. The comparison with the statistically reconstructed vertical profiles from ARMOR3D show that ocean data assimilation is able to embed variability into the model dynamics, constraining eddies with in situ and altimetry observation and generating them consistently with local environment.

Spatial variability of the Black Sea surface temperature from high resolution modeling and satellite measurements

NASA Astrophysics Data System (ADS)

Mizyuk, Artem; Senderov, Maxim; Korotaev, Gennady

2016-04-01

Large number of numerical ocean models were implemented for the Black Sea basin during last two decades. They reproduce rather similar structure of synoptical variability of the circulation. Since 00-s numerical studies of the mesoscale structure are carried out using high performance computing (HPC). With the growing capacity of computing resources it is now possible to reconstruct the Black Sea currents with spatial resolution of several hundreds meters. However, how realistic these results can be? In the proposed study an attempt is made to understand which spatial scales are reproduced by ocean model in the Black Sea. Simulations are made using parallel version of NEMO (Nucleus for European Modelling of the Ocean). A two regional configurations with spatial resolutions 5 km and 2.5 km are described. Comparison of the SST from simulations with two spatial resolutions shows rather qualitative difference of the spatial structures. Results of high resolution simulation are compared also with satellite observations and observation-based products from Copernicus using spatial correlation and spectral analysis. Spatial scales of correlations functions for simulated and observed SST are rather close and differs much from satellite SST reanalysis. Evolution of spectral density for modelled SST and reanalysis showed agreed time periods of small scales intensification. Using of the spectral analysis for satellite measurements is complicated due to gaps. The research leading to this results has received funding from Russian Science Foundation (project № 15-17-20020)

Aerosol Monitoring Mission using an Advanced Nanosatellite

NASA Astrophysics Data System (ADS)

Pranajaya, Freddy; Zee, Robert E.

The Space Flight Laboratory (SFL) at the University of Toronto Institute for Aerospace Studies (UTIAS) is currently developing a nanosatellite for the purpose of monitoring aerosol content in the atmosphere. The NEMO-AM (Nanosatellite for Earth Monitoring and Observation -Aerosol Monitoring) spacecraft is designed to perform multi-angle, dual-polarization observa-tions in three visible bands. The satellite is designed to detect aerosol content in the atmosphere over a specific region with a nominal ground resolution of up to 200 m and a minimum swath of 120 km. NEMO-AM is being built under a collaborative agreement between SFL and the Indian Space Research Organization (ISRO). SFL is responsible for the design, manufacturing and qualification of the spacecraft and the optical instrument. The NEMO-AM is based on the NEMO bus, which is the next evolution to the SFL Generic Nanosatellite Bus (GNB) technology. The NEMO bus has a primary structure measuring 20 cm by 20 cm by 40 cm and is capable of peak power generation up to 80W. A minimum of 30W is available to the payload. The high peak power generation enables the NEMO bus to support a dedicated state-of-the-art high speed transmitter. The NEMO bus is designed with a total mass of 15 kg, 9 kg of which is dedicated to the payload. It can be configured for full three-axis control with up to 1 arcmin pointing stability. NEMO spacecraft will be secured to launch vehicles using the XPOD Duo separation system. This paper will summarize the NEMO-AM mission and the innovative aspects of the NEMO bus.

Simulating the Agulhas system in global ocean models - nesting vs. multi-resolution unstructured meshes

NASA Astrophysics Data System (ADS)

Biastoch, Arne; Sein, Dmitry; Durgadoo, Jonathan V.; Wang, Qiang; Danilov, Sergey

2018-01-01

Many questions in ocean and climate modelling require the combined use of high resolution, global coverage and multi-decadal integration length. For this combination, even modern resources limit the use of traditional structured-mesh grids. Here we compare two approaches: A high-resolution grid nested into a global model at coarser resolution (NEMO with AGRIF) and an unstructured-mesh grid (FESOM) which allows to variably enhance resolution where desired. The Agulhas system around South Africa is used as a testcase, providing an energetic interplay of a strong western boundary current and mesoscale dynamics. Its open setting into the horizontal and global overturning circulations also requires global coverage. Both model configurations simulate a reasonable large-scale circulation. Distribution and temporal variability of the wind-driven circulation are quite comparable due to the same atmospheric forcing. However, the overturning circulation differs, owing each model's ability to represent formation and spreading of deep water masses. In terms of regional, high-resolution dynamics, all elements of the Agulhas system are well represented. Owing to the strong nonlinearity in the system, Agulhas Current transports of both configurations and in comparison with observations differ in strength and temporal variability. Similar decadal trends in Agulhas Current transport and Agulhas leakage are linked to the trends in wind forcing.

Evaluation of an operational ocean model configuration at 1/12° spatial resolution for the Indonesian seas - Part 1: Ocean physics

NASA Astrophysics Data System (ADS)

Tranchant, B.; Reffray, G.; Greiner, E.; Nugroho, D.; Koch-Larrouy, A.; Gaspar, P.

2015-08-01

INDO12, a 1/12° regional version of the NEMO physical ocean model covering the whole Indonesian EEZ has been developed and is now running every week in the framework of the INDESO project (Infrastructure Development of Space Oceanography) implemented by the Indonesian Ministry of Marine Affairs and Fisheries. The initial hydrographic conditions as well as open boundary conditions are derived from the operational global ocean forecasting system at 1/4° operated by Mercator Ocean. Atmospheric forcing fields (3 hourly ECMWF analyses) are used to force the regional model. INDO12 is also forced by tidal currents and elevations, and by the inverse barometer effect. The turbulent mixing induced by internal tides is taken into account through a specific parameterization. In this study we evaluate the model skill through comparisons with various datasets including outputs of the parent model, climatologies, in situ temperature and salinity measurements, and satellite data. The simulated and altimeter-derived Eddy Kinetic Energy fields display similar patterns and confirm that tides are a dominant forcing in the area. The volume transport of the Indonesian ThroughFlow is in good agreement with the INSTANT current meter estimates while the transport through Luzon Strait is, on average, westward but probably too weak. Significant water mass transformation occurs along the main routes of the Indonesian Throughflow (ITF) and compares well with observations. Vertical mixing is able to erode the South and North Pacific subtropical waters salinity maximum as seen in TS diagrams. Compared to satellite data, surface salinity and temperature fields display marked biases in the South China Sea. Altogether, INDO12 proves to be able to provide a very realistic simulation of the ocean circulation and water mass transformation through the Indonesian Archipelago. A few weaknesses are also detected. Work is on-going to reduce or eliminate these problems in the second INDO12 version.

Variable reactivity of particulate organic matter in a global ocean biogeochemical model

NASA Astrophysics Data System (ADS)

Aumont, Olivier; van Hulten, Marco; Roy-Barman, Matthieu; Dutay, Jean-Claude; Éthé, Christian; Gehlen, Marion

2017-05-01

The marine biological carbon pump is dominated by the vertical transfer of particulate organic carbon (POC) from the surface ocean to its interior. The efficiency of this transfer plays an important role in controlling the amount of atmospheric carbon that is sequestered in the ocean. Furthermore, the abundance and composition of POC is critical for the removal of numerous trace elements by scavenging, a number of which, such as iron, are essential for the growth of marine organisms, including phytoplankton. Observations and laboratory experiments have shown that POC is composed of numerous organic compounds that can have very different reactivities. However, this variable reactivity of POC has never been extensively considered, especially in modelling studies. Here, we introduced in the global ocean biogeochemical model NEMO-PISCES a description of the variable composition of POC based on the theoretical reactivity continuum model proposed by Boudreau and Ruddick (1991). Our model experiments show that accounting for a variable lability of POC increases POC concentrations in the ocean's interior by 1 to 2 orders of magnitude. This increase is mainly the consequence of a better preservation of small particles that sink slowly from the surface. Comparison with observations is significantly improved both in abundance and in size distribution. Furthermore, the amount of carbon that reaches the sediments is increased by more than a factor of 2, which is in better agreement with global estimates of the sediment oxygen demand. The impact on the major macronutrients (nitrate and phosphate) remains modest. However, iron (Fe) distribution is strongly altered, especially in the upper mesopelagic zone as a result of more intense scavenging: vertical gradients in Fe are milder in the upper ocean, which appears to be closer to observations. Thus, our study shows that the variable lability of POC can play a critical role in the marine biogeochemical cycles which advocates for more dedicated in situ and laboratory experiments.

Finding NEMO in preeclampsia.

PubMed

Sakowicz, Agata; Hejduk, Paulina; Pietrucha, Tadeusz; Nowakowska, Magdalena; Płuciennik, Elżbieta; Pospiech, Karolina; Gach, Agnieszka; Rybak-Krzyszkowska, Magda; Sakowicz, Bartosz; Kaminski, Marek; Krasomski, Grzegorz; Biesiada, Lidia

2016-04-01

The mechanism of preeclampsia and its way of inheritance are still a mystery. Biochemical and immunochemical studies reveal a substantial increase in tumor necrosis factor alpha, interleukin-1 beta, and interleukin-6 concentrations in the blood of women with preeclampsia. The level of these factors is regulated by nuclear facxtor-kappa B, whose activation in a classical pathway requires inhibitory kappa B kinase gamma (known as NEMO or IKBKG). Moreover, NEMO can schedule between cytoplasma and the nucleus. In the nucleus, IKBKG interacts with other proteins, and thus, it is implicated in the regulation of different gene expressions, which are related to cell cycle progression, proliferation, differentiation, and apoptosis. This is the first study investigating the association between the level of NEMO gene expression and the presence of preeclampsia. We tested the hypothesis that the simultaneous increase in NEMO gene expression both in the mother and her fetus may be responsible for the preeclampsia development. Moreover, the relationships between clinical risk factors of preeclampsia and the levels of NEMO gene expression in blood, umbilical cord blood, and placentas were investigated. A total of 91 women (43 preeclamptic women and 48 controls) and their children were examined. Real-time reverse transcription-polymerase chain reaction was used to assess the amount total NEMO messenger ribonucleic acid (mRNA) content and the mRNA level of each NEMO transcript from exons 1A, 1B, and 1C in maternal blood, umbilical cord blood, and placentas. Univariate analyses and correlation tests were performed to examine the association between NEMO gene expression and preeclampsia. Newborn weight and height, maternal platelet number, and gestational age (week of delivery) were lower in the group of women with preeclampsia than controls. NEMO gene expression level was found to be almost 7 times higher in the group of women with preeclampsia than healthy controls. The correlation analysis found that a simultaneous increase in the expression level of total NEMO mRNA in maternal blood and the mRNA for total NEMO (Rs = 0.311, P < .05), transcripts 1A (Rs = 0.463, P < .01), 1B (Rs = 0.454, P < .01), and 1C (Rs = 0.563, P < .001) in fetal blood was observed in preeclamptic pregnancies. In addition, the mRNA levels for total NEMO and transcripts 1A, 1B, and 1C were lower in placentas derived from pregnancies complicated by preeclampsia. Simultaneous increase of NEMO gene expression in maternal and fetal blood seems to be relevant for preeclampsia development. The results of our study also suggest that a decreased NEMO gene expression level in preeclamptic placentas may be the main reason for their intensified apoptosis. Copyright © 2016 Elsevier Inc. All rights reserved.

NEMO educational kit on micro-optics at the secondary school

NASA Astrophysics Data System (ADS)

Flores-Arias, M. T.; Bao-Varela, Carmen

2014-07-01

NEMO was the "Network of Excellence in Micro-Optics" granted in the "Sixth Framework Program" of the European Union. It aimed at providing Europe with a complete Micro-Optics food-chain, by setting up centers for optical modeling and design; measurement and instrumentation; mastering, prototyping and replication; integration and packaging and reliability and standardization. More than 300 researchers from 30 groups in 12 countries participated in the project. One of the objectives of NEMO was to spread excellence and disseminate knowledge on micro-optics and micro-photonics. To convince pupils, already from secondary school level on, about the crucial role of light and micro-optics and the opportunities this combination holds, several partners of NEMO had collaborate to create this Educational Kit. In Spain the partner involved in this aim was the "Microoptics and GRIN Optics Group" at the University of Santiago of Compostela (USC). The educational kits provided to the Secondary School were composed by two plastic cards with the following microoptical element: different kinds of diffractive optical elements or DOES and refractive optical elements or ROEs namely arrays of micro-lenses. The kit also included a DVD with a handbook for performing the experiments as well as a laser pointer source. This kit was distributed free of charge in the countries with partners in NEMO. In particular in Spain was offered to around 200 Secondary School Centers and only 80 answered accepting evaluate the kit.

Modelling the impacts of a dipole-like climatic state over the Arctic

NASA Astrophysics Data System (ADS)

Pasha Karami, Mehdi; de Vernal, Anne; Hu, Xianmin; Myers, Paul G.

2015-04-01

The Arctic dipole anomaly (ADA) features a pattern with opposite sea-level pressure anomalies over the Canadian Archipelago and the Barents Sea. Changes in the predominance of Arctic atmospheric circulation modes and the shift towards a dipole mode in the past decade played a role in the summer sea ice loss and sea ice-freshwater export from the Arctic to the North Atlantic. Reconstruction of sea ice cover variations during Holocene also suggests opposite anomalies in the Barents Sea versus either the western Arctic or the Fram Strait area similar to the ADA pattern. It is vital to study such physical processes that cause dramatic changes in the Arctic sea ice recalling the link between the ADA and the current climate change. Here we focus on the question of how a persistent ADA-like state affects the Arctic sea ice distribution and its outflow to the Atlantic Ocean. For this purpose, an eddy-permitting regional configuration of the NEMO coupled ocean/sea-ice model is used. The regional domain covers the Arctic Ocean and the Northern-Hemisphere Atlantic, with a horizontal resolution of 1/4 degree at the equator (ANHA4). For the present-day simulations, boundary conditions are obtained by taking the average over the years with a positive ADA and those with a negative ADA. In the Holocene scenario, global climate model data are used to force our regional model. To exclude the role of Bering Strait and the heat flux from the Pacific Ocean, we repeat the experiments with a closed Bering Strait since a nearly closed Bering configuration was possible for the Early Holocene. The model results are compared with the paleoclimate data from Arctic and subarctic seas.

Simulation of double beta decay in the ''SeXe'' TPC

NASA Astrophysics Data System (ADS)

Mauger, F.

2007-04-01

In 2004, the NEMO collaboration has started some preliminary studies for a next-generation double beta decay experiment: SuperNEMO. The possibility to use a large gaseous TPC has been investigated using simulation and extrapolation of former experiments. In this talk, I report on the reasons why such techniques have not been selected in 2004 and led the NEMO collaboration to reuse the techniques implemented within the NEMO3 detector.

Polyubiquitin conjugation to NEMO by triparite motif protein 23 (TRIM23) is critical in antiviral defense

PubMed Central

Arimoto, Kei-ichiro; Funami, Kenji; Saeki, Yasushi; Tanaka, Keiji; Okawa, Katsuya; Takeuchi, Osamu; Akira, Shizuo; Murakami, Yoshiki; Shimotohno, Kunitada

2010-01-01

The rapid induction of type I IFN is a central event of the innate defense against viral infections and is tightly regulated by a number of cellular molecules. Viral components induce strong type I IFN responses through the activation of toll-like receptors (TLRs) and intracellular cytoplasmic receptors such as an RNA helicase RIG-I and/or MDA5. According to recent studies, the NF-κB essential modulator (NEMO, also called IKKγ) is crucial for this virus-induced antiviral response. However, the precise roles of signal activation by NEMO adaptor have not been elucidated. Here, we show that virus-induced IRF3 and NF-κB activation depends on the K(lys)-27-linked polyubiquitination to NEMO by the novel ubiquitin E3 ligase triparite motif protein 23 (TRIM23). Virus-induced IRF3 and NF-κB activation, as well as K27-linked NEMO polyubiquitination, were abrogated in TRIM23 knockdown cells, whereas TRIM23 knockdown had no effect on TNFα-mediated NF-κB activation. Furthermore, in NEMO-deficient mouse embryo fibroblast cells, IFN-stimulated response element-driven reporter activity was restored by ectopic expression of WT NEMO, as expected, but only partial recovery by NEMO K165/309/325/326/344R multipoints mutant on which TRIM23-mediated ubiquitin conjugation was substantially reduced. Thus, we conclude that TRIM23-mediated ubiquitin conjugation to NEMO is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. PMID:20724660

Interannual variability of primary production and air-sea CO2 flux in the Atlantic and Indian sectors of the Southern Ocean.

NASA Astrophysics Data System (ADS)

Dufour, Carolina; Merlivat, Liliane; Le Sommer, Julien; Boutin, Jacqueline; Antoine, David

2013-04-01

As one of the major oceanic sinks of anthropogenic CO2, the Southern Ocean plays a critical role in the climate system. However, due to the scarcity of observations, little is known about physical and biological processes that control air-sea CO2 fluxes and how these processes might respond to climate change. It is well established that primary production is one of the major drivers of air-sea CO2 fluxes, consuming surface Dissolved Inorganic Carbon (DIC) during Summer. Southern Ocean primary production is though constrained by several limiting factors such as iron and light availability, which are both sensitive to mixed layer depth. Mixed layer depth is known to be affected by current changes in wind stress or freshwater fluxes over the Southern Ocean. But we still don't know how primary production may respond to anomalous mixed layer depth neither how physical processes may balance this response to set the seasonal cycle of air-sea CO2 fluxes. In this study, we investigate the impact of anomalous mixed layer depth on surface DIC in the Atlantic and Indian sectors of the Subantarctic zone of the Southern Ocean (60W-60E, 38S-55S) with a combination of in situ data, satellite data and model experiment. We use both a regional eddy permitting ocean biogeochemical model simulation based on NEMO-PISCES and data-based reconstruction of biogeochemical fields based on CARIOCA buoys and SeaWiFS data. A decomposition of the physical and biological processes driving the seasonal variability of surface DIC is performed with both the model data and observations. A good agreement is found between the model and the data for the amplitude of biological and air-sea flux contributions. The model data are further used to investigate the impact of winter and summer anomalies in mixed layer depth on surface DIC over the period 1990-2004. The relative changes of each physical and biological process contribution are quantified and discussed.

Effects of eustatic sea-level change, ocean dynamics, and nutrient utilization on atmospheric pCO2 and seawater composition over the last 130 000 years: a model study

NASA Astrophysics Data System (ADS)

Wallmann, K.; Schneider, B.; Sarnthein, M.

2016-02-01

We have developed and employed an Earth system model to explore the forcings of atmospheric pCO2 change and the chemical and isotopic evolution of seawater over the last glacial cycle. Concentrations of dissolved phosphorus (DP), reactive nitrogen, molecular oxygen, dissolved inorganic carbon (DIC), total alkalinity (TA), 13C-DIC, and 14C-DIC were calculated for 24 ocean boxes. The bi-directional water fluxes between these model boxes were derived from a 3-D circulation field of the modern ocean (Opa 8.2, NEMO) and tuned such that tracer distributions calculated by the box model were consistent with observational data from the modern ocean. To model the last 130 kyr, we employed records of past changes in sea-level, ocean circulation, and dust deposition. According to the model, about half of the glacial pCO2 drawdown may be attributed to marine regressions. The glacial sea-level low-stands implied steepened ocean margins, a reduced burial of particulate organic carbon, phosphorus, and neritic carbonate at the margin seafloor, a decline in benthic denitrification, and enhanced weathering of emerged shelf sediments. In turn, low-stands led to a distinct rise in the standing stocks of DIC, TA, and nutrients in the global ocean, promoted the glacial sequestration of atmospheric CO2 in the ocean, and added 13C- and 14C-depleted DIC to the ocean as recorded in benthic foraminifera signals. The other half of the glacial drop in pCO2 was linked to inferred shoaling of Atlantic meridional overturning circulation and more efficient utilization of nutrients in the Southern Ocean. The diminished ventilation of deep water in the glacial Atlantic and Southern Ocean led to significant 14C depletions with respect to the atmosphere. According to our model, the deglacial rapid and stepwise rise in atmospheric pCO2 was induced by upwelling both in the Southern Ocean and subarctic North Pacific and promoted by a drop in nutrient utilization in the Southern Ocean. The deglacial sea-level rise led to a gradual decline in nutrient, DIC, and TA stocks, a slow change due to the large size and extended residence times of dissolved chemical species in the ocean. Thus, the rapid deglacial rise in pCO2 can be explained by fast changes in ocean dynamics and nutrient utilization whereas the gradual pCO2 rise over the Holocene may be linked to the slow drop in nutrient and TA stocks that continued to promote an ongoing CO2 transfer from the ocean into the atmosphere.

Target Specificity of the E3 Ligase LUBAC for Ubiquitin and NEMO Relies on Different Minimal Requirements*

PubMed Central

Smit, Judith J.; van Dijk, Willem J.; El Atmioui, Dris; Merkx, Remco; Ovaa, Huib; Sixma, Titia K.

2013-01-01

The ubiquitination of NEMO with linear ubiquitin chains by the E3-ligase LUBAC is important for the activation of the canonical NF-κB pathway. NEMO ubiquitination requires a dual target specificity of LUBAC, priming on a lysine on NEMO and chain elongation on the N terminus of the priming ubiquitin. Here we explore the minimal requirements for these specificities. Effective linear chain formation requires a precise positioning of the ubiquitin N-terminal amine in a negatively charged environment on the top of ubiquitin. Whereas the RBR-LDD region on HOIP is sufficient for targeting the ubiquitin N terminus, the priming lysine modification on NEMO requires catalysis by the RBR domain of HOIL-1L as well as the catalytic machinery of the RBR-LDD domains of HOIP. Consequently, target specificity toward NEMO is determined by multiple LUBAC components, whereas linear ubiquitin chain elongation is realized by a specific interplay between HOIP and ubiquitin. PMID:24030825

Correlating interleukin-12 stimulated interferon-γ production and the absence of ectodermal dysplasia and anhidrosis (EDA) in patients with mutations in NF-κB essential modulator (NEMO).

PubMed

Haverkamp, Margje H; Marciano, Beatriz E; Frucht, David M; Jain, Ashish; van de Vosse, Esther; Holland, Steven M

2014-05-01

Patients with hypomorphic mutations in Nuclear Factor-κB Essential Modulator (NEMO) are immunodeficient (ID) and most display ectodermal dysplasia and anhidrosis (EDA). We compared cytokine production by NEMO-ID patients with and without EDA. PBMCs of NEMO-ID patients, four with EDA carrying E315A, C417R, D311N and Q403X, and three without EDA carrying E315A, E311_L333del and R254G, were cultured with PHA, PHA plus IL-12p70, LPS, LPS plus IFN-γ, TNF and IL-1β. The production of various cytokines was measured in the supernatants. Fifty-nine healthy individuals served as controls. PBMCs of NEMO-ID patients without EDA produce subnormal amounts of IFN-γ after stimulation with PHA, but normal amounts of IFN-γ after PHA plus IL-12p70. In contrast, IFN-γ production by patients with EDA was low in both cases. Patients with EDA also generate lower PHA-stimulated IL-10 and IL-1β than controls, whereas the production of these cytokines by patients without EDA was normal. Responses of PBMCs in NEMO-ID patients with EDA to PHA with and without IL-12p70 appear less robust than in NEMO-ID patients without EDA. This possibly indicates a better preserved NEMO function in our patients without EDA.

Ocean modelling aspects for drift applications

NASA Astrophysics Data System (ADS)

Stephane, L.; Pierre, D.

2010-12-01

Nowadays, many authorities in charge of rescue-at-sea operations lean on operational oceanography products to outline research perimeters. Moreover, current fields estimated with sophisticated ocean forecasting systems can be used as input data for oil spill/ adrift object fate models. This emphasises the necessity of an accurate sea state forecast, with a mastered level of reliability. This work focuses on several problems inherent to drift modeling, dealing in the first place with the efficiency of the oceanic current field representation. As we want to discriminate the relevance of a particular physical process or modeling option, the idea is to generate series of current fields of different characteristics and then qualify them in term of drift prediction efficiency. Benchmarked drift scenarios were set up from real surface drifters data, collected in the Mediterranean sea and off the coasts of Angola. The time and space scales that we are interested in are about 72 hr forecasts (typical timescale communicated in case of crisis), for distance errors that we hope about a few dozen of km around the forecast (acceptable for reconnaissance by aircrafts) For the ocean prediction, we used some regional oceanic configurations based on the NEMO 2.3 code, nested into Mercator 1/12° operational system. Drift forecasts were computed offline with Mothy (Météo France oil spill modeling system) and Ariane (B. Blanke, 1997), a Lagrangian diagnostic tool. We were particularly interested in the importance of the horizontal resolution, vertical mixing schemes, and any processes that may impact the surface layer. The aim of the study is to ultimately point at the most suitable set of parameters for drift forecast use inside operational oceanic systems. We are also motivated in assessing the relevancy of ensemble forecasts regarding determinist predictions. Several tests showed that mis-described observed trajectories can finally be modelled statistically by using uncertainties over the initial position of the drifting material. Works in the near future will explore that concept with ensemble of currents obtained with different initial conditions, phase shifted boundary forcings or perturbed atmospheric surface forcings.

Future change in ocean productivity: Is the Arctic the new Atlantic?

NASA Astrophysics Data System (ADS)

Yool, A.; Popova, E. E.; Coward, A. C.

2015-12-01

One of the most characteristic features in ocean productivity is the North Atlantic spring bloom. Responding to seasonal increases in irradiance and stratification, surface phytopopulations rise significantly, a pattern that visibly tracks poleward into summer. While blooms also occur in the Arctic Ocean, they are constrained by the sea-ice and strong vertical stratification that characterize this region. However, Arctic sea-ice is currently declining, and forecasts suggest this may lead to completely ice-free summers by the mid-21st century. Such change may open the Arctic up to Atlantic-style spring blooms, and do so at the same time as Atlantic productivity is threatened by climate change-driven ocean stratification. Here we use low and high-resolution instances of a coupled ocean-biogeochemistry model, NEMO-MEDUSA, to investigate productivity. Drivers of present-day patterns are identified, and changes in these across a climate change scenario (IPCC RCP 8.5) are analyzed. We find a globally significant decline in North Atlantic productivity (> -20%) by 2100, and a correspondingly significant rise in the Arctic (> +50%). However, rather than the future Arctic coming to resemble the current Atlantic, both regions are instead transitioning to a common, low nutrient regime. The North Pacific provides a counterexample where nutrients remain high and productivity increases with elevated temperature. These responses to climate change in the Atlantic and Arctic are common between model resolutions, suggesting an independence from resolution for key impacts. However, some responses, such as those in the North Pacific, differ between the simulations, suggesting the reverse and supporting the drive to more fine-scale resolutions. This article was corrected on 5 JAN 2016. See the end of the full text for details.

Toward variational assimilation of SARAL/Altika altimeter data in a North Atlantic circulation model at eddy-permitting resolution: assessment of a NEMO-based 4D-VAR system

NASA Astrophysics Data System (ADS)

Bouttier, Pierre-Antoine; Brankart, Jean-Michel; Candille, Guillem; Vidard, Arthur; Blayo, Eric; Verron, Jacques; Brasseur, Pierre

2015-04-01

In this project, the response of a variational data assimilation system based on NEMO and its linear tangent and adjoint model is investigated using a 4DVAR algorithm into a North-Atlantic model at eddy-permitting resolution. The assimilated data consist of Jason-2 and SARAL/AltiKA dataset collected during the 2013-2014 period. The main objective is to explore the robustness of the 4DVAR algorithm in the context of a realistic turbulent oceanic circulation at mid-latitude constrained by multi-satellite altimetry missions. This work relies on two previous studies. First, a study with similar objectives was performed based on academic double-gyre turbulent model and synthetic SARAL/AltiKA data, using the same DA experimental framework. Its main goal was to investigate the impact of turbulence on variational DA methods performance. The comparison with this previous work will bring to light the methodological and physical issues encountered by variational DA algorithms in a realistic context at similar, eddy-permitting spatial resolution. We also have demonstrated how a dataset mimicking future SWOT observations improves 4DVAR incremental performances at eddy-permitting resolution. Then, in the context of the OSTST and FP7 SANGOMA projects, an ensemble DA experiment based on the same model and observational datasets has been realized (see poster by Brasseur et al.). This work offers the opportunity to compare efficiency, pros and cons of both DA methods in the context of KA-band altimetric data, at spatial resolution commonly used today for research and operational applications. In this poster we will present the validation plan proposed to evaluate the skill of variational experiment vs. ensemble assimilation experiments covering the same period using independent observations (e.g. from Cryosat-2 mission).

The UKC2 regional coupled prediction system

NASA Astrophysics Data System (ADS)

Castillo, Juan; Lewis, Huw; Graham, Jennifer; Saulter, Andrew; Arnold, Alex; Fallmann, Joachim; Martinez de la Torre, Alberto; Blyth, Eleanor; Bricheno, Lucy

2017-04-01

It is hypothesized that more accurate prediction and warning of natural hazards, such as of the impacts of severe weather through the environment, requires a more integrated approach to forecasting. This approach also delivers research benefits through providing tools with which to explore the known interactions and feedbacks between different physical and biogeochemical components of the environment across sky, sea and land. This hypothesis is being tested in a UK regional context at km-scale through the UK Environmental Prediction Project. This presentation will provide an introduction to the UKC2 UK Environmental Prediction research system. This incorporates models of the atmosphere (Met Office Unified Model), land surface (JULES), shelf-sea ocean (NEMO) and ocean waves (WAVEWATCH III). These components are coupled (via OASIS3-MCT libraries) at unprecedentedly high resolution across the UK and the wider north-west European regional domain. A research framework has been established to explore the representation of feedback processes in coupled and uncoupled modes, providing a unique new research tool for UK environmental science. The presentation will highlight work undertaken to review and improve the computational cost of running these systems for efficient research application. Research will be presented highlighting case study evaluation on the sensitivity of the ocean and surface waves to the representation of feedbacks to the atmosphere, and on the sensitivity of weather systems and boundary layer cloud development to the exchange of heat and momentum at the ocean surface modified through sea surface temperature and wave-induced roughness. The presentation will discuss plans for future development through UKC3 and beyond.

Optimal boundary conditions for ORCA-2 model

NASA Astrophysics Data System (ADS)

Kazantsev, Eugene

2013-08-01

A 4D-Var data assimilation technique is applied to ORCA-2 configuration of the NEMO in order to identify the optimal parametrization of boundary conditions on the lateral boundaries as well as on the bottom and on the surface of the ocean. The influence of boundary conditions on the solution is analyzed both within and beyond the assimilation window. It is shown that the optimal bottom and surface boundary conditions allow us to better represent the jet streams, such as Gulf Stream and Kuroshio. Analyzing the reasons of the jets reinforcement, we notice that data assimilation has a major impact on parametrization of the bottom boundary conditions for u and v. Automatic generation of the tangent and adjoint codes is also discussed. Tapenade software is shown to be able to produce the adjoint code that can be used after a memory usage optimization.

The use of EuroCordex in marine climate projections

NASA Astrophysics Data System (ADS)

Tinker, Jonathan; Palmer, Matthew; Lowe, Jason; Howard, Tom

2017-04-01

The Northwest European Shelf seas (NWS, including the North Sea, Irish Sea and Celtic Sea) are of economic, environmental and cultural importance to a number of European countries. However, their representation by global climate models (GCMs) is very crude, due to their inability to represent the complex geometry and the absence of tides. Therefore, there is a need to employ dynamical downscaling methods when considering the potential impacts of climate change on the European (and other) shelf seas. Using a shelf seas model to dynamically downscale of the ocean component of the GCM is a well established method. While taking open ocean lateral boundary conditions from the GCM ocean is acceptable, using surface flux forcings from the GCM atmosphere is often problematic. The CORDEX project provides an important dataset of high spatial and temporal resolution atmospheric forcings, derived from 'parent' CMIP5 GCM simulations. We drive the NEMO shelf seas model with data from CMIP5 models and EURO-CORDEX Regional Climate Model (RCM) data to produce a set of NWS climate projections. We require relatively high temporal resolution output, and run-off (for the river forcings), and so are limited to a subset of the available EURO-CORDEX RCMs. From these we select two CMIP5 GCMs with the same RCM with two emissions scenarios to give a minimum estimate of GCM model structural and emission scenario uncertainty. Other experiments allow an initial estimate of the uncertainty associated with the model structure of both the shelf seas and the RCM. Our analysis is focused on the uncertainty associated with the mean change in a number of physical marine impacts and the drivers of coastal variability and change, including sea level and the propagation of open ocean signals onto the shelf. Our work is part of the UK Climate Projections (UKCP18) and will inform the following UK Climate Change Risk Assessments, required as part of the Climate Change Act.

Surface wave effects on water temperature in the Baltic Sea: simulations with the coupled NEMO-WAM model

NASA Astrophysics Data System (ADS)

Alari, Victor; Staneva, Joanna; Breivik, Øyvind; Bidlot, Jean-Raymond; Mogensen, Kristian; Janssen, Peter

2016-08-01

Coupled circulation (NEMO) and wave model (WAM) system was used to study the effects of surface ocean waves on water temperature distribution and heat exchange at regional scale (the Baltic Sea). Four scenarios—including Stokes-Coriolis force, sea-state dependent energy flux (additional turbulent kinetic energy due to breaking waves), sea-state dependent momentum flux and the combination these forcings—were simulated to test the impact of different terms on simulated temperature distribution. The scenario simulations were compared to a control simulation, which included a constant wave-breaking coefficient, but otherwise was without any wave effects. The results indicate a pronounced effect of waves on surface temperature, on the distribution of vertical temperature and on upwelling's. Overall, when all three wave effects were accounted for, did the estimates of temperature improve compared to control simulation. During the summer, the wave-induced water temperature changes were up to 1 °C. In northern parts of the Baltic Sea, a warming of the surface layer occurs in the wave included simulations in summer months. This in turn reduces the cold bias between simulated and measured data, e.g. the control simulation was too cold compared to measurements. The warming is related to sea-state dependent energy flux. This implies that a spatio-temporally varying wave-breaking coefficient is necessary, because it depends on actual sea state. Wave-induced cooling is mostly observed in near-coastal areas and is the result of intensified upwelling in the scenario, when Stokes-Coriolis forcing is accounted for. Accounting for sea-state dependent momentum flux results in modified heat exchange at the water-air boundary which consequently leads to warming of surface water compared to control simulation.

Oceanic N2O emissions in the 21st century

NASA Astrophysics Data System (ADS)

Martinez-Rey, J.; Bopp, L.; Gehlen, M.; Tagliabue, A.; Gruber, N.

2014-12-01

The ocean is a substantial source of nitrous oxide (N2O) to the atmosphere, but little is known on how this flux might change in the future. Here, we investigate the potential evolution of marine N2O emissions in the 21st century in response to anthropogenic climate change using the global ocean biogeochemical model NEMO-PISCES. We implemented two different parameterizations of N2O production, which differ primarily at low oxygen (O2) conditions. When forced with output from a climate model simulation run under the business-as-usual high CO2 concentration scenario (RCP8.5), our simulations suggest a decrease of 4 to 12% in N2O emissions from 2005 to 2100, i.e., a reduction from 4.03/3.71 to 3.54/3.56 Tg N yr-1 depending on the parameterization. The emissions decrease strongly in the western basins of the Pacific and Atlantic oceans, while they tend to increase above the Oxygen Minimum Zones (OMZs), i.e., in the Eastern Tropical Pacific and in the northern Indian Ocean. The reduction in N2O emissions is caused on the one hand by weakened nitrification as a consequence of reduced primary and export production, and on the other hand by stronger vertical stratification, which reduces the transport of N2O from the ocean interior to the ocean surface. The higher emissions over the OMZ are linked to an expansion of these zones under global warming, which leads to increased N2O production associated primarily with denitrification. From the perspective of a global climate system, the averaged feedback strength associated with the projected decrease in oceanic N2O emissions amounts to around -0.009 W m-2 K-1, which is comparable to the potential increase from terrestrial N2O sources. However, the assesment for a compensation between the terrestrial and marine feedbacks calls for an improved representation of N2O production terms in fully coupled next generation of Earth System Models.

Performance and Quality Assessment of the Forthcoming Copernicus Marine Service Global Ocean Monitoring and Forecasting Real-Time System

NASA Astrophysics Data System (ADS)

Lellouche, J. M.; Le Galloudec, O.; Greiner, E.; Garric, G.; Regnier, C.; Drillet, Y.

2016-02-01

Mercator Ocean currently delivers in real-time daily services (weekly analyses and daily forecast) with a global 1/12° high resolution system. The model component is the NEMO platform driven at the surface by the IFS ECMWF atmospheric analyses and forecasts. Observations are assimilated by means of a reduced-order Kalman filter with a 3D multivariate modal decomposition of the forecast error. It includes an adaptive-error estimate and a localization algorithm. Along track altimeter data, satellite Sea Surface Temperature and in situ temperature and salinity vertical profiles are jointly assimilated to estimate the initial conditions for numerical ocean forecasting. A 3D-Var scheme provides a correction for the slowly-evolving large-scale biases in temperature and salinity.Since May 2015, Mercator Ocean opened the Copernicus Marine Service (CMS) and is in charge of the global ocean analyses and forecast, at eddy resolving resolution. In this context, R&D activities have been conducted at Mercator Ocean these last years in order to improve the real-time 1/12° global system for the next CMS version in 2016. The ocean/sea-ice model and the assimilation scheme benefit among others from the following improvements: large-scale and objective correction of atmospheric quantities with satellite data, new Mean Dynamic Topography taking into account the last version of GOCE geoid, new adaptive tuning of some observational errors, new Quality Control on the assimilated temperature and salinity vertical profiles based on dynamic height criteria, assimilation of satellite sea-ice concentration, new freshwater runoff from ice sheets melting …This presentation doesn't focus on the impact of each update, but rather on the overall behavior of the system integrating all updates. This assessment reports on the products quality improvements, highlighting the level of performance and the reliability of the new system.

Study of water masses variability in the Mediterranean Sea using in-situ data / NEMO-Med12 model.

NASA Astrophysics Data System (ADS)

Margirier, Félix; Testor, Pierre; Mortier, Laurent; Arsouze, Thomas; Bosse, Anthony; Houpert, Loic; Hayes, Dan

2016-04-01

In the past 10 years, numerous observation programs in the Mediterranean deployed autonomous platforms (moorings, argo floats, gliders) and thus considerably increased the number of in-situ observations and the data coverage. In this study, we analyse time series built with profile data on interannual scales. Sorting data in regional boxes, we follow the evolution of different water masses in the basin and generate indexes to characterize their evolution. We then put those indexes in relation with external (atmospheric) forcings and present an intercomparison with the NEMO-Med12 model to estimate both the skill of the model and the relevance of the data-sampling in reproducing the evolution of water masses properties.

Towards a suite of test cases and a pycomodo library to assess and improve numerical methods in ocean models

NASA Astrophysics Data System (ADS)

Garnier, Valérie; Honnorat, Marc; Benshila, Rachid; Boutet, Martial; Cambon, Gildas; Chanut, Jérome; Couvelard, Xavier; Debreu, Laurent; Ducousso, Nicolas; Duhaut, Thomas; Dumas, Franck; Flavoni, Simona; Gouillon, Flavien; Lathuilière, Cyril; Le Boyer, Arnaud; Le Sommer, Julien; Lyard, Florent; Marsaleix, Patrick; Marchesiello, Patrick; Soufflet, Yves

2016-04-01

The COMODO group (http://www.comodo-ocean.fr) gathers developers of global and limited-area ocean models (NEMO, ROMS_AGRIF, S, MARS, HYCOM, S-TUGO) with the aim to address well-identified numerical issues. In order to evaluate existing models, to improve numerical approaches and methods or concept (such as effective resolution) to assess the behavior of numerical model in complex hydrodynamical regimes and to propose guidelines for the development of future ocean models, a benchmark suite that covers both idealized test cases dedicated to targeted properties of numerical schemes and more complex test case allowing the evaluation of the kernel coherence is proposed. The benchmark suite is built to study separately, then together, the main components of an ocean model : the continuity and momentum equations, the advection-diffusion of the tracers, the vertical coordinate design and the time stepping algorithms. The test cases are chosen for their simplicity of implementation (analytic initial conditions), for their capacity to focus on a (few) scheme or part of the kernel, for the availability of analytical solutions or accurate diagnoses and lastly to simulate a key oceanic processus in a controlled environment. Idealized test cases allow to verify properties of numerical schemes advection-diffusion of tracers, - upwelling, - lock exchange, - baroclinic vortex, - adiabatic motion along bathymetry, and to put into light numerical issues that remain undetected in realistic configurations - trajectory of barotropic vortex, - interaction current - topography. When complexity in the simulated dynamics grows up, - internal wave, - unstable baroclinic jet, the sharing of the same experimental designs by different existing models is useful to get a measure of the model sensitivity to numerical choices (Soufflet et al., 2016). Lastly, test cases help in understanding the submesoscale influence on the dynamics (Couvelard et al., 2015). Such a benchmark suite is an interesting bed to continue research in numerical approaches as well as an efficient tool to maintain any oceanic code and assure the users a stamped model in a certain range of hydrodynamical regimes. Thanks to a common netCDF format, this suite is completed with a python library that encompasses all the tools and metrics used to assess the efficiency of the numerical methods. References - Couvelard X., F. Dumas, V. Garnier, A.L. Ponte, C. Talandier, A.M. Treguier (2015). Mixed layer formation and restratification in presence of mesoscale and submesoscale turbulence. Ocean Modelling, Vol 96-2, p 243-253. doi:10.1016/j.ocemod.2015.10.004. - Soufflet Y., P. Marchesiello, F. Lemarié, J. Jouanno, X. Capet, L. Debreu , R. Benshila (2016). On effective resolution in ocean models. Ocean Modelling, in press. doi:10.1016/j.ocemod.2015.12.004

Forcing of global ocean models using an atmospheric boundary layer model: assessing consequences for the simulation of the AMOC

NASA Astrophysics Data System (ADS)

Abel, Rafael; Boening, Claus

2015-04-01

Current practice in the atmospheric forcing of ocean model simulations can lead to unphysical behaviours. The problem lies in the bulk formulation of the turbulent air-sea fluxes in conjunction with a prescribed, and unresponsive, atmospheric state as given, e.g., by reanalysis products. This forcing formulation corresponds to assuming an atmosphere with infinite heat capacity, and effectively damps SST anomalies even on basin scales. It thus curtails an important negative feedback between meridional ocean heat transport and SST in the North Atlantic, rendering simulations of the AMOC in such models excessively sensitive to details in the freshwater fluxes. As a consequence, such simulations are known for spurious drift behaviors which can only partially controlled by introducing some (and sometimes strong) unphysical restoring of sea surface salinity. There have been several suggestions during the last 20 years for at least partially alleviating the problem by including some simplified model of the atmospheric boundary layer (AML) which allows a feedback of SST anomalies on the near-surface air temperature and humidity needed to calculate the surface fluxes. We here present simulations with a simple, only thermally active AML formulation (based on the 'CheapAML' proposed by Deremble et al., 2013) implemented in a global model configuration based on NEMO (ORCA05). In a suite of experiments building on the CORE-bulk forcing methodology, we examine some general features of the AML-solutions (in which only the winds are prescribed) in comparison to solutions with a prescribed atmosperic state. The focus is on the North Atlantic, where we find that the adaptation of the atmospheric temperature the simulated ocean state can lead to strong local modifications in the surface heat fluxes in frontal regions (e.g., the 'Northwest Corner'). We particularly assess the potential of the AML-forcing concept for obtaining AMOC-simulations with reduced spurious drift, without employing the traditional remedy of salinity restoring.

GeNemo: a search engine for web-based functional genomic data.

PubMed

Zhang, Yongqing; Cao, Xiaoyi; Zhong, Sheng

2016-07-08

A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data science. Here, we present GeNemo, a web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. This distinguishes GeNemo from text or DNA sequence searches. The user can input any complete or partial functional genomic dataset, for example, a binding intensity file (bigWig) or a peak file. GeNemo reports any genomic regions, ranging from hundred bases to hundred thousand bases, from any of the online ENCODE datasets that share similar functional (binding, modification, accessibility) patterns. This is enabled by a Markov Chain Monte Carlo-based maximization process, executed on up to 24 parallel computing threads. By clicking on a search result, the user can visually compare her/his data with the found datasets and navigate the identified genomic regions. GeNemo is available at www.genemo.org. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Brain endothelial TAK1 and NEMO safeguard the neurovascular unit

PubMed Central

Ridder, Dirk A.; Wenzel, Jan; Müller, Kristin; Töllner, Kathrin; Tong, Xin-Kang; Assmann, Julian C.; Stroobants, Stijn; Weber, Tobias; Niturad, Cristina; Fischer, Lisanne; Lembrich, Beate; Wolburg, Hartwig; Grand’Maison, Marilyn; Papadopoulos, Panayiota; Korpos, Eva; Truchetet, Francois; Rades, Dirk; Sorokin, Lydia M.; Schmidt-Supprian, Marc; Bedell, Barry J.; Pasparakis, Manolis; Balschun, Detlef; D’Hooge, Rudi; Löscher, Wolfgang; Hamel, Edith

2015-01-01

Inactivating mutations of the NF-κB essential modulator (NEMO), a key component of NF-κB signaling, cause the genetic disease incontinentia pigmenti (IP). This leads to severe neurological symptoms, but the mechanisms underlying brain involvement were unclear. Here, we show that selectively deleting Nemo or the upstream kinase Tak1 in brain endothelial cells resulted in death of endothelial cells, a rarefaction of brain microvessels, cerebral hypoperfusion, a disrupted blood–brain barrier (BBB), and epileptic seizures. TAK1 and NEMO protected the BBB by activating the transcription factor NF-κB and stabilizing the tight junction protein occludin. They also prevented brain endothelial cell death in a NF-κB–independent manner by reducing oxidative damage. Our data identify crucial functions of inflammatory TAK1–NEMO signaling in protecting the brain endothelium and maintaining normal brain function, thus explaining the neurological symptoms associated with IP. PMID:26347470

Polyubiquitination events mediate polymethylmethacrylate (PMMA) particle activation of NF-kappaB pathway.

PubMed

Yamanaka, Yasuhiro; Karuppaiah, Kannan; Abu-Amer, Yousef

2011-07-08

The pathologic response to implant wear-debris constitutes a major component of inflammatory osteolysis and remains under intense investigation. Polymethylmethacrylate (PMMA) particles, which are released during implant wear and loosening, constitute a major culprit by virtue of inducing inflammatory and osteolytic responses by macrophages and osteoclasts, respectively. Recent work by several groups has identified important cellular entities and secreted factors that contribute to inflammatory osteolysis. In previous work, we have shown that PMMA particles contribute to inflammatory osteolysis through stimulation of major pathways in monocytes/macrophages, primarily NF-κB and MAP kinases. The former pathway requires assembly of large IKK complex encompassing IKK1, IKK2, and IKKγ/NEMO. We have shown recently that interfering with the NF-κB and MAPK activation pathways, through introduction of inhibitors and decoy molecules, impedes PMMA-induced inflammation and osteolysis in mouse models of experimental calvarial osteolysis and inflammatory arthritis. In this study, we report that PMMA particles activate the upstream transforming growth factor β-activated kinase-1 (TAK1), which is a key regulator of signal transduction cascades leading to activation of NF-κB and AP-1 factors. More importantly, we found that PMMA particles induce TAK1 binding to NEMO and UBC13. In addition, we show that PMMA particles induce TRAF6 and UBC13 binding to NEMO and that lack of TRAF6 significantly attenuates NEMO ubiquitination. Altogether, these observations suggest that PMMA particles induce ubiquitination of NEMO, an event likely mediated by TRAF6, TAK1, and UBC13. Our findings provide important information for better understanding of the mechanisms underlying PMMA particle-induced inflammatory responses.

NEMO Inhibits Programmed Necrosis in an NFκB-Independent Manner by Restraining RIP1

PubMed Central

Legarda, Diana; Ting, Adrian T.

2012-01-01

TNF can trigger two opposing responses: cell survival and cell death. TNFR1 activates caspases that orchestrate apoptosis but some cell types switch to a necrotic death when treated with caspase inhibitors. Several genes that are required to orchestrate cell death by programmed necrosis have been identified, such as the kinase RIP1, but very little is known about the inhibitory signals that keep this necrotic cell death pathway in check. We demonstrate that T cells lacking the regulatory subunit of IKK, NFκB essential modifier (NEMO), are hypersensitive to programmed necrosis when stimulated with TNF in the presence of caspase inhibitors. Surprisingly, this pro-survival activity of NEMO is independent of NFκB-mediated gene transcription. Instead, NEMO inhibits necrosis by binding to ubiquitinated RIP1 to restrain RIP1 from engaging the necrotic death pathway. In the absence of NEMO, or if ubiquitination of RIP1 is blocked, necrosis ensues when caspases are blocked. These results indicate that recruitment of NEMO to ubiquitinated RIP1 is a key step in the TNFR1 signaling pathway that determines whether RIP1 triggers a necrotic death response. PMID:22848449

Global assessment of Level 3 SMOS and Aquarius salinity measurements using Argo and an operational ocean model

NASA Astrophysics Data System (ADS)

Banks, Chris; Gommenginger, Christine; Srokosz, Meric; Snaith, Helen

2013-04-01

The launch of the European Space Agency (ESA) Soil Moisture and Ocean Salinity (SMOS) satellite in November 2009 marked a new era in satellite oceanography. SMOS was joined in orbit, in June 2011, by the NASA/Argentine Aquarius/SAC-D mission, specifically designed to measure sea surface salinity (SSS). These two satellites have significantly improved our ability to measure SSS synoptically. Despite significant differences in how the two satellites estimate SSS, both utilise passive systems to measure the response of the brightness temperature (Tb) at L-band (1.4 GHz) to SSS and initial results are encouraging. The UK National Oceanography Centre has produced 'Level 3' SSS data products for SMOS and Aquarius using monthly data on a 1° by 1° global grid, between 60°S and 60°N, from 1 September 2011 to 31 August 2012. Previous and on-going work shows for both satellites significant temporally varying differences between SSS from ascending passes (satellite moving south to north) and SSS from descending passes (satellite moving north to south). Therefore, for both SMOS and Aquarius, separate Level 3 products are produced from data for ascending and descending passes. For this study, two separate monthly validation datasets are used based on the same grid as the satellite data. The first is averaged near-surface salinity (depth less than 10 m) as derived from the drifting Argo float programme. The second validation data source is output from the UK Met Office Forecasting Ocean Assimilation Model (FOAM), which is based on NEMO (Nucleus for European Modelling of the Ocean). We calculate maps of the difference between all possible pairs of SSS data for each month, and consider their relationships using regression on the 1˚ values. The analysis is carried out for the global ocean, as well as for smaller, more homogeneous, study regions (e.g. SPURS in the subtropical North Atlantic).

I Feel You: The Design and Evaluation of a Domotic Affect-Sensitive Spoken Conversational Agent

PubMed Central

Lutfi, Syaheerah Lebai; Fernández-Martínez, Fernando; Lorenzo-Trueba, Jaime; Barra-Chicote, Roberto; Montero, Juan Manuel

2013-01-01

We describe the work on infusion of emotion into a limited-task autonomous spoken conversational agent situated in the domestic environment, using a need-inspired task-independent emotion model (NEMO). In order to demonstrate the generation of affect through the use of the model, we describe the work of integrating it with a natural-language mixed-initiative HiFi-control spoken conversational agent (SCA). NEMO and the host system communicate externally, removing the need for the Dialog Manager to be modified, as is done in most existing dialog systems, in order to be adaptive. The first part of the paper concerns the integration between NEMO and the host agent. The second part summarizes the work on automatic affect prediction, namely, frustration and contentment, from dialog features, a non-conventional source, in the attempt of moving towards a more user-centric approach. The final part reports the evaluation results obtained from a user study, in which both versions of the agent (non-adaptive and emotionally-adaptive) were compared. The results provide substantial evidences with respect to the benefits of adding emotion in a spoken conversational agent, especially in mitigating users' frustrations and, ultimately, improving their satisfaction. PMID:23945740

Numerical Modelling of Freshwater Inputs in the Shelf Area of the Ofanto River (Southern Italy)

NASA Astrophysics Data System (ADS)

Verri, G.; Pinardi, N.; Tribbia, J. J.; Gochis, D.; Bryan, F.; Tseng, Y. H.; Navarra, A.; Coppini, G.

2016-02-01

The aim of this study is to understand and to assess the effects of river freshwater release on the ocean circulation and dynamics focusing on the shelf area near estuaries. A sensitivity study to different modelling approaches, which point to the representation of the dynamics of the river inflow, are presented. The modeling strategy we chose consists of an integrated modeling chain including the atmosphere, the hydrology/hydraulics and the estuarine dynamics in order to force our regional ocean model at the Ofanto outlet in a reliable way. This meteo-hydrological modeling chain allows us to take into account all the physical processes involved in the local water cycle of the Ofanto catchment such as the rainfall, the land surface infiltration/evaporation, the partitioning of total runoff into surface and subsurface runoff and the channel streamflow. In order to achieve our goal, we chose the Ofanto river catchment and its estuary as case study. The Ofanto river is a torrential river flowing across the Southern Italy and ending in the Adriatic Sea; its annual averaged discharge is low (15 m3s-1 following Raicich, 1996) but may significantly increase when heavy rain events occur. In details our regional ocean model is a finite difference numerical model based on NEMO code (Madec, G., 2008) and implemented in the Central Mediterranean Sea with 2km as horizontal resolution. The meteo-hydrological modeling chain consists of: 1) the WRF-ARW model (Skamarock et al., 2008) including NOAH-MP as Land Surface Submodel,; 2) WRF-HYDRO model (Gochis D., et al., 2013) representing the hydrology/hydraulics component with 200m as horizontal resolution, simulating the streamflow discharge along the Ofanto river network.; 3) finally an estuarine box model (Garvine et al., 2006) is inserted downstream of WRF-Hydro and upstream of the regional ocean model. A set of sensitivity experiments has been performed aiming to evaluate the capability of the regional ocean model to decribe the Ofanto river plume by providing hindcast discharge and salinity from the estuary model at the river mouth with different methods. The time window of the simulations covers the first three months of year 2011, since 4 heavy rain events affected the Ofanto catchment in this period.

Projections of oceanic N2O emissions in the 21st century using the IPSL Earth system model

NASA Astrophysics Data System (ADS)

Martinez-Rey, J.; Bopp, L.; Gehlen, M.; Tagliabue, A.; Gruber, N.

2015-07-01

The ocean is a substantial source of nitrous oxide (N2O) to the atmosphere, but little is known about how this flux might change in the future. Here, we investigate the potential evolution of marine N2O emissions in the 21st century in response to anthropogenic climate change using the global ocean biogeochemical model NEMO-PISCES. Assuming nitrification as the dominant N2O formation pathway, we implemented two different parameterizations of N2O production which differ primarily under low-oxygen (O2) conditions. When forced with output from a climate model simulation run under the business-as-usual high-CO2 concentration scenario (RCP8.5), our simulations suggest a decrease of 4 to 12 % in N2O emissions from 2005 to 2100, i.e., a reduction from 4.03/3.71 to 3.54/3.56 TgN yr-1 depending on the parameterization. The emissions decrease strongly in the western basins of the Pacific and Atlantic oceans, while they tend to increase above the oxygen minimum zones (OMZs), i.e., in the eastern tropical Pacific and in the northern Indian Ocean. The reduction in N2O emissions is caused on the one hand by weakened nitrification as a consequence of reduced primary and export production, and on the other hand by stronger vertical stratification, which reduces the transport of N2O from the ocean interior to the ocean surface. The higher emissions over the OMZ are linked to an expansion of these zones under global warming, which leads to increased N2O production, associated primarily with denitrification. While there are many uncertainties in the relative contribution and changes in the N2O production pathways, the increasing storage seems unequivocal and determines largely the decrease in N2O emissions in the future. From the perspective of a global climate system, the averaged feedback strength associated with the projected decrease in oceanic N2O emissions amounts to around -0.009 W m-2 K-1, which is comparable to the potential increase from terrestrial N2O sources. However, the assessment for a potential balance between the terrestrial and marine feedbacks calls for an improved representation of N2O production terms in fully coupled next-generation Earth system models.

Arctic Ocean Pathways in the 21st century

NASA Astrophysics Data System (ADS)

Aksenov, Yevgeny; van Gennip, Simon J.; Kelly, Stephen J.; Popova, Ekaterina E.; Yool, Andrew

2017-04-01

In the last three decades, changes in the Arctic environment have been occurring at an increasing rate. The opening up of large areas of previously sea ice-covered ocean affects the marine environment with potential impacts on Arctic ecosystems, including through changes in Arctic access, industries and societies. Changes to sea ice and surface winds result in large-scale shifts in ocean circulation and oceanic pathways. This study presents a high-resolution analysis of the projected ocean circulation and pathways of the Arctic water masses across the 21st century. The analysis is based on an eddy-permitting high-resolution global simulation of the ocean general circulation model NEMO (Nucleus for European Modelling of the Ocean) at the 1/4-degree horizontal resolution. The atmospheric forcing is from HadGEM2-ES model output from IPCC Assessment Report 5 (AR5) simulations performed for Coupled Model Intercomparison Project 5 (CMIP5), and follow the Representative Concentration Pathway 8.5 (RCP8.5) scenario. During the 21st century the AO experiences a significant warming, with sea surface temperature increased by in excess of 4 deg. C. Annual mean Arctic sea ice thickness drops to less than 0.5m, and the Arctic Ocean is ice-free in summer from the mid-century. We use an off-line tracer technique to investigate Arctic pathways of the Atlantic and Pacific waters (AW and PW respectively) under this future climate. The AW tracers have been released in the eastern Fram Strait and in the western Barents Sea, whereas the PW tracer has been seeded in the Bering Strait. In the second half of the century the upper 1000 m ocean circulation shows a reduction in the eastward AW flow along the continental slopes towards the Makarov and Canada basins and a deviation of the PW flow away from the Beaufort Sea towards the Siberian coast. Strengthening of Arctic boundary current and intensification of the cyclonic gyre in the Nansen basin of the Arctic Ocean is accompanied by weakening of the current and an anti-cyclonic gyre spin-up in the Makarov Basin. This presents a shift of the Arctic circulation "dipole" and of the Transpolar Drift, with the consequence that the PW flow towards Fram Strait is significantly reduced by the end of the century, weakening the Pacific-Atlantic connection via the Arctic Ocean, and reducing the Arctic freshwater outflow into the North Atlantic. Examination of the simulations suggests that these circulation changes are primarily due to the shift in the wind.

Effects of wave-induced forcing on a circulation model of the North Sea

NASA Astrophysics Data System (ADS)

Staneva, Joanna; Alari, Victor; Breivik, Øyvind; Bidlot, Jean-Raymond; Mogensen, Kristian

2017-01-01

The effect of wind waves on water level and currents during two storms in the North Sea is investigated using a high-resolution Nucleus for European Modelling of the Ocean (NEMO) model forced with fluxes and fields from a high-resolution wave model. The additional terms accounting for wave-current interaction that are considered in this study are the Stokes-Coriolis force, the sea-state-dependent energy and momentum fluxes. The individual and collective role of these processes is quantified and the results are compared with a control run without wave effects as well as against current and water-level measurements from coastal stations. We find a better agreement with observations when the circulation model is forced by sea-state-dependent fluxes, especially in extreme events. The two extreme events, the storm Christian (25-27 October 2013), and about a month later, the storm Xaver (5-7 December 2013), induce different wave and surge conditions over the North Sea. Including the wave effects in the circulation model for the storm Xaver raises the modelled surge by more than 40 cm compared with the control run in the German Bight area. For the storm Christian, a difference of 20-30 cm in the surge level between the wave-forced and the stand-alone ocean model is found over the whole southern part of the North Sea. Moreover, the modelled vertical velocity profile fits the observations very well when the wave forcing is accounted for. The contribution of wave-induced forcing has been quantified indicating that this represents an important mechanism for improving water-level and current predictions.

Efficient Mobility Management Signalling in Network Mobility Supported PMIPV6

PubMed Central

Jebaseeli Samuelraj, Ananthi; Jayapal, Sundararajan

2015-01-01

Proxy Mobile IPV6 (PMIPV6) is a network based mobility management protocol which supports node's mobility without the contribution from the respective mobile node. PMIPV6 is initially designed to support individual node mobility and it should be enhanced to support mobile network movement. NEMO-BSP is an existing protocol to support network mobility (NEMO) in PMIPV6 network. Due to the underlying differences in basic protocols, NEMO-BSP cannot be directly applied to PMIPV6 network. Mobility management signaling and data structures used for individual node's mobility should be modified to support group nodes' mobility management efficiently. Though a lot of research work is in progress to implement mobile network movement in PMIPV6, it is not yet standardized and each suffers with different shortcomings. This research work proposes modifications in NEMO-BSP and PMIPV6 to achieve NEMO support in PMIPV6. It mainly concentrates on optimizing the number and size of mobility signaling exchanged while mobile network or mobile network node changes its access point. PMID:26366431

Phosphorylation and ubiquitination of the IkappaB kinase complex by two distinct signaling pathways.

PubMed

Shambharkar, Prashant B; Blonska, Marzenna; Pappu, Bhanu P; Li, Hongxiu; You, Yun; Sakurai, Hiroaki; Darnay, Bryant G; Hara, Hiromitsu; Penninger, Josef; Lin, Xin

2007-04-04

The IkappaB kinase (IKK) complex serves as the master regulator for the activation of NF-kappaB by various stimuli. It contains two catalytic subunits, IKKalpha and IKKbeta, and a regulatory subunit, IKKgamma/NEMO. The activation of IKK complex is dependent on the phosphorylation of IKKalpha/beta at its activation loop and the K63-linked ubiquitination of NEMO. However, the molecular mechanism by which these inducible modifications occur remains undefined. Here, we demonstrate that CARMA1, a key scaffold molecule, is essential to regulate NEMO ubiquitination upon T-cell receptor (TCR) stimulation. However, the phosphorylation of IKKalpha/beta activation loop is independent of CARMA1 or NEMO ubiquitination. Further, we provide evidence that TAK1 is activated and recruited to the synapses in a CARMA1-independent manner and mediate IKKalpha/beta phosphorylation. Thus, our study provides the biochemical and genetic evidence that phosphorylation of IKKalpha/beta and ubiquitination of NEMO are regulated by two distinct pathways upon TCR stimulation.

Successful treatment with infliximab for inflammatory colitis in a patient with X-linked anhidrotic ectodermal dysplasia with immunodeficiency.

PubMed

Mizukami, Tomoyuki; Obara, Megumi; Nishikomori, Ryuta; Kawai, Tomoki; Tahara, Yoshihiro; Sameshima, Naoki; Marutsuka, Kousuke; Nakase, Hiroshi; Kimura, Nobuhiro; Heike, Toshio; Nunoi, Hiroyuki

2012-02-01

X-linked anhidrotic ectodermal dysplasia with immunodeficiency (X-EDA-ID) is caused by hypomorphic mutations in the gene encoding nuclear factor-κB essential modulator protein (NEMO). Patients are susceptibile to diverse pathogens due to insufficient cytokine and frequently show severe chronic colitis. An 11-year-old boy with X-EDA-ID was hospitalized with autoimmune symptoms and severe chronic colitis which had been refractory to immunosuppressive drugs. Since tumor necrosis factor (TNF) α is responsible for the pathogenesis of NEMO colitis according to intestinal NEMO and additional TNFR1 knockout mice studies, and high levels of TNFα-producing mononuclear cells were detected in the patient due to the unexpected gene reversion mosaicism of NEMO, an anti-TNFα monoclonal antibody was administered to ameliorate his abdominal symptoms. Repeated administrations improved his colonoscopic findings as well as his dry skin along with a reduction of TNFα-expressing T cells. These findings suggest TNF blockade therapy is of value for refractory NEMO colitis with gene reversion.

Efficient Mobility Management Signalling in Network Mobility Supported PMIPV6.

PubMed

Samuelraj, Ananthi Jebaseeli; Jayapal, Sundararajan

2015-01-01

Proxy Mobile IPV6 (PMIPV6) is a network based mobility management protocol which supports node's mobility without the contribution from the respective mobile node. PMIPV6 is initially designed to support individual node mobility and it should be enhanced to support mobile network movement. NEMO-BSP is an existing protocol to support network mobility (NEMO) in PMIPV6 network. Due to the underlying differences in basic protocols, NEMO-BSP cannot be directly applied to PMIPV6 network. Mobility management signaling and data structures used for individual node's mobility should be modified to support group nodes' mobility management efficiently. Though a lot of research work is in progress to implement mobile network movement in PMIPV6, it is not yet standardized and each suffers with different shortcomings. This research work proposes modifications in NEMO-BSP and PMIPV6 to achieve NEMO support in PMIPV6. It mainly concentrates on optimizing the number and size of mobility signaling exchanged while mobile network or mobile network node changes its access point.

Withaferin A disrupts ubiquitin-based NEMO reorganization induced by canonical NF-κB signaling.

PubMed

Jackson, Shawn S; Oberley, Christopher; Hooper, Christopher P; Grindle, Kreg; Wuerzberger-Davis, Shelly; Wolff, Jared; McCool, Kevin; Rui, Lixin; Miyamoto, Shigeki

2015-02-01

The NF-κB family of transcription factors regulates numerous cellular processes, including cell proliferation and survival responses. The constitutive activation of NF-κB has also emerged as an important oncogenic driver in many malignancies, such as activated B-cell like diffuse large B cell lymphoma, among others. In this study, we investigated the impact and mechanisms of action of Withaferin A, a naturally produced steroidal lactone, against both signal-inducible as well as constitutive NF-κB activities. We found that Withaferin A is a robust inhibitor of canonical and constitutive NF-κB activities, leading to apoptosis of certain lymphoma lines. In the canonical pathway induced by TNF, Withaferin A did not disrupt RIP1 polyubiquitination or NEMO-IKKβ interaction and was a poor direct IKKβ inhibitor, but prevented the formation of TNF-induced NEMO foci which colocalized with TNF ligand. While GFP-NEMO efficiently formed TNF-induced foci, a GFP-NEMO(Y308S) mutant that is defective in binding to polyubiquitin chains did not form foci. Our study reveals that Withaferin A is a novel type of IKK inhibitor which acts by disrupting NEMO reorganization into ubiquitin-based signaling structures in vivo. Copyright © 2014 Elsevier Inc. All rights reserved.

Expanding the Substantial Interactome of NEMO Using Protein Microarrays

PubMed Central

Fenner, Beau J.; Scannell, Michael; Prehn, Jochen H. M.

2010-01-01

Signal transduction by the NF-kappaB pathway is a key regulator of a host of cellular responses to extracellular and intracellular messages. The NEMO adaptor protein lies at the top of this pathway and serves as a molecular conduit, connecting signals transmitted from upstream sensors to the downstream NF-kappaB transcription factor and subsequent gene activation. The position of NEMO within this pathway makes it an attractive target from which to search for new proteins that link NF-kappaB signaling to additional pathways and upstream effectors. In this work, we have used protein microarrays to identify novel NEMO interactors. A total of 112 protein interactors were identified, with the most statistically significant hit being the canonical NEMO interactor IKKbeta, with IKKalpha also being identified. Of the novel interactors, more than 30% were kinases, while at least 25% were involved in signal transduction. Binding of NEMO to several interactors, including CALB1, CDK2, SAG, SENP2 and SYT1, was confirmed using GST pulldown assays and coimmunoprecipitation, validating the initial screening approach. Overexpression of CALB1, CDK2 and SAG was found to stimulate transcriptional activation by NF-kappaB, while SYT1 overexpression repressed TNFalpha-dependent NF-kappaB transcriptional activation in human embryonic kidney cells. Corresponding with this finding, RNA silencing of CDK2, SAG and SENP2 reduced NF-kappaB transcriptional activation, supporting a positive role for these proteins in the NF-kappaB pathway. The identification of a host of new NEMO interactors opens up new research opportunities to improve understanding of this essential cell signaling pathway. PMID:20098747

Withaferin A disrupts ubiquitin-based NEMO reorganization induced by canonical NF-κB signaling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Shawn S.; Medical Scientist Training Program, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705; Cellular and Molecular Biology Program, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705

2015-02-01

The NF-κB family of transcription factors regulates numerous cellular processes, including cell proliferation and survival responses. The constitutive activation of NF-κB has also emerged as an important oncogenic driver in many malignancies, such as activated B-cell like diffuse large B cell lymphoma, among others. In this study, we investigated the impact and mechanisms of action of Withaferin A, a naturally produced steroidal lactone, against both signal-inducible as well as constitutive NF-κB activities. We found that Withaferin A is a robust inhibitor of canonical and constitutive NF-κB activities, leading to apoptosis of certain lymphoma lines. In the canonical pathway induced bymore » TNF, Withaferin A did not disrupt RIP1 polyubiquitination or NEMO–IKKβ interaction and was a poor direct IKKβ inhibitor, but prevented the formation of TNF-induced NEMO foci which colocalized with TNF ligand. While GFP-NEMO efficiently formed TNF-induced foci, a GFP-NEMO{sup Y308S} mutant that is defective in binding to polyubiquitin chains did not form foci. Our study reveals that Withaferin A is a novel type of IKK inhibitor which acts by disrupting NEMO reorganization into ubiquitin-based signaling structures in vivo. - Highlights: • Withaferin A, a NF-κB inhibitor, disrupts signaling induced NEMO localization, a novel point of inhibition. • NEMO can be localized to distinct signaling foci after treatment with TNF. • ABC-type DLCBL cells can be sensitized to apoptosis after treatment with Withaferin A.« less

Epithelial NEMO/IKKγ limits fibrosis and promotes regeneration during pancreatitis.

PubMed

Chan, Lap Kwan; Gerstenlauer, Melanie; Konukiewitz, Björn; Steiger, Katja; Weichert, Wilko; Wirth, Thomas; Maier, Harald Jakob

2017-11-01

Inhibitory κB kinase (IKK)/nuclear factor κB (NF-κB) signalling has been implicated in the pathogenesis of pancreatitis, but its precise function has remained controversial. Here, we analyse the contribution of IKK/NF-κB signalling in epithelial cells to the pathogenesis of pancreatitis by targeting the IKK subunit NF-κB essential modulator (NEMO) (IKKγ), which is essential for canonical NF-κB activation. Mice with a targeted deletion of NEMO in the pancreas were subjected to caerulein pancreatitis. Pancreata were examined at several time points and analysed for inflammation, fibrosis, cell death, cell proliferation, as well as cellular differentiation. Human samples were used to corroborate findings established in mice. In acute pancreatitis, NEMO deletion in the pancreatic parenchyma resulted in minor changes during the early phase but led to the persistence of inflammatory and fibrotic foci in the recovery phase. In chronic pancreatitis, NEMO deletion aggravated inflammation and fibrosis, inhibited compensatory acinar cell proliferation, and enhanced acinar atrophy and acinar-ductal metaplasia. Gene expression analysis revealed sustained activation of profibrogenic genes and the CXCL12/CXCR4 axis in the absence of epithelial NEMO. In human chronic pancreatitis samples, the CXCL12/CXCR4 axis was activated as well, with CXCR4 expression correlating with the degree of fibrosis. The aggravating effects of NEMO deletion were attenuated by the administration of the CXCR4 antagonist AMD3100. Our results suggest that NEMO in epithelial cells exerts a protective effect during pancreatitis by limiting inflammation and fibrosis and improving acinar cell regeneration. The CXCL12/CXCR4 axis is an important mediator of that effect and may also be of importance in human chronic pancreatitis. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Data assimilation experiments using diffusive back-and-forth nudging for the NEMO ocean model

NASA Astrophysics Data System (ADS)

Ruggiero, G. A.; Ourmières, Y.; Cosme, E.; Blum, J.; Auroux, D.; Verron, J.

2015-04-01

The diffusive back-and-forth nudging (DBFN) is an easy-to-implement iterative data assimilation method based on the well-known nudging method. It consists of a sequence of forward and backward model integrations, within a given time window, both of them using a feedback term to the observations. Therefore, in the DBFN, the nudging asymptotic behaviour is translated into an infinite number of iterations within a bounded time domain. In this method, the backward integration is carried out thanks to what is called backward model, which is basically the forward model with reversed time step sign. To maintain numeral stability, the diffusion terms also have their sign reversed, giving a diffusive character to the algorithm. In this article the DBFN performance to control a primitive equation ocean model is investigated. In this kind of model non-resolved scales are modelled by diffusion operators which dissipate energy that cascade from large to small scales. Thus, in this article, the DBFN approximations and their consequences for the data assimilation system set-up are analysed. Our main result is that the DBFN may provide results which are comparable to those produced by a 4Dvar implementation with a much simpler implementation and a shorter CPU time for convergence. The conducted sensitivity tests show that the 4Dvar profits of long assimilation windows to propagate surface information downwards, and that for the DBFN, it is worth using short assimilation windows to reduce the impact of diffusion-induced errors. Moreover, the DBFN is less sensitive to the first guess than the 4Dvar.

NBodyLab: A Testbed for Undergraduates Utilizing a Web Interface to NEMO and MD-GRAPE2 Hardware

NASA Astrophysics Data System (ADS)

Johnson, V. L.; Teuben, P. J.; Penprase, B. E.

An N-body simulation testbed called NBodyLab was developed at Pomona College as a teaching tool for undergraduates. The testbed runs under Linux and provides a web interface to selected back-end NEMO modeling and analysis tools, and several integration methods which can optionally use an MD-GRAPE2 supercomputer card in the server to accelerate calculation of particle-particle forces. The testbed provides a framework for using and experimenting with the main components of N-body simulations: data models and transformations, numerical integration of the equations of motion, analysis and visualization products, and acceleration techniques (in this case, special purpose hardware). The testbed can be used by students with no knowledge of programming or Unix, freeing such students and their instructor to spend more time on scientific experimentation. The advanced student can extend the testbed software and/or more quickly transition to the use of more advanced Unix-based toolsets such as NEMO, Starlab and model builders such as GalactICS. Cosmology students at Pomona College used the testbed to study collisions of galaxies with different speeds, masses, densities, collision angles, angular momentum, etc., attempting to simulate, for example, the Tadpole Galaxy and the Antenna Galaxies. The testbed framework is available as open-source to assist other researchers and educators. Recommendations are made for testbed enhancements.

Search for Neutrinoless Quadruple-β Decay of Nd 150 with the NEMO-3 Detector

NASA Astrophysics Data System (ADS)

Arnold, R.; Augier, C.; Barabash, A. S.; Basharina-Freshville, A.; Blondel, S.; Blot, S.; Bongrand, M.; Boursette, D.; Brudanin, V.; Busto, J.; Caffrey, A. J.; Calvez, S.; Cascella, M.; Cerna, C.; Cesar, J. P.; Chapon, A.; Chauveau, E.; Chopra, A.; Dawson, L.; Duchesneau, D.; Durand, D.; Egorov, V.; Eurin, G.; Evans, J. J.; Fajt, L.; Filosofov, D.; Flack, R.; Garrido, X.; Gómez, H.; Guillon, B.; Guzowski, P.; Hodák, R.; Huber, A.; Hubert, P.; Hugon, C.; Jullian, S.; Klimenko, A.; Kochetov, O.; Konovalov, S. I.; Kovalenko, V.; Lalanne, D.; Lang, K.; Lemière, Y.; Le Noblet, T.; Liptak, Z.; Liu, X. R.; Loaiza, P.; Lutter, G.; Macko, M.; Macolino, C.; Mamedov, F.; Marquet, C.; Mauger, F.; Morgan, B.; Mott, J.; Nemchenok, I.; Nomachi, M.; Nova, F.; Nowacki, F.; Ohsumi, H.; Patrick, C.; Pahlka, R. B.; Perrot, F.; Piquemal, F.; Povinec, P.; Přidal, P.; Ramachers, Y. A.; Remoto, A.; Reyss, J. L.; Riddle, C. L.; Rukhadze, E.; Saakyan, R.; Salazar, R.; Sarazin, X.; Shitov, Yu.; Simard, L.; Šimkovic, F.; Smetana, A.; Smolek, K.; Smolnikov, A.; Söldner-Rembold, S.; Soulé, B.; Štefánik, D.; Štekl, I.; Suhonen, J.; Sutton, C. S.; Szklarz, G.; Thomas, J.; Timkin, V.; Torre, S.; Tretyak, Vl. I.; Tretyak, V. I.; Umatov, V. I.; Vanushin, I.; Vilela, C.; Vorobel, V.; Waters, D.; Xie, F.; Žukauskas, A.; NEMO-3 Collaboration

2017-07-01

We report the results of a first experimental search for lepton number violation by four units in the neutrinoless quadruple-β decay of Nd 150 using a total exposure of 0.19 kg yr recorded with the NEMO-3 detector at the Modane Underground Laboratory. We find no evidence of this decay and set lower limits on the half-life in the range T1 /2>(1.1 - 3.2 )×1 021 yr at the 90% C.L., depending on the model used for the kinematic distributions of the emitted electrons.

Unusual Father-to-Daughter Transmission of Incontinentia Pigmenti Due to Mosaicism in IP Males.

