Science.gov

Sample records for advective mass exchange

  1. Efficient mass transport by optical advection

    PubMed Central

    Kajorndejnukul, Veerachart; Sukhov, Sergey; Dogariu, Aristide

    2015-01-01

    Advection is critical for efficient mass transport. For instance, bare diffusion cannot explain the spatial and temporal scales of some of the cellular processes. The regulation of intracellular functions is strongly influenced by the transport of mass at low Reynolds numbers where viscous drag dominates inertia. Mimicking the efficacy and specificity of the cellular machinery has been a long time pursuit and, due to inherent flexibility, optical manipulation is of particular interest. However, optical forces are relatively small and cannot significantly modify diffusion properties. Here we show that the effectiveness of microparticle transport can be dramatically enhanced by recycling the optical energy through an effective optical advection process. We demonstrate theoretically and experimentally that this new advection mechanism permits an efficient control of collective and directional mass transport in colloidal systems. The cooperative long-range interaction between large numbers of particles can be optically manipulated to create complex flow patterns, enabling efficient and tunable transport in microfluidic lab-on-chip platforms. PMID:26440069

  2. Controlling the column spacing in isothermal magnetic advection to enable tunable heat and mass transfer.

    DOE PAGES

    Solis, Kyle Jameson; Martin, James E.

    2012-11-01

    Isothermal magnetic advection is a recently discovered method of inducing highly organized, non-contact flow lattices in suspensions of magnetic particles, using only uniform ac magnetic fields of modest strength. The initiation of these vigorous flows requires neither a thermal gradient nor a gravitational field and so can be used to transfer heat and mass in circumstances where natural convection does not occur. These advection lattices are comprised of a square lattice of antiparallel flow columns. If the column spacing is sufficiently large compared to the column length, and the flow rate within the columns is sufficiently large, then one wouldmore » expect efficient transfer of both heat and mass. Otherwise, the flow lattice could act as a countercurrent heat exchanger and only mass will be efficiently transferred. Although this latter case might be useful for feeding a reaction front without extracting heat, it is likely that most interest will be focused on using IMA for heat transfer. In this paper we explore the various experimental parameters of IMA to determine which of these can be used to control the column spacing. These parameters include the field frequency, strength, and phase relation between the two field components, the liquid viscosity and particle volume fraction. We find that the column spacing can easily be tuned over a wide range, to enable the careful control of heat and mass transfer.« less

  3. Controlling the column spacing in isothermal magnetic advection to enable tunable heat and mass transfer.

    SciTech Connect

    Solis, Kyle Jameson; Martin, James E.

    2012-11-01

    Isothermal magnetic advection is a recently discovered method of inducing highly organized, non-contact flow lattices in suspensions of magnetic particles, using only uniform ac magnetic fields of modest strength. The initiation of these vigorous flows requires neither a thermal gradient nor a gravitational field and so can be used to transfer heat and mass in circumstances where natural convection does not occur. These advection lattices are comprised of a square lattice of antiparallel flow columns. If the column spacing is sufficiently large compared to the column length, and the flow rate within the columns is sufficiently large, then one would expect efficient transfer of both heat and mass. Otherwise, the flow lattice could act as a countercurrent heat exchanger and only mass will be efficiently transferred. Although this latter case might be useful for feeding a reaction front without extracting heat, it is likely that most interest will be focused on using IMA for heat transfer. In this paper we explore the various experimental parameters of IMA to determine which of these can be used to control the column spacing. These parameters include the field frequency, strength, and phase relation between the two field components, the liquid viscosity and particle volume fraction. We find that the column spacing can easily be tuned over a wide range, to enable the careful control of heat and mass transfer.

  4. Numerical simulation of advective-dispersive multisolute transport with sorption, ion exchange and equilibrium chemistry

    USGS Publications Warehouse

    Lewis, F.M.; Voss, C.I.; Rubin, Jacob

    1986-01-01

    A model was developed that can simulate the effect of certain chemical and sorption reactions simultaneously among solutes involved in advective-dispersive transport through porous media. The model is based on a methodology that utilizes physical-chemical relationships in the development of the basic solute mass-balance equations; however, the form of these equations allows their solution to be obtained by methods that do not depend on the chemical processes. The chemical environment is governed by the condition of local chemical equilibrium, and may be defined either by the linear sorption of a single species and two soluble complexation reactions which also involve that species, or binary ion exchange and one complexation reaction involving a common ion. Partial differential equations that describe solute mass balance entirely in the liquid phase are developed for each tenad (a chemical entity whose total mass is independent of the reaction process) in terms of their total dissolved concentration. These equations are solved numerically in two dimensions through the modification of an existing groundwater flow/transport computer code. (Author 's abstract)

  5. Jet-dominated advective systems of all mass scales

    NASA Astrophysics Data System (ADS)

    Körding, Elmar; Fender, R.

    We show that the radio emission of black hole (BH) and neutron star (NS) X-ray binaries (XRBs) follows the analytical prediction of a jet model where the jet carries a constant fraction of the accretion power. The radio emission can therefore be used as a tracer of the accretion rate. This measure is normalised with efficiently radiating objects. As it is independent of the X-ray fluxes, the measure allows us to compare the accretion rate dependency of the bolometric X-ray lumi- nosity of BHs and NSs. For NSs, it scales linearly with accretion rate while the scaling for BHs is quadratic - as expected for inefficient accretion flows. We find the same behaviour in AGN. This new approach uses the jet power to obtain the accretion rate. Thus, we know both the jet power and the radiated power of an accreting BH. This allows us to show that some accretion power is likely to be advected into the black hole, while the jet power dominates over the bolometric luminosity of a hard state BH.

  6. The impact of air mass advection on aerosol optical properties over Gotland (Baltic Sea)

    NASA Astrophysics Data System (ADS)

    Zdun, Agnieszka; Rozwadowska, Anna; Kratzer, Susanne

    2016-12-01

    In the present paper, measurements of aerosol optical properties from the Gotland station of the AERONET network, combined with a two-stage cluster analysis of back trajectories of air masses moving over Gotland, were used to identify the main paths of air mass advection to the Baltic Sea and to relate them to aerosol optical properties, i.e. the aerosol optical thickness at the wavelength λ = 500 nm, AOT (500) and the Ångström exponent for the spectral range from 440 to 870 nm, α(440,870). One- to six-day long back trajectories ending at 300, 500 and 3000 m above the station were computed using the HYSPLIT model. The study shows that in the Gotland region, variability in aerosol optical thickness AOT(500) is more strongly related to advections in the boundary layer than to those in the free troposphere. The observed variability in AOT(500) was best explained by the advection speeds and directions given by clustering of 4-day backward trajectories of air arriving in the boundary layer at 500 m above the station. 17 clusters of 4-day trajectories arriving at altitude 500 m above the Gotland station (sea level) derived using two-stage cluster analysis differ from each other with respect to trajectory length, the speed of air mass movement and the direction of advection. They also show different cluster means of AOT(500) and α(440,870). The cluster mean AOT(500) ranges from 0.342 ± 0.012 for the continental clusters M2 (east-southeast advection with moderate speed) and 0.294 ± 0.025 for S5 (slow south-southeast advection) to 0.064 ± 0.002 and 0.069 ± 0.002 for the respective marine clusters L3 (fast west-northwest advection) and M3 (north-northwest advection with moderate speed). The cluster mean α(440,870) varies from 1.65-1.70 for the short-trajectory clusters to 0.98 ± 0.03 and 1.06 ± 0.03 for the Arctic marine cluster L4 (fast inflow from the north) and marine cluster L5 (fast inflow from the west) respectively.

  7. The Effects of Heat Exchange and Thermal Advection on the Rate of Change of Temperature at Ocean Weather Station NOVEMBER.

    DTIC Science & Technology

    The effects of heat exchange across the sea surface and heat advection on the observed rate of change of temperature were examined using a physical...NOVEMBER during 1954 through 1970 were used. A three-dimensional plot of the annual variations of the monthly means of observed rate of change of...temperature produced three distinct trends. Heat exchange primarily contributed to the modification of the observed rate of change of temperature during the

  8. Assessment of advective porewater movement affecting mass transfer of hydrophobic organic contaminants in marine intertidal sediment.

    PubMed

    Cho, Yeo-Myoung; Werner, David; Moffett, Kevan B; Luthy, Richard G

    2010-08-01

    Advective porewater movement and molecular diffusion are important factors affecting the mass transfer of hydrophobic organic compounds (HOCs) in marsh and mudflat sediments. This study assessed porewater movement in an intertidal mudflat in South Basin adjacent to Hunters Point Shipyard, San Francisco, CA, where a pilot-scale test of sorbent amendment assessed the in situ stabilization of polychlorinated biphenyls (PCBs). To quantify advective porewater movement within the top 0-60 cm sediment layer, we used temperature as a tracer and conducted heat transport analysis using 14-day data from multidepth sediment temperature logging stations and one-dimensional heat transport simulations. The best-fit conditions gave an average Darcy velocity of 3.8cm/d in the downward vertical direction for sorbent-amended sediment with a plausible range of 0 cm/d to 8 cm/d. In a limiting case with no net advection, the best-fit depth-averaged mechanical dispersion coefficient was 2.2x10(-7) m2/s with a range of 0.9x10(-7) m2/s to 5.6x10(-7) m2/s. The Peclet number for PCB mobilization showed that molecular diffusion would control PCB mass transfer from sediment to sorbent particles for the case of uniform distribution of sorbent. However, the advective flow and mechanical dispersion in the test site would significantly benefit the stabilization effect of heterogeneously distributed sorbent by acting to smooth out the heterogeneities and homogenizing pollutant concentrations across the entire bioactive zone. These measurements and modeling techniques on intertidal sediment porewater transport could be useful for the development of more reliable mass transfer models for the prediction of contaminant release within the sediment bed, the movement of HOCs in the intertidal aquatic environment, and in situ sequestration by sorbent addition.

  9. Mass exchange processes with input

    NASA Astrophysics Data System (ADS)

    Krapivsky, P. L.

    2015-05-01

    We investigate a system of interacting clusters evolving through mass exchange and supplemented by input of small clusters. Three possibilities depending on the rate of exchange generically occur when input is homogeneous: continuous growth, gelation, and instantaneous gelation. We mostly study the growth regime using scaling methods. An exchange process with reaction rates equal to the product of reactant masses admits an exact solution which allows us to justify the validity of scaling approaches in this special case. We also investigate exchange processes with a localized input. We show that if the diffusion coefficients are mass-independent, the cluster mass distribution becomes stationary and develops an algebraic tail far away from the source.

  10. Investigation of the influence of groundwater advection on energy extraction rates for sustainable borehole heat exchanger operation

    NASA Astrophysics Data System (ADS)

    Schelenz, Sophie; Dietrich, Peter; Vienken, Thomas

    2016-04-01

    A sustainable thermal exploitation of the shallow subsurface requires a precise understanding of all relevant heat transport processes. Currently, planning practice of shallow geothermal systems (especially for systems < 30 kW) focuses on conductive heat transport as the main energy source while the impact of groundwater flow as the driver for advective heat transport is neglected or strongly simplified. The presented study proves that those simplifications of complex geological and hydrogeological subsurface characteristics are insufficient for a precise evaluation of site-specific energy extraction rates. Based on synthetic model scenarios with varying subsurface conditions (groundwater flow velocity and aquifer thickness) the impact of advection on induced long term temperature changes in 5 and 10 m distance of the borehole heat exchanger is presented. Extending known investigations, this study enhances the evaluation of shallow geothermal energy extraction rates by considering conductive and advective heat transport under varying aquifer thicknesses. Further, it evaluates the impact of advection on installation lengths of the borehole heat exchanger to optimize the initial financial investment. Finally, an evaluation approach is presented that classifies relevant heat transport processes according to their Péclet number to enable a first quantitative assessment of the subsurface energy regime and recommend further investigation and planning procedures.

  11. Thermal advection and stratification effects on surface winds and the low level meridional mass transport

    NASA Technical Reports Server (NTRS)

    Levy, Gad; Tiu, Felice S.

    1990-01-01

    Statistical tests are performed on the Seasat scatterometer observations to examine if and to what degree thermal advection and stratification effects manifest themselves in these remotely sensed measurements of mean wind and wind stress over the ocean. On the basis of a two layer baroclinic boundary layer model which is presented, it is shown that the thermal advection and stratification of the entire boundary layer as well as the geostrophic forcing influence the modeled near surface wind and wind stress profiles. Evidence of diurnal variation in the stratification under barotropic conditions is found in the data, with the daytime marine boundary layer being more convective than its nighttime counterpart. The temporal and spacial sampling pattern of the satellite makes it impossible to recover the full diurnal cycle, however. The observed effects of the thermal advection are shown to be statistically significant during the day (and presumed more convective) hours, causing a systematic increase in the poleward transport of mass and heat. The statistical results are in a qualitative agreement with the model simulations and cannot be reproduced in randomized control tests.

  12. A mass-conserving advection scheme for offline simulation of scalar transport in coastal ocean models

    NASA Astrophysics Data System (ADS)

    Gillibrand, P. A.; Herzfeld, M.

    2016-05-01

    We present a flux-form semi-Lagrangian (FFSL) advection scheme designed for offline scalar transport simulation with coastal ocean models using curvilinear horizontal coordinates. The scheme conserves mass, overcoming problems of mass conservation typically experienced with offline transport models, and permits long time steps (relative to the Courant number) to be used by the offline model. These attributes make the method attractive for offline simulation of tracers in biogeochemical or sediment transport models using archived flow fields from hydrodynamic models. We describe the FFSL scheme, and test it on two idealised domains and one real domain, the Great Barrier Reef in Australia. For comparison, we also include simulations using a traditional semi-Lagrangian advection scheme for the offline simulations. We compare tracer distributions predicted by the offline FFSL transport scheme with those predicted by the original hydrodynamic model, assess the conservation of mass in all cases and contrast the computational efficiency of the schemes. We find that the FFSL scheme produced very good agreement with the distributions of tracer predicted by the hydrodynamic model, and conserved mass with an error of a fraction of one percent. In terms of computational speed, the FFSL scheme was comparable with the semi-Lagrangian method and an order of magnitude faster than the full hydrodynamic model, even when the latter ran in parallel on multiple cores. The FFSL scheme presented here therefore offers a viable mass-conserving and computationally-efficient alternative to traditional semi-Lagrangian schemes for offline scalar transport simulation in coastal models.

  13. Diffusion or advection? Mass transfer and complex boundary layer landscapes of the brown alga Fucus vesiculosus.

    PubMed

    Lichtenberg, Mads; Nørregaard, Rasmus Dyrmose; Kühl, Michael

    2017-03-01

    The role of hyaline hairs on the thallus of brown algae in the genus Fucus is long debated and several functions have been proposed. We used a novel motorized set-up for two-dimensional and three-dimensional mapping with O2 microsensors to investigate the spatial heterogeneity of the diffusive boundary layer (DBL) and O2 flux around single and multiple tufts of hyaline hairs on the thallus of Fucus vesiculosus. Flow was a major determinant of DBL thickness, where higher flow decreased DBL thickness and increased O2 flux between the algal thallus and the surrounding seawater. However, the topography of the DBL varied and did not directly follow the contour of the underlying thallus. Areas around single tufts of hyaline hairs exhibited a more complex mass-transfer boundary layer, showing both increased and decreased thickness when compared with areas over smooth thallus surfaces. Over thallus areas with several hyaline hair tufts, the overall effect was an apparent increase in the boundary layer thickness. We also found indications for advective O2 transport driven by pressure gradients or vortex shedding downstream from dense tufts of hyaline hairs that could alleviate local mass-transfer resistances. Mass-transfer dynamics around hyaline hair tufts are thus more complex than hitherto assumed and may have important implications for algal physiology and plant-microbe interactions.

  14. Convection and interfacial mass exchange

    NASA Astrophysics Data System (ADS)

    Colinet, P.; Legros, J. C.; Dauby, P. C.; Lebon, G.; Bestehorn, M.; Stephan, P.; Tadrist, L.; Cerisier, P.; Poncelet, D.; Barremaecker, L.

    2005-10-01

    Mass-exchange through fluid interfaces is ubiquitous in many natural and industrial processes. Yet even basic phase-change processes such as evaporation of a pure liquid are not fully understood, in particular when coupled with fluid motions in the vicinity of the phase-change interface, or with microscopic physical phenomena in the vicinity of a triple line (where the interface meets a solid). Nowadays, many industries recognise that this lack of fundamental knowledge is hindering the optimisation of existing processes. Their modelling tools are too dependent on empirical correlations with a limited - and often unknown - range of applicability. In addition to the intrinsic multiscale nature of the phenomena involved in typical industrial processes linked to interfacial mass exchange, their study is highly multi-disciplinary, involving tools and techniques belonging to physical chemistry, chemical engineering, fluid dynamics, non-linear physics, non-equilibrium thermodynamics, chemistry and statistical physics. From the experimental point of view, microgravity offers a unique environment to obtain valuable data on phase-change processes, greatly reducing the influence of body forces and allowing the detailed and accurate study of interfacial dynamics. In turn, such improved understanding leads to optimisation of industrial processes and devices involving phase-change, both for space and ground applications.