PubMed

Fusco, Francesca; Conte, Matilde Immacolata; Diociaiuti, Andrea; Bigoni, Stefania; Branda, Maria Francesca; Ferlini, Alessandra; El Hachem, Maya; Ursini, Matilde Valeria

2017-09-01

Incontinentia pigmenti (IP; Online Mendelian Inheritance in Man catalog #308300) is an X-linked dominant ectodermal disorder caused by mutations of the inhibitor of κ polypeptide gene enchancer in B cells, kinase γ ( IKBKG )/ nuclear factor κB, essential modulator ( NEMO ) gene. Hemizygous IKBKG/NEMO loss-of-function (LoF) mutations are lethal in males, thus patients are female, and the disease is always transmitted from an IP-affected mother to her daughter. We present 2 families with father-to-daughter transmission of IP and provide for the first time molecular evidence that the combination of somatic and germ-line mosaicism for IKBKG/NEMO loss of function mutations in IP males resulted in the transmission of the disease to a female child. We searched for the IKBKG/NEMO mutant allele in blood, urine, skin, and sperm DNA and found that the 2 fathers were somatic and germ-line mosaics for the p.Gln132×mutation or the exon 4-10 deletion of IKBKG/NEMO , respectively. The highest level of IKBKG/NEMO mutant cells was detected in the sperm, which might explain the recurrence of the disease. We therefore recommend careful clinical evaluation in IP male cases and the genetic investigation in sperm DNA to ensure correct genetic counseling and prevent the risk of paternal transmission of IP. Copyright © 2017 by the American Academy of Pediatrics.

Implementation of Black Sea numerical model based on NEMO and 3DVAR data assimilation scheme for operational forecasting

NASA Astrophysics Data System (ADS)

Ciliberti, Stefania Angela; Peneva, Elisaveta; Storto, Andrea; Rostislav, Kandilarov; Lecci, Rita; Yang, Chunxue; Coppini, Giovanni; Masina, Simona; Pinardi, Nadia

2016-04-01

This study describes a new model implementation for the Black Sea, which uses data assimilation, towards operational forecasting, based on NEMO (Nucleus for European Modelling of the Ocean, Madec et al., 2012). The Black Sea domain is resolved with 1/27°×1/36° horizontal resolution (~3 km) and 31 z-levels with partial steps based on the GEBCO bathymetry data (Grayek et al., 2010). The model is forced by momentum, water and heat fluxes interactively computed by bulk formulae using high resolution atmospheric forcing provided by the European Centre for Medium-Range Forecast (ECMWF). The initial condition is calculated from long-term climatological temperature and salinity 3D fields. Precipitation field over the basin has been computed from the climatological GPCP rainfall monthly data (Adler et al., 2003; Huffman et al., 2009), while the evaporation is derived from the latent heat flux. The climatological monthly mean runoff of the major rivers in the Black Sea is computed using the hydrological dataset provided by SESAME project (Ludvig et al., 2009). The exchange with Mediterranean Sea through the Bosporus Straits is represented by a surface boundary condition taking into account the barotropic transport calculated to balance the fresh water fluxes on monthly bases (Stanev and Beckers, 1999, Peneva et al., 2001). A multi-annual run 2011-2015 has been completed in order to describe the main characteristics of the Black Sea circulation dynamics and thermohaline structure and the numerical results have been validated using in-situ (ARGO) and satellite (SST, SLA) data. The Black Sea model represents also the core of the new Black Sea Forecasting System, implemented at CMCC operationally since January 2016, which produces at daily frequency 10-day forecasts, 3-days analyses and 1-day simulation. Once a week, the system is run 15-day in the past in analysis mode to compute the new optimal initial condition for the forecast cycle. The assimilation is performed by a three-dimensional variational data assimilation system (3DVAR) that ingests all hydrographic profiles (mostly ARGO floats), sea level anomaly data from available altimetry missions and sea surface temperature measurements retrieved from infrared sensors on-board polar-orbiting satellites (Storto et al., 2014). All the data are taken from the CMEMS catalogue. The 3DVAR system implements a recursive filter to model horizontal correlations while vertical covariances are formulated through multivariate empirical orthogonal functions. The system produces hourly and daily means for temperature, salinity, currents and sea surface height with online validation against satellite observations for SST and in-situ ARGO measurements. Grayek, S., Stanev, E., Kandilarov, R., 2010. On the response of Black Sea level to external forcing: altimeter data and numerical modelling. Ocean Dyn. 60, 123-140. Ludwig W., E. Dumont, M. Meybeck, and S. Heussner, 2009. River discharges of water and nutrients to the Mediterranean and Black Sea: Major drivers for ecosystem changes during past and future decades? Progress in Oceanography, 80, 199-217. Peneva, E. L., E. Stanev, V. Belokopytov, and P.Y. Le Traon, 2001. Water transport in the Bosporus Straits estimated from hydro-meteorologycal and altimeter data: Seasonal to decadal variability. J. Mar. Sys., 31, 1-3, 21-35. Stanev E. and J.M. Beckers, 1999. Barotropic and baroclinic oscillations in strongly stratified ocean basins: Numerical study of the Black Sea. Journal of Marine Systems, 19, 65-112. Storto A., Masina S., Dobricic S., 2014. Estimation and impact of nonuniform horizontal correlation length scales for Global Ocean physical analyses. J. Atmos. Ocean. Technol., 31: 2330-2349.

Timing Calibration of the NEMO Optical Sensors

NASA Astrophysics Data System (ADS)

Circella, M.; de Marzo, C.; Megna, R.; Ruppi, M.

2006-04-01

This paper describes the timing calibration system for the NEMO underwater neutrino telescope. The NEMO Project aims at the construction of a km3 detector, equipped with a large number of photomultipliers, in the Mediterranean Sea. We foresee a redundant system to perform the time calibration of our apparatus: 1) A two-step procedure for measuring the offsets in the time measurements of the NEMO optical sensors, so as to measure separately the time delay for the synchronization signals to reach the offshore electronics and the response time of the photomultipliers to calibration signals delivered from optical pulsers through an optical fibre distribution system; 2) an all-optical procedure for measuring the differences in the time offsets of the different optical modules illuminated by calibration pulses. Such a system can be extended to work for a very large apparatus, even for complex arrangements of widely spaced sensors. The NEMO prototyping activities ongoing at a test site off the coast of Sicily will allow the system described in this work to be operated and tested in situ next year.

Novel hypomorphic mutation in IKBKG impairs NEMO-ubiquitylation causing ectodermal dysplasia, immunodeficiency, incontinentia pigmenti, and immune thrombocytopenic purpura.

PubMed

Ramírez-Alejo, Noé; Alcántara-Montiel, Julio C; Yamazaki-Nakashimada, Marco; Duran-McKinster, Carola; Valenzuela-León, Paola; Rivas-Larrauri, Francisco; Cedillo-Barrón, Leticia; Hernández-Rivas, Rosaura; Santos-Argumedo, Leopoldo

2015-10-01

NF-κB essential modulator (NEMO) is a component of the IKK complex, which participates in the activation of the NF-κB pathway. Hypomorphic mutations in the IKBKG gene result in different forms of anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) in males without affecting carrier females. Here, we describe a hypomorphic and missense mutation, designated c.916G>A (p.D306N), which affects our patient, his mother, and his sister. This mutation did not affect NEMO expression; however, an immunoprecipitation assay revealed reduced ubiquitylation upon CD40-stimulation in the patient's cells. Functional studies have demonstrated reduced phosphorylation and degradation of IκBα, affecting NF-κB recruitment into the nucleus. The patient presented with clinical features of ectodermal dysplasia, immunodeficiency, and immune thrombocytopenic purpura, the latter of which has not been previously reported in a patient with NEMO deficiency. His mother and sister displayed incontinentia pigmenti indicating that, in addition to amorphic mutations, hypomorphic mutations in NEMO can affect females. Copyright © 2015 Elsevier Inc. All rights reserved.

Inhibition of Canonical NF-κB Signaling by a Small Molecule Targeting NEMO-Ubiquitin Interaction

PubMed Central

Vincendeau, Michelle; Hadian, Kamyar; Messias, Ana C.; Brenke, Jara K.; Halander, Jenny; Griesbach, Richard; Greczmiel, Ute; Bertossi, Arianna; Stehle, Ralf; Nagel, Daniel; Demski, Katrin; Velvarska, Hana; Niessing, Dierk; Geerlof, Arie; Sattler, Michael; Krappmann, Daniel

2016-01-01

The IκB kinase (IKK) complex acts as the gatekeeper of canonical NF-κB signaling, thereby regulating immunity, inflammation and cancer. It consists of the catalytic subunits IKKα and IKKβ and the regulatory subunit NEMO/IKKγ. Here, we show that the ubiquitin binding domain (UBAN) in NEMO is essential for IKK/NF-κB activation in response to TNFα, but not IL-1β stimulation. By screening a natural compound library we identified an anthraquinone derivative that acts as an inhibitor of NEMO-ubiquitin binding (iNUB). Using biochemical and NMR experiments we demonstrate that iNUB binds to NEMOUBAN and competes for interaction with methionine-1-linked linear ubiquitin chains. iNUB inhibited NF-κB activation upon UBAN-dependent TNFα and TCR/CD28, but not UBAN-independent IL-1β stimulation. Moreover, iNUB was selectively killing lymphoma cells that are addicted to chronic B-cell receptor triggered IKK/NF-κB activation. Thus, iNUB disrupts the NEMO-ubiquitin protein-protein interaction interface and thereby inhibits physiological and pathological NF-κB signaling. PMID:26740240

Predicting the Arctic Ocean Environment in the 21st century

NASA Astrophysics Data System (ADS)

Aksenov, Yevgeny; Popova, Ekaterina; Yool, Andrew; Nurser, George

2015-04-01

Recent environmental changes in the Arctic have clearly demonstrated that climate change is faster and more vigorously in the Polar Regions than anywhere else. Significantly, change in the Arctic Ocean (AO) environment presents a variety of impacts, from ecological to social-economic and political. Mitigation of this change and adaptation to it requires detailed and robust environmental predictions. Here we present a detailed projection of ocean circulation and sea ice from the present until 2099, based on an eddy-permitting high-resolution global simulation of the NEMO ¼ degree ocean model. The model is forced at the surface with HadGEM2-ES atmosphere model output from the UK Met. Office IPCC Assessment Report 5 (AR5) Representative Concentration Pathways 8.5 (RCP8.5) scenario. The HadGEM2-ES simulations span 1860-2099 and are one of an ensemble of runs performed for the Coupled Model Intercomparison Project 5 (CMIP5) and IPCC AR5. Between 2000-2009 and 2090-2099 the AO experiences a significant warming, with sea surface temperature increasing on average by about 4° C, particularly in the Barents and Kara Seas, and in the Greenland Sea and Hudson Bay. By the end of the simulation, Arctic sea ice has an average annual thickness of less than 10 cm in the central AO, and less than 0.5 m in the East-Siberian Sea and Canadian Archipelago, and disappears entirely during the Arctic summer. In summer, opening of large areas of the Arctic Ocean to the wind and surface waves leads to the Arctic pack ice cover evolving into the Marginal Ice Zone (MIZ). In winter, sea ice persists until the 2030s; then it sharply declines and disappears from the Central Arctic Ocean by the end of the 21st century, with MIZ provinces remaining in winter along the Siberian, Alaskan coasts and in the Canadian Arctic Archipelago. Analysis of the AO circulation reveals evidence of (i) the reversal of the Arctic boundary currents in the Canadian Basin, from a weak cyclonic current in 2040-2049 to a strong anti-cyclonic current in 2090-2099, and (ii) increased anti-cyclonic surface ocean circulation in the eastern part of the AO, while the surface circulation in the western Arctic becomes more cyclonic. We relate the shift in the circulation to changes in the winds and reduction of sea ice cover, which modify momentum transfer from atmosphere to the ocean. Our simulation suggests a potentially complex picture of future AO change, and highlights the importance of high resolution modelling in forecasting it.

Operational skill assessment of the IBI-MFC Ocean Forecasting System within the frame of the CMEMS.

NASA Astrophysics Data System (ADS)

Lorente Jimenez, Pablo; Garcia-Sotillo, Marcos; Amo-Balandron, Arancha; Aznar Lecocq, Roland; Perez Gomez, Begoña; Levier, Bruno; Alvarez-Fanjul, Enrique

2016-04-01

Since operational ocean forecasting systems (OOFSs) are increasingly used as tools to support high-stakes decision-making for coastal management, a rigorous skill assessment of model performance becomes essential. In this context, the IBI-MFC (Iberia-Biscay-Ireland Monitoring & Forecasting Centre) has been providing daily ocean model estimates and forecasts for the IBI regional seas since 2011, first in the frame of MyOcean projects and later as part of the Copernicus Marine Environment Monitoring Service (CMEMS). A comprehensive web validation tool named NARVAL (North Atlantic Regional VALidation) has been developed to routinely monitor IBI performance and to evaluate model's veracity and prognostic capabilities. Three-dimensional comparisons are carried out on a different time basis ('online mode' - daily verifications - and 'delayed mode' - for longer time periods -) using a broad variety of in-situ (buoys, tide-gauges, ARGO-floats, drifters and gliders) and remote-sensing (satellite and HF radars) observational sources as reference fields to validate against the NEMO model solution. Product quality indicators and meaningful skill metrics are automatically computed not only averaged over the entire IBI domain but also over specific sub-regions of particular interest from a user perspective (i.e. coastal or shelf areas) in order to determine IBI spatial and temporal uncertainty levels. A complementary aspect of NARVAL web tool is the intercomparison of different CMEMS forecast model solutions in overlapping areas. Noticeable efforts are in progress in order to quantitatively assess the quality and consistency of nested system outputs by setting up specific intercomparison exercises on different temporal and spatial scales, encompassing global configurations (CMEMS Global system), regional applications (NWS and MED ones) and local high-resolution coastal models (i.e. the PdE SAMPA system in the Gibraltar Strait). NARVAL constitutes a powerful approach to increase our knowledge on the IBI-MFC forecast system and aids us to inform CMEMS end users about the provided ocean forecasting products' confidence level by routinely delivering QUality Information Documents (QUIDs). It allows the detection of strengths and weaknesses in the modeling of several key physical processes and the understanding of potential sources of discrepancies in IBI predictions. Once the numerical model shortcomings are identified, potential improvements can be achieved thanks to reliable upgrades, making evolve IBI OOFS towards more refined and advanced versions.

Sedimentary particulate iron: the missing micronutrients ?

NASA Astrophysics Data System (ADS)

Beghoura, Houda; Gorgues, Thomas; Aumont, Olivier; Planquette, Hélène

2017-04-01

Iron is known to regulate the marine primary production and to impact the structure of ecosystems. Indeed, iron is the limiting nutrient for the phytoplankton growth over about 30% of the global ocean. However, the nature of the external sources of iron to the ocean and their quantification remain uncertain. Among these external sources, the sediment sources have been recently shown to be underestimated. Besides, since the operationally defined dissolved iron (which is the sum of truly dissolved and colloidal iron) was traditionally assumed to be the only form available to phytoplankton and bacteria, most studies have focused on the supply of dissolved iron to the ocean, the role of the particulate fraction of iron being largely ignored. This traditional view has been recently challenged, noticeably, by observational evidences. Indeed, in situ observations have shown that large amounts of particulate iron are being resuspended from continental margins to the open ocean thanks to fine grained particles' transport over long distances. A fraction of this particulate iron may dissolve and thereby fuel the phytoplankton growth. The magnitude of the sedimentary sources of particulate iron and the releasing processes affecting this iron phase are not yet well constrained or quantified. As a consequence, the role of sedimentary particulate iron in the biogeochemical cycles is still unclear despite its potentially major widespread importance. Here, we propose a modeling exercise to assess the first order impacts of this newly considered particulate sedimentary iron on global ocean biogeochemistry. We designed global experiments with a coupled dynamical-biogeochemical model (NEMO-PISCES). First, a control simulation that includes only a sediment source of iron in the dissolved phase has been run. Then, this control simulation is being compared with simulations, in which we include a sediment source of iron in both phases (dissolved as well as particulate). Those latter simulations have been performed using a range of particulate iron dissolution rates (from published studies and laboratory experiment results) that will permit to test the sensitivity of the biogeochemical response.

EMPIRE and pyenda: Two ensemble-based data assimilation systems written in Fortran and Python

NASA Astrophysics Data System (ADS)

Geppert, Gernot; Browne, Phil; van Leeuwen, Peter Jan; Merker, Claire

2017-04-01

We present and compare the features of two ensemble-based data assimilation frameworks, EMPIRE and pyenda. Both frameworks allow to couple models to the assimilation codes using the Message Passing Interface (MPI), leading to extremely efficient and fast coupling between models and the data-assimilation codes. The Fortran-based system EMPIRE (Employing Message Passing Interface for Researching Ensembles) is optimized for parallel, high-performance computing. It currently includes a suite of data assimilation algorithms including variants of the ensemble Kalman and several the particle filters. EMPIRE is targeted at models of all kinds of complexity and has been coupled to several geoscience models, eg. the Lorenz-63 model, a barotropic vorticity model, the general circulation model HadCM3, the ocean model NEMO, and the land-surface model JULES. The Python-based system pyenda (Python Ensemble Data Assimilation) allows Fortran- and Python-based models to be used for data assimilation. Models can be coupled either using MPI or by using a Python interface. Using Python allows quick prototyping and pyenda is aimed at small to medium scale models. pyenda currently includes variants of the ensemble Kalman filter and has been coupled to the Lorenz-63 model, an advection-based precipitation nowcasting scheme, and the dynamic global vegetation model JSBACH.

Naval EarthMap Observer (NEMO) Hyperspectral Remote Sensing Program

DTIC Science & Technology

2000-10-01

The NEMO hyperspectral remote sensing program will provide unclassified, space-based hyperspectral passive imagery at moderate resolution that offers substantial potential for direct use by Naval forces and the Civil Sector.

Withaferin A disrupts ubiquitin-based NEMO reorganization induced by canonical NF-κB signaling

PubMed Central

Jackson, Shawn S.; Oberley, Christopher; Hooper, Christopher P.; Grindle, Kreg; Wuerzberger-Davis, Shelly; Wolff, Jared; McCool, Kevin; Rui, Lixin; Miyamoto, Shigeki

2014-01-01

The NF-κB family of transcription factors regulates numerous cellular processes, including cell proliferation and survival responses. The constitutive activation of NF-κB has also emerged as an important oncogenic driver in many malignancies, such as activated B-cell like diffuse large B cell lymphoma, among others. In this study, we investigated the impact and mechanisms of action of Withaferin A, a naturally produced steroidal lactone, against both signal-inducible as well as constitutive NF-κB activities. We found that Withaferin A is a robust inhibitor of canonical and constitutive NF-κB activities, leading to apoptosis of certain lymphoma lines. In the canonical pathway induced by TNF, Withaferin A did not disrupt RIP1 polyubiquitination or NEMO-IKKβ interaction and was a poor direct IKKβ inhibitor, but prevented the formation of TNF induced NEMO foci which colocalized with TNF ligand. While GFP-NEMO efficiently formed TNF-induced foci, a GFP-NEMOY308S mutant that is defective in binding to polyubiquitin chains did not form foci. Our study reveals that Withaferin A is a novel type of IKK inhibitor which acts by disrupting NEMO reorganization into ubiquitin-based signaling structures in vivo. PMID:25304104

NEMO: Status of the Project

NASA Astrophysics Data System (ADS)

Migneco, E.; Aiello, S.; Amato, E.; Ambriola, M.; Ameli, F.; Andronico, G.; Anghinolfi, M.; Battaglieri, M.; Bellotti, R.; Bersani, A.; Boldrin, A.; Bonori, M.; Cafagna, F.; Capone, A.; Caponnetto, L.; Chiarusi, T.; Circella, M.; Cocimano, R.; Coniglione, R.; Cordelli, M.; Costa, M.; Cuneo, S.; D'Amico, A.; D'Amico, V.; De Marzo, C.; De Vita, R.; Distefano, C.; Gabrielli, A.; Gandolfi, E.; Grimaldi, A.; Habel, R.; Italiano, A.; Leonardi, M.; Lo Nigro, L.; Lo Presti, D.; Margiotta, A.; Martini, A.; Masetti, M.; Masullo, R.; Montaruli, T.; Mosetti, R.; Musumeci, M.; Nicolau, C. A.; Occhipinti, R.; Papaleo, R.; Petta, C.; Piattelli, P.; Raia, G.; Randazzo, N.; Reito, S.; Ricco, G.; Riccobene, G.; Ripani, M.; Romita, M.; Rovelli, A.; Ruppi, M.; Russo, G. V.; Russo, M.; Sapienza, P.; Schuller, J. P.; Sedita, M.; Sokalski, I.; Spurio, M.; Taiuti, M.; Trasatti, L.; Ursella, L.; Valente, V.; Vicini, P.; Zanarini, G.

2004-11-01

The activities towards the realisation of a km3 Cherenkov neutrino detector, carried out by the NEMO Collaboration are described. Long term exploration of a 3500 m deep site close to the Sicilian coast has shown that it is optimal for the installation of the detector. A complete feasibility study, that has considered all the components of the detector as well as its deployment, has been carried out demonstrating that technological solutions exist for the realization of an underwater km3 detector. The realization of a technological demonstrator (the NEMO Phase 1 project) is under way.

Nemo:. a Project for a KM3 Underwater Detector for Astrophysical Neutrinos in the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Amore, I.; Aiello, S.; Ambriola, M.; Ameli, F.; Anghinolfi, M.; Anzalone, A.; Barbarino, G.; Barbarito, E.; Battaglieri, M.; Bellotti, R.; Beverini, N.; Bonori, M.; Bouhadef, B.; Brescia, M.; Cacopardo, G.; Cafagna, F.; Capone, A.; Caponetto, L.; Castorina, E.; Ceres, A.; Chiarusi, T.; Circella, M.; Cocimano, R.; Coniglione, R.; Cordelli, M.; Costa, M.; Cuneo, S.; D'Amico, A.; de Bonis, G.; de Marzo, C.; de Rosa, G.; de Vita, R.; Distefano, C.; Falchini, E.; Fiorello, C.; Flaminio, V.; Fratini, K.; Gabrielli, A.; Galeotti, S.; Gandolfi, E.; Giacomelli, G.; Giorgi, F.; Grimaldi, A.; Habel, R.; Leonora, E.; Lonardo, A.; Longo, G.; Lo Presti, D.; Lucarelli, F.; Maccioni, E.; Margiotta, A.; Martini, A.; Masullo, R.; Megna, R.; Migneco, E.; Mongelli, M.; Montaruli, T.; Morganti, M.; Musumeci, M. S.; Nicolau, C. A.; Orlando, A.; Osipenko, M.; Osteria, G.; Papaleo, R.; Pappalardo, V.; Petta, C.; Piattelli, P.; Raia, G.; Randazzo, N.; Reito, S.; Ricco, G.; Riccobene, G.; Ripani, M.; Rovelli, A.; Ruppi, M.; Russo, G. V.; Russo, S.; Sapienza, P.; Sedita, M.; Shirokov, E.; Simeone, F.; Sipala, V.; Spurio, M.; Taiuti, M.; Terreni, G.; Trasatti, L.; Urso, S.; Valente, V.; Vicini, P.

The status of the project is described: the activity on long term characterization of water optical and oceanographic parameters at the Capo Passero site candidate for the Mediterranean km3 neutrino telescope; the feasibility study; the physics performances and underwater technology for the km3; the activity on NEMO Phase 1, a technological demonstrator that has been deployed at 2000 m depth 25 km offshore Catania; the realization of an underwater infrastructure at 3500 m depth at the candidate site (NEMO Phase 2).

The UKC2 regional coupled environmental prediction system

NASA Astrophysics Data System (ADS)

Lewis, Huw W.; Castillo Sanchez, Juan Manuel; Graham, Jennifer; Saulter, Andrew; Bornemann, Jorge; Arnold, Alex; Fallmann, Joachim; Harris, Chris; Pearson, David; Ramsdale, Steven; Martínez-de la Torre, Alberto; Bricheno, Lucy; Blyth, Eleanor; Bell, Victoria A.; Davies, Helen; Marthews, Toby R.; O'Neill, Clare; Rumbold, Heather; O'Dea, Enda; Brereton, Ashley; Guihou, Karen; Hines, Adrian; Butenschon, Momme; Dadson, Simon J.; Palmer, Tamzin; Holt, Jason; Reynard, Nick; Best, Martin; Edwards, John; Siddorn, John

2018-01-01

It is hypothesized that more accurate prediction and warning of natural hazards, such as of the impacts of severe weather mediated through various components of the environment, require a more integrated Earth System approach to forecasting. This hypothesis can be explored using regional coupled prediction systems, in which the known interactions and feedbacks between different physical and biogeochemical components of the environment across sky, sea and land can be simulated. Such systems are becoming increasingly common research tools. This paper describes the development of the UKC2 regional coupled research system, which has been delivered under the UK Environmental Prediction Prototype project. This provides the first implementation of an atmosphere-land-ocean-wave modelling system focussed on the United Kingdom and surrounding seas at km-scale resolution. The UKC2 coupled system incorporates models of the atmosphere (Met Office Unified Model), land surface with river routing (JULES), shelf-sea ocean (NEMO) and ocean waves (WAVEWATCH III). These components are coupled, via OASIS3-MCT libraries, at unprecedentedly high resolution across the UK within a north-western European regional domain. A research framework has been established to explore the representation of feedback processes in coupled and uncoupled modes, providing a new research tool for UK environmental science. This paper documents the technical design and implementation of UKC2, along with the associated evaluation framework. An analysis of new results comparing the output of the coupled UKC2 system with relevant forced control simulations for six contrasting case studies of 5-day duration is presented. Results demonstrate that performance can be achieved with the UKC2 system that is at least comparable to its component control simulations. For some cases, improvements in air temperature, sea surface temperature, wind speed, significant wave height and mean wave period highlight the potential benefits of coupling between environmental model components. Results also illustrate that the coupling itself is not sufficient to address all known model issues. Priorities for future development of the UK Environmental Prediction framework and component systems are discussed.

Advanced energy systems and technologies - National R and D programme

NASA Astrophysics Data System (ADS)

Lund, P. D.

1992-08-01

The energy R and D in Finland is accomplished through the energy research programs of the Ministry of Trade and Industry. Today there are some 12 R and D programs in operation covering the various aspects of the energy sector. The NEMO-program deals with advanced new energy technologies and systems. The NEMO-program was launched in 1988 and it ends at the end of 1992. Helsinki University of Technology has been responsible for the coordination and most of the universities, research centers, and companies on new advanced energy technologies have been involved in the realization of NEMO. The objectives of the program have been to assess the potential of new technologies in the Finnish energy supply system, encourage and support businesses, and to create necessary research tradition in Finland. At the beginning in year 1988, several new technologies were included, but as the knowledge has increased, focusing on the most promising fields has taken place. Wind and solar energy show the best promises in respect to business activities and possibilities for utilization in Finland. Energy storage some other advanced technologies such as fuel cells and hydrogen technologies represented in the NEMO-program have an important role, but the commercial applications lie more distant in the future. The NEMO-program has reached its objectives. The international evaluation in fall 1990 gave very positive feedback and the scientific quality of the work was found good. At the same time, the contents was still focused more on commercial applications to support national industries in the field. The descriptions of the ongoing NEMO research projects are included in this report.

Design and validation of MEDRYS, a Mediterranean Sea reanalysis over the period 1992-2013

NASA Astrophysics Data System (ADS)

Hamon, Mathieu; Beuvier, Jonathan; Somot, Samuel; Lellouche, Jean-Michel; Greiner, Eric; Jordà, Gabriel; Bouin, Marie-Noëlle; Arsouze, Thomas; Béranger, Karine; Sevault, Florence; Dubois, Clotilde; Drevillon, Marie; Drillet, Yann

2016-04-01

The French research community in the Mediterranean Sea modeling and the French operational ocean forecasting center Mercator Océan have gathered their skill and expertise in physical oceanography, ocean modeling, atmospheric forcings and data assimilation to carry out a MEDiterranean sea ReanalYsiS (MEDRYS) at high resolution for the period 1992-2013. The ocean model used is NEMOMED12, a Mediterranean configuration of NEMO with a 1/12° ( ˜ 7 km) horizontal resolution and 75 vertical z levels with partial steps. At the surface, it is forced by a new atmospheric-forcing data set (ALDERA), coming from a dynamical downscaling of the ERA-Interim atmospheric reanalysis by the regional climate model ALADIN-Climate with a 12 km horizontal and 3 h temporal resolutions. This configuration is used to carry a 34-year hindcast simulation over the period 1979-2013 (NM12-FREE), which is the initial state of the reanalysis in October 1992. MEDRYS uses the existing Mercator Océan data assimilation system SAM2 that is based on a reduced-order Kalman filter with a three-dimensional (3-D) multivariate modal decomposition of the forecast error. Altimeter data, satellite sea surface temperature (SST) and temperature and salinity vertical profiles are jointly assimilated. This paper describes the configuration we used to perform MEDRYS. We then validate the skills of the data assimilation system. It is shown that the data assimilation restores a good average temperature and salinity at intermediate layers compared to the hindcast. No particular biases are identified in the bottom layers. However, the reanalysis shows slight positive biases of 0.02 psu and 0.15 °C above 150 m depth. In the validation stage, it is also shown that the assimilation allows one to better reproduce water, heat and salt transports through the Strait of Gibraltar. Finally, the ability of the reanalysis to represent the sea surface high-frequency variability is shown.

Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-κB Essential Modulator (NEMO)/IKKβ Protein-Protein Interface

PubMed Central

Golden, Mary S.; Cote, Shaun M.; Sayeg, Marianna; Zerbe, Brandon S.; Villar, Elizabeth A.; Beglov, Dmitri; Sazinsky, Stephen L.; Georgiadis, Rosina M.; Vajda, Sandor; Kozakov, Dima; Whitty, Adrian

2013-01-01

We report a comprehensive analysis of binding energy hot spots at the protein-protein interaction (PPI) interface between NF-κB Essential Modulator (NEMO) and IκB kinase subunit β (IKKβ), an interaction that is critical for NF-κB pathway signaling, using experimental alanine scanning mutagenesis and also the FTMap method for computational fragment screening. The experimental results confirm that the previously identified NBD region of IKKβ contains the highest concentration of hot spot residues, the strongest of which are W739, W741 and L742 (ΔΔG = 4.3, 3.5 and 3.2 kcal/mol, respectively). The region occupied by these residues defines a potentially druggable binding site on NEMO that extends for ~16 Å to additionally include the regions that bind IKKβ L737 and F734. NBD residues D738 and S740 are also important for binding but do not make direct contact with NEMO, instead likely acting to stabilize the active conformation of surrounding residues. We additionally found two previously unknown hot spot regions centered on IKKβ residues L708/V709 and L719/I723. The computational approach successfully identified all three hot spot regions on IKKβ. Moreover, the method was able to accurately quantify the energetic importance of all hot spots residues involving direct contact with NEMO. Our results provide new information to guide the discovery of small molecule inhibitors that target the NEMO/IKKβ interaction. They additionally clarify the structural and energetic complementarity between “pocket-forming” and “pocket occupying” hot spot residues, and further validate computational fragment mapping as a method for identifying hot spots at PPI interfaces. PMID:23506214

The 2004 Sumatra tsunami in the southeastern Pacific: Coastal and offshore measurements and numerical modeling

NASA Astrophysics Data System (ADS)

Moore, C. W.; Eble, M. C.; Rabinovich, A.; Titov, V. V.

2016-12-01

The Mw = 9.3 megathrust earthquake of December 26, 2004 off the coast of Sumatra generated a catastrophic tsunami that crossed the Indian Ocean and was widespread in the Pacific and Atlantic oceans being recorded by a great number of coastal tide gauges located in 15-25 thousand kilometers from the source area. The data from these instruments throughout the world oceans enabled estimates of various statistical parameters and energy decay of this event. However, only very few open-ocean records of this tsunami had been obtained. A unique high-resolution record of this tsunami from DART 32401 located offshore of northern Chile, combined with the South American mainland tide gauge measurements and the data from three island stations (San Felix, Juan Fernandez and Easter) enabled us to examine far-field characteristics of the event in the southeastern Pacific and to compare the results of global numerical simulations with observations. The maximum wave height measured at DART 32401 was only 1.8 cm but the signal was very clear and reliable. Despite their small heights, the waves demonstrated consistent spatial and temporal structure and good agreement with DART 46405/NeMO records in the NE Pacific. The travel time from the source area to DART 32401 was 25h 55min in good agreement with the computed travel time (25h 45min) and consistent with the times obtained from the nearby coastal tide gauges. This agreement was much better than it followed from the direct travel time estimation based classical kinematic theory that gave the travel time approximately 1.5 hrs shorter than observed. The later actual arrival of the 2004 tsunami waves corresponds to the most energetically economic path along the mid-ocean ridge wave-guides, which is distinctly reproduced by the numerical model. Also, the numerical model described well the frequency content, amplitudes and general structure of the observed waves at this DART and the three island stations. Maximum wave heights in this region were identified at Arica (72 cm) and Callao (65 cm). The open-ocean and coastal records indicate that the 2004 tsunami wave energy occupied the period band of 6 min to 3.7 hrs with the main energy concentrated at periods of 30 to 70 min and peak values at 40 min.

Earth Observations taken by Expedition 26 crewmember

NASA Image and Video Library

2011-01-09

ISS026-E-016287 (9 Jan. 2011) --- Onekotan Island, part of the Russian Federation in the western Pacific Ocean, is featured in this image photographed by an Expedition 26 crew member on the International Space Station. Snow cover highlights calderas and volcanic cones that form the northern and southern ends of the island. Calderas are depressions formed when a volcano empties its magma chamber in an explosive eruption, followed by collapse of the overlaying material into the newly evacuated space. The northern end of the island is dominated by the Nemo Peak volcano that began forming within an older caldera approximately 9,500 years ago, according to scientists. The last recorded eruptive activity at Nemo Peak occurred in the early 18th century. The southern end of the island is formed by the 7.5 kilometer wide Tao-Rusyr Caldera. The caldera is filled by Kal’tsevoe Lake and Krenitzyn Peak, a volcano that has only erupted once in recorded history during 1952. Extending between northeastern Japan and the Kamchatka Peninsula of Russia, the Kuril Islands are an island arc located along the Pacific “Ring of Fire”. Island arcs form along an active boundary between two tectonic plates where one plate is being driven beneath the other (subduction). Magma generated by the subduction process feeds volcanoes—which eventually form volcanic islands—over the subduction boundary.

The Nanoelectric Modeling Tool (NEMO) and Its Expansion to High Performance Parallel Computing

NASA Technical Reports Server (NTRS)

Klimeck, G.; Bowen, C.; Boykin, T.; Oyafuso, F.; Salazar-Lazaro, C.; Stoica, A.; Cwik, T.

1998-01-01

Material variations on an atomic scale enable the quantum mechanical functionality of devices such as resonant tunneling diodes (RTDs), quantum well infrared photodetectors (QWIPs), quantum well lasers, and heterostructure field effect transistors (HFETs).

North-western Mediterranean sea-breeze circulation in a regional climate system model

NASA Astrophysics Data System (ADS)

Drobinski, Philippe; Bastin, Sophie; Arsouze, Thomas; Béranger, Karine; Flaounas, Emmanouil; Stéfanon, Marc

2017-04-01

In the Mediterranean basin, moisture transport can occur over large distance from remote regions by the synoptic circulation or more locally by sea breezes, driven by land-sea thermal contrast. Sea breezes play an important role in inland transport of moisture especially between late spring and early fall. In order to explicitly represent the two-way interactions at the atmosphere-ocean interface in the Mediterranean region and quantify the role of air-sea feedbacks on regional meteorology and climate, simulations at 20 km resolution performed with WRF regional climate model (RCM) and MORCE atmosphere-ocean regional climate model (AORCM) coupling WRF and NEMO-MED12 in the frame of HyMeX/MED-CORDEX are compared. One result of this study is that these simulations reproduce remarkably well the intensity, direction and inland penetration of the sea breeze and even the existence of the shallow sea breeze despite the overestimate of temperature over land in both simulations. The coupled simulation provides a more realistic representation of the evolution of the SST field at fine scale than the atmosphere-only one. Temperature and moisture anomalies are created in direct response to the SST anomaly and are advected by the sea breeze over land. However, the SST anomalies are not of sufficient magnitude to affect the large-scale sea-breeze circulation. The temperature anomalies are quickly damped by strong surface heating over land, whereas the water vapor mixing ratio anomalies are transported further inland. The inland limit of significance is imposed by the vertical dilution in a deeper continental boundary-layer.

Biogeochemistry and plankton variabilities in the Mediterranean Sea: a long-term 3D coupled modelling approach

NASA Astrophysics Data System (ADS)

Dos Santos, Alex; Ulses, Caroline; Estournel, Claude; Marsaleix, Patrick

2017-04-01

The Mediterranean Sea is a semi-enclosed basin between Europe, Asia and North Africa. Around half a billion people (7% of the world population) live in this region, in 22 countries. The Mediterranean Sea is crossed by about one third of the world's total merchant shipping each year, representing a strong anthropogenic pressure on its ecosystems. Additionally, important climatic differences between Africa and Europe make the Mediterranean Sea a high gradients area, and thus can explain why it is very sensitive to climate change. Indeed, changes in temperature and salinity have already been observed in its deep waters. The semi-enclosed sea displays hydrodynamical processes which can be observed on a global scale, such as a thermohaline circulation or dense water formations, and a wide variety of trophic regimes. Studying environmental changes in the Mediterranean Sea can therefore bring insights for the global ocean. In this context, we propose to investigate the impact of climate and anthropogenic changes on the Mediterranean Sea pelagic planktonic ecosystems. A long-term historical simulation (hindcast) is performed in order to evaluate these changes. The regional ocean model NEMO-MED12, computing the circulation at a 1/12° resolution, is used to force offline the biogeochemical model ECO3M-S. After a validation of the simulation with existing data, a focus is made on the interannual variability of our key variables for the studied period: biogeochemical cycles are discussed, and nutrients budgets are computed on a basin scale. Finally, estimations of subsequent primary production and the structure of projected planktonic ecosystems are analysed.

Antarctic Climate Variability: Covariance of Ozone and Sea Ice in Atmosphere - Ocean Coupled Model Simulations

NASA Astrophysics Data System (ADS)

Jrrar, Amna; Abraham, N. Luke; Pyle, John A.; Holland, David

2014-05-01

Changes in sea ice significantly modulate climate change because of its high reflective and insulating nature. While Arctic Sea Ice Extent (SIE) shows a negative trend. Antarctic SIE shows a weak but positive trend, estimated at 0.127 x 106 km2 per decade. The trend results from large regional cancellations, more ice in the Weddell and the Ross seas, and less ice in the Amundsen - Bellingshausen seas. A number of studies had demonstrated that stratospheric ozone depletion has had a major impact on the atmospheric circulation, causing a positive trend in the Southern Annular Mode (SAM), which has been linked to the observed positive trend in autumn sea ice in the Ross Sea. However, other modelling studies show that models forced with prescribed ozone hole simulate decreased sea ice in all regions comparative to a control run. A recent study has also shown that stratospheric ozone recovery will mitigate Antarctic sea ice loss. To verify this assumed relationship, it is important first to investigate the covariance between ozone's natural (dynamical) variability and Antarctic sea ice distribution in pre-industrial climate, to estimate the trend due to natural variability. We investigate the relationship between anomalous Antarctic ozone years and the subsequent changes in Antarctic sea ice distribution in a multidecadal control simulation using the AO-UMUKCA model. The model has a horizontal resolution of 3.75 X 2.5 degrees in longitude and latitude; and 60 hybrid height levels in the vertical, from the surface up to a height of 84 km. The ocean component is the NEMO ocean model on the ORCA2 tripolar grid, and the sea ice model is CICE. We evaluate the model's performance in terms of sea ice distribution, and we calculate sea ice extent trends for composites of anomalously low versus anomalously high SH polar ozone column. We apply EOF analysis to the seasonal anomalies of sea ice concentration, MSLP, and Z 500, and identify the leading climate modes controlling the variability of Antarctic sea ice in each case, and study their relationship with SH polar ozone column.

Accurate Modelling of Surface Currents and Internal Tides in a Semi-enclosed Coastal Sea

NASA Astrophysics Data System (ADS)

Allen, S. E.; Soontiens, N. K.; Dunn, M. B. H.; Liu, J.; Olson, E.; Halverson, M. J.; Pawlowicz, R.

2016-02-01

The Strait of Georgia is a deep (400 m), strongly stratified, semi-enclosed coastal sea on the west coast of North America. We have configured a baroclinic model of the Strait of Georgia and surrounding coastal waters using the NEMO ocean community model. We run daily nowcasts and forecasts and publish our sea-surface results (including storm surge warnings) to the web (salishsea.eos.ubc.ca/storm-surge). Tides in the Strait of Georgia are mixed and large. The baroclinic model and previous barotropic models accurately represent tidal sea-level variations and depth mean currents. The baroclinic model reproduces accurately the diurnal but not the semi-diurnal baroclinic tidal currents. In the Southern Strait of Georgia, strong internal tidal currents at the semi-diurnal frequency are observed. Strong semi-diurnal tides are also produced in the model, but are almost 180 degrees out of phase with the observations. In the model, in the surface, the barotropic and baroclinic tides reinforce, whereas the observations show that at the surface the baroclinic tides oppose the barotropic. As such the surface currents are very poorly modelled. Here we will present evidence of the internal tidal field from observations. We will discuss the generation regions of the tides, the necessary modifications to the model required to correct the phase, the resulting baroclinic tides and the improvements in the surface currents.

Estimation of the atmosphere-ocean fluxes of greenhouse gases and aerosols at the finer resolution of the coastal ocean.

NASA Astrophysics Data System (ADS)

Vieira, Vasco; Sahlée, Erik; Jurus, Pavel; Clementi, Emanuela; Pettersson, Heidi; Mateus, Marcos

2016-04-01

The balances and fluxes of greenhouse gases and aerosols between atmosphere and ocean are fundamental for Earth's heat budget. Hence, the scientific community needs to know and simulate them with accuracy in order to monitor climate change from Earth-Observation satellites and to produce reliable estimates of climate change using Earth-System Models (ESM). So far, ESM have represented earth's surface with coarser resolutions so that each cell of the marine domain is dominated by the open ocean. In such case it is enough to use simple algorithms considering the wind speed 10m above sea-surface (u10) as sole driver of the gas transfer velocity. The formulation by Wanninkhof (1992) is broadly accepted as the best. However, the ESM community is becoming increasingly aware of the need to model with finer resolutions. Then, it is no longer enough to only consider u10 when modelling gas transfer velocities across the coastal oceans' surfaces. More comprehensive formulations are required that adjust better to local conditions by also accounting for the effects of sea-surface agitation, wave breaking, atmospheric stability of the Surface Boundary Layer, current drag with the bottom, surfactants and rain. Accurate algorithms are also fundamental to monitor atmosphere and ocean greenhouse gas concentrations using satellite data and reverse modelling. Past satellite missions ERS, Envisat, Jason-2, Aqua, Terra and Metop, have already been remotely sensing the ocean's surface at much finer resolutions than ESM using instruments like MERIS, MODIS, AMR, AATSR, MIPAS, Poseidon-3, SCIAMACHY, SeaWiFS, and IASI. The planned new satellite missions Sentinel-3, OCO-2 and GOSAT will further increase the resolutions. We developed a framework to congregate competing formulations for the estimation of the solubility and transfer velocity of virtually any gas on the biosphere taking into consideration the atmosphere and ocean fundamental variables and their derived geophysical processes mentioned above. First, we tested with measured data from the Baltic. Then, we adapted it to a coupler for atmosphere (WRF) and ocean (WW3-NEMO) model components and tested with simulated data relative to the Mediterranean and coastal North Atlantic. Computational speed was greatly improved by calculus vectorization and parallelization. The classical solubility formulation was compared to a recent alternative relying in a different chemistry background. Differences between solubility formulations resulted in a bias of 3.86×106 ton of CO2, 880.7 ton of CH4 and 401 ton of N2O dissolved in the first meter below the sea-surface of the modelled region, corresponding to 5.9% of the N2O yearly discharged by European estuaries. These differences concentrated in sensitive areas for Earth-System dynamics: the cooler polar waters and warmer less-saline coastal waters. The classical transfer velocity formulation using solely u10 was compared to alternatives using the friction velocity, atmospheric stability, sea-surface agitation and wave breaking. Differences between estimated transfer velocities concentrated at the coastal ocean and resulted in 55.82% of the gas volume transferred over the sea-surface of the modelled region during the 66h simulated period.

Inhibition of the NEMO/IKKβ association complex formation, a novel mechanism associated with the NF-κB activation suppression by Withania somnifera's key metabolite withaferin A.

PubMed

Grover, Abhinav; Shandilya, Ashutosh; Punetha, Ankita; Bisaria, Virendra S; Sundar, Durai

2010-12-02

Nuclear Factor kappa B (NF-κB) is a transcription factor involved in the regulation of cell signaling responses and is a key regulator of cellular processes involved in the immune response, differentiation, cell proliferation, and apoptosis. The constitutive activation of NF-κB contributes to multiple cellular outcomes and pathophysiological conditions such as rheumatoid arthritis, asthma, inflammatory bowel disease, AIDS and cancer. Thus there lies a huge therapeutic potential beneath inhibition of NF-κB signalling pathway for reducing these chronic ailments. Withania somnifera, a reputed herb in ayurvedic medicine, comprises a large number of steroidal lactones known as withanolides which show plethora of pharmacological activities like anti- inflammatory, antitumor, antibacterial, antioxidant, anticonvulsive, and immunosuppressive. Though a few studies have been reported depicting the effect of WA (withaferin A) on suppression of NF-κB activation, the mechanism behind this is still eluding the researchers. The study conducted here is an attempt to explore NF-κB signalling pathway modulating capability of Withania somnifera's major constituent WA and to elucidate its possible mode of action using molecular docking and molecular dynamics simulations studies. Formation of active IKK (IκB kinase) complex comprising NEMO (NF-κB Essential Modulator) and IKKβ subunits is one of the essential steps for NF-κB signalling pathway, non-assembly of which can lead to prevention of the above mentioned vulnerable disorders. As observed from our semi-flexible docking analysis, WA forms strong intermolecular interactions with the NEMO chains thus building steric as well as thermodynamic barriers to the incoming IKKβ subunits, which in turn pave way to naive complex formation capability of NEMO with IKKβ. Docking of WA into active NEMO/IKKβ complex using flexible docking in which key residues of the complex were kept flexible also suggest the disruption of the active complex. Thus the molecular docking analysis of WA into NEMO and active NEMO/IKKβ complex conducted in this study provides significant evidence in support of the proposed mechanism of NF-κB activation suppression by inhibition or disruption of active NEMO/IKKβ complex formation being accounted by non-assembly of the catalytically active NEMO/IKKβ complex. Results from the molecular dynamics simulations in water show that the trajectories of the native protein and the protein complexed with WA are stable over a considerably long time period of 2.6 ns. NF-κB is one of the most attractive topics in current biological, biochemical, and pharmacological research, and in the recent years the number of studies focusing on its inhibition/regulation has increased manifolds. Small ligands (both natural and synthetic) are gaining particular attention in this context. Our computational analysis provided a rationalization of the ability of naturally occurring withaferin A to alter the NF-κB signalling pathway along with its proposed mode of inhibition of the pathway. The absence of active IKK multisubunit complex would prevent degradation of IκB proteins, as the IκB proteins would not get phosphorylated by IKK. This would ultimately lead to non-release of NF-κB and its further translocation to the nucleus thus arresting its nefarious acts. Conclusively our results strongly suggest that withaferin A is a potent anticancer agent as ascertained by its potent NF-κB modulating capability. Moreover the present MD simulations made clear the dynamic structural stability of NEMO/IKKβ in complex with the drug WA, together with the inhibitory mechanism.

Dimensions of biodiversity of oceanic nitrogen cycling: nutrient co-limitation, nitrogen substrate preferences and more.

NASA Astrophysics Data System (ADS)

Zehr, J.; Mills, M. M.; Shilova, I. N.; Turk-Kubo, K.; Robidart, J.; van Dijken, G.; Bjorkman, K. M.; Whitt, D. B.; Wai, B.; Pampin Baro, J.; Hogan, M.; Rapp, I.; Zakem, E.; Fredrickson, A.; Leahy, B.; Linney, M.; Santiago, A.; Follows, M. J.; Achterberg, E. P.; Kolber, Z.; Church, M. J.; Arrigo, K. R.

2016-02-01

We conducted the research cruise: Nutrient Effects on Marine microOrganisms (NEMO) onboard the R/V New Horizon (NH1417: August 18 to September 16, 2014) between the ports of San Diego, CA and Honolulu, HI. The three major objectives of the cruise were to: 1) evaluate genetic, physiological and phylogenetic responses of marine phytoplankton communities in the North Pacific Subtropical Gyre to different nitrogen (N) substrates and to determine how other nutrients (iron, phosphorus) impact N utilization; 2) characterize the physical processes and dynamics in support of the biological processes; and 3) characterize the diversity and activities of microbial communities in the upper water column in relation to the nutrient availability. Several incubation experiments were conducted along the cruise transect to assess the effect of nutrients on microbial communities. The results showed that N addition resulted in increased chlorophyll a (chl a) and rates of CO2 fixation at most sites, but Prochlorococcus, Synechococcus and picoekaryotic phytoplankton had different responses to urea, ammonium and nitrate. In contrast, chl a and CO2 fixation did not respond to additions of single nutrient (e.g. N, P or Fe alone) at the westernmost experiment (151°W), where the simultaneous addition of N and P was required for stimulation. The physical dynamics were studied through high-resolution surveys of eddy dipole features as well as diel sampling at two locations. Additionally, we characterized an extensive bloom that occurred near the critical latitude (29°N, 140°W) from mid July to the end of September; a typical but still enigmatic event. Here, we present a summary of the initial observations and findings from the NEMO cruise with data including physics, nutrient concentrations, chl a, primary productivity and microbial community composition. The results of this research cruise will help in assessing how ocean N cycling and ecosystem functions will respond to global climate change.

CMIP5-downscaled projections for the NW European Shelf Seas: initial results and insights into uncertainties

NASA Astrophysics Data System (ADS)

Tinker, Jonathan; Palmer, Matthew; Lowe, Jason; Howard, Tom

2017-04-01

The North Sea, and wider Northwest European Shelf seas (NWS) are economically, environmentally, and culturally important for a number of European countries. They are protected by European legislation, often with specific reference to the potential impacts of climate change. Coastal climate change projections are an important source of information for effective management of European Shelf Seas. For example, potential changes in the marine environment are a key component of the climate change risk assessments (CCRAs) carried out under the UK Climate Change Act We use the NEMO shelf seas model combined with CMIP5 climate model and EURO-CORDEX regional atmospheric model data to generate new simulations of the NWS. Building on previous work using a climate model perturbed physics ensemble and the POLCOMS, this new model setup is used to provide first indication of the uncertainties associated with: (i) the driving climate model; (ii) the atmospheric downscaling model (iii) the shelf seas downscaling model; (iv) the choice of climate change scenario. Our analysis considers a range of physical marine impacts and the drivers of coastal variability and change, including sea level and the propagation of open ocean signals onto the shelf. The simulations are being carried out as part of the UK Climate Projections 2018 (UKCP18) and will feed into the following UK CCRA.

Performance and quality assessment of the recent updated CMEMS global ocean monitoring and forecasting real-time system

NASA Astrophysics Data System (ADS)

Le Galloudec, Olivier; Lellouche, Jean-Michel; Greiner, Eric; Garric, Gilles; Régnier, Charly; Drévillon, Marie; Drillet, Yann

2017-04-01

Since May 2015, Mercator Ocean opened the Copernicus Marine Environment and Monitoring Service (CMEMS) and is in charge of the global eddy resolving ocean analyses and forecast. In this context, Mercator Ocean currently delivers in real-time daily services (weekly analyses and daily forecast) with a global 1/12° high resolution system. The model component is the NEMO platform driven at the surface by the IFS ECMWF atmospheric analyses and forecasts. Observations are assimilated by means of a reduced-order Kalman filter with a 3D multivariate modal decomposition of the forecast error. It includes an adaptive-error estimate and a localization algorithm. Along track altimeter data, satellite Sea Surface Temperature and in situ temperature and salinity vertical profiles are jointly assimilated to estimate the initial conditions for numerical ocean forecasting. A 3D-Var scheme provides a correction for the slowly-evolving large-scale biases in temperature and salinity. R&D activities have been conducted at Mercator Ocean these last years to improve the real-time 1/12° global system for recent updated CMEMS version in 2016. The ocean/sea-ice model and the assimilation scheme benefited of the following improvements: large-scale and objective correction of atmospheric quantities with satellite data, new Mean Dynamic Topography taking into account the last version of GOCE geoid, new adaptive tuning of some observational errors, new Quality Control on the assimilated temperature and salinity vertical profiles based on dynamic height criteria, assimilation of satellite sea-ice concentration, new freshwater runoff from ice sheets melting, … This presentation will show the impact of some updates separately, with a particular focus on adaptive tuning experiments of satellite Sea Level Anomaly (SLA) and Sea Surface Temperature (SST) observations errors. For the SLA, the a priori prescribed observation error is globally greatly reduced. The median value of the error changed from 5cm to 2.5cm in a few assimilation cycles. For the SST, we chose to maintain the median value of the error to 0.4°C. The spatial distribution of the SST error follows the model physics and atmospheric variability. Either for SLA or SST, we improve the performances of the system using this adaptive tuning. The overall behavior of the system integrating all updates reporting on the products quality improvements will be also discussed, highlighting the level of performance and the reliability of the new system.

Evaluation of numerical models by FerryBox and Fixed Platform in-situ data in the southern North Sea

NASA Astrophysics Data System (ADS)

Haller, M.; Janssen, F.; Siddorn, J.; Petersen, W.; Dick, S.

2015-02-01

FerryBoxes installed on ships of opportunity (SoO) provide high-frequency surface biogeochemical measurements along selected tracks on a regular basis. Within the European FerryBox Community, several FerryBoxes are operated by different institutions. Here we present a comparison of model simulations applied to the North Sea with FerryBox temperature and salinity data from a transect along the southern North Sea and a more detailed analysis at three different positions located off the English East coast, at the Oyster Ground and in the German Bight. In addition to the FerryBox data, data from a Fixed Platform of the MARNET network are applied. Two operational hydrodynamic models have been evaluated for different time periods: results of BSHcmod v4 are analysed for 2009-2012, while simulations of FOAM AMM7 NEMO have been available from MyOcean data base for 2011 and 2012. The simulation of water temperatures is satisfying; however, limitations of the models exist, especially near the coast in the southern North Sea, where both models are underestimating salinity. Statistical errors differ between the models and the measured parameters, as the root mean square error (rmse) accounts for BSHcmod v4 to 0.92 K, for AMM7 only to 0.44 K. For salinity, BSHcmod is slightly better than AMM7 (0.98 and 1.1 psu, respectively). The study results reveal weaknesses of both models, in terms of variability, absolute levels and limited spatial resolution. In coastal areas, where the simulation of the transition zone between the coasts and the open ocean is still a demanding task for operational modelling, FerryBox data, combined with other observations with differing temporal and spatial scales serve as an invaluable tool for model evaluation and optimization. The optimization of hydrodynamical models with high frequency regional datasets, like the FerryBox data, is beneficial for their subsequent integration in ecosystem modelling.

Requirement of FADD, NEMO, and BAX/BAK for Aberrant Mitochondrial Function in Tumor Necrosis Factor Alpha-Induced Necrosis▿

PubMed Central

Irrinki, Krishna M.; Mallilankaraman, Karthik; Thapa, Roshan J.; Chandramoorthy, Harish C.; Smith, Frank J.; Jog, Neelakshi R.; Gandhirajan, Rajesh Kumar; Kelsen, Steven G.; Houser, Steven R.; May, Michael J.; Balachandran, Siddharth; Madesh, Muniswamy

2011-01-01

Necroptosis represents a form of alternative programmed cell death that is dependent on the kinase RIP1. RIP1-dependent necroptotic death manifests as increased reactive oxygen species (ROS) production in mitochondria and is accompanied by loss of ATP biogenesis and eventual dissipation of mitochondrial membrane potential. Here, we show that tumor necrosis factor alpha (TNF-α)-induced necroptosis requires the adaptor proteins FADD and NEMO. FADD was found to mediate formation of the TNF-α-induced pronecrotic RIP1-RIP3 kinase complex, whereas the IκB Kinase (IKK) subunit NEMO appears to function downstream of RIP1-RIP3. Interestingly, loss of RelA potentiated TNF-α-dependent necroptosis, indicating that NEMO regulates necroptosis independently of NF-κB. Using both pharmacologic and genetic approaches, we demonstrate that the overexpression of antioxidants alleviates ROS elevation and necroptosis. Finally, elimination of BAX and BAK or overexpression of Bcl-xL protects cells from necroptosis at a later step. These findings provide evidence that mitochondria play an amplifying role in inflammation-induced necroptosis. PMID:21746883

The SuperNemo ββ0ν enriched 82Se source foils and their radiopurity measurement with the BiPo-3 detector

NASA Astrophysics Data System (ADS)

Loaiza, P.; SuperNemo Collaboration

2017-09-01

The SuperNemo collaboration is currently building the SuperNemo demonstrator at the Modane Underground Laboratory, as the proof of concept for the full SuperNemo program. The enriched ββ0ν source consisting of thin foils containing 7 kg of 82Se is enclosed by the gas tracker and the plastic scintillator calorimeter. The full reconstruction of the ββ0ν event topology ensures an excellent background rejection and points at a true zero-background search. One of the most critical sources of background is a contamination in the source foils. The required radiopurity is 208Tl < 2 µBq/kg and 214Bi < 10 µBq/kg to achieve the sensitivity T1/2(ββ0ν) > 1026 years. The collaboration has developed a dedicated detector to measure the ultra high natural radiopurities requested, the BiPo-3 detector, installed in the Canfranc Underground Laboratory. The experimental design and performances of BiPo-3 are presented. Dedicated background measurements have been performed. After an exposure of about 2 years.m2 the surface activities of the scintillators of A(208Tl) = 1.0 ± 0.2 µBq/m2 and A(214Bi) = 1.0 ± 0.3 µBq/m2 are measured. Results of the 208Tl and 214Bi activity measurements of the first enriched 82Se foils of SuperNemo are also presented.

SN-1 and NEMO: the Italian cabled observatories

NASA Astrophysics Data System (ADS)

Favali, P.; Beranzoli, L.; Calore, D.; D'Anna, G.; Gasparoni, F.; NEMO Collaboration Team

2003-04-01

A fruitful synergy between Geophysics, Environmental Sciences, Nuclear Physics and Marine Technology has started through ongoing projects within different Italian research frameworks. The Neutrino Mediterranean Observatory (NEMO) project, funded by INFN, aims at the realization of a deep-sea experiment for the detection of cosmic neutrinos using an array of towers equipped by photosensors. To test the technological solutions proposed for the realization of the project, the Laboratiori Nazionali del Sud have set up an underwater Test Site off-shore Catania. A 25 km long submarine electro-optical cable was deployed in September 2001, in order to supply power from land and receive data from the underwater site located at a depth of 2000 m. A shore station has also been realize inside the Catania port area. In October 2001, Submarine Network-1 (SN-1), the first Italian deep-sea multidisciplinary observatory for geophysical and environmental monitoring was deployed at a depth of 2105 m, in the area of the Ibleo-maltese escarpment, in proximity of the marine tail of the NEMO cable. SN-1, funded by the Italian Gruppo Nazionale di Difesa dai Terremoti and coordinated by INGV, is presently operating in local mode storing measurements on hard disks and is powered by lithium batteries with an autonomy of approximately 200 days. In the view of mutual assistance, the coordinator institutions of NEMO and SN-1 have agreed that part of the optic fibres and power lines of the NEMO-1 underwater cable be made available to power SN-1 from land and to transfer in real time the signals acquired by the geophysical and environmental sensor packages of SN-1. On this latter's side, time series of environmental parameters useful for the analysis and interpretation of NEMO-1 detections will be available. A description of the two projects and of the 'state of the art' will be given and the benefits of the development of a submarine Italian prone site will be pointed out.

Progress on wave-ice interactions: satellite observations and model parameterizations

NASA Astrophysics Data System (ADS)

Ardhuin, Fabrice; Boutin, Guillaume; Dumont, Dany; Stopa, Justin; Girard-Ardhuin, Fanny; Accensi, Mickael

2017-04-01

In the open ocean, numerical wave models have their largest errors near sea ice, and, until recently, virtually no wave data was available in the sea ice to. Further, wave-ice interaction processes may play an important role in the Earth system. In particular, waves may break up an ice layer into floes, with significant impact on air-sea fluxes. With thinner Arctic ice, this process may contribut to the growing similarity between Arctic and Antarctic sea ice. In return, the ice has a strong damping impact on the waves that is highly variable and not understood. Here we report progress on parameterizations of waves interacting with a single ice layer, as implemented in the WAVEWATCH III model (WW3 Development Group, 2016), and based on few in situ observations, but extensive data derived from Synthetic Aperture Radars (SARs). Our parameterizations combine three processes. First a parameterization for the energy-conserving scattering of waves by ice floes (assuming isotropic back-scatter), which has very little effect on dominant waves of periods larger than 7 s, consistent with the observed narrow directional spectra and short travel times. Second, we implemented a basal friction below the ice layer (Stopa et al. The Cryosphere, 2016). Third, we use a secondary creep associated with ice flexure (Cole et al. 1998) adapted to random waves. These three processes (scattering, friction and creep) are strongly dependent on the maximum floe size. We have thus included an estimation of the potential floe size based on an ice flexure failure estimation adapted from Williams et al. (2013). This combination of dissipation and scattering is tested against measured patterns of wave height and directional spreading, and evidence of ice break-up, all obtained from SAR imagery (Ardhuin et al. 2017), and some in situ data (Collins et al. 2015). The combination of creep and friction is required to reproduce a strong reduction in wave attenuation in broken ice as observed by Collins et al. (2015). Ongoing developments include the coupling of WAVEWATCH III to the NEMO-LIM3 and NEMO-CICE models using the OASIS3-MCT communicator. This coupled system will provide a meaningful memory of the ice floe sizes, as the ice is advected. It will also make possible the investigation of feedback processes on the ice.

Evaluation of a new CNRM-CM6 model version for seasonal climate predictions

NASA Astrophysics Data System (ADS)

Volpi, Danila; Ardilouze, Constantin; Batté, Lauriane; Dorel, Laurant; Guérémy, Jean-François; Déqué, Michel

2017-04-01

This work presents the quality assessment of a new version of the Météo-France coupled climate prediction system, which has been developed in the EU COPERNICUS Climate Change Services framework to carry out seasonal forecast. The system is based on the CNRM-CM6 model, with Arpege-Surfex 6.2.2 as atmosphere/land component and Nemo 3.2 as ocean component, which has directly embedded the sea-ice component Gelato 6.0. In order to have a robust diagnostic, the experiment is composed by 60 ensemble members generated with stochastic dynamic perturbations. The experiment has been performed over a 37-year re-forecast period from 1979 to 2015, with two start dates per year, respectively in May 1st and November 1st. The evaluation of the predictive skill of the model is shown under two perspectives: on the one hand, the ability of the model to faithfully respond to positive or negative ENSO, NAO and QBO events, independently of the predictability of these events. Such assessment is carried out through a composite analysis, and shows that the model succeeds in reproducing the main patterns for 2-meter temperature, precipitation and geopotential height at 500 hPa during the winter season. On the other hand, the model predictive skill of the same events (positive and negative ENSO, NAO and QBO) is evaluated.

Evaluation of an operational water cycle prediction system for the Laurentian Great Lakes and St. Lawrence River

NASA Astrophysics Data System (ADS)

Fortin, Vincent; Durnford, Dorothy; Smith, Gregory; Dyck, Sarah; Martinez, Yosvany; Mackay, Murray; Winter, Barbara

2017-04-01

Environment and Climate Change Canada (ECCC) is implementing new numerical guidance products based on fully coupled numerical models to better inform the public as well as specialized users on the current and future state of various components of the water cycle, including stream flow and water levels. Outputs from this new system, named the Water Cycle Prediction System (WCPS), have been available for the Great Lakes and St. Lawrence River watershed since June 2016. WCPS links together ECCC's weather forecasting model, GEM, the 2-D ice model C-ICE, the 3-D lake and ocean model NEMO, and a 2-D hydrological model, WATROUTE. Information concerning the water cycle is passed between the models at intervals varying from a few minutes to one hour. It currently produces two forecasts per day for the next three days of the complete water cycle in the Great Lakes region, the largest freshwater lake system in the world. Products include spatially-varying precipitation, evaporation, river discharge, water level anomalies, surface water temperatures, ice coverage, and surface currents. These new products are of interest to water resources and management authority, flood forecasters, hydroelectricity producers, navigation, environmental disaster managers, search and rescue teams, agriculture, and the general public. This presentation focuses on the evaluation of various elements forecasted by the system, and weighs the advantages and disadvantages of running the system fully coupled.

Toward the assimilation of biogeochemical data in the CMEMS BIOMER coupled physical-biogeochemical operational system

NASA Astrophysics Data System (ADS)

Lamouroux, Julien; Testut, Charles-Emmanuel; Lellouche, Jean-Michel; Perruche, Coralie; Paul, Julien

2017-04-01

The operational production of data-assimilated biogeochemical state of the ocean is one of the challenging core projects of the Copernicus Marine Environment Monitoring Service. In that framework - and with the April 2018 CMEMS V4 release as a target - Mercator Ocean is in charge of improving the realism of its global ¼° BIOMER coupled physical-biogeochemical (NEMO/PISCES) simulations, analyses and re-analyses, and to develop an effective capacity to routinely estimate the biogeochemical state of the ocean, through the implementation of biogeochemical data assimilation. Primary objectives are to enhance the time representation of the seasonal cycle in the real time and reanalysis systems, and to provide a better control of the production in the equatorial regions. The assimilation of BGC data will rely on a simplified version of the SEEK filter, where the error statistics do not evolve with the model dynamics. The associated forecast error covariances are based on the statistics of a collection of 3D ocean state anomalies. The anomalies are computed from a multi-year numerical experiment (free run without assimilation) with respect to a running mean in order to estimate the 7-day scale error on the ocean state at a given period of the year. These forecast error covariances rely thus on a fixed-basis seasonally variable ensemble of anomalies. This methodology, which is currently implemented in the "blue" component of the CMEMS operational forecast system, is now under adaptation to be applied to the biogeochemical part of the operational system. Regarding observations - and as a first step - the system shall rely on the CMEMS GlobColour Global Ocean surface chlorophyll concentration products, delivered in NRT. The objective of this poster is to provide a detailed overview of the implementation of the aforementioned data assimilation methodology in the CMEMS BIOMER forecasting system. Focus shall be put on (1) the assessment of the capabilities of this data assimilation methodology to provide satisfying statistics of the model variability errors (through space-time analysis of dedicated representers of satellite surface Chla observations), (2) the dedicated features of the data assimilation configuration that have been implemented so far (e.g. log-transformation of the analysis state, multivariate Chlorophyll-Nutrient control vector, etc.) and (3) the assessment of the performances of this future operational data assimilation configuration.

Cascading of high salinity bottom waters from the Arabian/Persian Gulf to the northern Arabian Sea

NASA Astrophysics Data System (ADS)

Shapiro, Georgy; Wobus, Fred; Solovyev, Vladimir; Francis, Xavier; Hyder, Patrick; Chen, Feng; Asif, Muhammad

2017-04-01

Cascading (aka shelf convection) is a specific type of buoyancy driven current in which dense water is formed over the continental shelf and then descends down the slope to a greater depth. The cascades of dense water down continental slopes provide a mechanism for shelf-ocean exchange in many parts of the world's oceans (Shapiro et al, 2003). Dense water is formed on the shelf by a number of processes, with high evaporation, limited river discharge and low precipitation being the major processes in warm climates (Ivanov et al, 2004). The formation and outflow of high salinity waters in the near-bottom layer of the Arabian/Persian Gulf is an example of dense water cascading (Bower et al 2000). Despite of its importance for the self-cleaning and the state of the marine ecosystem in the Arabian/Persian Gulf, the properties of the outflow have so far mainly been analysed using climatologically averaged data or observations of a limited set of parameters (mainly temperature), see (Bower et al 2000). In this paper we study the dynamics of the flow using a comprehensive set of observational data (temperature, salinity velocity and turbidity profiles) obtained during the GRASP (Gulf Reconnaissance And Selective Profiling) observational campaign in the Gulf of Oman, which are complemented by the results of numerical modelling of the area using a number of 3D ocean models, and some ARGO T/S profiles. The GRASP measurements were carried out using an Aqualog climbing moored profiler, which was equipped with a Seabird CTD sensor, a Nortek Aquadopp current meter and a Seapoint turbidity meter. The Ocean circulation models used in the study include PGM4 and IND12 (UK Met Office); and AS20 and AG60 (University of Plymouth). All models are based on NEMO (Nucleus for European Modelling of the Ocean) codebase with a resolution from 9 km down to 1.8 km. The models were calibrated and validated against ARGO float profiles in the area. The study revealed the mesoscale and sub-mesoscale circulation patterns of the outflow, their spatial and temporal variability over time scales from a few days to seasonal. References Shapiro, G.I.; Huthnance, J.M.; Ivanov, V.V.. 2003 Dense water cascading off the continental shelf. Journal of Geophysical Research, 108 (C12). 3390.10.1029/2002JC001610 Ivanov, V.V.; Shapiro, G.I.; Huthnance, J.M.; Aleynik, D.L.; Golovin, P.N.. 2004 Cascades of dense water around the world ocean. Progress in Oceanography, 60 (1). 47-98.10.1016/j.pocean.2003.12.002 Bower, A. S., H. D. Hunt and J. Price, 2000. Character and Dynamics of the Red Sea and Persian Gulf Outflows. Journal of Geophysical Research - Oceans, Vol. 105, No. C3, pp. 6387-6414.

Ocean Mixed Layer responses to intense meteorological events during HyMeX-SOP1 from a high-resolution ocean simulation

NASA Astrophysics Data System (ADS)

Lebeaupin Brossier, Cindy; Arsouze, Thomas; Béranger, Karine; Bouin, Marie-Noëlle; Bresson, Emilie; Ducrocq, Véronique; Giordani, Hervé; Nuret, Mathieu; Rainaud, Romain; Taupier-Letage, Isabelle

2014-12-01

The western Mediterranean Sea is a source of heat and humidity for the atmospheric low-levels in autumn. Large exchanges take place at the air-sea interface, especially during intense meteorological events, such as heavy precipitation and/or strong winds. The Ocean Mixed Layer (OML), which is quite thin at this time of year (∼ 20 m-depth), evolves rapidly under such intense fluxes. This study investigates the ocean responses under intense meteorological events that occurred during HyMeX SOP1 (5 September-6 November 2012). The OML conditions and tendencies are derived from a high-resolution ocean simulation using the sub-regional eddy-resolving NEMO-WMED36 model (1/36°-resolution), driven at the surface by hourly air-sea fluxes from the AROME-WMED forecasts (2.5 km-resolution). The high space-time resolution of the atmospheric forcing allows the highly variable surface fluxes, which induce rapid changes in the OML, to be well represented and linked to small-scale atmospheric processes. First, the simulation results are compared to ocean profiles from several platforms obtained during the campaign. Then, this study focuses on the short-term OML evolution during three events. In particular, we examine the OML cooling and mixing under strong wind events, potentially associated with upwelling, as well as the surface freshening under heavy precipitation events, producing low-salinity lenses. Tendencies demonstrate the major role of the surface forcing in the temperature and/or salinity anomaly formation. At the same time, mixing [restratification] rapidly occurs. As expected, the sign of this tendency term is very dependent on the local vertical stratification which varies at fine scale in the Mediterranean. It also controls [disables] the vertical propagation. In the Alboran Sea, the strong dynamics redistribute the OML anomalies, sometimes up to 7 days after their formation. Elsewhere, despite local amplitude modulations due to internal wave excitation by strong winds, the integrated effect of the horizontal advection is almost null on the anomalies' spread and decay. Finally, diffusion has a small contribution.

Fibroblast growth factor homologous factor 1 interacts with NEMO to regulate NF-κB signaling in neurons.

PubMed

König, Hans-Georg; Fenner, Beau J; Byrne, Jennifer C; Schwamborn, Robert F; Bernas, Tytus; Jefferies, Caroline A; Prehn, Jochen H M

2012-12-15

Neuronal survival and plasticity critically depend on constitutive activity of the transcription factor nuclear factor-κB (NF-κB). We here describe a role for a small intracellular fibroblast growth factor homologue, the fibroblast growth factor homologous factor 1 (FHF1/FGF12), in the regulation of NF-κB activity in mature neurons. FHFs have previously been described to control neuronal excitability, and mutations in FHF isoforms give rise to a form of progressive spinocerebellar ataxia. Using a protein-array approach, we identified FHF1b as a novel interactor of the canonical NF-κB modulator IKKγ/NEMO. Co-immunoprecipitation, pull-down and GAL4-reporter experiments, as well as proximity ligation assays, confirmed the interaction of FHF1 and NEMO and demonstrated that a major site of interaction occurred within the axon initial segment. Fhf1 gene silencing strongly activated neuronal NF-κB activity and increased neurite lengths, branching patterns and spine counts in mature cortical neurons. The effects of FHF1 on neuronal NF-κB activity and morphology required the presence of NEMO. Our results imply that FHF1 negatively regulates the constitutive NF-κB activity in neurons.

NEMO-SMO acoustic array: A deep-sea test of a novel acoustic positioning system for a km3-scale underwater neutrino telescope

NASA Astrophysics Data System (ADS)

Viola, S.; Ardid, M.; Bertin, V.; Enzenhöfer, A.; Keller, P.; Lahmann, R.; Larosa, G.; Llorens, C. D.; NEMO Collaboration; SMO Collaboration

2013-10-01

Within the activities of the NEMO project, the installation of a 8-floors tower (NEMO-Phase II) at a depth of 3500 m is foreseen in 2012. The tower will be installed about 80 km off-shore Capo Passero, in Sicily. On board the NEMO tower, an array of 18 acoustic sensors will be installed, permitting acoustic detection of biological sources, studies for acoustic neutrino detection and primarily acoustic positioning of the underwater structures. For the latter purpose, the sensors register acoustic signals emitted by five acoustic beacons anchored on the sea-floor. The data acquisition system of the acoustic sensors is fully integrated with the detector data transport system and is based on an “all data to shore” philosophy. Signals coming from hydrophones are continuously sampled underwater at 192 kHz/24 bit and transmitted to shore through an electro-optical cable for real-time analysis. A novel technology for underwater GPS time-stamping of data has been implemented and tested. The operation of the acoustic array will permit long-term test of sensors and electronics technologies that are proposed for the acoustic positioning system of KM3NeT.

Long term monitoring of the optical background in the Capo Passero deep-sea site with the NEMO tower prototype

NASA Astrophysics Data System (ADS)

Adrián-Martínez, S.; Aiello, S.; Ameli, F.; Anghinolfi, M.; Ardid, M.; Barbarino, G.; Barbarito, E.; Barbato, F. C. T.; Beverini, N.; Biagi, S.; Biagioni, A.; Bouhadef, B.; Bozza, C.; Cacopardo, G.; Calamai, M.; Calì, C.; Calvo, D.; Capone, A.; Caruso, F.; Ceres, A.; Chiarusi, T.; Circella, M.; Cocimano, R.; Coniglione, R.; Costa, M.; Cuttone, G.; D'Amato, C.; D'Amico, A.; De Bonis, G.; De Luca, V.; Deniskina, N.; De Rosa, G.; di Capua, F.; Distefano, C.; Enzenhöfer, A.; Fermani, P.; Ferrara, G.; Flaminio, V.; Fusco, L. A.; Garufi, F.; Giordano, V.; Gmerk, A.; Grasso, R.; Grella, G.; Hugon, C.; Imbesi, M.; Kulikovskiy, V.; Lahmann, R.; Larosa, G.; Lattuada, D.; Leismüller, K. P.; Leonora, E.; Litrico, P.; Llorens Alvarez, C. D.; Lonardo, A.; Longhitano, F.; Lo Presti, D.; Maccioni, E.; Margiotta, A.; Marinelli, A.; Martini, A.; Masullo, R.; Migliozzi, P.; Migneco, E.; Miraglia, A.; Mollo, C. M.; Mongelli, M.; Morganti, M.; Musico, P.; Musumeci, M.; Nicolau, C. A.; Orlando, A.; Orzelli, A.; Papaleo, R.; Pellegrino, C.; Pellegriti, M. G.; Perrina, C.; Piattelli, P.; Pugliatti, C.; Pulvirenti, S.; Raffaelli, F.; Randazzo, N.; Real, D.; Riccobene, G.; Rovelli, A.; Saldaña, M.; Sanguineti, M.; Sapienza, P.; Sciacca, V.; Sgura, I.; Simeone, F.; Sipala, V.; Speziale, F.; Spitaleri, A.; Spurio, M.; Stellacci, S. M.; Taiuti, M.; Terreni, G.; Trasatti, L.; Trovato, A.; Ventura, C.; Vicini, P.; Viola, S.; Vivolo, D.

2016-02-01

The NEMO Phase-2 tower is the first detector which was operated underwater for more than 1 year at the "record" depth of 3500 m. It was designed and built within the framework of the NEMO (NEutrino Mediterranean Observatory) project. The 380 m high tower was successfully installed in March 2013 80 km offshore Capo Passero (Italy). This is the first prototype operated on the site where the Italian node of the KM3NeT neutrino telescope will be built. The installation and operation of the NEMO Phase-2 tower has proven the functionality of the infrastructure and the operability at 3500 m depth. A more than 1 year long monitoring of the deep water characteristics of the site has been also provided. In this paper the infrastructure and the tower structure and instrumentation are described. The results of long term optical background measurements are presented. The rates show stable and low baseline values, compatible with the contribution of ^{40}K light emission, with a small percentage of light bursts due to bioluminescence. All these features confirm the stability and good optical properties of the site.

Development from the seafloor to the sea surface of the cabled NEMO-SN1 observatory in the Western Ionian Sea

NASA Astrophysics Data System (ADS)

Sparnocchia, Stefania; Beranzoli, Laura; Borghini, Mireno; Durante, Sara; Favali, Paolo; Giovanetti, Gabriele; Italiano, Francesco; Marinaro, Giuditta; Meccia, Virna; Papaleo, Riccardo; Riccobene, Giorgio; Schroeder, Katrin

2015-04-01

A prototype of cabled deep-sea observatory has been operating in real-time since 2005 in Southern Italy (East Sicily, 37°30' N - 15°06'E), at 2100 m water depth, 25 km from the harbor of the city of Catania. It is the first-established real-time node of the "European Multidisciplinary Seafloor and water column Observatory" (EMSO, http://www.emso-eu.org) a research infrastructure of the Sector Environment of ESFRI. In the present configuration it consists of two components: the multi-parametric station NEMO-SN1 (TSN branch) equipped with geophysical and environmental sensors for measurements at the seafloor, and the NEMO-OνDE station (TSS branch) equipped with 4 wideband hydrophones. A 28 km long electro-optical cable connects the observatory to a shore laboratory in the Catania harbor, hosting the data acquisition system and supplying power and data transmission to the underwater instrumentation. The NEMO-SN1 observatory is located in an area particularly suited to multidisciplinary studies. The site is one of the most seismically active areas of the Mediterranean (some of the strongest earthquakes occurred in 1169, 1693 and 1908, also causing very intense tsunami waves) and is close to Mount Etna, one of the largest and most active volcanoes in Europe. The deployment area is also a key site for monitoring deep-water dynamics in the Ionian Sea, connecting the Levantine basin to the southern Adriatic basin where intermediate and deep waters are formed, and finally to the western Mediterranean Sea via the Strait of Sicily. The observatory is being further developed under EMSO MedIT (http://www.emso-medit.it/en/), a structural enhancement project contributing to the consolidation and enhancement of the European research infrastructure EMSO in Italian Convergence Regions. In this framework, a new Junction Box will be connected to the TSN branch and will provide wired and wireless (acoustic connections) for seafloor platforms and moorings. This will allow the implementation of new measurement capabilities at seafloor and along the water column with sensors for measurements of physical-chemical (pressure, temperature, salinity, dissolved oxygen, turbidity, pCO2, currents) and geophysical (magnetometer, seismometer and gravity meter) parameters. An imaging system for deep sea fauna will be deployed very soon at TSS. Furthermore, the data acquisition/elaboration system will be enhanced, and data will be shared in near real time through the Catania node of the high-speed telecommunication network for University and Scientific Research. An Open Access policy is adopted to favour the access of the international scientific community. According to the EMSO business plan and EC recommendations, the enhanced infrastructure will be open to scientists, companies and public actors on excellence research basis, for the development of innovative scientific and technological research products. The existing seafloor module is already offering this service under the TNA program of FixO3 EC Project (www.fixo3.eu). The ongoing development of NEMO-SN1 will strengthen its capabilities to monitor long-term variability of key physical, geophysical and biogeochemical parameters, with applications, for example, in studies on modifications of the properties of water masses and the marine circulation, changes in marine chemistry, with particular emphasis on the carbon system and its role in ocean acidification, evolving trends in global sea level, and to address geo-hazards issues, such as earthquake and tsunami risks, volcanic risk, instability and collapse of the slopes.

Projected Sea Level Rise and Changes in Extreme Storm Surge and Wave Events During the 21st Century in the Region of Singapore

NASA Astrophysics Data System (ADS)

Palmer, M. D.; Cannaby, H.; Howard, T.; Bricheno, L.

2016-02-01

Singapore is an island state with considerable population, industries, commerce and transport located in coastal areas at elevations less than 2 m making it vulnerable to sea-level rise. Mitigation against future inundation events requires a quantitative assessment of risk. To address this need, regional projections of changes in (i) long-term mean sea level and (ii) the frequency of extreme storm surge and wave events have been combined to explore potential changes to coastal flood risk over the 21st century. Local changes in time mean sea level were evaluated using the process-based climate model data and methods presented in the IPCC AR5. Regional surge and wave solutions extending from 1980 to 2100 were generated using 12 km resolution surge (Nucleus for European Modelling of the Ocean - NEMO) and wave (WaveWatchIII) models. Ocean simulations were forced by output from a selection of four downscaled ( 12 km resolution) atmospheric models, forced at the lateral boundaries by global climate model simulations generated for the IPCC AR5. Long-term trends in skew surge and significant wave height were then assessed using a generalised extreme value model, fit to the largest modelled events each year. An additional atmospheric solution downscaled from the ERA-Interim global reanalysis was used to force historical ocean model simulations extending from 1980-2010, enabling a quantitative assessment of model skill. Simulated historical sea surface height and significant wave height time series were compared to tide gauge data and satellite altimetry data respectively. Central estimates of the long-term mean sea level rise at Singapore by 2100 were projected to be 0.52 m(0.74 m) under the RCP 4.5(8.5) scenarios respectively. Trends in surge and significant wave height 2-year return levels were found to be statistically insignificant and/or physically very small under the more severe RCP8.5 scenario. We conclude that changes to long-term mean sea level constitute the dominant signal of change to the projected inundation risk for Singapore during the 21st century. We note that the largest recorded surge residual in the Singapore Strait of 84 cm lies between the central and upper estimates of sea level rise by 2100, highlighting the vulnerability of the region.

Projected sea level rise and changes in extreme storm surge and wave events during the 21st century in the region of Singapore

NASA Astrophysics Data System (ADS)

Cannaby, H.; Palmer, M. D.; Howard, T.; Bricheno, L.; Calvert, D.; Krijnen, J.; Wood, R.; Tinker, J.; Bunney, C.; Harle, J.; Saulter, A.; O'Neill, C.; Bellingham, C.; Lowe, J.

2015-12-01

Singapore is an island state with considerable population, industries, commerce and transport located in coastal areas at elevations less than 2 m making it vulnerable to sea-level rise. Mitigation against future inundation events requires a quantitative assessment of risk. To address this need, regional projections of changes in (i) long-term mean sea level and (ii) the frequency of extreme storm surge and wave events have been combined to explore potential changes to coastal flood risk over the 21st century. Local changes in time mean sea level were evaluated using the process-based climate model data and methods presented in the IPCC AR5. Regional surge and wave solutions extending from 1980 to 2100 were generated using ~ 12 km resolution surge (Nucleus for European Modelling of the Ocean - NEMO) and wave (WaveWatchIII) models. Ocean simulations were forced by output from a selection of four downscaled (~ 12 km resolution) atmospheric models, forced at the lateral boundaries by global climate model simulations generated for the IPCC AR5. Long-term trends in skew surge and significant wave height were then assessed using a generalised extreme value model, fit to the largest modelled events each year. An additional atmospheric solution downscaled from the ERA-Interim global reanalysis was used to force historical ocean model simulations extending from 1980-2010, enabling a quantitative assessment of model skill. Simulated historical sea surface height and significant wave height time series were compared to tide gauge data and satellite altimetry data respectively. Central estimates of the long-term mean sea level rise at Singapore by 2100 were projected to be 0.52 m (0.74 m) under the RCP 4.5 (8.5) scenarios respectively. Trends in surge and significant wave height 2 year return levels were found to be statistically insignificant and/or physically very small under the more severe RCP8.5 scenario. We conclude that changes to long-term mean sea level constitute the dominant signal of change to the projected inundation risk for Singapore during the 21st century. We note that the largest recorded surge residual in the Singapore Strait of ~ 84 cm lies between the central and upper estimates of sea level rise by 2100, highlighting the vulnerability of the region.

"Genetically Engineered" Nanoelectronics

NASA Technical Reports Server (NTRS)

Klimeck, Gerhard; Salazar-Lazaro, Carlos H.; Stoica, Adrian; Cwik, Thomas

2000-01-01

The quantum mechanical functionality of nanoelectronic devices such as resonant tunneling diodes (RTDs), quantum well infrared-photodetectors (QWIPs), quantum well lasers, and heterostructure field effect transistors (HFETs) is enabled by material variations on an atomic scale. The design and optimization of such devices requires a fundamental understanding of electron transport in such dimensions. The Nanoelectronic Modeling Tool (NEMO) is a general-purpose quantum device design and analysis tool based on a fundamental non-equilibrium electron transport theory. NEW was combined with a parallelized genetic algorithm package (PGAPACK) to evolve structural and material parameters to match a desired set of experimental data. A numerical experiment that evolves structural variations such as layer widths and doping concentrations is performed to analyze an experimental current voltage characteristic. The genetic algorithm is found to drive the NEMO simulation parameters close to the experimentally prescribed layer thicknesses and doping profiles. With such a quantitative agreement between theory and experiment design synthesis can be performed.

The Mercator Océan operational and reanalysis systems: overview of recent improvements and scientific key issues

NASA Astrophysics Data System (ADS)

Hernandez, F.; Benkiran, M.; Bourdalle-Badie, R.; Bricaud, C.; Cailleau, S.; Chanut, J.; Desportes, C.; Dombrowsky, E.; drevillon, M.; Drillet, Y.; Elmoussaoui, A.; Ferry, N.; Garric, G.; Greiner, E.; Le Galloudec, O.; Lellouche, J.; Levier, B.; Parent, L.; Perruche, C.; Reffray, G.; Regnier, C.; Rémy, E.; Testut, C.; Tranchant, B.

2011-12-01

In the framework of the European project GMES/MyOcean, Mercator Océan has designed a hierarchy of ocean analysis, forecasting and reanalysis systems based on numerical models of the ocean/sea-ice, data assimilation methods and biogeochemistry model. Operational weekly analysis provide initial conditions for daily predictions. All ocean model configurations are based on NEMO. The 1/4° global and 1/12° Atlantic and Mediterranean configurations are improved with (i) the use of high frequency (3h) atmospheric forcings including the diurnal cycle, (ii) the use of the CORE bulk formulation, (iii) the use of a new TKE vertical mixing scheme, (iv) the use of the LIM2-EVP ice model. Leading to a better representation of the diurnal cycle, the stratification in upper layers, the sea-ice interannual extensions, or mesoscale features and WBC in the 1/12°. The 1/36° IBI regional configuration, adds non linear free surface, atmospheric pressure and tidal forcing, barotropic/baroclinic time splitting, and specific boundary conditions for operational nesting with the global system. At regional scale, a number of improvements (bathymetry and bottom friction) make it suitable for coastal modelling, validated state-of-art coastal ocean models. Data assimilation is based on reduced order Kalman filter using 3D multivariate modal decomposition of the forecast error. It assimilates jointly satellite altimetry, SST and in situ observations (temperature and salinity profiles, including ARGO data). Among difficulties, the assimilation has to be operated in real time, with limited and less accurate set of observations. Recent improvements in the global systems include (v) the insertion of the zonal/meridional velocity components into the control vector, (vi) the use of the IAU procedure, (vii) the insertion of new observational operators, (viii) the use of a new MDT, (ix) the introduction of pseudo-observations, (x) the use of a bias correction method based on a variational approach to estimate large scale biases. These improvements limit noise introduced by sequential assimilation, like in in the vertical dynamics. Water masses, on the shelves or near major run-off, like the Amazon discharge, are preserved. A biogeochemistry prediction system has been added, based on PISCES model. it uses spatial degradation of the real time physic provides by the 1/4° global system. A reanalysis covering the "altimetric era" (1992-2009) has been carried out in collaboration with the Drakkar community. GLORYS reanalyses describe the evolution of the ocean and sea-ice states; It is based on Mercator operational 1/4° global system, but with 75 levels vertical grid, ERA-Interim atmospheric forcing fields (corrected with satellite-based fluxes) and the assimilation of delayed time reprocessed and quality controlled observations. First studies show the reanalysis usefulness for interannual assessment of the mesoscale dynamics, but also the thermohaline circulations changes like MOC.

Measurement of the atmospheric muon flux with the NEMO Phase-1 detector

NASA Astrophysics Data System (ADS)

Aiello, S.; Ameli, F.; Amore, I.; Anghinolfi, M.; Anzalone, A.; Barbarino, G.; Battaglieri, M.; Bazzotti, M.; Bersani, A.; Beverini, N.; Biagi, S.; Bonori, M.; Bouhadef, B.; Brunoldi, M.; Cacopardo, G.; Capone, A.; Caponetto, L.; Carminati, G.; Chiarusi, T.; Circella, M.; Cocimano, R.; Coniglione, R.; Cordelli, M.; Costa, M.; D'Amico, A.; De Bonis, G.; De Marzo, C.; De Rosa, G.; De Ruvo, G.; De Vita, R.; Distefano, C.; Falchini, E.; Flaminio, V.; Fratini, K.; Gabrielli, A.; Galatà, S.; Gandolfi, E.; Giacomelli, G.; Giorgi, F.; Giovanetti, G.; Grimaldi, A.; Habel, R.; Imbesi, M.; Kulikovsky, V.; Lattuada, D.; Leonora, E.; Lonardo, A.; Lo Presti, D.; Lucarelli, F.; Marinelli, A.; Margiotta, A.; Martini, A.; Masullo, R.; Migneco, E.; Minutoli, S.; Morganti, M.; Musico, P.; Musumeci, M.; Nicolau, C. A.; Orlando, A.; Osipenko, M.; Papaleo, R.; Pappalardo, V.; Piattelli, P.; Piombo, D.; Raia, G.; Randazzo, N.; Reito, S.; Ricco, G.; Riccobene, G.; Ripani, M.; Rovelli, A.; Ruppi, M.; Russo, G. V.; Russo, S.; Sapienza, P.; Sciliberto, D.; Sedita, M.; Shirokov, E.; Simeone, F.; Sipala, V.; Spurio, M.; Taiuti, M.; Trasatti, L.; Urso, S.; Vecchi, M.; Vicini, P.; Wischnewski, R.

2010-05-01

The NEMO Collaboration installed and operated an underwater detector including prototypes of the critical elements of a possible underwater km 3 neutrino telescope: a four-floor tower (called Mini-Tower) and a Junction Box. The detector was developed to test some of the main systems of the km 3 detector, including the data transmission, the power distribution, the timing calibration and the acoustic positioning systems as well as to verify the capabilities of a single tridimensional detection structure to reconstruct muon tracks. We present results of the analysis of the data collected with the NEMO Mini-Tower. The position of photomultiplier tubes (PMTs) is determined through the acoustic position system. Signals detected with PMTs are used to reconstruct the tracks of atmospheric muons. The angular distribution of atmospheric muons was measured and results compared to Monte Carlo simulations.

The trigger and data acquisition for the NEMO-Phase 2 tower

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pellegrino, C.; Biagi, S.; Fusco, L. A.

In the framework of the Phase 2 of the NEMO neutrino telescope project, a tower with 32 optical modules is being operated since march 2013. A new scalable Trigger and Data Acquisition System (TriDAS) has been developed and extensively tested with the data from this tower. Adopting the all-data-to-shore concept, the NEMO TriDAS is optimized to deal with a continuous data-stream from off-shore to on-shore with a large bandwidth. The TriDAS consists of four computing layers: (i) data aggregation of isochronal hits from all optical modules; (ii) data filtering by means of concurrent trigger algorithms; (iii) composition of the filteredmore » events into post-trigger files; (iv) persistent data storage. The TriDAS implementation is reported together with a review of dedicated on-line monitoring tools.« less

Response of water temperature to surface wave effects in the Baltic Sea: simulations with the coupled NEMO-WAM model

NASA Astrophysics Data System (ADS)

Alari, Victor; Staneva, Joanna; Breivik, Øyvind; Bidlot, Jean-Raymond; Mogensen, Kristian; Janssen, Peter

2016-04-01

The effects of wind waves on the Baltic Sea water temperature has been studied by coupling the hydrodynamical model NEMO with the wave model WAM. The wave forcing terms that have been taken into consideration are: Stokes-Coriolis force, seastate dependent energy flux and sea-state dependent momentum flux. The combined role of these processes as well as their individual contributions on simulated temperature is analysed. The results indicate a pronounced effect of waves on surface temperature, on the distribution of vertical temperature and on upwellinǵs. In northern parts of the Baltic Sea a warming of the surface layer occurs in the wave included simulations. This in turn reduces the cold bias between simulated and measured data. The warming is primarily caused by sea-state dependent energy flux. Wave induced cooling is mostly observed in near coastal areas and is mainly due to Stokes-Coriolis forcing. The latter triggers effect of intensifying upwellings near the coasts, depending on the direction of the wind. The effect of sea-state dependent momentum flux is predominantly to warm the surface layer. During the summer the wave induced water temperature changes were up to 1 °C.

Something black in the American Psyche: formal innovation and Freudian imagery in the comics of Winsor McCay and Robert Crumb.

PubMed

Shannon, Edward A

2010-01-01

Winsor McCay’s Little Nemo in Slumberland anticipates Robert Crumb’s work. McCay’s innocent dreamscapes seem antithetical to the sexually explicit work of anti-capitalist Crumb, but Nemo looks forward to Crumb in subject and form. Nemo’s presentation of class, gender, and race, and its pre-Freudian sensibility are ironic counterpoints to Crumb’s political, Freudian comix.

Towards a National Hydrological Forecasting system for Canada : Lessons Learned from the Great Lakes and St. Lawrence Prediction System

NASA Astrophysics Data System (ADS)

Fortin, V.; Durnford, D.; Gaborit, E.; Davison, B.; Dimitrijevic, M.; Matte, P.

2016-12-01

Environment and Climate Change Canada has recently deployed a water cycle prediction system for the Great Lakes and St. Lawrence River. The model domain includes both the Canadian and US portions of the watershed. It provides 84-h forecasts of weather elements, lake level, lake ice cover and surface currents based on two-way coupling of the GEM numerical weather prediction (NWP) model with the NEMO ocean model. Streamflow of all the major tributaries of the Great Lakes and St. Lawrence River are estimated by the WATROUTE routing model, which routes the surface runoff forecasted by GEM's land-surface scheme and assimilates streamflow observations where available. Streamflow forecasts are updated twice daily and are disseminated through an OGC compliant web map service (WMS) and a web feature service (WFS). In this presentation, in addition to describing the system and documenting its forecast skill, we show how it is being used by clients for various environmental prediction applications. We then discuss the importance of two-way coupling, land-surface and hillslope modelling and the impact of horizontal resolution on hydrological prediction skill. In the second portion of the talk, we discuss plans for implementing a similar system at the national scale, using what we have learned in the Great Lakes and St. Lawrence watershed. Early results obtained for the headwaters of the Saskatchewan River as well as for the whole Nelson-Churchill watershed are presented.

Modelling the influence of tides on ice-shelf melt rates in the Amundsen Sea, Antarctica.

NASA Astrophysics Data System (ADS)

Jourdain, Nicolas C.; Molines, Jean-Marc; Le Sommer, Julien; Mathiot, Pierre; Chanut, Jérome; Madec, Gurvan

2017-04-01

Variations in melt beneath ice- shelves may trigger ice-sheet instabilities, in particular in West Antarctica. Therefore, improving the understanding and modelling of ice-shelf basal melt rates has been a major focus over the last decades. In this presentation, we provide further insight into the role of tides on basal melt rates, and we assess several methods to account for tides in models that do not include an explicit representation of tides. First, we use an explicit representation of tides in a regional configuration of the NEMO-3.6 model deployed over the Amundsen Sea. We show that most of the tidal influence on ice-shelf melt is explained by four tidal constituents. Tides enhance melt by more than 30% in some cavities like Abbot, Cosgrove and Dotson, but by less than 10% in others like Thwaites and Pine Island. Over the entire Amundsen Sea sector, tides enhance melt by 92 Gt/yr, which is mostly induced by tidal velocities along ice drafts (+148 Gt/yr), partly compensated by tide-induced change in thermal forcing (-31 Gt/yr) and co-variations between tidal velocities and thermal forcing (-26 Gt/yr). In the second part of this presentation, we show that using uniform tidal velocities to account for tides effects in ocean models with no explicit tides produces large biases in melt rates. By contrast, prescribing non-uniform tidal velocities allows an accurate representation of the dynamical effects of tides on melt rates.

First results from the NEMO Test Site

NASA Astrophysics Data System (ADS)

Riccobene, Giorgio; NEMO Collaboration

2007-03-01

The NEMO (NEutrino Mediterranean Observatory) Collaboration is constructing, 25 km E from Catania (Sicily) at 2000 m depth, an underwater test site to perform long-term tests of prototypes and new technologies for an underwater high energy neutrino detector in the Mediterranean Sea. In this framework the collaboration deployed and operated an experimental apparatus for on-line monitoring of deep-sea noise. The station is equipped with 4 hydrophones operational in the range 30 Hz - 40 kHz. This interval of frequencies matches the range suitable for acoustic detection of high energy neutrino-induced showers in water. Hydrophone signals are digitized underwater at 96 kHz sampling frequency and 24 bits resolution. A custom software was developed to record data on high resolution 4-channels PCM .le. Data are used to model underwater acoustic noise as a function of frequency and time, a mandatory parametre for future acoustic neutrino detectors. Results indicate that the average noise in the site is compatible with noise produced in condition of sea surface agitation (sea state.)

Effects of wave-induced forcing on a circulation model of the North Sea

NASA Astrophysics Data System (ADS)

Staneva, Joanna; Alari, Victor; Breivik, Øyvind; Bidlot, Jean-Raymond; Mogensen, Kristian

2017-04-01

The effect of wind waves on water level and currents during two storms in the North Sea is investigated using a high-resolution NEMO model forced with fluxes and fields from a high-resolution wave model. The additional terms accounting for wave-current interaction that are considered in this study are the Stokes-Coriolis force and the sea-state dependent energy and momentum fluxes. The individual and collective role of these processes is quantified and the results are compared with a control run without wave effects as well as against current and water level measurements from coastal stations. We find a better agreement with observations when the circulation model is forced by sea-state dependent fluxes, especially in extreme events. The two extreme events, the storm Christian (25-27 October 2013), and about a month later, the storm Xaver (5-7 December 2013), induce different wave and surge conditions over the North Sea. Including the wave effects in the circulation model for the storm Xaver raises the modelled surge by more than 40 cm compared with the control run in the German Bight area. For the storm Christian, a difference of 20-30 cm in the surge level between the wave-forced and the stand-alone ocean model is found over the whole southern part of the North Sea. Moreover, the modelled vertical velocity profile fits the observations very well when the wave forcing is accounted for. The contribution of wave-induced forcing has been quantified indicating that this represents an important mechanism for improving water level and current predictions.

Exchanges between the shelf and the deep Black Sea: an integrated analysis of physical mechanisms

NASA Astrophysics Data System (ADS)

Shapiro, Georgy; Wobus, Fred; Zatsepin, Andrei; Akivis, Tatiana; Zhou, Feng

2017-04-01

This study provides an integrated analysis of exchanges of water, salt and heat between the north-western Black Sea shelf and the deep basin. Three contributing physical mechanisms are quantified, namely: Ekman drift, transport by mesoscale eddies at the edge of the NW Black Sea shelf and non-local cascading assisted by the rim current and mesoscale eddies. The semi-enclosed nature of the Black Sea together with its unique combination of an extensive shelf area in the North West and the deep central part make it sensitive to natural variations of fluxes, including the fluxes between the biologically productive shelf and predominantly anoxic deep sea. Exchanges between the shelf and deep sea play an important role in forming the balance of waters, nutrients and pollution within the coastal areas, and hence the level of human-induced eutrophication of coastal waters (MSFD Descriptor 5). In this study we analyse physical mechanisms and quantify shelf-deep sea exchange processes in the Black Sea sector using the NEMO ocean circulation model. The model is configured and optimized taking into account specific features of the Black Sea, and validated against in-situ and satellite observations. The study uses NEMO-BLS24 numerical model which is based on the NEMO codebase v3.2.1 with amendments introduced by the UK Met Office. The model has a horizontal resolution of 1/24×1/24° and a hybrid s-on-top-of-z vertical coordinate system with a total of 33 layers. The horizontal viscosity/diffusivity operator is rotated to reduce the contamination of vertical diffusion/viscosity by large values of their horizontal counterparts. The bathymetry is processed from ETOPO5 and capped to 1550m. Atmospheric forcing for the period 1989-2012 is given by the Drakkar Forcing Set v5.2. For comparison, the NCEP atmospheric forcing also used for 2005. The climatological runoff from 8 major rivers is included. We run the model individually for 24 calendar years without data assimilation. For the analysis of propagation of cold waters formed on the NW Black Sea shelf we use a passive tracer method. The tracer is treated as an artificial dye that "stains" a water parcel within the defined area as soon as it cooled below a 7°C temperature. To quantify the shelf-deep sea exchange, the transport of water, salt and heat between the NW shelf and deep-sea regions is calculated across an enclosed boundary (a "fence") approximating the 200 m isobath on the NW shelf plus two short segments connected to the coast. Partial transports are also calculated for the surface layer (top 20 m) and the under-surface layer (from 20 m to the bottom). The 20 m level is approximately equal to the Ekman depth in summer. It is also close to the depth of the biologically active euphotic layer. For validation of the NEMO-BLS24 configuration we present comparisons of the model with satellite-derived sea surface temperature measurements and with ship-derived cross-sections that show the vertical structure. We also compare the model to observations carried out during Black Sea cruises in 2004, 2007 and 2008. The model represents well the sea surface temperature, the depth of the upper mixed layer and the depth of the CIL, while overestimating the temperature in the core of the CIL by approx. 0.5 °C. Mechanism 1: exchanges due to a frontal eddy. Numerical simulations for the year 2005 (for which comprehensive remote sensed data is available) shows that a significant cross-shelf transport was generated by a long-lived anticyclonic eddy impinging on the shelf, sometimes assisted by a cyclonic meander of the Rim Current. Over 69 days between April 23 and June 30, 2005, a volume of 2.84×10^12 m3 of water (102% of the entire volume of the shelf waters) was transported out of the shelf and a similar amount onto the shelf (see details in Zhou et al. 2014). Mechanism 2: exchanges due to Ekman drift. During the short but intensive wind events of April 15 - 22 and July 1 - 4, 2005, 23% and 16% of shelf waters, were moved into the deep-sea region, respectively. Due to the high intensity of cross-shelf exchanges, the average renewal time for the NW shelf in the Black Sea was only 28 days in the summer of 2005 (Zhou et al. 2014). Mechanism 3: exchanges due to assisted cascading. Using the model run for 2003 as an example, we examine the fate of the tracer after 5.5 months of model integration. At 100m depth we identify four anti-cyclonic eddies: two eddies west of the Crimea peninsula, one north of Sinop and one west of Batumi. These eddies can be seen to assist cascading into the basin interior of cold waters formed on a shallow NW shelf to a depth greater than at which they were originally formed. The important result is that for many of the 24 studied years a significant proportion of dense shelf water does not cascade locally off the NW shelf, but is transported by the Rim Current over hundreds of kilometres before cascading into the deep basin in the southern and southeastern Black Sea. This work has been supported by EU FP7 PERSEUS, EU H2020 Sea Basin checkpoints Lot4 - Black Sea and a number of Chinese and Russian national projects. References Zhou, F., G. I. Shapiro, and F. Wobus, 2014: Cross-shelf exchange in the northwestern Black Sea. Journal of Geophysical Research: Oceans, 119, 2143-2164.

Extraction of pulse repetition intervals from sperm whale click trains for ocean acoustic data mining.

PubMed

Zaugg, Serge; van der Schaar, Mike; Houégnigan, Ludwig; André, Michel

2013-02-01

The analysis of acoustic data from the ocean is a valuable tool to study free ranging cetaceans and anthropogenic noise. Due to the typically large volume of acquired data, there is a demand for automated analysis techniques. Many cetaceans produce acoustic pulses (echolocation clicks) with a pulse repetition interval (PRI) remaining nearly constant over several pulses. Analyzing these pulse trains is challenging because they are often interleaved. This article presents an algorithm that estimates a pulse's PRI with respect to neighboring pulses. It includes a deinterleaving step that operates via a spectral dissimilarity metric. The sperm whale (SW) produces trains with PRIs between 0.5 and 2 s. As a validation, the algorithm was used for the PRI-based identification of SW click trains with data from the NEMO-ONDE observatory that contained other pulsed sounds, mainly from ship propellers. Separation of files containing SW clicks with a medium and high signal to noise ratio from files containing other pulsed sounds gave an area under the receiver operating characteristic curve value of 0.96. This study demonstrates that PRI can be used for the automated identification of SW clicks and that deinterleaving via spectral dissimilarity contributes to algorithm performance.

Recognition Memory for Realistic Synthetic Faces

PubMed Central

Yotsumoto, Yuko; Kahana, Michael J.; Wilson, Hugh R.; Sekuler, Robert

2006-01-01

A series of experiments examined short-term recognition memory for trios of briefly-presented, synthetic human faces derived from three real human faces. The stimuli were graded series of faces, which differed by varying known amounts from the face of the average female. Faces based on each of the three real faces were transformed so as to lie along orthogonal axes in a 3-D face space. Experiment 1 showed that the synthetic faces' perceptual similarity stucture strongly influenced recognition memory. Results were fit by NEMo, a noisy exemplar model of perceptual recognition memory. The fits revealed that recognition memory was influenced both by the similarity of the probe to series items, and by the similarities among the series items themselves. Non-metric multi-dimensional scaling (MDS) showed that faces' perceptual representations largely preserved the 3-D space in which the face stimuli were arrayed. NEMo gave a better account of the results when similarity was defined as perceptual, MDS similarity rather than physical proximity of one face to another. Experiment 2 confirmed the importance of within-list homogeneity directly, without mediation of a model. We discuss the affinities and differences between visual memory for synthetic faces and memory for simpler stimuli. PMID:17948069

Projected sea level rise and changes in extreme storm surge and wave events during the 21st century in the region of Singapore

NASA Astrophysics Data System (ADS)

Cannaby, Heather; Palmer, Matthew D.; Howard, Tom; Bricheno, Lucy; Calvert, Daley; Krijnen, Justin; Wood, Richard; Tinker, Jonathan; Bunney, Chris; Harle, James; Saulter, Andrew; O'Neill, Clare; Bellingham, Clare; Lowe, Jason

2016-05-01

Singapore is an island state with considerable population, industries, commerce and transport located in coastal areas at elevations less than 2 m making it vulnerable to sea level rise. Mitigation against future inundation events requires a quantitative assessment of risk. To address this need, regional projections of changes in (i) long-term mean sea level and (ii) the frequency of extreme storm surge and wave events have been combined to explore potential changes to coastal flood risk over the 21st century. Local changes in time-mean sea level were evaluated using the process-based climate model data and methods presented in the United Nations Intergovernmental Panel on Climate Change Fifth Assessment Report (IPCC AR5). Regional surge and wave solutions extending from 1980 to 2100 were generated using ˜ 12 km resolution surge (Nucleus for European Modelling of the Ocean - NEMO) and wave (WaveWatchIII) models. Ocean simulations were forced by output from a selection of four downscaled ( ˜ 12 km resolution) atmospheric models, forced at the lateral boundaries by global climate model simulations generated for the IPCC AR5. Long-term trends in skew surge and significant wave height were then assessed using a generalised extreme value model, fit to the largest modelled events each year. An additional atmospheric solution downscaled from the ERA-Interim global reanalysis was used to force historical ocean model simulations extending from 1980 to 2010, enabling a quantitative assessment of model skill. Simulated historical sea-surface height and significant wave height time series were compared to tide gauge data and satellite altimetry data, respectively. Central estimates of the long-term mean sea level rise at Singapore by 2100 were projected to be 0.52 m (0.74 m) under the Representative Concentration Pathway (RCP)4.5 (8.5) scenarios. Trends in surge and significant wave height 2-year return levels were found to be statistically insignificant and/or physically very small under the more severe RCP8.5 scenario. We conclude that changes to long-term mean sea level constitute the dominant signal of change to the projected inundation risk for Singapore during the 21st century. We note that the largest recorded surge residual in the Singapore Strait of ˜ 84 cm lies between the central and upper estimates of sea level rise by 2100, highlighting the vulnerability of the region.

A Hop-Sensitive Mechanism to Establish Route Optimization in Mobile Networks

NASA Astrophysics Data System (ADS)

Gnanaraj, J. Isac; Newton, P. Calduwel; Arockiam, L.; Kim, Tai-Hoon

The mobile network plays a vital role in mobile communications. It supports both host mobility and network mobility. The mobile network which supports network mobility can be called as NEMO. The NEMO refers to NEtwork MObility or mobile network that moves. Though NEMO provides many supports, it also suffers due to Quality of Service (QoS) issues. One such issue is Route Optimization (RO). When a Mobile Node (MN) is away from Home Network (HN), it will send a binding update to Home Agent (HA) in HN to inform its movement. If the Correspondent Node (CN) wants to send data to MN, it will send data through HA. In this scenario, three networks such as HN, Foreign Network (FN) and Correspondent Network are involved in data transfer. The involvement of these three networks affects the QoS. This paper concentrates on some of the QoS parameters to propose a QoS mechanism to establish RO among these three networks and significantly increases performance of the mobile network.

Major modes of short-term climate variability in the newly developed NUIST Earth System Model (NESM)

NASA Astrophysics Data System (ADS)

Cao, Jian; Wang, Bin; Xiang, Baoqiang; Li, Juan; Wu, Tianjie; Fu, Xiouhua; Wu, Liguang; Min, Jinzhong

2015-05-01

A coupled earth system model (ESM) has been developed at the Nanjing University of Information Science and Technology (NUIST) by using version 5.3 of the European Centre Hamburg Model (ECHAM), version 3.4 of the Nucleus for European Modelling of the Ocean (NEMO), and version 4.1 of the Los Alamos sea ice model (CICE). The model is referred to as NUIST ESM1 (NESM1). Comprehensive and quantitative metrics are used to assess the model's major modes of climate variability most relevant to subseasonal-to-interannual climate prediction. The model's assessment is placed in a multi-model framework. The model yields a realistic annual mean and annual cycle of equatorial SST, and a reasonably realistic precipitation climatology, but has difficulty in capturing the spring-fall asymmetry and monsoon precipitation domains. The ENSO mode is reproduced well with respect to its spatial structure, power spectrum, phase locking to the annual cycle, and spatial structures of the central Pacific (CP)-ENSO and eastern Pacific (EP)-ENSO; however, the equatorial SST variability, biennial component of ENSO, and the amplitude of CP-ENSO are overestimated. The model captures realistic intraseasonal variability patterns, the vertical-zonal structures of the first two leading predictable modes of Madden-Julian Oscillation (MJO), and its eastward propagation; but the simulated MJO speed is significantly slower than observed. Compared with the T42 version, the high resolution version (T159) demonstrates improved simulation with respect to the climatology, interannual variance, monsoon-ENSO lead-lag correlation, spatial structures of the leading mode of the Asian-Australian monsoon rainfall variability, and the eastward propagation of the MJO.

Improving the simulation of landfast ice by combining tensile strength and a parameterization for grounded ridges

NASA Astrophysics Data System (ADS)

Lemieux, Jean-François; Dupont, Frédéric; Blain, Philippe; Roy, François; Smith, Gregory C.; Flato, Gregory M.

2016-10-01

In some coastal regions of the Arctic Ocean, grounded ice ridges contribute to stabilizing and maintaining a landfast ice cover. Recently, a grounding scheme representing this effect on sea ice dynamics was introduced and tested in a viscous-plastic sea ice model. This grounding scheme, based on a basal stress parameterization, improves the simulation of landfast ice in many regions such as in the East Siberian Sea, the Laptev Sea, and along the coast of Alaska. Nevertheless, in some regions like the Kara Sea, the area of landfast ice is systematically underestimated. This indicates that another mechanism such as ice arching is at play for maintaining the ice cover fast. To address this problem, the combination of the basal stress parameterization and tensile strength is investigated using a 0.25° Pan-Arctic CICE-NEMO configuration. Both uniaxial and isotropic tensile strengths notably improve the simulation of landfast ice in the Kara Sea but also in the Laptev Sea. However, the simulated landfast ice season for the Kara Sea is too short compared to observations. This is especially obvious for the onset of the landfast ice season which systematically occurs later in the model and with a slower build up. This suggests that improvements to the sea ice thermodynamics could reduce these discrepancies with the data.

NEMO-Binding Domain Peptide Attenuates Lipopolysaccharide-Induced Acute Lung Injury by Inhibiting the NF-κB Signaling Pathway

PubMed Central

Huang, Jianhua; Li, Li; Yuan, Weifeng; Zheng, Linxin

2016-01-01

The aim of the present study is to investigate the protective effects and relevant mechanisms exerted by NEMO-binding domain peptide (NBD) against lipopolysaccharide- (LPS-) induced acute lung injury (ALI) in mice. The ALI model was induced by intratracheally administered atomized LPS (5 mg/kg) to BABL/c mice. Half an hour before LPS administration, we treated the mice with increasing concentrations of intratracheally administered NBD or saline aerosol. Two hours after LPS administration, each group of mice was sacrificed. We observed that NBD pretreatment significantly attenuated LPS-induced lung histopathological injury in a dose-dependent manner. Western blotting established that NBD pretreatment obviously attenuated LPS-induced IκB-α and NF-κBp65 activation and NOX1, NOX2, and NOX4 overexpression. Furthermore, NBD pretreatment increased SOD and T-AOC activity and decreased MDA levels in lung tissue. In addition, NBD also inhibited TNF-α and IL-1β secretion in BALF after LPS challenge. In conclusion, NBD protects against LPS-induced ALI in mice. PMID:27956761

Continuous monitoring of noise levels in the Gulf of Catania (Ionian Sea). Study of correlation with ship traffic.

PubMed

Viola, S; Grammauta, R; Sciacca, V; Bellia, G; Beranzoli, L; Buscaino, G; Caruso, F; Chierici, F; Cuttone, G; D'Amico, A; De Luca, V; Embriaco, D; Favali, P; Giovanetti, G; Marinaro, G; Mazzola, S; Filiciotto, F; Pavan, G; Pellegrino, C; Pulvirenti, S; Simeone, F; Speziale, F; Riccobene, G

2017-08-15

Acoustic noise levels were measured in the Gulf of Catania (Ionian Sea) from July 2012 to May 2013 by a low frequency (<1000Hz) hydrophone, installed on board the NEMO-SN1 multidisciplinary observatory. NEMO-SN1 is a cabled node of EMSO-ERIC, which was deployed at a water depth of 2100m, 25km off Catania. The study area is characterized by the proximity of mid-size harbors and shipping lanes. Measured noise levels were correlated with the passage of ships tracked with a dedicated AIS antenna. Noise power was measured in the frequency range between 10Hz and 1000Hz. Experimental data were compared with the results of a fast numerical model based on AIS data to evaluate the contribution of shipping noise in six consecutive 1/3 octave frequency bands, including the 1/3 octave frequency bands centered at 63Hz and 125Hz, indicated by the Marine Strategy Framework Directive (2008/56/EC). Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Specific NEMO mutations impair CD40-mediated c-Rel activation and B cell terminal differentiation

PubMed Central

Jain, Ashish; Ma, Chi A.; Lopez-Granados, Eduardo; Means, Gary; Brady, William; Orange, Jordan S.; Liu, Shuying; Holland, Steven; Derry, Jonathan M.J.

2004-01-01

Hypomorphic mutations in the zinc finger domain of NF-κB essential modulator (NEMO) cause X-linked hyper-IgM syndrome with ectodermal dysplasia (XHM-ED). Here we report that patient B cells are characterized by an absence of Ig somatic hypermutation (SHM) and defective class switch recombination (CSR) despite normal induction of activation-induced cytidine deaminase (AID) and Iε-Cε transcripts. This indicates that AID expression alone is insufficient to support neutralizing antibody responses. Furthermore, we show that patient B cells stimulated with CD40 ligand are impaired in both p65 and c-Rel activation, and whereas addition of IL-4 can enhance p65 activity, c-Rel activity remains deficient. This suggests that these NF-κB components have different activation requirements and that IL-4 can augment some but not all NEMO-dependent NF-κB signaling. Finally, using microarray analysis of patient B cells we identified downstream effects of impaired NF-κB activation and candidate factors that may be necessary for CSR and SHM in B cells. PMID:15578091

20th Annual Systems Engineering Conference, Thursday, Volume 4

DTIC Science & Technology

2017-10-26

Daniel Dault, Air Force Research Lab 19809 Physics Based Modeling & Simulation For Shock and Vulnerability Assessments - Navy Enhanced Sierra...19811 Version 1.0 of the New INCOSE Competency Framework u Mr. Don Gelosh 19515 A Proposed Engineering Training Framework and Competency Methodology...nonlinearity ▪ QEV, Transient, Frequency Domain ▪ Inverse Methods Capability ▪ Coupled Physics ▪ Fluids: nemo, aero and sigma ▪ Thermal (unidirection): fuego

AGAMA: Action-based galaxy modeling framework

NASA Astrophysics Data System (ADS)

Vasiliev, Eugene

2018-05-01

The AGAMA library models galaxies. It computes gravitational potential and forces, performs orbit integration and analysis, and can convert between position/velocity and action/angle coordinates. It offers a framework for finding best-fit parameters of a model from data and self-consistent multi-component galaxy models, and contains useful auxiliary utilities such as various mathematical routines. The core of the library is written in C++, and there are Python and Fortran interfaces. AGAMA may be used as a plugin for the stellar-dynamical software packages galpy (ascl:1411.008), AMUSE (ascl:1107.007), and NEMO (ascl:1010.051).

Status of NEMO

NASA Astrophysics Data System (ADS)

Migneco, E.; Aiello, S.; Ambriola, M.; Ameli, F.; Amore, I.; Anghinolfi, M.; Anzalone, A.; Barbarino, G.; Barbarito, E.; Battaglieri, M.; Bellotti, R.; Beverini, N.; Bonori, M.; Bouhdaef, B.; Brescia, M.; Cacopardo, G.; Cafagna, F.; Capone, A.; Caponetto, L.; Castorina, E.; Ceres, A.; Chiarusi, T.; Circella, M.; Cocimano, R.; Coniglione, R.; Cordelli, M.; Costa, M.; Cuneo, S.; D'Amico, A.; De Bonis, G.; De Marzo, C.; De Rosa, G.; De Vita, R.; Distefano, C.; Falchini, E.; Fiorello, C.; Flaminio, V.; Fratini, K.; Galeotti, S.; Gabrielli, A.; Gandolfi, E.; Giacomelli, G.; Grimaldi, A.; Habel, R.; Leonora, E.; Lonardo, A.; Longo, G.; Lo Presti, D.; Lucarelli, F.; Maccione, L.; Margiotta, A.; Martini, A.; Masullo, R.; Megna, R.; Mongelli, M.; Morganti, M.; Montaruli, T.; Musumeci, M.; Nicolau, C. A.; Orlando, A.; Osipenko, M.; Osteria, G.; Papaleo, R.; Pappalardo, V.; Petta, C.; Piattelli, P.; Raffaelli, F.; Raia, G.; Randazzo, N.; Reito, S.; Ricco, G.; Riccobene, G.; Ripani, M.; Rovelli, A.; Ruppi, M.; Russo, G. V.; Russo, S.; Sapienza, P.; Sedita, M.; Schuller, J.-P.; Shirokov, E.; Simeone, F.; Sipala, V.; Spurio, M.; Taiuti, M.; Terreni, G.; Trasatti, L.; Urso, S.; Valente, V.; Vicini, P.

2006-11-01

The activities towards the realization of a km3 Cherenkov neutrino detector carried out by the NEMO Collaboration are described. Long-term exploration of a 3500 m deep-sea site close to the Sicilian coast has shown that it is optimal for the installation of the detector. The realization of a Phase-1 project, which is under way, will validate the proposed technologies for the realization of the km3 detector on a Test Site at 2000 m depth. The realization of a new infrastructure on the candidate site (Phase-2 project) will provide the possibility to test detector components at 3500 m depth.

Robust and Cost-Efficient Communication Based on SNMP in Mobile Networks

NASA Astrophysics Data System (ADS)

Ryu, Sang-Hoon; Baik, Doo-Kwon

A main challenge in the design of this mobile network is the development of dynamic routing protocols that can efficiently find routes between two communicating nodes. Multimedia streaming services are receiving considerable interest in the mobile network business. An entire mobile network may change its point of attachment to the Internet. The mobile network is operated by a basic specification to support network mobility called Network Mobility (NEMO) Basic Support. However, NEMO basic Support mechanism has some problem in continuous communication. In this paper, we propose robust and cost-efficient algorithm. And we simulate proposed method and conclude some remarks.

New Geochemical Analyses Reveal Crustal Accretionary Processes at The Overlapping Spreading Center Near 3 N East Pacific Rise

NASA Astrophysics Data System (ADS)

Smithka, I. N.; Perfit, M. R.

2013-12-01

Mid-ocean ridges (MORs) are the sites of oceanic lithosphere creation and construction. Ridge discontinuities are a global phenomenom but are not as well understood as ridge axes. Geochemical analyses provide insights into upper mantle processes since elements fractionate with melting and freezing as well as reside in material to retain source signature. Lavas collected from ridge discontinuities consist of greater chemical diversity and represent variations in source, melting parameters, and local crustal processes. The small overlapping spreading center (OSC) near the third parallel north on the East Pacific Rise has been superficially analyzed previously, but here we present new isotope analyses and expand our understanding of MOR processes and processes near OSCs. Initial analyses of lavas collected in 2000 on AHA-NEMO2 revealed normal MOR basalt trends in rare earth element enrichments as well as in major element concentrations. Crystal fractionation varies along the tips of both axes, with MgO and TiO2 concentrations increasing towards the OSC basin. Newly analyzed Sr, Nd, and Pb isotope ratios will further constrain the nature of geochemical diversity along axis. As the northern tip seems to be propagating and the southern tip dying, lavas collected from each may reflect two different underlying mantle melting and magma storage processes.

Prospects for improving the representation of coastal and shelf seas in global ocean models

NASA Astrophysics Data System (ADS)

Holt, Jason; Hyder, Patrick; Ashworth, Mike; Harle, James; Hewitt, Helene T.; Liu, Hedong; New, Adrian L.; Pickles, Stephen; Porter, Andrew; Popova, Ekaterina; Icarus Allen, J.; Siddorn, John; Wood, Richard

2017-02-01

Accurately representing coastal and shelf seas in global ocean models represents one of the grand challenges of Earth system science. They are regions of immense societal importance through the goods and services they provide, hazards they pose and their role in global-scale processes and cycles, e.g. carbon fluxes and dense water formation. However, they are poorly represented in the current generation of global ocean models. In this contribution, we aim to briefly characterise the problem, and then to identify the important physical processes, and their scales, needed to address this issue in the context of the options available to resolve these scales globally and the evolving computational landscape.We find barotropic and topographic scales are well resolved by the current state-of-the-art model resolutions, e.g. nominal 1/12°, and still reasonably well resolved at 1/4°; here, the focus is on process representation. We identify tides, vertical coordinates, river inflows and mixing schemes as four areas where modelling approaches can readily be transferred from regional to global modelling with substantial benefit. In terms of finer-scale processes, we find that a 1/12° global model resolves the first baroclinic Rossby radius for only ˜ 8 % of regions < 500 m deep, but this increases to ˜ 70 % for a 1/72° model, so resolving scales globally requires substantially finer resolution than the current state of the art.We quantify the benefit of improved resolution and process representation using 1/12° global- and basin-scale northern North Atlantic nucleus for a European model of the ocean (NEMO) simulations; the latter includes tides and a k-ɛ vertical mixing scheme. These are compared with global stratification observations and 19 models from CMIP5. In terms of correlation and basin-wide rms error, the high-resolution models outperform all these CMIP5 models. The model with tides shows improved seasonal cycles compared to the high-resolution model without tides. The benefits of resolution are particularly apparent in eastern boundary upwelling zones.To explore the balance between the size of a globally refined model and that of multiscale modelling options (e.g. finite element, finite volume or a two-way nesting approach), we consider a simple scale analysis and a conceptual grid refining approach. We put this analysis in the context of evolving computer systems, discussing model turnaround time, scalability and resource costs. Using a simple cost model compared to a reference configuration (taken to be a 1/4° global model in 2011) and the increasing performance of the UK Research Councils' computer facility, we estimate an unstructured mesh multiscale approach, resolving process scales down to 1.5 km, would use a comparable share of the computer resource by 2021, the two-way nested multiscale approach by 2022, and a 1/72° global model by 2026. However, we also note that a 1/12° global model would not have a comparable computational cost to a 1° global model in 2017 until 2027. Hence, we conclude that for computationally expensive models (e.g. for oceanographic research or operational oceanography), resolving scales to ˜ 1.5 km would be routinely practical in about a decade given substantial effort on numerical and computational development. For complex Earth system models, this extends to about 2 decades, suggesting the focus here needs to be on improved process parameterisation to meet these challenges.

The km 3 Mediterranean neutrino observatory - the NEMO.RD project

NASA Astrophysics Data System (ADS)

De Marzo, C. N.

2001-05-01

The NEMO.RD Project is a feasibility study of a km 3 underwater telescope for high energy astrophysical neutrinos to be located in the Mediterranean Sea. Results on various issues of this project are presented on: i) Monte Carlo simulation study of the capabilities of various arrays of phototubes in order to determine the detector geometry that can optimize performance and cost; ii) oceanographic survey of various sites in search of the optimal one; iii) feasibility study of mechanics, deployment, connections and maintenance of such a detector. Parameters of a site near Capo Passero, Sicily, where depth, transparency and other water parameters seem optimal are shown.

Measurement of the BB Decay Half-Life of 130Te with the NEMO-3 Detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

A. J. Caffrey

2011-08-01

We report results from the NEMO-3 experiment based on an exposure of 1275 days with 661 g of 130Te in the form of enriched and natural tellurium foils. The double B decay rate of 130Te is found to be greater than zero with a significance of 7.7 standard deviations and the half-life is measured to be T2v 1/2 = [7.0 +/- 0.9(stat) +/- 1.1 (syst)] x 10{sup 20} yr. This represents the most precise measurement of this half-life yet published and the first real-time observation of this decay.

The BiPo-3 detector for the measurement of ultra low natural radioactivities of thin materials

NASA Astrophysics Data System (ADS)

Barabash, A. S.; Basharina-Freshville, A.; Birdsall, E.; Blondel, S.; Blot, S.; Bongrand, M.; Boursette, D.; Brudanin, V.; Busto, J.; Caffrey, A. J.; Calvez, S.; Cascella, M.; Cebrián, S.; Cerna, C.; Cesar, J. P.; Chauveau, E.; Chopra, A.; Dafní, T.; De Capua, S.; Duchesneau, D.; Durand, D.; Egorov, V.; Eurin, G.; Evans, J. J.; Fajt, L.; Filosofov, D.; Flack, R.; Garrido, X.; Gómez, H.; Guillon, B.; Guzowski, P.; Holý, K.; Hodák, R.; Huber, A.; Hugon, C.; Iguaz, F. J.; Irastorza, I. G.; Jeremie, A.; Jullian, S.; Kauer, M.; Klimenko, A.; Kochetov, O.; Konovalov, S. I.; Kovalenko, V.; Lang, K.; Lemière, Y.; Le Noblet, T.; Liptak, Z.; Liu, X. R.; Loaiza, P.; Lutter, G.; Luzón, G.; Macko, M.; Mamedov, F.; Marquet, C.; Mauger, F.; Morgan, B.; Mott, J.; Nemchenok, I.; Nomachi, M.; Nova, F.; Ohsumi, H.; Oliviéro, G.; Ortiz de Solórzano, A.; Pahlka, R. B.; Pater, J.; Perrot, F.; Piquemal, F.; Povinec, P.; Přidal, P.; Ramachers, Y. A.; Remoto, A.; Richards, B.; Riddle, C. L.; Rukhadze, E.; Saakyan, R.; Salazar, R.; Sarazin, X.; Shitov, Yu.; Simard, L.; Šimkovic, F.; Smetana, A.; Smolek, K.; Smolnikov, A.; Söldner-Rembold, S.; Soulé, B.; Štekl, I.; Thomas, J.; Timkin, V.; Torre, S.; Tretyak, Vl. I.; Tretyak, V. I.; Umatov, V. I.; Vilela, C.; Vorobel, V.; Waters, D.; Žukauskas, A.

2017-06-01

The BiPo-3 detector, running at the Canfranc Underground Laboratory (Laboratorio Subterr&aposaneo de Canfranc, LSC, Spain) since 2013, is a low-radioactivity detector dedicated to measuring ultra low natural radionuclide contaminations of 208Tl (232Th chain) and 214Bi (238U chain) in thin materials. The total sensitive surface area of the detector is 3.6 m2. The detector has been developed to measure the radiopurity of the selenium double β-decay source foils of the SuperNEMO experiment. In this paper the design and performance of the detector, and results of the background measurements in 208Tl and 214Bi, are presented, and the validation of the BiPo-3 measurement with a calibrated aluminium foil is discussed. Results of the 208Tl and 214Bi activity measurements of the first enriched 82Se foils of the double β-decay SuperNEMO experiment are reported. The sensitivity of the BiPo-3 detector for the measurement of the SuperNEMO 82Se foils is Script A(208Tl) <2 μBq/kg (90% C.L.) and Script A(214Bi) <140 μBq/kg (90% C.L.) after 6 months of measurement.

Conformational Analysis on structural perturbations of the zinc finger NEMO

NASA Astrophysics Data System (ADS)

Godwin, Ryan; Salsbury, Freddie; Salsbury Group Team

2014-03-01

The NEMO (NF-kB Essential Modulator) Zinc Finger protein (2jvx) is a functional Ubiquitin-binding domain, and plays a role in signaling pathways for immune/inflammatory responses, apoptosis, and oncogenesis [Cordier et al., 2008]. Characterized by 3 cysteines and 1 histidine residue at the active site, the biologically occurring, bound zinc configuration is a stable structural motif. Perturbations of the zinc binding residues suggest conformational changes in the 423-atom protein characterized via analysis of all-atom molecular dynamics simulations. Structural perturbations include simulations with and without a zinc ion and with and without de-protonated cysteines, resulting in four distinct configurations. Simulations of various time scales show consistent results, yet the longest, GPU driven, microsecond runs show more drastic structural and dynamic fluctuations when compared to shorter duration time-scales. The last cysteine residue (26 of 28) and the helix on which it resides exhibit a secondary, locally unfolded conformation in addition to its normal bound conformation. Combined analytics elucidate how the presence of zinc and/or protonated cysteines impact the dynamics and energetic fluctuations of NEMO. Comprehensive Cancer Center of Wake Forest University Computational Biosciences shared resource supported by NCI CCSG P30CA012197.

The Ups and Downs of Measuring Sea Surface Salinity from Space

NASA Astrophysics Data System (ADS)

Banks, C. J.; Gommenginger, C. P.; Srokosz, M. A.; Snaith, H. M.

2012-12-01

In November 2009, the European Space Agency (ESA) launched the Soil Moisture and Ocean Salinity (SMOS) satellite and a new era of satellite oceanography began vastly improving our ability to synoptically measure sea surface salinity (SSS). SMOS was joined in June 2011 by the NASA/Argentine Aquarius/SAC-D mission designed specifically to measure SSS. Although there are significant differences in how both satellites retrieve SSS, both utilise passive systems to measure the response of the brightness temperature (Tb) at L-band (1.4 GHz). We report on-going investigations into the validation of SMOS and Aquarius 'Level 3' measurements of SSS using monthly data on a 1° by 1° global grid between 60°S and 60°N. Previous studies have indicated significant temporally varying differences between SSS from SMOS ascending passes and from SMOS descending passes: therefore, for both SMOS and Aquarius, data from ascending and descending passes will be studied separately. Both satellites have sun-synchronous orbits but the direction of travel for the two satellites are twelve hours out of phase (i.e. at approximately 6 a.m. local time SMOS is travelling south-to-north (ascending) and Aquarius is travelling north-to-south (descending) whereas at 6 p.m. the directions of travel are switched). For validation purposes two separate monthly, 1° by 1° datasets are used over the same locations as the satellite data. The first is based on averaged near-surface salinity (depth less than 10 m) as derived from the drifting Argo float programme. The second validation data source is output from the UK Met Office Forecasting Ocean Assimilation Model (FOAM) based on NEMO (Nucleus for European Modelling of the Ocean). The SMOS Level 3 products are developed from ESA Level 2 products after quality control (QC) based on flags and SSS error provided in the ESA Level 2 products. Aquarius data (QC) is based only on data flags and a simple selection of in-range SSS values ([30, 40]). The study is based on monthly products over the period from September 2011 to May 2012. We calculate maps of the difference between each possible pair of SSS datasets for each month, and consider their relationships using regression on the 1° values. The analysis is carried out for the global ocean, as well as for smaller, more homogeneous, study regions (e.g. SPURS). In addition, a study is made of the differences and similarities, at Level 2, between the two satellites and the direction of travel.

A Transgenic Drosophila melanogaster Model To Study Human T-Lymphotropic Virus Oncoprotein Tax-1-Driven Transformation In Vivo

PubMed Central

Shirinian, Margret; Kambris, Zakaria; Hamadeh, Lama; Grabbe, Caroline; Journo, Chloé; Mahieux, Renaud

2015-01-01

Human T-cell lymphotropic virus type 1 (HTLV-1)-induced adult T-cell leukemia/lymphoma is an aggressive malignancy. HTLV-2 is genetically related to HTLV-1 but does not cause any malignant disease. HTLV-1 Tax transactivator (Tax-1) contributes to leukemogenesis via NF-κB. We describe transgenic Drosophila models expressing Tax in the compound eye and plasmatocytes. We demonstrate that Tax-1 but not Tax-2 induces ommatidial perturbation and increased plasmatocyte proliferation and that the eye phenotype is dependent on Kenny (IKKγ/NEMO), thus validating this new in vivo model. PMID:25995252

Performance and quality assessment of the global ocean eddy-permitting physical reanalysis GLORYS2V4.

NASA Astrophysics Data System (ADS)

Garric, Gilles; Parent, Laurent; Greiner, Eric; Drévillon, Marie; Hamon, Mathieu; Lellouche, Jean-Michel; Régnier, Charly; Desportes, Charles; Le Galloudec, Olivier; Bricaud, Clement; Drillet, Yann; Hernandez, Fabrice; Le Traon, Pierre-Yves

2017-04-01

The purpose of this presentation is to give an overview of the recent upgrade of GLORYS2 (version 4 and GLORYS2V4 hereafter), the latest ocean reanalysis produced at Mercator Ocean that covers the altimetry era (1993-2015) in the framework of Copernicus Marine Environment Monitoring Service (CMEMS; http://marine.copernicus.eu/). The reanalysis is run at eddy-permitting resolution (¼° horizontal resolution and 75 vertical levels) with the NEMO model and driven at the surface by ERA-Interim reanalysis from ECMWF (European Centre for Medium-Range Weather Forecasts). The reanalysis system uses a multi-data and multivariate reduced order Kalman filter based on the singular extended evolutive Kalman (SEEK) filter formulation together with a 3D-VAR large scale bias correction. The assimilated observations are along-track satellite altimetry, sea surface temperature, sea ice concentration and in-situ profiles of temperature and salinity. With respect to the previous version (GLORYS2V3), GLORYS2V4 contains a number of improvements. In particular: a) new initial temperature and salinity conditions derived from EN4 data base with a better mass equilibrium with altimetry, b) the use of the updated delayed mode CORA in situ observations from CMEMS, c) a new hybrid Mean Dynamical Topography (MDT) for the assimilation scheme referenced over the 1993-2013 period, d) a better observation operator for altimetry observations for the data assimilation scheme: e) A correction of large scale ERA-Interim atmospheric surface (precipitations and radiative) fluxes as in GLORYS2V3 but towards new satellite data set f) an update of the climatological runoff data base by using the latest version of Dai's 2009 data set for the global ocean together with better account of freshwater fluxes from polar ice sheet's glaciers. The presentation will show that the new reanalysis outperforms the previous version in many aspects such as biases and root mean squared error and, especially in representing the variability of global heat and salt content and associated steric sea level in the last two decades. The dataset is available in NetCDF format and GLORYS2V4 best analysis products are distributed onto the CMEMS data portal.

ESONET LIDO Demonstration Mission: the East Sicily node

NASA Astrophysics Data System (ADS)

Riccobene, Giorgio; Favali, Paolo; Andrè, Michel; Chierici, Francesco; Pavan, Gianni; Esonet Lido Demonstration Mission Team

2010-05-01

Off East Sicily (at 2100 m depth, 25 km off the harbour of Catania) a prototype of a cabled deep-sea observatory (NEMO-SN1) was set up and has been operational in real-time since 2005 (the cabled deep-sea multi-parameter station SN1, equipped with geophysical and environmental sensors and the cabled NEMO-OνDE, equipped with 4 broadband hydrophones). The Western Ionian Sea is one of the node sites for the upcoming European permanent underwater network (EMSO). Within the activities of the EC project ESONET-NoE some demonstration missions have been funded. The LIDO-DM (Listening to the Deep Ocean-Demonstration Mission) is one of these and is related to two sites, East Sicily and Iberian Margin (Gulf of Cadiz), the main aims being geo-hazards monitoring and warning (seismic, tsunami, and volcanic) and bio-acoustics. The LIDO-DM East Sicily installation represents a further major step within ESONET-NoE, resulting in a fully integrated system for multidisciplinary deep-sea science, capable to transmit and distribute data in real time to the scientific community and to the general public. LIDO-DM East Sicily hosts a large number of sensors aimed at monitoring and studying oceanographic and environmental parameters (by means of CTD, ADCP, 3-C single point current meter, turbidity meter), geophysical phenomena (low frequency hydrophones, accelerometer, gravity meter, vector and scalar magnetometers, seismometer, absolute and differential pressure gauges), ocean noise monitoring and identification and tracking of biological acoustic sources in deep sea. The latter will be performed using two tetrahedral arrays of 4 hydrophones, located at a relative distance of about 5 km, and at about 25 km from the shore. The whole system will be connected and powered from shore, by means of the electro-optical cable net installed at the East Sicily Site Infrastructure, and synchronised with GPS. Sensors data sampling is performed underwater and transmitted via optical fibre link, with optimal S/N ratio for all signals. This will also permit real-time data acquisition, analysis and distribution on-shore. Innovative electronics for the off-shore data acquisition and transmission systems has been designed, built and tested. A dedicated computing and networking infrastructure for data acquisition, storage and distribution through the internet has been also created. The deployment and connection of the deep sea structures will be performed using the dedicated ROV and Deep Sea Shuttle handling facilities (PEGASO, owned by INGV and INFN). LIDO-DM constitutes the enhancement of the Western Ionian site in view of the EMSO Research Infrastructure.

Hypohidrotic ectodermal dysplasia, osteopetrosis, lymphedema, and immunodeficiency in an infant with multiple opportunistic infections.

PubMed

Carlberg, Valerie M; Lofgren, Sabra M; Mann, Julianne A; Austin, Jared P; Nolt, Dawn; Shereck, Evan B; Davila-Saldana, Blachy; Zonana, Jonathan; Krol, Alfons L

2014-01-01

Osteopetrosis, lymphedema, hypohidrotic ectodermal dysplasia, and immunodeficiency (OL-HED-ID) is a rare X-linked disorder with only three reported prior cases in the English-language literature. We describe a case of OL-HED-ID in a male infant who initially presented with congenital lymphedema, leukocytosis, and thrombocytopenia of unknown etiology at 7 days of age. He subsequently developed gram-negative sepsis and multiple opportunistic infections including high-level cytomegalovirus viremia and Pneumocystis jiroveci pneumonia. The infant was noted to have mildly xerotic skin, fine sparse hair, and periorbital wrinkling, all features suggestive of ectodermal dysplasia. Skeletal imaging showed findings consistent with osteopetrosis, and immunologic investigation revealed hypogammaglobulinemia and mixed T- and B-cell dysfunction. Genetic testing revealed a novel mutation in the nuclear factor kappa beta (NF-KB) essential modulator (NEMO) gene, confirming the diagnosis of OL-HED-ID. Mutations in the NEMO gene have been reported in association with hypohidrotic ectodermal dysplasia with immunodeficiency (HED-ID), OL-HED-ID, and incontinentia pigmenti. In this case, we report a novel mutation in the NEMO gene associated with OL-HED-ID. This article highlights the dermatologic manifestations of a rare disorder, OL-HED-ID, and underscores the importance of early recognition and prompt intervention to prevent life-threatening infections. © 2013 Wiley Periodicals, Inc.

Implementation of a flow-dependent background error correlation length scale formulation in the NEMOVAR OSTIA system

NASA Astrophysics Data System (ADS)

Fiedler, Emma; Mao, Chongyuan; Good, Simon; Waters, Jennifer; Martin, Matthew

2017-04-01

OSTIA is the Met Office's Operational Sea Surface Temperature (SST) and Ice Analysis system, which produces L4 (globally complete, gridded) analyses on a daily basis. Work is currently being undertaken to replace the original OI (Optimal Interpolation) data assimilation scheme with NEMOVAR, a 3D-Var data assimilation method developed for use with the NEMO ocean model. A dual background error correlation length scale formulation is used for SST in OSTIA, as implemented in NEMOVAR. Short and long length scales are combined according to the ratio of the decomposition of the background error variances into short and long spatial correlations. The pre-defined background error variances vary spatially and seasonally, but not on shorter time-scales. If the derived length scales applied to the daily analysis are too long, SST features may be smoothed out. Therefore a flow-dependent component to determining the effective length scale has also been developed. The total horizontal gradient of the background SST field is used to identify regions where the length scale should be shortened. These methods together have led to an improvement in the resolution of SST features compared to the previous OI analysis system, without the introduction of spurious noise. This presentation will show validation results for feature resolution in OSTIA using the OI scheme, the dual length scale NEMOVAR scheme, and the flow-dependent implementation.

Evaluation of QoS supported in Network Mobility NEMO environments

NASA Astrophysics Data System (ADS)

Hussien, L. F.; Abdalla, A. H.; Habaebi, M. H.; Khalifa, O. O.; Hassan, W. H.

2013-12-01

Network mobility basic support (NEMO BS) protocol is an entire network, roaming as a unit which changes its point of attachment to the Internet and consequently its reachability in the network topology. NEMO BS doesn't provide QoS guarantees to its users same as traditional Internet IP and Mobile IPv6 as well. Typically, all the users will have same level of services without considering about their application requirements. This poses a problem to real-time applications that required QoS guarantees. To gain more effective control of the network, incorporated QoS is needed. Within QoS-enabled network the traffic flow can be distributed to various priorities. Also, the network bandwidth and resources can be allocated to different applications and users. Internet Engineering Task Force (IETF) working group has proposed several QoS solutions for static network such as IntServ, DiffServ and MPLS. These QoS solutions are designed in the context of a static environment (i.e. fixed hosts and networks). However, they are not fully adapted to mobile environments. They essentially demands to be extended and adjusted to meet up various challenges involved in mobile environments. With existing QoS mechanisms many proposals have been developed to provide QoS for individual mobile nodes (i.e. host mobility). In contrary, research based on the movement of the whole mobile network in IPv6 is still undertaking by the IETF working groups (i.e. network mobility). Few researches have been done in the area of providing QoS for roaming networks. Therefore, this paper aims to review and investigate (previous /and current) related works that have been developed to provide QoS in mobile network. Consequently, a new proposed scheme will be introduced to enhance QoS within NEMO environment, achieving by which seamless mobility to users of mobile network node (MNN).

Feasibility Studies for a Mediterranean Neutrino Observatory - The NEMO.RD Project

NASA Astrophysics Data System (ADS)

de Marzo, C.; Ambriola, M.; Bellotti, R.; Cafagna, F.; Calicchio, M.; Ciacio, F.; Circella, M.; de Marzo, C.; Montaruli, T.; Falchieri, D.; Gabrielli, A.; Gandolfi, E.; Masetti, M.; Vitullo, C.; Zanarini, G.; Habel, R.; Usai, I.; Aiello, S.; Burrafato, G.; Caponetto, L.; Costanzo, E.; Lopresti, D.; Pappalardo, L.; Petta, C.; Randazzo, N.; Russo, G. V.; Troia, O.; Barnà, R.; D'Amico, V.; de Domenico, E.; de Pasquale, D.; Giacobbe, S.; Italiano, A.; Migliardo, F.; Salvato, G.; Trafirò, A.; Trimarchi, M.; Ameli, F.; Bonori, M.; Bottai, S.; Capone, A.; Desiati, P.; Massa, F.; Masullo, R.; Salusti, E.; Vicini, M.; Coniglione, R.; Migneco, E.; Piattelli, P.; Riccobene, R.; Sapienza, P.; Cordelli, M.; Trasatti, L.; Valente, V.; de Marchis, G.; Piccari, L.; Accerboni, E.; Mosetti, R.; Astraldi, M.; Gasparini, G. P.; Ulzega, A.; Orrù, P.

2000-06-01

The NEMO.RD Project is a feasibility study of a km3 underwater telescope for high energy astrophysical neutrinos to be located in the Mediterranea Sea. At present this study concerns: i) Monte Carlo simulation study of the capabilities of various arrays of phototubes in order to determine the detector geometry that can optimize performance and cost; ii) design of low power consumption electronic cards for data acquisition and transmission to shore; iii) feasibility study of mechanics, deployment, connection and maintenance of such a detector in collaboration with petrol industries having experience of undersea operations; iv) oceanographic exploration of various sites in search for the optimal one. A brief report on the status of points i) and iv) is presented here

Listening to the Deep-Ocean Environment (LIDO): an ESONET Initiative for the Real-Time Monitoring of Geohazards and Marine Ambient Noise

NASA Astrophysics Data System (ADS)

André, Michel; Favali, Paolo; Piatteli, Paolo; Miranda, Jorge; Waldmann, Christoph; Esonet Lido Demonstration Mission Team

2010-05-01

Understanding the link between natural and anthropogenic processes is essential for predicting the magnitude and impact of future changes of the natural balance of the oceans. Deep-sea observatories have the potential to play a key role in the assessment and monitoring of these changes. ESONET is a European Network of Excellence of deep-sea observatories that includes 55 partners belonging to 14 countries. ESONET NoE is providing data on key parameters from the subsurface down to the seafloor at representative locations that transmit them to shore. The strategies of deployment, data sampling, technological development, standardisation and data management are being integrated with projects dealing with the spatial and near surface time series. LIDO (Listening to the Deep Ocean environment) is one of these projects and proposes to establish a first nucleus of a regional network of multidisciplinary seafloor observatories contributing to the coordination of high quality research in the ESONET NoE by allowing the real-time long-term monitoring of Geohazards and Marine Ambient Noise in the Mediterranean Sea and the adjacent Atlantic waters. Specific activities address the long-term monitoring of earthquakes and tsunamis and the characterisation of ambient noise, marine mammal sounds and anthropogenic sources. The objective of this demonstration mission will be achieved through the extension of the present capabilities of the observatories working in the ESONET key-sites of Eastern Sicily (NEMO-SN1) and of the Gulf of Cadiz (GEOSTAR configured for NEAREST pilot experiment) by installing new sensor equipments related to Bioacoustics and Geohazards, as well as by implementing international standard methods in data acquisition and management.

On the impact of the resolution on the surface and subsurface Eastern Tropical Atlantic warm bias

NASA Astrophysics Data System (ADS)

Martín-Rey, Marta; Lazar, Alban

2016-04-01

The tropical variability has a great importance for the climate of adjacent areas. Its sea surface temperature anomalies (SSTA) affect in particular the Brazilian Nordeste and the Sahelian region, as well as the tropical Pacific or the Euro-Atlantic sector. Nevertheless, the state-of the art climate models exhibits very large systematic errors in reproducing the seasonal cycle and inter-annual variability in the equatorial and coastal Africa upwelling zones (up to several °C for SST). Theses biases exist already, in smaller proportions though, in forced ocean models (several 1/10th of °C), and affect not only the mixed layer but also the whole thermocline. Here, we present an analysis of the impact of horizontal and vertical resolution changes on these biases. Three different DRAKKAR NEMO OGCM simulations have been analysed, associated to the same forcing set (DFS4.4) with different grid resolutions: "REF" for reference (1/4°, 46 vertical levels), "HH" with a finer horizontal grid (1/12°, 46 v.l.) and "HV" with a finer vertical grid (1/4°, 75 v.l.). At the surface, a more realistic seasonal SST cycle is produced in HH in the three upwellings, where the warm bias decreases (by 10% - 20%) during boreal spring and summer. A notable result is that increasing vertical resolution in HV causes a shift (in advance) of the upwelling SST seasonal cycles. In order to better understand these results, we estimate the three upwelling subsurface temperature errors, using various in-situ datasets, and provide thus a three-dimensional view of the biases.

A Transgenic Drosophila melanogaster Model To Study Human T-Lymphotropic Virus Oncoprotein Tax-1-Driven Transformation In Vivo.

PubMed

Shirinian, Margret; Kambris, Zakaria; Hamadeh, Lama; Grabbe, Caroline; Journo, Chloé; Mahieux, Renaud; Bazarbachi, Ali

2015-08-01

Human T-cell lymphotropic virus type 1 (HTLV-1)-induced adult T-cell leukemia/lymphoma is an aggressive malignancy. HTLV-2 is genetically related to HTLV-1 but does not cause any malignant disease. HTLV-1 Tax transactivator (Tax-1) contributes to leukemogenesis via NF-κB. We describe transgenic Drosophila models expressing Tax in the compound eye and plasmatocytes. We demonstrate that Tax-1 but not Tax-2 induces ommatidial perturbation and increased plasmatocyte proliferation and that the eye phenotype is dependent on Kenny (IKKγ/NEMO), thus validating this new in vivo model. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

MAVS ubiquitination by the E3 ligase TRIM25 and degradation by the proteasome is involved in type I interferon production after activation of the antiviral RIG-I-like receptors

PubMed Central

2012-01-01

Background During a viral infection, the intracellular RIG-I-like receptors (RLRs) sense viral RNA and signal through the mitochondrial antiviral signaling adaptor MAVS (also known as IPS-1, Cardif and VISA) whose activation triggers a rapid production of type I interferons (IFN) and of pro-inflammatory cytokines through the transcription factors IRF3/IRF7 and NF-κB, respectively. While MAVS is essential for this signaling and known to operate through the scaffold protein NEMO and the protein kinase TBK1 that phosphorylates IRF3, its mechanism of action and regulation remain unclear. Results We report here that RLR activation triggers MAVS ubiquitination on lysine 7 and 10 by the E3 ubiquitin ligase TRIM25 and marks it for proteasomal degradation concomitantly with downstream signaling. Inhibition of this MAVS degradation with a proteasome inhibitor does not affect NF-κB signaling but it hampers IRF3 activation, and NEMO and TBK1, two essential mediators in type I IFN production, are retained at the mitochondria. Conclusions These results suggest that MAVS functions as a recruitment platform that assembles a signaling complex involving NEMO and TBK1, and that the proteasome-mediated MAVS degradation is required to release the signaling complex into the cytosol, allowing IRF3 phosphorylation by TBK1. PMID:22626058

MAVS ubiquitination by the E3 ligase TRIM25 and degradation by the proteasome is involved in type I interferon production after activation of the antiviral RIG-I-like receptors.

PubMed

Castanier, Céline; Zemirli, Naima; Portier, Alain; Garcin, Dominique; Bidère, Nicolas; Vazquez, Aimé; Arnoult, Damien

2012-05-24

During a viral infection, the intracellular RIG-I-like receptors (RLRs) sense viral RNA and signal through the mitochondrial antiviral signaling adaptor MAVS (also known as IPS-1, Cardif and VISA) whose activation triggers a rapid production of type I interferons (IFN) and of pro-inflammatory cytokines through the transcription factors IRF3/IRF7 and NF-κB, respectively. While MAVS is essential for this signaling and known to operate through the scaffold protein NEMO and the protein kinase TBK1 that phosphorylates IRF3, its mechanism of action and regulation remain unclear. We report here that RLR activation triggers MAVS ubiquitination on lysine 7 and 10 by the E3 ubiquitin ligase TRIM25 and marks it for proteasomal degradation concomitantly with downstream signaling. Inhibition of this MAVS degradation with a proteasome inhibitor does not affect NF-κB signaling but it hampers IRF3 activation, and NEMO and TBK1, two essential mediators in type I IFN production, are retained at the mitochondria. These results suggest that MAVS functions as a recruitment platform that assembles a signaling complex involving NEMO and TBK1, and that the proteasome-mediated MAVS degradation is required to release the signaling complex into the cytosol, allowing IRF3 phosphorylation by TBK1.

Finding NEMO (novel electromaterial muscle oscillator): a polypyrrole powered robotic fish with real-time wireless speed and directional control

NASA Astrophysics Data System (ADS)

McGovern, Scott; Alici, Gursel; Truong, Van-Tan; Spinks, Geoffrey

2009-09-01

This paper presents the development of an autonomously powered and controlled robotic fish that incorporates an active flexural joint tail fin, activated through conducting polymer actuators based on polypyrrole (PPy). The novel electromaterial muscle oscillator (NEMO) tail fin assembly on the fish could be controlled wirelessly in real time by varying the frequency and duty cycle of the voltage signal supplied to the PPy bending-type actuators. Directional control was achieved by altering the duty cycle of the voltage input to the NEMO tail fin, which shifted the axis of oscillation and enabled turning of the robotic fish. At low speeds, the robotic fish had a turning circle as small as 15 cm (or 1.1 body lengths) in radius. The highest speed of the fish robot was estimated to be approximately 33 mm s-1 (or 0.25 body lengths s-1) and was achieved with a flapping frequency of 0.6-0.8 Hz which also corresponded with the most hydrodynamically efficient mode for tail fin operation. This speed is approximately ten times faster than those for any previously reported artificial muscle based device that also offers real-time speed and directional control. This study contributes to previously published studies on bio-inspired functional devices, demonstrating that electroactive polymer actuators can be real alternatives to conventional means of actuation such as electric motors.