  15. Mass-loss from advective accretion disc around rotating black holes

    NASA Astrophysics Data System (ADS)

    Aktar, Ramiz; Das, Santabrata; Nandi, Anuj

    2015-11-01

    We examine the properties of the outflowing matter from an advective accretion disc around a spinning black hole. During accretion, rotating matter experiences centrifugal pressure-supported shock transition that effectively produces a virtual barrier around the black hole in the form of post-shock corona (hereafter PSC). Due to shock compression, PSC becomes hot and dense that eventually deflects a part of the inflowing matter as bipolar outflows because of the presence of extra thermal gradient force. In our approach, we study the outflow properties in terms of the inflow parameters, namely specific energy (E) and specific angular momentum (λ) considering the realistic outflow geometry around the rotating black holes. We find that spin of the black hole (ak) plays an important role in deciding the outflow rate R_{dot{m}} (ratio of mass flux of outflow to inflow); in particular, R_{dot{m}} is directly correlated with ak for the same set of inflow parameters. It is found that a large range of the inflow parameters allows global accretion-ejection solutions, and the effective area of the parameter space (E, λ) with and without outflow decreases with black hole spin (ak). We compute the maximum outflow rate (R^{max}_{dot{m}}) as a function of black hole spin (ak) and observe that R^{max}_{dot{m}} weakly depends on ak that lies in the range ˜10-18 per cent of the inflow rate for the adiabatic index (γ) with 1.5 ≥ γ ≥ 4/3. We present the observational implication of our approach while studying the steady/persistent jet activities based on the accretion states of black holes. We discuss that our formalism seems to have the potential to explain the observed jet kinetic power for several Galactic black hole sources and active galactic nuclei.

  16. Flipping the thin film model: Mass transfer by hyporheic exchange in gaining and losing streams

    NASA Astrophysics Data System (ADS)

    McCluskey, Alexander H.; Grant, Stanley B.; Stewardson, Michael J.

    2016-10-01

    The exchange of mass between a stream and its hyporheic zone, or "hyporheic exchange," is central to many important ecosystem services. In this paper we show that mass transfer across the streambed by linear mechanisms of hyporheic exchange in a gaining or losing stream can be represented by a thin film model in which (a) the mass transfer coefficient is replaced with the average Darcy flux of water downwelling into the sediment and (b) the driving force for mass transfer is "flipped" from normal to the surface (concentration difference across a boundary layer) to parallel to the surface (concentration difference across downwelling and upwelling zones). Our analysis is consistent with previously published analytical, computational, and experimental studies of hyporheic exchange in the presence of stream-groundwater interactions, and links stream network, advection-dispersion, and stochastic descriptions of solute fate and transport in rivers.

  17. Analytical aspects of hydrogen exchange mass spectrometry

    PubMed Central

    Engen, John R.; Wales, Thomas E.

    2016-01-01

    The analytical aspects of measuring hydrogen exchange by mass spectrometry are reviewed. The nature of analytical selectivity in hydrogen exchange is described followed by review of the analytical tools required to accomplish fragmentation, separation, and the mass spectrometry measurements under restrictive exchange quench conditions. In contrast to analytical quantitation that relies on measurements of peak intensity or area, quantitation in hydrogen exchange mass spectrometry depends on measuring a mass change with respect to an undeuterated or deuterated control, resulting in a value between zero and the maximum amount of deuterium that could be incorporated. Reliable quantitation is a function of experimental fidelity and to achieve high measurement reproducibility, a large number of experimental variables must be controlled during sample preparation and analysis. The method also reports on important qualitative aspects of the sample, including conformational heterogeneity and population dynamics. PMID:26048552

  18. Extratropical Stratosphere-Troposphere Mass Exchange

    NASA Technical Reports Server (NTRS)

    Schoeberl, Mark R.

    2004-01-01

    Understanding the exchange of gases between the stratosphere and the troposphere is important for determining how pollutants enter the stratosphere and how they leave. This study does a global analysis of that the exchange of mass between the stratosphere and the troposphere. While the exchange of mass is not the same as the exchange of constituents, you can t get the constituent exchange right if you have the mass exchange wrong. Thus this kind of calculation is an important test for models which also compute trace gas transport. In this study I computed the mass exchange for two assimilated data sets and a GCM. The models all agree that amount of mass descending from the stratosphere to the troposphere in the Northern Hemisphere extra tropics is approx. 10(exp 10) kg/s averaged over a year. The value for the Southern Hemisphere by about a factor of two. ( 10(exp 10) kg of air is the amount of air in 100 km x 100 km area with a depth of 100 m - roughly the size of the D.C. metro area to a depth of 300 feet.) Most people have the idea that most of the mass enters the stratosphere through the tropics. But this study shows that almost 5 times more mass enters the stratosphere through the extra-tropics. This mass, however, is quickly recycled out again. Thus the lower most stratosphere is a mixture of upper stratospheric air and tropospheric air. This is an important result for understanding the chemistry of the lower stratosphere.

  19. Multiphase, multicomponent numerical model of bioventing with nonequilibrium mass exchange

    SciTech Connect

    Lang, J.R.; Rathfelder, K.M.; Abriola, L.M.

    1995-12-31

    A numerical model is presented that has been specifically designed to simulate the combined processes of soil vapor extraction and enhanced bioremediation known as bioventing. In this model, equations describing multiphase flow, multicomponent advective diffusive transport, and biodegradation are coupled. An entrapped organic residual, mobile gas and aqueous phases, and a reactive biophase are modeled. Components include n organic contaminants, oxygen, nitrogen, and water. Rate-limited mass exchange between the phases is simulated using linear driving force expressions. These expressions model volatilization and dissolution of the entrapped organic residual, rate-limited transport between the gas and aqueous phases, and rate-limited transport to the biophase. Monod-type kinetic expressions are employed to describe biophase utilization of substrates, the electron acceptor, and a limiting nutrient, as well as the growth of the microbial population. The coupled nonlinear governing equations are solved using a set iterative finite element method. Numerical simulations are presented for one-dimensional bench-scale column studies. These simulations illustrate the potential importance of biological degradation in the remediation of systems that are subject to mass transfer limitations.

  20. Overcoming diffusion-limited processes using enhanced advective fields

    SciTech Connect

    Rasmussen, T.C.

    1995-12-31

    Many subsurface cleanup activities focus on the remediation of organic contaminants using induced advective fields. Subsurface heterogeneities cause most advective transport to occur in more permeable zones, with transport from the lower permeability units being limited by diffusion to the higher permeable units. While diffusion rates can be enhanced using thermal sources, many of the treatment strategies, including pump and treat, vapor extraction and bioremediation, are limited by mass exchange rates between the higher and lower permeability sand and clay mixtures. Instead of relying on the enhancement of diffusion rates, it is proposed that remediation strategies should focus on the enhancement of induced advective transport rates through the lower permeability units. Injection-extraction strategies using crosshole and huff-and-puff methods are presented for maximizing advective transport through lower permeability units. Optimization of the design can incorporate diffusion-enhancement technologies, bionourishment, capillary confinement in the unsaturated zone, and DNAPL slurping.

  1. Microchannel laminated mass exchanger and method of making

    DOEpatents

    Martin, Peter M [Kennewick, WA; Bennett, Wendy D [Kennewick, WA; Matson, Dean W [Kennewick, WA; Stewart, Donald C [Richland, WA; Drost, Monte K [Pasco, WA; Wegeng, Robert S [Richland, WA; Perez, Joseph M [Richland, WA; Feng, Xiangdong [West Richland, WA; Liu, Jun [West Richland, WA

    2002-03-05

    The present invention is a microchannel mass exchanger having a first plurality of inner thin sheets and a second plurality of outer thin sheets. The inner thin sheets each have a solid margin around a circumference, the solid margin defining a slot through the inner thin sheet thickness. The outer thin sheets each have at least two header holes on opposite ends and when sandwiching an inner thin sheet. The outer thin sheets further have a mass exchange medium. The assembly forms a closed flow channel assembly wherein fluid enters through one of the header holes into the slot and exits through another of the header holes after contacting the mass exchange medium.

  2. Microchannel laminated mass exchanger and method of making

    DOEpatents

    Martin, Peter M.; Bennett, Wendy D.; Matson, Dean W.; Stewart, Donald C.; Drost, Monte K.; Wegeng, Robert S.; Perez, Joseph M.; Feng, Xiangdong; Liu, Jun

    2000-01-01

    The present invention is a microchannel mass exchanger having a first plurality of inner thin sheets and a second plurality of outer thin sheets. The inner thin sheets each have a solid margin around a circumference, the solid margin defining a slot through the inner thin sheet thickness. The outer thin sheets each have at least two header holes on opposite ends and when sandwiching an inner thin sheet. The outer thin sheets further have a mass exchange medium. The assembly forms a closed flow channel assembly wherein fluid enters through one of the header holes into the slot and exits through another of the header holes after contacting the mass exchange medium.

  3. Microchannel laminated mass exchanger and method of making

    DOEpatents

    Martin, Peter M [Kennewick, WA; Bennett, Wendy D [Kennewick, WA; Matson, Dean W [Kennewick, WA; Stewart, Donald C [Richland, WA; Drost, Monte K [Pasco, WA; Wegeng, Robert S [Richland, WA; Perez, Joseph M [Richland, WA; Feng, Xiangdong [West Richland, WA; Liu, Jun [West Richland, WA

    2003-03-18

    The present invention is a microchannel mass exchanger having a first plurality of inner thin sheets and a second plurality of outer thin sheets. The inner thin sheets each have a solid margin around a circumference, the solid margin defining a slot through the inner thin sheet thickness. The outer thin sheets each have at least two header holes on opposite ends and when sandwiching an inner thin sheet. The outer thin sheets further have a mass exchange medium. The assembly forms a closed flow channel assembly wherein fluid enters through one of the header holes into the slot and exits through another of the header holes after contacting the mass exchange medium.

  4. Membrane device and process for mass exchange, separation, and filtration

    DOEpatents

    Liu, Wei; Canfield, Nathan L.

    2016-11-15

    A membrane device and processes for fabrication and for using are disclosed. The membrane device may include a number of porous metal membranes that provide a high membrane surface area per unit volume. The membrane device provides various operation modes that enhance throughput and selectivity for mass exchange, mass transfer, separation, and/or filtration applications between feed flow streams and permeate flow streams.

  5. Kinetic model of mass exchange with dynamic Arrhenius transition rates

    NASA Astrophysics Data System (ADS)

    Hristopulos, Dionissios T.; Muradova, Aliki

    2016-02-01

    We study a nonlinear kinetic model of mass exchange between interacting grains. The transition rates follow the Arrhenius equation with an activation energy that depends dynamically on the grain mass. We show that the activation parameter can be absorbed in the initial conditions for the grain masses, and that the total mass is conserved. We obtain numerical solutions of the coupled, nonlinear, ordinary differential equations of mass exchange for the two-grain system, and we compare them with approximate theoretical solutions in specific neighborhoods of the phase space. Using phase plane methods, we determine that the system exhibits regimes of diffusive and growth-decay (reverse diffusion) kinetics. The equilibrium states are determined by the mass equipartition and separation nullcline curves. If the transfer rates are perturbed by white noise, numerical simulations show that the system maintains the diffusive and growth-decay regimes; however, the noise can reverse the sign of equilibrium mass difference. Finally, we present theoretical analysis and numerical simulations of a system with many interacting grains. Diffusive and growth-decay regimes are established as well, but the approach to equilibrium is considerably slower. Potential applications of the mass exchange model involve coarse-graining during sintering and wealth exchange in econophysics.

  6. Thermally-driven advections of aerosol-rich air masses to an Alpine valley: Theoretical considerations and experimental evidences

    NASA Astrophysics Data System (ADS)

    Diémoz, Henri; Magri, Tiziana; Pession, Giordano; Zublena, Manuela; Campanelli, Monica; Gobbi, Gian Paolo; Barnaba, Francesca; Di Liberto, Luca; Dionisi, Davide

    2016-04-01

    A CHM-15k laser radar (lidar) was installed in April 2015 at the solar observatory of the Environmental Protection Agency (ARPA) of the Aosta Valley (Northern Italy, 45.74N, 7.36E, 560 m a.s.l.). The instrument operates at 1064 nm, is capable of mapping the vertical profile of aerosols and clouds up to the tropopause and is part of the Alice-net ceilometers network (www.alice-net.eu). The site is in a large Alpine valley floor, in a semi-rural context. Among the most interesting cases observed in the first months of operation, several days characterised by weak synoptic circulation and well-developed, thermally-driven up-valley winds are accompanied by the appearance of a thick aerosol layer in the afternoon. The phenomenon is frequent in Spring and Summer and is likely to be related to easterly airmass advections from polluted sites (e.g., the Po basin) rather than to local emissions. To test this hypothesis, the following method was adopted. First, some case studies were selected and the respective meteorological fields were analysed based on both observations at ground and the high-resolution output of the nonhydrostatic limited-area atmospheric prediction model maintained by the COnsortium for Small-scale MOdelling (COSMO) over the complex orography of the domain. Then, to evaluate the dynamics of the aerosol diffusion in the valley, the chemical transport 2D/3D eulerian Flexible Air quality Regional Model (FARM) was run. Finally, the three-dimensional output of the model was compared to the vertically-resolved aerosol field derived from the lidar-ceilometer soundings. The effects of up-slope winds, and the resulting subsidence along the main axis of the valley, is hypothesised to break up the aerosol layer close to the ground in the middle of the day and to drag the residual layer down into the mixing layer. The measurements by a co-located sun/sky photometer operating in the framework of the EuroSkyRad (ESR) network were additionally analysed to detect any

  7. Gas Exchange with Mass Cultures of Algae

    PubMed Central

    Hannan, P. J.; Patouillet, Constance

    1963-01-01

    Comparisons of oxygen production and carbon dioxide absorption by an algal gas exchanger were made over a 3-month period. The data do not represent a continuous test, but they do represent results obtained when identical light intensities, CO2 supply rates, and dilution rates with fresh culture medium had been used for more than 1 day. Steady-state conditions were thus assured, and the agreement in the data was excellent. Under the same experimental conditions, the unit was operated continuously for a 5-day period, and the daily variability in this test was less than in the results obtained from month to month. The variation between the average O2 production during the 5-day test and the average of the tests over a several-month period was less than 3%. It is concluded, therefore, that the reliability of the algae in producing oxygen is sufficient to warrant their use in either submarine or space ship use. PMID:14063790

  8. Gas Exchange with Mass Cultures of Algae

    PubMed Central

    Hannan, P. J.; Patouillet, Constance

    1963-01-01

    The performance of a small photosynthetic gas exchanger is described in which simultaneous measurements of suspension density, O2 production, and CO2 absorption are readily accomplished. The volume of suspension was 6200 ml. With the Sorokin strain of Chlorella pyrenoidosa 7-11-05, this unit produced 4500 cc of O2 per hr at a light intensity of 34,000 ft-c from each of six Quartzline lamps. At any given light intensity, the O2 production was proportional to the rate of CO2 input up to a maximum. The impetus for this study was the consideration of the algal system as a means of oxygen generation in a submarine. Based on the performance of this unit, the power requirement per man for a system having the geometry described would be 52 kw, but reasons are given for the hope that this may be reduced to less than 5 kw. PMID:14063789

  9. Mass exchange during simultaneous grinding and dissolution

    SciTech Connect

    Aksel'rud, G.A.; Semenishin, E.M.; Kopyt, S.Ya.; Trotskii, V.I.

    1988-03-20

    Extraction of ore components of interest has a number of disadvantages, one of which being low efficiency. Combining the grinding and dissolution steps in one apparatus makes the process more efficient. Adoption of this technology, however, requires theoretical and mathematical studies. This paper reports the kinetics of simultaneous grinding and dissolution of copper-containing minerals. Simultaneous grinding and dissolution accelerated several fold the mass transfer of components of interest in the interaction of malachite and azurite with sulfuric acid solutions. The complete dissolution time was determined by adding the experimental rates of dissolution and abrasion.

  10. Pathways for Advective Transport

    DTIC Science & Technology

    2001-01-19

    the approach is given and an application to the Gulf of Mexico is described where the analysis precisely identifies the boundaries of coherent vortical structures as well as pathways for advective transport.

  11. Minimizing back exchange in the hydrogen exchange-mass spectrometry experiment.

    PubMed

    Walters, Benjamin T; Ricciuti, Alec; Mayne, Leland; Englander, S Walter

    2012-12-01

    The addition of mass spectrometry (MS) analysis to the hydrogen exchange (HX) proteolytic fragmentation experiment extends powerful HX methodology to the study of large biologically important proteins. A persistent problem is the degradation of HX information due to back exchange of deuterium label during the fragmentation-separation process needed to prepare samples for MS measurement. This paper reports a systematic analysis of the factors that influence back exchange (solution pH, ionic strength, desolvation temperature, LC column interaction, flow rates, system volume). The many peptides exhibit a range of back exchange due to intrinsic amino acid HX rate differences. Accordingly, large back exchange leads to large variability in D-recovery from one residue to another as well as one peptide to another that cannot be corrected for by reference to any single peptide-level measurement. The usual effort to limit back exchange by limiting LC time provides little gain. Shortening the LC elution gradient by 3-fold only reduced back exchange by ~2%, while sacrificing S/N and peptide count. An unexpected dependence of back exchange on ionic strength as well as pH suggests a strategy in which solution conditions are changed during sample preparation. Higher salt should be used in the first stage of sample preparation (proteolysis and trapping) and lower salt (<20 mM) and pH in the second stage before electrospray injection. Adjustment of these and other factors together with recent advances in peptide fragment detection yields hundreds of peptide fragments with D-label recovery of 90% ± 5%.

  12. HEMP advection model

    SciTech Connect

    Sharp, R.W. Jr.; Barton, R.T.

    1981-01-21

    A continuous rezoning procedure has been implemented in the computational cycle of a version of the HEMP two-dimensional, Lagrange, fluid dynamics code. The rezoning problem is divided into two steps. The first step requires the solving of ordinary Lagrange equations of motion; the second step consists of adding equipotential grid relaxation along with an advective remapping scheme.

  13. Fu Ori outbursts and the planet-disc mass exchange

    NASA Astrophysics Data System (ADS)

    Nayakshin, Sergei; Lodato, Giuseppe

    2012-10-01

    It has been recently proposed that giant protoplanets migrating inwards through the disc more rapidly than they contract could be tidally disrupted when they fill their Roche lobes ˜0.1 au away from their parent protostars. Here we consider the process of mass and angular momentum exchange between the tidally disrupted planet and the surrounding disc in detail. We find that the planet's adiabatic mass-radius relation and its ability to open a deep gap in the disc determine whether the disruption proceeds as a sudden runaway or a balanced quasi-static process. In the latter case, the planet feeds the inner disc through its Lagrangian L1 point like a secondary star in a stellar binary system. As the planet loses mass, it gains specific angular momentum and normally migrates in the outward direction until the gap closes. Numerical experiments show that planet disruption outbursts are preceded by long 'quiescent' periods during which the disc inward of the planet is empty. The hole in the disc is created when the planet opens a deep gap, letting the inner disc to drain on to the star while keeping the outer one stalled behind the planet. We find that the mass-losing planet embedded in a realistic protoplanetary disc spawns an extremely rich set of variability patterns. In a subset of parameter space, there is a limit cycle behaviour caused by non-linear interaction between the planet mass-loss and the disc hydrogen ionization instability. We suggest that tidal disruptions of young massive planets near their stars may be responsible for the observed variability of young accreting protostars such as FU Ori, EXor and T Tauri stars in general.

  14. The Area Between Exchange Curves as a Measure of Conformational Differences in Hydrogen-Deuterium Exchange Mass Spectrometry Studies

    NASA Astrophysics Data System (ADS)

    Mazur, Sharlyn J.; Weber, Daniel P.

    2017-02-01

    Hydrogen-deuterium exchange mass spectrometry (HDX-MS) provides information about protein conformational mobility under native conditions. The area between exchange curves, A bec , a functional data analysis concept, was adapted to the interpretation of HDX-MS data and provides a useful measure of exchange curve dissimilarity for tests of significance. Importantly, for most globular proteins under native conditions, A bec values provide an estimate of the log ratio of exchange-competent fractions in the two states, and thus are related to differences in the free energy of microdomain unfolding.

  15. Hydrogen exchange mass spectrometry of proteins at Langmuir monolayers

    PubMed Central

    Pirrone, Gregory F.; Vernon, Briana C.; Kent, Michael S.; Engen, John R.

    2015-01-01

    Hydrogen exchange (HX) mass spectrometry (MS) is valuable for providing conformational information for proteins/peptides that are very difficult to analyze with other methods such as peripheral membrane proteins and peptides that interact with membranes. We developed a new type of HX MS measurement that integrates Langmuir monolayers. A lipid monolayer was generated, a peptide or protein associated with it, and then the monolayer-associated peptide or protein was exposed to deuterium. The deuterated species was recovered from the monolayer, digested, and deuterium incorporation monitored by MS. Test peptides showed that deuterium recovery in an optimized protocol was equivalent to deuterium recovery in conventional solution HX MS. The reproducibility of the measurements was high despite the requirement of generating a new monolayer for each deuterium labeling time. We validated that known conformational changes in the presence of a monolayer/membrane could be observed with the peptide melittin and the myristoylated protein Arf-1. Results in an accompanying paper show that the method can reveal details of conformational changes in a protein (HIV-1 Nef) which adopts a different conformation depending on if it can insert into the lipid layer. Overall, the HX MS Langmuir monolayer method provided new and meaningful conformational information for proteins that associate with lipid layers. The combination of HX MS results with neutron or X-ray reflection of the same proteins in Langmuir monolayers can be more informative than isolated use of either method. PMID:26134943

  16. Gas circulation and mass exchange between animal and plant units

    NASA Astrophysics Data System (ADS)

    Liu, Hong; Tong, Ling; Hu, Enzhu

    To investigate the gas circulation and mass exchange relations among animal, plant and other biological units in the bioregenarative life support system, a closed cultivating system consisting of animal breeding chamber and plant growing chamber was established. This facility is 1.4 m high with the bottom area measuring 1.4 m X 0.8 m. In the animal chamber, silkworms in the multistage instars from the first instar to the third day in the fifth instar were bred; in the plant chamber, lettuce with sharp leaves were grown in a staggered manner. After transferring the silkworms in different instars hatched in the artificial climate box proportionally, utilizing mulberry leaves supplied from the outside of the closed cultivating system to feed the silkworms from the first instar to the third instar; fed the silkworms after the third instar to the third day in the fifth instar with the lettuce leaves grown in the closed facility, meanwhile, took out silkworms' excretion whose amount was in proportion to that of the mulberry leaves input into the facility. Furthermore, the silkworms on the third day in the fifth instar were took out to provide animal protein with high quality for astronauts at certain intervals and the next batch of the silkworms in the first instar were put into the animal chamber. In this cultivating process, the O2 cycle period and CO2 concentration change were investigated, moreover, the transfer and transforming ways of carbon and other elements were determined.

  17. Ion-exchange reactions on clay minerals coupled with advection/dispersion processes. Application to Na+/Ca2+ exchange on vermiculite: Reactive-transport modeling, batch and stirred flow-through reactor experiments

    NASA Astrophysics Data System (ADS)

    Tertre, E.; Hubert, F.; Bruzac, S.; Pacreau, M.; Ferrage, E.; Prêt, D.

    2013-07-01

    The present study aims at testing the validity of using an Na+/Ca2+ ion-exchange model, derived from batch data to interpret experimental Ca2+-for-Na+ exchange breakthrough curves obtained on vermiculite (a common swelling clay mineral in surface environments). The ion-exchange model was constructed considering the multi-site nature of the vermiculite surface as well as the exchange of all aqueous species (Mg2+ derived from the dissolution of the solid and H+). The proposed ion-exchange model was then coupled with a transport model, and the predicted breakthrough curves were compared with the experimental ones obtained using a well stirred flow-through reactor. For a given solute residence time in the reactor (typically 50 min), our thermodynamic model based on instantaneous equilibrium was found to accurately reproduce several of the experimental breakthrough curves, depending on the Na+ and Ca2+ concentrations of the influents pumped through the reactor. However the model failed to reproduce experimental breakthrough curves obtained at high flow rates and low chemical gradient between the exchanger phase and the solution. An alternative model based on a hybrid equilibrium/kinetic approach was thus used and allowed predicting experimental data. Based on these results, we show that a simple parameter can be used to differentiate between thermodynamic and kinetic control of the exchange reaction with water flow. The results of this study are relevant for natural systems where two aquatic environments having contrasted chemistries interact. Indeed, the question regarding the attainment of a full equilibrium in such a system during the contact time of the aqueous phase with the particle/colloid remains most often open. In this context, we show that when a river (a flow of fresh water) encounters marine colloids, a systematic full equilibrium can be assumed (i.e., the absence of kinetic effects) when the residence time of the solute in 1 m3 of the system is ⩾6200 h.

  18. LAYER DEPENDENT ADVECTION IN CMAQ

    EPA Science Inventory

    The advection methods used in CMAQ require that the Courant-Friedrichs-Lewy (CFL) condition be satisfied for numerical stability and accuracy. In CMAQ prior to version 4.3, the ADVSTEP algorithm established CFL-safe synchronization and advection timesteps that were uniform throu...

  19. A Mass Computation Model for Lightweight Brayton Cycle Regenerator Heat Exchangers

    NASA Technical Reports Server (NTRS)

    Juhasz, Albert J.

    2010-01-01

    Based on a theoretical analysis of convective heat transfer across large internal surface areas, this paper discusses the design implications for generating lightweight gas-gas heat exchanger designs by packaging such areas into compact three-dimensional shapes. Allowances are made for hot and cold inlet and outlet headers for assembly of completed regenerator (or recuperator) heat exchanger units into closed cycle gas turbine flow ducting. Surface area and resulting volume and mass requirements are computed for a range of heat exchanger effectiveness values and internal heat transfer coefficients. Benefit cost curves show the effect of increasing heat exchanger effectiveness on Brayton cycle thermodynamic efficiency on the plus side, while also illustrating the cost in heat exchanger required surface area, volume, and mass requirements as effectiveness is increased. The equations derived for counterflow and crossflow configurations show that as effectiveness values approach unity, or 100 percent, the required surface area, and hence heat exchanger volume and mass tend toward infinity, since the implication is that heat is transferred at a zero temperature difference. To verify the dimensional accuracy of the regenerator mass computational procedure, calculation of a regenerator specific mass, that is, heat exchanger weight per unit working fluid mass flow, is performed in both English and SI units. Identical numerical values for the specific mass parameter, whether expressed in lb/(lb/sec) or kg/(kg/sec), show the dimensional consistency of overall results.

  20. A Mass Computation Model for Lightweight Brayton Cycle Regenerator Heat Exchangers

    NASA Technical Reports Server (NTRS)

    Juhasz, Albert J.

    2010-01-01

    Based on a theoretical analysis of convective heat transfer across large internal surface areas, this paper discusses the design implications for generating lightweight gas-gas heat exchanger designs by packaging such areas into compact three-dimensional shapes. Allowances are made for hot and cold inlet and outlet headers for assembly of completed regenerator (or recuperator) heat exchanger units into closed cycle gas turbine flow ducting. Surface area and resulting volume and mass requirements are computed for a range of heat exchanger effectiveness values and internal heat transfer coefficients. Benefit cost curves show the effect of increasing heat exchanger effectiveness on Brayton cycle thermodynamic efficiency on the plus side, while also illustrating the cost in heat exchanger required surface area, volume, and mass requirements as effectiveness is increased. The equations derived for counterflow and crossflow configurations show that as effectiveness values approach unity, or 100 percent, the required surface area, and hence heat exchanger volume and mass tend toward infinity, since the implication is that heat is transferred at a zero temperature difference. To verify the dimensional accuracy of the regenerator mass computational procedure, calculation of a regenerator specific mass, that is, heat exchanger weight per unit working fluid mass flow, is performed in both English and SI units. Identical numerical values for the specific mass parameter, whether expressed in lb/(lb/sec) or kg/ (kg/sec), show the dimensional consistency of overall results.

  1. Advanced Heat/Mass Exchanger Technology for Geothermal and Solar Renewable Energy Systems

    SciTech Connect

    Greiner, Miles; Childress, Amy; Hiibel, Sage; Kim, Kwang; Park, Chanwoo; Wirtz, Richard

    2014-12-16

    Northern Nevada has abundant geothermal and solar energy resources, and these renewable energy sources provide an ample opportunity to produce economically viable power. Heat/mass exchangers are essential components to any energy conversion system. Improvements in the heat/mass exchange process will lead to smaller, less costly (more efficient) systems. There is an emerging heat transfer technology, based on micro/nano/molecular-scale surface science that can be applied to heat/mass exchanger design. The objective is to develop and characterize unique coating materials, surface configurations and membranes capable of accommodating a 10-fold increase in heat/mass exchanger performance via phase change processes (boiling, condensation, etc.) and single phase convective heat/mass transfer.

  2. Advective hydrogel membrane chromatography for monoclonal antibody purification in bioprocessing.

    PubMed

    Hou, Ying; Brower, Mark; Pollard, David; Kanani, Dharmesh; Jacquemart, Renaud; Kachuik, Bradley; Stout, James

    2015-01-01

    Protein A chromatography is widely employed for the capture and purification of monoclonal antibodies (mAbs). Because of the high cost of protein A resins, there is a significant economic driving force to seek new downstream processing strategies. Membrane chromatography has emerged as a promising alternative to conventional resin based column chromatography. However, to date, the application has been limited to mostly ion exchange flow through (FT) mode. Recently, significant advances in Natrix hydrogel membrane has resulted in increased dynamic binding capacities for proteins, which makes membrane chromatography much more attractive for bind/elute operations. The dominantly advective mass transport property of the hydrogel membrane has also enabled Natrix membrane to be run at faster volumetric flow rates with high dynamic binding capacities. In this work, the potential of using Natrix weak cation exchange membrane as a mAb capture step is assessed. A series of cycle studies was also performed in the pilot scale device (> 30 cycles) with good reproducibility in terms of yield and product purities, suggesting potential for improved manufacturing flexibility and productivity. In addition, anion exchange (AEX) hydrogel membranes were also evaluated with multiple mAb programs in FT mode. Significantly higher binding capacity for impurities (support mAb loads up to 10Kg/L) and 40X faster processing speed were observed compared with traditional AEX column chromatography. A proposed protein A free mAb purification process platform could meet the demand of a downstream purification process with high purity, yield, and throughput.

  3. Water mass formation and circulation in the Persian Gulf and water exchange with the Indian Ocean

    NASA Astrophysics Data System (ADS)

    Yao, Fengchao

    The Persian Gulf is a shallow, semi-enclosed marginal sea where the Persian Gulf Water (PGW), one of the most saline water masses in the world, is formed due to the arid climate. The PGW flushes out of the Persian Gulf as a deep outflow and induces a surface inflow of the Indian Ocean Surface Water (IOSW), driving an inverse-estuarine type water exchange through the Strait of Hormuz. In this dissertation, the circulation and water mass transformation processes in the Persian Gulf and the water exchange with the Indian Ocean through the Strait of Hormuz, in response to the atmospheric forcing, are studied using the HYbrid Coordinate Ocean Model (HYCOM). The model is driven by surface wind stress, heat and fresh water fluxes derived from two sources: the COADS (Comprehensive Ocean-Atmosphere Data Set) monthly climatology and high frequency (2-hourly) MM5 (The Fifth-Generation NCAR/Penn State Mesoscale Model) output. This study is motivated by the time series measurements in the Strait during December 1996 to March 1998 by Johns et al. (2003), which also serve as a major benchmark for evaluating the model results. The simulations with climatological forcing show that the IOSW propagates in two branches into the Gulf, one along the Iranian coast toward the northern gulf and the other one onto the southern banks driven by the Ekman drift by the prevailing northwesterly winds. These two branches of inflow form two cyclonic gyres in the northern and in the southern gulf respectively. Cold, saline deep waters are formed both in the northern gulf and in the southern gulf during the wintertime cooling period and their exports contribute seasonally to the outflow in the strait. After formation in winter, the dense water in the shallow southwestern gulf spills off into the strait and causes high-salinity pulses in the outflow in the strait, a phenomenon also present in the observations. The export of dense waters from the northern gulf persists throughout the year, with the

  4. Intensification of heat and mass transfer by ultrasound: application to heat exchangers and membrane separation processes.

    PubMed

    Gondrexon, N; Cheze, L; Jin, Y; Legay, M; Tissot, Q; Hengl, N; Baup, S; Boldo, P; Pignon, F; Talansier, E

    2015-07-01

    This paper aims to illustrate the interest of ultrasound technology as an efficient technique for both heat and mass transfer intensification. It is demonstrated that the use of ultrasound results in an increase of heat exchanger performances and in a possible fouling monitoring in heat exchangers. Mass transfer intensification was observed in the case of cross-flow ultrafiltration. It is shown that the enhancement of the membrane separation process strongly depends on the physico-chemical properties of the filtered suspensions.

  5. GAS EXCHANGE WITH MASS CULTURES OF ALGAE. II. RELIABILITY OF A PHOTOSYNTHETIC GAS EXCHANGER.

    PubMed

    HANNAN, P J; PATOUILLET, C

    1963-09-01

    Comparisons of oxygen production and carbon dioxide absorption by an algal gas exchanger were made over a 3-month period. The data do not represent a continuous test, but they do represent results obtained when identical light intensities, CO(2) supply rates, and dilution rates with fresh culture medium had been used for more than 1 day. Steady-state conditions were thus assured, and the agreement in the data was excellent. Under the same experimental conditions, the unit was operated continuously for a 5-day period, and the daily variability in this test was less than in the results obtained from month to month. The variation between the average O(2) production during the 5-day test and the average of the tests over a several-month period was less than 3%. It is concluded, therefore, that the reliability of the algae in producing oxygen is sufficient to warrant their use in either submarine or space ship use.

  6. Mathematical modeling of heat exchange between mine air and rock mass during fire

    SciTech Connect

    A.E. Krasnoshtein; B.P. Kazakov; A.V. Shalimov

    2006-05-15

    Solution of problems on heat exchange between ventilating air and rock mass and on gas admixture propagation in mine workings serve as a base for considering changes in heat-gas-air state at a mine after inflammation. The presented mathematical relations allow calculation of a varied velocity and movement direction of air flows, their temperatures and smoking conditions during fire.