Assessing the sampling strategy in the Northwestern Mediterranean Sea

NASA Astrophysics Data System (ADS)

Margirier, Félix; Testor, Pierre; Bosse, Anthony; Heslop, Emma; L'Hévéder, Blandine; Arsouze, Thomas; Houpert, Loic; Mortier, Laurent

2017-04-01

The deployment of numerous autonomous platforms (gliders, argo floats, moorings) added to the repeated ship cruises in the Northwestern Mediterranean Sea account for a considerable data coverage of the area through the past 10 years. In this study, we analyse the in-situ observations' ability to assess for the changes in the Northwester Mediterranean basin water masses properties over time. Comparing the observed time series for the different regions and different water masses to that of a glider simulator in the NEMO-Med12 model, we estimate both the quality of the model and the skill of the in-situ observations in reproducing the evolution of the basin properties.

Background noise levels and correlation with ship traffic in the Gulf of Catania

NASA Astrophysics Data System (ADS)

Viola, Salvatore; Buscaino, Giuseppa; Caruso, Francesco; Chierici, Francesco; Embriaco, Davide; Favali, Paolo; Giovanetti, Gabriele; Grammauta, Roasario; Larosa, Giuseppina; Pavan, Gianni; Pellegrino, Carmelo; Pulvirenti, Sara; Riccobene, Giorgio; Sciacca, Virginia; Simeone, Francesco; Beranzoli, Laura; Marinaro, Giuditta

2015-04-01

In the last decades the growing interest in the evaluation of the underwater acoustic noise for studies in the fields of geology, biology and high-energy physics is driving the scientific community to collaborate towards a multidisciplinary approach to the topic. In June 2012 in the framework of the European project EMSO, a multidisciplinary underwater observatory, named NEMO-SN1, was installed 25 km off-shore the port of Catania, at a depth of 2100 m and operated until May 2013 by INFN (Istituto Nazionale di Fisica Nucleare) and INGV (Istituto Nazionale di Geofisica e Vulcanologia). NEMO-SN1 hosted aboard geophysical, oceanographic and acoustic sensors: among these a seismic hydrophone model SMID DT-405D(V). In this work, conducted within the activity of the SMO project, the results on the evaluation of the underwater acoustic pollution in the Gulf of Catania through SMID DT-405D(V) recordings are presented. The seismic hydrophone provided a data set of about 11 months of continuous (24/7) recordings. Underwater sounds have been continuously digitized at a sampling frequency of 2 kHz and the acquired data have been stored in 10min long files for off-line analysis. To describe one-year background noise levels, the mean integrated acoustic noise was measured every second (sampling frequency 2000, NFFT 2048) in the 1/3 octave bands with centre frequency 63 Hz and for each 10 minutes-long file the 5th, the 50th and the 98th percentiles were calculated. Measured noise was correlated with the shipping traffic in the area, thanks to the data provided by an AIS receiver installed at the INFN-Laboratori Nazionali del Sud. An acoustic noise increment was measured in coincidence with the passing of crafts in the area and it was possible to identify the characteristic spectrum of each ship. A simple model for the estimation of the acoustic noise induced by the ships passing through the area was developed. The model was applied by using AIS data acquired during the operation of the NEMO-SN1 and the results of the model were compared with the experimental acoustic data. This approach paves the way for further studies on the acoustic identification of the ships producing high noise levels to find solutions to mitigate the underwater acoustic pollution. Further studies on the whole water column are foreseen, taking advantage of the data provided by the acoustic antennas that are going to be installed between 3500 m and 3000 m water depth, off-shore Portopalo di Capo Passero, in South-East Sicily.

Numerical modelling of the buoyant marine microplastics in the South-Eastern Baltic Sea

NASA Astrophysics Data System (ADS)

Bagaev, Andrei; Mizyuk, Artem; Chubarenko, Irina; Khatmullilna, Liliya

2017-04-01

Microplastics is a burning issue in the marine pollution science. Its sources, ways of propagation and final destiny pose a lot of questions to the modern oceanographers. Hence, a numerical model is an optimal tool for reconstruction of microplastics pathways and fate. Within the MARBLE project (lamp.ocean.ru), a model of Lagrangian particles transport was developed. It was tested coupled with oceanographic transport fields from the operational oceanography product of Copernicus Marine Monitoring Environment Service. Our model deals with two major types of microplastics such as microfibres and buoyant spheroidal particles. We are currently working to increase the grid resolution by means of the NEMO regional configuration for the south-eastern Baltic Sea. Several expeditions were organised to the three regions of the Baltic Sea (the Gotland, the Bornholm, and the Gdansk basins). Water samples from the surface and different water layers were collected, processed, and analysed by our team. A set of laboratory experiments was specifically designed to establish the settling velocity of particles of various shapes and densities. The analysis in question provided us with the understanding necessary for the model to reproduce the large-scale dynamics of microfibres. In the simulation, particles were spreading from the shore to the deep sea, slowly sinking to the bottom, while decreasing in quantity due to conditional sedimentation. Our model is expected to map out the microplastics life cycle and to account for its distribution patterns under the impact of wind and currents. For this purpose, we have already included the parameterization for the wind drag force applied to a particle. Initial results of numerical experiments seem to indicate the importance of proper implicit parameterization of the particle dynamics at the vertical solid boundary. Our suggested solutions to that problem will be presented at the EGU-2017. The MARBLE project is supported by Russian Science Foundation grant #15-17-10020.

Ultra-low level radon assays in gases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Xin Ran

The SuperNEMO experiment aims to search for the neutrinoless double beta decay (0νβ β) to T{sub 1{sub /{sub 2}}}(0ν) > 10{sup 26} years, this corresponds to an effective neutrino mass of 50-100 meV. The extremely rare event rate means the minimisation of background is of critical concern. The stringent strategy instigated to ensure detector radiopurity is outlined here for all construction materials. In particular the large R&D programme undertaken to reach the challengingly low level of radon, < 0.15 mBq/m{sup 3}, required inside the SuperNEMO gaseous tracker will be detailed. This includes an experiment designed to measure radon diffusion throughmore » various materials. A “Radon Concentration Line” (RnCL) was developed to be used in conjunction with a state-of-the-art radon detector in order to achieve world leading sensitivity to {sup 222}Rn content in large gas volumes at the level of a few µBq/m{sup 3}. A radon purification system was developed and installed which has demonstrated radon suppression by several orders of magnitude depending on the carrier gas. This apparatus has now been commissioned and measurements of cylindered gas have been made to confirm radon suppression by a factor 20 when using nitrogen as the carrier gas. The results from measurements of radon content in various gases, used inside SuperNEMO, using the RnCL will be presented.« less

Kilometric Scale Modeling of the North West European Shelf Seas: Exploring the Spatial and Temporal Variability of Internal Tides

NASA Astrophysics Data System (ADS)

Guihou, K.; Polton, J.; Harle, J.; Wakelin, S.; O'Dea, E.; Holt, J.

2018-01-01

The North West European Shelf break acts as a barrier to the transport and exchange between the open ocean and the shelf seas. The strong spatial variability of these exchange processes is hard to fully explore using observations, and simulations generally are too coarse to simulate the fine-scale processes over the whole region. In this context, under the FASTNEt program, a new NEMO configuration of the North West European Shelf and Atlantic Margin at 1/60° (˜1.8 km) has been developed, with the objective to better understand and quantify the seasonal and interannual variability of shelf break processes. The capability of this configuration to reproduce the seasonal cycle in SST, the barotropic tide, and fine-resolution temperature profiles is assessed against a basin-scale (1/12°, ˜9 km) configuration and a standard regional configuration (7 km resolution). The seasonal cycle is well reproduced in all configurations though the fine-resolution allows the simulation of smaller scale processes. Time series of temperature at various locations on the shelf show the presence of internal waves with a strong spatiotemporal variability. Spectral analysis of the internal waves reveals peaks at the diurnal, semidiurnal, inertial, and quarter-diurnal bands, which are only realistically reproduced in the new configuration. Tidally induced pycnocline variability is diagnosed in the model and shown to vary with the spring neap cycle with mean displacement amplitudes in excess of 2 m for 30% of the stratified domain. With sufficiently fine resolution, internal tides are shown to be generated at numerous bathymetric features resulting in a complex pycnocline displacement superposition pattern.

Nested high resolution models for the coastal areas of the North Indian Ocean

NASA Astrophysics Data System (ADS)

Wobus, Fred; Shapiro, Georgy

2017-04-01

Oceanographic processes at coastal scales require much higher horizontal resolution from both ocean models and observations as compared to deep water oceanography. Aside from a few exceptions such as land-locked seas, the hydrodynamics of coastal shallow waters is strongly influenced by the tides, which in turn control the mixing, formation of temperature fronts and other phenomena. The numerical modelling of the coastal domains requires good knowledge of the lateral boundary conditions. The application of lateral boundary conditions to ocean models is a notoriously tricky task, but can only be avoided with global ocean models. Smaller scale regional ocean models are typically nested within global models, and even smaller-scale coastal models may be nested within regional models, creating a nesting chain. However a direct nesting of a very high resolution coastal model into a coarse resolution global model results in degrading of the accuracy of the outputs due to the large difference between the model resolutions. This is why a nesting chain has to be applied, so that every increase in resolution is kept within a reasonable minimum (typically by a factor of 3 to 5 at each step). Global models are traditionally non-tidal, so at some stage of the nesting chain the tides need to be introduced. This is typically done by calculating the tidal constituents from a dedicated tidal model (e.g. TPXO) for all boundary points of a nested model. The tidal elevation at each boundary location can then be calculated from the harmonics at every model time step and the added to the parent model non-tidal SSH. This combination of harmonics-derived tidal SSH and non-tidal parent model SSH is typically applied to the nested domain using the Flather condition, together with the baroclinic velocities from the parent model. The harmonics-derived SSH cannot be added to an SSH signal that is already tidal, so the parent model SSH has to be either detided or taken from a non-tidal model. Due to the lack of effective detiding methods and the prevailing view that harmonics-derived SSH provide a cleaner tidal signal over the SSH taken from a tidal parent model it has traditionally only been the last model in a nesting chain that is tidal. But to our knowledge these assumptions haven't been sufficiently tested and need to be re-visited. Furthermore, the lack of tides in the larger-scale regional models limits their capability and we would like to push for a nesting chain where all regional models (including the intermediate ones) are tidal. In this study we have conducted a number of numerical experiments where we have tested whether a tidal regional model can effectively force a tidal nested model without resorting to detiding techniques and the use of a dedicated tidal model such as TPXO. We have tested whether it's possible to use a tidal parent model and use the total SSH (combined geostrophic SSH and tidal component) to force the child model at the boundary. We call this strategy "tidal nesting" as opposed to TPXO tidal forcing which is used in "traditional nesting". For our experiments we have developed 2 models based on the same NEMO 3.6 codebase. The medium resolution AS20 model covers the Arabian Sea at 1/20 ̊ with 50 layers using a hybrid s-on-top-of-z vertical discretisation scheme (Shapiro et al., 2013); and the high resolution AG60 model covers the Arabian/Persian Gulf at 1/60 ̊ with 50 layers. The AS20 model is "traditionally" nested within the UK Met Office non-tidal large-scale Indian Ocean model at 1/12 ̊ resolution and tidal constituents at the boundary are taken from the TPXO7.2 Global Tidal Solution. Our "tidal nesting" experiments use different forcing frequencies at which the tidal SSH is fed from the larger-scale AS20 into the smaller-scale AG60 model. These strategies are compared with "traditional nesting" where the inner AG60 uses boundary conditions from a non-tidal AS20 parent model and tides are computed from TPXO harmonics. The results reveal an optimal tidal nesting strategy which forces tidal SSH from the parent model at 1-hourly intervals whilst non-tidal parameters are forced at 24-hourly intervals. The analysis includes comparisons with tidal gauges in the Gulf of Oman and inside the Arabian Gulf. The accuracy of tides inside the Gulf is inhibited by the narrow Straits of Hormuz, and tidal nesting doesn't achieve the same level of agreement with observation as traditional nesting. We also found that a further increase in the SSH forcing frequency to 30 minutes does not further improve the results. The forcing at intervals of 1h/24h for tidal/non-tidal parameters shows that a 2-step tidal nesting chain is viable and thus tides can be represented in more than just the last model of a nesting chain. References: Shapiro, G., Luneva, M., Pickering, J., and Storkey, D.: The effect of various vertical discretization schemes and horizontal diffusion parameterization on the performance of a 3-D ocean model: the Black Sea case study, Ocean Sci., 9, 377-390, doi:10.5194/os-9-377-2013, 2013.

Cyclone: java-based querying and computing with Pathway/Genome databases.

PubMed

Le Fèvre, François; Smidtas, Serge; Schächter, Vincent

2007-05-15

Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL). In addition, Cyclone interfaces easily with Java software including the Eclipse IDE for HQL edition, the Jung API for graph algorithms or Cytoscape for graph visualization. Cyclone is freely available under an open source license at: http://sourceforge.net/projects/nemo-cyclone. For download and installation instructions, tutorials, use cases and examples, see http://nemo-cyclone.sourceforge.net.

PORFIDO on the NEMO Phase 2 tower

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ciaffoni, Orlando; Cordelli, Marco; Habel, Roberto

We have designed and built an underwater measurement system, PORFIDO (Physical Oceanography by RFID Outreach) to gather oceanographic data from the Optical Modules of a neutrino telescope with a minimum of disturbance to the main installation. PORFIDO is composed of a sensor glued to the outside of an Optical Module, in contact with seawater, and of a reader placed inside the sphere, facing the sensor. Data are transmitted to the reader through the glass by RFID and to shore in real time for periods of years. The sensor gathers power from the radio frequency, thus eliminating the need for batteriesmore » or connectors through the glass. We have deployed four PORFIDO probes measuring temperatures with the NEMO-KM3Net-Italy Phase 2 tower in april 2013. The four probes are operative and are transmitting temperature data from 3500 m depth.« less

Numerical simulation of inter-annual variations in the properties of the upper mixed layer in the Black Sea over the last 34 years

NASA Astrophysics Data System (ADS)

Shapiro, Georgy I.; Wobus, Fred; Zatsepin, Andrei G.; Akivis, Tatiana M.; Zanacchi, Marcus; Stanichny, Sergey

2014-05-01

The Black Sea is a nearly land-locked basin where a combination of salt and heat budgets results in a unique thermohaline water mass structure. An important feature of the Black Sea is that oxygen is dissolved and rich sea life made possible only in the upper water levels. This is due to a strong pycnocline which cannot be mixed even by strong winds or winter convection (Shapiro, 2008). The upper mixed layer (UML) with a nearly uniform temperature profile and a very sharp seasonal thermocline at its lower boundary develops during the summer season (Sur & Ilyin, 1997). The deepening of the UML has an important effect on the supply of nutrients into the euphotic upper layer from the underlying nutrient-rich water mass. The temperature of the UML at any given location is dependent on the surface heat flux, horizontal advection of heat, the depth and the rate of deepening of the UML. In this study we use a 3D ocean circulation model, NEMO-SHELF (O'Dea et al, 2012) to simulate the parameters of the UML in the Black Sea over the last 34 years. The model has horizontal resolution of 1/12×1/16 degrees and 33 layers in the vertical. The vertical discretization uses a hybrid enveloped s-z grid developed in Shapiro et al. (2012). The model is spun up from climatology (Suvorov et al., 2004); it is forced by the Drakkar Forcing Set v5.2 (Brodeau et al., 2010, Meinvielle et al., 2013) and river discharges from 8 major rivers are included. For each year the model is run from 1st January and the data for the period April to October are used for analysis. The sea surface temperature produced by the model is compared with satellite data ( Modis-Aqua, 2013) to show a good agreement. The model simulations are validated against in-situ observations (BSERP-3, 2004; Piotukh et al., 2011). The analysis is performed for the deep basin where the depth of the sea is greater than 1000m. It clearly shows the inter-annual variations of both the SST and the depth of UML. The depth of UML is calculated using the method by Thomson (1976). It is highly dependent on the meteorological forcing, in particular the wind speed. The correlation between the variations of parameters of UML, the weather patterns, buoyancy fluxes and the kinetic energy of the UML circulation is analysed. This study was supported by EU FP7 PERSEUS and EU FP7 MyOcean2 projects. References BSERP-3. Black Sea Ecosystem Recovery Project. BSERP-3 cruise, May 2004. http://www.research.plymouth.ac.uk/shelf/projects/Black_sea/C_S_BSERP3_final.pdf, 2004. Brodeau, L., B. Barnier, A-M. Treguier, T. Penduff, S. Gulev : An ERA40-based atmospheric forcing for global ocean circulation models, Ocean Modelling, 31, (3-4), 88-104, 2010, http://dx.doi.org/10.1016/j.ocemod.2009.10.005 Meinvielle, M., Brankart, J.-M., Brasseur, P., Barnier, B., Dussin, R., and Verron, J.: Optimal adjustment of the atmospheric forcing parameters of ocean models using sea surface temperature data assimilation, Ocean Sci., 9, 867-883, doi:10.5194/os-9-867-2013, 2013. MODIS-AQUA. http://aqua.nasa.gov/science/images_data.php, 2013. O'Dea, E. J., While, J., Furner, R., Arnold, A., Hyder, P., Storkey, D., Edwards, K.P., Siddorn, J.R., Martin, M.J., Liu, H., Holt, J.T.: An operational ocean forecast system incorporating SST data assimilation for the tidally driven European North-West European shelf. Journal of Operational Oceanography, 5, 3-17, 2012. Piotukh V.B., Zatsepin A.G., Kazmin A.S., Yakubenko V.G.: Impact of the winter cooling on the variability of the thermohaline characteristics of the active layer in the Black Sea. Oceanology, 41, 2, 221-230, 2011 Shapiro, G.I.: Black Sea Circulation. In: Encyclopedia of Ocean Sciences (Second Edition). Eds: J. H. Steele, K. K. Turekian, and S. A. Thorpe. ISBN: 978-0-12-374473-9, P.3519-3532, 2008. Sur, H. I., and Y. P. Ilyin: Evolution of satellite derived mesoscale thermal patterns in the Black Sea, Prog. Oceanogr., 39, 109-151, 1997 Suvorov, A.M., Eremeev, V.N., Belokopytov, V.N., Khaliulin, A.H., Godin, E.A., Ingerov, A.V., Palmer, D.R. and Levitus, S.: Digital Atlas: Physical Oceanography of the Black Sea. (CD-ROM), Environmental Services Data and Information Management Program, Marine Hydrophysical Institute of the National Academy of Sciences of Ukraine, 2004. Thompson, R. O. R. Y.: Climatological numerical models of the surface mixed layer of the ocean, J. Phys. Oceanogr., 6, 496-603, 1976

The Superimposed Deubiquitination Effect of OTULIN and Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Nsp11 Promotes Multiplication of PRRSV.

PubMed

Su, Yanxin; Shi, Peidian; Zhang, Lilin; Lu, Dong; Zhao, Chengxue; Li, Ruiqiao; Zhang, Lei; Huang, Jinhai

2018-05-01

Linear ubiquitination plays an important role in the regulation of the immune response by regulating nuclear factor κB (NF-κB). The linear ubiquitination-specific deubiquitinase ovarian tumor domain deubiquitinase with linear linkage specificity (OTULIN) can control the immune signaling transduction pathway by restricting the Met1-linked ubiquitination process. In our study, the porcine OTLLIN gene was cloned and deubiquitin functions were detected in a porcine reproductive and respiratory syndrome virus (PRRSV)-infected-cell model. PRRSV infection promotes the expression of the OTULIN gene; in turn, overexpression of OTULIN contributes to PRRSV proliferation. There is negative regulation of innate immunity with OTULIN during viral infection. The cooperative effects of swine OTULIN and PRRSV Nsp11 potentiate the ability to reduce levels of cellular protein ubiquitin associated with innate immunity. Importantly, PRRSV Nsp11 recruits OTULIN through a nonenzymatic combination to enhance its ability to remove linear ubiquitination targeting NEMO, resulting in a superimposed effect that inhibits the production of type I interferons (IFNs). Our report presents a new model of virus utilization of the ubiquitin-protease system in vivo from the perspective of the viral proteins that interact with cell deubiquitination enzymes, providing new ideas for prevention and control of PRRSV. IMPORTANCE Deubiquitination effects of swine OTULIN were identified. The interaction between porcine OTULIN and PRRSV Nsp11 is dependent on the OTU domain. PRRSV Nsp11 recruits OTULIN through a nonenzymatic combination to promote removal of linear ubiquitination targeting NEMO, resulting in a superimposed effect that inhibits the production of type I IFNs. Copyright © 2018 American Society for Microbiology.

NEMO: Extraction and normalization of organization names from PubMed affiliations.

PubMed

Jonnalagadda, Siddhartha Reddy; Topham, Philip

2010-10-04

Today, there are more than 18 million articles related to biomedical research indexed in MEDLINE, and information derived from them could be used effectively to save the great amount of time and resources spent by government agencies in understanding the scientific landscape, including key opinion leaders and centers of excellence. Associating biomedical articles with organization names could significantly benefit the pharmaceutical marketing industry, health care funding agencies and public health officials and be useful for other scientists in normalizing author names, automatically creating citations, indexing articles and identifying potential resources or collaborators. Large amount of extracted information helps in disambiguating organization names using machine-learning algorithms. We propose NEMO, a system for extracting organization names in the affiliation and normalizing them to a canonical organization name. Our parsing process involves multi-layered rule matching with multiple dictionaries. The system achieves more than 98% f-score in extracting organization names. Our process of normalization that involves clustering based on local sequence alignment metrics and local learning based on finding connected components. A high precision was also observed in normalization. NEMO is the missing link in associating each biomedical paper and its authors to an organization name in its canonical form and the Geopolitical location of the organization. This research could potentially help in analyzing large social networks of organizations for landscaping a particular topic, improving performance of author disambiguation, adding weak links in the co-author network of authors, augmenting NLM's MARS system for correcting errors in OCR output of affiliation field, and automatically indexing the PubMed citations with the normalized organization name and country. Our system is available as a graphical user interface available for download along with this paper.

Nailfold videocapillaroscopy micro-haemorrhage and giant capillary counting as an accurate approach for a steady state definition of disease activity in systemic sclerosis.

PubMed

Sambataro, Domenico; Sambataro, Gianluca; Zaccara, Eleonora; Maglione, Wanda; Polosa, Riccardo; Afeltra, Antonella M V; Vitali, Claudio; Del Papa, Nicoletta

2014-10-09

Nailfold videocapillaroscopy (NVC) in systemic sclerosis (SSc) is a procedure commonly used for patient classification and subsetting, but not to define disease activity (DA). This study aimed to evaluate whether the number of micro-haemorrhages (MHE), micro-thrombosis (MT), giant capillaries (GC), and normal/dilated capillaries (Cs) in NVC could predict DA in SSc. Eight-finger NVC was performed in 107 patients with SSc, and the total number of MHE/MT, GC, and the mean number of Cs were counted and defined as number of micro-haemorrhages (NEMO), GC and Cs scores, respectively. The European Scleroderma Study Group (ESSG) index constituted the gold standard for DA assessment, and scores ≥ 3.5 and = 3 were considered indicative of high and moderate activity, respectively. NEMO and GC scores were positively correlated with ESSG index (R = 0.65, P < 0.0001, and R = 0.47, P <0.0001, respectively), whilst Cs score showed a negative correlation with that DA index (R = -0.30, P <0.001). The area under the curve (AUC) of receiver operating characteristic plots, obtained by NEMO score sensitivity and specificity values in classifying patients with ESSG index ≥ 3.5, was significantly higher than the corresponding AUC derived from either GC or Cs scores (P <0.03 and P <0.0006, respectively). A modified score, defined by the presence of a given number of MHE/MT and GC, had a good performance in classifying active patients (ESSG index ≥ 3, sensitivity 95.1%, specificity 84.8%, accuracy 88.7%). MHE/MT and GC appear to be good indicators of DA in SSc, and enhances the role of NVC as an easy technique to identify active patients.

Assessing activity of Hepatitis A virus 3C protease using a cyclized luciferase-based biosensor.

PubMed

Zhou, Junwei; Wang, Dang; Xi, Yongqiang; Zhu, Xinyu; Yang, Yuting; Lv, Mengting; Luo, Chuanzhen; Chen, Jiyao; Ye, Xu; Fang, Liurong; Xiao, Shaobo

2017-07-08

Hepatitis A is an acute infection caused by Hepatitis A virus (HAV), which is widely distributed throughout the world. The HAV 3C cysteine protease (3C pro ), an important nonstructural protein, is responsible for most cleavage within the viral polyprotein and is critical for the processes of viral replication. Our group has previously demonstrated that HAV 3C pro cleaves human NF-κB essential modulator (NEMO), a kinase required in interferon signaling. Based on this finding, we generated four luciferase-based biosensors containing the NEMO sequence (PVLKAQ↓ADIYKA) that is cleaved by HAV 3C pro and/or the Nostoc punctiforme DnaE intein, to monitor the activity of HAV 3C pro in human embryonic kidney cells (HEK-293T). Western blotting showed that HAV 3C pro recognized and cleaved the NEMO cleavage sequence incorporated in the four biosensors, whereas only one cyclized luciferase-based biosensor (233-DnaE-HAV, 233DH) showed a measurable and reliable increase in firefly luciferase activity, with very low background, in the presence of HAV 3C pro . With this biosensor (233DH), we monitored HAV 3C pro activity in HEK-293T cells, and tested it against a catalytically deficient mutant HAV 3C pro and other virus-encoded proteases. The results showed that the activity of this luciferase biosensor is specifically dependent on HAV 3C pro . Collectively, our data demonstrate that the luciferase biosensor developed here might provide a rapid, sensitive, and efficient evaluation of HAV 3C pro activity, and should extend our better understanding of the biological relevance of HAV 3C pro . Copyright © 2017 Elsevier Inc. All rights reserved.

2013 Mt. Etna Pyroclastic Activity through the ADCP Recordings of NEMO-SN1 Multidisciplinary Seafloor Observatory

NASA Astrophysics Data System (ADS)

Lo Bue, N.; Sgroi, T.; Giovinetti, G.; Marinaro, G.; Favali, P.

2014-12-01

The Acoustic Doppler Current Profiler (ADCP) is one of the most useful sensor used to measure speed and direction of sea currents in the water column. More often ADCPs are being also used to monitor concentration of suspended matter in rivers or in marine environments by the analysis of the acoustic backscatter intensity. In the framework of the European Research Infrastructure EMSO (European Multidisciplinary Seafloor and water-column Observatory, www.emso-eu.org), its cabled node, the NEMO-SN1 multidisciplinary seafloor observatory, was deployed in the Western Ionian Sea (Southern Italy) at a depth of 2100 m, about 25 km off-shore Eastern Sicily close to the submarine slope of the Mt. Etna volcano. Starting from February 2013, the Mt. Etna was interested by thirteen different parossistic events producing intense eruption followed by pyroclastic fallout that reached distances of tens kilometres from the eruptive centre. Four of these events affected the ESE sector with a consequent fallout in the Western Ionian Sea and they were detected by NEMO-SN1. In fact, its scientific payload also included an ADCP (RDI WorkHorse 600 kHz) with the main aim to monitor the hydrodynamic conditions of about 30 metres of the water column above the station. Surprisingly, this sensor offered spectacular recordings of the Mt. Etna pyroclastic activity occurred on 2013 wich affected the ESE sector. This work aims to present new records of pyroclastic fallout associated to explosive events observed at sea bottom by the analysis of backscatter signal of the ADCP. A multidisciplinary approach taking into account the Mt. Etna eruptive activity as well as the local oceanographic dynamic is necessary to describe marine processes involved in volcanic ash sedimentation.

Inorganic carbon fluxes on the Mackenzie Shelf of the Beaufort Sea

NASA Astrophysics Data System (ADS)

Mol, Jacoba; Thomas, Helmuth; Myers, Paul G.; Hu, Xianmin; Mucci, Alfonso

2018-02-01

The Mackenzie Shelf in the southeastern Beaufort Sea is a region that has experienced large changes in the past several decades as warming, sea-ice loss, and increased river discharge have altered carbon cycling. Upwelling and downwelling events are common on the shelf, caused by strong, fluctuating along-shore winds, resulting in cross-shelf Ekman transport, and an alternating estuarine and anti-estuarine circulation. Downwelling carries dissolved inorganic carbon (DIC) and other remineralization products off the shelf and into the deep basin for possible long-term storage in the world's oceans. Upwelling carries DIC and nutrient-rich waters from the Pacific-origin upper halocline layer (UHL) onto the shelf. Profiles of DIC and total alkalinity (TA) taken in August and September of 2014 are used to investigate the cycling of carbon on the Mackenzie Shelf. The along-shore transport of water and the cross-shelf transport of DIC are quantified using velocity field output from a simulation of the Arctic and Northern Hemisphere Atlantic (ANHA4) configuration of the Nucleus of European Modelling of the Ocean (NEMO) framework. A strong upwelling event prior to sampling on the Mackenzie Shelf took place, bringing CO2-rich (elevated pCO2) water from the UHL onto the shelf bottom. The maximum on-shelf DIC flux was estimated at 16.9×103 mol C d-1 m-2 during the event. The maximum on-shelf transport of DIC through the upwelling event was found to be 65±15×10-3 Tg C d-1. TA and the oxygen isotope ratio of water (δ18O-H2O) are used to examine water-mass distributions in the study area and to investigate the influence of Pacific Water, Mackenzie River freshwater, and sea-ice melt on carbon dynamics and air-sea fluxes of carbon dioxide (CO2) in the surface mixed layer. Understanding carbon transfer in this seasonally dynamic environment is key to quantify the importance of Arctic shelf regions to the global carbon cycle and provide a basis for understanding how it will respond to the aforementioned climate-induced changes.

Usage of satellite data SMOS in order to characterize Sea Surface Salinity in the western Mediterranean

NASA Astrophysics Data System (ADS)

Brook, Anna; Robins, Lotem; Olmedo Casal, Estrella

2017-04-01

Measuring the level of Sea Surface Salinity (SSS) is a principle component in order to understand climate processes that occur today and for better understanding of climate change in the future; Different processes create different salt concentration in different places in the oceans. This different salinity level had a role in determining the vertical and horizontal water fluxes. As the first three meters of the ocean surface contain more heat than that in the whole atmosphere, the influence of the salinity level on the layering of the different water levels and the different fluxes, thus, it is an important factor determining air sea interaction. An existing problem in predicting the oceans is the lack of salinity samples in the oceans. While Sea surface Temperature (SST) could be evaluated easier from remote sensed devices, analyzing data at the Near Infra-Red and Visual wavelength. Measuring and locating salinity spectral signature was an obstacle. This lack of data caused problems running different models that describe different parameters of the ocean, both in depth and surface. One of the main goals of a program called: Soil Moisture and Ocean Salinity (SMOS), is to deliver data on a global scale concerning the sea surface salinity (SSS). The main idea of the SMOS technology is based on the differences between the electro-magnetic properties (spectral signatures) of distilled water and salted water. High concentration of salt revealed by analyzing the energy emitted from the ocean's surface, using detectors that are sensitive for the wavelength at the range of 21 cm (L-band: 1.4 GHz). One of the main problems, measuring this wavelength, is that it requires very large antennas. In order to solve this problem, a Y shaped satellite was built, on each of its arms, 69 antennas were attached, with equal distances between each antenna. Each antenna is 165 mm on the diameter and their height is 19 mm. This antenna transmits all the information they receive to a central device. By using interferometry and a matching algorithm between the signals of each possible couple of antennas, synthesis of all the antennas is preformed, which makes it possible to overcome the problem of using large antennas. The SMOS satellite delivers data at accuracy of 0.1psu, with spatial resolution of 200 km. The data is available in different forms, starting from unprocessed data to final products of brightness temperature that are temporally and spatially synchronized (L2 level). By downscaling those products, models of spatial resolution of 25 km and temporal daily resolution are calculated. The meaning of this long process is that the data is going through long process before arriving to scientific analysis. The process from raw data until L2 level involves radiometric and physical corrections, detection and exclusion of atmospheric disturbance, geographical anchor etc. In order to check the possible usage of the processed data of SMOS in the Mediterranean, a simple comparison was held between SMOS and MEDRYS1V2 - reanalysis of the Mediterranean sea during the years 1992-2013, which is based on the oceanic model of NEMO12, and forced by the atmospheric model of ALDERA. While doing this comparison, it is important to remember that the goal of the SMOS program is to deliver data in a global scale, while MEDRYS1V2 was created especially for the Mediterranean. From the comparison of the two data sets, it is possible to detect to main issues: The first issue is that it seems that the SMOS satellite uses more linear interpolation, to describe the space, while the reanalysis is based on the primitive physical equations and data assimilation. The second issue is a large anomaly that occurs probably due to the river spill, which is getting a different signature, as the low resolution of SMOS might be a problem detecting correctly the spill, without another local data source. To conclude, the SMOS program which one of its main goals is to create a reliable data source of SSS, on a global scale, has an important role for understanding oceanic process and climate change patterns. While the global goal is contributing for research and development, on a more local scale it is possible to observe that analyzation of the Mediterranean, that mainly being held in high spatial resolution is not represented well using SMOS products. The main reason is the low spatial resolution, of the satellite, but owing to its unique technology, different methods could be applied, to better represent smaller scaled research.

The CMEMS IBI-MFC Forecasting Service in 2017: Evolution and Novelties associated to the CMEMS service release

NASA Astrophysics Data System (ADS)

Lorente, Pablo; Sotillo, Marcos G.; Gutknecht, Elodie; Dabrowski, Tomasz; Aouf, Lotfi; Toledano, Cristina; Amo-Baladron, Arancha; Aznar, Roland; De Pascual, Alvaro; Levier, Bruno; Bowyer, Peter; Rainaud, Romain; Alvarez-Fanjul, Enrique

2017-04-01

The IBI-MFC (Iberia-Biscay-Ireland Monitoring & Forecasting Centre) has been providing daily ocean model estimates and forecasts of diverse physical parameters for the IBI regional seas since 2011, first in the frame of MyOcean projects and later as part of the Copernicus Marine Environment Monitoring Service (CMEMS). By April 2017, coincident with the V3 CMEMS Service Release, the IBI-MFC will extend their near real time (NRT) forecast capabilities. Two new operational IBI forecast systems will be operationally run to generate high resolution biochemical (BIO) and wave (WAV) products on the IBI area. The IBI-NRT-BIO forecast system, based on a 1/36° NEMO-PISCES model application, is run once a week coupled with the IBI physical forecast solution and nested to the CMEMS GLOBAL-BIO solution. On the other hand, the IBI-NRT-WAV system, based on a MeteoFrance-WAM 10km resolution model application, runs twice a day using ECMWF wind forcing. Among other novelties related to the evolution of the IBI physical (PHY) solution, it is worthwhile mentioning the provision, as part of the IBI-NRT-PHY product daily updated, of three-dimensional hourly data on specific areas within the IBI domain. The delivery of these new hourly data along the whole water column has been achieved after the request from IBI users, in order to foster downscaling approaches by providing coherent open boundary conditions to any potential high-resolution coastal model nested to IBI regional solution. An extensive skill assessment of IBI-NRT forecast products has been conducted through the NARVAL (North Atlantic Regional VALidation) web tool, by means of the automatic computation of statistical metrics and quality indicators. By now, this tool has been focused on the validation of the IBI-NRT-PHY system. Nowadays, NARVAL is facing a significant upgrade to validate the aforementioned new biogeochemical and wave IBI products. To this aim, satellite derived observations of chlorophyll and significant wave height will be used, together with in-situ wave parameters measured by mooring buoys. Within this validation framework, special emphasis has been placed on the intercomparison of different forecast model solutions in overlapping areas in order to evaluate models' performances and prognostic capabilities. This common uncertainty estimates of IBI and other model solution is currently performed by NARVAL using both CMEMS forecast model sources (i.e. GLOBAL-MFC, MED-MFC and NWS-MFC) and non-CMEMS operational forecast solutions (mostly downstream application nested to the IBI solution). With respect to the IBI multi-year (MY) products, it is worth mentioning that the actual biogeochemical and physical reanalysis products will be re-run along year 2017, extending its time coverage backwards until 1992. Based on these IBI-MY products, a variety of climatic indicators related to essential oceanographic processes (i.e. western coastal upwelling or the Mediterranean Outflow Water) are currently being computed.

NEMO Binding Domain peptide inhibits constitutive NF-κB activity and reduces tumor burden in a canine model of relapsed, refractory Diffuse Large B-Cell Lymphoma

PubMed Central

Gaurnier-Hausser, Anita; Patel, Reema; Baldwin, Albert S.; May, Michael J.; Mason, Nicola J.

2011-01-01

Purpose Activated B-Cell Diffuse Large B-Cell Lymphoma (ABC-DLBCL) is an aggressive, poorly chemoresponsive lymphoid malignancy characterized by constitutive canonical NF-κB activity that promotes lymphomagenesis and chemotherapy resistance via over-expression of anti-apoptotic NF-κB target genes. Inhibition of the canonical NF-κB pathway may therefore have therapeutic relevance in ABC-DLBCL. Here we set out to determine whether dogs with spontaneous DLBCL have comparative aberrant constitutive NF-κB activity and to determine the therapeutic relevance of NF-κB inhibition in dogs with relapsed, resistant DLBCL. Experimental Design Canonical NF-κB activity was evaluated by electrophoretic mobility shift assays and immunoblot analyses, and NF-κB target gene expression was measured by qRT-PCR. Primary malignant canine B lymphocytes were treated with the selective IKK complex inhibitor Nemo Binding Domain (NBD) peptide, and evaluated for NF-κB activity and apoptosis. NBD peptide was administered intra-nodally to dogs with relapsed B-cell lymphoma and NF-κB target gene expression and tumor burden were evaluated pre and post treatment. Results Constitutive canonical NF-κB activity and increased NF-κB target gene expression was detected in primary DLBCL tissue. NBD peptide inhibited this activity and induced apoptosis of primary malignant B cells in vitro. Intra-tumoral injections of NBD peptide to dogs with relapsed DLBCL inhibited NF-κB target gene expression and reduced tumor burden. Conclusions This work shows that dogs with spontaneous DLBCL represent a clinically relevant, spontaneous, large animal model for human ABC-DLBCL and demonstrates the therapeutic relevance of NF-κB inhibition in the treatment of ABC-DLBCL. These results have important translational relevance for ABC-DLBCL treatment in human patients. PMID:21610150

Data transmission and acquisition in NEMO

NASA Astrophysics Data System (ADS)

Bunkheila, G.

2006-11-01

A comprehensive system for data transmission and acquisition has been developed for an "à la NEMO" underwater neutrino telescope based on Čerenkov light detection using photomultipliers (PMTs) as sensors. Signals generated by each sensor are triggered, sampled and tagged by an electronics board, called Front End Module (FEM). Data streams from up to eight FEMs located on one tower floor are collected by a concentration board called Floor Control Module (FCM) and sent to a twin FCM board—located at the onshore station and plugged into an interface machine (FCM Interface, or FCMI) via a PCI bus—through a DWDM-compliant optical fiber and using a self-synchronous serial protocol. All sensor data reach the onshore lab through FCMI where they are made available to subsequent elaboration processes, such as time-wise alignment and muon track event-triggering. To meet requirements of the latter, onshore data unpacking is carried out with respect to their topological origin. The system promised, and keeps on showing, very light charges on power consumption and infrastructure complexity, while having recently proved to behave at high performance levels in its optical part.

Minimal Information for Neural Electromagnetic Ontologies (MINEMO): A standards-compliant method for analysis and integration of event-related potentials (ERP) data

PubMed Central

Frishkoff, Gwen; Sydes, Jason; Mueller, Kurt; Frank, Robert; Curran, Tim; Connolly, John; Kilborn, Kerry; Molfese, Dennis; Perfetti, Charles; Malony, Allen

2011-01-01

We present MINEMO (Minimal Information for Neural ElectroMagnetic Ontologies), a checklist for the description of event-related potentials (ERP) studies. MINEMO extends MINI (Minimal Information for Neuroscience Investigations)to the ERP domain. Checklist terms are explicated in NEMO, a formal ontology that is designed to support ERP data sharing and integration. MINEMO is also linked to an ERP database and web application (the NEMO portal). Users upload their data and enter MINEMO information through the portal. The database then stores these entries in RDF (Resource Description Framework), along with summary metrics, i.e., spatial and temporal metadata. Together these spatial, temporal, and functional metadata provide a complete description of ERP data and the context in which these data were acquired. The RDF files then serve as inputs to ontology-based labeling and meta-analysis. Our ultimate goal is to represent ERPs using a rich semantic structure, so results can be queried at multiple levels, to stimulate novel hypotheses and to promote a high-level, integrative account of ERP results across diverse study methods and paradigms. PMID:22180824

The Scaffold Protein TANK/I-TRAF Inhibits NF-κB Activation by Recruiting Polo-like Kinase 1

PubMed Central

Zhang, Wanqiao; Zhang, Ying; Yuan, Yanzhi; Guan, Wei; Jin, Chaozhi; Chen, Hui; Wang, Xiaohui

2010-01-01

TANK/I-TRAF is a TRAF-binding protein that negatively regulates NF-κB activation. The underlying mechanism of this activity remains unclear. Here we show that TANK directly interacts with PLK1, a conserved cell cycle–regulated kinase. PLK1 inhibits NF-κB transcriptional activation induced by TNF-α, IL-1β, or several activators, but not by nuclear transcription factor p65. PLK1 expression reduces the DNA-binding activity of NF-κB induced by TNF-α. Moreover, endogenous activation of PLK1 reduces the TNF-induced phosphorylation of endogenous IκBα. PLK1 is bound to NEMO (IKKγ) through TANK to form a ternary complex in vivo. We describe a new regulatory mechanism for PLK1: PLK1 negatively regulates TNF-induced IKK activation by inhibiting the ubiquitination of NEMO. These findings reveal that the scaffold protein TANK recruits PLK1 to negatively regulate NF-κB activation and provide direct evidence that PLK1 is required for the repression function of TANK. PMID:20484576

Measurement of the double-{beta} decay half-life of {sup 150}Nd and search for neutrinoless decay modes with the NEMO-3 detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Argyriades, J.; Augier, C.; Bongrand, M.

2009-09-15

The half-life for double-{beta} decay of {sup 150}Nd has been measured by the NEMO-3 experiment at the Modane Underground Laboratory. Using 924.7 days of data recorded with 36.55 g of {sup 150}Nd, we measured the half-life for 2{nu}{beta}{beta} decay to be T{sub 1/2}{sup 2{nu}}=(9.11{sub -0.22}{sup +0.25}(stat.){+-}0.63(syst.))x10{sup 18} yr. The observed limit on the half-life for neutrinoless double-{beta} decay is found to be T{sub 1/2}{sup 0{nu}}>1.8x10{sup 22} yr at 90% confidence level. This translates into a limit on the effective Majorana neutrino mass of <4.0-6.3 eV if the nuclear deformation is taken into account. We also set limits on modelsmore » involving Majoron emission, right-handed currents, and transitions to excited states.« less

Radon emanation based material measurement and selection for the SuperNEMO double beta experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cerna, Cédric, E-mail: cerna@cenbg.in2p3.fr; Soulé, Benjamin; Perrot, Frédéric

The SuperNEMO Demonstrator experiment aims to study the neutrinoless double beta decay of 7 kg of {sup 82}Se in order to reach a limit on the light Majorana neutrino mass mechanism T{sub 1/2} (ββ0ν) > 6.5 10{sup 24} years (90%CL) equivalent to a mass sensitivity mβ{sub β} < 0.20 - 0.40 eV (90%CL) in two years of data taking. The detector construction started in 2014 and its installation in the Laboratoire Souterrain de Modane (LSM) is expected during the course of 2015. The remaining level of {sup 226}Ra ({sup 238}U chain) in the detector components can lead to the emanationmore » of {sup 222}Rn gas. This isotope should be controlled and reduced down to the level of a 150 µBq/m{sup 3} in the tracker chamber of the detector to achieve the physics goals. Besides the HPGe selection of the detector materials for their radiopurity, the most critical materials have been tested and selected in a dedicated setup facility able to measure their {sup 222}Rn emanation level. The operating principle relies on a large emanation tank (0.7m{sup 3}) that allows measuring large material surfaces or large number of construction pieces. The emanation tank is coupled to an electrostatic detector equipped with a silicon diode to perform the alpha spectroscopy of the gas it contains and extract the {sup 222}Rn daughters. The transfer efficiency and the detector efficiency have been carefully calibrated through different methods. The intrinsic background of the system allows one to measure 222Rn activities down to 3 mBq, leading to a typical emanation sensitivity of 20 µBq/m{sup 2}/day for a 30 m{sup 2} surface sample. Several construction materials have been measured and selected, such as nylon and aluminized Mylar films, photomultipliers and tracking of the SuperNEMO Demonstrator.« less

Nemo-like kinase (NLK) expression in osteoblastic cells and suppression of osteoblastic differentiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nifuji, Akira, E-mail: nifuji-a@tsurumi-u.ac.jp; Department of Pharmacology, Tsurumi University School of Dental Medicine, Yokohama; Ideno, Hisashi

2010-04-15

Mitogen-activated protein kinases (MAPKs) regulate proliferation and differentiation in osteoblasts. The vertebral homologue of nemo, nemo-like kinase (NLK), is an atypical MAPK that targets several signaling components, including the T-cell factor/lymphoid enhancer factor (TCF/Lef1) transcription factor. Recent studies have shown that NLK forms a complex with the histone H3-K9 methyltransferase SETDB1 and suppresses peroxisome proliferator-activated receptor (PPAR)-gamma:: action in the mesenchymal cell line ST2. Here we investigated whether NLK regulates osteoblastic differentiation. We showed that NLK mRNA is expressed in vivo in osteoblasts at embryonic day 18.5 (E18.5) mouse calvariae. By using retrovirus vectors, we performed forced expression of NLKmore » in primary calvarial osteoblasts (pOB cells) and the mesenchymal cell line ST2. Wild-type NLK (NLK-WT) suppressed alkaline phosphatase activity and expression of bone marker genes such as alkaline phosphatase, type I procollagen, runx2, osterix, steopontin and osteocalcin in these cells. NLK-WT also decreased type I collagen protein expression in pOB and ST2 cells. Furthermore, mineralized nodule formation was reduced in pOB cells overexpressing NLK-WT. In contrast, kinase-negative form of NLK (NLK-KN) did not suppress or partially suppress ALP activity and bone marker gene expression in pOB and ST2 cells. NLK-KN did not suppress nodule formation in pOB cells. In addition to forced expression, suppression of endogenous NLK expression by siRNA increased bone marker gene expression in pOB and ST2 cells. Finally, transcriptional activity analysis of gene promoters revealed that NLK-WT suppressed Wnt1 activation of TOP flash promoter and Runx2 activation of the osteocalcin promoter. Taken together, these results suggest that NLK negatively regulates osteoblastic differentiation.« less

Incontinentia pigmenti: learning disabilities are a fundamental hallmark of the disease.

PubMed

Pizzamiglio, Maria Rosa; Piccardi, Laura; Bianchini, Filippo; Canzano, Loredana; Palermo, Liana; Fusco, Francesca; D'Antuono, Giovanni; Gelmini, Chiara; Garavelli, Livia; Ursini, Matilde Valeria

2014-01-01

Studies suggest that genetic factors are associated with the etiology of learning disabilities. Incontinentia Pigmenti (IP, OMIM#308300), which is caused by mutations of the IKBKG/NEMO gene, is a rare X-linked genomic disorder (1:10000/20:000) that affects the neuroectodermal tissues. It always affects the skin and sometimes the hair, teeth, nails, eyes and central nervous system (CNS). Data from IP patients demonstrate the heterogeneity of the clinical phenotype; about 30% have CNS manifestations. This extreme variability suggests that IP patients might also have learning disabilities. However, no studies in the literature have evaluated the cognitive profile of IP patients. In fact, the learning disability may go unnoticed in general neurological analyses, which focus on major disabling manifestations of the CNS. Here, we investigated the neuropsychological outcomes of a selected group of IP-patients by focusing on learning disabilities. We enrolled 10 women with IP (7 without mental retardation and 3 with mild to severe mental retardation) whose clinical diagnosis had been confirmed by the presence of a recurrent deletion in the IKBKG/NEMO gene. The participants were recruited from the Italian patients' association (I.P.A.SS.I. Onlus). They were submitted to a cognitive assessment that included the Wechsler Adult Intelligence scale and a battery of tests examining reading, arithmetic and writing skills. We found that 7 patients had deficits in calculation/arithmetic reasoning and reading but not writing skills; the remaining 3 had severe to mild intellectual disabilities. Results of this comprehensive evaluation of the molecular and psychoneurological aspects of IP make it possible to place "learning disabilities" among the CNS manifestations of the disease and suggest that the IKBKG/NEMO gene is a genetic determinant of this CNS defect. Our findings indicate the importance of an appropriate psychoneurological evaluation of IP patients, which includes early assessment of learning abilities, to prevent the onset of this deficit.

Thermodynamic and dynamic ice thickness contributions in the Canadian Arctic Archipelago in NEMO-LIM2 numerical simulations

NASA Astrophysics Data System (ADS)

Hu, Xianmin; Sun, Jingfan; Chan, Ting On; Myers, Paul G.

2018-04-01

Sea ice thickness evolution within the Canadian Arctic Archipelago (CAA) is of great interest to science, as well as local communities and their economy. In this study, based on the NEMO numerical framework including the LIM2 sea ice module, simulations at both 1/4 and 1/12° horizontal resolution were conducted from 2002 to 2016. The model captures well the general spatial distribution of ice thickness in the CAA region, with very thick sea ice (˜ 4 m and thicker) in the northern CAA, thick sea ice (2.5 to 3 m) in the west-central Parry Channel and M'Clintock Channel, and thin ( < 2 m) ice (in winter months) on the east side of CAA (e.g., eastern Parry Channel, Baffin Island coast) and in the channels in southern areas. Even though the configurations still have resolution limitations in resolving the exact observation sites, simulated ice thickness compares reasonably (seasonal cycle and amplitudes) with weekly Environment and Climate Change Canada (ECCC) New Ice Thickness Program data at first-year landfast ice sites except at the northern sites with high concentration of old ice. At 1/4 to 1/12° scale, model resolution does not play a significant role in the sea ice simulation except to improve local dynamics because of better coastline representation. Sea ice growth is decomposed into thermodynamic and dynamic (including all non-thermodynamic processes in the model) contributions to study the ice thickness evolution. Relatively smaller thermodynamic contribution to ice growth between December and the following April is found in the thick and very thick ice regions, with larger contributions in the thin ice-covered region. No significant trend in winter maximum ice volume is found in the northern CAA and Baffin Bay while a decline (r2 ≈ 0.6, p < 0.01) is simulated in Parry Channel region. The two main contributors (thermodynamic growth and lateral transport) have high interannual variabilities which largely balance each other, so that maximum ice volume can vary interannually by ±12 % in the northern CAA, ±15 % in Parry Channel, and ±9 % in Baffin Bay. Further quantitative evaluation is required.

75 FR 25268 - Submission for OMB Review; Comment Request; REDS-II-Does Pre-Donation Behavioral Deferral...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

... on sexual behavior deferrals and their impact on blood safety. The two main study aims are: (1) To assess infectious disease marker prevalence in donors who are deferred for higher risk sexual and non.... George Nemo, Project Officer, NHLBI, Two Rockledge Center, Suite 10042, 6701 Rockledge Drive, Bethesda...

Variability of the volume and thickness of sea ice in the Bay of Bothnia

NASA Astrophysics Data System (ADS)

Ronkainen, Iina; Lehtiranta, Jonni; Lensu, Mikko; Rinne, Eero; Hordoir, Robinson; Haapala, Jari

2017-04-01

Variability of the volume and thickness of sea ice in the Bay of Bothnia In our study, we want to quantify the variability of sea ice volume and thickness in the Bay of Bothnia and to introduce the drivers of the observed variability. There has been similar studies, but only for fast ice. We use various different data sets: in-situ ice thickness data, remote sensing data, model data and ice charts. In-situ data is from the regular monitoring stations in the coastal fast ice zone and from field campaigns. The remote sensing data is helicopter-borne and ship-borne electromagnetic data. The models we use are HELMI and NEMO-Nordic. We analyze the different data sets and compare them to each other to solve the inter-annual variability and to discuss the ratio of level and deformed ice.

Propagation of uncertainties through the oil spill model MEDSLIK-II: operational application to the Black Sea

NASA Astrophysics Data System (ADS)

Liubartseva, Svitlana; Coppini, Giovanni; Ciliberti, Stefania Angela; Lecci, Rita

2017-04-01

In operational oil spill modeling, MEDSLIK-II (De Dominicis et al., 2013) focuses on the reliability of the oil drift and fate predictions routinely fed by operational oceanographic and atmospheric forecasting chain. Uncertainty calculations enhance oil spill forecast efficiency, supplying probability maps to quantify the propagation of various uncertainties. Recently, we have developed the methodology that allows users to evaluate the variability of oil drift forecast caused by uncertain data on the initial oil spill conditions (Liubartseva et al., 2016). One of the key methodological aspects is a reasonable choice of a way of parameter perturbation. In case of starting oil spill location and time, these scalars might be treated as independent random parameters. If we want to perturb the underlying ocean currents and wind, we have to deal with deterministic vector parameters. To a first approximation, we suggest rolling forecasts as a set of perturbed ocean currents and wind. This approach does not need any extra hydrodynamic calculations, and it is quick enough to be performed in web-based applications. The capabilities of the proposed methodology are explored using the Black Sea Forecasting System (BSFS) recently implemented by Ciliberti et al. (2016) for the Copernicus Marine Environment Monitoring Service (http://marine.copernicus.eu/services-portfolio/access-to-products). BSFS horizontal resolution is 1/36° in zonal and 1/27° in meridional direction (ca. 3 km). Vertical domain discretization is represented by 31 unevenly spaced vertical levels. Atmospheric wind data are provided by the European Centre for Medium-Range Weather Forecasts (ECMWF) forecasts, at 1/8° (ca. 12.5 km) horizontal and 6-hour temporal resolution. A great variety of probability patterns controlled by different underlying flows is represented including the cyclonic Rim Current, flow bifurcations in anticyclonic eddies (e.g., Sevastopol and Batumi), northwestern shelf circulation, etc. Uncertainty imprints in the oil mass balance components are also analyzed. This work is conducted in the framework of the REACT Project funded by Fondazione CON IL SUD/Brains2South. References Ciliberti, S.A., Peneva, E., Storto, A., Kandilarov, R., Lecci, R., Yang, C., Coppini, G., Masina, S., Pinardi, N., 2016. Implementation of Black Sea numerical model based on NEMO and 3DVAR data assimilation scheme for operational forecasting, Geophys. Res. Abs., 18, EGU2016-16222. De Dominicis, M., Pinardi, N., Zodiatis, G., Lardner, R., 2013. MEDSLIK-II, a Lagrangian marine surface oil spill model for short term forecasting-Part 1: Theory, Geosci. Model Dev., 6, 1851-1869. Liubartseva, S., Coppini, G., Pinardi, N., De Dominicis, M., Lecci, R., Turrisi, G., Cretì, S., Martinelli, S., Agostini, P., Marra, P., Palermo, F., 2016. Decision support system for emergency management of oil spill accidents in the Mediterranean Sea, Nat. Hazards Earth Syst. Sci., 16, 2009-2020.

The Sea around Us: Social Climbing in "Seabiscuit," "Whale Rider," and "Finding Nemo"

ERIC Educational Resources Information Center

Beck, Bernard

2004-01-01

All life begins in the sea, people are taught, and a great transformation extends it to new places on land. The sea has always echoed this transformation in images of human aspiration in myths and metaphors. In the summer of 2003, this powerful image appeared again in the movies. In three very different films, "Seabiscuit," "Whale Rider," and…

Finding Difference: Nemo and Friends Opening the Door to Disability Theory

ERIC Educational Resources Information Center

Preston, Daniel L.

2010-01-01

While middle school and high school students may have watched the Disney and Disney/Pixar films when they were younger, chances are they did not do so with a critical eye toward difference and disability, despite the fact that these films serve as excellent tools for teaching about difference. Recent estimates label 20% of the world's population…

Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator).

PubMed

Godwin, Ryan C; Melvin, Ryan L; Gmeiner, William H; Salsbury, Freddie R

2017-01-31

Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein structure, dynamics, and ultimately function, as these pivotal regulatory proteins are increasingly important for protein engineering and therapeutic discovery. To better understand the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB essential modulator), as well as the role of zinc, we present results of 20 μs molecular dynamics trajectories, 5 μs for each of four active site configurations. Consistent with experimental evidence, the zinc ion is essential for mechanical stabilization of the functional, folded conformation. Hydrogen bond motifs are unique for deprotonated configurations yet overlap in protonated cases. Correlated motions and principal component analysis corroborate the similarity of the protonated configurations and highlight unique relationships of the zinc-bound configuration. We hypothesize a potential mechanism for zinc binding from results of the thiol configurations. The deprotonated, zinc-bound configuration alone predominantly maintains its tertiary structure throughout all 5 μs and alludes rare conformations potentially important for (im)proper zinc-finger-related protein-protein or protein-DNA interactions.

SENP1-mediated NEMO deSUMOylation in adipocytes limits inflammatory responses and type-1 diabetes progression

PubMed Central

Shao, Lan; Zhou, Huanjiao Jenny; Zhang, Haifeng; Qin, Lingfeng; Hwa, John; Yun, Zhong; Ji, Weidong; Min, Wang

2015-01-01

Adipocyte dysfunction correlates with the development of diabetes. Here we show that mice with a adipocyte-specific deletion of the SUMO-specific protease SENP1 gene develop symptoms of type-1 diabetes mellitus (T1DM), including hyperglycaemia and glucose intolerance with mild insulin resistance. Peri-pancreatic adipocytes from SENP1-deficient mice exhibit heightened NF-κB activity and production of proinflammatory cytokines, which induce CCL5 expression in adjacent pancreatic islets and direct cytotoxic effects on pancreatic islets. Mechanistic studies show that SENP1 deletion in adipocytes enhances SUMOylation of the NF-κB essential molecule, NEMO, at lysine 277/309, leading to increased NF-κB activity, cytokine production and pancreatic inflammation. We further show that NF-κB inhibitors could inhibit pre-diabetic cytokine production, β-cell damages and ameliorate the T1DM phenotype in SENP1-deficient mice. Feeding a high-fat diet augments both type-1 and type-2 diabetes phenotypes in SENP1-deficient mice, consistent with the effects on adipocyte-derived NF-κB and cytokine signalling. Our study reveals previously unrecognized mechanism regulating the onset and progression of T1DM associated with adipocyte dysfunction. PMID:26596471

SENP1-mediated NEMO deSUMOylation in adipocytes limits inflammatory responses and type-1 diabetes progression.

PubMed

Shao, Lan; Zhou, Huanjiao Jenny; Zhang, Haifeng; Qin, Lingfeng; Hwa, John; Yun, Zhong; Ji, Weidong; Min, Wang

2015-11-24

Adipocyte dysfunction correlates with the development of diabetes. Here we show that mice with a adipocyte-specific deletion of the SUMO-specific protease SENP1 gene develop symptoms of type-1 diabetes mellitus (T1DM), including hyperglycaemia and glucose intolerance with mild insulin resistance. Peri-pancreatic adipocytes from SENP1-deficient mice exhibit heightened NF-κB activity and production of proinflammatory cytokines, which induce CCL5 expression in adjacent pancreatic islets and direct cytotoxic effects on pancreatic islets. Mechanistic studies show that SENP1 deletion in adipocytes enhances SUMOylation of the NF-κB essential molecule, NEMO, at lysine 277/309, leading to increased NF-κB activity, cytokine production and pancreatic inflammation. We further show that NF-κB inhibitors could inhibit pre-diabetic cytokine production, β-cell damages and ameliorate the T1DM phenotype in SENP1-deficient mice. Feeding a high-fat diet augments both type-1 and type-2 diabetes phenotypes in SENP1-deficient mice, consistent with the effects on adipocyte-derived NF-κB and cytokine signalling. Our study reveals previously unrecognized mechanism regulating the onset and progression of T1DM associated with adipocyte dysfunction.

The Leading Edge of the Galapagos Hotspot: Geochemistry and Geochronology of Submarine Glasses Coupled to New Sidescan Sonar Imagery

NASA Astrophysics Data System (ADS)

Kurz, M. D.; Fornari, D. J.; Geist, D. J.; Johnson, P. D.; Curtice, J. M.; Lott, D. E.; Harpp, K.; Saal, A. E.; Peckman, U. G.

2001-12-01

Fernandina, the western-most volcano in the Galapagos archipelago, is at the leading edge of the hotspot with respect to plate motion. Recent mapping of the ocean floor west of Fernandina (on R/V Revelle, using the HMRG towed sidescan sonar MR1, and Simrad EM120 multibeam) provides a dramatic new view of the volcanic constructional processes that have created the islands. The western flank of the volcano is characterized by the prominent Northwest, West, and Southwest rift zones, which are constructed of hummocky pillow lavas. Older lava flow terrain is distinguished by weaker acoustic return, whereas extensive younger flows are characterized by strong backscatter patterns with distinctive flow-like margins. MR1 sidescan sonar mapping provides an important new geologic and stratigraphic context for understanding the submarine Galapagos platform, particularly from a geochemical perspective. Fernandina lavas have high 3He/4He ratios, up to 29 times atmospheric, and solar-like neon isotopic compositions, characteristics which suggest they are derived from the deep mantle. The high 3He/4He ratios, and rapid eruption rates at Fernandina also indicate that it lies directly above the center of the Galapagos hotspot. In order to place these geochemical data into a chronological framework, we have determined ages for Fernandina submarine glasses using the Th-U-He crushing/melting disequilibrium method. Preliminary Th-U-He ages (from the 2000 R/V Melville AHA-Nemo expedition), combined with the new MR1 sonar mapping, shows that the rift zones are characterized by extremely young ages (0 to 30 Ka) while older submarine lava flows with lower acoustic backscatter have significantly older ages ( ~ 100 Ka). The geochronological data, and the geological context from the side-scan sonar, provide new evidence for volcano growth rates in oceanic hotspot provinces, and will be used to determine the growth rate of the Galapagos platform.

Systemic delivery of NEMO binding domain/IKKγ inhibitory peptide to young mdx mice improves dystrophic skeletal muscle histopathology.

PubMed

Reay, Daniel P; Yang, Michele; Watchko, Jon F; Daood, Molly; O'Day, Terrence L; Rehman, Khaleel K; Guttridge, Denis C; Robbins, Paul D; Clemens, Paula R

2011-09-01

The activation of nuclear factor κB (NF-κB) contributes to muscle degeneration that results from dystrophin deficiency in human Duchenne muscular dystrophy (DMD) and in the mdx mouse. In dystrophic muscle, NF-κB participates in inflammation and failure of muscle regeneration. Peptides containing the NF-κB Essential Modulator (NEMO) binding domain (NBD) disrupt the IκB kinase complex, thus blocking NF-κB activation. The NBD peptide, which is linked to a protein transduction domain to achieve in vivo peptide delivery to muscle tissue, was systemically delivered to mdx mice for 4 or 7 weeks to study NF-κB activation, histological changes in hind limb and diaphragm muscle and ex vivo function of diaphragm muscle. Decreased NF-κB activation, decreased necrosis and increased regeneration were observed in hind limb and diaphragm muscle in mdx mice treated systemically with NBD peptide, as compared to control mdx mice. NBD peptide treatment resulted in improved generation of specific force and greater resistance to lengthening activations in diaphragm muscle ex vivo. Together these data support the potential of NBD peptides for the treatment of DMD by modulating dystrophic pathways in muscle that are downstream of dystrophin deficiency. Published by Elsevier Inc.

Design and first tests of an acoustic positioning and detection system for KM3NeT

NASA Astrophysics Data System (ADS)

Simeone, F.; Ameli, F.; Ardid, M.; Bertin, V.; Bonori, M.; Bou-Cabo, M.; Calì, C.; D'Amico, A.; Giovanetti, G.; Imbesi, M.; Keller, P.; Larosa, G.; Llorens, C. D.; Masullo, R.; Randazzo, N.; Riccobene, G.; Speziale, F.; Viola, S.; KM3NeT Consortium

2012-01-01

In a deep-sea neutrino telescope it is mandatory to locate the position of the optical sensors with a precision of about 10 cm. To achieve this requirement, an innovative Acoustic Positioning System (APS) has been designed in the frame work of the KM3NeT neutrino telescope. The system will also be able to provide an acoustic guide during the deployment of the telescope’s components and seafloor infrastructures (junction boxes, cables, etc.). A prototype of the system based on the successful acoustic systems of ANTARES and NEMO is being developed. It will consist of an array of hydrophones and a network of acoustic transceivers forming the Long Baseline. All sensors are connected to the telescope data acquisition system and are in phase and synchronised with the telescope master clock. Data from the acoustic sensors, continuously sampled at 192 kHz, will be sent to shore where signal recognition and analysis will be carried out. The design and first tests of the system elements will be presented. This new APS is expected to have better precision compared to the systems used in ANTARES and NEMO, and can also be used as a real-time monitor of acoustic sources and environmental noise in deep sea.

TNFα- and IKKβ-mediated TANK/I-TRAF phosphorylation: implications for interaction with NEMO/IKKγ and NF-κB activation

PubMed Central

Bonif, Marianne; Meuwis, Marie-Alice; Close, Pierre; Benoit, Valérie; Heyninck, Karen; Chapelle, Jean-Paul; Bours, Vincent; Merville, Marie-Paule; Piette, Jacques; Beyaert, Rudi; Chariot, Alain

2005-01-01

Pro-inflammatory cytokines trigger signalling cascades leading to NF-κB (nuclear factor-κB)-dependent gene expression through IKK [IκB (inhibitory κB) kinase]-dependent phosphorylation and subsequent degradation of the IκB proteins and via induced phosphorylation of p65. These signalling pathways rely on sequentially activated kinases which are assembled by essential and non-enzymatic scaffold proteins into functional complexes. Here, we show that the pro-inflammatory cytokine TNFα (tumour necrosis factor α) promotes TANK [TRAF (TNF receptor-associated factor) family member associated NF-κB activator] recruitment to the IKK complex via a newly characterized C-terminal zinc finger. Moreover, we show that TANK is phosphorylated by IKKβ upon TNFα stimulation and that this modification negatively regulates TANK binding to NEMO (NF-κB essential modulator). Interestingly, reduced TANK expression by RNA interference attenuates TNFα-mediated induction of a subset of NF-κB target genes through decreased p65 transactivation potential. Therefore the scaffold protein TANK is required for the cellular response to TNFα by connecting upstream signalling molecules to the IKKs and p65, and its subsequent IKKβ-mediated phosphorylation may be a mechanism to terminate the TANK-dependent wave of NF-κB activation. PMID:16336209

CIKS, a connection to Ikappa B kinase and stress-activated protein kinase.

PubMed

Leonardi, A; Chariot, A; Claudio, E; Cunningham, K; Siebenlist, U

2000-09-12

Pathogens, inflammatory signals, and stress cause acute transcriptional responses in cells. The induced expression of genes in response to these signals invariably involves transcription factors of the NF-kappaB and AP-1/ATF families. Activation of NF-kappaB factors is thought to be mediated primarily via IkappaB kinases (IKK), whereas that of AP-1/ATF can be mediated by stress-activated protein kinases (SAPKs; also named Jun kinases or JNKs). IKKalpha and IKKbeta are two catalytic subunits of a core IKK complex that also contains the regulatory subunit NEMO (NF-kappaB essential modulator)/IKKgamma. The latter protein is essential for activation of the IKKs, but its mechanism of action is not known. Here we describe the molecular cloning of CIKS (connection to IKK and SAPK/JNK), a previously unknown protein that directly interacts with NEMO/IKKgamma in cells. When ectopically expressed, CIKS stimulates IKK and SAPK/JNK kinases and it transactivates an NF-kappaB-dependent reporter. Activation of NF-kappaB is prevented in the presence of kinase-deficient, interfering mutants of the IKKs. CIKS may help to connect upstream signaling events to IKK and SAPK/JNK modules. CIKS could coordinate the activation of two stress-induced signaling pathways, functions reminiscent of those noted for tumor necrosis factor receptor-associated factor adaptor proteins.

A parapoxviral virion protein inhibits NF-κB signaling early in infection

PubMed Central

Khatiwada, Sushil; Delhon, Gustavo; Nagendraprabhu, Ponnuraj; Chaulagain, Sabal; Luo, Shuhong; Diel, Diego G.; Flores, Eduardo F.

2017-01-01

Poxviruses have evolved unique proteins and mechanisms to counteract the nuclear factor κB (NF-κB) signaling pathway, which is an essential regulatory pathway of host innate immune responses. Here, we describe a NF-κB inhibitory virion protein of orf virus (ORFV), ORFV073, which functions very early in infected cells. Infection with ORFV073 gene deletion virus (OV-IA82Δ073) led to increased accumulation of NF-κB essential modulator (NEMO), marked phosphorylation of IκB kinase (IKK) subunits IKKα and IKKβ, IκBα and NF-κB subunit p65 (NF-κB-p65), and to early nuclear translocation of NF-κB-p65 in virus-infected cells (≤ 30 min post infection). Expression of ORFV073 alone was sufficient to inhibit TNFα induced activation of the NF-κB signaling in uninfected cells. Consistent with observed inhibition of IKK complex activation, ORFV073 interacted with the regulatory subunit of the IKK complex NEMO. Infection of sheep with OV-IA82Δ073 led to virus attenuation, indicating that ORFV073 is a virulence determinant in the natural host. Notably, ORFV073 represents the first poxviral virion-associated NF-κB inhibitor described, highlighting the significance of viral inhibition of NF-κB signaling very early in infection. PMID:28787456

Nuclear lamina defects cause ATM-dependent NF-κB activation and link accelerated aging to a systemic inflammatory response.

PubMed

Osorio, Fernando G; Bárcena, Clea; Soria-Valles, Clara; Ramsay, Andrew J; de Carlos, Félix; Cobo, Juan; Fueyo, Antonio; Freije, José M P; López-Otín, Carlos

2012-10-15

Alterations in the architecture and dynamics of the nuclear lamina have a causal role in normal and accelerated aging through both cell-autonomous and systemic mechanisms. However, the precise nature of the molecular cues involved in this process remains incompletely defined. Here we report that the accumulation of prelamin A isoforms at the nuclear lamina triggers an ATM- and NEMO-dependent signaling pathway that leads to NF-κB activation and secretion of high levels of proinflammatory cytokines in two different mouse models of accelerated aging (Zmpste24(-/-) and Lmna(G609G/G609G) mice). Causal involvement of NF-κB in accelerated aging was demonstrated by the fact that both genetic and pharmacological inhibition of NF-κB signaling prevents age-associated features in these animal models, significantly extending their longevity. Our findings provide in vivo proof of principle for the feasibility of pharmacological modulation of the NF-κB pathway to slow down the progression of physiological and pathological aging.

Hepatic tissue environment in NEMO-deficient mice critically regulates positive selection of donor cells after hepatocyte transplantation.

PubMed

Kaldenbach, Michaela; Cubero, Francisco Javier; Erschfeld, Stephanie; Liedtke, Christian; Trautwein, Christian; Streetz, Konrad

2014-01-01

Hepatocyte transplantation (HT) is a promising alternative treatment strategy for end-stage liver diseases compared with orthotopic liver transplantation. A limitation for this approach is the low engraftment of donor cells. The deletion of the I-kappa B kinase-regulatory subunit IKKγ/NEMO in hepatocytes prevents nuclear factor (NF)-kB activation and triggers spontaneous liver apoptosis, chronic hepatitis and the development of liver fibrosis and hepatocellular carcinoma. We hypothesized that NEMOΔhepa mice may therefore serve as an experimental model to study HT. Pre-conditioned NEMOΔhepa mice were transplanted with donor-hepatocytes from wildtype (WT) and mice deficient for the pro-apoptotic mediator Caspase-8 (Casp8Δhepa). Transplantation of isolated WT-hepatocytes into pre-conditioned NEMOΔhepa mice resulted in a 6-7 fold increase of donor cells 12 weeks after HT, while WT-recipients showed no liver repopulation. The use of apoptosis-resistant Casp8Δhepa-derived donor cells further enhanced the selection 3-fold after 12-weeks and up to 10-fold increase after 52 weeks compared with WT donors. While analysis of NEMOΔhepa mice revealed strong liver injury, HT-recipient NEMOΔhepa mice showed improved liver morphology and decrease in serum transaminases. Concomitant with these findings, the histological examination elicited an improved liver tissue architecture associated with significantly lower levels of apoptosis, decreased proliferation and a lesser amount of liver fibrogenesis. Altogether, our data clearly support the therapeutic benefit of the HT procedure into NEMOΔhepa mice. This study demonstrates the feasibility of the NEMOΔhepa mouse as an in vivo tool to study liver repopulation after HT. The improvement of the characteristic phenotype of chronic liver injury in NEMOΔhepa mice after HT suggests the therapeutic potential of HT in liver diseases with a chronic inflammatory phenotype and opens a new door for the applicability of this technique to combat liver disease in the human clinic.

Hepatic Tissue Environment in NEMO-Deficient Mice Critically Regulates Positive Selection of Donor Cells after Hepatocyte Transplantation

PubMed Central

Kaldenbach, Michaela; Cubero, Francisco Javier; Erschfeld, Stephanie; Liedtke, Christian; Trautwein, Christian; Streetz, Konrad

2014-01-01

Background Hepatocyte transplantation (HT) is a promising alternative treatment strategy for end-stage liver diseases compared with orthotopic liver transplantation. A limitation for this approach is the low engraftment of donor cells. The deletion of the I-kappa B kinase-regulatory subunit IKKγ/NEMO in hepatocytes prevents nuclear factor (NF)-kB activation and triggers spontaneous liver apoptosis, chronic hepatitis and the development of liver fibrosis and hepatocellular carcinoma. We hypothesized that NEMOΔhepa mice may therefore serve as an experimental model to study HT. Methods Pre-conditioned NEMOΔhepa mice were transplanted with donor-hepatocytes from wildtype (WT) and mice deficient for the pro-apoptotic mediator Caspase-8 (Casp8Δhepa). Results Transplantation of isolated WT-hepatocytes into pre-conditioned NEMOΔhepa mice resulted in a 6-7 fold increase of donor cells 12 weeks after HT, while WT-recipients showed no liver repopulation. The use of apoptosis-resistant Casp8Δhepa-derived donor cells further enhanced the selection 3-fold after 12-weeks and up to 10-fold increase after 52 weeks compared with WT donors. While analysis of NEMOΔhepa mice revealed strong liver injury, HT-recipient NEMOΔhepa mice showed improved liver morphology and decrease in serum transaminases. Concomitant with these findings, the histological examination elicited an improved liver tissue architecture associated with significantly lower levels of apoptosis, decreased proliferation and a lesser amount of liver fibrogenesis. Altogether, our data clearly support the therapeutic benefit of the HT procedure into NEMOΔhepa mice. Conclusion This study demonstrates the feasibility of the NEMOΔhepa mouse as an in vivo tool to study liver repopulation after HT. The improvement of the characteristic phenotype of chronic liver injury in NEMOΔhepa mice after HT suggests the therapeutic potential of HT in liver diseases with a chronic inflammatory phenotype and opens a new door for the applicability of this technique to combat liver disease in the human clinic. PMID:24979756

Rainfall as a trigger for stratification and winter phytoplankton growth in temperate shelf seas

NASA Astrophysics Data System (ADS)

Jardine, Jenny; Palmer, Matthew; Mahaffey, Claire; Holt, Jason; Mellor, Adam; Wakelin, Sarah

2017-04-01

We present new data from ocean gliders to investigate physical controls on stratification and phytoplankton dynamics, collected in the Celtic Sea between November 2014 and August 2015 as part of the UK Shelf Sea Biogeochemistry programme. This presentation focuses on the winter period (Jan-March) when the diurnal heating cycle results in regular but weak near surface stratification followed by night-time convection. Despite low light conditions, this daily cycle often promotes a daytime increase in observed chlorophyll fluorescence, indicative of phytoplankton growth. This daily cycle is occasionally interrupted when buoyancy inputs are sufficient to outcompete night-time convection and result in short-term periods of sustained winter stratification, typically lasting 2-3 days. Sustained stratification often coincides with periods of heavy rainfall, suggesting freshwater input from precipitation may play a role on these events by producing a subtle yet significant freshening of the surface layer of the order of 0.005 PSU. Comparing rainfall estimates with observed salinity changes confirms rainfall to often be the initiator of these winter stratification periods. As winter winds subside and solar heating increases towards spring, the water column becomes more susceptible to periods of halo-stratification, such that heavy rainfall during the winter-spring transition is likely to promote sustained stratification. The timing and extent of a heavy rainfall event in March 2015 does suggest it may be the critical trigger for shelf-wide stratification that eventually instigates the spring bloom. We propose that the timing of these downpours relative to the daily heating cycle can be a triggering mechanism for both short term and seasonal stratification in shelf seas, and so play a critical role in winter and early spring phytoplankton growth and the shelf sea carbon cycle. We further test the importance of this process using historical data, and results from the NEMO-AMM7 model to test how rainfall events have affected previous winter and spring conditions.

Analysis of twitter users' sharing of official new york storm response messages.