  7. Kinetic study of the mass transfer of bovine serum albumin in anion-exchange chromatography.

    PubMed

    Miyabe, K; Guiochon, G

    2000-01-14

    A kinetic study was made on the mass transfer phenomena of bovine serum albumin (BSA) in two different anion-exchange columns (Resource-Q and TSK-GEL-DEAE-5PW). The analysis of the concentration dependence of the lumped mass transfer rate coefficient (km,L) provided the information about the kinetics of the several mass transfer processes in the columns and the anion exchangers, i.e., the axial dispersion, the fluid-to-particle mass transfer, the intraparticle diffusion, and the adsorption/desorption. In the Resource-Q column, the intraparticle diffusion had a dominant contribution to the band broadening compared with those of the other processes. The surface diffusion coefficient (Ds) of BSA showed a positive concentration dependence, by which the linear dependence of km,L on the BSA concentration seemed to be interpreted. On the other hand, in the TSK-GEL-DEAE-5PW column, the contribution of the adsorption/desorption was also important and almost same as that due to the intraparticle diffusion. There are some differences between the intrinsic properties of the mass transfer kinetics inside the two anion exchangers. It was likely that the positive concentration dependence of Ds was explained by the heterogeneous surface model.

  8. Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 1. Peptides to Proteins

    NASA Astrophysics Data System (ADS)

    Donohoe, Gregory C.; Khakinejad, Mahdiar; Valentine, Stephen J.

    2015-04-01

    Ion mobility spectrometry (IMS) coupled with hydrogen deuterium exchange (HDX)-mass spectrometry (MS) has been used to study the conformations of negatively-charged peptide and protein ions. Results are presented for ion conformers of angiotensin 1, a synthetic peptide (SP), bovine insulin, ubiquitin, and equine cytochrome c. In general, the SP ion conformers demonstrate a greater level of HDX efficiency as a greater proportion of the sites undergo HDX. Additionally, these ions exhibit the fastest rates of exchange. Comparatively, the angiotensin 1 ions exhibit a lower rate of exchange and HDX level presumably because of decreased accessibility of exchange sites by charge sites. The latter are likely confined to the peptide termini. Insulin ions show dramatically reduced HDX levels and exchange rates, which can be attributed to decreased conformational flexibility resulting from the disulfide bonds. For the larger ubiquitin and protein ions, increased HDX is observed for larger ions of higher charge state. For ubiquitin, a conformational transition from compact to more elongated species (from lower to higher charge states) is reflected by an increase in HDX levels. These results can be explained by a combination of interior site protection by compact conformers as well as decreased access by charge sites. The elongated cytochrome c ions provide the largest HDX levels where higher values correlate with charge state. These results are consistent with increased exchange site accessibility by additional charge sites. The data from these enhanced IMS-HDX experiments are described in terms of charge site location, conformer rigidity, and interior site protection.

  9. Ion mobility spectrometry-hydrogen deuterium exchange mass spectrometry of anions: part 1. Peptides to proteins.

    PubMed

    Donohoe, Gregory C; Khakinejad, Mahdiar; Valentine, Stephen J

    2015-04-01

    Ion mobility spectrometry (IMS) coupled with hydrogen deuterium exchange (HDX)-mass spectrometry (MS) has been used to study the conformations of negatively-charged peptide and protein ions. Results are presented for ion conformers of angiotensin 1, a synthetic peptide (SP), bovine insulin, ubiquitin, and equine cytochrome c. In general, the SP ion conformers demonstrate a greater level of HDX efficiency as a greater proportion of the sites undergo HDX. Additionally, these ions exhibit the fastest rates of exchange. Comparatively, the angiotensin 1 ions exhibit a lower rate of exchange and HDX level presumably because of decreased accessibility of exchange sites by charge sites. The latter are likely confined to the peptide termini. Insulin ions show dramatically reduced HDX levels and exchange rates, which can be attributed to decreased conformational flexibility resulting from the disulfide bonds. For the larger ubiquitin and protein ions, increased HDX is observed for larger ions of higher charge state. For ubiquitin, a conformational transition from compact to more elongated species (from lower to higher charge states) is reflected by an increase in HDX levels. These results can be explained by a combination of interior site protection by compact conformers as well as decreased access by charge sites. The elongated cytochrome c ions provide the largest HDX levels where higher values correlate with charge state. These results are consistent with increased exchange site accessibility by additional charge sites. The data from these enhanced IMS-HDX experiments are described in terms of charge site location, conformer rigidity, and interior site protection.

  10. Black Hole Advective Accretion Disks with Optical Depth Transition

    SciTech Connect

    Artemove, Y.V.; Bisnovatyi-Kogan, G.S.; Igumenshchev, I.V.; Novikov, I.D.

    2006-02-01

    We have constructed numerically global solutions of advective accretion disks around black holes that describe a continuous transition between the effectively optically thick outer and optically thin inner disk regions. We have concentrated on models of accretion flows with large mass accretion rates, and we have employed a bridging formula for radiative losses at high and low effective optical depths.

  11. EXCHANGE

    SciTech Connect

    Boltz, J.C.

    1992-09-01

    EXCHANGE is published monthly by the Idaho National Engineering Laboratory (INEL), a multidisciplinary facility operated for the US Department of Energy (DOE). The purpose of EXCHANGE is to inform computer users about about recent changes and innovations in both the mainframe and personal computer environments and how these changes can affect work being performed at DOE facilities.

  12. Mass exchange in an experimental new-generation LSS model based on biological regeneration of envirnment

    NASA Astrophysics Data System (ADS)

    Tikhomirov, A.; Ushakova, S.; Gribovskaya, I.; Tirranen, L.; Manukovsky, N.; Zolotukhin, I.; Gros, J.; Lasseur, C.

    Experimental model of a biological life support system (LSS) was used to evaluate qualitative and quantitative parameters of inner mass exchange. The photosynthesizing block was the higher plants component (wheat, 3 radish), the heterotroph block consisted of the soil-like substrate (SLS) California worms, mushrooms and microbial microflora. In terms of gas composition the mass exchange process involved emission of oxygen by the photosynthesiz ing component and its uptake by the heterotroph component along with formation and maintaining the SLS structure, growth of mushrooms, California worms, human respiration and several other processes. Human presence in the system had the form of a "part of virtual human" that at regular intervals took part in the respiration gas exchange to get engaged in the respiration gas exchange in the course of calculated period of time. Experimental data demonstrated good agreement of ? 2 /? ? 2 balance which, in these gas components, was close to complete. Basic component in the water mass exchange were transpiration water and aqueous watering solution with mineral elements. Human consumption of the harvest biomass of plants (seeds and roots) was simulated by processing hese production by a genuine physical - chemicalt method of oxidizing to inorganic mineral compounds that were returned into the system and fully assimilated by the plants. Such an oxidation was achieved by "wet incineration" of organic biomass using hydrogen peroxide by a special process where high temperature and pressure are not needed, and hydrogen peroxide is produced from the water inside the system. The turnover was estimated in terms of individual biogenous elements. Specifically, experiments showed that in terms of sulfur, carbon and several other elements the closedness was almost 100%. Applications opportunities of the experimental biological system considered are under discussion.

  13. Mass transfer model liquid phase catalytic exchange column simulation applicable to any column composition profile

    SciTech Connect

    Busigin, A.

    2015-03-15

    Liquid Phase Catalytic Exchange (LPCE) is a key technology used in water detritiation systems. Rigorous simulation of LPCE is complicated when a column may have both hydrogen and deuterium present in significant concentrations in different sections of the column. This paper presents a general mass transfer model for a homogenous packed bed LPCE column as a set of differential equations describing composition change, and equilibrium equations to define the mass transfer driving force within the column. The model is used to show the effect of deuterium buildup in the bottom of an LPCE column from non-negligible D atom fraction in the bottom feed gas to the column. These types of calculations are important in the design of CECE (Combined Electrolysis and Catalytic Exchange) water detritiation systems.

  14. Subunit exchange of polydisperse proteins: mass spectrometry reveals consequences of alphaA-crystallin truncation.

    PubMed

    Aquilina, J Andrew; Benesch, Justin L P; Ding, Lin Lin; Yaron, Orna; Horwitz, Joseph; Robinson, Carol V

    2005-04-15

    The small heat shock protein, alpha-crystallin, plays a key role in maintaining lens transparency by chaperoning structurally compromised proteins. This is of particular importance in the human lens, where proteins are exposed to post-translational modifications over the life-time of an individual. Here, we examine the structural and functional consequences of one particular modification of alphaA-crystallin involving the truncation of 5 C-terminal residues (alphaA(1-168)). Using novel mass spectrometry approaches and established biophysical techniques, we show that alphaA(1-168) forms oligomeric assemblies with a lower average molecular mass than wild-type alphaA-crystallin (alphaA(WT)). Also apparent from the mass spectra of both alphaA(WT) and alphaA(1-168) assemblies is the predominance of oligomers containing even numbers of subunits; interestingly, this preference is more marked for alphaA(1-168). To examine the rate of exchange of subunits between assemblies, we mixed alphaB crystallin with either alphaA(WT) or alphaA(1-168) and monitored in a real-time mass spectrometry experiment the formation of heteroligomers. The results show that there is a significant decrease in the rate of exchange when alphaA(1-168) is involved. These reduced exchange kinetics, however, have no effect upon chaperone efficiency, which is found to be closely similar for both alphaA(WT) and alphaA(1-168). Overall, therefore, our results allow us to conclude that, in contrast to mechanisms established for analogous proteins from plants, yeast, and bacteria, the rate of subunit exchange is not the critical parameter in determining efficient chaperone behavior for mammalian alphaA-crystallin.

  15. General Formalism of Mass Scaling Approach for Replica-Exchange Molecular Dynamics and its Application

    NASA Astrophysics Data System (ADS)

    Nagai, Tetsuro

    2017-01-01

    Replica-exchange molecular dynamics (REMD) has demonstrated its efficiency by combining trajectories of a wide range of temperatures. As an extension of the method, the author formalizes the mass-manipulating replica-exchange molecular dynamics (MMREMD) method that allows for arbitrary mass scaling with respect to temperature and individual particles. The formalism enables the versatile application of mass-scaling approaches to the REMD method. The key change introduced in the novel formalism is the generalized rules for the velocity and momentum scaling after accepted replica-exchange attempts. As an application of this general formalism, the refinement of the viscosity-REMD (V-REMD) method [P. H. Nguyen, J. Chem. Phys. 132, 144109 (2010)] is presented. Numerical results are provided using a pilot system, demonstrating easier and more optimized applicability of the new version of V-REMD as well as the importance of adherence to the generalized velocity scaling rules. With the new formalism, more sound and efficient simulations will be performed.

  16. On the vertical exchange of heat, mass and momentum over complex, mountainous terrain

    NASA Astrophysics Data System (ADS)

    Rotach, Mathias; Gohm, Alexander; Lang, Moritz; Leukauf, Daniel; Stiperski, Ivana; Wagner, Johannes

    2015-12-01

    The role of the atmospheric boundary layer (ABL) in the atmosphere-climate system is the exchange of heat, mass and momentum between 'the earth's surface' and the atmosphere. Traditionally, it is understood that turbulent transport is responsible for this exchange and hence the understanding and physical description of the turbulence structure of the boundary layer is key to assess the effectiveness of earth-atmosphere exchange. This understanding is rooted in the (implicit) assumption of a scale separation or spectral gap between turbulence and mean atmospheric motions, which in turn leads to the assumption of a horizontally homogeneous and flat (HHF) surface as a reference, for which both physical understanding and model parameterizations have successfully been developed over the years. Over mountainous terrain, however, the ABL is generically inhomogeneous due to both thermal (radiative) and dynamic forcing. This inhomogeneity leads to meso-scale and even sub-meso-scale flows such as slope and valley winds or wake effects. It is argued here that these (sub)meso-scale motions can significantly contribute to the vertical structure of the boundary layer and hence vertical exchange of heat and mass between the surface and the atmosphere. If model grid resolution is not high enough the latter will have to be parameterized (in a similar fashion as gravity wave drag parameterizations take into account the momentum transport due to gravity waves in large-scale models). In this contribution we summarize the available evidence of the contribution of (sub)meso-scale motions to vertical exchange in mountainous terrain from observational and numerical modeling studies. In particular, a number of recent simulation studies using idealized topography will be summarized and put into perspective - so as to identify possible limitations and areas of necessary future research.

  17. Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR.

    PubMed Central

    Yi, Q.; Baker, D.

    1996-01-01

    We use mass spectrometry in conjunction with hydrogen-deuterium exchange and NMR to characterize the conformational dynamics of the 62-residue IgG binding domain of protein L under conditions in which the native state is marginally stable. Mass spectra of protein L after short incubations in D2O reveal the presence of two distinct populations containing different numbers of protected protons. NMR experiments indicate that protons in the hydrophobic core are protected in one population, whereas all protons are exchanged for deuterons in the other. As the exchange period is increased, molecules are transferred from the former population to the latter. The absence of molecules with a subset of the core protons protected suggests that exchange occurs in part via a highly concerted transition to an excited state in which all protons exchange rapidly with deuterons. A steady increase in the molecular weight of the population with protected protons, and variation in the exchange rates of the individual protected protons indicates the presence of an additional exchange mechanism. A simple model in which exchange results from rapid (> 10(5)/s) local fluctuations around the native state superimposed upon transitions to an unfolded excited state at approximately 0.06/s is supported by qualitative agreement between the observed mass spectra and the mass spectra simulated according to the model using NMR-derived estimates of the proton exchange rates. PMID:8762137

  18. Polar Aprotic Modifiers for Chromatographic Separation and Back-Exchange Reduction for Protein Hydrogen/Deuterium Exchange Monitored by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Valeja, Santosh G.; Emmett, Mark R.; Marshall, Alan G.

    2012-04-01

    Hydrogen/deuterium exchange monitored by mass spectrometry is an important non-perturbing tool to study protein structure and protein-protein interactions. However, water in the reversed-phase liquid chromatography mobile phase leads to back-exchange of D for H during chromatographic separation of proteolytic peptides following H/D exchange, resulting in incorrect identification of fast-exchanging hydrogens as unexchanged hydrogens. Previously, fast high-performance liquid chromatography (HPLC) and supercritical fluid chromatography have been shown to decrease back-exchange. Here, we show that replacement of up to 40% of the water in the LC mobile phase by the modifiers, dimethylformamide (DMF) and N-methylpyrrolidone (NMP) (i.e., polar organic modifiers that lack rapid exchanging hydrogens), significantly reduces back-exchange. On-line LC micro-ESI FT-ICR MS resolves overlapped proteolytic peptide isotopic distributions, allowing for quantitative determination of the extent of back-exchange. The DMF modified solvent composition also improves chromatographic separation while reducing back-exchange relative to conventional solvent.

  19. Polar Aprotic Modifiers for Chromatographic Separation and Back-Exchange Reduction for Protein Hydrogen/Deuterium Exchange Monitored by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    PubMed Central

    Valeja, Santosh G.; Emmett, Mark R.; Marshall, Alan G.

    2013-01-01

    Hydrogen/deuterium exchange monitored by mass spectrometry is an important non-perturbing tool to study protein structure and protein–protein interactions. However, water in the reversed-phase liquid chromatography mobile phase leads to back-exchange of D for H during chromatographic separation of proteolytic peptides following H/D exchange, resulting in incorrect identification of fast-exchanging hydrogens as unexchanged hydrogens. Previously, fast high-performance liquid chromatography (HPLC) and supercritical fluid chromatography have been shown to decrease back-exchange. Here, we show that replacement of up to 40% of the water in the LC mobile phase by the modifiers, dimethylformamide (DMF) and N-methylpyrrolidone (NMP) (i.e., polar organic modifiers that lack rapid exchanging hydrogens), significantly reduces back-exchange. On-line LC micro-ESI FT-ICR MS resolves overlapped proteolytic peptide isotopic distributions, allowing for quantitative determination of the extent of back-exchange. The DMF modified solvent composition also improves chromatographic separation while reducing back-exchange relative to conventional solvent. PMID:22298288

  20. Observing the Invisible through Imaging Mass Spectrometry, a Window into the Metabolic Exchange Patterns of Microbes

    PubMed Central

    Gonzalez, David J.; Xu, Yuquan; Yang, Yu-Liang; Esquenazi, Eduardo; Liu, Wei-Ting; Edlund, Anna; Duong, Tram; Du, Liangcheng; Molnár, István; Gerwick, William H.; Jensen, Paul R.; Fischbach, Michael; Liaw, Chih-Chuang; Straight, Paul; Nizet, Victor; Dorrestein, Pieter C.

    2012-01-01

    Many microbes can be cultured as single-species communities. Often, these colonies are controlled and maintained via the secretion of metabolites. Such metabolites have been an invaluable resource for the discovery of therapeutics (e.g. penicillin, taxol, rapamycin, epothilone). In this article, written for a special issue on imaging mass spectrometry, we show that MALDI-imaging mass spectrometry can be adapted to observe, in a spatial manner, the metabolic exchange patterns of a diverse array of microbes, including thermophilic and mesophilic fungi, cyanobacteria, marine and terrestrial actinobacteria, and pathogenic bacteria. Dependent on media conditions, on average and based on manual analysis, we observed 11.3 molecules associated with each microbial IMS experiment, which was split nearly 50:50 between secreted and colony-associated molecules. The spatial distributions of these metabolic exchange factors are related to the biological and ecological functions of the organisms. This work establishes that MALDI-based IMS can be used as a general tool to study a diverse array of microbes. Furthermore the article forwards the notion of the IMS platform as a window to discover previously unreported molecules by monitoring the metabolic exchange patterns of organisms when grown on agar substrates. PMID:22641157

  1. Hydrogen exchange-mass spectrometry measures stapled peptide conformational dynamics and predicts pharmacokinetic properties.

    PubMed

    Shi, Xiangguo Eric; Wales, Thomas E; Elkin, Carl; Kawahata, Noriyuki; Engen, John R; Annis, D Allen

    2013-12-03

    Peptide drugs have traditionally suffered from poor pharmacokinetic properties due to their conformational flexibility and the interaction of proteases with backbone amide bonds. "Stapled Peptides" are cyclized using an all-hydrocarbon cross-linking strategy to reinforce their α-helical conformation, yielding improved protease resistance and drug-like properties. Here we demonstrate that hydrogen exchange-mass spectrometry (HX-MS) effectively probes the conformational dynamics of Stapled Peptides derived from the survivin-borealin protein-protein interface and predicts their susceptibility to proteolytic degradation. In Stapled Peptides, amide exchange was reduced by over five orders-of-magnitude versus the native peptide sequence depending on staple placement. Furthermore, deuteration kinetics correlated directly with rates of proteolysis to reveal the optimal staple placement for improved drug properties.

  2. An Efficient and Inexpensive Refrigerated LC System for H/D Exchange Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Keppel, Theodore R.; Jacques, Martin E.; Young, Robert W.; Ratzlaff, Kenneth L.; Weis, David D.

    2011-08-01

    Loss of deuterium label during the LC step in amide hydrogen/deuterium exchange mass spectrometry (H/D-MS) is minimized by maintaining an acidic mobile phase pH and low temperature (pH 2.5, 0 °C). Here we detail the construction and performance of a low-cost, thermoelectrically refrigerated enclosure to house high-performance liquid chromatography (HPLC) components and cool mobile phases. Small volume heat exchangers rapidly decrease mobile phase temperature and keep the temperature stable to ±0.2 °C. Using a superficially porous reversed-phase column, we obtained excellent chromatographic performance in the separation of peptides with a median peak width of 4.4 s. Average deuterium recovery was 80.2% with an average relative precision of 0.91%.

  3. Utilizing Microchip Capillary Electrophoresis Electrospray Ionization for Hydrogen Exchange Mass Spectrometry

    PubMed Central

    Black, William A.; Stocks, Bradley B.; Mellors, J. Scott; Engen, John R.; Ramsey, J. Michael

    2015-01-01

    Hydrogen exchange (HX) mass spectrometry (MS) of complex mixtures requires a fast, reproducible, and high peak capacity separation prior to MS detection. The current paradigm relies on liquid chromatography (LC) with fast gradients performed at low temperatures to minimize back exchange. Unfortunately, under these conditions, the efficiency of LC is limited due to resistance to mass transfer, reducing the capability to analyze complex samples. Capillary electrophoresis (CE), on the other hand, is not limited by resistance to mass transfer, enabling very rapid separations that are not adversely affected by low temperature. Previously, we have demonstrated an integrated microfluidic device coupling CE with electrospray ionization (ESI) capable of very rapid and high efficiency separations. In this work, we demonstrate the utility of this microchip CE-ESI device for HX MS. High speed CE-ESI of a bovine hemoglobin pepsin digestion was performed in 1 minute with a peak capacity of 62 versus a similar LC separation performed in 7 minutes with peak capacity of 31. A room temperature CE method performed in 1.25 minutes provided similar deuterium retention as an 8.5 minute LC method conducted at 0 °C. Separation of a complex mixture with CE was done with considerably better speed and nearly triple the peak capacity than the equivalent separation by LC. Overall the results indicate the potential utility of microchip CE-ESI for HX MS. PMID:25992468

  4. Guanine nucleotide induced conformational change of Cdc42 revealed by hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Yang, Sheng-Wei; Ting, Hsiu-Chi; Lo, Yi-Ting; Wu, Ting-Yuan; Huang, Hung-Wei; Yang, Chia-Jung; Chan, Jui-Fen Riva; Chuang, Min-Chieh; Hsu, Yuan-Hao Howard

    2016-01-01

    Cdc42 regulates pathways related to cell division. Dysregulation of Cdc42 can lead to cancer, cardiovascular diseases and neurodegenerative diseases. GTP induced activation mechanism plays an important role in the activity and biological functions of Cdc42. P-loop, Switch I and Switch II are critical regions modulating the enzymatic activity of Cdc42. We applied amide hydrogen/deuterium exchange coupled with liquid chromatography mass spectrometry (HDXMS) to investigate the dynamic changes of apo-Cdc42 after GDP, GTP and GMP-PCP binding. The natural substrate GTP induced significant decreases of deuteration in P-loop and Switch II, moderate changes of deuteration in Switch I and significant changes of deuteration in the α7 helix, a region far away from the active site. GTP binding induced similar effects on H/D exchange to its non-hydrolysable analog, GMP-PCP. HDXMS results indicate that GTP binding blocked the solvent accessibility in the active site leading to the decrease of H/D exchange rate surrounding the active site, and further triggered a conformational change resulting in the drastic decrease of H/D exchange rate at the remote α7 helix. Comparing the deuteration levels in three activation states of apo-Cdc42, Cdc42-GDP and Cdc42-GMP-PCP, the apo-Cdc42 has the most flexible structure, which can be stabilized by guanine nucleotide binding. The rates of H/D exchange of Cdc42-GDP are between the GMP-PCP-bound and the apo form, but more closely to the GMP-PCP-bound form. Our results show that the activation of Cdc42 is a process of conformational changes involved with P-loop, Switch II and α7 helix for structural stabilization.

  5. The arc of Mass Spectrometry Exchange Formats is long, but it bends toward HDF5.

    PubMed

    Askenazi, Manor; Ben Hamidane, Hisham; Graumann, Johannes

    2016-10-14

    The evolution of data exchange in Mass Spectrometry spans decades and has ranged from human-readable text files representing individual scans or collections thereof (McDonald et al., 2004) through the official standard XML-based (Harold, Means, & Udemadu, 2005) data interchange standard (Deutsch, 2012), to increasingly compressed (Teleman et al., 2014) variants of this standard sometimes requiring purely binary adjunct files (Römpp et al., 2011). While the desire to maintain even partial human readability is understandable, the inherent mismatch between XML's textual and irregular format relative to the numeric and highly regular nature of actual spectral data, along with the explosive growth in dataset scales and the resulting need for efficient (binary and indexed) access has led to a phenomenon referred to as "technical drift" (Davis, 2013). While the drift is being continuously corrected using adjunct formats, compression schemes, and programs (Röst et al., 2015), we propose that the future of Mass Spectrometry Exchange Formats lies in the continued reliance and development of the PSI-MS (Mayer et al., 2014) controlled vocabulary, along with an expedited shift to an alternative, thriving and well-supported ecosystem for scientific data-exchange, storage, and access in binary form, namely that of HDF5 (Koranne, 2011). Indeed, pioneering efforts to leverage this universal, binary, and hierarchical data-format have already been published (Wilhelm et al., 2012; Rübel et al., 2013) though they have under-utilized self-description, a key property shared by HDF5 and XML. We demonstrate that a straightforward usage of plain ("vanilla") HDF5 yields immediate returns including, but not limited to, highly efficient data access, platform independent data viewers, a variety of libraries (Collette, 2014) for data retrieval and manipulation in many programming languages and remote data access through comprehensive RESTful data-servers. © 2016 Wiley Periodicals, Inc. Mass

  6. Droplet infiltration and OM composition of intact soil structural surfaces for studying mass exchange

    NASA Astrophysics Data System (ADS)

    Leue, Martin, ,, Dr.; Gerke, PD Horst H., ,, Dr.; Godow, Sophie Ch.; Ellerbrock, PD Ruth H., ,, Dr.

    2014-05-01

    During rapid percolation through macropores with local nonequilibrium conditions water and solute mass exchange with the porous matrix and sorption of reactive components is both taken place at the surface of preferential flow paths. Aggregate surfaces can be coated by illuviated clayey particles and biopores covered by plant residues or earthworm casts. By controlling wettability and sorption properties, the organic matter (OM) of surface coatings may also affect the transport properties of structured soils. Composition of OM in wall coatings was found spatially distributed at the mm-scale; thus, it remained unclear if water absorption by the soil matrix (i.e., mass exchange) was affected by locally-distributed OM. For samples with intact aggregate surfaces and biopore walls taken at clay-illuvial subsoil horizon of Luvisols developed from Loess and glacial till, the mm-scale spatial distribution of OM composition was measured using diffuse reflectance infrared spectroscopy (DRIFT). Spectra were analysed with respect to alkyl and carboxyl functional groups in OM to obtain an estimate for its potential wettability. The infiltration dynamic of water droplets was evaluated using contact angle measurements and droplet penetration time. The potential wettability of OM differed for coatings and burrow walls and was generally lower for the Loess-derived than for the till-derived samples. The droplet infiltration times were significantly lower only for the Loess Luvisol samples. The results suggest that mass exchange between flow path and matrix can be affected by OM composition of structural surfaces among other factors such as texture, moisture, and chemical status (pH).

  7. Advective-diffusive/dispersive transport of chemically reacting species in hydrothermal systems. Final report, FY83-85

    SciTech Connect

    Lichtner, P.C.; Helgeson, H.C.

    1986-06-20

    A general formulation of multi-phase fluid flow coupled to chemical reactions was developed based on a continuum description of porous media. A preliminary version of the computer code MCCTM was constructed which implemented the general equations for a single phase fluid. The computer code MCCTM incorporates mass transport by advection-diffusion/dispersion in a one-dimensional porous medium coupled to reversible and irreversible, homogeneous and heterogeneous chemical reactions. These reactions include aqueous complexing, oxidation/reduction reactions, ion exchange, and hydrolysis reactions of stoichiometric minerals. The code MCCTM uses a fully implicit finite difference algorithm. The code was tested against analytical calculations. Applications of the code included investigation of the propagation of sharp chemical reaction fronts, metasomatic alteration of microcline at elevated temperatures and pressures, and ion-exchange in a porous column. Finally numerical calculations describing fluid flow in crystalline rock in the presence of a temperature gradient were compared with experimental results for quartzite.

  8. Higher order structure characterization of protein therapeutics by hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Huang, Richard Y-C; Chen, Guodong

    2014-10-01

    Characterization of therapeutic drugs is a crucial step in drug development in the biopharmaceutical industry. Analysis of protein therapeutics is a challenging task because of the complexities associated with large molecular size and 3D structures. Recent advances in hydrogen/deuterium-exchange mass spectrometry (HDX-MS) have provided a means to assess higher-order structure of protein therapeutics in solution. In this review, the principles and procedures of HDX-MS for protein therapeutics characterization are presented, focusing on specific applications of epitope mapping for protein-protein interactions and higher-order structure comparison studies for conformational dynamics of protein therapeutics.

  9. High-resolution two dimensional advective transport

    USGS Publications Warehouse

    Smith, P.E.; Larock, B.E.

    1989-01-01

    The paper describes a two-dimensional high-resolution scheme for advective transport that is based on a Eulerian-Lagrangian method with a flux limiter. The scheme is applied to the problem of pure-advection of a rotated Gaussian hill and shown to preserve the monotonicity property of the governing conservation law.

  10. Evolution and advection of solar mesogranulation

    NASA Technical Reports Server (NTRS)

    Muller, Richard; Auffret, Herve; Roudier, Thierry; Vigneau, Jean; Simon, George W.; Frank, Zoe; Shine, Richard A.; Title, Alan M.

    1992-01-01

    A three-hour sequence of observations at the Pic du Midi observatory has been obtained which shows the evolution of solar mesogranules from appearance to disappearance with unprecedented clarity. It is seen that the supergranules, which are known to advect the granules with their convective motion, also advect the mesogranules to their boundaries. This process controls the evolution and disappearance of mesogranules.

  11. Aerosol particles and the formation of advection fog

    NASA Technical Reports Server (NTRS)

    Hung, R. J.; Liaw, G. S.; Vaughan, O. H., Jr.

    1979-01-01

    A study of numerical simulation of the effects of concentration, particle size, mass of nuclei, and chemical composition on the dynamics of warm fog formation, particularly the formation of advection fog, is presented. This formation is associated with the aerosol particle characteristics, and both macrophysical and microphysical processes are considered. In the macrophysical model, the evolution of wind components, water vapor content, liquid water content, and potential temperature under the influences of vertical turbulent diffusion, turbulent momentum, and turbulent energy transfers are taken into account. In the microphysical model, the supersaturation effect is incorporated with the surface tension and hygroscopic material solution. It is shown that the aerosol particles with the higher number density, larger size nuclei, the heavier nuclei mass, and the higher ratio of the Van't Hoff factor to the molecular weight favor the formation of the lower visibility advection fogs with stronger vertical energy transfer during the nucleation and condensation time period.

  12. Protein Conformation in Amorphous Solids by FTIR and by Hydrogen/Deuterium Exchange with Mass Spectrometry

    PubMed Central

    Sinha, Sandipan; Li, Yunsong; Williams, Todd D.; Topp, Elizabeth M.

    2008-01-01

    Solid-state hydrogen/deuterium exchange (ssHDX) with electrospray ionization mass spectrometry (ESI-MS) and Fourier transform infrared (FTIR) spectroscopy were used to assess protein conformation in amorphous solids. Myoglobin, lysozyme, β-lactoglobulin, ribonuclease A, E-cadherin 5, and concanavalin A were co-lyophilized with carbohydrates (trehalose, raffinose, and dextran 5000), linear polymers (polyvinyl alcohol and polyvinyl pyrrolidone) or guanidine hydrochloride (negative control). For ssHDX, samples were exposed to D2O vapor at 33% relative humidity and room temperature, and then reconstituted at low temperature (4°C) and pH 2.5 and analyzed by ESI-MS. Peptic digestion of selected proteins was used to provide region-specific information on exchange. FTIR spectra were acquired using attenuated total reflectance. FTIR and ssHDX of intact proteins showed preservation of structure by raffinose and trehalose, as indicated by FTIR band intensity and protection from exchange. ssHDX of peptic digests further indicated that these protective effects were not exerted uniformly along the protein sequence but were observed primarily in α-helical regions, a level of structural resolution not afforded by FTIR. The results thus demonstrate the utility of HDX with ESI-MS for analyzing protein conformation in amorphous solid samples. PMID:18835903

  13. Towards a theory of tropical/midlatitude mass exchange from the earth's surface through the stratosphere

    NASA Technical Reports Server (NTRS)

    Hartley, Dana

    1995-01-01

    The main focus of this work is to understand the dynamics of mass exchange between the tropics and the midlatitudes and to determine any links between tropospheric exchange and that in the stratosphere. We have approached this problem from two different perspectives. The first is aimed towards understanding the troposphere's role in inducing lower stratospheric tropical/midlatitude exchange. For this project we focus on observational analysis of the lower stratosphere to assess the key regions of transport in/out of the tropics and to what extent this transport is driven by tropospheric processes. The second approach is to determine the extent to which stratospheric processes influence the troposphere. In this project we are performing potential vorticity (PV) inversions to assess the winds induced near the tropopause when the stratospheric polar vortex is displaced equatorward. These are each discussed in more detail in the subsections below. Also, we have organized a session on Tropical/Midlatitude Interaction and Transport at the Fall AGU where we will be showing our latest results.

  14. CFD analysis of the plate heat exchanger - Mathematical modelling of mass and heat transfer in serial connection with tubular heat exchanger

    NASA Astrophysics Data System (ADS)

    Bojko, Marian; Kocich, Radim

    2016-06-01

    Application of numerical simulations based on the CFD calculation when the mass and heat transfer between the fluid flows is essential component of thermal calculation. In this article the mathematical model of the heat exchanger is defined, which is subsequently applied to the plate heat exchanger, which is connected in series with the other heat exchanger (tubular heat exchanger). The present contribution deals with the possibility to use the waste heat of the flue gas produced by small micro turbine. Inlet boundary conditions to the mathematical model of the plate heat exchanger are obtained from the results of numerical simulation of the tubular heat exchanger. Required parameters such for example inlet temperature was evaluated from temperature field, which was subsequently imported to the inlet boundary condition to the simulation of plate heat exchanger. From the results of 3D numerical simulations are evaluated basic flow variables including the evaluation of dimensionless parameters such as Colburn j-factor and friction ft factor. Numerical simulation is realized by software ANSYS Fluent15.0.

  15. The dominant mechanisms of hyporheic exchange

    NASA Astrophysics Data System (ADS)

    McCluskey, Alexander H.; Stewardson, Michael J.; Grant, Stanley B.

    2013-04-01

    The mechanisms driving hyporheic exchange are of significant interest facilitating transfer of nutrients, oxygen and energy essential for benthic ecology. The hyporheic zone is the region directly beneath the sediment-water interface (SWI) marking the transition from stream to porous flow. Hyporheic exchange is controlled by a range of variables of the stream, streambed and the geometry of the SWI. The boundary layer of a stream is characterized by a slip velocity across the SWI, facilitating transition from free fluid to Darcian flow. Mass and momentum transfer across the SWI are driven by either (1) advective pumping from variation in dynamic head at the SWI causing potential flow into and out of the streambed, or; (2) turbulent structures in the boundary layer which penetrate into the streambed. Unlike the advective pumping, turbulent structures penetrate well beyond the characteristic mixing length scale and lead to permanent displacement of fluid. The advective pumping model assumes a potential field directly beneath the SWI, despite the slip layer propagating into the bed. Furthermore, turbulent exchange can lead to a permanent displacement of fluid, while advective pumping is multidirectional and periodic. Models derived from flume experiments have been based on one of these mechanisms and have been presented as two alternative approaches for modelling hyporheic exchange. However, the incongruence of these mechanisms leads us to investigate and model each individually. Our investigation treats coherent turbulent penetration and advective pumping as unique mechanisms which both contribute to rates of hyporheic exchange. Using bedforms as a proxy for advective pumping allowed us to gain insight into the dynamics of exchange mechanisms. Analysis of 93 past flume experiments has shown that bedforms alter the dependence of hyporheic exchange on these exchange mechanisms. Power models developed through a multilinear regression analysis showed that exchange in

  16. The influence of cryogenic mass exchange on the distribution of viable microfauna in cryozems

    NASA Astrophysics Data System (ADS)

    Gubin, S. V.; Lupachev, A. V.; Shatilovich, A. V.; Myl'nikov, A. P.; Ryss, A. Yu.; Veremeeva, A. A.