PubMed

Genes, Nicholas; Chary, Michael; Chason, Kevin

2014-01-01

Twitter is a social network where users read, send, and share snippets of text ("tweets"). Tweets can be disseminated through multiple means; on desktop computers, laptops, and mobile devices, over ethernet, Wi-Fi or cellular networks. This redundancy positions Twitter as a useful tool for disseminating information to the public during emergencies or disasters. Previous research on dissemination of information using Twitter has mostly investigated the characteristics of tweets that are most effective in raising consumer awareness about a new product or event. In particular, they describe characteristics that increase the chance the messages will be shared ("retweeted") by users. In comparison, little has been published on how information from municipal or state government agencies spreads on Twitter during emergency situations. Retweeting these messages is a way to enhance public awareness of potentially important instructions from public officials in a disaster. The aim of this study is to (1) describe the tweets of select New York State and New York City agencies by public officials surrounding two notable recent winter storms that required a large-scale emergency response, and (2) identify the characteristics of the tweets of public officials that were most disseminated (retweeted). For one week surrounding Superstorm Sandy (October 2012) and the winter blizzard Nemo (February 2013), we collected (1) tweets from the official accounts for six New York governmental agencies, and (2) all tweets containing the hashtags #sandy (or #nemo) and #nyc. From these data we calculated how many times a tweet was retweeted, controlling for differences in baseline activity in each account. We observed how many hashtags and links each tweet contained. We also calculated the lexical diversity of each tweet, a measure of the range of vocabulary used. During the Sandy storm, 3242 shared (retweeted) messages from public officials were collected. The lexical diversity of official tweets was similar (2.25-2.49) and well below the average for non-official tweets mentioning #sandy and #nyc (3.82). Most official tweets were with substantial retweets including a link for further reading. Of the 448 tweets analyzed from six official city and state Twitter accounts from the Nemo blizzard, 271 were related to the storm, and 174 had actionable information for the public. Actionable storm messages were retweeted approximately 24x per message, compared to 31x per message for general storm information. During two weather emergencies, New York public officials were able to convey storm-related information that was shared widely beyond existing follower bases, potentially improving situational awareness and disaster response. Official Sandy tweets, characterized by a lower lexical diversity score than other city- and Sandy-related tweets, were likely easier to understand, and often linked to further information and resources. Actionable information in the Nemo blizzard, such as specific instructions and cancellation notices, was not shared as often as more general warnings and "fun facts," suggesting agencies mix important instructions with more general news and trivia, as a way of reaching the broadest audience during a disaster.

A new real-time tsunami detection algorithm

NASA Astrophysics Data System (ADS)

Chierici, F.; Embriaco, D.; Pignagnoli, L.

2016-12-01

Real-time tsunami detection algorithms play a key role in any Tsunami Early Warning System. We have developed a new algorithm for tsunami detection based on the real-time tide removal and real-time band-pass filtering of sea-bed pressure recordings. The algorithm greatly increases the tsunami detection probability, shortens the detection delay and enhances detection reliability, at low computational cost. The algorithm is designed to be used also in autonomous early warning systems with a set of input parameters and procedures which can be reconfigured in real time. We have also developed a methodology based on Monte Carlo simulations to test the tsunami detection algorithms. The algorithm performance is estimated by defining and evaluating statistical parameters, namely the detection probability, the detection delay, which are functions of the tsunami amplitude and wavelength, and the occurring rate of false alarms. Pressure data sets acquired by Bottom Pressure Recorders in different locations and environmental conditions have been used in order to consider real working scenarios in the test. We also present an application of the algorithm to the tsunami event which occurred at Haida Gwaii on October 28th, 2012 using data recorded by the Bullseye underwater node of Ocean Networks Canada. The algorithm successfully ran for test purpose in year-long missions onboard the GEOSTAR stand-alone multidisciplinary abyssal observatory, deployed in the Gulf of Cadiz during the EC project NEAREST and on NEMO-SN1 cabled observatory deployed in the Western Ionian Sea, operational node of the European research infrastructure EMSO.

Dive and Explore: An Interactive Exhibit That Simulates Making an ROV Dive to a Submarine Volcano, Hatfield Marine Science Visitor Center, Newport, Oregon

NASA Astrophysics Data System (ADS)

Weiland, C.; Chadwick, W. W.; Hanshumaker, W.; Osis, V.; Hamilton, C.

2002-12-01

We have created a new interactive exhibit in which the user can sit down and simulate that they are making a dive to the seafloor with the remotely operated vehicle (ROV) named ROPOS. The exhibit immerses the user in an interactive experience that is naturally fun but also educational. This new public display is located at the Hatfield Marine Science Visitor Center in Newport, Oregon. The exhibit is designed to look like the real ROPOS control console and includes three video monitors, a PC, a DVD player, an overhead speaker, graphic panels, buttons, lights, dials, and a seat in front of a joystick. The dives are based on real seafloor settings at Axial seamount, an active submarine volcano on the Juan de Fuca Ridge (NE Pacific) that is also the location of a seafloor observatory called NeMO. The user can choose between 1 of 3 different dives sites in the caldera of Axial Volcano. Once a dive is chosen, then the user watches ROPOS being deployed and then arrives into a 3-D computer-generated seafloor environment that is based on the real world but is easier to visualize and navigate. Once on the bottom, the user is placed within a 360 degree panorama and can look in all directions by manipulating the joystick. By clicking on markers embedded in the scene, the user can then either move to other panorama locations via movies that travel through the 3-D virtual environment, or they can play video clips from actual ROPOS dives specifically related to that scene. Audio accompanying the video clips informs the user where they are going or what they are looking at. After the user is finished exploring the dive site they end the dive by leaving the bottom and watching the ROV being recovered onto the ship at the surface. The user can then choose a different dive or make the same dive again. Within the three simulated dives there are a total of 6 arrival and departure movies, 7 seafloor panoramas, 12 travel movies, and 23 ROPOS video clips. The exhibit software was created with Macromedia Director using Apple Quicktime and Quicktime VR. The exhibit is based on the NeMO Explorer web site (http://www.pmel.noaa.gov/vents/nemo/explorer.html).

Studying Si/SiGe disordered alloys within effective mass theory

NASA Astrophysics Data System (ADS)

Gamble, John; Montaño, Inès; Carroll, Malcolm S.; Muller, Richard P.

Si/SiGe is an attractive material system for electrostatically-defined quantum dot qubits due to its high-quality crystalline quantum well interface. Modeling the properties of single-electron quantum dots in this system is complicated by the presence of alloy disorder, which typically requires atomistic techniques in order to treat properly. Here, we use the NEMO-3D empirical tight binding code to calibrate a multi-valley effective mass theory (MVEMT) to properly handle alloy disorder. The resulting MVEMT simulations give good insight into the essential physics of alloy disorder, while being extremely computationally efficient and well-suited to determining statistical properties. Sandia is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the US Department of Energy's National Nuclear Security Administration under Contract No. DE-AC04-94AL85000.

Design and Development of nEMoS, an All-in-One, Low-Cost, Web-Connected and 3D-Printed Device for Environmental Analysis

PubMed Central

Salamone, Francesco; Belussi, Lorenzo; Danza, Ludovico; Ghellere, Matteo; Meroni, Italo

2015-01-01

The Indoor Environmental Quality (IEQ) refers to the quality of the environment in relation to the health and well-being of the occupants. It is a holistic concept, which considers several categories, each related to a specific environmental parameter. This article describes a low-cost and open-source hardware architecture able to detect the indoor variables necessary for the IEQ calculation as an alternative to the traditional hardware used for this purpose. The system consists of some sensors and an Arduino board. One of the key strengths of Arduino is the possibility it affords of loading the script into the board’s memory and letting it run without interfacing with computers, thus granting complete independence, portability and accuracy. Recent works have demonstrated that the cost of scientific equipment can be reduced by applying open-source principles to their design using a combination of the Arduino platform and a 3D printer. The evolution of the 3D printer has provided a new means of open design capable of accelerating self-directed development. The proposed nano Environmental Monitoring System (nEMoS) instrument is shown to have good reliability and it provides the foundation for a more critical approach to the use of professional sensors as well as for conceiving new scenarios and potential applications. PMID:26053749

Emergence of the A20/ABIN-mediated inhibition of NF-κB signaling via modifying the ubiquitinated proteins in a basal chordate.

PubMed

Yuan, Shaochun; Dong, Xiangru; Tao, Xin; Xu, Liqun; Ruan, Jie; Peng, Jian; Xu, Anlong

2014-05-06

In the past decade, ubiquitination has been well documented to have multifaceted roles in regulating NF-κB activation in mammals. However, its function, especially how deubiquitinating enzymes balance the NF-κB activation, remains largely elusive in invertebrates. Investigating bbtA20 and its binding proteins, bbt A20-binding inhibitor of NF-κB (bbtABIN1) and bbtABIN2, in Chinese amphioxus Branchiostoma belcheri tsingtauense, we found that bbtABIN2 can colocalize and compete with bbt TNF receptor-associated factor 6 to connect the K63-linked polyubiquitin chains, whereas bbtABIN1 physically links bbtA20 to bbt NF-κB essential modulator (bbtNEMO) to facilitate the K48-linked ubiquitination of bbtNEMO. Similar to human A20, bbtA20 is a dual enzyme that removes the K63-linked polyubiquitin chains and builds the K48-linked polyubiquitin chains on bbt receptor-interacting serine/threonine protein kinase 1b, leading to the inhibition of NF-κB signaling. Our study not only suggests that ubiquitination is an ancient strategy in regulating NF-κB activation but also provides the first evidence, to our knowledge, for ABINs/A20-mediated inhibition of NF-κB via modifying the ubiquitinated proteins in a basal chordate, adding information on the stepwise development of vertebrate innate immune signaling.

BK virus encephalopathy and sclerosing vasculopathy in a patient with hypohidrotic ectodermal dysplasia and immunodeficiency.

PubMed

Darbinyan, Armine; Major, Eugene O; Morgello, Susan; Holland, Steven; Ryschkewitsch, Caroline; Monaco, Maria Chiara; Naidich, Thomas P; Bederson, Joshua; Malaczynska, Joanna; Ye, Fei; Gordon, Ronald; Cunningham-Rundles, Charlotte; Fowkes, Mary; Tsankova, Nadejda M

2016-07-13

Human BK polyomavirus (BKV) is reactivated under conditions of immunosuppression leading most commonly to nephropathy or cystitis; its tropism for the brain is rare and poorly understood. We present a unique case of BKV-associated encephalopathy in a man with hypohidrotic ectodermal dysplasia and immunodeficiency (HED-ID) due to IKK-gamma (NEMO) mutation, who developed progressive neurological symptoms. Brain biopsy demonstrated polyomavirus infection of gray and white matter, with predominant involvement of cortex and distinct neuronal tropism, in addition to limited demyelination and oligodendroglial inclusions. Immunohistochemistry demonstrated polyoma T-antigen in neurons and glia, but expression of VP1 capsid protein only in glia. PCR analysis on both brain biopsy tissue and cerebrospinal fluid detected high levels of BKV DNA. Sequencing studies further identified novel BKV variant and disclosed unique rearrangements in the noncoding control region of the viral DNA (BKVN NCCR). Neuropathological analysis also demonstrated an unusual form of obliterative fibrosing vasculopathy in the subcortical white matter with abnormal lysosomal accumulations, possibly related to the patient's underlying ectodermal dysplasia. Our report provides the first neuropathological description of HED-ID due to NEMO mutation, and expands the diversity of neurological presentations of BKV infection in brain, underscoring the importance of its consideration in immunodeficient patients with unexplained encephalopathy. We also document novel BKVN NCCR rearrangements that may be associated with the unique neuronal tropism in this patient.

CIKS, a connection to IκB kinase and stress-activated protein kinase

PubMed Central

Leonardi, Antonio; Chariot, Alain; Claudio, Estefania; Cunningham, Kirk; Siebenlist, Ulrich

2000-01-01

Pathogens, inflammatory signals, and stress cause acute transcriptional responses in cells. The induced expression of genes in response to these signals invariably involves transcription factors of the NF-κB and AP-1/ATF families. Activation of NF-κB factors is thought to be mediated primarily via IκB kinases (IKK), whereas that of AP-1/ATF can be mediated by stress-activated protein kinases (SAPKs; also named Jun kinases or JNKs). IKKα and IKKβ are two catalytic subunits of a core IKK complex that also contains the regulatory subunit NEMO (NF-κB essential modulator)/IKKγ. The latter protein is essential for activation of the IKKs, but its mechanism of action is not known. Here we describe the molecular cloning of CIKS (connection to IKK and SAPK/JNK), a previously unknown protein that directly interacts with NEMO/IKKγ in cells. When ectopically expressed, CIKS stimulates IKK and SAPK/JNK kinases and it transactivates an NF-κB-dependent reporter. Activation of NF-κB is prevented in the presence of kinase-deficient, interfering mutants of the IKKs. CIKS may help to connect upstream signaling events to IKK and SAPK/JNK modules. CIKS could coordinate the activation of two stress-induced signaling pathways, functions reminiscent of those noted for tumor necrosis factor receptor-associated factor adaptor proteins. PMID:10962033

Design and development of nEMoS, an all-in-one, low-cost, web-connected and 3D-printed device for environmental analysis.

PubMed

Salamone, Francesco; Belussi, Lorenzo; Danza, Ludovico; Ghellere, Matteo; Meroni, Italo

2015-06-04

The Indoor Environmental Quality (IEQ) refers to the quality of the environment in relation to the health and well-being of the occupants. It is a holistic concept, which considers several categories, each related to a specific environmental parameter. This article describes a low-cost and open-source hardware architecture able to detect the indoor variables necessary for the IEQ calculation as an alternative to the traditional hardware used for this purpose. The system consists of some sensors and an Arduino board. One of the key strengths of Arduino is the possibility it affords of loading the script into the board's memory and letting it run without interfacing with computers, thus granting complete independence, portability and accuracy. Recent works have demonstrated that the cost of scientific equipment can be reduced by applying open-source principles to their design using a combination of the Arduino platform and a 3D printer. The evolution of the 3D printer has provided a new means of open design capable of accelerating self-directed development. The proposed nano Environmental Monitoring System (nEMoS) instrument is shown to have good reliability and it provides the foundation for a more critical approach to the use of professional sensors as well as for conceiving new scenarios and potential applications.

The numerics of hydrostatic structured-grid coastal ocean models: State of the art and future perspectives

NASA Astrophysics Data System (ADS)

Klingbeil, Knut; Lemarié, Florian; Debreu, Laurent; Burchard, Hans

2018-05-01

The state of the art of the numerics of hydrostatic structured-grid coastal ocean models is reviewed here. First, some fundamental differences in the hydrodynamics of the coastal ocean, such as the large surface elevation variation compared to the mean water depth, are contrasted against large scale ocean dynamics. Then the hydrodynamic equations as they are used in coastal ocean models as well as in large scale ocean models are presented, including parameterisations for turbulent transports. As steps towards discretisation, coordinate transformations and spatial discretisations based on a finite-volume approach are discussed with focus on the specific requirements for coastal ocean models. As in large scale ocean models, splitting of internal and external modes is essential also for coastal ocean models, but specific care is needed when drying & flooding of intertidal flats is included. As one obvious characteristic of coastal ocean models, open boundaries occur and need to be treated in a way that correct model forcing from outside is transmitted to the model domain without reflecting waves from the inside. Here, also new developments in two-way nesting are presented. Single processes such as internal inertia-gravity waves, advection and turbulence closure models are discussed with focus on the coastal scales. Some overview on existing hydrostatic structured-grid coastal ocean models is given, including their extensions towards non-hydrostatic models. Finally, an outlook on future perspectives is made.

A review of ocean chlorophyll algorithms and primary production models

NASA Astrophysics Data System (ADS)

Li, Jingwen; Zhou, Song; Lv, Nan

2015-12-01

This paper mainly introduces the five ocean chlorophyll concentration inversion algorithm and 3 main models for computing ocean primary production based on ocean chlorophyll concentration. Through the comparison of five ocean chlorophyll inversion algorithm, sums up the advantages and disadvantages of these algorithm,and briefly analyzes the trend of ocean primary production model.

Modeling High-Resolution Coastal Ocean Dynamics with COAMPS: System Overview, Applications and Future Directions

NASA Astrophysics Data System (ADS)

Allard, R. A.; Campbell, T. J.; Edwards, K. L.; Smith, T.; Martin, P.; Hebert, D. A.; Rogers, W.; Dykes, J. D.; Jacobs, G. A.; Spence, P. L.; Bartels, B.

2014-12-01

The Coupled Ocean Atmosphere Mesoscale Prediction System (COAMPS®) is an atmosphere-ocean-wave modeling system developed by the Naval Research Laboratory which can be configured to cycle regional forecasts/analysis models in single-model (atmosphere, ocean, and wave) or coupled-model (atmosphere-ocean, ocean-wave, and atmosphere-ocean-wave) modes. The model coupling is performed using the Earth System Modeling Framework (ESMF). The ocean component is the Navy Coastal Ocean Model (NCOM), and the wave components include Simulating WAves Nearshore (SWAN) and WaveWatch-III. NCOM has been modified to include wetting and drying, the effects of Stokes drift current, wave radiation stresses due to horizontal gradients of the momentum flux of surface waves, enhancement of bottom drag in shallow water, and enhanced vertical mixing due to Langmuir turbulence. An overview of the modeling system including ocean data assimilation and specification of boundary conditions will be presented. Results from a high-resolution (10-250m) modeling study from the Surfzone Coastal Oil Pathways Experiment (SCOPE) near Ft. Walton Beach, Florida in December 2013 will be presented. ®COAMPS is a registered trademark of the Naval Research Laboratory

Methods of testing parameterizations: Vertical ocean mixing

NASA Technical Reports Server (NTRS)

Tziperman, Eli

1992-01-01

The ocean's velocity field is characterized by an exceptional variety of scales. While the small-scale oceanic turbulence responsible for the vertical mixing in the ocean is of scales a few centimeters and smaller, the oceanic general circulation is characterized by horizontal scales of thousands of kilometers. In oceanic general circulation models that are typically run today, the vertical structure of the ocean is represented by a few tens of discrete grid points. Such models cannot explicitly model the small-scale mixing processes, and must, therefore, find ways to parameterize them in terms of the larger-scale fields. Finding a parameterization that is both reliable and plausible to use in ocean models is not a simple task. Vertical mixing in the ocean is the combined result of many complex processes, and, in fact, mixing is one of the less known and less understood aspects of the oceanic circulation. In present models of the oceanic circulation, the many complex processes responsible for vertical mixing are often parameterized in an oversimplified manner. Yet, finding an adequate parameterization of vertical ocean mixing is crucial to the successful application of ocean models to climate studies. The results of general circulation models for quantities that are of particular interest to climate studies, such as the meridional heat flux carried by the ocean, are quite sensitive to the strength of the vertical mixing. We try to examine the difficulties in choosing an appropriate vertical mixing parameterization, and the methods that are available for validating different parameterizations by comparing model results to oceanographic data. First, some of the physical processes responsible for vertically mixing the ocean are briefly mentioned, and some possible approaches to the parameterization of these processes in oceanographic general circulation models are described in the following section. We then discuss the role of the vertical mixing in the physics of the large-scale ocean circulation, and examine methods of validating mixing parameterizations using large-scale ocean models.

Development of a new model for short period ocean tidal variations of Earth rotation

NASA Astrophysics Data System (ADS)

Schuh, Harald

2015-08-01

Within project SPOT (Short Period Ocean Tidal variations in Earth rotation) we develop a new high frequency Earth rotation model based on empirical ocean tide models. The main purpose of the SPOT model is its application to space geodetic observations such as GNSS and VLBI.We consider an empirical ocean tide model, which does not require hydrodynamic ocean modeling to determine ocean tidal angular momentum. We use here the EOT11a model of Savcenko & Bosch (2012), which is extended for some additional minor tides (e.g. M1, J1, T2). As empirical tidal models do not provide ocean tidal currents, which are re- quired for the computation of oceanic relative angular momentum, we implement an approach first published by Ray (2001) to estimate ocean tidal current veloci- ties for all tides considered in the extended EOT11a model. The approach itself is tested by application to tidal heights from hydrodynamic ocean tide models, which also provide tidal current velocities. Based on the tidal heights and the associated current velocities the oceanic tidal angular momentum (OTAM) is calculated.For the computation of the related short period variation of Earth rotation, we have re-examined the Euler-Liouville equation for an elastic Earth model with a liquid core. The focus here is on the consistent calculation of the elastic Love num- bers and associated Earth model parameters, which are considered in the Euler- Liouville equation for diurnal and sub-diurnal periods in the frequency domain.

Modeling the biogeochemical impact of atmospheric phosphate deposition from desert dust and combustion sources to the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Richon, Camille; Dutay, Jean-Claude; Dulac, François; Wang, Rong; Balkanski, Yves

2018-04-01

Daily modeled fields of phosphate deposition to the Mediterranean from natural dust, anthropogenic combustion and wildfires were used to assess the effect of this external nutrient on marine biogeochemistry. The ocean model used is a high-resolution (1/12°) regional coupled dynamical-biogeochemical model of the Mediterranean Sea (NEMO-MED12/PISCES). The input fields of phosphorus are for 2005, which are the only available daily resolved deposition fields from the global atmospheric chemical transport model LMDz-INCA. Traditionally, dust has been suggested to be the main atmospheric source of phosphorus, but the LMDz-INCA model suggests that combustion is dominant over natural dust as an atmospheric source of phosphate (PO4, the bioavailable form of phosphorus in seawater) for the Mediterranean Sea. According to the atmospheric transport model, phosphate deposition from combustion (Pcomb) brings on average 40.5×10-6 mol PO4 m-2 yr-1 over the entire Mediterranean Sea for the year 2005 and is the primary source over the northern part (e.g., 101×10-6 mol PO4 m-2 yr-1 from combustion deposited in 2005 over the north Adriatic against 12.4×10-6 from dust). Lithogenic dust brings 17.2×10-6 mol PO4 m-2 yr-1 on average over the Mediterranean Sea in 2005 and is the primary source of atmospheric phosphate to the southern Mediterranean Basin in our simulations (e.g., 31.8×10-6 mol PO4 m-2 yr-1 from dust deposited in 2005 on average over the south Ionian basin against 12.4×10-6 from combustion). The evaluation of monthly averaged deposition flux variability of Pdust and Pcomb for the 1997-2012 period indicates that these conclusions may hold true for different years. We examine separately the two atmospheric phosphate sources and their respective flux variability and evaluate their impacts on marine surface biogeochemistry (phosphate concentration, chlorophyll a, primary production). The impacts of the different phosphate deposition sources on the biogeochemistry of the Mediterranean are found localized, seasonally varying and small, but yet statistically significant. Differences in the geographical deposition patterns between phosphate from dust and from combustion will cause contrasted and significant changes in the biogeochemistry of the basin. We contrast the effects of combustion in the northern basin (Pcomb deposition effects are found to be 10 times more important in the northern Adriatic, close to the main source region) to the effects of dust in the southern basin. These different phosphorus sources should therefore be accounted for in modeling studies.

Study of strain boundary conditions and GaAs buffer sizes in InGaAs quantum dots

NASA Technical Reports Server (NTRS)

Oyafuso, F.; Klimeck, G.; Boykin, T. B.; Bowen, R. C.; Allmen, P. von

2003-01-01

NEMO 3-D has been developed for the simulation of electronic structure in self-assembled InGaAs quantum dots on GaAs substrates. Typical self-assembled quantum dots in that material system contain about 0.5 to 1 million atoms. Effects of strain by the surrounding GaAs buffer modify the electronic structure inside the quantum dot significantly and a large GaAs buffer must be included in the strain and electronic structure.

Icing Characteristics of Low Altitude, Supercooled Layer Clouds. Revision

DTIC Science & Technology

1980-05-01

Droplet Size Distribution 5. Icing Rate Meters C. Accuracy and Sources of Error in the Measurements from the Period 1944-1950 11 1. Rotating...whether currently available LWC meters and icing rate detectors will give re- liable results when flown on helicopters. Concerning the forecasting...Max Dia. Size Distrib. Meter Samples 4 1944 MSP DP -- Al .... 4 6 1946 OR 2,4RC 2,4RHC Al 4RMC -- 3 7 1946-47 NEMO, 4RMC 4RMC AI 4RMC - 31 TN,OH, IN

Earth observations taken from shuttle orbiter Atlantis during STS-84 mission

NASA Image and Video Library

1997-05-20

STS084-712-003 (15-24 May 1997) --- Early morning sun highlights the volcanic features on Onekotan Island which is one of several volcanic islands in the Russian owned Kurile Island chain. Onekotan lies just south of Kamchatka. Two volcanoes are active on the island -- the small island surrounded by a moat-like lake in the south (Tao-Rusyr caldera) last erupted in 1952, and the cone-shaped peak at the north end of the island, Nemo peak, erupted in 1938.

Nuclear lamina defects cause ATM-dependent NF-κB activation and link accelerated aging to a systemic inflammatory response

PubMed Central

Osorio, Fernando G.; Bárcena, Clea; Soria-Valles, Clara; Ramsay, Andrew J.; de Carlos, Félix; Cobo, Juan; Fueyo, Antonio; Freije, José M.P.; López-Otín, Carlos

2012-01-01

Alterations in the architecture and dynamics of the nuclear lamina have a causal role in normal and accelerated aging through both cell-autonomous and systemic mechanisms. However, the precise nature of the molecular cues involved in this process remains incompletely defined. Here we report that the accumulation of prelamin A isoforms at the nuclear lamina triggers an ATM- and NEMO-dependent signaling pathway that leads to NF-κB activation and secretion of high levels of proinflammatory cytokines in two different mouse models of accelerated aging (Zmpste24−/− and LmnaG609G/G609G mice). Causal involvement of NF-κB in accelerated aging was demonstrated by the fact that both genetic and pharmacological inhibition of NF-κB signaling prevents age-associated features in these animal models, significantly extending their longevity. Our findings provide in vivo proof of principle for the feasibility of pharmacological modulation of the NF-κB pathway to slow down the progression of physiological and pathological aging. PMID:23019125

Representing grounding line migration in synchronous coupling between a marine ice sheet model and a z-coordinate ocean model

NASA Astrophysics Data System (ADS)

Goldberg, D. N.; Snow, K.; Holland, P.; Jordan, J. R.; Campin, J.-M.; Heimbach, P.; Arthern, R.; Jenkins, A.

2018-05-01

Synchronous coupling is developed between an ice sheet model and a z-coordinate ocean model (the MITgcm). A previously-developed scheme to allow continuous vertical movement of the ice-ocean interface of a floating ice shelf ("vertical coupling") is built upon to allow continuous movement of the grounding line, or point of floatation of the ice sheet ("horizontal coupling"). Horizontal coupling is implemented through the maintenance of a thin layer of ocean ( ∼ 1 m) under grounded ice, which is inflated into the real ocean as the ice ungrounds. This is accomplished through a modification of the ocean model's nonlinear free surface evolution in a manner akin to a hydrological model in the presence of steep bathymetry. The coupled model is applied to a number of idealized geometries and shown to successfully represent ocean-forced marine ice sheet retreat while maintaining a continuous ocean circulation.

Sea state indices for a coastal strait

NASA Astrophysics Data System (ADS)

Gemmrich, Johannes; Dewey, Richard

2017-04-01

The Strait of Georgia at the west coast of Canada is an enclosed coastal strait, about 250km long and 25 to 50 km wide, with great socio-economic importance. Regular freighter traffic, ferry services, commercial and sport fisheries, and recreational boating, makes the area one of the busiest marine areas in the world. Waves in SoG are generally small, with the median value of the significant wave height Hs=0.3m. However, strong outflows off the mountainous terrain can generate significant wave heights Hs > 2.5m, with high spatial and temporal variability. In addition, strong tidal currents and the Fraser River outflow generate localized regions of steep and breaking waves that are of particular concern. We have implemented the Wavewatch III model at 500m-resolution, forced by Environment Canada's high resolution atmospheric model winds and currents from the UBC NEMO implementation of the Salish Sea. The final output combines GIS layers of the predicted wave field (Hs, dominant wave length and direction), the modeled wind field and currents, observed currents from a set of CODAR systems, and a sea state index that highlights regions of potentially steep and dangerous waves.

A perspective on sustained marine observations for climate modelling and prediction

PubMed Central

Dunstone, Nick J.

2014-01-01

Here, I examine some of the many varied ways in which sustained global ocean observations are used in numerical modelling activities. In particular, I focus on the use of ocean observations to initialize predictions in ocean and climate models. Examples are also shown of how models can be used to assess the impact of both current ocean observations and to simulate that of potential new ocean observing platforms. The ocean has never been better observed than it is today and similarly ocean models have never been as capable at representing the real ocean as they are now. However, there remain important unanswered questions that can likely only be addressed via future improvements in ocean observations. In particular, ocean observing systems need to respond to the needs of the burgeoning field of near-term climate predictions. Although new ocean observing platforms promise exciting new discoveries, there is a delicate balance to be made between their funding and that of the current ocean observing system. Here, I identify the need to secure long-term funding for ocean observing platforms as they mature, from a mainly research exercise to an operational system for sustained observation over climate change time scales. At the same time, considerable progress continues to be made via ship-based observing campaigns and I highlight some that are dedicated to addressing uncertainties in key ocean model parametrizations. The use of ocean observations to understand the prominent long time scale changes observed in the North Atlantic is another focus of this paper. The exciting first decade of monitoring of the Atlantic meridional overturning circulation by the RAPID-MOCHA array is highlighted. The use of ocean and climate models as tools to further probe the drivers of variability seen in such time series is another exciting development. I also discuss the need for a concerted combined effort from climate models and ocean observations in order to understand the current slow-down in surface global warming. PMID:25157195

Assimilation of SeaWiFS Ocean Chlorophyll Data into a Three-Dimensional Global Ocean Model

NASA Technical Reports Server (NTRS)

Gregg, Watson W.

2005-01-01

Assimilation of satellite ocean color data is a relatively new phenomenon in ocean sciences. However, with routine observations from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS), launched in late 1997, and now with new data from the Moderate Resolution Imaging Spectroradometer (MODIS) Aqua, there is increasing interest in ocean color data assimilation. Here SeaWiFS chlorophyll data were assimilated with an established thre-dimentional global ocean model. The assimilation improved estimates of hlorophyll and primary production relative to a free-run (no assimilation) model. This represents the first attempt at ocean color data assimilation using NASA satellites in a global model. The results suggest the potential of assimilation of satellite ocean chlorophyll data for improving models.

Results from ISOMIP+ and MISOMIP1, two interrelated marine ice sheet and ocean model intercomparison projects

NASA Astrophysics Data System (ADS)

Asay-Davis, X.; Galton-Fenzi, B.; Gwyther, D.; Jourdain, N.; Martin, D. F.; Nakayama, Y.; Seroussi, H. L.

2016-12-01

MISMIP+ (the third Marine Ice Sheet MIP), ISOMIP+ (the second Ice Shelf-Ocean MIP) and MISOMIP1 (the first Marine Ice Sheet-Ocean MIP) prescribe a set of idealized experiments for marine ice-sheet models, ocean models with ice-shelf cavities, and coupled ice sheet-ocean models, respectively. Here, we present results from ISOMIP+ and MISOMIP1 experiments using several ocean-only and coupled ice sheet-ocean models. Among the ocean models, we show that differences in model behavior are significant enough that similar results can only be achieved by tuning model parameters (the heat- and salt-transfer coefficients across the sub-ice-shelf boundary layer) for each model. This tuning is constrained by a desired mean melt rate in quasi-steady state under specified forcing conditions, akin to tuning the models to match observed melt rates. We compare the evolution of ocean temperature transects, melt rate, friction velocity and thermal driving between ocean models for the five ISOMIP+ experiments (Ocean0-4), which have prescribed ice-shelf topography. We find that melt patterns differ between models based on the relative importance of overturning strength and vertical mixing of temperature even when the models have been tuned to achieve similar melt rates near the grounding line. For the two MISOMIP1 experiments (IceOcean1 without dynamic calving and IceOcean2 with a simple calving parameterization), we compare temperature transects, melt rate, ice-shelf topography and grounded area across models and for several model configurations. Consistent with preliminary results from MISMIP+, we find that for a given coupled model, the use of a Coulomb-limited basal friction parameterization below grounded ice and the application of dynamic calving both significantly increase the rate of grounding-line retreat, whereas the rate of retreat appears to be less sensitive to the ice stress approximation (shallow-shelf approximation, higher-order, etc.). We show that models with similar mean melt rates, stress approximations and basal friction parameterizations produce markedly different rates of grounding-line retreat, and we investigate possible sources of these disparities (e.g. differences in coupling strategy or melt distribution).

Southern Ocean vertical iron fluxes; the ocean model effect

NASA Astrophysics Data System (ADS)

Schourup-Kristensen, V.; Haucke, J.; Losch, M. J.; Wolf-Gladrow, D.; Voelker, C. D.

2016-02-01

The Southern Ocean plays a key role in the climate system, but commonly used large-scale ocean general circulation biogeochemical models give different estimates of current and future Southern Ocean net primary and export production. The representation of the Southern Ocean iron sources plays an important role for the modeled biogeochemistry. Studies of the iron supply to the surface mixed layer have traditionally focused on the aeolian and sediment contributions, but recent work has highlighted the importance of the vertical supply from below. We have performed a model study in which the biogeochemical model REcoM2 was coupled to two different ocean models, the Finite Element Sea-ice Ocean Model (FESOM) and the MIT general circulation model (MITgcm) and analyzed the magnitude of the iron sources to the surface mixed layer from below in the two models. Our results revealed a remarkable difference in terms of mechanism and magnitude of transport. The mean iron supply from below in the Southern Ocean was on average four times higher in MITgcm than in FESOM and the dominant pathway was entrainment in MITgcm, whereas diffusion dominated in FESOM. Differences in the depth and seasonal amplitude of the mixed layer between the models affect on the vertical iron profile, the relative position of the base of the mixed layer and ferricline and thereby also on the iron fluxes. These differences contribute to differences in the phytoplankton composition in the two models, as well as in the timing of the onset of the spring bloom. The study shows that the choice of ocean model has a significant impact on the iron supply to the Southern Ocean mixed layer and thus on the modeled carbon cycle, with possible implications for model runs predicting the future carbon uptake in the region.

Decoupling of Iron and Phosphate in the Global Ocean

NASA Technical Reports Server (NTRS)

Parekh, Payal

2003-01-01

Iron is an essential micronutrient for marine phytoplankton, limiting their growth in high nutrient, low chlorophyll regions of the ocean. I use a hierarchy of ocean circulation and biogeochemistry models to understand controls on global iron distribution. I formulate a mechanistic model of iron cycling which includes scavenging onto sinking particles and complexation with an organic ligand. The iron cycle is coupled to a phosphorus cycling model. Iron's aeolian source is prescribed. In the context of a highly idealized multi-box model scheme, the model can be brought into consistency with the relatively sparse ocean observations of iron in the oceans. This biogeochemical scheme is also implemented in a coarse resolution ocean general circulation model. This model also successfully reproduces the broad regional patterns of iron and phosphorus. In particular, the high macronutrient concentrations of the Southern Ocean result from iron limitation in the model. Due to the potential ability of iron to change the efficiency of the carbon pump in the remote Southern Ocean, I study Southern Ocean surface phosphate response to increased aeolian dust flux. My box model and GCM results suggest that a global ten fold increase in dust flux can support a phosphate drawdown of 0.25-0.5 micromolar.

A real-time photo-realistic rendering algorithm of ocean color based on bio-optical model

NASA Astrophysics Data System (ADS)

Ma, Chunyong; Xu, Shu; Wang, Hongsong; Tian, Fenglin; Chen, Ge

2016-12-01

A real-time photo-realistic rendering algorithm of ocean color is introduced in the paper, which considers the impact of ocean bio-optical model. The ocean bio-optical model mainly involves the phytoplankton, colored dissolved organic material (CDOM), inorganic suspended particle, etc., which have different contributions to absorption and scattering of light. We decompose the emergent light of the ocean surface into the reflected light from the sun and the sky, and the subsurface scattering light. We establish an ocean surface transmission model based on ocean bidirectional reflectance distribution function (BRDF) and the Fresnel law, and this model's outputs would be the incident light parameters of subsurface scattering. Using ocean subsurface scattering algorithm combined with bio-optical model, we compute the scattering light emergent radiation in different directions. Then, we blend the reflection of sunlight and sky light to implement the real-time ocean color rendering in graphics processing unit (GPU). Finally, we use two kinds of radiance reflectance calculated by Hydrolight radiative transfer model and our algorithm to validate the physical reality of our method, and the results show that our algorithm can achieve real-time highly realistic ocean color scenes.

Description and verification of a U.S. Naval Research Lab's loosely coupled data assimilation system for the Navy's Earth System Model

NASA Astrophysics Data System (ADS)

Barton, N. P.; Metzger, E. J.; Smedstad, O. M.; Ruston, B. C.; Wallcraft, A. J.; Whitcomb, T.; Ridout, J. A.; Zamudio, L.; Posey, P.; Reynolds, C. A.; Richman, J. G.; Phelps, M.

2017-12-01

The Naval Research Laboratory is developing an Earth System Model (NESM) to provide global environmental information to meet Navy and Department of Defense (DoD) operations and planning needs from the upper atmosphere to under the sea. This system consists of a global atmosphere, ocean, ice, wave, and land prediction models and the individual models include: atmosphere - NAVy Global Environmental Model (NAVGEM); ocean - HYbrid Coordinate Ocean Model (HYCOM); sea ice - Community Ice CodE (CICE); WAVEWATCH III™; and land - NAVGEM Land Surface Model (LSM). Data assimilation is currently loosely coupled between the atmosphere component using a 6-hour update cycle in the Naval Research Laboratory (NRL) Atmospheric Variational Data Assimilation System - Accelerated Representer (NAVDAS-AR) and the ocean/ice components using a 24-hour update cycle in the Navy Coupled Ocean Data Assimilation (NCODA) with 3 hours of incremental updating. This presentation will describe the US Navy's coupled forecast model, the loosely coupled data assimilation, and compare results against stand-alone atmosphere and ocean/ice models. In particular, we will focus on the unique aspects of this modeling system, which includes an eddy resolving ocean model and challenges associated with different update-windows and solvers for the data assimilation in the atmosphere and ocean. Results will focus on typical operational diagnostics for atmosphere, ocean, and ice analyses including 500 hPa atmospheric height anomalies, low-level winds, temperature/salinity ocean depth profiles, ocean acoustical proxies, sea ice edge, and sea ice drift. Overall, the global coupled system is performing with comparable skill to the stand-alone systems.

On the assimilation of absolute geodetic dynamic topography in a global ocean model: impact on the deep ocean state

NASA Astrophysics Data System (ADS)

Androsov, Alexey; Nerger, Lars; Schnur, Reiner; Schröter, Jens; Albertella, Alberta; Rummel, Reiner; Savcenko, Roman; Bosch, Wolfgang; Skachko, Sergey; Danilov, Sergey

2018-05-01

General ocean circulation models are not perfect. Forced with observed atmospheric fluxes they gradually drift away from measured distributions of temperature and salinity. We suggest data assimilation of absolute dynamical ocean topography (DOT) observed from space geodetic missions as an option to reduce these differences. Sea surface information of DOT is transferred into the deep ocean by defining the analysed ocean state as a weighted average of an ensemble of fully consistent model solutions using an error-subspace ensemble Kalman filter technique. Success of the technique is demonstrated by assimilation into a global configuration of the ocean circulation model FESOM over 1 year. The dynamic ocean topography data are obtained from a combination of multi-satellite altimetry and geoid measurements. The assimilation result is assessed using independent temperature and salinity analysis derived from profiling buoys of the AGRO float data set. The largest impact of the assimilation occurs at the first few analysis steps where both the model ocean topography and the steric height (i.e. temperature and salinity) are improved. The continued data assimilation over 1 year further improves the model state gradually. Deep ocean fields quickly adjust in a sustained manner: A model forecast initialized from the model state estimated by the data assimilation after only 1 month shows that improvements induced by the data assimilation remain in the model state for a long time. Even after 11 months, the modelled ocean topography and temperature fields show smaller errors than the model forecast without any data assimilation.

A coupled ice-ocean model of upwelling in the marginal ice zone

NASA Technical Reports Server (NTRS)

Roed, L. P.; Obrien, J. J.

1983-01-01

A dynamical coupled ice-ocean numerical model for the marginal ice zone (MIZ) is suggested and used to study upwelling dynamics in the MIZ. The nonlinear sea ice model has a variable ice concentration and includes internal ice stress. The model is forced by stresses on the air/ocean and air/ice surfaces. The main coupling between the ice and the ocean is in the form of an interfacial stress on the ice/ocean interface. The ocean model is a linear reduced gravity model. The wind stress exerted by the atmosphere on the ocean is proportional to the fraction of open water, while the interfacial stress ice/ocean is proportional to the concentration of ice. A new mechanism for ice edge upwelling is suggested based on a geostrophic equilibrium solution for the sea ice medium. The upwelling reported in previous models invoking a stationary ice cover is shown to be replaced by a weak downwelling due to the ice motion. Most of the upwelling dynamics can be understood by analysis of the divergence of the across ice edge upper ocean transport. On the basis of numerical model, an analytical model is suggested that reproduces most of the upwelling dynamics of the more complex numerical model.

The Spectral Ocean Wave Model (SOWM), a Northern Hemisphere Computer Model for Specifying and Forecasting Ocean Wave Spectra

DTIC Science & Technology

1982-07-01

directions. SIGNIFICANT WAVE HEIGHT A further sua-tion of (3) over the 15 frequency bands yields, within a linear model , the variance of a time history of...SPECTRAL Of.EAN WAVE MODEL (SOWM), A NORTHERN Final Report HEMtISPHEE COMPUTER MODELL Foyt SPECIFYING AND FORECASTING OCEAN WAVE .SftfTRA S EFRIGOG...Ocean Wave Model (SWM() In use at the Fleet Numerical Oceanography Center si.nce 1974 has been used to produce spectra for a 20- year ocean wave

Multimillennium changes in dissolved oxygen under global warming: results from an AOGCM and offline ocean biogeochemical model

NASA Astrophysics Data System (ADS)

Yamamoto, A.; Abe-Ouchi, A.; Shigemitsu, M.; Oka, A.; Takahashi, K.; Ohgaito, R.; Yamanaka, Y.

2016-12-01

Long-term oceanic oxygen change due to global warming is still unclear; most future projections (such as CMIP5) are only performed until 2100. Indeed, few previous studies using conceptual models project oxygen change in the next thousands of years, showing persistent global oxygen reduction by about 30% in the next 2000 years, even after atmospheric carbon dioxide stops rising. Yet, these models cannot sufficiently represent the ocean circulation change: the key driver of oxygen change. Moreover, considering serious effect oxygen reduction has on marine life and biogeochemical cycling, long-term oxygen change should be projected for higher validity. Therefore, we used a coupled atmosphere-ocean general circulation model (AOGCM) and an offline ocean biogeochemical model, investigating realistic long-term changes in oceanic oxygen concentration and ocean circulation. We integrated these models for 2000 years under atmospheric CO2 doubling and quadrupling. After global oxygen reduction in the first 500 years, oxygen concentration in deep ocean globally recovers and overshoots, despite surface oxygen decrease and weaker Atlantic Meridional Overturning Circulation. Deep ocean convection in the Weddell Sea recovers and overshoots, after initial cessation. Thus, enhanced deep convection and associated Antarctic Bottom Water supply oxygen-rich surface waters to deep ocean, resulting global deep ocean oxygenation. We conclude that the change in ocean circulation in the Southern Ocean potentially drives millennial-scale oxygenation in the deep ocean; contrary to past reported long-term oxygen reduction and general expectation. In presentation, we will discuss the mechanism of response of deep ocean convection in the Weddell Sea and show the volume changes of hypoxic waters.

Natural ocean carbon cycle sensitivity to parameterizations of the recycling in a climate model

NASA Astrophysics Data System (ADS)

Romanou, A.; Romanski, J.; Gregg, W. W.

2014-02-01

Sensitivities of the oceanic biological pump within the GISS (Goddard Institute for Space Studies ) climate modeling system are explored here. Results are presented from twin control simulations of the air-sea CO2 gas exchange using two different ocean models coupled to the same atmosphere. The two ocean models (Russell ocean model and Hybrid Coordinate Ocean Model, HYCOM) use different vertical coordinate systems, and therefore different representations of column physics. Both variants of the GISS climate model are coupled to the same ocean biogeochemistry module (the NASA Ocean Biogeochemistry Model, NOBM), which computes prognostic distributions for biotic and abiotic fields that influence the air-sea flux of CO2 and the deep ocean carbon transport and storage. In particular, the model differences due to remineralization rate changes are compared to differences attributed to physical processes modeled differently in the two ocean models such as ventilation, mixing, eddy stirring and vertical advection. GISSEH(GISSER) is found to underestimate mixed layer depth compared to observations by about 55% (10%) in the Southern Ocean and overestimate it by about 17% (underestimate by 2%) in the northern high latitudes. Everywhere else in the global ocean, the two models underestimate the surface mixing by about 12-34%, which prevents deep nutrients from reaching the surface and promoting primary production there. Consequently, carbon export is reduced because of reduced production at the surface. Furthermore, carbon export is particularly sensitive to remineralization rate changes in the frontal regions of the subtropical gyres and at the Equator and this sensitivity in the model is much higher than the sensitivity to physical processes such as vertical mixing, vertical advection and mesoscale eddy transport. At depth, GISSER, which has a significant warm bias, remineralizes nutrients and carbon faster thereby producing more nutrients and carbon at depth, which eventually resurfaces with the global thermohaline circulation especially in the Southern Ocean. Because of the reduced primary production and carbon export in GISSEH compared to GISSER, the biological pump efficiency, i.e., the ratio of primary production and carbon export at 75 m, is half in the GISSEH of that in GISSER, The Southern Ocean emerges as a key region where the CO2 flux is as sensitive to biological parameterizations as it is to physical parameterizations. The fidelity of ocean mixing in the Southern Ocean compared to observations is shown to be a good indicator of the magnitude of the biological pump efficiency regardless of physical model choice.

Natural Ocean Carbon Cycle Sensitivity to Parameterizations of the Recycling in a Climate Model

NASA Technical Reports Server (NTRS)

Romanou, A.; Romanski, J.; Gregg, W. W.

2014-01-01

Sensitivities of the oceanic biological pump within the GISS (Goddard Institute for Space Studies ) climate modeling system are explored here. Results are presented from twin control simulations of the air-sea CO2 gas exchange using two different ocean models coupled to the same atmosphere. The two ocean models (Russell ocean model and Hybrid Coordinate Ocean Model, HYCOM) use different vertical coordinate systems, and therefore different representations of column physics. Both variants of the GISS climate model are coupled to the same ocean biogeochemistry module (the NASA Ocean Biogeochemistry Model, NOBM), which computes prognostic distributions for biotic and abiotic fields that influence the air-sea flux of CO2 and the deep ocean carbon transport and storage. In particular, the model differences due to remineralization rate changes are compared to differences attributed to physical processes modeled differently in the two ocean models such as ventilation, mixing, eddy stirring and vertical advection. GISSEH(GISSER) is found to underestimate mixed layer depth compared to observations by about 55% (10 %) in the Southern Ocean and overestimate it by about 17% (underestimate by 2%) in the northern high latitudes. Everywhere else in the global ocean, the two models underestimate the surface mixing by about 12-34 %, which prevents deep nutrients from reaching the surface and promoting primary production there. Consequently, carbon export is reduced because of reduced production at the surface. Furthermore, carbon export is particularly sensitive to remineralization rate changes in the frontal regions of the subtropical gyres and at the Equator and this sensitivity in the model is much higher than the sensitivity to physical processes such as vertical mixing, vertical advection and mesoscale eddy transport. At depth, GISSER, which has a significant warm bias, remineralizes nutrients and carbon faster thereby producing more nutrients and carbon at depth, which eventually resurfaces with the global thermohaline circulation especially in the Southern Ocean. Because of the reduced primary production and carbon export in GISSEH compared to GISSER, the biological pump efficiency, i.e., the ratio of primary production and carbon export at 75 m, is half in the GISSEH of that in GISSER, The Southern Ocean emerges as a key region where the CO2 flux is as sensitive to biological parameterizations as it is to physical parameterizations. The fidelity of ocean mixing in the Southern Ocean compared to observations is shown to be a good indicator of the magnitude of the biological pump efficiency regardless of physical model choice.

On Verifying Currents and Other Features in the Hawaiian Islands Region Using Fully Coupled Ocean/Atmosphere Mesoscale Prediction System Compared to Global Ocean Model and Ocean Observations

NASA Astrophysics Data System (ADS)

Jessen, P. G.; Chen, S.

2014-12-01

This poster introduces and evaluates features concerning the Hawaii, USA region using the U.S. Navy's fully Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS-OS™) coupled to the Navy Coastal Ocean Model (NCOM). It also outlines some challenges in verifying ocean currents in the open ocean. The system is evaluated using in situ ocean data and initial forcing fields from the operational global Hybrid Coordinate Ocean Model (HYCOM). Verification shows difficulties in modelling downstream currents off the Hawaiian islands (Hawaii's wake). Comparing HYCOM to NCOM current fields show some displacement of small features such as eddies. Generally, there is fair agreement from HYCOM to NCOM in salinity and temperature fields. There is good agreement in SSH fields.

Drivers of Arctic Ocean warming in CMIP5 models

NASA Astrophysics Data System (ADS)

Burgard, Clara; Notz, Dirk

2017-05-01

We investigate changes in the Arctic Ocean energy budget simulated by 26 general circulation models from the Coupled Model Intercomparison Project Phase 5 framework. Our goal is to understand whether the Arctic Ocean warming between 1961 and 2099 is primarily driven by changes in the net atmospheric surface flux or by changes in the meridional oceanic heat flux. We find that the simulated Arctic Ocean warming is driven by positive anomalies in the net atmospheric surface flux in 11 models, by positive anomalies in the meridional oceanic heat flux in 11 models, and by positive anomalies in both energy fluxes in four models. The different behaviors are mainly characterized by the different changes in meridional oceanic heat flux that lead to different changes in the turbulent heat loss to the atmosphere. The multimodel ensemble mean is hence not representative of a consensus across the models in Arctic climate projections.

A perspective on sustained marine observations for climate modelling and prediction.

PubMed

Dunstone, Nick J

2014-09-28

Here, I examine some of the many varied ways in which sustained global ocean observations are used in numerical modelling activities. In particular, I focus on the use of ocean observations to initialize predictions in ocean and climate models. Examples are also shown of how models can be used to assess the impact of both current ocean observations and to simulate that of potential new ocean observing platforms. The ocean has never been better observed than it is today and similarly ocean models have never been as capable at representing the real ocean as they are now. However, there remain important unanswered questions that can likely only be addressed via future improvements in ocean observations. In particular, ocean observing systems need to respond to the needs of the burgeoning field of near-term climate predictions. Although new ocean observing platforms promise exciting new discoveries, there is a delicate balance to be made between their funding and that of the current ocean observing system. Here, I identify the need to secure long-term funding for ocean observing platforms as they mature, from a mainly research exercise to an operational system for sustained observation over climate change time scales. At the same time, considerable progress continues to be made via ship-based observing campaigns and I highlight some that are dedicated to addressing uncertainties in key ocean model parametrizations. The use of ocean observations to understand the prominent long time scale changes observed in the North Atlantic is another focus of this paper. The exciting first decade of monitoring of the Atlantic meridional overturning circulation by the RAPID-MOCHA array is highlighted. The use of ocean and climate models as tools to further probe the drivers of variability seen in such time series is another exciting development. I also discuss the need for a concerted combined effort from climate models and ocean observations in order to understand the current slow-down in surface global warming. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Improving model biases in an ESM with an isopycnic ocean component by accounting for wind work on oceanic near-inertial motions.

NASA Astrophysics Data System (ADS)

de Wet, P. D.; Bentsen, M.; Bethke, I.

2016-02-01

It is well-known that, when comparing climatological parameters such as ocean temperature and salinity to the output of an Earth System Model (ESM), the model exhibits biases. In ESMs with an isopycnic ocean component, such as NorESM, insufficient vertical mixing is thought to be one of the causes of such differences between observational and model data. However, enhancing the vertical mixing of the model's ocean component not only requires increasing the energy input, but also sound physical reasoning for doing so. Various authors have shown that the action of atmospheric winds on the ocean's surface is a major source of energy input into the upper ocean. However, due to model and computational constraints, oceanic processes linked to surface winds are incompletely accounted for. Consequently, despite significantly contributing to the energy required to maintain ocean stratification, most ESMs do not directly make provision for this energy. In this study we investigate the implementation of a routine in which the energy from work done on oceanic near-inertial motions is calculated in an offline slab model. The slab model, which has been well-documented in the literature, runs parallel to but independently from the ESM's ocean component. It receives wind fields with a frequency higher than that of the coupling frequency, allowing it to capture the fluctuations in the winds on shorter time scales. The additional energy calculated thus is then passed to the ocean component, avoiding the need for increased coupling between the components of the ESM. Results show localised reduction in, amongst others, the salinity and temperature biases of NorESM, confirming model sensitivity to wind-forcing and points to the need for better representation of surface processes in ESMs.

Effects of surface wave breaking on the oceanic boundary layer

NASA Astrophysics Data System (ADS)

He, Hailun; Chen, Dake

2011-04-01

Existing laboratory studies suggest that surface wave breaking may exert a significant impact on the formation and evolution of oceanic surface boundary layer, which plays an important role in the ocean-atmosphere coupled system. However, present climate models either neglect the effects of wave breaking or treat them implicitly through some crude parameterization. Here we use a one-dimensional ocean model (General Ocean Turbulence Model, GOTM) to investigate the effects of wave breaking on the oceanic boundary layer on diurnal to seasonal time scales. First a set of idealized experiments are carried out to demonstrate the basic physics and the necessity to include wave breaking. Then the model is applied to simulating observations at the northern North Sea and the Ocean Weather Station Papa, which shows that properly accounting for wave breaking effects can improve model performance and help it to successfully capture the observed upper ocean variability.

The DEBOT Model, a New Global Barotropic Ocean Tidal Model: Test Computations and an Application in Related Geophysical Disciplines

NASA Astrophysics Data System (ADS)

Einspigel, D.; Sachl, L.; Martinec, Z.

2014-12-01

We present the DEBOT model, which is a new global barotropic ocean model. The DEBOT model is primarily designed for modelling of ocean flow generated by the tidal attraction of the Moon and the Sun, however it can be used for other ocean applications where the barotropic model is sufficient, for instance, a tsunami wave propagation. The model has been thoroughly tested by several different methods: 1) synthetic example which involves a tsunami-like wave propagation of an initial Gaussian depression and testing of the conservation of integral invariants, 2) a benchmark study with another barotropic model, the LSGbt model, has been performed and 3) results of realistic simulations have been compared with data from tide gauge measurements around the world. The test computations prove the validity of the numerical code and demonstrate the ability of the DEBOT model to simulate the realistic ocean tides. The DEBOT model will be principaly applied in related geophysical disciplines, for instance, in an investigation of an influence of the ocean tides on the geomagnetic field or the Earth's rotation. A module for modelling of the secondary poloidal magnetic field generated by an ocean flow is already implemented in the DEBOT model and preliminary results will be presented. The future aim is to assimilate magnetic data provided by the Swarm satellite mission into the ocean flow model.

Impact of the Fraser River Geometry on Tides and the River Plumes in a Model of the Fraser River Plume

NASA Astrophysics Data System (ADS)

Liu, J.; Allen, S. E.; Soontiens, N. K.

2016-02-01

Fraser River is the largest river on the west coast of Canada. It empties into the Strait of Georgia, which is a large, semi-enclosed body of water between Vancouver Island and the mainland of British Columbia. We have developed a three-dimensional model of the Strait of Georgia, including the Fraser River plume, using the NEMO model in its regional configuration. This operational model produces daily nowcasts and forecasts for salinity, temperature, currents and sea surface heights. Observational data available for evaluation of the model includes daily British Columbia ferry salinity data, profile data and surface drifter data. The salinity of the modelled Fraser River plume agrees well with ferry based measurements of salinity. However, large discrepencies exist between the modelled and observed position of the plume. Modelled surface currents compared to drifter observations show that the model has too strong along-strait velocities and too weak cross-strait velocities. We investigated the impact of river geometry. A sensitivity experiment was performed comparing the original, short, shallow river channel to an extended and deepened river channel. With the latter bathymetry, tidal amplitudes within Fraser River correspond well with observations. Comparisons to drifter tracks show that the surface currents have been improved with the new bathymetry. However, substantial discrepencies remain. We will discuss how reducing vertical eddy viscosity and other changes further improve the modelled position of the plume.

Excitation of the Earth's Chandler wobble by a turbulent oceanic double-gyre

NASA Astrophysics Data System (ADS)

Naghibi, S. E.; Jalali, M. A.; Karabasov, S. A.; Alam, M.-R.

2017-04-01

We develop a layer-averaged, multiple-scale spectral ocean model and show how an oceanic double-gyre can communicate with the Earth's Chandler wobble. The overall transfers of energy and angular momentum from the double-gyre to the Chandler wobble are used to calibrate the turbulence parameters of the layer-averaged model. Our model is tested against a multilayer quasi-geostrophic ocean model in turbulent regime, and base states used in parameter identification are obtained from mesoscale eddy resolving numerical simulations. The Chandler wobble excitation function obtained from the model predicts a small role of North Atlantic ocean region on the wobble dynamics as compared to all oceans, in agreement with the existing observations.

Sensitivity of simulated deep ocean natural radiocarbon to gas exchange velocity and historical atmospheric Δ14C variations

NASA Astrophysics Data System (ADS)

Wagner, Hannes; Koeve, Wolfgang; Kriest, Iris; Oschlies, Andreas

2015-04-01

Simulated deep ocean natural radiocarbon is frequently used to assess model performance of deep ocean ventilation in Ocean General Circulation Models (OGCMs). It has been shown to be sensitive to a variety of model parameters, such as the mixing parameterization, convection scheme and vertical resolution. Here we use three different ocean models (MIT2.8, ECCO, UVic) to evaluate the sensitivity of simulated deep ocean natural radiocarbon to two other factors, while keeping the model physics constant: (1) the gas exchange velocity and (2) historic variations in atmospheric Δ^1^4C boundary conditions. We find that simulated natural Δ^1^4C decreases by 14-20 ‰ throughout the deep ocean and consistently in all three models, if the gas exchange velocity is lowered by 30 % with respect to the OCMIP-2 protocol, to become more consistent with newer estimates of the oceans uptake of bomb derived ^1^4C. Simulated deep ocean natural Δ^1^4C furthermore decreases by 3-9 ‰ throughout the deep Pacific, Indian and Southern Oceans and consistently in all three models, if the models are forced with the observed atmospheric Δ^1^4C history, instead of an often made pragmatic assumption of a constant atmospheric Δ^1^4C value of zero. Applying both improvements (gas exchange reduction, as well as atmospheric Δ^1^4C history implementation) concomitantly and accounting for the present uncertainty in gas exchange velocity estimates (between 10 and 40 % reduction with respect to the OCMIP-2 protocol) simulated deep ocean Δ^1^4C decreases by 10-30 ‰ throughout the deep Pacific, Indian and Southern Ocean. This translates to a ^1^4C-age increase of 100-300 years and indicates, that models, which in former assessments (based on the OCMIP-2 protocol) had been identified to have an accurate deep ocean ventilation, should now be regarded as rather having a bit too sluggish a ventilation. Models, which on the other hand had been identified to have a bit too fast a deep ocean ventilation, should now be regarded as rather having a more accurate ventilation.

High-resolution coupled ice sheet-ocean modeling using the POPSICLES model

NASA Astrophysics Data System (ADS)

Ng, E. G.; Martin, D. F.; Asay-Davis, X.; Price, S. F.; Collins, W.

2014-12-01

It is expected that a primary driver of future change of the Antarctic ice sheet will be changes in submarine melting driven by incursions of warm ocean water into sub-ice shelf cavities. Correctly modeling this response on a continental scale will require high-resolution modeling of the coupled ice-ocean system. We describe the computational and modeling challenges in our simulations of the full Southern Ocean coupled to a continental-scale Antarctic ice sheet model at unprecedented spatial resolutions (0.1 degree for the ocean model and adaptive mesh refinement down to 500m in the ice sheet model). The POPSICLES model couples the POP2x ocean model, a modified version of the Parallel Ocean Program (Smith and Gent, 2002), with the BISICLES ice-sheet model (Cornford et al., 2012) using a synchronous offline-coupling scheme. Part of the PISCEES SciDAC project and built on the Chombo framework, BISICLES makes use of adaptive mesh refinement to fully resolve dynamically-important regions like grounding lines and employs a momentum balance similar to the vertically-integrated formulation of Schoof and Hindmarsh (2009). Results of BISICLES simulations have compared favorably to comparable simulations with a Stokes momentum balance in both idealized tests like MISMIP3D (Pattyn et al., 2013) and realistic configurations (Favier et al. 2014). POP2x includes sub-ice-shelf circulation using partial top cells (Losch, 2008) and boundary layer physics following Holland and Jenkins (1999), Jenkins (2001), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008) and other continental-scale simulations and melt-rate observations (Kimura et al., 2013; Rignot et al., 2013). For the POPSICLES Antarctic-Southern Ocean simulations, ice sheet and ocean models communicate at one-month coupling intervals.

High sensitivity detectors for measurement of diffusion, emanation and low activity of radon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mamedov, Fadahat; Štekl, Ivan; Smolek, Karel

Today's underground experiments require ultra-low background conditions. One of the most important source of background is radon. It is necessary to suppress it and consequently to detect very low radon concentration. In the frame of SuperNEMO collaboration experimental setups for measurement of low radon activity, radon diffusion through shielding foils and radon emanation from construction materials have been constructed in IEAP CTU in Prague and the obtained results are presented. The application of Timepix device in radon detection is briefly discussed.

R&D for an innovative acoustic positioning system for the KM3NeT neutrino telescope

NASA Astrophysics Data System (ADS)

Ameli, F.; Ardid, M.; Bertin, V.; Bonori, M.; Bou-Cabo, M.; Calì, C.; D'Amico, A.; Giovanetti, G.; Imbesi, M.; Keller, P.; Larosa, G.; Llorens, C. D.; Masullo, R.; Randazzo, N.; Riccobene, G.; Speziale, F.; Viola, S.; KM3NeT Consortium

2011-01-01

An innovative Acoustic Positioning System for the km3-scale neutrino telescope has been designed and is under realization within the KM3NeT Consortium. Compared to the Acoustic Positioning Systems used for the km3 demonstrators, ANTARES and NEMO Phase 1, this new system is based on the “all data to shore” concept and it will permit the enhancement of detector positioning performances, reduction of costs and its use as real-time monitor of environmental acoustic noise.

DOE Office of Scientific and Technical Information (OSTI.GOV)

NEMO Collaboration

Double beta decay of {sup 100}Mo (172g) is studied with the NEMO 2 detector in the Frejus Underground Laboratory. The experiment has now accumulated 2485 hours of data taking. A clear signal of 380 events for 2{beta}2{nu} decay has been obtained corresponding to a half-life of T{sub {1/2}} = 1.0 {plus_minus} 0.08 (syst.) 10{sup 19} y. Limits are presented for 2{beta}(0{nu}, {chi}), 2{beta}0{nu} (ground state and excited states 2{sub 1}{sup +} and 0{sub 1}{sup +}). The experiment will run til October 1993.

High Resolution Simulations of Arctic Sea Ice, 1979-1993

DTIC Science & Technology

2003-01-01

William H. Lipscomb * PO[ARISSP To evaluate improvements in modelling Arctic sea ice, we compare results from two regional models at 1/120 horizontal...resolution. The first is a coupled ice-ocean model of the Arctic Ocean, consisting of an ocean model (adapted from the Parallel Ocean Program, Los...Alamos National Laboratory [LANL]) and the "old" sea ice model . The second model uses the same grid but consists of an improved "new" sea ice model (LANL

Neutrinoless double-β decay of Se82 in the shell model: Beyond the closure approximation

NASA Astrophysics Data System (ADS)

Sen'kov, R. A.; Horoi, M.; Brown, B. A.

2014-05-01

We recently proposed a method [R. A. Senkov and M. Horoi, Phys. Rev. C 88, 064312 (2013), 10.1103/PhysRevC.88.064312] to calculate the standard nuclear matrix elements for neutrinoless double-β decay (0νββ) of Ca48 going beyond the closure approximation. Here we extend this analysis to the important case of Se82, which was chosen as the base isotope for the upcoming SuperNEMO experiment. We demonstrate that by using a mixed method that considers information from closure and nonclosure approaches, one can get excellent convergence properties for the nuclear matrix elements, which allows one to avoid unmanageable computational costs. We show that in contrast with the closure approximation the mixed approach has a very weak dependence on the average closure energy. The matrix elements for the heavy neutrino-exchange mechanism that could contribute to the 0νββ decay of Se82 are also presented.

NBodyLab Simulation Experiments with GRAPE-6a AND MD-GRAPE2 Acceleration

NASA Astrophysics Data System (ADS)

Johnson, V.; Ates, A.

2005-12-01

NbodyLab is an astrophysical N-body simulation testbed for student research. It is accessible via a web interface and runs as a backend framework under Linux. NbodyLab can generate data models or perform star catalog lookups, transform input data sets, perform direct summation gravitational force calculations using a variety of integration schemes, and produce analysis and visualization output products. NEMO (Teuben 1994), a popular stellar dynamics toolbox, is used for some functions. NbodyLab integrators can optionally utilize two types of low-cost desktop supercomputer accelerators, the newly available GRAPE-6a (125 Gflops peak) and the MD-GRAPE2 (64-128 Gflops peak). The initial version of NBodyLab was presented at ADASS 2002. This paper summarizes software enhancements developed subsequently, focusing on GRAPE-6a related enhancements, and gives examples of computational experiments and astrophysical research, including star cluster and solar system studies, that can be conducted with the new testbed functionality.

Biogeochemical modelling of dissolved oxygen in a changing ocean.

PubMed

Andrews, Oliver; Buitenhuis, Erik; Le Quéré, Corinne; Suntharalingam, Parvadha

2017-09-13

Secular decreases in dissolved oxygen concentration have been observed within the tropical oxygen minimum zones (OMZs) and at mid- to high latitudes over the last approximately 50 years. Earth system model projections indicate that a reduction in the oxygen inventory of the global ocean, termed ocean deoxygenation, is a likely consequence of on-going anthropogenic warming. Current models are, however, unable to consistently reproduce the observed trends and variability of recent decades, particularly within the established tropical OMZs. Here, we conduct a series of targeted hindcast model simulations using a state-of-the-art global ocean biogeochemistry model in order to explore and review biases in model distributions of oceanic oxygen. We show that the largest magnitude of uncertainty is entrained into ocean oxygen response patterns due to model parametrization of p CO 2 -sensitive C : N ratios in carbon fixation and imposed atmospheric forcing data. Inclusion of a p CO 2 -sensitive C : N ratio drives historical oxygen depletion within the ocean interior due to increased organic carbon export and subsequent remineralization. Atmospheric forcing is shown to influence simulated interannual variability in ocean oxygen, particularly due to differences in imposed variability of wind stress and heat fluxes.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'. © 2017 The Author(s).

Biogeochemical modelling of dissolved oxygen in a changing ocean

NASA Astrophysics Data System (ADS)

Andrews, Oliver; Buitenhuis, Erik; Le Quéré, Corinne; Suntharalingam, Parvadha

2017-08-01

Secular decreases in dissolved oxygen concentration have been observed within the tropical oxygen minimum zones (OMZs) and at mid- to high latitudes over the last approximately 50 years. Earth system model projections indicate that a reduction in the oxygen inventory of the global ocean, termed ocean deoxygenation, is a likely consequence of on-going anthropogenic warming. Current models are, however, unable to consistently reproduce the observed trends and variability of recent decades, particularly within the established tropical OMZs. Here, we conduct a series of targeted hindcast model simulations using a state-of-the-art global ocean biogeochemistry model in order to explore and review biases in model distributions of oceanic oxygen. We show that the largest magnitude of uncertainty is entrained into ocean oxygen response patterns due to model parametrization of pCO2-sensitive C : N ratios in carbon fixation and imposed atmospheric forcing data. Inclusion of a pCO2-sensitive C : N ratio drives historical oxygen depletion within the ocean interior due to increased organic carbon export and subsequent remineralization. Atmospheric forcing is shown to influence simulated interannual variability in ocean oxygen, particularly due to differences in imposed variability of wind stress and heat fluxes. This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.

A recipe for simulating the interannual variability of the Asian summer monsoon and its relation with ENSO

NASA Astrophysics Data System (ADS)

Bracco, Annalisa; Kucharski, Fred; Molteni, Franco; Hazeleger, Wilco; Severijns, Camiel

2007-04-01

This study investigates how accurately the interannual variability over the Indian Ocean basin and the relationship between the Indian summer monsoon and the El Niño Southern Oscillation (ENSO) can be simulated by different modelling strategies. With a hierarchy of models, from an atmospherical general circulation model (AGCM) forced by observed SST, to a coupled model with the ocean component limited to the tropical Pacific and Indian Oceans, the role of heat fluxes and of interactive coupling is analyzed. Whenever sea surface temperature anomalies in the Indian basin are created by the coupled model, the inverse relationship between the ENSO index and the Indian summer monsoon rainfall is recovered, and it is preserved if the atmospherical model is forced by the SSTs created by the coupled model. If the ocean model domain is limited to the Indian Ocean, changes in the Walker circulation over the Pacific during El-Niño years induce a decrease of rainfall over the Indian subcontinent. However, the observed correlation between ENSO and the Indian Ocean zonal mode (IOZM) is not properly modelled and the two indices are not significantly correlated, independently on season. Whenever the ocean domain extends to the Pacific, and ENSO can impact both the atmospheric circulation and the ocean subsurface in the equatorial Eastern Indian Ocean, modelled precipitation patterns associated both to ENSO and to the IOZM closely resemble the observations.

"One-Stop Shopping" for Ocean Remote-Sensing and Model Data

NASA Technical Reports Server (NTRS)

Li, P. Peggy; Vu, Quoc; Chao, Yi; Li, Zhi-Jin; Choi, Jei-Kook

2006-01-01

OurOcean Portal 2.0 (http:// ourocean.jpl.nasa.gov) is a software system designed to enable users to easily gain access to ocean observation data, both remote-sensing and in-situ, configure and run an Ocean Model with observation data assimilated on a remote computer, and visualize both the observation data and the model outputs. At present, the observation data and models focus on the California coastal regions and Prince William Sound in Alaska. This system can be used to perform both real-time and retrospective analyses of remote-sensing data and model outputs. OurOcean Portal 2.0 incorporates state-of-the-art information technologies (IT) such as MySQL database, Java Web Server (Apache/Tomcat), Live Access Server (LAS), interactive graphics with Java Applet at the Client site and MatLab/GMT at the server site, and distributed computing. OurOcean currently serves over 20 real-time or historical ocean data products. The data are served in pre-generated plots or their native data format. For some of the datasets, users can choose different plotting parameters and produce customized graphics. OurOcean also serves 3D Ocean Model outputs generated by ROMS (Regional Ocean Model System) using LAS. The Live Access Server (LAS) software, developed by the Pacific Marine Environmental Laboratory (PMEL) of the National Oceanic and Atmospheric Administration (NOAA), is a configurable Web-server program designed to provide flexible access to geo-referenced scientific data. The model output can be views as plots in horizontal slices, depth profiles or time sequences, or can be downloaded as raw data in different data formats, such as NetCDF, ASCII, Binary, etc. The interactive visualization is provided by graphic software, Ferret, also developed by PMEL. In addition, OurOcean allows users with minimal computing resources to configure and run an Ocean Model with data assimilation on a remote computer. Users may select the forcing input, the data to be assimilated, the simulation period, and the output variables and submit the model to run on a backend parallel computer. When the run is complete, the output will be added to the LAS server for

Ocean acidification over the next three centuries using a simple global climate carbon-cycle model: projections and sensitivities

DOE PAGES

Hartin, Corinne A.; Bond-Lamberty, Benjamin; Patel, Pralit; ...

2016-08-01

Continued oceanic uptake of anthropogenic CO 2 is projected to significantly alter the chemistry of the upper oceans over the next three centuries, with potentially serious consequences for marine ecosystems. Relatively few models have the capability to make projections of ocean acidification, limiting our ability to assess the impacts and probabilities of ocean changes. In this study we examine the ability of Hector v1.1, a reduced-form global model, to project changes in the upper ocean carbonate system over the next three centuries, and quantify the model's sensitivity to parametric inputs. Hector is run under prescribed emission pathways from the Representativemore » Concentration Pathways (RCPs) and compared to both observations and a suite of Coupled Model Intercomparison (CMIP5) model outputs. Current observations confirm that ocean acidification is already taking place, and CMIP5 models project significant changes occurring to 2300. Hector is consistent with the observational record within both the high- (> 55°) and low-latitude oceans (< 55°). The model projects low-latitude surface ocean pH to decrease from preindustrial levels of 8.17 to 7.77 in 2100, and to 7.50 in 2300; aragonite saturation levels (Ω Ar) decrease from 4.1 units to 2.2 in 2100 and 1.4 in 2300 under RCP 8.5. These magnitudes and trends of ocean acidification within Hector are largely consistent with the CMIP5 model outputs, although we identify some small biases within Hector's carbonate system. Of the parameters tested, changes in [H +] are most sensitive to parameters that directly affect atmospheric CO 2 concentrations – Q 10 (terrestrial respiration temperature response) as well as changes in ocean circulation, while changes in Ω Ar saturation levels are sensitive to changes in ocean salinity and Q 10. We conclude that Hector is a robust tool well suited for rapid ocean acidification projections and sensitivity analyses, and it is capable of emulating both current observations and large-scale climate models under multiple emission pathways.« less

Ocean acidification over the next three centuries using a simple global climate carbon-cycle model: projections and sensitivities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hartin, Corinne A.; Bond-Lamberty, Benjamin; Patel, Pralit

Continued oceanic uptake of anthropogenic CO 2 is projected to significantly alter the chemistry of the upper oceans over the next three centuries, with potentially serious consequences for marine ecosystems. Relatively few models have the capability to make projections of ocean acidification, limiting our ability to assess the impacts and probabilities of ocean changes. In this study we examine the ability of Hector v1.1, a reduced-form global model, to project changes in the upper ocean carbonate system over the next three centuries, and quantify the model's sensitivity to parametric inputs. Hector is run under prescribed emission pathways from the Representativemore » Concentration Pathways (RCPs) and compared to both observations and a suite of Coupled Model Intercomparison (CMIP5) model outputs. Current observations confirm that ocean acidification is already taking place, and CMIP5 models project significant changes occurring to 2300. Hector is consistent with the observational record within both the high- (> 55°) and low-latitude oceans (< 55°). The model projects low-latitude surface ocean pH to decrease from preindustrial levels of 8.17 to 7.77 in 2100, and to 7.50 in 2300; aragonite saturation levels (Ω Ar) decrease from 4.1 units to 2.2 in 2100 and 1.4 in 2300 under RCP 8.5. These magnitudes and trends of ocean acidification within Hector are largely consistent with the CMIP5 model outputs, although we identify some small biases within Hector's carbonate system. Of the parameters tested, changes in [H +] are most sensitive to parameters that directly affect atmospheric CO 2 concentrations – Q 10 (terrestrial respiration temperature response) as well as changes in ocean circulation, while changes in Ω Ar saturation levels are sensitive to changes in ocean salinity and Q 10. We conclude that Hector is a robust tool well suited for rapid ocean acidification projections and sensitivity analyses, and it is capable of emulating both current observations and large-scale climate models under multiple emission pathways.« less

Ocean acidification over the next three centuries using a simple global climate carbon-cycle model: projections and sensitivities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hartin, Corinne A.; Bond-Lamberty, Benjamin; Patel, Pralit

Continued oceanic uptake of anthropogenic CO 2 is projected to significantly alter the chemistry of the upper oceans over the next three centuries, with potentially serious consequences for marine ecosystems. Relatively few models have the capability to make projections of ocean acidification, limiting our ability to assess the impacts and probabilities of ocean changes. In this study we examine the ability of Hector v1.1, a reduced-form global model, to project changes in the upper ocean carbonate system over the next three centuries, and quantify the model's sensitivity to parametric inputs. Hector is run under prescribed emission pathways from the Representativemore » Concentration Pathways (RCPs) and compared to both observations and a suite of Coupled Model Intercomparison (CMIP5) model outputs. Current observations confirm that ocean acidification is already taking place, and CMIP5 models project significant changes occurring to 2300. Hector is consistent with the observational record within both the high- (> 55°) and low-latitude oceans (< 55°). The model projects low-latitude surface ocean pH to decrease from preindustrial levels of 8.17 to 7.77 in 2100, and to 7.50 in 2300; aragonite saturation levels (Ω Ar) decrease from 4.1 units to 2.2 in 2100 and 1.4 in 2300 under RCP 8.5. These magnitudes and trends of ocean acidification within Hector are largely consistent with the CMIP5 model outputs, although we identify some small biases within Hector's carbonate system. Of the parameters tested, changes in [H +] are most sensitive to parameters that directly affect atmospheric CO 2 concentrations – Q 10 (terrestrial respiration temperature response) as well as changes in ocean circulation, while changes in Ω Ar saturation levels are sensitive to changes in ocean salinity and Q 10. We conclude that Hector is a robust tool well suited for rapid ocean acidification projections and sensitivity analyses, and it is capable of emulating both current observations and large-scale climate models under multiple emission pathways.« less

An iceberg model implementation in ACME.

NASA Astrophysics Data System (ADS)

Comeau, D.; Turner, A. K.; Hunke, E. C.

2017-12-01

Icebergs represent approximately half of the mass flux from the Antarctic ice sheet, transporting freshwater and nutrients away from the coast to the Southern Ocean. Icebergs impact the surrounding ocean and sea ice environment, and serve as nutrient sources for biogeochemical activity, yet these processes are typically not resolved in current climate models. We have implemented a parameterization for iceberg drift and decay into the Department of Energy's Accelerated Climate Model for Energy (ACME), where the ocean, sea ice, and land ice components are based on the unstructured grid modeling framework Multiple Prediction Across Scales (MPAS), to improve the representation of Antarctic mass flux to the Southern Ocean and its impacts on ocean stratification and circulation, sea ice, and biogeochemical processes in a fully coupled global climate model. The iceberg model is implemented in two frameworks: Lagrangian and Eulerian. The Lagrangian framework embeds individual icebergs into the ocean and sea ice grids, and will be useful in modeling `giant' (>10 nautical miles) iceberg events, which may have highly localized impacts on ocean and sea ice. The Eulerian framework allows us to model a realistic population of Antarctic icebergs without the computational expense of individual particle tracking to simulate the aggregate impact on the Southern Ocean climate system. This capability, together with under ice-shelf ocean cavities and dynamic ice-shelf fronts, will allow for extremely high fidelity simulation of the southern cryosphere within ACME.

A simple model of the effect of ocean ventilation on ocean heat uptake

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nadiga, Balasubramanya T.; Urban, Nathan Mark

Presentation includes slides on Earth System Models vs. Simple Climate Models; A Popular SCM: Energy Balance Model of Anomalies; On calibrating against one ESM experiment, the SCM correctly captures that ESM's surface warming response with other forcings; Multi-Model Analysis: Multiple ESMs, Single SCM; Posterior Distributions of ECS; However In Excess of 90% of TOA Energy Imbalance is Sequestered in the World Oceans; Heat Storage in the Two Layer Model; Heat Storage in the Two Layer Model; Including TOA Rad. Imbalance and Ocean Heat in Calibration Improves Repr., but Significant Errors Persist; Improved Vertical Resolution Does Not Fix Problem; A Seriesmore » of Expts. Confirms That Anomaly-Diffusing Models Cannot Properly Represent Ocean Heat Uptake; Physics of the Thermocline; Outcropping Isopycnals and Horizontally-Averaged Layers; Local interactions between outcropping isopycnals leads to non-local interactions between horizontally-averaged layers; Both Surface Warming and Ocean Heat are Well Represented With Just 4 Layers; A Series of Expts. Confirms That When Non-Local Interactions are Allowed, the SCMs Can Represent Both Surface Warming and Ocean Heat Uptake; and Summary and Conclusions.« less

Evaluating the Ocean Component of the US Navy Earth System Model

NASA Astrophysics Data System (ADS)

Zamudio, L.

2017-12-01

Ocean currents, temperature, and salinity observations are used to evaluate the ocean component of the US Navy Earth System Model. The ocean and atmosphere components of the system are an eddy-resolving (1/12.5° equatorial resolution) version of the HYbrid Coordinate Ocean Model (HYCOM), and a T359L50 version of the NAVy Global Environmental Model (NAVGEM), respectively. The system was integrated in hindcast mode and the ocean results are compared against unassimilated observations, a stand-alone version of HYCOM, and the Generalized Digital Environment Model ocean climatology. The different observation types used in the system evaluation are: drifting buoys, temperature profiles, salinity profiles, and acoustical proxies (mixed layer depth, sonic layer depth, below layer gradient, and acoustical trapping). To evaluate the system's performance in each different metric, a scorecard is used to translate the system's errors into scores, which provide an indication of the system's skill in both space and time.

Collaborative Project. Understanding the effects of tides and eddies on the ocean dynamics, sea ice cover and decadal/centennial climate prediction using the Regional Arctic Climate Model (RACM)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchings, Jennifer; Joseph, Renu

2013-09-14

The goal of this project is to develop an eddy resolving ocean model (POP) with tides coupled to a sea ice model (CICE) within the Regional Arctic System Model (RASM) to investigate the importance of ocean tides and mesoscale eddies in arctic climate simulations and quantify biases associated with these processes and how their relative contribution may improve decadal to centennial arctic climate predictions. Ocean, sea ice and coupled arctic climate response to these small scale processes will be evaluated with regard to their influence on mass, momentum and property exchange between oceans, shelf-basin, ice-ocean, and ocean-atmosphere. The project willmore » facilitate the future routine inclusion of polar tides and eddies in Earth System Models when computing power allows. As such, the proposed research addresses the science in support of the BER’s Climate and Environmental Sciences Division Long Term Measure as it will improve the ocean and sea ice model components as well as the fully coupled RASM and Community Earth System Model (CESM) and it will make them more accurate and computationally efficient.« less

Climate Ocean Modeling on Parallel Computers

NASA Technical Reports Server (NTRS)

Wang, P.; Cheng, B. N.; Chao, Y.

1998-01-01

Ocean modeling plays an important role in both understanding the current climatic conditions and predicting future climate change. However, modeling the ocean circulation at various spatial and temporal scales is a very challenging computational task.

A simple model of the effect of ocean ventilation on ocean heat uptake

NASA Astrophysics Data System (ADS)

Nadiga, Balu; Urban, Nathan

2017-11-01

Transport of water from the surface mixed layer into the ocean interior is achieved, in large part, by the process of ventilation-a process associated with outcropping isopycnals. Starting from such a configuration of outcropping isopycnals, we derive a simple model of the effect of ventilation on ocean uptake of anomalous radiative forcing. This model can be seen as an improvement of the popular anomaly-diffusing class of energy balance models (AD-EBM) that are routinely employed to analyze and emulate the warming response of both observed and simulated Earth system. We demonstrate that neither multi-layer, nor continuous-diffusion AD-EBM variants can properly represent both surface-warming and the vertical distribution of ocean heat uptake. The new model overcomes this deficiency. The simplicity of the models notwithstanding, the analysis presented and the necessity of the modification is indicative of the role played by processes related to the down-welling branch of global ocean circulation in shaping the vertical distribution of ocean heat uptake.

Ocean (de)oxygenation from the Last Glacial Maximum to the twenty-first century: insights from Earth System models.

PubMed

Bopp, L; Resplandy, L; Untersee, A; Le Mezo, P; Kageyama, M

2017-09-13

All Earth System models project a consistent decrease in the oxygen content of oceans for the coming decades because of ocean warming, reduced ventilation and increased stratification. But large uncertainties for these future projections of ocean deoxygenation remain for the subsurface tropical oceans where the major oxygen minimum zones are located. Here, we combine global warming projections, model-based estimates of natural short-term variability, as well as data and model estimates of the Last Glacial Maximum (LGM) ocean oxygenation to gain some insights into the major mechanisms of oxygenation changes across these different time scales. We show that the primary uncertainty on future ocean deoxygenation in the subsurface tropical oceans is in fact controlled by a robust compensation between decreasing oxygen saturation (O 2sat ) due to warming and decreasing apparent oxygen utilization (AOU) due to increased ventilation of the corresponding water masses. Modelled short-term natural variability in subsurface oxygen levels also reveals a compensation between O 2sat and AOU, controlled by the latter. Finally, using a model simulation of the LGM, reproducing data-based reconstructions of past ocean (de)oxygenation, we show that the deoxygenation trend of the subsurface ocean during deglaciation was controlled by a combination of warming-induced decreasing O 2sat and increasing AOU driven by a reduced ventilation of tropical subsurface waters.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'. © 2017 The Author(s).

Ocean (de)oxygenation from the Last Glacial Maximum to the twenty-first century: insights from Earth System models

NASA Astrophysics Data System (ADS)

Bopp, L.; Resplandy, L.; Untersee, A.; Le Mezo, P.; Kageyama, M.

2017-08-01

All Earth System models project a consistent decrease in the oxygen content of oceans for the coming decades because of ocean warming, reduced ventilation and increased stratification. But large uncertainties for these future projections of ocean deoxygenation remain for the subsurface tropical oceans where the major oxygen minimum zones are located. Here, we combine global warming projections, model-based estimates of natural short-term variability, as well as data and model estimates of the Last Glacial Maximum (LGM) ocean oxygenation to gain some insights into the major mechanisms of oxygenation changes across these different time scales. We show that the primary uncertainty on future ocean deoxygenation in the subsurface tropical oceans is in fact controlled by a robust compensation between decreasing oxygen saturation (O2sat) due to warming and decreasing apparent oxygen utilization (AOU) due to increased ventilation of the corresponding water masses. Modelled short-term natural variability in subsurface oxygen levels also reveals a compensation between O2sat and AOU, controlled by the latter. Finally, using a model simulation of the LGM, reproducing data-based reconstructions of past ocean (de)oxygenation, we show that the deoxygenation trend of the subsurface ocean during deglaciation was controlled by a combination of warming-induced decreasing O2sat and increasing AOU driven by a reduced ventilation of tropical subsurface waters. This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.

Impact of Targeted Ocean Observations for Improving Ocean Model Initialization for Coupled Hurricane Forecasting

NASA Astrophysics Data System (ADS)

Halliwell, G. R.; Srinivasan, A.; Kourafalou, V. H.; Yang, H.; Le Henaff, M.; Atlas, R. M.

2012-12-01

The accuracy of hurricane intensity forecasts produced by coupled forecast models is influenced by errors and biases in SST forecasts produced by the ocean model component and the resulting impact on the enthalpy flux from ocean to atmosphere that powers the storm. Errors and biases in fields used to initialize the ocean model seriously degrade SST forecast accuracy. One strategy for improving ocean model initialization is to design a targeted observing program using airplanes and in-situ devices such as floats and drifters so that assimilation of the additional data substantially reduces errors in the ocean analysis system that provides the initial fields. Given the complexity and expense of obtaining these additional observations, observing system design methods such as OSSEs are attractive for designing efficient observing strategies. A new fraternal-twin ocean OSSE system based on the HYbrid Coordinate Ocean Model (HYCOM) is used to assess the impact of targeted ocean profiles observed by hurricane research aircraft, and also by in-situ float and drifter deployments, on reducing errors in initial ocean fields. A 0.04-degree HYCOM simulation of the Gulf of Mexico is evaluated as the nature run by determining that important ocean circulation features such as the Loop Current and synoptic cyclones and anticyclones are realistically simulated. The data-assimilation system is run on a 0.08-degree HYCOM mesh with substantially different model configuration than the nature run, and it uses a new ENsemble Kalman Filter (ENKF) algorithm optimized for the ocean model's hybrid vertical coordinates. The OSSE system is evaluated and calibrated by first running Observing System Experiments (OSEs) to evaluate existing observing systems, specifically quantifying the impact of assimilating more than one satellite altimeter, and also the impact of assimilating targeted ocean profiles taken by the NOAA WP-3D hurricane research aircraft in the Gulf of Mexico during the Deepwater Horizon oil spill. OSSE evaluation and calibration is then performed by repeating these two OSEs with synthetic observations and comparing the resulting observing system impact to determine if it differs from the OSE results. OSSEs are first run to evaluate different airborne sampling strategies with respect to temporal frequency of flights and the horizontal separation of upper-ocean profiles during each flight. They are then run to assess the impact of releasing multiple floats and gliders. Evaluation strategy focuses on error reduction in fields important for hurricane forecasting such as the structure of ocean currents and eddies, upper ocean heat content distribution, and upper-ocean stratification.

Simulations of Antarctic ice shelves and the Southern Ocean in the POP2x ocean model coupled with the BISICLES ice-sheet model

NASA Astrophysics Data System (ADS)

Asay-Davis, Xylar; Martin, Daniel; Price, Stephen; Maltrud, Mathew

2014-05-01

We present initial results from Antarctic, ice-ocean coupled simulations using large-scale ocean circulation and ice-sheet evolution models. This presentation focuses on the ocean model, POP2x, which is a modified version of POP, a fully eddying, global-scale ocean model (Smith and Gent, 2002). POP2x allows for circulation beneath ice shelf cavities using the method of partial top cells (Losch, 2008). Boundary layer physics, which control fresh water and salt exchange at the ice-ocean interface, are implemented following Holland and Jenkins (1999), Jenkins (2001), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008) and other continental-scale simulations and melt-rate observations (Kimura et al., 2013; Rignot et al., 2013) and with results from other idealized ice-ocean coupling test cases (e.g., Goldberg et al., 2012). A companion presentation, 'Fully resolved whole-continent Antarctica simulations using the BISICLES AMR ice sheet model coupled with the POP2x Ocean Model', concentrates more on the ice-sheet model, BISICLES (Cornford et al., 2012), which includes a 1st-order accurate momentum balance (L1L2) and uses block structured, adaptive-mesh refinement to more accurately model regions of dynamic complexity, such as ice streams, outlet glaciers, and grounding lines. For idealized test cases focused on marine-ice sheet dynamics, BISICLES output compares very favorably relative to simulations based on the full, nonlinear Stokes momentum balance (MISMIP-3d; Pattyn et al., 2013). Here, we present large-scale (Southern Ocean) simulations using POP2x at 0.1 degree resolution with fixed ice shelf geometries, which are used to obtain and validate modeled submarine melt rates against observations. These melt rates are, in turn, used to force evolution of the BISICLES model. An offline-coupling scheme, which we compare with the ice-ocean coupling work of Goldberg et al. (2012), is then used to sequentially update the sub-shelf cavity geometry seen by POP2x.

Development and Utilization of Regional Oceanic Modeling System (ROMS). Delicacy, Imprecision, and Uncertainty of Oceanic Simulations: An Investigation with the Regional Oceanic Modeling System (ROMS). Mixing in the Ocean Surface Layer Using the Regional Oceanic Modeling System (ROMS).

DTIC Science & Technology

2011-09-30

community use for ROMS is biogeochemisty: chemical cycles, water quality, blooms , micro-nutrients, larval dispersal, biome transitions, and coupling to...J.C. McWilliams, X. Capet, and J. Kurian, 2010: Heat balance and eddies in the Peru- Chile Current System. Climate Dynamics, 37, in press. doi10.1007

Characteristics of the ocean simulations in the Max Planck Institute Ocean Model (MPIOM) the ocean component of the MPI-Earth system model

NASA Astrophysics Data System (ADS)

Jungclaus, J. H.; Fischer, N.; Haak, H.; Lohmann, K.; Marotzke, J.; Matei, D.; Mikolajewicz, U.; Notz, D.; von Storch, J. S.

2013-06-01

MPI-ESM is a new version of the global Earth system model developed at the Max Planck Institute for Meteorology. This paper describes the ocean state and circulation as well as basic aspects of variability in simulations contributing to the fifth phase of the Coupled Model Intercomparison Project (CMIP5). The performance of the ocean/sea-ice model MPIOM, coupled to a new version of the atmosphere model ECHAM6 and modules for land surface and ocean biogeochemistry, is assessed for two model versions with different grid resolution in the ocean. The low-resolution configuration has a nominal resolution of 1.5°, whereas the higher resolution version features a quasiuniform, eddy-permitting global resolution of 0.4°. The paper focuses on important oceanic features, such as surface temperature and salinity, water mass distribution, large-scale circulation, and heat and freshwater transports. In general, these integral quantities are simulated well in comparison with observational estimates, and improvements in comparison with the predecessor system are documented; for example, for tropical variability and sea ice representation. Introducing an eddy-permitting grid configuration in the ocean leads to improvements, in particular, in the representation of interior water mass properties in the Atlantic and in the representation of important ocean currents, such as the Agulhas and Equatorial current systems. In general, however, there are more similarities than differences between the two grid configurations, and several shortcomings, known from earlier versions of the coupled model, prevail.

Assessment of ocean models in Mediterranean Sea against altimetry and gravimetry measurements

NASA Astrophysics Data System (ADS)

Fenoglio-Marc, Luciana; Uebbing, Bernd; Kusche, Jürgen

2017-04-01

This work aims at assessing in a regional study in the Mediterranean Sea the agreement between ocean model outputs and satellite altimetry and satellite gravity observations. Satellite sea level change are from altimeter data made available by the Sea Level Climate Change Initiative (SLCCI) and from satellite gravity data made available by GRACE. We consider two ocean simulations not assimilating satellite altimeter data and one ocean model reanalysis assimilating satellite altimetry. Ocean model simulations can provide some insight on the ocean variability, but they are affected by biases due to errors in model formulation, specification of initial states and forcing, and are not directly constrained by observations. Their trend can be quite different from the altimetric observations due to surface radiation biases, however they are physically consistent. Ocean reanalyses are the combination of ocean models, atmospheric forcing fluxes and ocean observations via data assimilation methods and have the potential to provide more accurate information than observation-only or model-only based ocean estimations. They will be closer to altimetry at long and short timescales, but assimilation may destroy mass consistency. We use two ocean simulations which are part of the Med-CORDEX initiative (https://www.medcordex.eu). The first is the CNRM-RCM4 fully-coupled Regional Climate System Model (RCMS) simulation developed at METEOFRANCE for 1980-2012. The second is the PROTHEUS standalone hindcast simulation developed at ENEA and covers the interval 1960-2012. The third model is the regional model MEDSEA_REANALYSIS_PHIS_006_004 assimilating satellite altimeter data (http://marine.copernicus.eu/) and available over 1987-2014. Comparison at basin and regional scale are made. First the steric, thermo-steric, halosteric and dynamic components output of the models are compared. Then the total sea level given by the models is compared to the altimeter observations. Finally the mass component derived from GRACE is compared to the difference between the total sea level and the steric component. We observe large differences between the ocean models and discuss the model which best agrees with the CCI sea level product at short and at longer timescales. We consider departure in sea level trends, inter-annual variability and seasonal cycle. The work is part of the Sea Level Climate Change Initiative project.

Application of the Convolution Formalism to the Ocean Tide Potential: Results from the Gravity and Recovery and Climate Experiment (GRACE)

NASA Technical Reports Server (NTRS)

Desai, S. D.; Yuan, D. -N.

2006-01-01

A computationally efficient approach to reducing omission errors in ocean tide potential models is derived and evaluated using data from the Gravity Recovery and Climate Experiment (GRACE) mission. Ocean tide height models are usually explicitly available at a few frequencies, and a smooth unit response is assumed to infer the response across the tidal spectrum. The convolution formalism of Munk and Cartwright (1966) models this response function with a Fourier series. This allows the total ocean tide height, and therefore the total ocean tide potential, to be modeled as a weighted sum of past, present, and future values of the tide-generating potential. Previous applications of the convolution formalism have usually been limited to tide height models, but we extend it to ocean tide potential models. We use luni-solar ephemerides to derive the required tide-generating potential so that the complete spectrum of the ocean tide potential is efficiently represented. In contrast, the traditionally adopted harmonic model of the ocean tide potential requires the explicit sum of the contributions from individual tidal frequencies. It is therefore subject to omission errors from neglected frequencies and is computationally more intensive. Intersatellite range rate data from the GRACE mission are used to compare convolution and harmonic models of the ocean tide potential. The monthly range rate residual variance is smaller by 4-5%, and the daily residual variance is smaller by as much as 15% when using the convolution model than when using a harmonic model that is defined by twice the number of parameters.

The new version of the Institute of Numerical Mathematics Sigma Ocean Model (INMSOM) for simulation of Global Ocean circulation and its variability

NASA Astrophysics Data System (ADS)

Gusev, Anatoly; Fomin, Vladimir; Diansky, Nikolay; Korshenko, Evgeniya

2017-04-01

In this paper, we present the improved version of the ocean general circulation sigma-model developed in the Institute of Numerical Mathematics of the Russian Academy of Sciences (INM RAS). The previous version referred to as INMOM (Institute of Numerical Mathematics Ocean Model) is used as the oceanic component of the IPCC climate system model INMCM (Institute of Numerical Mathematics Climate Model (Volodin et al 2010,2013). Besides, INMOM as the only sigma-model was used for simulations according to CORE-II scenario (Danabasoglu et al. 2014,2016; Downes et al. 2015; Farneti et al. 2015). In general, INMOM results are comparable to ones of other OGCMs and were used for investigation of climatic variations in the North Atlantic (Gusev and Diansky 2014). However, detailed analysis of some CORE-II INMOM results revealed some disadvantages of the INMOM leading to considerable errors in reproducing some ocean characteristics. So, the mass transport in the Antarctic Circumpolar Current (ACC) was overestimated. As well, there were noticeable errors in reproducing thermohaline structure of the ocean. After analysing the previous results, the new version of the OGCM was developed. It was decided to entitle is INMSOM (Institute of Numerical Mathematics Sigma Ocean Model). The new title allows one to distingwish the new model, first, from its older version, and second, from another z-model developed in the INM RAS and referred to as INMIO (Institute of Numerical Mathematics and Institute of Oceanology ocean model) (Ushakov et al. 2016). There were numerous modifications in the model, some of them are as follows. 1) Formulation of the ocean circulation problem in terms of full free surface with taking into account water amount variation. 2) Using tensor form of lateral viscosity operator invariant to rotation. 3) Using isopycnal diffusion including Gent-McWilliams mixing. 4) Using atmospheric forcing computation according to NCAR methodology (Large and Yeager 2009). 5) Improvement river runoff algorithm accounting the total amount of discharged water. 6) Using explicit leapfrog time scheme for all lateral operators and implicit Euler scheme for vertical diffusion and viscosity. The INMSOM is tested by reproducing World Ocean circulation and thermohaline characteristics using the well-proved CORE dataset. The presentation is devoted to the analysis of new INMSOM simulation results, estimation of their quality and comparison to the ones previously obtained with the INMOM. The main aim of the INMSOM development is using it as the oceanic component of the next version of INMCM. The work was supported by the Russian Foundation for Basic Research (grants № 16-05-00534 and № 15-05-07539) References 1. Danabasoglu, G., Yeager S.G., Bailey D., et al., 2014: North Atlantic simulations in Coordinated Ocean-ice Reference Experiments phase II (CORE-II). Part I: Mean states. Ocean Modelling, 73, 76-107. 2. Danabasoglu, G., Yeager S.G., Kim W.M. et al., 2016: North Atlantic simulations in Coordinated Ocean-ice Reference Experiments phase II (CORE-II). Part II: Inter-annual to decadal variability. Ocean Modelling, 97, 65-90. 3. Downes S.M., Farneti R., Uotila P. et al. An assessment of Southern Ocean water masses and sea ice during 1988-2007 in a suite of interannual CORE-II simulations. Ocean Modelling (2015), 94, 67-94. 4. Farneti R., Downes S.M., Griffies S.M. et al. An assessment of Antarctic Circumpolar Current and Southern Ocean Meridional Overturning Circulation during 1958-2007 in a suite of interannual CORE-II simulations, Ocean Modelling (2015), 93, 84-120. 5. Gusev A.V. and Diansky N.A. Numerical simulation of the World ocean circulation and its climatic variability for 1948-2007 using the INMOM. Izvestiya, Atmospheric and Oceanic Physics, 2014, V. 50, N. 1, P. 1-12 6. Large, W., Yeager, S., 2009. The global climatology of an interannually varying air-sea flux data set. Clim Dyn, V. 33, P. 341-364. 7. Ushakov K.V., Grankina T.B., Ibraev R.A. Modeling the water circulation in the North Atlantic in the scope of the CORE-II experiment. Izvestiya, Atmospheric and Oceanic Physics. 2016. V. 52, № 4, P. 365-375

Oceanic sources of predictability for MJO propagation across the Maritime Continent in a subset of S2S forecast models

NASA Astrophysics Data System (ADS)

DeMott, C. A.; Klingaman, N. P.

2017-12-01

Skillful prediction of the Madden-Julian oscillation (MJO) passage across the Maritime Continent (MC) has important implications for global forecasts of high-impact weather events, such as atmospheric rivers and heat waves. The North American teleconnection response to the MJO is strongest when MJO convection is located in the western Pacific Ocean, but many climate and forecast models are deficient in their simulation of MC-crossing MJO events. Compared to atmosphere-only general circulation models (AGCMs), MJO simulation skill generally improves with the addition of ocean feedbacks in coupled GCMs (CGCMs). Using observations, previous studies have noted that the degree of ocean coupling may vary considerably from one MJO event to the next. The coupling mechanisms may be linked to the presence of ocean Equatorial Rossby waves, the sign and amplitude of Equatorial surface currents, and the upper ocean temperature and salinity profiles. In this study, we assess the role of ocean feedbacks to MJO prediction skill using a subset of CGCMs participating in the Subseasonal-to-Seasonal (S2S) Project database. Oceanic observational and reanalysis datasets are used to characterize the upper ocean background state for observed MJO events that do and do not propagate beyond the MC. The ability of forecast models to capture the oceanic influence on the MJO is first assessed by quantifying SST forecast skill. Next, a set of previously developed air-sea interaction diagnostics is applied to model output to measure the role of SST perturbations on the forecast MJO. The "SST effect" in forecast MJO events is compared to that obtained from reanalysis data. Leveraging all ensemble members of a given forecast helps disentangle oceanic model biases from atmospheric model biases, both of which can influence the expression of ocean feedbacks in coupled forecast systems. Results of this study will help identify areas of needed model improvement for improved MJO forecasts.

The PP4R1 sub-unit of protein phosphatase PP4 is essential for inhibition of NF-κB by merkel polyomavirus small tumour antigen.

PubMed

Abdul-Sada, Hussein; Müller, Marietta; Mehta, Rajni; Toth, Rachel; Arthur, J Simon C; Whitehouse, Adrian; Macdonald, Andrew

2017-04-11

Merkel cell carcinoma (MCC) is a highly aggressive skin cancer with a high metastatic potential. The majority of MCC cases are caused by the Merkel cell polyomavirus (MCPyV), through expression of the virus-encoded tumour antigens. Whilst mechanisms attributing tumour antigen expression to transformation are being uncovered, little is known of the mechanisms by which MCPyV persists in the host. We previously identified the MCPyV small T antigen (tAg) as a novel inhibitor of nuclear factor kappa B (NF-kB) signalling and a modulator of the host anti-viral response. Here we demonstrate that regulation of NF-kB activation involves a previously undocumented interaction between tAg and regulatory sub-unit 1 of protein phosphatase 4 (PP4R1). Formation of a complex with PP4R1 and PP4c is required to bridge MCPyV tAg to the NEMO adaptor protein, allowing deactivation of the NF-kB pathway. Mutations in MCPyV tAg that fail to interact with components of this complex, or siRNA depletion of PP4R1, prevents tAg-mediated inhibition of NF-kB and pro-inflammatory cytokine production. Comparison of tAg binding partners from other human polyomavirus demonstrates that interactions with NEMO and PP4R1 are unique to MCPyV. Collectively, these data identify PP4R1 as a novel target for virus subversion of the host anti-viral response.

The Effects of Better Environmental Inputs in Estimating Sea Clutter

DTIC Science & Technology

1988-01-01

3.2 A Spectral Ocean Wave Model: DWAVE 11 3.3 Limitations of DWAVE 11 4. HYBRID MODEL DEVELOPMENT 12 4.1 Overall Plan 12 4.2 High Resolution...intensive. 10 3.2 A Spectral Ocean Wave Model: DWAVE Most of the spectral ocean wave models give essentially the same type of outputs, for example, the...sea clutter estimation. A deep ocean wave model DWAVE by Offshore & Coastal Technologies, Inc. (OCTI) has been chosen because it can be run on a

Role of buccal corridor in smile esthetics and its correlation with underlying skeletal and dental structures.

PubMed

Tikku, Tripti; Khanna, Rohit; Maurya, R P; Ahmad, Nabeel

2012-01-01

This study was designed to evaluate the buccal corridor in smile esthetics and to correlate it with underlying hard tissues. Posed smiling frontal photographs, digital posterior-anterior (PA) cephalograms, and study models of 25 males and 25 females in age range of 18-25 years were taken. Photographs were evaluated for smile esthetics by eight orthodontists, eight plastic surgeons, eight beauticians and eight lay people to group them into three groups with least attractive, average and attractive smile and buccal corridor width was measured. Digital PA cephalograms were transferred on Nemo-tech software for frontal facial analysis. Intercanine and intermolar widths were measured on upper study model with the help of a digital calliper. The buccal corridor width was least in attractive smile group and maximum in least attractive smile group. The buccal corridor width had a negligible correlation with hard tissues and a mild to moderate inverse correlation with intercanine and intermolar widths within the groups. As the amount of buccal corridor display was increased, smiling images were scored less attractive by the evaluators. The buccal corridor is not influenced by underlying skeletal hard tissues but have mild to moderate inverse correlation with the intercanine and intermolar width.

LES Modeling of Lateral Dispersion in the Ocean on Scales of 10 m to 10 km

DTIC Science & Technology

2015-10-20

ocean on scales of 0.1-10 km that can be implemented in larger-scale ocean models. These parameterizations will incorporate the effects of local...ocean on scales of 0.1-10 km that can be implemented in larger-scale ocean models. These parameterizations will incorporate the effects of local...www.fields.utoronto.ca/video-archive/static/2013/06/166-1766/mergedvideo.ogv) and at the Nonlinear Effects in Internal Waves Conference held at Cornell University

Impact of Typhoons on the Western Pacific Ocean (ITOP) DRI: Numerical Modeling of Ocean Mixed Layer Turbulence and Entrainment at High Winds

DTIC Science & Technology

2013-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Impact of Typhoons on the Western Pacific Ocean (ITOP...The measurement and modeling activities include a focus on the impact of surface waves, air-sea fluxes and the temperature, salinity and velocity...SUBTITLE Impact of Typhoons on the Western Pacific Ocean (ITOP) DRI: Numerical Modeling of Ocean Mixed Layer Turbulence and Entrainment at High Winds

New Observationally-Based Metrics for the Analysis of Coupled Climate Model and Earth System Model Simulations of the Southern Ocean

NASA Astrophysics Data System (ADS)

Russell, J. L.

2014-12-01

The exchange of heat and carbon dioxide between the atmosphere and ocean are major controls on Earth's climate under conditions of anthropogenic forcing. The Southern Ocean south of 30°S, occupying just over ¼ of the surface ocean area, accounts for a disproportionate share of the vertical exchange of properties between the deep and surface waters of the ocean and between the surface ocean and the atmosphere; thus this region can be disproportionately influential on the climate system. Despite the crucial role of the Southern Ocean in the climate system, understanding of the particular mechanisms involved remains inadequate, and the model studies underlying many of these results are highly controversial. As part of the overall goal of working toward reducing uncertainties in climate projections, we present an analysis using new data/model metrics based on a unified framework of theory, quantitative datasets, and numerical modeling. These new metrics quantify the mechanisms, processes, and tendencies relevant to the role of the Southern Ocean in climate.

Deep Ocean Warming Assessed from Altimeters, GRACE, 3 In-situ Measurements, and a Non-Boussinesq OGCM

NASA Technical Reports Server (NTRS)

Song, Y. Tony; Colberg, Frank

2011-01-01

Observational surveys have shown significant oceanic bottom water warming, but they are too spatially and temporally sporadic to quantify the deep ocean contribution to the present-day sea level rise (SLR). In this study, altimetry sea surface height (SSH), Gravity Recovery and Climate Experiment (GRACE) ocean mass, and in situ upper ocean (0-700 m) steric height have been assessed for their seasonal variability and trend maps. It is shown that neither the global mean nor the regional trends of altimetry SLR can be explained by the upper ocean steric height plus the GRACE ocean mass. A non-Boussinesq ocean general circulation model (OGCM), allowing the sea level to rise as a direct response to the heat added into the ocean, is then used to diagnose the deep ocean steric height. Constrained by sea surface temperature data and the top of atmosphere (TOA) radiation measurements, the model reproduces the observed upper ocean heat content well. Combining the modeled deep ocean steric height with observational upper ocean data gives the full depth steric height. Adding a GRACE-estimated mass trend, the data-model combination explains not only the altimetry global mean SLR but also its regional trends fairly well. The deep ocean warming is mostly prevalent in the Atlantic and Indian oceans, and along the Antarctic Circumpolar Current, suggesting a strong relation to the oceanic circulation and dynamics. Its comparison with available bottom water measurements shows reasonably good agreement, indicating that deep ocean warming below 700 m might have contributed 1.1 mm/yr to the global mean SLR or one-third of the altimeter-observed rate of 3.11 +/- 0.6 mm/yr over 1993-2008.

Global Modeling of Internal Tides Within an Eddying Ocean General Circulation Model

DTIC Science & Technology

2012-06-01

atmosphere and ocean (Yu and Weller, 2007 ). Salinities in the upper ocean are set by the difference between evaporation and precipitation at the ocean...surface (Yu, 2007 ; Schmitt, 2008). Because the buoyancy (density) of seawater at the ocean surface is con- trolled by temperature and salinity, the...days, these currents mean- der and generate highly energetic meso- scale eddies (Schmitz, 1996a,b; Stammer , 1997), the spinning oceanic dynamical

Model study of the ship emissions impact on the air quality in the Adriatic/Ionian area

NASA Astrophysics Data System (ADS)

Karagiannidis, Athanasios; Poupkou, Anastasia; Liora, Natalia; Dimopoulos, Spiros; Giannaros, Christos; Melas, Dimitrios; Argiriou, Athanassios

2015-04-01

The increase of the ship traffic for touristic and commercial purposes is one of the EU Blue Growth targets. The Adriatic/Ionian is one of the sea-basin strategic areas for this target. The purpose of the study is the examination of the impact of the ship emissions on the gaseous and particulate pollutants concentrations in the Adriatic/Ionian area for which the current scientific knowledge is limited. The impact is simulated over a domain covering the Central and Eastern Mediterranean in 10 km resolution during a summer period (July) and a winter period (January) of the year 2012. The modeling system used consists of the photochemical model CAMx off line coupled with the meteorological model WRF. The zero-out modeling method is implemented involving CAMx simulations performed while including and omitting the ship emission data. The simulations are based on the European scale anthropogenic emission inventory of The Netherlands Organisation (TNO) for the reference year 2009. Natural emissions (NMVOCs from the vegetation, sea salt, wind-blown dust), estimated with the use of the Natural Emission MOdel (NEMO) developed by the Aristotle University of Thessaloniki, are accounted for in the photochemical model runs. The spatial distribution of the resulting differences in the gaseous and particulate pollutant concentration fields for both emission scenarios are presented and discussed, providing an estimation of the contribution of ship emissions on the determination of the air quality in the Adriatic/Ionian countries

Ethane ocean on Titan

NASA Technical Reports Server (NTRS)

Lunine, J. I.; Stevenson, D. J.; Yung, Y.L.

1983-01-01

Voyager I radio occultation data is employed to develop a qualitative model of an ethane ocean on Titan. It is suggested that the ocean contains 25 percent CH4 and that the ocean is in dynamic equilibrium with an N2 atmosphere. Previous models of a CH4 ocean are discounted due to photolysis rates of CH4 gas. Tidal damping of Titan's orbital eccentricity is taken as evidence for an ocean layer approximately 1 km deep, with the ocean floor being covered with a solid C2H2 layer 100 to 200 m thick. The photolytic process disrupting the CH4, if the estimates of the oceanic content of CH4 are correct, could continue for at least one billion years. Verification of the model is dependent on detecting CH4 clouds in the lower atmosphere, finding C2H6 saturation in the lower troposphere, or obtaining evidence of a global ocean.

The influence of the ocean circulation state on ocean carbon storage and CO2 drawdown potential in an Earth system model

NASA Astrophysics Data System (ADS)

Ödalen, Malin; Nycander, Jonas; Oliver, Kevin I. C.; Brodeau, Laurent; Ridgwell, Andy

2018-03-01

During the four most recent glacial cycles, atmospheric CO2 during glacial maxima has been lowered by about 90-100 ppm with respect to interglacials. There is widespread consensus that most of this carbon was partitioned in the ocean. It is, however, still debated which processes were dominant in achieving this increased carbon storage. In this paper, we use an Earth system model of intermediate complexity to explore the sensitivity of ocean carbon storage to ocean circulation state. We carry out a set of simulations in which we run the model to pre-industrial equilibrium, but in which we achieve different states of ocean circulation by changing forcing parameters such as wind stress, ocean diffusivity and atmospheric heat diffusivity. As a consequence, the ensemble members also have different ocean carbon reservoirs, global ocean average temperatures, biological pump efficiencies and conditions for air-sea CO2 disequilibrium. We analyse changes in total ocean carbon storage and separate it into contributions by the solubility pump, the biological pump and the CO2 disequilibrium component. We also relate these contributions to differences in the strength of the ocean overturning circulation. Depending on which ocean forcing parameter is tuned, the origin of the change in carbon storage is different. When wind stress or ocean diapycnal diffusivity is changed, the response of the biological pump gives the most important effect on ocean carbon storage, whereas when atmospheric heat diffusivity or ocean isopycnal diffusivity is changed, the solubility pump and the disequilibrium component are also important and sometimes dominant. Despite this complexity, we obtain a negative linear relationship between total ocean carbon and the combined strength of the northern and southern overturning cells. This relationship is robust to different reservoirs dominating the response to different forcing mechanisms. Finally, we conduct a drawdown experiment in which we investigate the capacity for increased carbon storage by artificially maximising the efficiency of the biological pump in our ensemble members. We conclude that different initial states for an ocean model result in different capacities for ocean carbon storage due to differences in the ocean circulation state and the origin of the carbon in the initial ocean carbon reservoir. This could explain why it is difficult to achieve comparable responses of the ocean carbon pumps in model inter-comparison studies in which the initial states vary between models. We show that this effect of the initial state is quantifiable. The drawdown experiment highlights the importance of the strength of the biological pump in the control state for model studies of increased biological efficiency.

Global Climate Impacts of Fixing the Southern Ocean Shortwave Radiation Bias in the Community Earth System Model (CESM)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kay, Jennifer E.; Wall, Casey; Yettella, Vineel

Here, a large, long-standing, and pervasive climate model bias is excessive absorbed shortwave radiation (ASR) over the midlatitude oceans, especially the Southern Ocean. This study investigates both the underlying mechanisms for and climate impacts of this bias within the Community Earth System Model, version 1, with the Community Atmosphere Model, version 5 [CESM1(CAM5)]. Excessive Southern Ocean ASR in CESM1(CAM5) results in part because low-level clouds contain insufficient amounts of supercooled liquid. In a present-day atmosphere-only run, an observationally motivated modification to the shallow convection detrainment increases supercooled cloud liquid, brightens low-level clouds, and substantially reduces the Southern Ocean ASR bias.more » Tuning to maintain global energy balance enables reduction of a compensating tropical ASR bias. In the resulting preindustrial fully coupled run with a brighter Southern Ocean and dimmer tropics, the Southern Ocean cools and the tropics warm. As a result of the enhanced meridional temperature gradient, poleward heat transport increases in both hemispheres (especially the Southern Hemisphere), and the Southern Hemisphere atmospheric jet strengthens. Because northward cross-equatorial heat transport reductions occur primarily in the ocean (80%), not the atmosphere (20%), a proposed atmospheric teleconnection linking Southern Ocean ASR bias reduction and cooling with northward shifts in tropical precipitation has little impact. In summary, observationally motivated supercooled liquid water increases in shallow convective clouds enable large reductions in long-standing climate model shortwave radiation biases. Of relevance to both model bias reduction and climate dynamics, quantifying the influence of Southern Ocean cooling on tropical precipitation requires a model with dynamic ocean heat transport.« less

Global Climate Impacts of Fixing the Southern Ocean Shortwave Radiation Bias in the Community Earth System Model (CESM)

DOE PAGES

Kay, Jennifer E.; Wall, Casey; Yettella, Vineel; ...

2016-06-10

Here, a large, long-standing, and pervasive climate model bias is excessive absorbed shortwave radiation (ASR) over the midlatitude oceans, especially the Southern Ocean. This study investigates both the underlying mechanisms for and climate impacts of this bias within the Community Earth System Model, version 1, with the Community Atmosphere Model, version 5 [CESM1(CAM5)]. Excessive Southern Ocean ASR in CESM1(CAM5) results in part because low-level clouds contain insufficient amounts of supercooled liquid. In a present-day atmosphere-only run, an observationally motivated modification to the shallow convection detrainment increases supercooled cloud liquid, brightens low-level clouds, and substantially reduces the Southern Ocean ASR bias.more » Tuning to maintain global energy balance enables reduction of a compensating tropical ASR bias. In the resulting preindustrial fully coupled run with a brighter Southern Ocean and dimmer tropics, the Southern Ocean cools and the tropics warm. As a result of the enhanced meridional temperature gradient, poleward heat transport increases in both hemispheres (especially the Southern Hemisphere), and the Southern Hemisphere atmospheric jet strengthens. Because northward cross-equatorial heat transport reductions occur primarily in the ocean (80%), not the atmosphere (20%), a proposed atmospheric teleconnection linking Southern Ocean ASR bias reduction and cooling with northward shifts in tropical precipitation has little impact. In summary, observationally motivated supercooled liquid water increases in shallow convective clouds enable large reductions in long-standing climate model shortwave radiation biases. Of relevance to both model bias reduction and climate dynamics, quantifying the influence of Southern Ocean cooling on tropical precipitation requires a model with dynamic ocean heat transport.« less

Ocean Hydrodynamics Numerical Model in Curvilinear Coordinates for Simulating Circulation of the Global Ocean and its Separate Basins.

NASA Astrophysics Data System (ADS)

Gusev, Anatoly; Diansky, Nikolay; Zalesny, Vladimir

2010-05-01

The original program complex is proposed for the ocean circulation sigma-model, developed in the Institute of Numerical Mathematics (INM), Russian Academy of Sciences (RAS). The complex can be used in various curvilinear orthogonal coordinate systems. In addition to ocean circulation model, the complex contains a sea ice dynamics and thermodynamics model, as well as the original system of the atmospheric forcing implementation on the basis of both prescribed meteodata and atmospheric model results. This complex can be used as the oceanic block of Earth climate model as well as for solving the scientific and practical problems concerning the World ocean and its separate oceans and seas. The developed program complex can be effectively used on parallel shared memory computational systems and on contemporary personal computers. On the base of the complex proposed the ocean general circulation model (OGCM) was developed. The model is realized in the curvilinear orthogonal coordinate system obtained by the conformal transformation of the standard geographical grid that allowed us to locate the system singularities outside the integration domain. The horizontal resolution of the OGCM is 1 degree on longitude, 0.5 degree on latitude, and it has 40 non-uniform sigma-levels in depth. The model was integrated for 100 years starting from the Levitus January climatology using the realistic atmospheric annual cycle calculated on the base of CORE datasets. The experimental results showed us that the model adequately reproduces the basic characteristics of large-scale World Ocean dynamics, that is in good agreement with both observational data and results of the best climatic OGCMs. This OGCM is used as the oceanic component of the new version of climatic system model (CSM) developed in INM RAS. The latter is now ready for carrying out the new numerical experiments on climate and its change modelling according to IPCC (Intergovernmental Panel on Climate Change) scenarios in the scope of the CMIP-5 (Coupled Model Intercomparison Project). On the base of the complex proposed the Pacific Ocean circulation eddy-resolving model was realized. The integration domain covers the Pacific from Equator to Bering Strait. The model horizontal resolution is 0.125 degree and it has 20 non-uniform sigma-levels in depth. The model adequately reproduces circulation large-scale structure and its variability: Kuroshio meandering, ocean synoptic eddies, frontal zones, etc. Kuroshio high variability is shown. The distribution of contaminant was simulated that is admittedly wasted near Petropavlovsk-Kamchatsky. The results demonstrate contaminant distribution structure and provide us understanding of hydrological fields formation processes in the North-West Pacific.

Ocean Raman Scattering in Satellite Backscatter UV Measurements

NASA Technical Reports Server (NTRS)

Vasilkov, Alexander P.; Joiner, Joanna; Gleason, James; Bhartia, Pawan; Bhartia, P. K. (Technical Monitor)

2002-01-01

Ocean Raman scattering significantly contributes to the filling-in of solar Fraunhofer lines measured by satellite backscatter ultraviolet (buy) instruments in the cloudless atmosphere over clear ocean waters. A model accounting for this effect in buy measurements is developed and compared with observations from the Global Ozone Monitoring Experiment (GONE). The model extends existing models for ocean Raman scattering to the UV spectral range. Ocean Raman scattering radiance is propagated through the atmosphere using a concept of the Lambert equivalent reflectively and an accurate radiative transfer model for Rayleigh scattering. The model and observations can be used to evaluate laboratory measurements of pure water absorption in the UV. The good agreement between model and observations suggests that buy instruments may be useful for estimating chlorophyll content.

The Crossover Time as an Evaluation of Ocean Models Against Persistence

NASA Astrophysics Data System (ADS)

Phillipson, L. M.; Toumi, R.

2018-01-01

A new ocean evaluation metric, the crossover time, is defined as the time it takes for a numerical model to equal the performance of persistence. As an example, the average crossover time calculated using the Lagrangian separation distance (the distance between simulated trajectories and observed drifters) for the global MERCATOR ocean model analysis is found to be about 6 days. Conversely, the model forecast has an average crossover time longer than 6 days, suggesting limited skill in Lagrangian predictability by the current generation of global ocean models. The crossover time of the velocity error is less than 3 days, which is similar to the average decorrelation time of the observed drifters. The crossover time is a useful measure to quantify future ocean model improvements.

Southern Ocean bottom water characteristics in CMIP5 models

NASA Astrophysics Data System (ADS)

Heuzé, CéLine; Heywood, Karen J.; Stevens, David P.; Ridley, Jeff K.

2013-04-01

Southern Ocean deep water properties and formation processes in climate models are indicative of their capability to simulate future climate, heat and carbon uptake, and sea level rise. Southern Ocean temperature and density averaged over 1986-2005 from 15 CMIP5 (Coupled Model Intercomparison Project Phase 5) climate models are compared with an observed climatology, focusing on bottom water. Bottom properties are reasonably accurate for half the models. Ten models create dense water on the Antarctic shelf, but it mixes with lighter water and is not exported as bottom water as in reality. Instead, most models create deep water by open ocean deep convection, a process occurring rarely in reality. Models with extensive deep convection are those with strong seasonality in sea ice. Optimum bottom properties occur in models with deep convection in the Weddell and Ross Gyres. Bottom Water formation processes are poorly represented in ocean models and are a key challenge for improving climate predictions.

Coupled ice sheet-ocean modelling to investigate ocean driven melting of marine ice sheets in Antarctica

NASA Astrophysics Data System (ADS)

Jong, Lenneke; Gladstone, Rupert; Galton-Fenzi, Ben

2017-04-01

Ocean induced melting below the ice shelves of marine ice sheets is a major source of uncertainty for predictions of ice mass loss and Antarctica's resultant contribution to future sea level rise. The floating ice shelves provide a buttressing force against the flow of ice across the grounding line into the ocean. Thinning of these ice shelves due to an increase in melting reduces this force and can lead to an increase in the discharge of grounded ice. Fully coupled modelling of ice sheet-ocean interactions is key to improving understanding the influence of the Southern ocean on the evolution of the Antarctic ice sheet, and to predicting its future behaviour under changing climate conditions. Coupling of ocean and ice sheet models is needed to provide more realistic melt rates at the base of ice shelves and hence make better predictions of the behaviour of the grounding line and the shape of the ice-shelf cavity as the ice sheet evolves. The Framework for Ice Sheet - Ocean Coupling (FISOC) has been developed to provide a flexible platform for performing coupled ice sheet - ocean modelling experiments. We present preliminary results using FISOC to couple the Regional Ocean Modelling System (ROMS) with Elmer/Ice in idealised experiments Marine Ice Sheet-Ocean Model Intercomparison Project (MISOMIP). These experiments use an idealised geometry motivated by that of Pine Island glacier and the adjacent Amundsen Sea in West Antarctica, a region which has shown shown signs of thinning ice and grounding line retreat.

Global Paleobathymetry Reconstruction with Realistic Shelf-Slope and Sediment Wedge

NASA Astrophysics Data System (ADS)

Goswami, A.; Hinnov, L. A.; Gnanadesikan, A.; Olson, P.

2013-12-01

We present paleo-ocean bathymetry reconstructions in a 0.1°x0.1° resolution, using simple geophysical models (Plate Model Equation for oceanic lithosphere), published ages of the ocean floor (Müller et al. 2008), and modern world sediment thickness data (Divins 2003). The motivation is to create realistic paleobathymetry to understand the effect of ocean floor roughness on tides and heat transport in paleoclimate simulations. The values for the parameters in the Plate Model Equation are deduced from Crosby et al. (2006) and are used together with ocean floor age to model Depth to Basement. On top of the Depth to Basement, we added an isostatically adjusted multilayer sediment layer, as indicated from sediment thickness data of the modern oceans and marginal seas (Divins 2003). We also created another version of the sediment layer from the Müller et al. dataset. The Depth to Basement with the appropriate sediment layer together represent a realistic paleobathymetry. A Sediment Wedge was modeled to complement the reconstructed paleobathymetry by extending it to the coastlines. In this process we added a modeled Continental Shelf and Continental Slope to match the extent of the reconstructed paleobathymetry. The Sediment Wedge was prepared by studying the modern ocean where a complete history of seafloor spreading is preserved (north, south and central Atlantic Ocean, Southern Ocean between Australia-Antarctica, and the Pacific Ocean off the west coast of South America). The model takes into account the modern continental shelf-slope structure (as evident from ETOPO1/ETOPO5), tectonic margin type (active vs. passive margin) and age of the latest tectonic activity (USGS & CGMW). Once the complete ocean bathymetry is modeled, we combine it with PALEOMAP (Scotese, 2011) continental reconstructions to produce global paleoworld elevation-bathymetry maps. Modern time (00 Ma) was assumed as a test case. Using the above-described methodology we reconstructed modern ocean bathymetry, starting with age of the oceanic crust. We then reconstructed paleobathymetry for PETM (55 Ma) and Cenomanian-Turonian (90 Ma) times. For each case, the final products are: a) a global depth to basement measurement map based on plate model and EarthByte published age of the ocean crust for modern world; b) global oceanic crust bathymetry maps with a multilayer sediment layer (two versions with two types of sediment layers based on: i) observed total sediment thickness of the modern oceans and marginal seas, and ii) EarthByte-estimated global sediment data for 00 Ma); c) global oceanic bathymetry maps (two versions with two types of sediment layers) with reconstructed shelf and slope; and d) global elevation-bathymetry maps (two versions with two types of sediment layers) with continental elevations (PALEOMAP) and ocean bathymetry. Similar maps for other geological times can be produced using this method provided that ocean crustal age is known.

Upper oceanic response to tropical cyclone Phailin in the Bay of Bengal using a coupled atmosphere-ocean model

NASA Astrophysics Data System (ADS)

Prakash, Kumar Ravi; Pant, Vimlesh

2017-01-01

A numerical simulation of very severe cyclonic storm `Phailin', which originated in southeastern Bay of Bengal (BoB) and propagated northwestward during 10-15 October 2013, was carried out using a coupled atmosphere-ocean model. A Model Coupling Toolkit (MCT) was used to make exchanges of fluxes consistent between the atmospheric model `Weather Research and Forecasting' (WRF) and ocean circulation model `Regional Ocean Modelling System' (ROMS) components of the `Coupled Ocean-Atmosphere-Wave-Sediment Transport' (COAWST) modelling system. The track and intensity of tropical cyclone (TC) Phailin simulated by the WRF component of the coupled model agrees well with the best-track estimates reported by the India Meteorological Department (IMD). Ocean model component (ROMS) was configured over the BoB domain; it utilized the wind stress and net surface heat fluxes from the WRF model to investigate upper oceanic response to the passage of TC Phailin. The coupled model shows pronounced sea surface cooling (2-2.5 °C) and an increase in sea surface salinity (SSS) (2-3 psu) after 06 GMT on 12 October 2013 over the northwestern BoB. Signature of this surface cooling was also observed in satellite data and buoy measurements. The oceanic mixed layer heat budget analysis reveals relative roles of different oceanic processes in controlling the mixed layer temperature over the region of observed cooling. The heat budget highlighted major contributions from horizontal advection and vertical entrainment processes in governing the mixed layer cooling (up to -0.1 °C h-1) and, thereby, reduction in sea surface temperature (SST) in the northwestern BoB during 11-12 October 2013. During the post-cyclone period, the net heat flux at surface regained its diurnal variations with a noontime peak that provided a warming tendency up to 0.05 °C h-1 in the mixed layer. Clear signatures of TC-induced upwelling are seen in vertical velocity (about 2.5 × 10-3 m s-1), rise in isotherms and isohalines along 85-88° E longitudes in the northwestern BoB. The study demonstrates that a coupled atmosphere-ocean model (WRF + ROMS) serves as a useful tool to investigate oceanic response to the passage of cyclones.

Air-Sea Momentum and Enthalpy Exchange in Coupled Atmosphere-Wave-Ocean Modeling of Tropical Cyclones

NASA Astrophysics Data System (ADS)

Curcic, M.; Chen, S. S.

2016-02-01

The atmosphere and ocean are coupled through momentum, enthalpy, and mass fluxes. Accurate representation of these fluxes in a wide range of weather and climate conditions is one of major challenges in prediction models. Their current parameterizations are based on sparse observations in low-to-moderate winds and are not suited for high wind conditions such as tropical cyclones (TCs) and winter storms. In this study, we use the Unified Wave INterface - Coupled Model (UWIN-CM), a high resolution, fully-coupled atmosphere-wave-ocean model, to better understand the role of ocean surface waves in mediating air-sea momentum and enthalpy exchange in TCs. In particular, we focus on the explicit treatment of wave growth and dissipation for calculating atmospheric and oceanic stress, and its role in upper ocean mixing and surface cooling in the wake of the storm. Wind-wave misalignment and local wave disequilibrium result in difference between atmospheric and oceanic stress being largest on the left side of the storm. We find that explicit wave calculation in the coupled model reduces momentum transfer into the ocean by more than 10% on average, resulting in reduced cooling in TC's wake and subsequent weakening of the storm. We also investigate the impacts of sea surface temperature and upper ocean parameterization on air-sea enthalpy fluxes in the fully coupled model. High-resolution UWIN-CM simulations of TCs with various intensities and structure are conducted in this study to better understand the complex TC-ocean interaction and improve the representation of air-sea coupling processes in coupled prediction models.

Climate variability and predictability associated with the Indo-Pacific Oceanic Channel Dynamics in the CCSM4 Coupled System Model

NASA Astrophysics Data System (ADS)

Yuan, Dongliang; Xu, Peng; Xu, Tengfei

2017-01-01

An experiment using the Community Climate System Model (CCSM4), a participant of the Coupled Model Intercomparison Project phase-5 (CMIP5), is analyzed to assess the skills of this model in simulating and predicting the climate variabilities associated with the oceanic channel dynamics across the Indo-Pacific Oceans. The results of these analyses suggest that the model is able to reproduce the observed lag correlation between the oceanic anomalies in the southeastern tropical Indian Ocean and those in the cold tongue in the eastern equatorial Pacific Ocean at a time lag of 1 year. This success may be largely attributed to the successful simulation of the interannual variations of the Indonesian Throughflow, which carries the anomalies of the Indian Ocean Dipole (IOD) into the western equatorial Pacific Ocean to produce subsurface temperature anomalies, which in turn propagate to the eastern equatorial Pacific to generate ENSO. This connection is termed the "oceanic channel dynamics" and is shown to be consistent with the observational analyses. However, the model simulates a weaker connection between the IOD and the interannual variability of the Indonesian Throughflow transport than found in the observations. In addition, the model overestimates the westerly wind anomalies in the western-central equatorial Pacific in the year following the IOD, which forces unrealistic upwelling Rossby waves in the western equatorial Pacific and downwelling Kelvin waves in the east. This assessment suggests that the CCSM4 coupled climate system has underestimated the oceanic channel dynamics and overestimated the atmospheric bridge processes.

Long-Term Evaluation of Ocean Tidal Variation Models of Polar Motion and UT1

NASA Astrophysics Data System (ADS)

Karbon, Maria; Balidakis, Kyriakos; Belda, Santiago; Nilsson, Tobias; Hagedoorn, Jan; Schuh, Harald

2018-04-01

Recent improvements in the development of VLBI (very long baseline interferometry) and other space geodetic techniques such as the global navigation satellite systems (GNSS) require very precise a-priori information of short-period (daily and sub-daily) Earth rotation variations. One significant contribution to Earth rotation is caused by the diurnal and semi-diurnal ocean tides. Within this work, we developed a new model for the short-period ocean tidal variations in Earth rotation, where the ocean tidal angular momentum model and the Earth rotation variation have been setup jointly. Besides the model of the short-period variation of the Earth's rotation parameters (ERP), based on the empirical ocean tide model EOT11a, we developed also ERP models, that are based on the hydrodynamic ocean tide models FES2012 and HAMTIDE. Furthermore, we have assessed the effect of uncertainties in the elastic Earth model on the resulting ERP models. Our proposed alternative ERP model to the IERS 2010 conventional model considers the elastic model PREM and 260 partial tides. The choice of the ocean tide model and the determination of the tidal velocities have been identified as the main uncertainties. However, in the VLBI analysis all models perform on the same level of accuracy. From these findings, we conclude that the models presented here, which are based on a re-examined theoretical description and long-term satellite altimetry observation only, are an alternative for the IERS conventional model but do not improve the geodetic results.

Comparison of MERRA-2 and ECCO-v4 ocean surface heat fluxes: Consequences of different forcing feedbacks on ocean circulation and implications for climate data assimilation.

NASA Astrophysics Data System (ADS)

Strobach, E.; Molod, A.; Menemenlis, D.; Forget, G.; Hill, C. N.; Campin, J. M.; Heimbach, P.

2017-12-01

Forcing ocean models with reanalysis data is a common practice in ocean modeling. As part of this practice, prescribed atmospheric state variables and interactive ocean SST are used to calculate fluxes between the ocean and the atmosphere. When forcing an ocean model with reanalysis fields, errors in the reanalysis data, errors in the ocean model and errors in the forcing formulation will generate a different solution compared to other ocean reanalysis solutions (which also have their own errors). As a first step towards a consistent coupled ocean-atmosphere reanalysis, we compare surface heat fluxes from a state-of-the-art atmospheric reanalysis, the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2), to heat fluxes from a state-of-the-art oceanic reanalysis, the Estimating the Circulation and Climate of the Ocean Version 4, Release 2 (ECCO-v4). Then, we investigate the errors associated with the MITgcm ocean model in its ECCO-v4 ocean reanalysis configuration (1992-2011) when it is forced with MERRA-2 atmospheric reanalysis fields instead of with the ECCO-v4 adjoint optimized ERA-interim state variables. This is done by forcing ECCO-v4 ocean with and without feedbacks from MERRA-2 related to turbulent fluxes of heat and moisture and the outgoing long wave radiation. In addition, we introduce an intermediate forcing method that includes only the feedback from the interactive outgoing long wave radiation. The resulting ocean circulation is compared with ECCO-v4 reanalysis and in-situ observations. We show that, without feedbacks, imbalances in the energy and the hydrological cycles of MERRA-2 (which are directly related to the fact it was created without interactive ocean) result in considerable SST drifts and a large reduction in sea level. The bulk formulae and interactive outgoing long wave radiation, although providing air-sea feedbacks and reducing model-data misfit, strongly relax the ocean to observed SST and may result in unwanted features such as large change in the water budget. These features have implications in on desired forcing recipe to be used. The results strongly and unambiguously argue for next generation data assimilation climate studies to involve fully coupled systems.

Vulnerability of Population and Transportation Infrastructure at the East Bank of Delaware Bay Due to Coastal Flooding in Sea-Level Rise Conditions

DTIC Science & Technology

2013-04-30

resulting impact on residents and transportation infrastructure. The three-dimensional coastal ocean model FVCOM coupled with a two-dimensional...shallow water model is used to simulate hydrodynamic flooding from coastal ocean water with fine-resolution meshes, and a topography-based hydrologic... ocean model FVCOM coupled with a two-dimensional shallow water model is used to simulate hydrodynamic flooding from coastal ocean water with fine

Magma oceanography. I - Thermal evolution. [of lunar surface

NASA Technical Reports Server (NTRS)

Solomon, S. C.; Longhi, J.

1977-01-01

Fractional crystallization and flotation of cumulate plagioclase in a cooling 'magma ocean' provides the simplest explanation for early emplacement of a thick feldspar-rich lunar crust. The complementary mafic cumulates resulting from the differentiation of such a magma ocean have been identified as the ultimate source of mare basalt liquids on the basis or rare-earth abundance patterns and experimental petrology studies. A study is conducted concerning the thermal evolution of the early differentiation processes. A range of models of increasing sophistication are considered. The models developed contain the essence of the energetics and the time scale for magma ocean differentiation. Attention is given to constraints on a magma ocean, modeling procedures, single-component magma oceans, fractionating magma oceans, and evolving magma oceans.

Effects of Southern Hemisphere Wind Changes on the Meridional Overturning Circulation in Ocean Models.

PubMed

Gent, Peter R

2016-01-01

Observations show that the Southern Hemisphere zonal wind stress maximum has increased significantly over the past 30 years. Eddy-resolving ocean models show that the resulting increase in the Southern Ocean mean flow meridional overturning circulation (MOC) is partially compensated by an increase in the eddy MOC. This effect can be reproduced in the non-eddy-resolving ocean component of a climate model, providing the eddy parameterization coefficient is variable and not a constant. If the coefficient is a constant, then the Southern Ocean mean MOC change is balanced by an unrealistically large change in the Atlantic Ocean MOC. Southern Ocean eddy compensation means that Southern Hemisphere winds cannot be the dominant mechanism driving midlatitude North Atlantic MOC variability.

Parallel Computation of the Regional Ocean Modeling System (ROMS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, P; Song, Y T; Chao, Y

2005-04-05

The Regional Ocean Modeling System (ROMS) is a regional ocean general circulation modeling system solving the free surface, hydrostatic, primitive equations over varying topography. It is free software distributed world-wide for studying both complex coastal ocean problems and the basin-to-global scale ocean circulation. The original ROMS code could only be run on shared-memory systems. With the increasing need to simulate larger model domains with finer resolutions and on a variety of computer platforms, there is a need in the ocean-modeling community to have a ROMS code that can be run on any parallel computer ranging from 10 to hundreds ofmore » processors. Recently, we have explored parallelization for ROMS using the MPI programming model. In this paper, an efficient parallelization strategy for such a large-scale scientific software package, based on an existing shared-memory computing model, is presented. In addition, scientific applications and data-performance issues on a couple of SGI systems, including Columbia, the world's third-fastest supercomputer, are discussed.« less

Eddy-resolving 1/10° model of the World Ocean

NASA Astrophysics Data System (ADS)

Ibrayev, R. A.; Khabeev, R. N.; Ushakov, K. V.

2012-02-01

The first results on simulating the intra-annual variability of the World Ocean circulation by use of the eddy-resolving model are considered. For this purpose, a model of the World Ocean with a 1/10° horizontal resolution and 49 vertical levels was developed (a 1/10 × 1/10 × 49 model of the World Ocean). This model is based on the traditional system of three-dimensional equations of the large-scale dynamics of the ocean and boundary conditions with an explicit allowance for water fluxes on the free surface of the ocean. The equations are written in the tripolar coordinate system. The numerical method is based on the separation of the barotropic and baroclinic components of the solution. Discretization in time is implemented using explicit schemes allowing effective parallelization for a large number of processors. The model uses the sub-models of the boundary layer of the atmosphere and the submodel of sea-ice thermodynamics. The model of the World Ocean was developed at the Institute of Numerical Mathematics of the Russian Academy of Sciences (INM RAS) and the P.P. Shirshov Institute of Oceanogy (IO RAS). The formulation of the problem of simulating the intra-annual variability of thermohydrodynamic processes of the World Ocean and the parameterizations that were used are considered. In the numerical experiment, the temporal evolution of the atmospheric effect is determined by the normal annual cycle according to the conditions of the international Coordinated Ocean-Ice Reference Experiment (CORE-I). The calculation was carried out on a multiprocessor computer with distributed memory; 1601 computational cores were used. The presented analysis demonstrates that the obtained results are quite satisfactory when compared to the results that were obtained by other eddy-resolving models of the global ocean. The analysis of the model solution is, to a larger extent, of a descriptive character. A detailed analysis of the results is to be presented in following works. This experiment is a significant first step in developing the eddy-resolving model of the World Ocean.

A conceptual model of oceanic heat transport in the Snowball Earth scenario

NASA Astrophysics Data System (ADS)

Comeau, Darin; Kurtze, Douglas A.; Restrepo, Juan M.

2016-12-01

Geologic evidence suggests that the Earth may have been completely covered in ice in the distant past, a state known as Snowball Earth. This is still the subject of controversy, and has been the focus of modeling work from low-dimensional models up to state-of-the-art general circulation models. In our present global climate, the ocean plays a large role in redistributing heat from the equatorial regions to high latitudes, and as an important part of the global heat budget, its role in the initiation a Snowball Earth, and the subsequent climate, is of great interest. To better understand the role of oceanic heat transport in the initiation of Snowball Earth, and the resulting global ice covered climate state, the goal of this inquiry is twofold: we wish to propose the least complex model that can capture the Snowball Earth scenario as well as the present-day climate with partial ice cover, and we want to determine the relative importance of oceanic heat transport. To do this, we develop a simple model, incorporating thermohaline dynamics from traditional box ocean models, a radiative balance from energy balance models, and the more contemporary "sea glacier" model to account for viscous flow effects of extremely thick sea ice. The resulting model, consisting of dynamic ocean and ice components, is able to reproduce both Snowball Earth and present-day conditions through reasonable changes in forcing parameters. We find that including or neglecting oceanic heat transport may lead to vastly different global climate states, and also that the parameterization of under-ice heat transfer in the ice-ocean coupling plays a key role in the resulting global climate state, demonstrating the regulatory effect of dynamic ocean heat transport.

Numerical Modeling of Ocean Circulation

NASA Astrophysics Data System (ADS)

Miller, Robert N.

2007-01-01

The modelling of ocean circulation is important not only for its own sake, but also in terms of the prediction of weather patterns and the effects of climate change. This book introduces the basic computational techniques necessary for all models of the ocean and atmosphere, and the conditions they must satisfy. It describes the workings of ocean models, the problems that must be solved in their construction, and how to evaluate computational results. Major emphasis is placed on examining ocean models critically, and determining what they do well and what they do poorly. Numerical analysis is introduced as needed, and exercises are included to illustrate major points. Developed from notes for a course taught in physical oceanography at the College of Oceanic and Atmospheric Sciences at Oregon State University, this book is ideal for graduate students of oceanography, geophysics, climatology and atmospheric science, and researchers in oceanography and atmospheric science. Features examples and critical examination of ocean modelling and results Demonstrates the strengths and weaknesses of different approaches Includes exercises to illustrate major points and supplement mathematical and physical details

Report for Oregon State University Reporting Period: June 2016 to June 2017

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchings, Jennifer

The goal of this project is to develop an eddy resolving ocean model (POP) with tides coupled to a sea ice model (CICE) within the Regional Arctic System Model (RASM) to investigate the importance of ocean tides and mesoscale eddies in arctic climate simulations and quantify biases associated with these processes and how their relative contribution may improve decadal to centennial arctic climate predictions. Ocean, sea ice and coupled arctic climate response to these small scale processes will be evaluated with regard to their influence on mass, momentum and property exchange between oceans, shelf-basin, ice-ocean, and ocean-atmosphere. The project willmore » facilitate the future routine inclusion of polar tides and eddies in Earth System Models when computing power allows. As such, the proposed research addresses the science in support of the BER’s Climate and Environmental Sciences Division Long Term Measure as it will improve the ocean and sea ice model components as well as the fully coupled RASM and Community Earth System Model (CESM) and it will make them more accurate and computationally efficient.« less

Connecting Ocean Heat Transport Changes from the Midlatitudes to the Arctic Ocean

NASA Astrophysics Data System (ADS)

Hezel, P.; Nummelin, A.; Li, C.

2017-12-01

Under greenhouse warming, climate models simulate a weakening of the Atlantic Meridional Overturning Circulation and the associated ocean heat transport at midlatitudes but an increase in the ocean heat transport to the Arctic Ocean. These opposing trends lead to what could appear to be a discrepancy in the reported ocean contribution to Arctic amplification. This study clarifies how ocean heat transport affects Arctic climate under strong greenhouse warming using a set of the 21st century simulations performed within the Coupled Model Intercomparison Project. The results suggest that a future reduction in subpolar ocean heat loss enhances ocean heat transport to the Arctic Ocean, driving an increase in Arctic Ocean heat content and contributing to the intermodel spread in Arctic amplification. The results caution against extrapolating the forced oceanic signal from the midlatitudes to the Arctic.

Evaluation and Sensitivity Analysis of an Ocean Model Response to Hurricane Ivan (PREPRINT)

DTIC Science & Technology

2009-05-18

analysis of upper-limb meridional overturning circulation interior ocean pathways in the tropical/subtropical Atlantic . In: Interhemispheric Water...diminishing returns are encountered when either resolution is increased. 3 1. Introduction Coupled ocean-atmosphere general circulation models have become...northwest Caribbean Sea 4 and GOM. Evaluation is difficult because ocean general circulation models incorporate a large suite of numerical algorithms

Effect of Global Warming and Increased Freshwater Flux on Northern Hemispheric Cooling

NASA Astrophysics Data System (ADS)

Girihagama, L. N.; Nof, D.

2016-02-01

We wish to answer the, fairly complicated, question of whether global warming and an increased freshwater flux can cause Northern Hemispheric warming or cooling. Starting from the assumption that the ocean is the primary source of variability in the Northern hemispheric ocean-atmosphere coupled system, we employed a simple non-linear one-dimensional coupled ocean-atmosphere model. The simplicity of the model allows us to analytically predict the evolution of many dynamical variables of interest such as, the strength of the Atlantic Meridional overturning circulation (AMOC), temperatures of the ocean and atmosphere, mass transports, salinity, and ocean-atmosphere heat fluxes. The model results show that a reduced AMOC transport due to an increased freshwater flux causes cooling in both the atmosphere and ocean in the North Atlantic (NA) deep-water formation region. Cooling in both the ocean and atmosphere can cause reduction of the ocean-atmosphere temperature difference, which in turn reduces heat fluxes in both the ocean and atmosphere. For present day climate parameters, the calculated critical freshwater flux needed to arrest AMOC is 0.08 Sv. For a constant atmospheric zonal flow, there is minimal reduction in the AMOC strength, as well as minimal warming of the ocean and atmosphere. This model provides a conceptual framework for a dynamically sound response of the ocean and atmosphere to AMOC variability as a function of increased freshwater flux. The results are qualitatively consistent with numerous realistic coupled numerical models of varying complexity.

A two-dimensional ocean model for long-term climatic simulations: Stability and coupling to atmospheric and sea ice models

NASA Astrophysics Data System (ADS)

Harvey, L. D. Danny

1992-06-01

A two-dimensional (latitude-depth) deep ocean model is presented which is coupled to a sea ice model and an Energy Balance Climate Model (EBCM), the latter having land-sea and surface-air resolution. The processes which occur in the ocean model are thermohaline overturning driven by the horizontal density gradient, shallow wind-driven overturning cells, convective overturning, and vertical and horizontal diffusion of heat and salt. The density field is determined from the temperature and salinity fields using a nonlinear equation of state. Mixed layer salinity is affected by evaporation, precipitation, runoff from continents, and sea ice freezing and melting, as well as by advective, convective, and diffusive exchanges with the deep ocean. The ocean model is first tested in an uncoupled mode, in which hemispherically symmetric mixed layer temperature and salinity, or salinity flux, are specified as upper boundary conditions. An experiment performed with previous models is repeated in which a mixed layer salinity perturbation is introduced in the polar half of one hemisphere after switching from a fixed salinity to a fixed salinity flux boundary condition. For small values of the vertical diffusion coefficient KV, the model undergoes self-sustained oscillations with a period of about 1500 years. With larger values of KV, the model locks into either an asymmetric mode with a single overturning cell spanning both hemispheres, or a symmetric quiescent state with downwelling near the equator, upwelling at high latitudes, and a warm deep ocean (depending on the value of KV). When the ocean model is forced with observed mixed layer temperature and salinity, no oscillations occur. The model successfully simulates the very weak meridional overturning and strong Antarctic Circumpolar Current at the latitudes of the Drake Passage. The coupled EBCM-deep ocean model displays internal oscillations with a period of 3000 years if the ocean fraction is uniform with latitude and KV and the horizontal diffusion coefficient in the mixed layer are not too large. Globally averaged atmospheric temperature changes of 2 K are driven by oscillations in the heat flux into or out of the deep ocean, with the sudden onset of a heat flux out of the deep ocean associated with the rapid onset of thermohaline overturning after a quiescent period, and the sudden onset of a heat flux into the deep ocean associated with the collapse of thermohaline overturning. When the coupled model is run with prescribed parameters (such as land-sea fraction and precipitation) varying with latitude based on observations, the model does not oscillate and produces a reasonable deep ocean temperature field but a completely unrealistic salinity field. Resetting the mixed layer salinity to observations on each time step (equivalent to the "flux correction" method used in atmosphere-ocean general circulation models) is sufficient to give a realistic salinity field throughout the ocean depth, but dramatically alters the flow field and associated heat transport. Although the model is highly idealized, the finding that the maximum perturbation in globally averaged heat flux from the deep ocean to the surface over a 100-year period is 1.4 W m-2 suggests that effect of continuing greenhouse gas increases, which could result in a heating perturbation of 10 W m-2 by the end of the next century, will swamp possible surface heating perturbations due to changes in oceanic circulation. On the other hand, the extreme sensitivity of the oceanic flow field to variations in precipitation and evaporation suggests that it will not be possible to produce accurate projections of regional climatic change in the near term, if at all.

Effect of Ocean Tide Models on the Precise Orbit Determination of Geodetic Satellites

NASA Astrophysics Data System (ADS)

Kubo-Oka, T.; Matsumoto, K.; Otsubo, T.; Gotoh, T.

2005-12-01

Several ocean tide models are tested with precise observation data of satellite laser ranging to geodetic satellites, Starlette and Stella. Four ocean models, NAO.99b, CSR 3.0 (standard model in IERS Conventions 2003), CSR 4.0, and GOT99.2b were implemented in our orbit analysis software "concerto ver. 4". NAO.99b model was developed by assimilating tidal solutions from TOPEX/POSEIDON altimeter data into hydrodynamical model. Eight constituents (M2, S2, K1, O1, N2, P1, K2, Q1) were taken into account in each ocean tide model. Moreover, eight additional constituents (M1, J1, OO1, 2N2, Mu2, Nu2, L2, T2) can be included in NAO.99b model. Effect of ocean tides on geopotential coefficients were computed to 20th order. SLR data to Starlette and Stella were divided into arcs of 7 days length and 52 arcs (Jan. 2 - Dec. 30, 2004) were analyzed. Using different ocean tide model, orbits of these satellites were determined and weighted rms of postfit residuals are compared. We found that the NAO.99b model with 16 constituents can reduce weighted rms of postfit residuals using to the level of about 6.0 cm (Starlette) and 9.6 cm (Stella). These values are about 3-5 % smaller compared to other ocean tide models.

Oceanic response to tropical cyclone `Phailin' in the Bay of Bengal

NASA Astrophysics Data System (ADS)

Pant, V.; Prakash, K. R.

2016-02-01

Vertical mixing largely explains surface cooling induced by Tropical Cyclones (TCs). However, TC-induced upwelling of deeper waters plays an important role as it partly balances the warming of subsurface waters induced by vertical mixing. Below 100 m, vertical advection results in cooling that persists for a few days after the storm. The present study investigates the integrated ocean response to tropical cyclone `Phaillin' (10-14 October 2013) in the Bay of Bengal (BoB) through both coupled and stand-alone ocean-atmosphere models. Two numerical experiments with different coupling configurations between Regional Ocean Modelling System (ROMS) and Weather Research and Forecasting (WRF) were performed to investigate the impact of Phailin cyclone on the surface and sub-surface oceanic parameters. In the first experiment, ocean circulation model ROMS observe surface wind forcing from a mesoscale atmospheric model (WRF with nested damin setup), while rest forcing parameters are supplied to ROMS from NCEP data. In the second experiment, all surface forcing data to ROMS directly comes from WRF. The modeling components and data fields exchanged between atmospheric and oceanic models are described. The coupled modeling system is used to identify model sensitivity by exchanging prognostic variable fields between the two model components during simulation of Phallin cyclone (10-14 October 2013) in the BoB.In general, the simulated Phailin cyclone track and intensities agree well with observations in WRF simulations. Further, the inter-comparison between stand-alone and coupled model simulations validated against observations highlights better performance of coupled modeling system in simulating the oceanic conditions during the Phailin cyclone event.

Southern Ocean warming due to human influence

NASA Astrophysics Data System (ADS)

Fyfe, John C.

2006-10-01

I show that the latest series of climate models reproduce the observed mid-depth Southern Ocean warming since the 1950s if they include time-varying changes in anthropogenic greenhouse gases, sulphate aerosols and volcanic aerosols in the Earth's atmosphere. The remarkable agreement between observations and state-of-the art climate models suggests significant human influence on Southern Ocean temperatures. I also show that climate models that do not include volcanic aerosols produce mid-depth Southern Ocean warming that is nearly double that produced by climate models that do include volcanic aerosols. This implies that the full effect of human-induced warming of the Southern Ocean may yet to be realized.

The Role of Air-sea Coupling in the Response of Climate Extremes to Aerosols

NASA Astrophysics Data System (ADS)

Mahajan, S.