    2016-12-01

    The role of cryogenic mass exchange in the distribution of the viable microfauna (ciliates, heterotrophic flagellates, and nematodes) in the profiles of cryoturbated cryogenic soils and in the upper layers of permafrost was revealed. The material for microbiological investigations was collected from the main horizons of cryozem profiles, including the zones with morphologically manifested processes of cryogenic mass exchange (the development of barren spots, cryoturbation, and suprapermafrost accumulation) and the zones affected by solifluction. The radiocarbon dating of the soil samples showed that the age of the organic cryogenic material and material buried in the course of solifluction varied from 2100 to 4500 years. Some zones with specific ecological conditions promoting the preservation of species diversity of the microfauna were found to develop in the cryozem profiles. A considerable part of the community (38% of ciliates, 58% of flagellates, and 50% of nematodes) maintained its viability in the dormant state, and in some cases, it could pass to the state of long-term cryobiosis in the upper layer of permafrost.

  17. Removal of chlorofluorocarbons by increased mass exchange between the stratosphere and troposphere in a changing climate.

    PubMed

    Butchart, N; Scaife, A A

    2001-04-12

    Chlorofluorocarbons (CFCs), along with bromine compounds, have been unequivocally identified as being responsible for most of the anthropogenic destruction of stratospheric ozone. With curbs on emissions of these substances, the recovery of the ozone layer will depend on their removal from the atmosphere. As CFCs have no significant tropospheric removal process, but are rapidly photolysed above the lower stratosphere, the timescale for their removal is set mainly by the rate at which air is transported from the troposphere into the stratosphere. Using a global climate model we predict that, in response to the projected changes in greenhouse-gas concentrations during the first half of the twenty-first century, this rate of mass exchange will increase by 3% per decade. This increase is due to more vigorous extra-tropical planetary waves emanating from the troposphere. We estimate that this increase in mass exchange will accelerate the removal of CFCs to an extent that recovery to levels currently predicted for 2050 and 2080 will occur 5 and 10 years earlier, respectively.

  18. Localizing Carbohydrate Binding Sites in Proteins Using Hydrogen/Deuterium Exchange Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Zhang, Jingjing; Kitova, Elena N.; Li, Jun; Eugenio, Luiz; Ng, Kenneth; Klassen, John S.

    2016-01-01

    The application of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to localize ligand binding sites in carbohydrate-binding proteins is described. Proteins from three bacterial toxins, the B subunit homopentamers of Cholera toxin and Shiga toxin type 1 and a fragment of Clostridium difficile toxin A, and their interactions with native carbohydrate receptors, GM1 pentasaccharides (β-Gal-(1→3)-β-GalNAc-(1→4)[α-Neu5Ac-(2→3)]-β-Gal-(1→4)-Glc), Pk trisaccharide (α-Gal-(1→4)-β-Gal-(1→4)-Glc) and CD-grease (α-Gal-(1→3)-β-Gal-(1→4)-β-GlcNAcO(CH2)8CO2CH3), respectively, served as model systems for this study. Comparison of the differences in deuterium uptake for peptic peptides produced in the absence and presence of ligand revealed regions of the proteins that are protected against deuterium exchange upon ligand binding. Notably, protected regions generally coincide with the carbohydrate binding sites identified by X-ray crystallography. However, ligand binding can also result in increased deuterium exchange in other parts of the protein, presumably through allosteric effects. Overall, the results of this study suggest that HDX-MS can serve as a useful tool for localizing the ligand binding sites in carbohydrate-binding proteins. However, a detailed interpretation of the changes in deuterium exchange upon ligand binding can be challenging because of the presence of ligand-induced changes in protein structure and dynamics.

  19. Lattice Boltzmann method for the fractional advection-diffusion equation.

    PubMed

    Zhou, J G; Haygarth, P M; Withers, P J A; Macleod, C J A; Falloon, P D; Beven, K J; Ockenden, M C; Forber, K J; Hollaway, M J; Evans, R; Collins, A L; Hiscock, K M; Wearing, C; Kahana, R; Villamizar Velez, M L

    2016-04-01

    Mass transport, such as movement of phosphorus in soils and solutes in rivers, is a natural phenomenon and its study plays an important role in science and engineering. It is found that there are numerous practical diffusion phenomena that do not obey the classical advection-diffusion equation (ADE). Such diffusion is called abnormal or superdiffusion, and it is well described using a fractional advection-diffusion equation (FADE). The FADE finds a wide range of applications in various areas with great potential for studying complex mass transport in real hydrological systems. However, solution to the FADE is difficult, and the existing numerical methods are complicated and inefficient. In this study, a fresh lattice Boltzmann method is developed for solving the fractional advection-diffusion equation (LabFADE). The FADE is transformed into an equation similar to an advection-diffusion equation and solved using the lattice Boltzmann method. The LabFADE has all the advantages of the conventional lattice Boltzmann method and avoids a complex solution procedure, unlike other existing numerical methods. The method has been validated through simulations of several benchmark tests: a point-source diffusion, a boundary-value problem of steady diffusion, and an initial-boundary-value problem of unsteady diffusion with the coexistence of source and sink terms. In addition, by including the effects of the skewness β, the fractional order α, and the single relaxation time τ, the accuracy and convergence of the method have been assessed. The numerical predictions are compared with the analytical solutions, and they indicate that the method is second-order accurate. The method presented will allow the FADE to be more widely applied to complex mass transport problems in science and engineering.

  20. Lattice Boltzmann method for the fractional advection-diffusion equation

    NASA Astrophysics Data System (ADS)

    Zhou, J. G.; Haygarth, P. M.; Withers, P. J. A.; Macleod, C. J. A.; Falloon, P. D.; Beven, K. J.; Ockenden, M. C.; Forber, K. J.; Hollaway, M. J.; Evans, R.; Collins, A. L.; Hiscock, K. M.; Wearing, C.; Kahana, R.; Villamizar Velez, M. L.

    2016-04-01

    Mass transport, such as movement of phosphorus in soils and solutes in rivers, is a natural phenomenon and its study plays an important role in science and engineering. It is found that there are numerous practical diffusion phenomena that do not obey the classical advection-diffusion equation (ADE). Such diffusion is called abnormal or superdiffusion, and it is well described using a fractional advection-diffusion equation (FADE). The FADE finds a wide range of applications in various areas with great potential for studying complex mass transport in real hydrological systems. However, solution to the FADE is difficult, and the existing numerical methods are complicated and inefficient. In this study, a fresh lattice Boltzmann method is developed for solving the fractional advection-diffusion equation (LabFADE). The FADE is transformed into an equation similar to an advection-diffusion equation and solved using the lattice Boltzmann method. The LabFADE has all the advantages of the conventional lattice Boltzmann method and avoids a complex solution procedure, unlike other existing numerical methods. The method has been validated through simulations of several benchmark tests: a point-source diffusion, a boundary-value problem of steady diffusion, and an initial-boundary-value problem of unsteady diffusion with the coexistence of source and sink terms. In addition, by including the effects of the skewness β , the fractional order α , and the single relaxation time τ , the accuracy and convergence of the method have been assessed. The numerical predictions are compared with the analytical solutions, and they indicate that the method is second-order accurate. The method presented will allow the FADE to be more widely applied to complex mass transport problems in science and engineering.

  1. Advection, diffusion, and delivery over a network.

    PubMed

    Heaton, Luke L M; López, Eduardo; Maini, Philip K; Fricker, Mark D; Jones, Nick S

    2012-08-01

    Many biological, geophysical, and technological systems involve the transport of a resource over a network. In this paper, we present an efficient method for calculating the exact quantity of the resource in each part of an arbitrary network, where the resource is lost or delivered out of the network at a given rate, while being subject to advection and diffusion. The key conceptual step is to partition the resource into material that does or does not reach a node over a given time step. As an example application, we consider resource allocation within fungal networks, and analyze the spatial distribution of the resource that emerges as such networks grow over time. Fungal growth involves the expansion of fluid filled vessels, and such growth necessarily involves the movement of fluid. We develop a model of delivery in growing fungal networks, and find good empirical agreement between our model and experimental data gathered using radio-labeled tracers. Our results lead us to suggest that in foraging fungi, growth-induced mass flow is sufficient to account for long-distance transport, if the system is well insulated. We conclude that active transport mechanisms may only be required at the very end of the transport pathway, near the growing tips.

  2. Isentropic mass exchange between the Tropics and extratropics in the stratosphere

    NASA Technical Reports Server (NTRS)

    Chen, Ping; Holton, James R.; O'Neill, Alan; Swinbank, Richard

    1994-01-01

    The isentropic mass exchange between the Tropics and extratropics in the stratosphere is investigated with a semi-Lagrangian transport model for the periods from 1 June to 31 October 1992 and from 1 December 1992 to 30 April 1993 using winds from the U.K. Meteorological Office data assimilation system. Calculations with an idealized, initially zonally symmetric tracer show that in the middle and upper stratosphere the bulk of tropical air is transported into the midlatitudes of the winter hemisphere although there exist quasi-permeable barriers in the subtropics. The transport takes place in the form of planetary-scale 'tongues' of material that are drawn poleward in association with the episodic amplification of planetary-scale waves in high latitudes of the winter hemisphere. Once air of tropical origin is transported to the midlatitudes it is irreversibly mixed with the midlatitude air in the 'surf zone.' Air of tropical origin can, however, hardly penetrate into the interior of the winter polar vortex until the breakdown of the vortex. Transport of tropical air into the midlatitudes of the summer hemisphere is strongly inhibited. In the lower stratosphere, tropical air is transported into the northern and southern midlatitudes. During the period from 1 June to 31 October 1992, the amount of tropical air transported into the Northern Hemisphere is, however, much smaller than that transported into the Southern Hemisphere, and there exist strong gradients in the tracer field in the equatorial region, indicating that there is a quasi-permeable barrier to cross-equator mass exchange. During the period from 1 December 1992 to 30 April 1993, on the other hand, roughly the same amounts of tropical air are transported into the Southern Hemisphere, and there exist strong gradients in the tracer field in the equatorial region, indicating that there is a quasi-permeable barrier to cross-equator mass exchange. During the period from 1 December 1992 to 30 April 1993, on the

  3. Towards a Theory of Tropical/Midlatitude Mass Exchange from the Earth's Surface through the Stratosphere

    NASA Technical Reports Server (NTRS)

    Hartley, Dana

    1998-01-01

    The main findings of this research project have been the following: (1) there is a significant feedback from the stratosphere on tropospheric dynamics, and (2) a detailed analysis of the interaction between tropical and polar wave breaking in controlling stratospheric mixing. Two papers are were written and are included. The first paper is titled, "A New Perspective on the Dynamical Link Between the Stratosphere and Troposphere." Atmospheric processes of tropospheric origin can perturb the stratosphere, but direct feedback in the opposite direction is usually assumed to be negligible, despite the troposphere's sensitivity to changes in the release of wave activity into the stratosphere. Here, however, we present evidence that such a feedback exists and can be significant. We find that if the wintertime Arctic polar stratospheric vortex is distorted, either by waves propagating upward from the troposphere or by eastward-travelling stratospheric waves, then there is a concomitant redistribution of stratospheric potential vorticity that induces perturbations in key meteorological fields in the upper troposphere. The feedback is large despite the much greater mass of the troposphere: it can account for up to half of the geopotential height anomaly at the tropopause. Although the relative strength of the feedback is partly due to a cancellation between contributions to these anomalies from lower altitudes, our results imply that stratospheric dynamics and its feedback on the troposphere are more significant for climate modelling and data assimilation than was previously assumed. The second article is titled "Diagnosing the Polar Excitation of Subtropical Waves in the Stratosphere". The poleward migration of planetary scale tongues of subtropical air has often been associated with intense polar vortex disturbances in the stratosphere. This question of vortex influence is reexamined from a potential vorticity (PV) perspective. Anomalous geopotential height and wind fields

  4. Mass spectrometric measurement of protein amide hydrogen exchange rates of apo- and holo-myoglobin.

    PubMed Central

    Johnson, R. S.; Walsh, K. A.

    1994-01-01

    Measurement of backbone amide hydrogen exchange rates can provide detailed information concerning protein structure, dynamics, and interactions. Although nuclear magnetic resonance is typically used to provide these data, its use is restricted to lower molecular weight proteins that are soluble at millimolar concentrations. Not subject to these limitations is a mass spectrometric approach for measuring deuterium incorporation into proteins that are subsequently proteolyzed by pepsin; the resulting peptide masses are measured using a flowing-fast atom bombardment ionization source (Zhang Z, Smith DL, 1993, Protein Sci 2:522-531). In the current study, amide deuterium incorporation for intact apo- and holo-myoglobin was measured using liquid chromatography coupled directly to an electrospray ionization (LC/MS) source. Electrospray ionization provided a more complete coverage of the protein sequence and permitted the measurement of deuterium incorporation into intact proteins. Tandem mass spectrometry was used to rapidly identify the peptic peptides. It was found that within 30 s, the amides in apo-myoglobin were 47% deuterated, whereas holo-myoglobin was 12% deuterated. Peptic digestion and LC/MS demonstrated that regions represented by peptic peptides encompassing positions 1-7, 12-29, and 110-134 were not significantly altered by removal of the heme. Likewise, destabilized regions were identified within positions 33-106 and 138-153. PMID:7756994

  5. Activation of AMP-activated protein kinase revealed by hydrogen/deuterium exchange Mass Spectrometry

    PubMed Central

    Landgraf, Rachelle R.; Goswami, Devrishi; Rajamohan, Francis; Harris, Melissa S.; Calabrese, Matthew; Hoth, Lise R.; Magyar, Rachelle; Pascal, Bruce D.; Chalmers, Michael J.; Busby, Scott A.; Kurumbail, Ravi; Griffin, Patrick R.

    2013-01-01

    Summary AMP-Activated protein kinase (AMPK) monitors cellular energy, regulates genes involved in ATP synthesis and consumption, and is allosterically activated by nucleotides and synthetic ligands. Analysis of the intact enzyme by hydrogen/deuterium exchange mass spectrometry reveals conformational perturbations of AMPK in response to binding of nucleotides, cyclodextrin and a synthetic small molecule activator, A769662. Results from this analysis clearly show that binding of AMP leads to conformational changes primarily in the γ subunit of AMPK and subtle changes in the α and β subunits. In contrast, A769662 causes profound conformational changes in the glycogen binding module of the β subunit and in the kinase domain of the α subunit suggesting that the molecular binding site of latter resides between the α and β subunits. The distinct short and long-range perturbations induced upon binding of AMP and A769662 suggest fundamentally different molecular mechanisms for activation of AMPK by these two ligands. PMID:24076403

  6. Ion exchange separation of chromium from natural water matrix for stable isotope mass spectrometric analysis

    USGS Publications Warehouse

    Ball, J.W.; Bassett, R.L.

    2000-01-01

    A method has been developed for separating the Cr dissolved in natural water from matrix elements and determination of its stable isotope ratios using solid-source thermal-ionization mass spectrometry (TIMS). The separation method takes advantage of the existence of the oxidized form of Cr as an oxyanion to separate it from interfering cations using anion-exchange chromatography, and of the reduced form of Cr as a positively charged ion to separate it from interfering anions such as sulfate. Subsequent processing of the separated sample eliminates residual organic material for application to a solid source filament. Ratios for 53Cr/52Cr for National Institute of Standards and Technology Standard Reference Material 979 can be measured using the silica gel-boric acid technique with a filament-to-filament standard deviation in the mean 53Cr/52Cr ratio for 50 replicates of 0.00005 or less. (C) 2000 Elsevier Science B.V. All rights reserved.

  7. Evolution and Advection of Solar Mesogranulation

    DTIC Science & Technology

    1992-03-01

    unprecedented clarity. We see that the supergranules, which are known to carry along (advect) the granules with their convective motion, also advect...I Solar mesogranulation, Solar observations, Solar super- 2 granulation 16. PRICE COCE 1i7. SECJ-3T LSiIATO 8 EUITY CLASSIFICA ION 19. SECURITY CLAS...mo~iesý sho~ed that granules are adl~ectedl b• Richard Muller*, Hers& Auffret*, Thierry Roudiert, the larger-scale consectie flowss. and thu, could

  8. Evidence of mass exchange between inside and outside of sonoluminescing bubble in aqueous solution of terbium chloride

    NASA Astrophysics Data System (ADS)

    Liang, Jinfu; Chen, Weizhong; Wang, Xun; Yang, Jing; Chen, Zhan

    2016-12-01

    Spectra of single-bubble sonoluminescence (SBSL) were obtained for Tb3+ ions emission lines from bubbles in an aqueous solution of terbium chloride (TbCl3). The spectra provide experimental evidence to prove that an air bubble driven by strong ultrasound will not eventually become a rectified pure argon bubble, which is not as predicted by the argon rectification hypothesis. The time-resolved spectra of SBSL show a mass exchange of material such as Tb3+ ions between the inside and outside of the bubble. With increasing sound pressure, the rate of mass exchange and the SBSL intensity increases.