2017-12-01

Air-sea interactions dominate the climate of surrounding regions and thus also modulate the climate response to local and remote aerosol forcings. To clearly isolate the role of air-sea coupling in the climate response to aerosols, we conduct experiments with a full complexity atmosphere model that is coupled to a series of ocean models progressively increasing in complexity. The ocean models range from a data ocean model with prescribed SSTs, to a slab ocean model that only allows thermodynamic interactions, to a full dynamic ocean model. In a preliminary study, we have conducted single forcing experiments with black carbon aerosols in an atmosphere GCM coupled to a data ocean model and a slab ocean model. We find that while black carbon aerosols can intensify mean and extreme summer monsoonal precipitation over the Indian sub-continent, air-sea coupling can dramatically modulate this response. Black carbon aerosols in the vicinity of the Arabian Sea result in an increase of sea surface temperatures there in the slab ocean model, which intensify the low-level Somali Jet. The associated increase in moisture transport into Western India enhances the mean as well as extreme precipitation. In prescribed SST experiments, where SSTs are not allowed to respond BC aerosols, the response is muted. We will present results from a hierarchy of GCM simulations that investigate the role of air-sea coupling in the climate response to aerosols in more detail.

Development and validation of a regional coupled forecasting system for S2S forecasts

NASA Astrophysics Data System (ADS)

Sun, R.; Subramanian, A. C.; Hoteit, I.; Miller, A. J.; Ralph, M.; Cornuelle, B. D.

2017-12-01

Accurate and efficient forecasting of oceanic and atmospheric circulation is essential for a wide variety of high-impact societal needs, including: weather extremes; environmental protection and coastal management; management of fisheries, marine conservation; water resources; and renewable energy. Effective forecasting relies on high model fidelity and accurate initialization of the models with observed state of the ocean-atmosphere-land coupled system. A regional coupled ocean-atmosphere model with the Weather Research and Forecasting (WRF) model and the MITGCM ocean model coupled using the ESMF (Earth System Modeling Framework) coupling framework is developed to resolve mesoscale air-sea feedbacks. The regional coupled model allows oceanic mixed layer heat and momentum to interact with the atmospheric boundary layer dynamics at the mesoscale and submesoscale spatiotemporal regimes, thus leading to feedbacks which are otherwise not resolved in coarse resolution global coupled forecasting systems or regional uncoupled forecasting systems. The model is tested in two scenarios in the mesoscale eddy rich Red Sea and Western Indian Ocean region as well as mesoscale eddies and fronts of the California Current System. Recent studies show evidence for air-sea interactions involving the oceanic mesoscale in these two regions which can enhance predictability on sub seasonal timescale. We will present results from this newly developed regional coupled ocean-atmosphere model for forecasts over the Red Sea region as well as the California Current region. The forecasts will be validated against insitu observations in the region as well as reanalysis fields.

Current State and Recent Changes in the Arctic Ocean from the HYCOM-NCODA Global Ocean and Sea Ice Prediction System

NASA Astrophysics Data System (ADS)

Dukhovskoy, D. S.; Chassignet, E. P.; Hogan, P. J.; Metzger, E. J.; Posey, P.; Smedstad, O. M.; Stefanova, L. B.; Wallcraft, A. J.

2016-12-01

The great potential of numerical models to provide a high-resolution continuous picture of the environmental characteristics of the Arctic system is related to the problem of reliability and accuracy of the simulations. Recent Arctic Ocean model intercomparison projects have identified substantial disagreements in water mass distribution and circulation among the models over the last two decades. In situ and satellite observations cannot yield enough continuous in time and space information to interpret the observed changes in the Arctic system. Observations combined with Arctic Ocean models via data assimilation provide perhaps the most complete knowledge about the state of the Arctic system. We use outputs from the US Navy Global Ocean Forecast System (20-year reanalysis + analysis) to investigate several hypotheses that have been put forward regarding the current state and recent changes in the Arctic Ocean. The system is based on the 0.08-degree HYbrid Coordinate Ocean Model (HYCOM) and can be run with two-way coupling to the Los Alamos Community Ice CodE (CICE) or with an energy-loan ice model. Observations are assimilated by the Navy Coupled Ocean Data Assimilation (NCODA) algorithm. HYCOM temperature and salinity fields are shown to be in good agreement with observational data in the Arctic and North Atlantic. The model reproduces changes in the freshwater budget in the Arctic as reported in other studies. The modeled freshwater fluxes between the Arctic Ocean and the North Atlantic are analyzed to document and discuss the interaction between the two regions over the last two decades.

North Atlantic Ocean OSSE system development: Nature Run evaluation and application to hurricane interaction with the Gulf Stream

NASA Astrophysics Data System (ADS)

Kourafalou, Vassiliki H.; Androulidakis, Yannis S.; Halliwell, George R.; Kang, HeeSook; Mehari, Michael M.; Le Hénaff, Matthieu; Atlas, Robert; Lumpkin, Rick

2016-11-01

A high resolution, free-running model has been developed for the hurricane region of the North Atlantic Ocean. The model is evaluated with a variety of observations to ensure that it adequately represents both the ocean climatology and variability over this region, with a focus on processes relevant to hurricane-ocean interactions. As such, it can be used as the "Nature Run" (NR) model within the framework of Observing System Simulation Experiments (OSSEs), designed specifically to improve the ocean component of coupled ocean-atmosphere hurricane forecast models. The OSSE methodology provides quantitative assessment of the impact of specific observations on the skill of forecast models and enables the comprehensive design of future observational platforms and the optimization of existing ones. Ocean OSSEs require a state-of-the-art, high-resolution free-running model simulation that represents the true ocean (the NR). This study concentrates on the development and data based evaluation of the NR model component, which leads to a reliable model simulation that has a dual purpose: (a) to provide the basis for future hurricane related OSSEs; (b) to explore process oriented studies of hurricane-ocean interactions. A specific example is presented, where the impact of Hurricane Bill (2009) on the eastward extension and transport of the Gulf Stream is analyzed. The hurricane induced cold wake is shown in both NR simulation and observations. Interaction of storm-forced currents with the Gulf Stream produced a temporary large reduction in eastward transport downstream from Cape Hatteras and had a marked influence on frontal displacement in the upper ocean. The kinetic energy due to ageostrophic currents showed a significant increase as the storm passed, and then decreased to pre-storm levels within 8 days after the hurricane advanced further north. This is a unique result of direct hurricane impact on a western boundary current, with possible implications on the ocean feedback on hurricane evolution.

Research on strategy marine noise map based on i4ocean platform: Constructing flow and key approach

NASA Astrophysics Data System (ADS)

Huang, Baoxiang; Chen, Ge; Han, Yong

2016-02-01

Noise level in a marine environment has raised extensive concern in the scientific community. The research is carried out on i4Ocean platform following the process of ocean noise model integrating, noise data extracting, processing, visualizing, and interpreting, ocean noise map constructing and publishing. For the convenience of numerical computation, based on the characteristics of ocean noise field, a hybrid model related to spatial locations is suggested in the propagation model. The normal mode method K/I model is used for far field and ray method CANARY model is used for near field. Visualizing marine ambient noise data is critical to understanding and predicting marine noise for relevant decision making. Marine noise map can be constructed on virtual ocean scene. The systematic marine noise visualization framework includes preprocessing, coordinate transformation interpolation, and rendering. The simulation of ocean noise depends on realistic surface. Then the dynamic water simulation gird was improved with GPU fusion to achieve seamless combination with the visualization result of ocean noise. At the same time, the profile and spherical visualization include space, and time dimensionality were also provided for the vertical field characteristics of ocean ambient noise. Finally, marine noise map can be published with grid pre-processing and multistage cache technology to better serve the public.

Spin-Up and Tuning of the Global Carbon Cycle Model Inside the GISS ModelE2 GCM

NASA Technical Reports Server (NTRS)

Aleinov, Igor; Kiang, Nancy Y.; Romanou, Anastasia

2015-01-01

Planetary carbon cycle involves multiple phenomena, acting at variety of temporal and spacial scales. The typical times range from minutes for leaf stomata physiology to centuries for passive soil carbon pools and deep ocean layers. So, finding a satisfactory equilibrium state becomes a challenging and computationally expensive task. Here we present the spin-up processes for different configurations of the GISS Carbon Cycle model from the model forced with MODIS observed Leaf Area Index (LAI) and prescribed ocean to the prognostic LAI and to the model fully coupled to the dynamic ocean and ocean biology. We investigate the time it takes the model to reach the equilibrium and discuss the ways to speed up this process. NASA Goddard Institute for Space Studies General Circulation Model (GISS ModelE2) is currently equipped with all major algorithms necessary for the simulation of the Global Carbon Cycle. The terrestrial part is presented by Ent Terrestrial Biosphere Model (Ent TBM), which includes leaf biophysics, prognostic phenology and soil biogeochemistry module (based on Carnegie-Ames-Stanford model). The ocean part is based on the NASA Ocean Biogeochemistry Model (NOBM). The transport of atmospheric CO2 is performed by the atmospheric part of ModelE2, which employs quadratic upstream algorithm for this purpose.

Impact of Parameterized Lee Wave Drag on the Energy Budget of an Eddying Global Ocean Model

DTIC Science & Technology

2013-08-26

Teixeira, J., Peng, M., Hogan, T.F., Pauley, R., 2002. Navy Operational Global Atmospheric Prediction System (NOGAPS): Forcing for ocean models...Impact of parameterized lee wave drag on the energy budget of an eddying global ocean model David S. Trossman a,⇑, Brian K. Arbic a, Stephen T...input and output terms in the total mechanical energy budget of a hybrid coordinate high-resolution global ocean general circulation model forced by winds

Regular network model for the sea ice-albedo feedback in the Arctic.

PubMed

Müller-Stoffels, Marc; Wackerbauer, Renate

2011-03-01

The Arctic Ocean and sea ice form a feedback system that plays an important role in the global climate. The complexity of highly parameterized global circulation (climate) models makes it very difficult to assess feedback processes in climate without the concurrent use of simple models where the physics is understood. We introduce a two-dimensional energy-based regular network model to investigate feedback processes in an Arctic ice-ocean layer. The model includes the nonlinear aspect of the ice-water phase transition, a nonlinear diffusive energy transport within a heterogeneous ice-ocean lattice, and spatiotemporal atmospheric and oceanic forcing at the surfaces. First results for a horizontally homogeneous ice-ocean layer show bistability and related hysteresis between perennial ice and perennial open water for varying atmospheric heat influx. Seasonal ice cover exists as a transient phenomenon. We also find that ocean heat fluxes are more efficient than atmospheric heat fluxes to melt Arctic sea ice.

Effects of Precipitation on Ocean Mixed-Layer Temperature and Salinity as Simulated in a 2-D Coupled Ocean-Cloud Resolving Atmosphere Model

NASA Technical Reports Server (NTRS)

Li, Xiaofan; Sui, C.-H.; Lau, K-M.; Adamec, D.

1999-01-01

A two-dimensional coupled ocean-cloud resolving atmosphere model is used to investigate possible roles of convective scale ocean disturbances induced by atmospheric precipitation on ocean mixed-layer heat and salt budgets. The model couples a cloud resolving model with an embedded mixed layer-ocean circulation model. Five experiment are performed under imposed large-scale atmospheric forcing in terms of vertical velocity derived from the TOGA COARE observations during a selected seven-day period. The dominant variability of mixed-layer temperature and salinity are simulated by the coupled model with imposed large-scale forcing. The mixed-layer temperatures in the coupled experiments with 1-D and 2-D ocean models show similar variations when salinity effects are not included. When salinity effects are included, however, differences in the domain-mean mixed-layer salinity and temperature between coupled experiments with 1-D and 2-D ocean models could be as large as 0.3 PSU and 0.4 C respectively. Without fresh water effects, the nocturnal heat loss over ocean surface causes deep mixed layers and weak cooling rates so that the nocturnal mixed-layer temperatures tend to be horizontally-uniform. The fresh water flux, however, causes shallow mixed layers over convective areas while the nocturnal heat loss causes deep mixed layer over convection-free areas so that the mixed-layer temperatures have large horizontal fluctuations. Furthermore, fresh water flux exhibits larger spatial fluctuations than surface heat flux because heavy rainfall occurs over convective areas embedded in broad non-convective or clear areas, whereas diurnal signals over whole model areas yield high spatial correlation of surface heat flux. As a result, mixed-layer salinities contribute more to the density differences than do mixed-layer temperatures.

Observationally-based Metrics of Ocean Carbon and Biogeochemical Variables are Essential for Evaluating Earth System Model Projections

NASA Astrophysics Data System (ADS)

Russell, J. L.; Sarmiento, J. L.

2017-12-01

The Southern Ocean is central to the climate's response to increasing levels of atmospheric greenhouse gases as it ventilates a large fraction of the global ocean volume. Global coupled climate models and earth system models, however, vary widely in their simulations of the Southern Ocean and its role in, and response to, the ongoing anthropogenic forcing. Due to its complex water-mass structure and dynamics, Southern Ocean carbon and heat uptake depend on a combination of winds, eddies, mixing, buoyancy fluxes and topography. Understanding how the ocean carries heat and carbon into its interior and how the observed wind changes are affecting this uptake is essential to accurately projecting transient climate sensitivity. Observationally-based metrics are critical for discerning processes and mechanisms, and for validating and comparing climate models. As the community shifts toward Earth system models with explicit carbon simulations, more direct observations of important biogeochemical parameters, like those obtained from the biogeochemically-sensored floats that are part of the Southern Ocean Carbon and Climate Observations and Modeling project, are essential. One goal of future observing systems should be to create observationally-based benchmarks that will lead to reducing uncertainties in climate projections, and especially uncertainties related to oceanic heat and carbon uptake.

In-surface confinement of topological insulator nanowire surface states

NASA Astrophysics Data System (ADS)

Chen, Fan W.; Jauregui, Luis A.; Tan, Yaohua; Manfra, Michael; Klimeck, Gerhard; Chen, Yong P.; Kubis, Tillmann

2015-09-01

The bandstructures of [110] and [001] Bi2Te3 nanowires are solved with the atomistic 20 band tight binding functionality of NEMO5. The theoretical results reveal: The popular assumption that all topological insulator (TI) wire surfaces are equivalent is inappropriate. The Fermi velocity of chemically distinct wire surfaces differs significantly which creates an effective in-surface confinement potential. As a result, topological insulator surface states prefer specific surfaces. Therefore, experiments have to be designed carefully not to probe surfaces unfavorable to the surface states (low density of states) and thereby be insensitive to the TI-effects.

Spectroscopic Studies of Double Beta Decays and MOON

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ejiri, H.; Nuclear Science, Czech Technical University, Brehova, Prague, Czech Republic, National Institute of Radiological Sciences, Chiba, 263-8555

2007-10-12

This is a brief review of future spectroscopic experiments of neutrino-less double beta decays (0{nu}{beta}{beta}) and the MOON (Mo Observatory Of Neutrinos) project. Spectroscopic 0{nu}{beta}{beta} experiments of MOON, SuperNEMO and DCBA are planned to study Majorana masses in the quasi-degenerate (QD) and inverted mass hierarchy (IH) regions. MOON aims at 0{nu}{beta}{beta} studies with the {nu}-mass sensitivities of 100-30 meV by means of a super ensemble of multi-layer modules, each being consist of a scintillator plate, two tracking detector planes and a thin {beta}{beta} source film.

Improved Climate Simulations through a Stochastic Parameterization of Ocean Eddies

NASA Astrophysics Data System (ADS)

Williams, Paul; Howe, Nicola; Gregory, Jonathan; Smith, Robin; Joshi, Manoj

2016-04-01

In climate simulations, the impacts of the sub-grid scales on the resolved scales are conventionally represented using deterministic closure schemes, which assume that the impacts are uniquely determined by the resolved scales. Stochastic parameterization relaxes this assumption, by sampling the sub-grid variability in a computationally inexpensive manner. This presentation shows that the simulated climatological state of the ocean is improved in many respects by implementing a simple stochastic parameterization of ocean eddies into a coupled atmosphere-ocean general circulation model. Simulations from a high-resolution, eddy-permitting ocean model are used to calculate the eddy statistics needed to inject realistic stochastic noise into a low-resolution, non-eddy-permitting version of the same model. A suite of four stochastic experiments is then run to test the sensitivity of the simulated climate to the noise definition, by varying the noise amplitude and decorrelation time within reasonable limits. The addition of zero-mean noise to the ocean temperature tendency is found to have a non-zero effect on the mean climate. Specifically, in terms of the ocean temperature and salinity fields both at the surface and at depth, the noise reduces many of the biases in the low-resolution model and causes it to more closely resemble the high-resolution model. The variability of the strength of the global ocean thermohaline circulation is also improved. It is concluded that stochastic ocean perturbations can yield reductions in climate model error that are comparable to those obtained by refining the resolution, but without the increased computational cost. Therefore, stochastic parameterizations of ocean eddies have the potential to significantly improve climate simulations. Reference PD Williams, NJ Howe, JM Gregory, RS Smith, and MM Joshi (2016) Improved Climate Simulations through a Stochastic Parameterization of Ocean Eddies. Journal of Climate, under revision.

Contrasting Indian Ocean SST Variability With and Without ENSO Influence: A Coupled Atmosphere-Ocean GCM Study

NASA Technical Reports Server (NTRS)

Yu, Jin-Yi; Lau, K. M.

2004-01-01

In this study, we perform experiments with a coupled atmosphere-ocean general circulation model (CGCM) to examine ENSO's influence on the interannual sea surface temperature (SST) variability of the tropical Indian Ocean. The control experiment includes both the Indian and Pacific Oceans in the ocean model component of the CGCM (the Indo-Pacific Run). The anomaly experiment excludes ENSOs influence by including only the Indian Ocean while prescribing monthly-varying climatological SSTs for the Pacific Ocean (the Indian-Ocean Run). In the Indo-Pacific Run, an oscillatory mode of the Indian Ocean SST variability is identified by a multi-channel singular spectral analysis (MSSA). The oscillatory mode comprises two patterns that can be identified with the Indian Ocean Zonal Mode (IOZM) and a basin-wide warming/cooling mode respectively. In the model, the IOZM peaks about 3-5 months after ENSO reaches its maximum intensity. The basin mode peaks 8 months after the IOZM. The timing and associated SST patterns suggests that the IOZM is related to ENSO, and the basin- wide warming/cooling develops as a result of the decay of the IOZM spreading SST anomalies from western Indian Ocean to the eastern Indian Ocean. In contrast, in the Indian-Ocean Run, no oscillatory modes can be identified by the MSSA, even though the Indian Ocean SST variability is characterized by east-west SST contrast patterns similar to the IOZM. In both control and anomaly runs, IOZM-like SST variability appears to be associated with forcings from fluctuations of the Indian monsoon. Our modeling results suggest that the oscillatory feature of the IOZM is primarily forced by ENSO.

Application of a Topological Metric for Assessing Numerical Ocean Models with Satellite Observations

NASA Astrophysics Data System (ADS)

Morey, S. L.; Dukhovskoy, D. S.; Hiester, H. R.; Garcia-Pineda, O. G.; MacDonald, I. R.

2015-12-01

Satellite-based sensors provide a vast amount of observational data over the world ocean. Active microwave radars measure changes in sea surface height and backscattering from surface waves. Data from passive radiometers sensing emissions in multiple spectral bands can directly measure surface temperature, be combined with other data sources to estimate salinity, or processed to derive estimates of optically significant quantities, such as concentrations of biochemical properties. Estimates of the hydrographic variables can be readily used for assimilation or assessment of hydrodynamic ocean models. Optical data, however, have been underutilized in ocean circulation modeling. Qualitative assessments of oceanic fronts and other features commonly associated with changes in optically significant quantities are often made through visual comparison. This project applies a topological approach, borrowed from the field of computer image recognition, to quantitatively evaluate ocean model simulations of features that are related to quantities inferred from satellite imagery. The Modified Hausdorff Distance (MHD) provides a measure of the similarity of two shapes. Examples of applications of the MHD to assess ocean circulation models are presented. The first application assesses several models' representation of the freshwater plume structure from the Mississippi River, which is associated with a significant expression of color, using a satellite-derived ocean color index. Even though the variables being compared (salinity and ocean color index) differ, the MHD allows contours of the fields to be compared topologically. The second application assesses simulations of surface oil transport driven by winds and ocean model currents using surface oil maps derived from synthetic aperture radar backscatter data. In this case, maps of time composited oil coverage are compared between the simulations and satellite observations.

A 4.5 km resolution Arctic Ocean simulation with the global multi-resolution model FESOM 1.4

NASA Astrophysics Data System (ADS)

Wang, Qiang; Wekerle, Claudia; Danilov, Sergey; Wang, Xuezhu; Jung, Thomas

2018-04-01

In the framework of developing a global modeling system which can facilitate modeling studies on Arctic Ocean and high- to midlatitude linkage, we evaluate the Arctic Ocean simulated by the multi-resolution Finite Element Sea ice-Ocean Model (FESOM). To explore the value of using high horizontal resolution for Arctic Ocean modeling, we use two global meshes differing in the horizontal resolution only in the Arctic Ocean (24 km vs. 4.5 km). The high resolution significantly improves the model's representation of the Arctic Ocean. The most pronounced improvement is in the Arctic intermediate layer, in terms of both Atlantic Water (AW) mean state and variability. The deepening and thickening bias of the AW layer, a common issue found in coarse-resolution simulations, is significantly alleviated by using higher resolution. The topographic steering of the AW is stronger and the seasonal and interannual temperature variability along the ocean bottom topography is enhanced in the high-resolution simulation. The high resolution also improves the ocean surface circulation, mainly through a better representation of the narrow straits in the Canadian Arctic Archipelago (CAA). The representation of CAA throughflow not only influences the release of water masses through the other gateways but also the circulation pathways inside the Arctic Ocean. However, the mean state and variability of Arctic freshwater content and the variability of freshwater transport through the Arctic gateways appear not to be very sensitive to the increase in resolution employed here. By highlighting the issues that are independent of model resolution, we address that other efforts including the improvement of parameterizations are still required.

Simulations of coupled, Antarctic ice-ocean evolution using POP2x and BISICLES (Invited)

NASA Astrophysics Data System (ADS)

Price, S. F.; Asay-Davis, X.; Martin, D. F.; Maltrud, M. E.; Hoffman, M. J.

2013-12-01

We present initial results from Antarctic, ice-ocean coupled simulations using large-scale ocean circulation and land ice evolution models. The ocean model, POP2x is a modified version of POP, a fully eddying, global-scale ocean model (Smith and Gent, 2002). POP2x allows for circulation beneath ice shelf cavities using the method of partial top cells (Losch, 2008). Boundary layer physics, which control fresh water and salt exchange at the ice-ocean interface, are implemented following Holland and Jenkins (1999), Jenkins (1999), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008; Kimura et al., 2013) and with results from other idealized ice-ocean coupling test cases (e.g., Goldberg et al., 2012). The land ice model, BISICLES (Cornford et al., 2012), includes a 1st-order accurate momentum balance (L1L2) and uses block structured, adaptive-mesh refinement to more accurately model regions of dynamic complexity, such as ice streams, outlet glaciers, and grounding lines. For idealized test cases focused on marine-ice sheet dynamics, BISICLES output compares very favorably relative to simulations based on the full, nonlinear Stokes momentum balance (MISMIP-3d; Pattyn et al., 2013). Here, we present large-scale (southern ocean) simulations using POP2x with fixed ice shelf geometries, which are used to obtain and validate modeled submarine melt rates against observations. These melt rates are, in turn, used to force evolution of the BISICLES model. An offline-coupling scheme, which we compare with the ice-ocean coupling work of Goldberg et al. (2012), is then used to sequentially update the sub-shelf cavity geometry seen by POP2x.

OMIP contribution to CMIP6: experimental and diagnostic protocol for the physical component of the Ocean Model Intercomparison Project

NASA Astrophysics Data System (ADS)

Griffies, Stephen M.; Danabasoglu, Gokhan; Durack, Paul J.; Adcroft, Alistair J.; Balaji, V.; Böning, Claus W.; Chassignet, Eric P.; Curchitser, Enrique; Deshayes, Julie; Drange, Helge; Fox-Kemper, Baylor; Gleckler, Peter J.; Gregory, Jonathan M.; Haak, Helmuth; Hallberg, Robert W.; Heimbach, Patrick; Hewitt, Helene T.; Holland, David M.; Ilyina, Tatiana; Jungclaus, Johann H.; Komuro, Yoshiki; Krasting, John P.; Large, William G.; Marsland, Simon J.; Masina, Simona; McDougall, Trevor J.; Nurser, A. J. George; Orr, James C.; Pirani, Anna; Qiao, Fangli; Stouffer, Ronald J.; Taylor, Karl E.; Treguier, Anne Marie; Tsujino, Hiroyuki; Uotila, Petteri; Valdivieso, Maria; Wang, Qiang; Winton, Michael; Yeager, Stephen G.

2016-09-01

The Ocean Model Intercomparison Project (OMIP) is an endorsed project in the Coupled Model Intercomparison Project Phase 6 (CMIP6). OMIP addresses CMIP6 science questions, investigating the origins and consequences of systematic model biases. It does so by providing a framework for evaluating (including assessment of systematic biases), understanding, and improving ocean, sea-ice, tracer, and biogeochemical components of climate and earth system models contributing to CMIP6. Among the WCRP Grand Challenges in climate science (GCs), OMIP primarily contributes to the regional sea level change and near-term (climate/decadal) prediction GCs.OMIP provides (a) an experimental protocol for global ocean/sea-ice models run with a prescribed atmospheric forcing; and (b) a protocol for ocean diagnostics to be saved as part of CMIP6. We focus here on the physical component of OMIP, with a companion paper (Orr et al., 2016) detailing methods for the inert chemistry and interactive biogeochemistry. The physical portion of the OMIP experimental protocol follows the interannual Coordinated Ocean-ice Reference Experiments (CORE-II). Since 2009, CORE-I (Normal Year Forcing) and CORE-II (Interannual Forcing) have become the standard methods to evaluate global ocean/sea-ice simulations and to examine mechanisms for forced ocean climate variability. The OMIP diagnostic protocol is relevant for any ocean model component of CMIP6, including the DECK (Diagnostic, Evaluation and Characterization of Klima experiments), historical simulations, FAFMIP (Flux Anomaly Forced MIP), C4MIP (Coupled Carbon Cycle Climate MIP), DAMIP (Detection and Attribution MIP), DCPP (Decadal Climate Prediction Project), ScenarioMIP, HighResMIP (High Resolution MIP), as well as the ocean/sea-ice OMIP simulations.

Tropical Atlantic climate response to different freshwater input in high latitudes with an ocean-only general circulation model

NASA Astrophysics Data System (ADS)

Men, Guang; Wan, Xiuquan; Liu, Zedong

2016-10-01

Tropical Atlantic climate change is relevant to the variation of Atlantic meridional overturning circulation (AMOC) through different physical processes. Previous coupled climate model simulation suggested a dipole-like SST structure cooling over the North Atlantic and warming over the South Tropical Atlantic in response to the slowdown of the AMOC. Using an ocean-only global ocean model here, an attempt was made to separate the total influence of various AMOC change scenarios into an oceanic-induced component and an atmospheric-induced component. In contrast with previous freshwater-hosing experiments with coupled climate models, the ocean-only modeling presented here shows a surface warming in the whole tropical Atlantic region and the oceanic-induced processes may play an important role in the SST change in the equatorial south Atlantic. Our result shows that the warming is partly governed by oceanic process through the mechanism of oceanic gateway change, which operates in the regime where freshwater forcing is strong, exceeding 0.3 Sv. Strong AMOC change is required for the gateway mechanism to work in our model because only when the AMOC is sufficiently weak, the North Brazil Undercurrent can flow equatorward, carrying warm and salty north Atlantic subtropical gyre water into the equatorial zone. This threshold is likely to be model-dependent. An improved understanding of these issues may have help with abrupt climate change prediction later.

Advancing coastal ocean modelling, analysis, and prediction for the US Integrated Ocean Observing System

USGS Publications Warehouse

Wilkin, John L.; Rosenfeld, Leslie; Allen, Arthur; Baltes, Rebecca; Baptista, Antonio; He, Ruoying; Hogan, Patrick; Kurapov, Alexander; Mehra, Avichal; Quintrell, Josie; Schwab, David; Signell, Richard; Smith, Jane

2017-01-01

This paper outlines strategies that would advance coastal ocean modelling, analysis and prediction as a complement to the observing and data management activities of the coastal components of the US Integrated Ocean Observing System (IOOS®) and the Global Ocean Observing System (GOOS). The views presented are the consensus of a group of US-based researchers with a cross-section of coastal oceanography and ocean modelling expertise and community representation drawn from Regional and US Federal partners in IOOS. Priorities for research and development are suggested that would enhance the value of IOOS observations through model-based synthesis, deliver better model-based information products, and assist the design, evaluation, and operation of the observing system itself. The proposed priorities are: model coupling, data assimilation, nearshore processes, cyberinfrastructure and model skill assessment, modelling for observing system design, evaluation and operation, ensemble prediction, and fast predictors. Approaches are suggested to accomplish substantial progress in a 3–8-year timeframe. In addition, the group proposes steps to promote collaboration between research and operations groups in Regional Associations, US Federal Agencies, and the international ocean research community in general that would foster coordination on scientific and technical issues, and strengthen federal–academic partnerships benefiting IOOS stakeholders and end users.

Nested ocean models: Work in progress

NASA Technical Reports Server (NTRS)

Perkins, A. Louise

1991-01-01

The ongoing work of combining three existing software programs into a nested grid oceanography model is detailed. The HYPER domain decomposition program, the SPEM ocean modeling program, and a quasi-geostrophic model written in England are being combined into a general ocean modeling facility. This facility will be used to test the viability and the capability of two-way nested grids in the North Atlantic.

Assimilation of TOPEX/POSEIDON Altimeter Data into a Global Ocean Circulation Model: Are the Results Any Good?

NASA Technical Reports Server (NTRS)

Fukumori, I.; Fu, L. L.; Chao, Y.

1998-01-01

The feasibility of assimilating satellite altimetry data into a global ocean general ocean general circulation model is studied. Three years of TOPEX/POSEIDON data is analyzed using a global, three-dimensional, nonlinear primitive equation model.

Modeling seasonality of ice and ocean carbon production in the Arctic

NASA Astrophysics Data System (ADS)

Jin, M.; Deal, C. M.; Ji, R.

2011-12-01

In the Arctic Ocean, both phytoplankton and sea ice algae are important contributors to the primary production and the arctic food web. Copepod in the arctic regions have developed their feeding habit depending on the timing between the ice algal bloom and the subsequent phytoplankton bloom. A mismatch of the timing due to climate changes could have dramatic consequences on the food web as shown by some regional observations. In this study, a global coupled ice-ocean-ecosystem model was used to assess the seasonality of the ice algal and phytoplankton blooms in the arctic. The ice-ocean ecosystem modules are fully coupled in the physical model POP-CICE (Parallel Ocean Program- Los Alamos Sea Ice Model). The model results are compared with various observations. The modeled ice and ocean carbon production were analyzed by regions and their linkage to the physical environment changes (such as changes of ice concentration and water temperature, and light intensity etc.) between low- and high-ice years.

Intercomparison of Antarctic ice-shelf, ocean, and sea-ice interactions simulated by MetROMS-iceshelf and FESOM 1.4

NASA Astrophysics Data System (ADS)

Naughten, Kaitlin A.; Meissner, Katrin J.; Galton-Fenzi, Benjamin K.; England, Matthew H.; Timmermann, Ralph; Hellmer, Hartmut H.; Hattermann, Tore; Debernard, Jens B.

2018-04-01

An increasing number of Southern Ocean models now include Antarctic ice-shelf cavities, and simulate thermodynamics at the ice-shelf/ocean interface. This adds another level of complexity to Southern Ocean simulations, as ice shelves interact directly with the ocean and indirectly with sea ice. Here, we present the first model intercomparison and evaluation of present-day ocean/sea-ice/ice-shelf interactions, as simulated by two models: a circumpolar Antarctic configuration of MetROMS (ROMS: Regional Ocean Modelling System coupled to CICE: Community Ice CodE) and the global model FESOM (Finite Element Sea-ice Ocean Model), where the latter is run at two different levels of horizontal resolution. From a circumpolar Antarctic perspective, we compare and evaluate simulated ice-shelf basal melting and sub-ice-shelf circulation, as well as sea-ice properties and Southern Ocean water mass characteristics as they influence the sub-ice-shelf processes. Despite their differing numerical methods, the two models produce broadly similar results and share similar biases in many cases. Both models reproduce many key features of observations but struggle to reproduce others, such as the high melt rates observed in the small warm-cavity ice shelves of the Amundsen and Bellingshausen seas. Several differences in model design show a particular influence on the simulations. For example, FESOM's greater topographic smoothing can alter the geometry of some ice-shelf cavities enough to affect their melt rates; this improves at higher resolution, since less smoothing is required. In the interior Southern Ocean, the vertical coordinate system affects the degree of water mass erosion due to spurious diapycnal mixing, with MetROMS' terrain-following coordinate leading to more erosion than FESOM's z coordinate. Finally, increased horizontal resolution in FESOM leads to higher basal melt rates for small ice shelves, through a combination of stronger circulation and small-scale intrusions of warm water from offshore.

Deep Water Ocean Acoustics

DTIC Science & Technology

2015-07-17

under- ice scattering, bathymetric diffraction and the application of the ocean acoustic Parabolic Equation to infrasound. 2. Tasks a. Task 1...and Climate of the Ocean, Phase II (ECCO2): High-Resolution Global-Ocean and Sea- Ice Data Synthesis) model re- analysis for the years 1992 and 1993...The ECCO2 model is a state estimation based upon data syntheses obtained by least squares fitting of the global ocean and sea- ice configuration of

Investigation of land ice-ocean interaction with a fully coupled ice-ocean model: 1. Model description and behavior

NASA Astrophysics Data System (ADS)

Goldberg, D. N.; Little, C. M.; Sergienko, O. V.; Gnanadesikan, A.; Hallberg, R.; Oppenheimer, M.

2012-06-01

Antarctic ice shelves interact closely with the ocean cavities beneath them, with ice shelf geometry influencing ocean cavity circulation, and heat from the ocean driving changes in the ice shelves, as well as the grounded ice streams that feed them. We present a new coupled model of an ice stream-ice shelf-ocean system that is used to study this interaction. The model is capable of representing a moving grounding line and dynamically responding ocean circulation within the ice shelf cavity. Idealized experiments designed to investigate the response of the coupled system to instantaneous increases in ocean temperature show ice-ocean system responses on multiple timescales. Melt rates and ice shelf basal slopes near the grounding line adjust in 1-2 years, and downstream advection of the resulting ice shelf thinning takes place on decadal timescales. Retreat of the grounding line and adjustment of grounded ice takes place on a much longer timescale, and the system takes several centuries to reach a new steady state. During this slow retreat, and in the absence of either an upward-or downward-sloping bed or long-term trends in ocean heat content, the ice shelf and melt rates maintain a characteristic pattern relative to the grounding line.

Ocean alkalinity and the Cretaceous/Tertiary boundary

NASA Technical Reports Server (NTRS)

Caldeira, K. G.; Rampino, Michael R.

1988-01-01

A biogeochemical cycle model resolving ocean carbon and alkalinity content is applied to the Maestrichtian and Danian. The model computes oceanic concentrations and distributions of Ca(2+), Mg(2+), and Sigma-CO2. From these values an atmospheric pCO2 value is calculated, which is used to estimate rates of terrestrial weathering of calcite, dolomite, and calcium and magnesium silicates. Metamorphism of carbonate rocks and the subsequent outgassing of CO2 to the atmosphere are parameterized in terms of carbonate rock reservoir sizes, total land area, and a measure of overall tectonic activity, the sea-floor generation rate. The ocean carbon reservoir computed by the model is used with Deep Sea Drilling Project (DSDP) C-13 data to estimate organic detrital fluxes under a variety of ocean mixing rate assumptions. Using Redfield ratios, the biogenic detrital flux estimate is used to partition the ocean carbon and alkalinity reservoirs between the mixed layer and deep ocean. The calcite flux estimate and carbonate ion concentrations are used to determine the rate of biologically mediated CaCO3 titration. Oceanic productivity was severely limited for approximately 500 kyr following the K/T boundary resulting in significant increases in total ocean alkalinity. As productivity returned to the ocean, excess carbon and alkalinity was removed from the ocean as CaCO3. Model runs indicate that this resulted in a transient imbalance in the other direction. Ocean chemistry returned to near-equilibrium by about 64 mybp.

Crustal control of dissipative ocean tides in Enceladus and other icy moons

NASA Astrophysics Data System (ADS)

Beuthe, Mikael

2016-12-01

Could tidal dissipation within Enceladus' subsurface ocean account for the observed heat flow? Earthlike models of dynamical tides give no definitive answer because they neglect the influence of the crust. I propose here the first model of dissipative tides in a subsurface ocean, by combining the Laplace Tidal Equations with the membrane approach. For the first time, it is possible to compute tidal dissipation rates within the crust, ocean, and mantle in one go. I show that oceanic dissipation is strongly reduced by the crustal constraint, and thus contributes little to Enceladus' present heat budget. Tidal resonances could have played a role in a forming or freezing ocean less than 100 m deep. The model is general: it applies to all icy satellites with a thin crust and a shallow ocean. Scaling rules relate the resonances and dissipation rate of a subsurface ocean to the ones of a surface ocean. If the ocean has low viscosity, the westward obliquity tide does not move the crust. Therefore, crustal dissipation due to dynamical obliquity tides can differ from the static prediction by up to a factor of two.

Subsurface Ocean Tides in Enceladus and Other Icy Moons

NASA Astrophysics Data System (ADS)

Beuthe, M.

2016-12-01

Could tidal dissipation within Enceladus' subsurface ocean account for the observed heat flow? Earthlike models of dynamical tides give no definitive answer because they neglect the influence of the crust. I propose here the first model of dissipative tides in a subsurface ocean, by combining the Laplace Tidal Equations with the membrane approach. For the first time, it is possible to compute tidal dissipation rates within the crust, ocean, and mantle in one go. I show that oceanic dissipation is strongly reduced by the crustal constraint, and thus contributes little to Enceladus' present heat budget. Tidal resonances could have played a role in a forming or freezing ocean less than 100 meters deep. The model is general: it applies to all icy satellites with a thin crust and a shallow or stratified ocean. Scaling rules relate the resonances and dissipation rate of a subsurface ocean to the ones of a surface ocean. If the ocean has low viscosity, the westward obliquity tide does not move the crust. Therefore, crustal dissipation due to dynamical obliquity tides can differ from the static prediction by up to a factor of two.

On the origin of the marine zinc-silicon correlation

NASA Astrophysics Data System (ADS)

de Souza, Gregory F.; Khatiwala, Samar P.; Hain, Mathis P.; Little, Susan H.; Vance, Derek

2018-06-01

The close linear correlation between the distributions of dissolved zinc (Zn) and silicon (Si) in seawater has puzzled chemical oceanographers since its discovery almost forty years ago, due to the apparent lack of a mechanism for coupling these two nutrient elements. Recent research has shown that such a correlation can be produced in an ocean model without any explicit coupling between Zn and Si, via the export of Zn-rich biogenic particles in the Southern Ocean, consistent with the observation of elevated Zn quotas in Southern Ocean diatoms. Here, we investigate the physical and biological mechanisms by which Southern Ocean uptake and export control the large-scale marine Zn distribution, using suites of sensitivity simulations in an ocean general circulation model (OGCM) and a box-model ensemble. These simulations focus on the sensitivity of the Zn distribution to the stoichiometry of Zn uptake relative to phosphate (PO4), drawing directly on observations in culture. Our analysis reveals that OGCM model variants that produce a well-defined step between relatively constant, high Zn:PO4 uptake ratios in the Southern Ocean and low Zn:PO4 ratios at lower latitudes fare best in reproducing the marine Zn-Si correlation at both the global and the regional Southern Ocean scale, suggesting the presence of distinct Zn-biogeochemical regimes in the high- and low-latitude oceans that may relate to differences in physiology, ecology or (micro-)nutrient status. Furthermore, a study of the systematics of both the box model and the OGCM reveals that regional Southern Ocean Zn uptake exerts control over the global Zn distribution via its modulation of the biogeochemical characteristics of the surface Southern Ocean. Specifically, model variants with elevated Southern Ocean Zn:PO4 uptake ratios produce near-complete Zn depletion in the Si-poor surface Subantarctic Zone, where upper-ocean water masses with key roles in the global oceanic circulation are formed. By setting the main preformed covariation trend within the ocean interior, the subduction of these Zn- and Si-poor water masses produces a close correlation between the Zn and Si distributions that is barely altered by their differential remineralisation during low-latitude cycling. We speculate that analogous processes in the high-latitude oceans may operate for other trace metal micronutrients as well, splitting the ocean into two fundamentally different biogeochemical, and thus biogeographic, regimes.

Models for ecological models: Ocean primary productivity

USGS Publications Warehouse

Wikle, Christopher K.; Leeds, William B.; Hooten, Mevin B.

2016-01-01

The ocean accounts for more than 70% of planet Earth's surface, and it processes are critically important to marine and terrestrial life.  Ocean ecosystems are strongly dependent on the physical state of the ocean (e.g., transports, mixing, upwelling, runoff, and ice dynamics(.  As an example, consider the Coastal Gulf of Alaska (CGOA) region.

Baroclinic stabilization effect of the Atlantic-Arctic water exchange simulated by the eddy-permitting ocean model and global atmosphere-ocean model

NASA Astrophysics Data System (ADS)

Moshonkin, Sergey; Bagno, Alexey; Gritsun, Andrey; Gusev, Anatoly

2017-04-01

Numerical experiments were performed with the global atmosphere-ocean model INMCM5 (for version of the international project CMIP6, resolution for atmosphere is 2°x1.5°, 21 level) and with the three-dimensional, free surface, sigma coordinate eddy-permitting ocean circulation model for Atlantic (from 30°S) - Arctic and Bering sea domain (0.25 degrees resolution, Institute of Numerical Mathematics Ocean Model or INMOM). Spatial resolution of the INMCM5 oceanic component is 0.5°x0.25°. Both models have 40 s-levels in ocean. Previously, the simulations were carried out for INMCM5 to generate climatic system stable state. Then model was run for 180 years. In the experiment with INMOM, CORE-II data for 1948-2009 were used. As the goal for comparing results of two these numerical models, we selected evolution of the density and velocity anomalies in the 0-300m active ocean layer near Fram Strait in the Greenland Sea, where oceanic cyclonic circulation influences Atlantic-Arctic water exchange. Anomalies were count without climatic seasonal cycle for time scales smaller than 30 years. We use Singular Value Decomposition analysis (SVD) for density-velocity anomalies with time lag from minus one to six months. Both models perform identical stable physical result. They reveal that changes of heat and salt transports by West Spitsbergen and East Greenland currents, caused by atmospheric forcing, produce the baroclinic modes of velocity anomalies in 0-300m layer, thereby stabilizing ocean response on the atmospheric forcing, which stimulates keeping water exchange between the North Atlantic and Arctic Ocean at the certain climatological level. The first SVD-mode of density-velocity anomalies is responsible for the cyclonic circulation variability. The second and third SVD-modes stabilize existing ocean circulation by the anticyclonic vorticity generation. The second and third SVD-modes give 35% of the input to the total dispersion of density anomalies and 16-18% of the input to the total dispersion of velocity anomalies for numerical results as in INMCM5 so in INMOM models. Input to the total dispersion of velocity anomalies for the first SVD-mode is equal to 50% for INMCM5 and only 19% for INMOM. The research was done in the INM RAS. The model INMOM was supported by Russian Foundation for Basic Research (grant №16-05-00534), and the model INMCM was supported by the Russian Scientific Foundation (grant №14-27-00126).

Geostrophic Turbulence in the Frequency-Wavenumber Domain: Eddy-Driven Low-Frequency Variability

DTIC Science & Technology

2014-01-01

in ASFMRS. Previous studies of oceanic frequency– wavenumber spectra include Wunsch and Stammer (1995), Chelton and Schlax (1996), Farrar (2008...ASFMRS. However, the realistic eddying ocean model utilized here is the Hy- brid Coordinate Ocean Model (HYCOM; Chassignet et al. 2007 ), in place of...the Naval Research Laboratory (NRL) Layered Ocean Model (NLOM; Hurlburt and AUGUST 2014 ARB I C ET AL . 2051 Thompson 1980; Shriver et al. 2007 ) used

1/f model for long-time memory of the ocean surface temperature

NASA Astrophysics Data System (ADS)

Fraedrich, Klaus; Luksch, Ute; Blender, Richard

2004-09-01

The 1/f spectrum of the ocean surface temperature in the Atlantic and Pacific midlatitudes is explained by a simple vertical diffusion model with a shallow mixed layer on top of a deep ocean. The model is forced at the air-sea interface with the total surface heat flux from a 1000 year climate simulation. The analysis reveals the role of ocean advection and substantiates estimates of internal thermal diffusivities.

The effects of mixed layer dynamics on ice growth in the central Arctic

NASA Astrophysics Data System (ADS)

Kitchen, Bruce R.

1992-09-01

The thermodynamic model of Thorndike (1992) is coupled to a one dimensional, two layer ocean entrainment model to study the effect of mixed layer dynamics on ice growth and the variation in the ocean heat flux into the ice due to mixed layer entrainment. Model simulations show the existence of a negative feedback between the ice growth and the mixed layer entrainment, and that the underlying ocean salinity has a greater effect on the ocean beat flux than does variations in the underlying ocean temperature. Model simulations for a variety of surface forcings and initial conditions demonstrate the need to include mixed layer dynamics for realistic ice prediction in the arctic.

NCAR CSM ocean model by the NCAR oceanography section. Technical note

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

This technical note documents the ocean component of the NCAR Climate System Model (CSM). The ocean code has been developed from the Modular Ocean Model (version 1.1) which was developed and maintained at the NOAA Geophysical Fluid Dynamics Laboratory in Princeton. As a tribute to Mike Cox, and because the material is still relevant, the first four sections of this technical note are a straight reproduction from the GFDL Technical Report that Mike wrote in 1984. The remaining sections document how the NCAR Oceanography Section members have developed the MOM 1.1 code, and how it is forced, in order tomore » produce the NCAR CSM Ocean Model.« less

MMAB Operational Products

Science.gov Websites

Atlantic Real-Time Ocean Forecast System NOAA Wavewatch III® Ocean Wave Model Sea Ice Concentration Analysis Satellite Derived Ocean Surface Winds Daily Sea Surface Temperature Analysis Sea Ice Drift Model

Natural biogeochemical cycle of mercury in a global three-dimensional ocean tracer model

NASA Astrophysics Data System (ADS)

Zhang, Yanxu; Jaeglé, Lyatt; Thompson, LuAnne

2014-05-01

We implement mercury (Hg) biogeochemistry in the offline global 3-D ocean tracer model (OFFTRAC) to investigate the natural Hg cycle, prior to any anthropogenic input. The simulation includes three Hg tracers: dissolved elemental (Hg0aq), dissolved divalent (HgIIaq), and particle-bound mercury (HgPaq). Our Hg parameterization takes into account redox chemistry in ocean waters, air-sea exchange of Hg0, scavenging of HgIIaq onto sinking particles, and resupply of HgIIaq at depth by remineralization of sinking particles. Atmospheric boundary conditions are provided by a global simulation of the natural atmospheric Hg cycle in the GEOS-Chem model. In the surface ocean, the OFFTRAC model predicts global mean concentrations of 0.16 pM for total Hg, partitioned as 80% HgIIaq, 14% Hg0aq, and 6% HgPaq. Total Hg concentrations increase to 0.38 pM in the thermocline/intermediate waters (between the mixed layer and 1000 m depth) and 0.82 pM in deep waters (below 1000 m), reflecting removal of Hg from the surface to the subsurface ocean by particle sinking followed by remineralization at depth. Our model predicts that Hg concentrations in the deep North Pacific Ocean (>2000 m) are a factor of 2-3 higher than in the deep North Atlantic Ocean. This is the result of cumulative input of Hg from particle remineralization as deep waters transit from the North Atlantic to the North Pacific on their ~2000 year journey. The model is able to reproduce the relatively uniform concentrations of total Hg observed in the old deep waters of the North Pacific Ocean (observations: 1.2 ± 0.4 pM; model: 1.1 ± 0.04 pM) and Southern Ocean (observations: 1.1 ± 0.2 pM; model: 0.8 ± 0.02 pM). However, the modeled concentrations are factors of 5-6 too low compared to observed concentrations in the surface ocean and in the young water masses of the deep North Atlantic Ocean. This large underestimate for these regions implies a factor of 5-6 anthropogenic enhancement in Hg concentrations.

Technical Report Series on Global Modeling and Data Assimilation. Volume 22; A Coupled Ocean-Atmosphere Radiative Model for Global Ocean Biogeochemical Models

NASA Technical Reports Server (NTRS)

Gregg, Watson W.; Suarez, Max J. (Editor)

2002-01-01

An ocean-atmosphere radiative model (OARM) evaluates irradiance availability and quality in the water column to support phytoplankton growth and drive ocean thermodynamics. An atmospheric component incorporates spectral and directional effects of clear and cloudy skies as a function of atmospheric optical constituents, and spectral reflectance across the air-sea interface. An oceanic component evaluates the propagation of spectral and directional irradiance through the water column as a function of water, five phytoplankton groups, and chromophoric dissolved organic matter. It tracks the direct and diffuse streams from the atmospheric component, and a third stream, upwelling diffuse irradiance. The atmospheric component of OARM was compared to data sources at the ocean surface with a coefficient of determination (r2) of 0.97 and a root mean square of 12.1%.

The differentiation history of the terrestrial planets as recorded on the moon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borg, L

2007-02-20

The outline for this report is: (1) Factors Leading to Lunar Magma Ocean Model for Planetary Differentiation (2) Rationale for Magma Oceans on Other Planets Means for early efficient differentiation (Works on Moon why not here?) (3) Some Inconsistencies between the Lunar Magma Ocean Model and Observations. The conclusions are: (1) Differentiation via solidification of a magma ocean is derived from geologic observations of the Moon (2) Although geologic observations on other bodies are often consistent with differentiation via magma ocean solidification, it is not generally required. (3) There are some fundamental inconsistencies between observed lunar data and the model,more » that will require this model to be modified (4) Nevertheless, the Moon is the only location we know of to study magma ocean process in detail.« less

Sensitivity of a climatologically-driven sea ice model to the ocean heat flux

NASA Technical Reports Server (NTRS)

Parkinson, C. L.; Good, M. R.

1982-01-01

Ocean heat flux sensitivity was studied on a numerical model of sea ice covering the Weddell Sea region of the southern ocean. The model is driven by mean monthly climatological atmospheric variables. For each model run, the ocean heat flux is uniform in both space and time. Ocean heat fluxes below 20 W m to the minus 2 power do not provide sufficient energy to allow the ice to melt to its summertime thicknesses and concentrations by the end of the 14 month simulation, whereas ocean heat fluxes of 30 W m to the minus 2 power and above result in too much ice melt, producing the almost total disappearance of ice in the Weddell Sea by the end of the 14 months. These results are dependent on the atmospheric forcing fields.

Sensitivity of the ocean overturning circulation to wind and mixing: theoretical scalings and global ocean models

NASA Astrophysics Data System (ADS)

Nikurashin, Maxim; Gunn, Andrew

2017-04-01

The meridional overturning circulation (MOC) is a planetary-scale oceanic flow which is of direct importance to the climate system: it transports heat meridionally and regulates the exchange of CO2 with the atmosphere. The MOC is forced by wind and heat and freshwater fluxes at the surface and turbulent mixing in the ocean interior. A number of conceptual theories for the sensitivity of the MOC to changes in forcing have recently been developed and tested with idealized numerical models. However, the skill of the simple conceptual theories to describe the MOC simulated with higher complexity global models remains largely unknown. In this study, we present a systematic comparison of theoretical and modelled sensitivity of the MOC and associated deep ocean stratification to vertical mixing and southern hemisphere westerlies. The results show that theories that simplify the ocean into a single-basin, zonally-symmetric box are generally in a good agreement with a realistic, global ocean circulation model. Some disagreement occurs in the abyssal ocean, where complex bottom topography is not taken into account by simple theories. Distinct regimes, where the MOC has a different sensitivity to wind or mixing, as predicted by simple theories, are also clearly shown by the global ocean model. The sensitivity of the Indo-Pacific, Atlantic, and global basins is analysed separately to validate the conceptual understanding of the upper and lower overturning cells in the theory.

Experimental design for three interrelated marine ice sheet and ocean model intercomparison projects: MISMIP v. 3 (MISMIP +), ISOMIP v. 2 (ISOMIP +) and MISOMIP v. 1 (MISOMIP1)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asay-Davis, Xylar S.; Cornford, Stephen L.; Durand, Gaël

Coupled ice sheet-ocean models capable of simulating moving grounding lines are just becoming available. Such models have a broad range of potential applications in studying the dynamics of marine ice sheets and tidewater glaciers, from process studies to future projections of ice mass loss and sea level rise. The Marine Ice Sheet-Ocean Model Intercomparison Project (MISOMIP) is a community effort aimed at designing and coordinating a series of model intercomparison projects (MIPs) for model evaluation in idealized setups, model verification based on observations, and future projections for key regions of the West Antarctic Ice Sheet (WAIS). Here we describe computationalmore » experiments constituting three interrelated MIPs for marine ice sheet models and regional ocean circulation models incorporating ice shelf cavities. These consist of ice sheet experiments under the Marine Ice Sheet MIP third phase (MISMIP+), ocean experiments under the Ice Shelf-Ocean MIP second phase (ISOMIP+) and coupled ice sheet-ocean experiments under the MISOMIP first phase (MISOMIP1). All three MIPs use a shared domain with idealized bedrock topography and forcing, allowing the coupled simulations (MISOMIP1) to be compared directly to the individual component simulations (MISMIP+ and ISOMIP+). The experiments, which have qualitative similarities to Pine Island Glacier Ice Shelf and the adjacent region of the Amundsen Sea, are designed to explore the effects of changes in ocean conditions, specifically the temperature at depth, on basal melting and ice dynamics. In future work, differences between model results will form the basis for the evaluation of the participating models.« less

Development of a High-Resolution Climate Model for Future Climate Change Projection on the Earth Simulator

NASA Astrophysics Data System (ADS)

Kanzawa, H.; Emori, S.; Nishimura, T.; Suzuki, T.; Inoue, T.; Hasumi, H.; Saito, F.; Abe-Ouchi, A.; Kimoto, M.; Sumi, A.

2002-12-01

The fastest supercomputer of the world, the Earth Simulator (total peak performance 40TFLOPS) has recently been available for climate researches in Yokohama, Japan. We are planning to conduct a series of future climate change projection experiments on the Earth Simulator with a high-resolution coupled ocean-atmosphere climate model. The main scientific aims for the experiments are to investigate 1) the change in global ocean circulation with an eddy-permitting ocean model, 2) the regional details of the climate change including Asian monsoon rainfall pattern, tropical cyclones and so on, and 3) the change in natural climate variability with a high-resolution model of the coupled ocean-atmosphere system. To meet these aims, an atmospheric GCM, CCSR/NIES AGCM, with T106(~1.1o) horizontal resolution and 56 vertical layers is to be coupled with an oceanic GCM, COCO, with ~ 0.28ox 0.19o horizontal resolution and 48 vertical layers. This coupled ocean-atmosphere climate model, named MIROC, also includes a land-surface model, a dynamic-thermodynamic seaice model, and a river routing model. The poles of the oceanic model grid system are rotated from the geographic poles so that they are placed in Greenland and Antarctic land masses to avoild the singularity of the grid system. Each of the atmospheric and the oceanic parts of the model is parallelized with the Message Passing Interface (MPI) technique. The coupling of the two is to be done with a Multi Program Multi Data (MPMD) fashion. A 100-model-year integration will be possible in one actual month with 720 vector processors (which is only 14% of the full resources of the Earth Simulator).

Real-Time Ocean Prediction System for the East Coast of India

NASA Astrophysics Data System (ADS)

Warrior, H. V.

2016-02-01

The primary objective of the research work reported in this abstract was to develop a Realtime Environmental model for Ocean Dispersion and Impact (as part of an already in-place Decision Support System) for the purpose of radiological safety for the area along Kalpakkam (East Indian) coast. This system involves combining real-time ocean observations with numerical models of ocean processes to provide hindcasts, nowcasts and forecasts of currents, tides and waves. In this work we present the development of an Automated Coupled Atmospheric - Ocean Model (we call it IIT-CAOM) used to forecast the sea surface currents, sea surface temperature (SST) and salinity etc of the Bay of Bengal region under the influence of transient and unsteady atmospheric conditions. This method uses a coupling of Atmosphere and Ocean model. The models used here are the WRF for atmospheric simulations and POM for the ocean counterpart. It has a 3 km X 3 km resolution. This Coupled Model uses GFS (Global Forecast System) Data or FNL (Final Analyses) Data as initial conditions for jump-starting the atmospheric model. The Atmospheric model is run first thus extracting air temperature, wind speed and relative humidity. The heat flux subroutine computes the net heat flux, using above mentioned parameters data. The net heat flux feeds to the ocean model by simply adding net heat flux subroutine to the ocean model code without changing the model original structure. The online forecast of the IIT-CAOM is currently available in the web. The whole system has been automized and runs without any more manual support. The IIT-CAOM simulations have been carried out for Kalpakkam region, which is located on the East coast of India, about 70 km south of Chennai in Tamilnadu State and a three day forecast of sea surface currents, sea surface temperature (SST) and salinity, etc have been obtained.

Development and applications of a Coupled-Ocean-Atmosphere-Wave-Sediment Transport (COAWST) Modeling System

NASA Astrophysics Data System (ADS)

Warner, J. C.; Armstrong, B. N.; He, R.; Zambon, J. B.; Olabarrieta, M.; Voulgaris, G.; Kumar, N.; Haas, K. A.

2012-12-01

Understanding processes responsible for coastal change is important for managing both our natural and economic coastal resources. Coastal processes respond from both local scale and larger regional scale forcings. Understanding these processes can lead to significant insight into how the coastal zone evolves. Storms are one of the primary driving forces causing coastal change from a coupling of wave and wind driven flows. Here we utilize a numerical modeling approach to investigate these dynamics of coastal storm impacts. We use the Coupled Ocean - Atmosphere - Wave - Sediment Transport (COAWST) Modeling System that utilizes the Model Coupling Toolkit to exchange prognostic variables between the ocean model ROMS, atmosphere model WRF, wave model SWAN, and the Community Sediment Transport Modeling System (CSTMS) sediment routines. The models exchange fields of sea-surface temperature, ocean currents, water levels, bathymetry, wave heights, lengths, periods, bottom orbital velocities, and atmospheric surface heat and momentum fluxes, atmospheric pressure, precipitation, and evaporation. Data fields are exchanged using regridded flux conservative sparse matrix interpolation weights computed from the SCRIP spherical coordinate remapping interpolation package. We describe the modeling components and the model field exchange methods. As part of the system, the wave and ocean models run with cascading, refined, spatial grids to provide increased resolution, scaling down to resolve nearshore wave driven flows simulated by the vortex force formulation, all within selected regions of a larger, coarser-scale coastal modeling system. The ocean and wave models are driven by the atmospheric component, which is affected by wave dependent ocean-surface roughness and sea surface temperature which modify the heat and momentum fluxes at the ocean-atmosphere interface. We describe the application of the modeling system to several regions of multi-scale complexity to identify the significance of larger scale forcing cascading down to smaller scales and to investigate the interactions of the coupled system with increasing degree of model-model interactions. Three examples include the impact of Hurricane Ivan in 2004 in the Gulf of Mexico, Hurricane Ida in 2009 that evolved into a tropical storm on the US East coast, and passage of strong cold fronts across the US southeast. Results identify that hurricane intensity is extremely sensitive to sea-surface temperature, with a reduction in intensity when the atmosphere is coupled to the ocean model due to rapid cooling of the ocean from the surface through the mixed layer. Coupling of the ocean to the atmosphere also results in decreased boundary layer stress and coupling of the waves to the atmosphere results in increased sea-surface stress. Wave results are sensitive to both ocean and atmospheric coupling due to wave-current interactions with the ocean and wave-growth from the atmospheric wind stress. Sediment resuspension at regional scale during the hurricane is controlled by shelf width and wave propagation during hurricane approach. Results from simulation of passage of cold fronts suggest that synoptic meteorological systems can strongly impact surf zone and inner shelf response, therefore act as a strong driver for long term littoral sediment transport. We will also present some of the challenges faced to develop the modeling system.

Comparison between geodetic and oceanographic approaches to estimate mean dynamic topography for vertical datum unification: evaluation at Australian tide gauges

NASA Astrophysics Data System (ADS)

Filmer, M. S.; Hughes, C. W.; Woodworth, P. L.; Featherstone, W. E.; Bingham, R. J.

2018-04-01

The direct method of vertical datum unification requires estimates of the ocean's mean dynamic topography (MDT) at tide gauges, which can be sourced from either geodetic or oceanographic approaches. To assess the suitability of different types of MDT for this purpose, we evaluate 13 physics-based numerical ocean models and six MDTs computed from observed geodetic and/or ocean data at 32 tide gauges around the Australian coast. We focus on the viability of numerical ocean models for vertical datum unification, classifying the 13 ocean models used as either independent (do not contain assimilated geodetic data) or non-independent (do contain assimilated geodetic data). We find that the independent and non-independent ocean models deliver similar results. Maximum differences among ocean models and geodetic MDTs reach >150 mm at several Australian tide gauges and are considered anomalous at the 99% confidence level. These differences appear to be of geodetic origin, but without additional independent information, or formal error estimates for each model, some of these errors remain inseparable. Our results imply that some ocean models have standard deviations of differences with other MDTs (using geodetic and/or ocean observations) at Australian tide gauges, and with levelling between some Australian tide gauges, of ˜ ± 50 mm . This indicates that they should be considered as an alternative to geodetic MDTs for the direct unification of vertical datums. They can also be used as diagnostics for errors in geodetic MDT in coastal zones, but the inseparability problem remains, where the error cannot be discriminated between the geoid model or altimeter-derived mean sea surface.

On the Land-Ocean Contrast of Tropical Convection and Microphysics Statistics Derived from TRMM Satellite Signals and Global Storm-Resolving Models

NASA Technical Reports Server (NTRS)

Matsui, Toshihisa; Chern, Jiun-Dar; Tao, Wei-Kuo; Lang, Stephen E.; Satoh, Masaki; Hashino, Tempei; Kubota, Takuji

2016-01-01

A 14-year climatology of Tropical Rainfall Measuring Mission (TRMM) collocated multi-sensor signal statistics reveal a distinct land-ocean contrast as well as geographical variability of precipitation type, intensity, and microphysics. Microphysics information inferred from the TRMM precipitation radar and Microwave Imager (TMI) show a large land-ocean contrast for the deep category, suggesting continental convective vigor. Over land, TRMM shows higher echo-top heights and larger maximum echoes, suggesting taller storms and more intense precipitation, as well as larger microwave scattering, suggesting the presence of morelarger frozen convective hydrometeors. This strong land-ocean contrast in deep convection is invariant over seasonal and multi-year time-scales. Consequently, relatively short-term simulations from two global storm-resolving models can be evaluated in terms of their land-ocean statistics using the TRMM Triple-sensor Three-step Evaluation via a satellite simulator. The models evaluated are the NASA Multi-scale Modeling Framework (MMF) and the Non-hydrostatic Icosahedral Cloud Atmospheric Model (NICAM). While both simulations can represent convective land-ocean contrasts in warm precipitation to some extent, near-surface conditions over land are relatively moisture in NICAM than MMF, which appears to be the key driver in the divergent warm precipitation results between the two models. Both the MMF and NICAM produced similar frequencies of large CAPE between land and ocean. The dry MMF boundary layer enhanced microwave scattering signals over land, but only NICAM had an enhanced deep convection frequency over land. Neither model could reproduce a realistic land-ocean contrast in in deep convective precipitation microphysics. A realistic contrast between land and ocean remains an issue in global storm-resolving modeling.

Ocean-Atmosphere Coupled Model Simulations of Precipitation in the Central Andes

NASA Technical Reports Server (NTRS)

Nicholls, Stephen D.; Mohr, Karen I.

2015-01-01

The meridional extent and complex orography of the South American continent contributes to a wide diversity of climate regimes ranging from hyper-arid deserts to tropical rainforests to sub-polar highland regions. In addition, South American meteorology and climate are also made further complicated by ENSO, a powerful coupled ocean-atmosphere phenomenon. Modelling studies in this region have typically resorted to either atmospheric mesoscale or atmosphere-ocean coupled global climate models. The latter offers full physics and high spatial resolution, but it is computationally inefficient typically lack an interactive ocean, whereas the former offers high computational efficiency and ocean-atmosphere coupling, but it lacks adequate spatial and temporal resolution to adequate resolve the complex orography and explicitly simulate precipitation. Explicit simulation of precipitation is vital in the Central Andes where rainfall rates are light (0.5-5 mm hr-1), there is strong seasonality, and most precipitation is associated with weak mesoscale-organized convection. Recent increases in both computational power and model development have led to the advent of coupled ocean-atmosphere mesoscale models for both weather and climate study applications. These modelling systems, while computationally expensive, include two-way ocean-atmosphere coupling, high resolution, and explicit simulation of precipitation. In this study, we use the Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST), a fully-coupled mesoscale atmosphere-ocean modeling system. Previous work has shown COAWST to reasonably simulate the entire 2003-2004 wet season (Dec-Feb) as validated against both satellite and model analysis data when ECMWF interim analysis data were used for boundary conditions on a 27-9-km grid configuration (Outer grid extent: 60.4S to 17.7N and 118.6W to 17.4W).

Natural Air-Sea Flux of CO2 in Simulations of the NASA-GISS Climate Model: Sensitivity to the Physical Ocean Model Formulation

NASA Technical Reports Server (NTRS)

Romanou, A.; Gregg, Watson W.; Romanski, J.; Kelley, M.; Bleck, R.; Healy, R.; Nazarenko, L.; Russell, G.; Schmidt, G. A.; Sun, S.;

World Ocean Circulation Experiment

NASA Technical Reports Server (NTRS)

Clarke, R. Allyn

1992-01-01

The oceans are an equal partner with the atmosphere in the global climate system. The World Ocean Circulation Experiment is presently being implemented to improve ocean models that are useful for climate prediction both by encouraging more model development but more importantly by providing quality data sets that can be used to force or to validate such models. WOCE is the first oceanographic experiment that plans to generate and to use multiparameter global ocean data sets. In order for WOCE to succeed, oceanographers must establish and learn to use more effective methods of assembling, quality controlling, manipulating and distributing oceanographic data.

A coupled ice-ocean model of ice breakup and banding in the marginal ice zone

NASA Technical Reports Server (NTRS)

Smedstad, O. M.; Roed, L. P.

1985-01-01

A coupled ice-ocean numerical model for the marginal ice zone is considered. The model consists of a nonlinear sea ice model and a two-layer (reduced gravity) ocean model. The dependence of the upwelling response on wind stress direction is discussed. The results confirm earlier analytical work. It is shown that there exist directions for which there is no upwelling, while other directions give maximum upwelling in terms of the volume of uplifted water. The ice and ocean is coupled directly through the stress at the ice-ocean interface. An interesting consequence of the coupling is found in cases when the ice edge is almost stationary. In these cases the ice tends to break up a few tenths of kilometers inside of the ice edge.

An ensemble Kalman filter with a high-resolution atmosphere-ocean coupled model for tropical cyclone forecasts

NASA Astrophysics Data System (ADS)

Kunii, M.; Ito, K.; Wada, A.

2015-12-01

An ensemble Kalman filter (EnKF) using a regional mesoscale atmosphere-ocean coupled model was developed to represent the uncertainties of sea surface temperature (SST) in ensemble data assimilation strategies. The system was evaluated through data assimilation cycle experiments over a one-month period from July to August 2014, during which a tropical cyclone as well as severe rainfall events occurred. The results showed that the data assimilation cycle with the coupled model could reproduce SST distributions realistically even without updating SST and salinity during the data assimilation cycle. Therefore, atmospheric variables and radiation applied as a forcing to ocean models can control oceanic variables to some extent in the current data assimilation configuration. However, investigations of the forecast error covariance estimated in EnKF revealed that the correlation between atmospheric and oceanic variables could possibly lead to less flow-dependent error covariance for atmospheric variables owing to the difference in the time scales between atmospheric and oceanic variables. A verification of the analyses showed positive impacts of applying the ocean model to EnKF on precipitation forecasts. The use of EnKF with the coupled model system captured intensity changes of a tropical cyclone better than it did with an uncoupled atmosphere model, even though the impact on the track forecast was negligibly small.

How well-connected is the surface of the global ocean?

PubMed

Froyland, Gary; Stuart, Robyn M; van Sebille, Erik

2014-09-01

The Ekman dynamics of the ocean surface circulation is known to contain attracting regions such as the great oceanic gyres and the associated garbage patches. Less well-known are the extents of the basins of attractions of these regions and how strongly attracting they are. Understanding the shape and extent of the basins of attraction sheds light on the question of the strength of connectivity of different regions of the ocean, which helps in understanding the flow of buoyant material like plastic litter. Using short flow time trajectory data from a global ocean model, we create a Markov chain model of the surface ocean dynamics. The surface ocean is not a conservative dynamical system as water in the ocean follows three-dimensional pathways, with upwelling and downwelling in certain regions. Using our Markov chain model, we easily compute net surface upwelling and downwelling, and verify that it matches observed patterns of upwelling and downwelling in the real ocean. We analyze the Markov chain to determine multiple attracting regions. Finally, using an eigenvector approach, we (i) identify the five major ocean garbage patches, (ii) partition the ocean into basins of attraction for each of the garbage patches, and (iii) partition the ocean into regions that demonstrate transient dynamics modulo the attracting garbage patches.

Response of the Antarctic ice sheet to ocean forcing using the POPSICLES coupled ice sheet-ocean model

NASA Astrophysics Data System (ADS)

Martin, D. F.; Asay-Davis, X.; Price, S. F.; Cornford, S. L.; Maltrud, M. E.; Ng, E. G.; Collins, W.

2014-12-01

We present the response of the continental Antarctic ice sheet to sub-shelf-melt forcing derived from POPSICLES simulation results covering the full Antarctic Ice Sheet and the Southern Ocean spanning the period 1990 to 2010. Simulations are performed at 0.1 degree (~5 km) ocean resolution and ice sheet resolution as fine as 500 m using adaptive mesh refinement. A comparison of fully-coupled and comparable standalone ice-sheet model results demonstrates the importance of two-way coupling between the ice sheet and the ocean. The POPSICLES model couples the POP2x ocean model, a modified version of the Parallel Ocean Program (Smith and Gent, 2002), and the BISICLES ice-sheet model (Cornford et al., 2012). BISICLES makes use of adaptive mesh refinement to fully resolve dynamically-important regions like grounding lines and employs a momentum balance similar to the vertically-integrated formulation of Schoof and Hindmarsh (2009). Results of BISICLES simulations have compared favorably to comparable simulations with a Stokes momentum balance in both idealized tests like MISMIP3D (Pattyn et al., 2013) and realistic configurations (Favier et al. 2014). POP2x includes sub-ice-shelf circulation using partial top cells (Losch, 2008) and boundary layer physics following Holland and Jenkins (1999), Jenkins (2001), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008) and other continental-scale simulations and melt-rate observations (Kimura et al., 2013; Rignot et al., 2013). A companion presentation, "Present-day circum-Antarctic simulations using the POPSICLES coupled land ice-ocean model" in session C027 describes the ocean-model perspective of this work, while we focus on the response of the ice sheet and on details of the model. The figure shows the BISICLES-computed vertically-integrated ice velocity field about 1 month into a 20-year coupled Antarctic run. Groundling lines are shown in green.

GFDL's ESM2 global coupled climate-carbon Earth System Models. Part I: physical formulation and baseline simulation characteristics

USGS Publications Warehouse

Dunne, John P.; John, Jasmin G.; Adcroft, Alistair J.; Griffies, Stephen M.; Hallberg, Robert W.; Shevalikova, Elena; Stouffer, Ronald J.; Cooke, William; Dunne, Krista A.; Harrison, Matthew J.; Krasting, John P.; Malyshev, Sergey L.; Milly, P.C.D.; Phillipps, Peter J.; Sentman, Lori A.; Samuels, Bonita L.; Spelman, Michael J.; Winton, Michael; Wittenberg, Andrew T.; Zadeh, Niki

2012-01-01

We describe the physical climate formulation and simulation characteristics of two new global coupled carbon-climate Earth System Models, ESM2M and ESM2G. These models demonstrate similar climate fidelity as the Geophysical Fluid Dynamics Laboratory's previous CM2.1 climate model while incorporating explicit and consistent carbon dynamics. The two models differ exclusively in the physical ocean component; ESM2M uses Modular Ocean Model version 4.1 with vertical pressure layers while ESM2G uses Generalized Ocean Layer Dynamics with a bulk mixed layer and interior isopycnal layers. Differences in the ocean mean state include the thermocline depth being relatively deep in ESM2M and relatively shallow in ESM2G compared to observations. The crucial role of ocean dynamics on climate variability is highlighted in the El Niño-Southern Oscillation being overly strong in ESM2M and overly weak ESM2G relative to observations. Thus, while ESM2G might better represent climate changes relating to: total heat content variability given its lack of long term drift, gyre circulation and ventilation in the North Pacific, tropical Atlantic and Indian Oceans, and depth structure in the overturning and abyssal flows, ESM2M might better represent climate changes relating to: surface circulation given its superior surface temperature, salinity and height patterns, tropical Pacific circulation and variability, and Southern Ocean dynamics. Our overall assessment is that neither model is fundamentally superior to the other, and that both models achieve sufficient fidelity to allow meaningful climate and earth system modeling applications. This affords us the ability to assess the role of ocean configuration on earth system interactions in the context of two state-of-the-art coupled carbon-climate models.

Understanding variability of the Southern Ocean overturning circulation in CORE-II models

NASA Astrophysics Data System (ADS)

Downes, S. M.; Spence, P.; Hogg, A. M.

2018-03-01

The current generation of climate models exhibit a large spread in the steady-state and projected Southern Ocean upper and lower overturning circulation, with mechanisms for deep ocean variability remaining less well understood. Here, common Southern Ocean metrics in twelve models from the Coordinated Ocean-ice Reference Experiment Phase II (CORE-II) are assessed over a 60 year period. Specifically, stratification, surface buoyancy fluxes, and eddies are linked to the magnitude of the strengthening trend in the upper overturning circulation, and a decreasing trend in the lower overturning circulation across the CORE-II models. The models evolve similarly in the upper 1 km and the deep ocean, with an almost equivalent poleward intensification trend in the Southern Hemisphere westerly winds. However, the models differ substantially in their eddy parameterisation and surface buoyancy fluxes. In general, models with a larger heat-driven water mass transformation where deep waters upwell at the surface ( ∼ 55°S) transport warmer waters into intermediate depths, thus weakening the stratification in the upper 2 km. Models with a weak eddy induced overturning and a warm bias in the intermediate waters are more likely to exhibit larger increases in the upper overturning circulation, and more significant weakening of the lower overturning circulation. We find the opposite holds for a cool model bias in intermediate depths, combined with a more complex 3D eddy parameterisation that acts to reduce isopycnal slope. In summary, the Southern Ocean overturning circulation decadal trends in the coarse resolution CORE-II models are governed by biases in surface buoyancy fluxes and the ocean density field, and the configuration of the eddy parameterisation.

Will high-resolution global ocean models benefit coupled predictions on short-range to climate timescales?

NASA Astrophysics Data System (ADS)

Hewitt, Helene T.; Bell, Michael J.; Chassignet, Eric P.; Czaja, Arnaud; Ferreira, David; Griffies, Stephen M.; Hyder, Pat; McClean, Julie L.; New, Adrian L.; Roberts, Malcolm J.

2017-12-01

As the importance of the ocean in the weather and climate system is increasingly recognised, operational systems are now moving towards coupled prediction not only for seasonal to climate timescales but also for short-range forecasts. A three-way tension exists between the allocation of computing resources to refine model resolution, the expansion of model complexity/capability, and the increase of ensemble size. Here we review evidence for the benefits of increased ocean resolution in global coupled models, where the ocean component explicitly represents transient mesoscale eddies and narrow boundary currents. We consider lessons learned from forced ocean/sea-ice simulations; from studies concerning the SST resolution required to impact atmospheric simulations; and from coupled predictions. Impacts of the mesoscale ocean in western boundary current regions on the large-scale atmospheric state have been identified. Understanding of air-sea feedback in western boundary currents is modifying our view of the dynamics in these key regions. It remains unclear whether variability associated with open ocean mesoscale eddies is equally important to the large-scale atmospheric state. We include a discussion of what processes can presently be parameterised in coupled models with coarse resolution non-eddying ocean models, and where parameterizations may fall short. We discuss the benefits of resolution and identify gaps in the current literature that leave important questions unanswered.

Development and Utilization of Regional Oceanic Modeling System (ROMS). Delicacy, Imprecision, and Uncertainty of Oceanic Simulations: An Investigation with the Regional Oceanic Modeling System (ROMS). Submesoscale Flows and Mixing in the Ocean Surface Layer Using the Regional Oceanic Modeling System (ROMS). Eddy Effects in General Circulation, Spanning Mean Currents, Mesoscale Eddies, and Topographic Generation, including Submesoscale Nests

DTIC Science & Technology

2012-09-30

unbalanced motions is likely to occur. Due to an rapidly expanding set of investigation on oceanic flows at submesoscales, it is increasingly clear...Uchiyama, E. M. Lane, J. M. Restrepo, & J. C. McWilliams, 2011: A vortex force analysis of the interaction of rip currents and gravity waves. J. Geophys...particular topographic features, the torque is pervasively positive (cyclonic) along the Stream, in opposition to the anticyclonic wind curl in the

Modeling Studies of the Effects of Winds and Heat Flux on the Tropical Oceans

NASA Technical Reports Server (NTRS)

Seager, R.