  9. A New Methodology For Estimating CO2 Advective Fluxes In Complex Terrain

    NASA Astrophysics Data System (ADS)

    Montagnani, L.; Manca, G.; Canepa, E.; Georgieva, E.; Kerschbaumer, G.; Minerbi, S.; Seufert, G.

    2007-12-01

    A key problem in using the eddy correlation (EC) technique for estimating the carbon dioxide Net Ecosystem Exchange (NEE) of terrestrial ecosystems is the potential bias caused by advective fluxes of CO2. Advective fluxes are often not considered since they are difficult to identify and to quantify, especially in complex mountainous terrain with highly variable wind patterns and drainage flows. We propose a methodology to estimate these fluxes based on a full 3-Dimensional (3D) approach applied to the topographically complex alpine forest site of Renon (1736 m a.s.l.). This is an aerodynamic method based on the computation of advective fluxes across the aerial faces of a control volume including the plant ecosystem. Data used for the computation of CO2 advective fluxes were collected during an extensive field campaign performed in 2005 in the framework of CarboEurope-IP research project. Vertical profiles of wind, air temperature and CO2 concentration have been measured at five towers and a spatial interpolation was performed in order to get 3D fields of such variables. The frame of reference used was orthogonal and the vertical direction was parallel to the gravity. Each anemometer was aligned in this frame of reference and no rotations were applied to the wind velocity components. The analysis of the 3D fields of wind velocity, CO2 mixing ratio and air density highlighted the spatial heterogeneity of CO2 source/sink strength and the strong de-coupling between air flow below and above the canopy during stable nights. The total CO2 advection calculated using the proposed methodology exhibited prevailing positive values during the night-time period. Advective fluxes estimated during windy nights were of the same magnitude and sign of vertical turbulent flux measured above canopy by the EC technique. This observation suggests that the friction velocity correction routinely applied to night-time periods may not be efficient at the Renon site. During light windy nights

  10. Elucidation of tRNA-cytochrome c interactions through hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Lo, Yi-Ting; Huang, Hung-Wei; Huang, Yi-Chuan; Chan, Jui-Fen; Hsu, Yuan-Hao Howard

    2017-02-27

    Cytochrome c (cyt c) is a mitochondrial protein responsible for transferring electrons between electron transport chain complexes III and IV. The release of cyt c from the mitochondria has been considered as a commitment step in intrinsic apoptosis. Transfer RNA (tRNA) has recently been found to interact with the released cyt c to prevent the formation of the apoptosome complex, thus preventing cell apoptosis. To understand the molecular basis of tRNA-cyt c interactions, we applied hydrogen/deuterium exchange mass spectrometry (HDXMS) to analyze the interactions between tRNA and cyt c. tRNA(Phe) binding to cyt c reduced the deuteration level of cyt c in all analyzed regions, indicating that tRNA binding blocks the solvent-accessible regions and results in the formation of a more compact conformation. Substitution of the tRNA(Phe) with the total tRNA from brewer's yeast in the HDXMS experiment significantly reduced deuteration in the N-terminus and the region 18-32 residue of cyt c, where all tRNAs are bound. To clarify the cause of binding, we used synthesized single-stranded oligonucleotides of 12-mer dA and dT to form complexes with cyt c. The exchange of the nucleotide bases between adenine and thymine did not affect the deuteration level of cyt c. However, the regions 1-10 and 65-82 showed minor decreases after unstructured dA or dT DNA binding. Collectively, these results reveal that cyt c maintains its globular structure to interact with tRNA. The region 18-32 selectively interacts with tRNA, and N-terminal 1-10 interacts with oligonucleotides electrostatically.

  11. Hydrogen/deuterium exchange of hydrophobic peptides in model membranes by electrospray ionization mass spectrometry.

    PubMed

    Hansen, Raino K; Broadhurst, R William; Skelton, Paul C; Arkin, Isaiah T

    2002-12-01

    We demonstrate here that the hydrogen/deuterium solvent exchange (HDX) properties of the transmembrane fragment of the M2 protein of Influenza A (M2-TM) incorporated into lipid vesicles or detergent micelles can be studied with straightforward electrospray (ESI) and nanospray mass spectrometry (MS) configurations provided that key factors, including sample preparation techniques, are optimized. Small unilamellar vesicle preparations were obtained by solubilizing dimyristoyl phosphatidylcholine (DMPC) and the M2-TM peptide in aqueous solution with n-octyl-beta-D-glycopyranoside, followed by dialysis to remove the detergent. Electron microscopy experiments revealed that subsequent concentration by centrifugation introduced large multilamellar aggregates that were not compatible with ESI-MS. By contrast, a lyophilization-based concentration procedure, followed by thawing above the liquid crystal transition temperature of the lipid component, maintained the liposome size profile and yielded excellent ion fluxes in both ESI-MS and nano-ESI-MS. Using these methods the global HDX profile of M2-TM in aqueous DMPC vesicles was compared with that in methanol, demonstrating that several amide sites were protected from exchange by the lipid membrane. We also show that hydrophobic peptides can be detected by ESI-MS in the presence of a large molar excess of the detergent Triton X-100. The rate of HDX of M2-TM in Triton X-100 micelles was faster than that in DMPC vesicles but slower than when the peptide had been denatured in methanol. These results indicate that the accessibility of backbone amide sites to the solvent can be profoundly affected by membrane protein structure and dynamics, as well as the properties of model bilayer systems.

  12. Surfzone alongshore advective accelerations: observations and modeling

    NASA Astrophysics Data System (ADS)

    Hansen, J.; Raubenheimer, B.; Elgar, S.

    2014-12-01

    The sources, magnitudes, and impacts of non-linear advective accelerations on alongshore surfzone currents are investigated with observations and a numerical model. Previous numerical modeling results have indicated that advective accelerations are an important contribution to the alongshore force balance, and are required to understand spatial variations in alongshore currents (which may result in spatially variable morphological change). However, most prior observational studies have neglected advective accelerations in the alongshore force balance. Using a numerical model (Delft3D) to predict optimal sensor locations, a dense array of 26 colocated current meters and pressure sensors was deployed between the shoreline and 3-m water depth over a 200 by 115 m region near Duck, NC in fall 2013. The array included 7 cross- and 3 alongshore transects. Here, observational and numerical estimates of the dominant forcing terms in the alongshore balance (pressure and radiation-stress gradients) and the advective acceleration terms will be compared with each other. In addition, the numerical model will be used to examine the force balance, including sources of velocity gradients, at a higher spatial resolution than possible with the instrument array. Preliminary numerical results indicate that at O(10-100 m) alongshore scales, bathymetric variations and the ensuing alongshore variations in the wave field and subsequent forcing are the dominant sources of the modeled velocity gradients and advective accelerations. Additional simulations and analysis of the observations will be presented. Funded by NSF and ASDR&E.

  13. Freshwater mass balance and exchange of water masses with the open sea: the Mljet Lakes (Croatia, Adriatic Sea)

    NASA Astrophysics Data System (ADS)

    Martincic, Urska; Bezak, Nejc; Zagar, Dusan; Makovec, Tihomir; Lucic, Davor; Onofri, Vladimir; Malacic, Vlado

    2016-04-01

    Two karstic seawater lakes (Veliko - Big and Malo - Small Lake) located in the National Park Mljet on the Mljet Island in Croatia were investigated in this study. The Small and the Big Lake cover 0.25 and 1.45 km2, respectively. The two lakes are connected to each other and to the sea by narrow channels. The connecting channel between the Big Lake and the sea is 12 m wide and 3 m deep. The connection to the Small Lake leads through another artificial channel (2.7 m wide and 0.8 m deep). The average salinity of the Big and the Small lake is 37.75 and 36.9, respectively, and the average salinity of the open sea is 38.5. While previous studies have been conducted due to the lakes' unique ecosystem and the karstic characteristics of the area, the main aim of this study was to determine the freshwater mass balance and exchange of water masses with the nearby sea. Several measurement campaigns were performed between 2008 and 2015 when meteorological parameters as well as salinity, water temperature and water velocities in both lakes and the channels were observed. A perpetual year was determined using available meteorological data. The contribution of the surface runoff to both lakes was modelled using the hydrological rainfall-runoff HEC-HMS model. Curve number parameter was estimated using the CLC Corine Land cover and geomorphological maps. Evaporation from the lake was calculated using the Verburg, Kondo and Coare equations. We found that the annual evaporation approximately equals the annual rainfall to the lake surface (cca. 550-600 mm). From the hydrological model and the difference between precipitation and evaporation from the lake surface we calculated the annual net excess of freshwater between 0.5 106 and 0.7 106 m3. The average salinity in both lakes is lower than the salinity in the sea; therefore, we hypothesize that the excess water should be discharged either through the channel between the Big Lake and the open sea or through underwater karstic sink

  14. Glacial-interglacial 3D ice sheet modelling of Antarctica; Validation by age-isotope advection

    NASA Astrophysics Data System (ADS)

    Springer, S. R.; Padman, L.; Dinniman, M. S.

    2014-12-01

    Wintertime sea ice extent around Antarctica has shown a positive trend during at least the past decade. The maximum northward expansion of sea ice is likely to be limited by the strong ocean temperature gradients associated with fronts of the Antarctic Circumpolar Current (ACC). The ACC is, however, very dynamically unstable, with mesoscale eddies accounting for a large fraction of the variance in surface currents and sea surface temperature (SST). We combine satellite-observed sea-ice concentration, SST, and geostrophic eddy velocities to explore the hypothesis that dynamic and thermodynamic interactions between mesoscale eddies and sea ice exert an additional influence on the location of the winter sea ice margin. Advancing sea ice develops meridional deviations at horizontal scales of ~100 km, lengthening the perimeter of the ice-covered area by 30-70%. In many cases, this "scalloping" of the ice margin can be attributed to advection by eddy velocities. The effect varies regionally, depending on the proximity of the ice edge to the ACC. From the Amundsen Sea eastward through the Drake Passage the southern limit of eddy variability coincides with the northernmost extent of sea ice, and scalloping is common. By deforming the ice margin, eddies increase the potential for ice-edge melting and destruction by Southern Ocean surface wave action, while eddy-driven ice advection modifies the mean thermodynamic exchanges responsible for mass loss from the base of the ice pack. We use observations and models to estimate sea-ice loss caused by eddy/ice interactions.

  15. Dynamic Structural Changes During Complement C3 Activation Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry

    PubMed Central

    Schuster, Michael C.; Ricklin, Daniel; Papp, Krisztián; Molnar, Kathleen S.; Coales, Stephen J.; Hamuro, Yoshitomo; Sfyroera, Georgia; Chen, Hui; Winters, Michael S.; Lambris, John D.

    2008-01-01

    Proteolytic cleavage of component C3 to C3b is a central step in the activation of complement. Whereas C3 is largely biologically inactive, C3b is directly involved in various complement activities. While the recently described crystal structures of C3 and C3b provide a molecular basis of complement activation, they do not reflect the dynamic changes that occur in solution. In addition, the available C3b structures diverge in some important aspects. Here we have utilized hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) to investigate relative changes in the solution-phase structures of C3 and C3b. By combining two forms of mass spectrometry we could maximize the primary sequence coverage of C3b and demonstrate the feasibility of this method for large plasma proteins. While the majority of the 82 peptides that could be followed over time showed only minor alterations in HDX, we observed clear changes in solvent accessibility for 16 peptides, primarily in the α-chain (α’NT, MG6-8, CUB, TED, C345C domains). Most of these peptides could be directly linked to the structural transitions visible in the crystal structures and revealed additional information about the probability of the structural variants of C3b. In addition, a discontinuous cluster of seven peptides in the MG3, MG6, LNK and α’NT domains showed a decreased accessibility after activation to C3b. Although no gross conformational changes are detected in the crystal structure, this area may reflect a structurally flexible region in solution that contributes to C3 activation and function. PMID:18456336

  16. qcML: an exchange format for quality control metrics from mass spectrometry experiments.

    PubMed

    Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W P; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A; Kelstrup, Christian D; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S; Olsen, Jesper V; Heck, Albert J R; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

    2014-08-01

    Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml.

  17. [Analysis of mouse liver membrane proteins using multidimensional ion exchange chromatography and tandem mass spectrometry].

    PubMed

    Wang, Zhuowei; Peng, Fuli; Wang, Yuan; Tong, Wei; Ren, Yan; Xu, Ningzhi; Liu, Siqi

    2010-02-01

    The analysis of membrane proteins is still a technical obstacle in proteomic investigation. A fundamental question is how to allow the hydrophobic proteins fully solubilizing in a proper solvent environment. We propose that the denatured membrane proteins in high denaturant solution are fully ionized and separated through ion exchange chromatography. The membrane proteins prepared from a mouse liver were dissolved in 4 mol/L urea, 20 mmol/L Tris-HCl buffer (pH 9.0), and loaded onto a tandem chromatography coupled with Q-Sepharose FF and Sephacryl S-200HR. With a linear NaCl gradient elution, the bound proteins were eluted and collected followed by sodium-dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) to further separate the eluted proteins. The protein bound on SDS-PAGE were excised and in-gel digested by trypsin, while the digested peptides were delivered to reversed-phase high performance liquid chromatography (HPLC) and ion-trap mass spectrometry for the peptide identifications. Of a total of 392 proteins identified, 306 were membrane proteins or membrane associated proteins reported by literature. Based on the calculation of hydrophobicity, the GRAVY (grand average of hydropathicity) scores of 83 proteins are over or equal to 0.00. Taking all the evidence, we have established an effective approach which is feasible in the investigation towards mouse liver membrane proteomics.

  18. Differential hydrogen/deuterium exchange mass spectrometry analysis of protein–ligand interactions

    PubMed Central

    Chalmers, Michael J; Busby, Scott A; Pascal, Bruce D; West, Graham M; Griffin, Patrick R

    2011-01-01

    Functional regulation of ligand-activated receptors is driven by alterations in the conformational dynamics of the protein upon ligand binding. Differential hydrogen/deuterium exchange (HDX) coupled with mass spectrometry has emerged as a rapid and sensitive approach for characterization of perturbations in conformational dynamics of proteins following ligand binding. While this technique is sensitive to detecting ligand interactions and alterations in receptor dynamics, it also can provide important mechanistic insights into ligand regulation. For example, HDX has been used to determine a novel mechanism of ligand activation of the nuclear receptor peroxisome proliferator activated receptor-γ, perform detailed analyses of binding modes of ligands within the ligand-binding pocket of two estrogen receptor isoforms, providing insight into selectivity, and helped classify different types of estrogen receptor-α ligands by correlating their pharmacology with the way they interact with the receptor based solely on hierarchical clustering of receptor HDX signatures. Beyond small-molecule–receptor interactions, this technique has also been applied to study protein–protein complexes, such as mapping antibody–antigen interactions. In this article, we summarize the current state of the differential HDX approaches and the future outlook. We summarize how HDX analysis of protein–ligand interactions has had an impact on biology and drug discovery. PMID:21329427

  19. qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments*

    PubMed Central

    Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W. P.; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A.; Kelstrup, Christian D.; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S.; Olsen, Jesper V.; Heck, Albert J. R.; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

    2014-01-01

    Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml. PMID:24760958

  20. Electrospray ionization mass spectrometric observation of ligand exchange of zinc pyrithione with amino acids.

    PubMed

    Moriwaki, Hiroshi; Okabayashi, Masanori; Watanabe, Takehiro; Kawasaki, Hideya; Arakawa, Ryuichi

    2009-07-01

    Zinc pyrithione (ZnPT) is widely used as an antidandruff or antifouling reagent. However, this compound is considered toxic, such as the teratogenic effect, to aquatic lives, and it is important to clarify the mechanism of its toxicity. In this study, the interactions between ZnPT and amino acids were observed using electrospray ionization mass spectrometry (ESI-MS) in order to obtain information on the activity of ZnPT within the living body. The ZnPT complex ([ZnPT-ligand+Amino acid]+), in which the ligand of ZnPT was exchanged by the amino acid, was detected in ZnPT solutions mixed with one of 20 amino acids by ESI-MS. Histidine and cysteine, in particular, showed a high reactivity with ZnPT, while serine and glycine showed a low reactivity. The complexes of ZnPT and a peptide were also observed by the ESI-MS measurement of the solution containing ZnPT with the peptide. These results would be useful to understand the mechanism of ZnPT toxicities to living creatures.

  1. Use of the mass exchange theory for describing soil erosion by water and wind

    NASA Astrophysics Data System (ADS)

    Gendugov, V. M.; Glazunov, G. P.; Larionov, G. A.; Nazarov, N. F.

    2012-02-01

    It was shown that the soil loss equation for different types of erosion should and can be theoretically derived in a general form. An analogy was drawn between the detachment of soil particles by water or air flows, on the one hand, and the heat and mass exchange in the boundary layer on a plate flowed around by a flow, on the other hand, which allowed finding the thermodynamic parameters of the circumfluent flow analogous to the mechanical parameters of a flow eroding the soil. On this basis, the Clausius-Clapeyron equation for equilibrium sublimation was transformed into an equation describing the removal of soil by both water and wind. The validity of the obtained equation for the description of the soil loss rate as a function of the eroding flow parameters was confirmed using the data on the physical simulation of wind erosion in wind tunnels and water erosion in hydraulic flumes. The confirmed adequacy of the derived equation to the phenomena of soil erosion by water and wind provides the theoretical substantiation of the equations previously derived for soil loss by washing [6] and blowing [3] and forms the basis for the further development of the theory of soil erosion.