1999-01-01

Over a decade ago, funding from this NASA grant supported the development of the Cane-Zebiak ENSO prediction model which remains in use to this day. It also supported our work developing schemes for modeling the air-sea heat flux in ocean models used for studying climate variability. We introduced a succession of simple boundary layer models that allow the fluxes to be computed internally in the model and avoid the need to specify the atmospheric thermodynamic state. These models have now reached a level of generality that allows modeling of the global, rather than just tropical, ocean, including sea ice cover. The most recent versions of these boundary layer models have been widely distributed around the world and are in use by many ocean modeling groups.

Transient rheology of the oceanic asthenosphere following the 2012 Indian Ocean Earthquake inferred from geodetic data

NASA Astrophysics Data System (ADS)

Pratama, Cecep; Ito, Takeo; Sasajima, Ryohei; Tabei, Takao; Kimata, Fumiaki; Gunawan, Endra; Ohta, Yusaku; Yamashina, Tadashi; Ismail, Nazli; Nurdin, Irwandi; Sugiyanto, Didik; Muksin, Umar; Meilano, Irwan

2017-10-01

Postseismic motion in the middle-field (100-500 km from the epicenter) geodetic data resulting from the 2012 Indian Ocean earthquake exhibited rapid change during the two months following the rupture. This pattern probably indicates multiple postseismic deformation mechanisms and might have been controlled by transient rheology. Therefore, the relative contribution of transient rheology in the oceanic asthenosphere and afterslip in the oceanic lithosphere should be incorporated to explain short- and long-term transitional features of postseismic signals. In this study, using two years of post-earthquake geodetic data from northern Sumatra, a three-dimensional spherical-earth finite-element model was constructed based on a heterogeneous structure and incorporating transient rheology. A rheology model combined with stress-driven afterslip was estimated. Our best-fit model suggests an oceanic lithosphere thickness of 75 km with oceanic asthenosphere viscosity values of 1 × 1017 Pa s and 2 × 1018 Pa s for the Kelvin and Maxwell viscosity models, respectively. The model results indicate that horizontal landward motion and vertical uplift in northern Sumatra require viscoelastic relaxation of the oceanic asthenosphere coupled with afterslip in the lithosphere. The present study demonstrates that transient rheology is essential for reproducing the rapidly changing motion of postseismic deformation in the middle-field area.

Quantifying Key Climate Parameter Uncertainties Using an Earth System Model with a Dynamic 3D Ocean

NASA Astrophysics Data System (ADS)

Olson, R.; Sriver, R. L.; Goes, M. P.; Urban, N.; Matthews, D.; Haran, M.; Keller, K.

2011-12-01

Climate projections hinge critically on uncertain climate model parameters such as climate sensitivity, vertical ocean diffusivity and anthropogenic sulfate aerosol forcings. Climate sensitivity is defined as the equilibrium global mean temperature response to a doubling of atmospheric CO2 concentrations. Vertical ocean diffusivity parameterizes sub-grid scale ocean vertical mixing processes. These parameters are typically estimated using Intermediate Complexity Earth System Models (EMICs) that lack a full 3D representation of the oceans, thereby neglecting the effects of mixing on ocean dynamics and meridional overturning. We improve on these studies by employing an EMIC with a dynamic 3D ocean model to estimate these parameters. We carry out historical climate simulations with the University of Victoria Earth System Climate Model (UVic ESCM) varying parameters that affect climate sensitivity, vertical ocean mixing, and effects of anthropogenic sulfate aerosols. We use a Bayesian approach whereby the likelihood of each parameter combination depends on how well the model simulates surface air temperature and upper ocean heat content. We use a Gaussian process emulator to interpolate the model output to an arbitrary parameter setting. We use Markov Chain Monte Carlo method to estimate the posterior probability distribution function (pdf) of these parameters. We explore the sensitivity of the results to prior assumptions about the parameters. In addition, we estimate the relative skill of different observations to constrain the parameters. We quantify the uncertainty in parameter estimates stemming from climate variability, model and observational errors. We explore the sensitivity of key decision-relevant climate projections to these parameters. We find that climate sensitivity and vertical ocean diffusivity estimates are consistent with previously published results. The climate sensitivity pdf is strongly affected by the prior assumptions, and by the scaling parameter for the aerosols. The estimation method is computationally fast and can be used with more complex models where climate sensitivity is diagnosed rather than prescribed. The parameter estimates can be used to create probabilistic climate projections using the UVic ESCM model in future studies.

Analyzing coastal turbidity under complex terrestrial loads characterized by a 'stress connectivity matrix' with an atmosphere-watershed-coastal ocean coupled model

NASA Astrophysics Data System (ADS)

Yamamoto, Takahiro; Nadaoka, Kazuo

2018-04-01

Atmospheric, watershed and coastal ocean models were integrated to provide a holistic analysis approach for coastal ocean simulation. The coupled model was applied to coastal ocean in the Philippines where terrestrial sediment loads provided from several adjacent watersheds play a major role in influencing coastal turbidity and are partly responsible for the coastal ecosystem degradation. The coupled model was validated using weather and hydrologic measurement to examine its potential applicability. The results revealed that the coastal water quality may be governed by the loads not only from the adjacent watershed but also from the distant watershed via coastal currents. This important feature of the multiple linkages can be quantitatively characterized by a "stress connectivity matrix", which indicates the complex underlying structure of environmental stresses in coastal ocean. The multiple stress connectivity concept shows the potential advantage of the integrated modelling approach for coastal ocean assessment, which may also serve for compensating the lack of measured data especially in tropical basins.

Seasonal Atmospheric and Oceanic Predictions

NASA Technical Reports Server (NTRS)

Roads, John; Rienecker, Michele (Technical Monitor)

2003-01-01

Several projects associated with dynamical, statistical, single column, and ocean models are presented. The projects include: 1) Regional Climate Modeling; 2) Statistical Downscaling; 3) Evaluation of SCM and NSIPP AGCM Results at the ARM Program Sites; and 4) Ocean Forecasts.

Attenuation of microglial RANTES by NEMO-binding domain peptide inhibits the infiltration of CD8(+) T cells in the nigra of hemiparkinsonian monkey.

PubMed

Roy, A; Mondal, S; Kordower, J H; Pahan, K

2015-08-27

Parkinson's disease (PD) is a progressive neurodegenerative disease characterized by the loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc). Despite intense investigations, little is known about its pathological mediators. Here, we report the marked upregulation of RANTES (regulated on activation, normal T cell expressed and secreted) and eotaxin, chemokines that are involved in T cell trafficking, in the serum of hemiparkinsonian monkeys. Interestingly, 1-methyl-4-phenylpyridinium (MPP(+)), a Parkinsonian toxin, increased the expression of RANTES and eotaxin in mouse microglial cells. The presence of NF-κB binding sites in promoters of RANTES and eotaxin and down-regulation of these genes by NEMO-binding domain (NBD) peptide, selective inhibitor of induced NF-κB activation, in MPP(+)-stimulated microglial cells suggest that the activation of NF-κB plays an important role in the upregulation of these two chemokines. Consistently, serum enzyme-linked immuno assay (ELISA) and nigral immunohistochemistry further confirmed that these chemokines were strongly upregulated in MPTP-induced hemiparkinsonian monkeys and that treatment with NBD peptides effectively inhibited the level of these chemokines. Furthermore, the microglial upregulation of RANTES in the nigra of hemiparkinsonian monkeys could be involved in the altered adaptive immune response in the brain as we observed greater infiltration of CD8(+) T cells around the perivascular niche and deep brain parenchyma of hemiparkinsonian monkeys as compared to control. The treatment of hemiparkinsonian monkeys with NBD peptides decreased the microglial expression of RANTES and attenuated the infiltration of CD8(+) T cells in nigra. These results indicate the possible involvement of chemokine-dependent adaptive immune response in Parkinsonism. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

Nemo regulates cell dynamics and represses the expression of miple, a midkine/pleiotrophin cytokine, during ommatidial rotation

PubMed Central

Muñoz-Soriano, Verónica; Ruiz, Carlos; Pérez-Alonso, Manuel; Mlodzik, Marek; Paricio, Nuria

2013-01-01

Ommatidial rotation is one of the most important events for correct patterning of the Drosophila eye. Although several signaling pathways are involved in this process, few genes have been shown to specifically affect it. One of them is nemo (nmo), which encodes a MAP-like protein kinase that regulates the rate of rotation throughout the entire process, and serves as a link between core planar cell polarity (PCP) factors and the E-cadherin–β-catenin complex. To determine more precisely the role of nmo in ommatidial rotation, live-imaging analyses in nmo mutant and wild-type early pupal eye discs were performed. We demonstrate that ommatidial rotation is not a continuous process, and that rotating and non-rotating interommatidial cells are very dynamic. Our in vivo analyses also show that nmo regulates the speed of rotation and is required in cone cells for correct ommatidial rotation, and that these cells as well as interommatidial cells are less dynamic in nmo mutants. Furthermore, microarray analyses of nmo and wild-type larval eye discs led us to identify new genes and signaling pathways related to nmo function during this process. One of them, miple, encodes the Drosophila ortholog of the midkine/pleiotrophin secreted cytokines that are involved in cell migration processes. miple is highly up-regulated in nmo mutant discs. Indeed, phenotypic analyses reveal that miple overexpression leads to ommatidial rotation defects. Genetic interaction assays suggest that miple is signaling through Ptp99A, the Drosophila ortholog of the vertebrate midkine/pleiotrophin PTPζ receptor. Accordingly, we propose that one of the roles of Nmo during ommatial rotation is to repress miple expression, which may in turn affect the dynamics in E-cadherin–β-catenin complexes. PMID:23428616

Intestinal exposure to PCB 153 induces inflammation via the ATM/NEMO pathway.

PubMed

Phillips, Matthew C; Dheer, Rishu; Santaolalla, Rebeca; Davies, Julie M; Burgueño, Juan; Lang, Jessica K; Toborek, Michal; Abreu, Maria T

2018-01-15

Polychlorinated biphenyls (PCBs) are persistent organic pollutants that adversely affect human health. PCBs bio-accumulate in organisms important for human consumption. PCBs accumulation in the body leads to activation of the transcription factor NF-κB, a major driver of inflammation. Despite dietary exposure being one of the main routes of exposure to PCBs, the gut has been widely ignored when studying the effects of PCBs. We investigated the effects of PCB 153 on the intestine and addressed whether PCB 153 affected intestinal permeability or inflammation and the mechanism by which this occurred. Mice were orally exposed to PCB 153 and gut permeability was assessed. Intestinal epithelial cells (IECs) were collected and evaluated for evidence of genotoxicity and inflammation. A human IEC line (SW480) was used to examine the direct effects of PCB 153 on epithelial function. NF-кB activation was measured using a reporter assay, DNA damage was assessed, and cytokine expression was ascertained with real-time PCR. Mice orally exposed to PCB 153 had an increase in intestinal permeability and inflammatory cytokine expression in their IECs; inhibition of NF-кB ameliorated both these effects. This inflammation was associated with genotoxic damage and NF-кB activation. Exposure of SW480 cells to PCB 153 led to similar effects as seen in vivo. We found that activation of the ATM/NEMO pathway by genotoxic stress was upstream of NF-kB activation. These results demonstrate that oral exposure to PCB 153 is genotoxic to IECs and induces downstream inflammation and barrier dysfunction in the intestinal epithelium. Copyright © 2017 Elsevier Inc. All rights reserved.

A Phase I Clinical Trial of Systemically Delivered NEMO Binding Domain Peptide in Dogs with Spontaneous Activated B-Cell like Diffuse Large B-Cell Lymphoma

PubMed Central

Habineza Ndikuyeze, Georges; Gaurnier-Hausser, Anita; Patel, Reema; Baldwin, Albert S.; May, Michael J.; Flood, Patrick; Krick, Erika; Propert, Kathleen J.; Mason, Nicola J.

2014-01-01

Activated B-Cell (ABC) Diffuse Large B-Cell Lymphoma (DLBCL) is a common, aggressive and poorly chemoresponsive subtype of DLBCL, characterized by constitutive canonical NF-κB signaling. Inhibition of NF-κB signaling leads to apoptosis of ABC-DLBCL cell lines, suggesting targeted disruption of this pathway may have therapeutic relevance. The selective IKK inhibitor, NEMO Binding Domain (NBD) peptide effectively blocks constitutive NF-κB activity and induces apoptosis in ABC-DLBCL cells in vitro. Here we used a comparative approach to determine the safety and efficacy of systemic NBD peptide to inhibit constitutive NF-κB signaling in privately owned dogs with spontaneous newly diagnosed or relapsed ABC-like DLBCL. Malignant lymph nodes biopsies were taken before and twenty-four hours after peptide administration to determine biological effects. Intravenous administration of <2 mg/kg NBD peptide was safe and inhibited constitutive canonical NF-κB activity in 6/10 dogs. Reductions in mitotic index and Cyclin D expression also occurred in a subset of dogs 24 hours post peptide and in 3 dogs marked, therapeutically beneficial histopathological changes were identified. Mild, grade 1 toxicities were noted in 3 dogs at the time of peptide administration and one dog developed transient subclinical hepatopathy. Long term toxicities were not identified. Pharmacokinetic data suggested rapid uptake of peptide into tissues. No significant hematological or biochemical toxicities were identified. Overall the results from this phase I study indicate that systemic administration of NBD peptide is safe and effectively blocks constitutive NF-κB signaling and reduces malignant B cell proliferation in a subset of dogs with ABC-like DLBCL. These results have potential translational relevance for human ABC-DLBCL. PMID:24798348

Uncertainty in Earth System Models: Benchmarks for Ocean Model Performance and Validation

NASA Astrophysics Data System (ADS)

Ogunro, O. O.; Elliott, S.; Collier, N.; Wingenter, O. W.; Deal, C.; Fu, W.; Hoffman, F. M.

2017-12-01

The mean ocean CO2 sink is a major component of the global carbon budget, with marine reservoirs holding about fifty times more carbon than the atmosphere. Phytoplankton play a significant role in the net carbon sink through photosynthesis and drawdown, such that about a quarter of anthropogenic CO2 emissions end up in the ocean. Biology greatly increases the efficiency of marine environments in CO2 uptake and ultimately reduces the impact of the persistent rise in atmospheric concentrations. However, a number of challenges remain in appropriate representation of marine biogeochemical processes in Earth System Models (ESM). These threaten to undermine the community effort to quantify seasonal to multidecadal variability in ocean uptake of atmospheric CO2. In a bid to improve analyses of marine contributions to climate-carbon cycle feedbacks, we have developed new analysis methods and biogeochemistry metrics as part of the International Ocean Model Benchmarking (IOMB) effort. Our intent is to meet the growing diagnostic and benchmarking needs of ocean biogeochemistry models. The resulting software package has been employed to validate DOE ocean biogeochemistry results by comparison with observational datasets. Several other international ocean models contributing results to the fifth phase of the Coupled Model Intercomparison Project (CMIP5) were analyzed simultaneously. Our comparisons suggest that the biogeochemical processes determining CO2 entry into the global ocean are not well represented in most ESMs. Polar regions continue to show notable biases in many critical biogeochemical and physical oceanographic variables. Some of these disparities could have first order impacts on the conversion of atmospheric CO2 to organic carbon. In addition, single forcing simulations show that the current ocean state can be partly explained by the uptake of anthropogenic emissions. Combined effects of two or more of these forcings on ocean biogeochemical cycles and ecosystems are challenging to predict since additive or antagonistic effects may occur. A benchmarking tool for accurate assessment and validation of marine biogeochemical outputs will be indispensable as the model community continues to improve ESM developments. It will provide a first order tool in understanding climate-carbon cycle feedbacks.

Global Modeling of Internal Tides Within an Eddying Ocean General Circulation Model

DTIC Science & Technology

2012-05-31

heat between the atmosphere and ocean (Yu and Weller, 2007 ). Salinities in the upper ocean are set by the difference between evaporation and...precipitation at the ocean surface (Yu, 2007 ; Schmitt, 2008). Because the buoyancy (density) of seawater at the ocean surface is con- trolled by...timescales of about 10–200 days, these currents mean- der and generate highly energetic meso- scale eddies (Schmitz, 1996a,b; Stammer , 1997), the spinning

Carbonate dissolution in mixed waters due to ocean acidification

NASA Astrophysics Data System (ADS)

Koski, K.; Wilson, J. L.

2009-12-01

Much of the anthropogenically released carbon dioxide has been stored as a dissolved gas in the ocean, causing a 0.1 decrease in ocean surface pH, with models predicting that by 2100 the surface ocean pH will be 0.5 below pre-industrial levels. In mixed ocean water - fresh water environments (e.g. estuaries, coastal aquifers, and edges of ice sheets), the decreased ocean pH couples with the mixed water geochemistry to make water more undersaturated with respect to calcium carbonate than ocean acidification alone. Mixed-water calcite dissolution may be one of the first directly observable effects of ocean acidification, as the ocean water and the fresh water can both be saturated with respect to calcium carbonate while their mixture will be undersaturated. We present a basic quantitative model describing mixed water dissolution in coastal or island freshwater aquifers, using temporally changing ocean pH, sea level, precipitation, and groundwater pumping. The model describes the potential for an increased rate of speleogenesis and porosity/permeability development along the lower edge of a fresh water lens aquifer. The model accounts the indirect effects of rising sea level and a growing coastal population on these processes. Applications are to freshwater carbonate aquifers on islands (e.g. the Bahamas) and in coastal areas (e.g. the unconfined Floridan aquifer of the United States, the Yucatan Peninsula of Mexico).

Going with the flow: the role of ocean circulation in global marine ecosystems under a changing climate.

PubMed

van Gennip, Simon J; Popova, Ekaterina E; Yool, Andrew; Pecl, Gretta T; Hobday, Alistair J; Sorte, Cascade J B

2017-07-01

Ocean warming, acidification, deoxygenation and reduced productivity are widely considered to be the major stressors to ocean ecosystems induced by emissions of CO 2 . However, an overlooked stressor is the change in ocean circulation in response to climate change. Strong changes in the intensity and position of the western boundary currents have already been observed, and the consequences of such changes for ecosystems are beginning to emerge. In this study, we address climatically induced changes in ocean circulation on a global scale but relevant to propagule dispersal for species inhabiting global shelf ecosystems, using a high-resolution global ocean model run under the IPCC RCP 8.5 scenario. The ¼ degree model resolution allows improved regional realism of the ocean circulation beyond that of available CMIP5-class models. We use a Lagrangian approach forced by modelled ocean circulation to simulate the circulation pathways that disperse planktonic life stages. Based on trajectory backtracking, we identify present-day coastal retention, dominant flow and dispersal range for coastal regions at the global scale. Projecting into the future, we identify areas of the strongest projected circulation change and present regional examples with the most significant modifications in their dominant pathways. Climatically induced changes in ocean circulation should be considered as an additional stressor of marine ecosystems in a similar way to ocean warming or acidification. © 2017 John Wiley & Sons Ltd.

Response of an eddy-permitting ocean model to the assimilation of sparse in situ data

NASA Astrophysics Data System (ADS)

Li, Jian-Guo; Killworth, Peter D.; Smeed, David A.

2003-04-01

The response of an eddy-permitting ocean model to changes introduced by data assimilation is studied when the available in situ data are sparse in both space and time (typical for the majority of the ocean). Temperature and salinity (T&S) profiles from the WOCE upper ocean thermal data set were assimilated into a primitive equation ocean model over the North Atlantic, using a simple nudging scheme with a time window of about 2 days and a horizontal spatial radius of about 1°. When data are sparse the model returns to its unassimilated behavior, locally "forgetting" or rejecting the assimilation, on timescales determined by the local advection and diffusion. Increasing the spatial weighting radius effectively reduces both processes and hence lengthens the model restoring time (and with it, the impact of assimilation). Increasing the nudging factor enhances the assimilation effect but has little effect on the model restoring time.

An Integrated Assessment Model for Helping the United States Sea Scallop (Placopecten magellanicus) Fishery Plan Ahead for Ocean Acidification and Warming

PubMed Central

2015-01-01

Ocean acidification, the progressive change in ocean chemistry caused by uptake of atmospheric CO2, is likely to affect some marine resources negatively, including shellfish. The Atlantic sea scallop (Placopecten magellanicus) supports one of the most economically important single-species commercial fisheries in the United States. Careful management appears to be the most powerful short-term factor affecting scallop populations, but in the coming decades scallops will be increasingly influenced by global environmental changes such as ocean warming and ocean acidification. In this paper, we describe an integrated assessment model (IAM) that numerically simulates oceanographic, population dynamic, and socioeconomic relationships for the U.S. commercial sea scallop fishery. Our primary goal is to enrich resource management deliberations by offering both short- and long-term insight into the system and generating detailed policy-relevant information about the relative effects of ocean acidification, temperature rise, fishing pressure, and socioeconomic factors on the fishery using a simplified model system. Starting with relationships and data used now for sea scallop fishery management, the model adds socioeconomic decision making based on static economic theory and includes ocean biogeochemical change resulting from CO2 emissions. The model skillfully reproduces scallop population dynamics, market dynamics, and seawater carbonate chemistry since 2000. It indicates sea scallop harvests could decline substantially by 2050 under RCP 8.5 CO2 emissions and current harvest rules, assuming that ocean acidification affects P. magellanicus by decreasing recruitment and slowing growth, and that ocean warming increases growth. Future work will explore different economic and management scenarios and test how potential impacts of ocean acidification on other scallop biological parameters may influence the social-ecological system. Future empirical work on the effect of ocean acidification on sea scallops is also needed. PMID:25945497

An Integrated Assessment Model for Helping the United States Sea Scallop (Placopecten magellanicus) Fishery Plan Ahead for Ocean Acidification and Warming.

PubMed

Cooley, Sarah R; Rheuban, Jennie E; Hart, Deborah R; Luu, Victoria; Glover, David M; Hare, Jonathan A; Doney, Scott C

2015-01-01

Ocean acidification, the progressive change in ocean chemistry caused by uptake of atmospheric CO2, is likely to affect some marine resources negatively, including shellfish. The Atlantic sea scallop (Placopecten magellanicus) supports one of the most economically important single-species commercial fisheries in the United States. Careful management appears to be the most powerful short-term factor affecting scallop populations, but in the coming decades scallops will be increasingly influenced by global environmental changes such as ocean warming and ocean acidification. In this paper, we describe an integrated assessment model (IAM) that numerically simulates oceanographic, population dynamic, and socioeconomic relationships for the U.S. commercial sea scallop fishery. Our primary goal is to enrich resource management deliberations by offering both short- and long-term insight into the system and generating detailed policy-relevant information about the relative effects of ocean acidification, temperature rise, fishing pressure, and socioeconomic factors on the fishery using a simplified model system. Starting with relationships and data used now for sea scallop fishery management, the model adds socioeconomic decision making based on static economic theory and includes ocean biogeochemical change resulting from CO2 emissions. The model skillfully reproduces scallop population dynamics, market dynamics, and seawater carbonate chemistry since 2000. It indicates sea scallop harvests could decline substantially by 2050 under RCP 8.5 CO2 emissions and current harvest rules, assuming that ocean acidification affects P. magellanicus by decreasing recruitment and slowing growth, and that ocean warming increases growth. Future work will explore different economic and management scenarios and test how potential impacts of ocean acidification on other scallop biological parameters may influence the social-ecological system. Future empirical work on the effect of ocean acidification on sea scallops is also needed.

State estimation improves prospects for ocean research

NASA Astrophysics Data System (ADS)

Stammer, Detlef; Wunsch, C.; Fukumori, I.; Marshall, J.

Rigorous global ocean state estimation methods can now be used to produce dynamically consistent time-varying model/data syntheses, the results of which are being used to study a variety of important scientific problems. Figure 1 shows a schematic of a complete ocean observing and synthesis system that includes global observations and state-of-the-art ocean general circulation models (OGCM) run on modern computer platforms. A global observing system is described in detail in Smith and Koblinsky [2001],and the present status of ocean modeling and anticipated improvements are addressed by Griffies et al. [2001]. Here, the focus is on the third component of state estimation: the synthesis of the observations and a model into a unified, dynamically consistent estimate.

The use of Argo for validation and tuning of mixed layer models

NASA Astrophysics Data System (ADS)

Acreman, D. M.; Jeffery, C. D.

We present results from validation and tuning of 1-D ocean mixed layer models using data from Argo floats and data from Ocean Weather Station Papa (145°W, 50°N). Model tests at Ocean Weather Station Papa showed that a bulk model could perform well provided it was tuned correctly. The Large et al. [Large, W.G., McWilliams, J.C., Doney, S.C., 1994. Oceanic vertical mixing: a review and a model with a nonlocal boundary layer parameterisation. Rev. Geophys. 32 (Novermber), 363-403] K-profile parameterisation (KPP) model also gave a good representation of mixed layer depth provided the vertical resolution was sufficiently high. Model tests using data from a single Argo float indicated a tendency for the KPP model to deepen insufficiently over an annual cycle, whereas the tuned bulk model and general ocean turbulence model (GOTM) gave a better representation of mixed layer depth. The bulk model was then tuned using data from a sample of Argo floats and a set of optimum parameters was found; these optimum parameters were consistent with the tuning at OWS Papa.

The Global Ocean Observing System

NASA Technical Reports Server (NTRS)

Kester, Dana

1992-01-01

A Global Ocean Observing System (GOOS) should be established now with international coordination (1) to address issues of global change, (2) to implement operational ENSO forecasts, (3) to provide the data required to apply global ocean circulation models, and (4) to extract the greatest value from the one billion dollar investment over the next ten years in ocean remote sensing by the world's space agencies. The objectives of GOOS will focus on climatic and oceanic predictions, on assessing coastal pollution, and in determining the sustainability of living marine resources and ecosystems. GOOS will be a complete system including satellite observations, in situ observations, numerical modeling of ocean processes, and data exchange and management. A series of practical and economic benefits will be derived from the information generated by GOOS. In addition to the marine science community, these benefits will be realized by the energy industries of the world, and by the world's fisheries. The basic oceanic variables that are required to meet the oceanic and predictability objectives of GOOS include wind velocity over the ocean, sea surface temperature and salinity, oceanic profiles of temperature and salinity, surface current, sea level, the extent and thickness of sea ice, the partial pressure of CO2 in surface waters, and the chlorophyll concentration of surface waters. Ocean circulation models and coupled ocean-atmosphere models can be used to evaluate observing system design, to assimilate diverse data sets from in situ and remotely sensed observations, and ultimately to predict future states of the system. The volume of ocean data will increase enormously over the next decade as new satellite systems are launched and as complementary in situ measuring systems are deployed. These data must be transmitted, quality controlled, exchanged, analyzed, and archived with the best state-of-the-art computational methods.

Determining the Ocean's Role on the Variable Gravity Field and Earth Rotation

NASA Technical Reports Server (NTRS)

Ponte, Rui M.

2000-01-01

Our three year investigation, carried out over the period 18-19 Nov 2000, focused on the study of the variability in ocean angular momentum and mass signals and their relation to the Earth's variable rotation and gravity field. This final report includes a summary description of our work and a list of related publications and presentations. One thrust of the investigation was to determine and interpret the changes in the ocean mass field, as they impact on the variable gravity field and Earth rotation. In this regard, the seasonal cycle in local vertically-integrated ocean mass was analyzed using two ocean models of different complexity: (1) the simple constant-density, coarse resolution model of Ponte; and (2) the fully stratified, eddy-resolving model of Semtner and Chervin. The dynamics and thermodynamics of the seasonal variability in ocean mass were examined in detail, as well as the methodologies to calculate those changes under different model formulations. Another thrust of the investigation was to examine signals in ocean angular momentum (OAM) in relation to Earth rotation changes. A number of efforts were undertaken in this regard. Sensitivity of the oceanic excitation to different assumptions about how the ocean is forced and how it dissipates its energy was explored.

Ocean Model Impact Study for Coupled Hurricane Forecasting: An HFIP Initiative

NASA Astrophysics Data System (ADS)

Kim, H. S. S.; Halliwell, G. R., Jr.; Tallapragada, V.; Black, P. G.; Bond, N.; Chen, S.; Cione, J.; Cronin, M. F.; Ginis, I.; Liu, B.; Miller, L.; Jayne, S. R.; Sanabia, E.; Shay, L. K.; Uhlhorn, E.; Zhu, L.

2016-02-01

Established in 2009, the NOAA Hurricane Forecast Improvement Project (HFIP) is a ten-year project to promote accelerated improvements hurricane track and intensity forecasts (Gall et al. 2013). The Ocean Model Impact Tiger Team (OMITT) consisting of model developers and research scientists was formed as one of HFIP working groups in December 2014, to evaluate the impact of ocean coupling in tropical cyclone (TC) forecasts. The team investigated the ocean model impact in real cases for Category 3 Hurricane Edouard in 2014, using simulations and observations that were collected for different stages of the hurricane. Two Eastern North Pacific Hurricanes in 2015, Blanca and Dolores, are also of special interest. These two powerful Category 4 storms followed a similar track, however, they produced dramatically different ocean cooling, about 7.2oC for Hurricane Blanca but only about 2.7oC for Hurricane Dolores, and the corresponding intensity changes were negative 40 ms-1 and 20 ms-1, respectively. Two versions of operational HWRF and COAMPS-TC coupled prediction systems are employed in the study. These systems are configured to have 1D and 3D ocean dynamics coupled to the atmosphere. The ocean components are initialized separately with climatology, analysis and nowcast products to evaluate the impact of ocean initialization on hurricane forecasts. Real storm forecast experiments are being designed and performed with different levels of the ocean model complexity and various model configurations to study model sensitivity. In this talk, we report the OMITT activities conducted during the past year, present preliminary results of on-going investigation of air-sea interactions in the simulations, and discuss future plans toward improving coupled TC predictions. Gall, R., J. Franklin, F. Marks, E.N. Rappaport, and F. Toepfer, 2013: THE HURRICANE FORECAST IMPROVEMENT PROJECT. Bull. Amer. Meteor. Soc., 329-343.

Importance of ocean salinity for climate and habitability

PubMed Central

Cullum, Jodie; Stevens, David P.; Joshi, Manoj M.

2016-01-01

Modeling studies of terrestrial extrasolar planetary climates are now including the effects of ocean circulation due to a recognition of the importance of oceans for climate; indeed, the peak equator-pole ocean heat transport on Earth peaks at almost half that of the atmosphere. However, such studies have made the assumption that fundamental oceanic properties, such as salinity, temperature, and depth, are similar to Earth. This assumption results in Earth-like circulations: a meridional overturning with warm water moving poleward at the surface, being cooled, sinking at high latitudes, and traveling equatorward at depth. Here it is shown that an exoplanetary ocean with a different salinity can circulate in the opposite direction: an equatorward flow of polar water at the surface, sinking in the tropics, and filling the deep ocean with warm water. This alternative flow regime results in a dramatic warming in the polar regions, demonstrated here using both a conceptual model and an ocean general circulation model. These results highlight the importance of ocean salinity for exoplanetary climate and consequent habitability and the need for its consideration in future studies. PMID:27044090

Importance of ocean salinity for climate and habitability.

PubMed

Cullum, Jodie; Stevens, David P; Joshi, Manoj M

2016-04-19

Modeling studies of terrestrial extrasolar planetary climates are now including the effects of ocean circulation due to a recognition of the importance of oceans for climate; indeed, the peak equator-pole ocean heat transport on Earth peaks at almost half that of the atmosphere. However, such studies have made the assumption that fundamental oceanic properties, such as salinity, temperature, and depth, are similar to Earth. This assumption results in Earth-like circulations: a meridional overturning with warm water moving poleward at the surface, being cooled, sinking at high latitudes, and traveling equatorward at depth. Here it is shown that an exoplanetary ocean with a different salinity can circulate in the opposite direction: an equatorward flow of polar water at the surface, sinking in the tropics, and filling the deep ocean with warm water. This alternative flow regime results in a dramatic warming in the polar regions, demonstrated here using both a conceptual model and an ocean general circulation model. These results highlight the importance of ocean salinity for exoplanetary climate and consequent habitability and the need for its consideration in future studies.

Dispersal of Fine Sediment in the Coastal Ocean: Sensitivity to Aggregation and Stratification

DTIC Science & Technology

2008-01-01

Venice. They have used this model as both a research tool (Bignami et al., 2007) and to construct an operational model ( Chiggiato and Oddo, 2006... Chiggiato , J. and Oddo, P., 2006. Operational ocean models in the Adriatic Sea: a skill assessment. Ocean Science Discussions, 3: 2087 - 2116. Haidvogel

Computed and observed turbulent heat fluxes during an extreme Bora event in the Adriatic using atmosphere-ocean coupling

NASA Astrophysics Data System (ADS)

Ličer, Matjaž; Smerkol, Peter; Fettich, Anja; Ravdas, Michalis; Papapostolou, Alexandros; Mantziafou, Anneta; Strajnar, Benedikt; Cedilnik, Jure; Jeromel, Maja; Jerman, Jure; Petan, Sašo; Benetazzo, Alvise; Carniel, Sandro; Malačič, Vlado; Sofianos, Sarantis

2016-04-01

We have studied the performances of (a) a two-way coupled atmosphere-ocean modeling system and (b) one-way coupled ocean model (forced by the atmosphere model), as compared to the available in situ measurements during and after a strong Adriatic Bora wind event in February 2012, which led to extreme air-sea interactions. The simulations span the period between January and March 2012. The models used were ALADIN (4.4 km resolution) on the atmosphere side and Adriatic setup of POM (1°/30 × 1°/30 angular resolution) on the ocean side. The atmosphere-ocean coupling was implemented using the OASIS3-MCT model coupling toolkit. Two-way coupling ocean feedback to the atmosphere is limited to sea surface temperature. We have compared modeled atmosphere-ocean fluxes (computed using modified Louis scheme) and sea temperatures from both setups to platform and CTD measurements of fluxes (computed using COARE scheme) and temperatures from three observational platforms (Vida, Paloma, Acqua Alta) in the Northern Adriatic. We show that turbulent fluxes from both setups differ up to 20% during the Bora but not significantly before and after the event. The impact of the coupling on the ocean is significant while the impact on the atmosphere is less pronounced. When compared to observations, two way coupling ocean temperatures exhibit a four times lower RMSE than those from one-way coupled system. Two-way coupling improves sensible heat fluxes at all stations but does not improve latent heat loss.

Ocean processes at the Antarctic continental slope.

PubMed

Heywood, Karen J; Schmidtko, Sunke; Heuzé, Céline; Kaiser, Jan; Jickells, Timothy D; Queste, Bastien Y; Stevens, David P; Wadley, Martin; Thompson, Andrew F; Fielding, Sophie; Guihen, Damien; Creed, Elizabeth; Ridley, Jeff K; Smith, Walker

2014-07-13

The Antarctic continental shelves and slopes occupy relatively small areas, but, nevertheless, are important for global climate, biogeochemical cycling and ecosystem functioning. Processes of water mass transformation through sea ice formation/melting and ocean-atmosphere interaction are key to the formation of deep and bottom waters as well as determining the heat flux beneath ice shelves. Climate models, however, struggle to capture these physical processes and are unable to reproduce water mass properties of the region. Dynamics at the continental slope are key for correctly modelling climate, yet their small spatial scale presents challenges both for ocean modelling and for observational studies. Cross-slope exchange processes are also vital for the flux of nutrients such as iron from the continental shelf into the mixed layer of the Southern Ocean. An iron-cycling model embedded in an eddy-permitting ocean model reveals the importance of sedimentary iron in fertilizing parts of the Southern Ocean. Ocean gliders play a key role in improving our ability to observe and understand these small-scale processes at the continental shelf break. The Gliders: Excellent New Tools for Observing the Ocean (GENTOO) project deployed three Seagliders for up to two months in early 2012 to sample the water to the east of the Antarctic Peninsula in unprecedented temporal and spatial detail. The glider data resolve small-scale exchange processes across the shelf-break front (the Antarctic Slope Front) and the front's biogeochemical signature. GENTOO demonstrated the capability of ocean gliders to play a key role in a future multi-disciplinary Southern Ocean observing system.

Sensitivity of the Arctic Ocean gas hydrate to climate changes in the period of 1948-2015

NASA Astrophysics Data System (ADS)

Malakhova, Valentina V.; Golubeva, Elena N.; Iakshina, Dina F.

2017-11-01

The objective of the present study is to analyze the interactions between a methane hydrates stability zone and the ocean temperature variations and to define the hydrate sensitivity to the contemporary warming in the Arctic Ocean. To obtain the spatial-temporary variability of the ocean bottom temperature we employ the ICMMG regional Arctic-North Atlantic ocean model that has been developed in the Institute of Computational Mathematics and Mathematical Geophysics. With the ice-ocean model the Arctic bottom water temperatures were analyzed. The resulting warming ocean bottom water is spatially inhomogeneous, with a strong impact by the Atlantic inflow on shallow regions of 200-500 m depth. Results of the mathematical modeling of the dynamics of methane hydrate stability zone in the Arctic Ocean sediment are reported. We find that the reduction of the methane hydrate stability zone occurs in the Arctic Ocean between 250 and 400 m water depths within the upper 100 m of sediment in the area influenced by the Atlantic inflow. We have identified the areas of the Arctic Ocean where an increase in methane release is probable to occur at the present time.

On the interrelationship between temporal trends in. delta. sup 13 C,. delta. sup 18 O, and. delta. sup 34 S in the world ocean

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoffman, A.; Gruszczynski, M.; Malkowski, K.

1991-05-01

The phenomena of (i) inverse correlation between the oceanic carbon and sulfur isotopic curves, and (ii) covariation between the oceanic carbon and oxygen isotopic curves at all their major excursions appear as paradoxes in the current paradigm of global biogeochemical cycles. These phenomena, however, are fully explicable by a model proposing that the ocean alternates between two general modes: stagnant, stratified, and net autotrophic (overfed) ocean, on the one hand, and vigorously mixed and net heterotrophic (hungry) ocean, on the other. This model is in fact strongly supported by the carbon isotopic evidence. The directions of change in the isotopicmore » ratios of carbon, oxygen, and sulfur should be different in the lower, anoxic box of a stratified ocean than in the upper, oxic box; whereas ocean destratification and mixing of the two boxes should lead to coeval shifts in the oceanic isotopic curves of these elements. The model has far-reaching implications for (i) the causal explanation of both secular trends and major shifts in the oceanic isotopic curves, and (ii) for the application of oxygen isotopic data for paleotemperature and paleoenvironment determinations.« less

The Impact of Ocean Observations in Seasonal Climate Prediction

NASA Technical Reports Server (NTRS)

Rienecker, Michele; Keppenne, Christian; Kovach, Robin; Marshak, Jelena

2010-01-01

The ocean provides the most significant memory for the climate system. Hence, a critical element in climate forecasting with coupled models is the initialization of the ocean with states from an ocean data assimilation system. Remotely-sensed ocean surface fields (e.g., sea surface topography, SST, winds) are now available for extensive periods and have been used to constrain ocean models to provide a record of climate variations. Since the ocean is virtually opaque to electromagnetic radiation, the assimilation of these satellite data is essential to extracting the maximum information content. More recently, the Argo drifters have provided unprecedented sampling of the subsurface temperature and salinity. Although the duration of this observation set has been too short to provide solid statistical evidence of its impact, there are indications that Argo improves the forecast skill of coupled systems. This presentation will address the impact these different observations have had on seasonal climate predictions with the GMAO's coupled model.

Impacts of dynamical ocean coupling in MJO experiments using NICAM/NICOCO

NASA Astrophysics Data System (ADS)

Miyakawa, T.

2016-12-01

The cloud-system resolving atmosphereic model NICAM has been successfull in producing Madden-Julian Oscillations(MJOs), having it's prediction skill estimated to be about 4 weeks in a series of hindcast experiments for winter MJO events during 2003-2012 (Miyakawa et al. 2014). A simple mixed-layer ocean model has been applied with nudging towards a prescribed "persistent anomaly SST", which maintains the initial anomaly with a time-varying climatological seasonal cycle. This setup enables the model to interact with an ocean with reasonably realistic SST, and also run in a "forecast mode", without using any observational information after the initial date. A limitation is that under this setup, the model skill drops if the oceanic anomaly rapidly changes after the initial date in the real world. Here we run a recently developed, full 3D-ocean coupled version NICAM-COCO (NICOCO) and explore its impact on MJO simulations. Dynamical ocean models can produce oceanic waves/currents, but will also have a bias and drift away from reality. In a sub-seasonal simulation (an initial problem), it is essential to compare the merit of having better represented oceanic signals and the demerit of bias/drift. A test case simulation series featuring an MJO that triggered the abrupt termination of a major El Nino in 1998 shows that the abrupt termination occurs in all 9 simulation members, highlighting the merit of ocean coupling. However, this is a case where oceanic signals are at its extremes. We carried out an estimation of MJO prediction skill for a preliminary 1-degree mesh ocean version of NICOCO in a similar manner to Miyakawa et al. (2014). The MJO skill was degraded for simulations that was initialized at RMM phases 1 and 2 (corresponding to the Indian Ocean), while those initialized at phase 8 (Africa) was not strongly affected. The tendency of the model ocean to overestimate the Maritime Continent warm pool SST possibly delays the eastward propagation of MJO convective envelope, accounting for the degrade of prediction skills (phases 1 and 2). Reference:Madden-Julian Oscillation prediction skill of a new-generation global model demonstrated using a supercomputer. Miyakawa, T., M. Satoh, H. Miura, H. Tomita, H. Yashiro, A. T. Noda, Y. Yamada, C. Kodama, M. Kimoto & K. Yoneyama. Nature Comm. 5, 3769, doi:10.1038/ncomms4769.

Advances in a distributed approach for ocean model data interoperability

USGS Publications Warehouse

Signell, Richard P.; Snowden, Derrick P.

2014-01-01

An infrastructure for earth science data is emerging across the globe based on common data models and web services. As we evolve from custom file formats and web sites to standards-based web services and tools, data is becoming easier to distribute, find and retrieve, leaving more time for science. We describe recent advances that make it easier for ocean model providers to share their data, and for users to search, access, analyze and visualize ocean data using MATLAB® and Python®. These include a technique for modelers to create aggregated, Climate and Forecast (CF) metadata convention datasets from collections of non-standard Network Common Data Form (NetCDF) output files, the capability to remotely access data from CF-1.6-compliant NetCDF files using the Open Geospatial Consortium (OGC) Sensor Observation Service (SOS), a metadata standard for unstructured grid model output (UGRID), and tools that utilize both CF and UGRID standards to allow interoperable data search, browse and access. We use examples from the U.S. Integrated Ocean Observing System (IOOS®) Coastal and Ocean Modeling Testbed, a project in which modelers using both structured and unstructured grid model output needed to share their results, to compare their results with other models, and to compare models with observed data. The same techniques used here for ocean modeling output can be applied to atmospheric and climate model output, remote sensing data, digital terrain and bathymetric data.

On the sensitivity of the global ocean circulation to reconstructions of paleo-bathymetry

NASA Astrophysics Data System (ADS)

Weber, Tobias; Thomas, Maik

2013-04-01

The ability to model the long-term evolution of the climate does considerably depend on the accuracy of ocean models and their interaction with the atmosphere. Thereby, the ocean model's behavior with respect to uncertain and changing boundary conditions is of crucial importance. One of the remaining questions is, how different reconstructions of the ocean floor influence the model. Although of general interest, this effect has mostly been neglected, so far. We modeled Pliocene and pre-industrial ocean currents with the Max-Planck-Institute Ocean Model (MPIOM), forced by climatologies derived from an atmospheric and vegetational Global Circulation Model (GCM). We equipped it with different reconstructions of the bathymetry, what allowed us to study the model's sensitivity regarding changes in bathymetry. On the one hand we examined the influence of reconstructions with different locations of major ridges, but the same treatment of the shelf. On the other hand, reconstruction techniques that treated the shelf areas differently were taken into consideration. This leads to different oceanic circulation realizations, which induce changes in deep ocean temperature and salinity. Some of the simulations result in unrealistic behavior, such as an increase in surface temperature by several degrees. Most important, small bathymetric changes in the areas of deep water formation near Greenland and the Antarctic alter the thermohaline circulation strongly. This leads to its complete cessation in some of the simulations and therefore to stationary deep laying ocean masses. This shows that not all bathymetric reconstruction sequences are applicable for the generation of boundary conditions for GCMs. In order to obtain reliable and physically realistic data from the models, the reconstruction method to be used for the paleo-bathymetry also needs to be applied to the present day bathymetry. This reconstruction can then be used in a control simulation which can be validated against measurements. Hereby systematic errors introduced by the reconstruction technique are identified.

Improved Climate Simulations through a Stochastic Parameterization of Ocean Eddies

NASA Astrophysics Data System (ADS)

Williams, Paul; Howe, Nicola; Gregory, Jonathan; Smith, Robin; Joshi, Manoj

2017-04-01

In climate simulations, the impacts of the subgrid scales on the resolved scales are conventionally represented using deterministic closure schemes, which assume that the impacts are uniquely determined by the resolved scales. Stochastic parameterization relaxes this assumption, by sampling the subgrid variability in a computationally inexpensive manner. This study shows that the simulated climatological state of the ocean is improved in many respects by implementing a simple stochastic parameterization of ocean eddies into a coupled atmosphere-ocean general circulation model. Simulations from a high-resolution, eddy-permitting ocean model are used to calculate the eddy statistics needed to inject realistic stochastic noise into a low-resolution, non-eddy-permitting version of the same model. A suite of four stochastic experiments is then run to test the sensitivity of the simulated climate to the noise definition by varying the noise amplitude and decorrelation time within reasonable limits. The addition of zero-mean noise to the ocean temperature tendency is found to have a nonzero effect on the mean climate. Specifically, in terms of the ocean temperature and salinity fields both at the surface and at depth, the noise reduces many of the biases in the low-resolution model and causes it to more closely resemble the high-resolution model. The variability of the strength of the global ocean thermohaline circulation is also improved. It is concluded that stochastic ocean perturbations can yield reductions in climate model error that are comparable to those obtained by refining the resolution, but without the increased computational cost. Therefore, stochastic parameterizations of ocean eddies have the potential to significantly improve climate simulations. Reference Williams PD, Howe NJ, Gregory JM, Smith RS, and Joshi MM (2016) Improved Climate Simulations through a Stochastic Parameterization of Ocean Eddies. Journal of Climate, 29, 8763-8781. http://dx.doi.org/10.1175/JCLI-D-15-0746.1

Equivalent magnetization over the World's Ocean

NASA Astrophysics Data System (ADS)

Dyment, J.; Choi, Y.; Hamoudi, M.; Erwan, T.; Lesur, V.

2014-12-01

As a by-product of our recent work to build a candidate model over the oceans for the World Digital Magnetic Anomaly Map (WDMAM) version 2, we derived global distributions of the equivalent magnetization in oceanic domains. In a first step, we use classic point source forward modeling on a spherical Earth to build a forward model of the marine magnetic anomalies at sea-surface. We estimate magnetization vectors using the age map of the ocean floor, the relative plate motions, the apparent polar wander path for Africa, and a geomagnetic reversal time scale. As magnetized source geometry, we assume 1 km-thick layer bearing a 10 A/m magnetization following the topography of the oceanic basement as defined by the bathymetry and sedimentary thickness. Adding a present-day geomagnetic field model allows the computation of our initial magnetic anomaly model. In a second step, we adjust this model to the existing marine magnetic anomaly data, in order to make it consistent with these data. To do so, we extract synthetic magnetic along the ship tracks for which real data are available and we compare quantitatively the measured and computed anomalies on 100, 200 or 400 km-long sliding windows (depending the spreading rate). Among the possible comparison criteria, we discard the maximal range - too dependent on local values - and the correlation and coherency - the geographical adjustment between model and data being not accurate enough - to favor the standard deviation around the mean value. The ratio between the standard deviations of data and model on each sliding window represent an estimate of the magnetization ratio causing the anomalies, which we interpolate to adjust the initial magnetic anomaly model to the data and therefore compute a final model to be included in our WDMAM candidate over the oceanic regions lacking data. The above ratio, after division by the magnetization of 10 A/m used in the model, represents an estimate of the equivalent magnetization under the considered magnetized source geometry. The resulting distributions of equivalent magnetization are discussed in terms of mid-ocean ridges, presence of hotspots and oceanic plateaus, and the age of the oceanic lithosphere. Global marine magnetic data sets and models represent a useful tool to assess first order magnetic properties of the oceanic lithosphere.

Sensitivity of climate and atmospheric CO2 to deep-ocean and shallow-ocean carbonate burial

NASA Technical Reports Server (NTRS)

Volk, Tyler

1989-01-01

A model of the carbonate-silicate geochemical cycle is presented that distinguishes carbonate masses produced by shallow-ocean and deep-ocean carbonate burial and shows that reasonable increases in deep-ocean burial could produce substantial warmings over a few hundred million years. The model includes exchanges between crust and mantle; transients from burial shifts are found to be sensitive to the fraction of nondegassed carbonates subducted into the mantle. Without the habitation of the open ocean by plankton such as foraminifera and coccolithophores, today's climate would be substantially colder.

Wave–turbulence interaction-induced vertical mixing and its effects in ocean and climate models

PubMed Central

Qiao, Fangli; Yuan, Yeli; Deng, Jia; Dai, Dejun; Song, Zhenya

2016-01-01

Heated from above, the oceans are stably stratified. Therefore, the performance of general ocean circulation models and climate studies through coupled atmosphere–ocean models depends critically on vertical mixing of energy and momentum in the water column. Many of the traditional general circulation models are based on total kinetic energy (TKE), in which the roles of waves are averaged out. Although theoretical calculations suggest that waves could greatly enhance coexisting turbulence, no field measurements on turbulence have ever validated this mechanism directly. To address this problem, a specially designed field experiment has been conducted. The experimental results indicate that the wave–turbulence interaction-induced enhancement of the background turbulence is indeed the predominant mechanism for turbulence generation and enhancement. Based on this understanding, we propose a new parametrization for vertical mixing as an additive part to the traditional TKE approach. This new result reconfirmed the past theoretical model that had been tested and validated in numerical model experiments and field observations. It firmly establishes the critical role of wave–turbulence interaction effects in both general ocean circulation models and atmosphere–ocean coupled models, which could greatly improve the understanding of the sea surface temperature and water column properties distributions, and hence model-based climate forecasting capability. PMID:26953182

Exploring the southern ocean response to climate change

NASA Technical Reports Server (NTRS)

Martinson, Douglas G.; Rind, David; Parkinson, Claire

1993-01-01

The purpose of this project was to couple a regional (Southern Ocean) ocean/sea ice model to the existing Goddard Institute for Space Science (GISS) atmospheric general circulation model (GCM). This modification recognizes: the relative isolation of the Southern Ocean; the need to account, prognostically, for the significant air/sea/ice interaction through all involved components; and the advantage of translating the atmospheric lower boundary (typically the rapidly changing ocean surface) to a level that is consistent with the physical response times governing the system evolution (that is, to the base of the fast responding ocean surface layer). The deeper ocean beneath this layer varies on time scales several orders of magnitude slower than the atmosphere and surface ocean, and therefore the boundary between the upper and deep ocean represents a more reasonable fixed boundary condition.

Interbasin effects of the Indian Ocean on Pacific decadal climate change

NASA Astrophysics Data System (ADS)

Mochizuki, Takashi; Kimoto, Masahide; Watanabe, Masahiro; Chikamoto, Yoshimitsu; Ishii, Masayoshi

2016-07-01

We demonstrate the significant impact of the Indian Ocean on the Pacific climate on decadal timescales by comparing two sets of data assimilation experiments (pacemaker experiments) conducted over recent decades. For the Indian Ocean of an atmosphere-ocean coupled global climate model, we assimilate ocean temperature and salinity anomalies defined as deviations from climatology or as anomalies with the area-averaged changes for the Indian Ocean subtracted. When decadal sea surface temperature (SST) trends are observed to be strong over the Indian Ocean, the equatorial thermocline uniformly deepens, and the model simulates the eastward tendencies of surface wind aloft. Surface winds strongly converge around the maritime continent, and the associated strengthening of the Walker circulation suppresses an increasing trend in the equatorial Pacific SST through ocean thermocline shoaling, similar to common changes associated with seasonal Indian Ocean warming.

Statistical and dynamical assessment of land-ocean-atmosphere interactions across North Africa

NASA Astrophysics Data System (ADS)

Yu, Yan

North Africa is highly vulnerable to hydrologic variability and extremes, including impacts of climate change. The current understanding of oceanic versus terrestrial drivers of North African droughts and pluvials is largely model-based, with vast disagreement among models in terms of the simulated oceanic impacts and vegetation feedbacks. Regarding oceanic impacts, the relative importance of the tropical Pacific, tropical Indian, and tropical Atlantic Oceans in regulating the North African rainfall variability, as well as the underlying mechanism, remains debated among different modeling studies. Classic theory of land-atmosphere interactions across the Sahel ecotone, largely based on climate modeling experiments, has promoted positive vegetation-rainfall feedbacks associated with a dominant surface albedo mechanism. However, neither the proposed positive vegetation-rainfall feedback with its underlying albedo mechanism, nor its relative importance compared with oceanic drivers, has been convincingly demonstrated up to now using observational data. Here, the multivariate Generalized Equilibrium Feedback Assessment (GEFA) is applied in order to identify the observed oceanic and terrestrial drivers of North African climate and quantify their impacts. The reliability of the statistical GEFA method is first evaluated against dynamical experiments within the Community Earth System Model (CESM). In order to reduce the sampling error caused by short data records, the traditional GEFA approach is refined through stepwise GEFA, in which unimportant forcings are dropped through stepwise selection. In order to evaluate GEFA's reliability in capturing oceanic impacts, the atmospheric response to a sea-surface temperature (SST) forcing across the tropical Pacific, tropical Indian, and tropical Atlantic Ocean is estimated independently through ensembles of dynamical experiments and compared with GEFA-based assessments. Furthermore, GEFA's performance in capturing terrestrial impacts is evaluated through ensembles of fully coupled CESM dynamical experiments, with modified leaf area index (LAI) and soil moisture across the Sahel or West African Monsoon (WAM) region. The atmospheric responses to oceanic and terrestrial forcings are generally consistent between the dynamical experiments and statistical GEFA, confirming GEFA's capability of isolating the individual impacts of oceanic and terrestrial forcings on North African climate. Furthermore, with the incorporation of stepwise selection, GEFA can now provide reliable estimates of the oceanic and terrestrial impacts on the North African climate with the typical length of observational datasets, thereby enhancing the method's applicability. After the successful validation of GEFA, the key observed oceanic and terrestrial drivers of North African climate are identified through the application of GEFA to gridded observations, remote sensing products, and reanalyses. According to GEFA, oceanic drivers dominate over terrestrial drivers in terms of their observed impacts on North African climate in most seasons. Terrestrial impacts are comparable to, or more important than, oceanic impacts on rainfall during the post-monsoon across the Sahel and WAM region, and after the short rain across the Horn of Africa (HOA). The key ocean basins that regulate North African rainfall are typically located in the tropics. While the observed impacts of SST variability across the tropical Pacific and tropical Atlantic Oceans on the Sahel rainfall are largely consistent with previous model-based findings, minimal impacts from tropical Indian Ocean variability on Sahel rainfall are identified in observations, in contrast to previous modeling studies. The current observational analysis verifies model-hypothesized positive vegetation-rainfall feedback across the Sahel and HOA, which is confined to the post-monsoon and post-short rains season, respectively. However, the observed positive vegetation feedback to rainfall in the semi-arid Sahel and HOA is largely due to moisture recycling, rather than the classic albedo mechanism. Future projections of Sahel rainfall remain highly uncertain in terms of both sign and magnitude within phases three and five of the Coupled Model Intercomparison Project (CMIP3 and CMIP5). The GEFA-based observational analyses will provide a benchmark for evaluating climate models, which will facilitate effective process-based model weighting for more reliable projections of regional climate, as well as model development.

Can increased poleward oceanic heat flux explain the warm Cretaceous climate?

NASA Astrophysics Data System (ADS)

Schmidt, Gavin A.; Mysak, Lawrence A.

1996-10-01

The poleward transport of heat in the mid-Cretaceous (100 Ma) is examined using an idealized coupled ocean-atmosphere model. The oceanic component consists of two zonally averaged basins representing the proto-Pacific and proto-Indian oceans and models the dynamics of the meridional thermohaline circulation. The atmospheric component is a simple energy and moisture balance model which includes the diffusive meridional transport of sensible heat and moisture. The ocean model is spun up with a variety of plausible Cretaceous surface temperature and salinity profiles, and a consistent atmosphere is objectively derived based on the resultant sea surface temperature and the surface heat and freshwater fluxes. The coupled model does not exhibit climate drift. Multiple equilibria of the coupled model are found that break the initial symmetry of the ocean circulation; several of these equilibria have one-cell (northern or southern sinking) thermohaline circulation patterns. Two main classes of circulation are found: circulations where the densest water is relatively cool and is formed at the polar latitudes and circulations where the densest water is warm, but quite saline, and the strongest sinking occurs at the tropics. In all cases, significant amounts of warm, saline bottom water are formed in the proto-Indian basin which modify the deepwater characteristics in the larger (proto-Pacific) basin. Temperatures in the deep ocean are warm, 10°-17°C, in agreement with benthic foraminiferal oxygen isotope data. The poleward transport of heat in the modeled Cretaceous oceans is larger than in some comparable models of the present day thermohaline circulation and significantly larger than estimates of similar processes in the present-day ocean. It is consistently larger in the polar sinking cases when compared with that seen in the tropical sinking cases, but this represents an increase of only 10%. The largest increase over present-day model transports is in the atmospheric latent heat transport, where an increased hydrological cycle (especially in the tropical sinking cases) contributes up to an extra 1 PW of poleward heat transport. Better constraints on the oceanic deepwater circulation during this period are necessary before the meridional circulation can be unambiguously described.

OceanNOMADS: Real-time and retrospective access to operational U.S. ocean prediction products

NASA Astrophysics Data System (ADS)

Harding, J. M.; Cross, S. L.; Bub, F.; Ji, M.

2011-12-01

The National Oceanic and Atmospheric Administration (NOAA) National Operational Model Archive and Distribution System (NOMADS) provides both real-time and archived atmospheric model output from servers at the National Centers for Environmental Prediction (NCEP) and National Climatic Data Center (NCDC) respectively (http://nomads.ncep.noaa.gov/txt_descriptions/marRutledge-1.pdf). The NOAA National Ocean Data Center (NODC) with NCEP is developing a complementary capability called OceanNOMADS for operational ocean prediction models. An NCEP ftp server currently provides real-time ocean forecast output (http://www.opc.ncep.noaa.gov/newNCOM/NCOM_currents.shtml) with retrospective access through NODC. A joint effort between the Northern Gulf Institute (NGI; a NOAA Cooperative Institute) and the NOAA National Coastal Data Development Center (NCDDC; a division of NODC) created the developmental version of the retrospective OceanNOMADS capability (http://www.northerngulfinstitute.org/edac/ocean_nomads.php) under the NGI Ecosystem Data Assembly Center (EDAC) project (http://www.northerngulfinstitute.org/edac/). Complementary funding support for the developmental OceanNOMADS from U.S. Integrated Ocean Observing System (IOOS) through the Southeastern University Research Association (SURA) Model Testbed (http://testbed.sura.org/) this past year provided NODC the analogue that facilitated the creation of an NCDDC production version of OceanNOMADS (http://www.ncddc.noaa.gov/ocean-nomads/). Access tool development and storage of initial archival data sets occur on the NGI/NCDDC developmental servers with transition to NODC/NCCDC production servers as the model archives mature and operational space and distribution capability grow. Navy operational global ocean forecast subsets for U.S waters comprise the initial ocean prediction fields resident on the NCDDC production server. The NGI/NCDDC developmental server currently includes the Naval Research Laboratory Inter-America Seas Nowcast/Forecast System over the Gulf of Mexico from 2004-Mar 2011, the operational Naval Oceanographic Office (NAVOCEANO) regional USEast ocean nowcast/forecast system from early 2009 to present, and the NAVOCEANO operational regional AMSEAS (Gulf of Mexico/Caribbean) ocean nowcast/forecast system from its inception 25 June 2010 to present. AMSEAS provided one of the real-time ocean forecast products accessed by NOAA's Office of Response and Restoration from the NGI/NCDDC developmental OceanNOMADS during the Deep Water Horizon oil spill last year. The developmental server also includes archived, real-time Navy coastal forecast products off coastal Japan in support of U.S./Japanese joint efforts following the 2011 tsunami. Real-time NAVOCEANO output from regional prediction systems off Southern California and around Hawaii, currently available on the NCEP ftp server, are scheduled for archival on the developmental OceanNOMADS by late 2011 along with the next generation Navy/NOAA global ocean prediction output. Accession and archival of additional regions is planned as server capacities increase.

Elemental mercury concentrations and fluxes in the tropical atmosphere and ocean.

PubMed

Soerensen, Anne L; Mason, Robert P; Balcom, Prentiss H; Jacob, Daniel J; Zhang, Yanxu; Kuss, Joachim; Sunderland, Elsie M

2014-10-07

Air-sea exchange of elemental mercury (Hg(0)) is a critical component of the global biogeochemical Hg cycle. To better understand variability in atmospheric and oceanic Hg(0), we collected high-resolution measurements across large gradients in seawater temperature, salinity, and productivity in the Pacific Ocean (20°N-15°S). We modeled surface ocean Hg inputs and losses using an ocean general circulation model (MITgcm) and an atmospheric chemical transport model (GEOS-Chem). Observed surface seawater Hg(0) was much more variable than atmospheric concentrations. Peak seawater Hg(0) concentrations (∼ 130 fM) observed in the Pacific intertropical convergence zone (ITCZ) were ∼ 3-fold greater than surrounding areas (∼ 50 fM). This is similar to observations from the Atlantic Ocean. Peak evasion in the northern Pacific ITCZ was four times higher than surrounding regions and located at the intersection of high wind speeds and elevated seawater Hg(0). Modeling results show that high Hg inputs from enhanced precipitation in the ITCZ combined with the shallow ocean mixed layer in this region drive elevated seawater Hg(0) concentrations. Modeled seawater Hg(0) concentrations reproduce observed peaks in the ITCZ of both the Atlantic and Pacific Oceans but underestimate its magnitude, likely due to insufficient deep convective scavenging of oxidized Hg from the upper troposphere. Our results demonstrate the importance of scavenging of reactive mercury in the upper atmosphere driving variability in seawater Hg(0) and net Hg inputs to biologically productive regions of the tropical ocean.

A Real-time 1/16° Global Ocean Nowcast/Forecast System

NASA Astrophysics Data System (ADS)

Shriver, J. F.; Rhodes, R. C.; Hurlburt, H. E.; Wallcraft, A. J.; Metzger, E. J.; Smedstad, O. M.; Kara, A. B.

2001-05-01

A 1/16° eddy-resolving global ocean prediction system that uses the NRL Layered Ocean Model (NLOM) has been transitioned to the Naval Oceanographic Office (NAVO), Stennis Space Center, MS. The system gives a real time view of the ocean down to the 50-100 mile scale of ocean eddies and the meandering of ocean currents and fronts, a view with unprecedented resolution and clarity, and demonstrated forecast skill for a month or more for many ocean features. It has been running in real time at NAVO since 19 Oct 2000 with assimilation of real-time altimeter sea surface height (SSH) data (currently ERS-2, GFO and TOPEX/POSEIDON) and sea surface temperature (SST). The model is updated daily and 4-day forecasts are made daily. 30-day forecasts are made once a week. Nowcasts and forecasts using this model are viewable on the web, including SSH, SST and 30-day forecast verification statistics for many zoom regions. The NRL web address is http://www7320.nrlssc.navy.mil/global_nlom/index.html. The NAVO web address is: http://www.navo.navy.mil. Click on "Operational Products", then "Product Search Form", then "Product Type View", then select "Model Navy Layered Ocean Model" and a region and click on "Submit Query". This system is used at NAVO for ocean front and eddy analyses and predictions and to provide accurate sea surface height for use in computing synthetic temperature and salinity profiles, among other applications.

Garnet Signatures in Geophysical and Geochemical Observations: Insights into the Thermo-Petrological Structure of Oceanic Upper Mantle

NASA Astrophysics Data System (ADS)

Grose, C. J.; Afonso, J. C.

2013-12-01

We have developed new physically comprehensive thermal plate models of the oceanic lithosphere which incorporate temperature- and pressure-dependent heat transport properties and thermal expansivity, melting beneath ridges, hydrothermal circulation near ridge axes, and insulating oceanic crust. These models provide good fits to global databases of seafloor topography and heat flow, and seismic evidence of thermal structure near ridge axes. We couple these thermal plate models with thermodynamic models to predict the petrology of oceanic lithosphere. Geoid height predictions from our models suggest that there is a strong anomaly in geoid slope (over age) above ~25 Ma lithosphere due to the topography of garnet-field mantle. A similar anomaly is also present in geoid data over fracture zones. In addition, we show that a new assessment of a large database of ocean island basalt Sm/Yb systematics indicates that there is an unmistakable step-like increase in Sm/Yb values around 15-20 Ma, indicating the presence of garnet. To explain this feature, we have attempted to couple our thermo-petrological models of oceanic upper mantle with an open system, non-modal, dynamic melting model with diffusion kinetics to investigate trace element partitioning in an ascending mantle column.

Thermal and mechanical structure of the upper mantle: A comparison between continental and oceanic models

NASA Technical Reports Server (NTRS)

Froidevaux, C.; Schubert, G.; Yuen, D. A.

1976-01-01

Temperature, velocity, and viscosity profiles for coupled thermal and mechanical models of the upper mantle beneath continental shields and old ocean basins show that under the continents, both tectonic plates and the asthenosphere, are thicker than they are beneath the oceans. The minimum value of viscosity in the continental asthenosphere is about an order of magnitude larger than in the shear zone beneath oceans. The shear stress or drag underneath continental plates is also approximately an order of magnitude larger than the drag on oceanic plates. Effects of shear heating may account for flattening of ocean floor topography and heat flux in old ocean basins.

Long-term measurements of acoustic background noise in very deep sea

NASA Astrophysics Data System (ADS)

Riccobene, G.; NEMO Collaboration

2009-06-01

The NEMO (NEutrino Mediterranean Observatory) Collaboration installed, 25 km E offshore the port of Catania (Sicily) at 2000 m depth, an underwater laboratory to perform long-term tests of prototypes and new technologies for an underwater high energy neutrino km-scale detector in the Mediterranean Sea. In this framework the Collaboration deployed and successfully operated for about two years, starting from January 2005, an experimental apparatus for on-line monitoring of deep-sea noise. The station was equipped with four hydrophones and it is operational in the range 30 Hz-43 kHz. This interval of frequencies matches the range suitable for the proposed acoustic detection technique of high energy neutrinos. Hydrophone signals were digitized underwater at 96 kHz sampling frequency and 24 bits resolution. The stored data library, consisting of more than 2000 h of recordings, is a unique tool to model underwater acoustic noise at large depth, to characterize its variations as a function of environmental parameters, biological sources and human activities (ship traffic, etc.), and to determine the presence of cetaceans in the area.

Mapping Global Ocean Surface Albedo from Satellite Observations: Models, Algorithms, and Datasets

NASA Astrophysics Data System (ADS)

Li, X.; Fan, X.; Yan, H.; Li, A.; Wang, M.; Qu, Y.

2018-04-01

Ocean surface albedo (OSA) is one of the important parameters in surface radiation budget (SRB). It is usually considered as a controlling factor of the heat exchange among the atmosphere and ocean. The temporal and spatial dynamics of OSA determine the energy absorption of upper level ocean water, and have influences on the oceanic currents, atmospheric circulations, and transportation of material and energy of hydrosphere. Therefore, various parameterizations and models have been developed for describing the dynamics of OSA. However, it has been demonstrated that the currently available OSA datasets cannot full fill the requirement of global climate change studies. In this study, we present a literature review on mapping global OSA from satellite observations. The models (parameterizations, the coupled ocean-atmosphere radiative transfer (COART), and the three component ocean water albedo (TCOWA)), algorithms (the estimation method based on reanalysis data, and the direct-estimation algorithm), and datasets (the cloud, albedo and radiation (CLARA) surface albedo product, dataset derived by the TCOWA model, and the global land surface satellite (GLASS) phase-2 surface broadband albedo product) of OSA have been discussed, separately.

A Coupled Ocean General Circulation, Biogeochemical, and Radiative Model of the Global Oceans: Seasonal Distributions of Ocean Chlorophyll and Nutrients

NASA Technical Reports Server (NTRS)

Gregg, Watson W.; Busalacchi, Antonio (Technical Monitor)

2000-01-01

A coupled ocean general circulation, biogeochemical, and radiative model was constructed to evaluate and understand the nature of seasonal variability of chlorophyll and nutrients in the global oceans. Biogeochemical processes in the model are determined from the influences of circulation and turbulence dynamics, irradiance availability. and the interactions among three functional phytoplankton groups (diatoms. chlorophytes, and picoplankton) and three nutrients (nitrate, ammonium, and silicate). Basin scale (greater than 1000 km) model chlorophyll results are in overall agreement with CZCS pigments in many global regions. Seasonal variability observed in the CZCS is also represented in the model. Synoptic scale (100-1000 km) comparisons of imagery are generally in conformance although occasional departures are apparent. Model nitrate distributions agree with in situ data, including seasonal dynamics, except for the equatorial Atlantic. The overall agreement of the model with satellite and in situ data sources indicates that the model dynamics offer a reasonably realistic simulation of phytoplankton and nutrient dynamics on synoptic scales. This is especially true given that initial conditions are homogenous chlorophyll fields. The success of the model in producing a reasonable representation of chlorophyll and nutrient distributions and seasonal variability in the global oceans is attributed to the application of a generalized, processes-driven approach as opposed to regional parameterization and the existence of multiple phytoplankton groups with different physiological and physical properties. These factors enable the model to simultaneously represent many aspects of the great diversity of physical, biological, chemical, and radiative environments encountered in the global oceans.

Biological production in the Indian Ocean upwelling zones - Part 1: refined estimation via the use of a variable compensation depth in ocean carbon models

NASA Astrophysics Data System (ADS)

Geethalekshmi Sreeush, Mohanan; Valsala, Vinu; Pentakota, Sreenivas; Venkata Siva Rama Prasad, Koneru; Murtugudde, Raghu

2018-04-01

Biological modelling approach adopted by the Ocean Carbon-Cycle Model Intercomparison Project (OCMIP-II) provided amazingly simple but surprisingly accurate rendition of the annual mean carbon cycle for the global ocean. Nonetheless, OCMIP models are known to have seasonal biases which are typically attributed to their bulk parameterisation of compensation depth. Utilising the criteria of surface Chl a-based attenuation of solar radiation and the minimum solar radiation required for production, we have proposed a new parameterisation for a spatially and temporally varying compensation depth which captures the seasonality in the production zone reasonably well. This new parameterisation is shown to improve the seasonality of CO2 fluxes, surface ocean pCO2, biological export and new production in the major upwelling zones of the Indian Ocean. The seasonally varying compensation depth enriches the nutrient concentration in the upper ocean yielding more faithful biological exports which in turn leads to accurate seasonality in the carbon cycle. The export production strengthens by ˜ 70 % over the western Arabian Sea during the monsoon period and achieves a good balance between export and new production in the model. This underscores the importance of having a seasonal balance in the model export and new productions for a better representation of the seasonality of the carbon cycle over upwelling regions. The study also implies that both the biological and solubility pumps play an important role in the Indian Ocean upwelling zones.

Spurious sea ice formation caused by oscillatory ocean tracer advection schemes

NASA Astrophysics Data System (ADS)

Naughten, Kaitlin A.; Galton-Fenzi, Benjamin K.; Meissner, Katrin J.; England, Matthew H.; Brassington, Gary B.; Colberg, Frank; Hattermann, Tore; Debernard, Jens B.

2017-08-01

Tracer advection schemes used by ocean models are susceptible to artificial oscillations: a form of numerical error whereby the advected field alternates between overshooting and undershooting the exact solution, producing false extrema. Here we show that these oscillations have undesirable interactions with a coupled sea ice model. When oscillations cause the near-surface ocean temperature to fall below the freezing point, sea ice forms for no reason other than numerical error. This spurious sea ice formation has significant and wide-ranging impacts on Southern Ocean simulations, including the disappearance of coastal polynyas, stratification of the water column, erosion of Winter Water, and upwelling of warm Circumpolar Deep Water. This significantly limits the model's suitability for coupled ocean-ice and climate studies. Using the terrain-following-coordinate ocean model ROMS (Regional Ocean Modelling System) coupled to the sea ice model CICE (Community Ice CodE) on a circumpolar Antarctic domain, we compare the performance of three different tracer advection schemes, as well as two levels of parameterised diffusion and the addition of flux limiters to prevent numerical oscillations. The upwind third-order advection scheme performs better than the centered fourth-order and Akima fourth-order advection schemes, with far fewer incidents of spurious sea ice formation. The latter two schemes are less problematic with higher parameterised diffusion, although some supercooling artifacts persist. Spurious supercooling was eliminated by adding flux limiters to the upwind third-order scheme. We present this comparison as evidence of the problematic nature of oscillatory advection schemes in sea ice formation regions, and urge other ocean/sea-ice modellers to exercise caution when using such schemes.

Cloud-radiative effects on implied oceanic energy transport as simulated by atmospheric general circulation models

NASA Technical Reports Server (NTRS)

Gleckler, P. J.; Randall, D. A.; Boer, G.; Colman, R.; Dix, M.; Galin, V.; Helfand, M.; Kiehl, J.; Kitoh, A.; Lau, W.

1995-01-01

This paper summarizes the ocean surface net energy flux simulated by fifteen atmospheric general circulation models constrained by realistically-varying sea surface temperatures and sea ice as part of the Atmospheric Model Intercomparison Project. In general, the simulated energy fluxes are within the very large observational uncertainties. However, the annual mean oceanic meridional heat transport that would be required to balance the simulated surface fluxes is shown to be critically sensitive to the radiative effects of clouds, to the extent that even the sign of the Southern Hemisphere ocean heat transport can be affected by the errors in simulated cloud-radiation interactions. It is suggested that improved treatment of cloud radiative effects should help in the development of coupled atmosphere-ocean general circulation models.

A model of ocean basin crustal magnetization appropriate for satellite elevation anomalies

NASA Technical Reports Server (NTRS)

Thomas, Herman H.

1987-01-01

A model of ocean basin crustal magnetization measured at satellite altitudes is developed which will serve both as background to which anomalous magnetizations can be contrasted and as a beginning point for studies of tectonic modification of normal ocean crust. The model is based on published data concerned with the petrology and magnetization of the ocean crust and consists of viscous magnetization and induced magnetization estimated for individual crustal layers. Thermal remanent magnetization and chemical remanent magnetization are excluded from the model because seafloor spreading anomalies are too short in wavelength to be resolved at satellite altitudes. The exception to this generalization is found at the oceanic magnetic quiet zones where thermal remanent magnetization and chemical remanent magnetization must be considered along with viscous magnetization and induced magnetization.

Ocean color modeling: Parameterization and interpretation

NASA Astrophysics Data System (ADS)

Feng, Hui

The ocean color as observed near the water surface is determined mainly by dissolved and particulate substances, known as "optically-active constituents," in the upper water column. The goal of ocean color modeling is to interpret an ocean color spectrum quantitatively to estimate the suite of optically-active constituents near the surface. In recent years, ocean color modeling efforts have been centering upon three major optically-active constituents: chlorophyll concentration, colored dissolved organic matter, and scattering particulates. Many challenges are still being faced in this arena. This thesis generally addresses and deals with some critical issues in ocean color modeling. In chapter one, an extensive literature survey on ocean color modeling is given. A general ocean color model is presented to identify critical candidate uncertainty sources in modeling the ocean color. The goal for this thesis study is then defined as well as some specific objectives. Finally, a general overview of the dissertation is portrayed, defining each of the follow-up chapters to target some relevant objectives. In chapter two, a general approach is presented to quantify constituent concentration retrieval errors induced by uncertainties in inherent optical property (IOP) submodels of a semi-analytical forward model. Chlorophyll concentrations are retrieved by inverting a forward model with nonlinear IOPs. The study demonstrates how uncertainties in individual IOP submodels influence the accuracy of the chlorophyll concentration retrieval at different chlorophyll concentration levels. The important finding for this study shows that precise knowledge of spectral shapes of IOP submodels is critical for accurate chlorophyll retrieval, suggesting an improvement in retrieval accuracy requires precise spectral IOP measurements. In chapter three, three distinct inversion techniques, namely, nonlinear optimization (NLO), principal component analysis (PCA) and artificial neural network (ANN) are compared to assess their inversion performances to retrieve optically-active constituents for a complex nonlinear bio-optical system simulated by a semi-analytical ocean color model. A well-designed simulation scheme was implemented to simulate waters of different bio-optical complexity, and then the three inversion methods were applied to these simulated datasets for performance evaluation. In chapter four, an approach is presented for optimally parameterizing an irradiance reflectance model on the basis of a bio-optical dataset made at 45 stations in the Tokyo Bay and nearby regions between 1982 and 1984. (Abstract shortened by UMI.)