  2. Online deuterium hydrogen exchange and protein digestion coupled with ion mobility spectrometry and tandem mass spectrometry.

    PubMed

    Donohoe, Gregory C; Arndt, James R; Valentine, Stephen J

    2015-05-19

    Online deuterium hydrogen exchange (DHX) and pepsin digestion (PD) is demonstrated using drift tube ion mobility spectrometry (DTIMS) coupled with linear ion trap (LTQ) mass spectrometry (MS) with electron transfer dissociation (ETD) capabilities. DHX of deuterated ubiquitin, followed by subsequent quenching and digestion, is performed within ∼60 s, yielding 100% peptide sequence coverage. The high reproducibility of the IMS separation allows spectral feature matching between two-dimensional IMS-MS datasets (undeuterated and deuterated) without the need for dataset alignment. Extracted ion drift time distributions (XIDTDs) of deuterated peptic peptides are mobility-matched to corresponding XIDTDs of undeuterated peptic peptides that were identified using collision-induced dissociation (CID). Matching XIDTDs allows a straightforward identification and deuterium retention evaluation for labeled peptides. Aside from the mobility separation, the ion trapping capabilities of the LTQ, combined with ETD, are demonstrated to provide single-residue resolution. Deuterium retention for the c- series ions across residues M(1)-L(15) and N(25)-R(42) are in good agreement with the known secondary structural elements within ubiquitin.

  3. Modelling heat and mass transfer in a membrane-based air-to-air enthalpy exchanger

    NASA Astrophysics Data System (ADS)

    Dugaria, S.; Moro, L.; Del, D., Col

    2015-11-01

    The diffusion of total energy recovery systems could lead to a significant reduction in the energy demand for building air-conditioning. With these devices, sensible heat and humidity can be recovered in winter from the exhaust airstream, while, in summer, the incoming air stream can be cooled and dehumidified by transferring the excess heat and moisture to the exhaust air stream. Membrane based enthalpy exchangers are composed by different channels separated by semi-permeable membranes. The membrane allows moisture transfer under vapour pressure difference, or water concentration difference, between the two sides and, at the same time, it is ideally impermeable to air and other contaminants present in exhaust air. Heat transfer between the airstreams occurs through the membrane due to the temperature gradient. The aim of this work is to develop a detailed model of the coupled heat and mass transfer mechanisms through the membrane between the two airstreams. After a review of the most relevant models published in the scientific literature, the governing equations are presented and some simplifying assumptions are analysed and discussed. As a result, a steady-state, two-dimensional finite difference numerical model is setup. The developed model is able to predict temperature and humidity evolution inside the channels. Sensible and latent heat transfer rate, as well as moisture transfer rate, are determined. A sensitive analysis is conducted in order to determine the more influential parameters on the thermal and vapour transfer.

  4. CO2 and O2 Gas Exchange in an Experimental Model of the Btlss with Plant Wastes and Human Wastes Included in the Mass Exchange

    NASA Astrophysics Data System (ADS)

    Ushakova, Sofya; Tikhomirov, Alexander A.; Velichko, Vladimir; Tikhomirova, Natalia; Trifonov, Sergey V.

    2016-07-01

    Mass exchange processes in the new experimental model of the biotechnical life support system (BTLSS) constructed at the Institute of Biophysics SB RAS have a higher degree of closure than in the previous BTLSS, and, thus, the technologies employed in the new system are more complex. Therefore, before closing the loops of mass exchange processes for several months, the new model of the BTLSS was run to match the technologies employed to cultivate plants and the methods used to involve inedible plant parts and human wastes into the mass exchange with the CO2 absorption rate and the amount of the resulting O2. The plant compartment included vegetables grown on the soil-like substrate (SLS) (chufa, beet, carrot, radish, and lettuce), plants hydroponically grown on expanded clay aggregate (wheat, soybean, watercress), and plants grown in aquaculture (common glasswort and watercress). Nutrient solutions for hydroponically grown plants were prepared by using products of physicochemical mineralization of human wastes. Growing the plants in aquaculture enabled maintaining NaCl concentration in the irrigation solution for hydroponically grown plants at a level safe for the plants. Inedible plant biomass was added to the SLS. Three cycles of closing the system were run, which lasted 7, 7, and 10 days. The comparison of the amount of CO2 fed into the system over 24 h (simulating human respiration) and the amount of CO2 daily exhaled by a 70-kg middle-aged human showed that between 1% and 4% of the daily emissions of CO2 were assimilated in the system, and about 3% of the average human daily O2 requirement accumulated in the system. Plant productivity was between 4 and 4.7% of the human daily vegetable requirement, or between 3 and 3.5% of the total human daily food requirement. Thus, testing of the BTLSS showed a match between the technologies employed to arrange mass exchange processes. This study was supported by the grant of the Russian Science Foundation (Project No. 14-14-00599).

  5. Diffusion and Advection using Cellular Potts Model

    NASA Astrophysics Data System (ADS)

    Dan, Debasis; Glazier, James

    2005-03-01

    The Cellular Potts Model (CPM) is a robust cell level methodology for simulation of biological tissues and morphogenesis. Standard diffusion solvers in the CPM use finite difference methods on the underlying CPM lattice. These methods have difficulty in simulating local advection in the ECM due to physiology and morphogenesis. To circumvent the problem of instabilities we simulate advection-diffusion within the framework of CPM using off-lattice finite-difference methods. We define a set of generalised fluid "cells" or particles which separate advection and diffusion from the lattice. Diffusion occurs between neighboring fluid cells by local averaging rules which approximate the Laplacian. CPM movement of the cells by spin flips handles the advection. The extension allows the CPM to model viscosity explicitly by including a relative velocity constraint on the fluid. The extended CPM correctly reproduces flow profiles of viscous fluids in cylindrical tube, during Stokes flow across a sphere and in flow in concentric cylindrical shells. We illustrate various conditions for diffusion including multiple instantaneous sources, continuous sources, moving sources and different boundary geometries and conditions to validate our approximation by comparing with analytical and established numerical solutions.

  6. 3D Flow Visualization Using Texture Advection

    NASA Technical Reports Server (NTRS)

    Kao, David; Zhang, Bing; Kim, Kwansik; Pang, Alex; Moran, Pat (Technical Monitor)

    2001-01-01

    Texture advection is an effective tool for animating and investigating 2D flows. In this paper, we discuss how this technique can be extended to 3D flows. In particular, we examine the use of 3D and 4D textures on 3D synthetic and computational fluid dynamics flow fields.

  7. A cryogenic circulating advective multi-pass absorption cell

    NASA Astrophysics Data System (ADS)

    Stockett, M. H.; Lawler, J. E.

    2012-03-01

    A novel absorption cell has been developed to enable a spectroscopic survey of a broad range of polycyclic aromatic hydrocarbons (PAH) under astrophysically relevant conditions and utilizing a synchrotron radiation continuum to test the still controversial hypothesis that these molecules or their ions could be carriers of the diffuse interstellar bands. The cryogenic circulating advective multi-pass absorption cell resembles a wind tunnel; molecules evaporated from a crucible or injected using a custom gas feedthrough are entrained in a laminar flow of cryogenically cooled buffer gas and advected into the path of the synchrotron beam. This system includes a multi-pass optical White cell enabling absorption path lengths of hundreds of meters and a detection sensitivity to molecular densities on the order of 107 cm-3. A capacitively coupled radio frequency dielectric barrier discharge provides ionized and metastable buffer gas atoms for ionizing the candidate molecules via charge exchange and the Penning effect. Stronger than expected clustering of PAH molecules has slowed efforts to record gas phase PAH spectra at cryogenic temperatures, though such clusters may play a role in other interstellar phenomena.

  8. A cryogenic circulating advective multi-pass absorption cell.

    PubMed

    Stockett, M H; Lawler, J E

    2012-03-01

    A novel absorption cell has been developed to enable a spectroscopic survey of a broad range of polycyclic aromatic hydrocarbons (PAH) under astrophysically relevant conditions and utilizing a synchrotron radiation continuum to test the still controversial hypothesis that these molecules or their ions could be carriers of the diffuse interstellar bands. The cryogenic circulating advective multi-pass absorption cell resembles a wind tunnel; molecules evaporated from a crucible or injected using a custom gas feedthrough are entrained in a laminar flow of cryogenically cooled buffer gas and advected into the path of the synchrotron beam. This system includes a multi-pass optical White cell enabling absorption path lengths of hundreds of meters and a detection sensitivity to molecular densities on the order of 10(7) cm(-3). A capacitively coupled radio frequency dielectric barrier discharge provides ionized and metastable buffer gas atoms for ionizing the candidate molecules via charge exchange and the Penning effect. Stronger than expected clustering of PAH molecules has slowed efforts to record gas phase PAH spectra at cryogenic temperatures, though such clusters may play a role in other interstellar phenomena.

  9. A cryogenic circulating advective multi-pass absorption cell

    SciTech Connect

    Stockett, M. H.; Lawler, J. E.

    2012-03-15

    A novel absorption cell has been developed to enable a spectroscopic survey of a broad range of polycyclic aromatic hydrocarbons (PAH) under astrophysically relevant conditions and utilizing a synchrotron radiation continuum to test the still controversial hypothesis that these molecules or their ions could be carriers of the diffuse interstellar bands. The cryogenic circulating advective multi-pass absorption cell resembles a wind tunnel; molecules evaporated from a crucible or injected using a custom gas feedthrough are entrained in a laminar flow of cryogenically cooled buffer gas and advected into the path of the synchrotron beam. This system includes a multi-pass optical White cell enabling absorption path lengths of hundreds of meters and a detection sensitivity to molecular densities on the order of 10{sup 7} cm{sup -3}. A capacitively coupled radio frequency dielectric barrier discharge provides ionized and metastable buffer gas atoms for ionizing the candidate molecules via charge exchange and the Penning effect. Stronger than expected clustering of PAH molecules has slowed efforts to record gas phase PAH spectra at cryogenic temperatures, though such clusters may play a role in other interstellar phenomena.

  10. Anion exchange SPE and liquid chromatography-tandem mass spectrometry in GHB analysis.

    PubMed

    Elian, Albert A; Hackett, Jeffery

    2011-12-01

    In this study, the extraction of γ-hydroxybutyrate (GHB) from urine using solid-phase extraction (SPE) is described. SPE was performed on anion exchange columns after samples of urine had been diluted with de-ionized water. After application of the diluted samples containing GHB-d(6) as an internal standard, the sorbent was washed with deionized water and methanol and dried. The GHB was eluted from the SPE column with a solvent consisting of methanol containing 6% glacial acetic acid. The eluent was collected, evaporated to dryness, and dissolved in mobile phase (100 μL) for analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in negative multiple reaction monitoring (MRM) mode. Liquid chromatography was performed in gradient mode employing a biphenyl column and a mobile phase consisting of acetontitrile (containing 0.1% formic acid) and 0.1% aqueous formic acid. The total run time for each analysis was less than 5 min. The limits of detection/quantification for this method were determined to be 50 and 100 ng/mL, respectively. The method was found to be linear from 500 ng/mL to 10,000 ng/mL (r(2)>0.995). The recovery of GHB was found to be greater than 75%. In this report, results of authentic urine samples analyzed for GHB by this method are presented. GHB concentrations in these samples were found to be range from less than 500 ng/mL to 5110 ng/mL.

  11. Protein structural dynamics at the gas/water interface examined by hydrogen exchange mass spectrometry.

    PubMed

    Xiao, Yiming; Konermann, Lars

    2015-08-01

    Gas/water interfaces (such as air bubbles or foam) are detrimental to the stability of proteins, often causing aggregation. This represents a potential problem for industrial processes, for example, the production and handling of protein drugs. Proteins possess surfactant-like properties, resulting in a high affinity for gas/water interfaces. The tendency of previously buried nonpolar residues to maximize contact with the gas phase can cause significant structural distortion. Most earlier studies in this area employed spectroscopic tools that could only provide limited information. Here we use hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for probing the conformational dynamics of the model protein myoglobin (Mb) in the presence of N(2) bubbles. HDX/MS relies on the principle that unfolded and/or highly dynamic regions undergo faster deuteration than tightly folded segments. In bubble-free solution Mb displays EX2 behavior, reflecting the occurrence of short-lived excursions to partially unfolded conformers. A dramatically different behavior is seen in the presence of N(2) bubbles; EX2 dynamics still take place, but in addition the protein shows EX1 behavior. The latter results from interconversion of the native state with conformers that are globally unfolded and long-lived. These unfolded species likely correspond to Mb that is adsorbed to the surface of gas bubbles. N(2) sparging also induces aggregation. To explain the observed behavior we propose a simple model, that is, "semi-unfolded" ↔ "native" ↔ "globally unfolded" → "aggregated". This model quantitatively reproduces the experimentally observed kinetics. To the best of our knowledge, the current study marks the first exploration of surface denaturation phenomena by HDX/MS.

  12. Protein structural dynamics at the gas/water interface examined by hydrogen exchange mass spectrometry

    PubMed Central

    Xiao, Yiming; Konermann, Lars

    2015-01-01

    Gas/water interfaces (such as air bubbles or foam) are detrimental to the stability of proteins, often causing aggregation. This represents a potential problem for industrial processes, for example, the production and handling of protein drugs. Proteins possess surfactant-like properties, resulting in a high affinity for gas/water interfaces. The tendency of previously buried nonpolar residues to maximize contact with the gas phase can cause significant structural distortion. Most earlier studies in this area employed spectroscopic tools that could only provide limited information. Here we use hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for probing the conformational dynamics of the model protein myoglobin (Mb) in the presence of N2 bubbles. HDX/MS relies on the principle that unfolded and/or highly dynamic regions undergo faster deuteration than tightly folded segments. In bubble-free solution Mb displays EX2 behavior, reflecting the occurrence of short-lived excursions to partially unfolded conformers. A dramatically different behavior is seen in the presence of N2 bubbles; EX2 dynamics still take place, but in addition the protein shows EX1 behavior. The latter results from interconversion of the native state with conformers that are globally unfolded and long-lived. These unfolded species likely correspond to Mb that is adsorbed to the surface of gas bubbles. N2 sparging also induces aggregation. To explain the observed behavior we propose a simple model, that is, “semi-unfolded” ↔ “native” ↔ “globally unfolded” → “aggregated”. This model quantitatively reproduces the experimentally observed kinetics. To the best of our knowledge, the current study marks the first exploration of surface denaturation phenomena by HDX/MS. PMID:25761782

  13. South Atlantic interbasin exchanges of mass, heat, salt and anthropogenic carbon

    NASA Astrophysics Data System (ADS)

    Evans, G. R.; McDonagh, E. L.; King, B. A.; Bryden, H. L.; Bakker, D. C. E.; Brown, P. J.; Schuster, U.; Speer, K. G.; van Heuven, S. M. A. C.

    2017-02-01

    The exchange of mass, heat, salt and anthropogenic carbon (Cant) between the South Atlantic, south of 24°S, and adjacent ocean basins is estimated from hydrographic data obtained during 2008-2009 using an inverse method. Transports of anthropogenic carbon are calculated across the western (Drake Passage), eastern (30°E) and northern (24°S) boundaries. The freshwater overturning transport of 0.09 Sv is southward, consistent with an overturning circulation that exports freshwater from the North Atlantic, and consistent with a bistable Meridional Overturning Circulation (MOC), under conditions of excess freshwater perturbation. At 30°E, net eastward Antarctic Circumpolar Current (ACC) transport, south of the Subtropical Front, is compensated by a 15.9 ± 2.3 Sv westward flow along the Antarctic boundary. The region as a whole is a substantial sink for atmospheric anthropogenic carbon of 0.51 ± 0.37 Pg C yr-1, of which 0.18 ± 0.12 Pg C yr-1 accumulates and is stored within the water column. At 24°S, a 20.2 Sv meridional overturning is associated with a 0.11 Pg C yr-1 Cant overturning. The remainder is transported into the Atlantic Ocean north of 24°S (0.28 ± 0.16 Pg C yr-1) and Indian sector of Southern Ocean (1.12 ± 0.43 Pg C yr-1), having been enhanced by inflow through Drake Passage (1.07 ± 0.44 Pg C yr-1). This underlines the importance of the South Atlantic as a crucial element of the anthropogenic carbon sink in the global oceans.

  14. Mass exchange in an experimental new-generation life support system model based on biological regeneration of environment

    NASA Astrophysics Data System (ADS)

    Tikhomirov, A. A.; Ushakova, S. A.; Manukovsky, N. S.; Lisovsky, G. M.; Kudenko, Yu. A.; Kovalev, V. S.; Gubanov, V. G.; Barkhatov, Yu. V.; Gribovskaya, I. V.; Zolotukhin, I. G.; Gros, J. B.; Lasseur, Ch.

    An experimental model of a biological life support system was used to evaluate qualitative and quantitative parameters of the internal mass exchange. The photosynthesizing unit included the higher plant component (wheat and radish), and the heterotrophic unit consisted of a soil-like substrate, California warms, mushrooms and microbial microflora. The gas mass exchange involved evolution of oxygen by the photosynthesizing component and its uptake by the heterotroph component along with the formation and maintaining of the SLS structure, growth of mushrooms and California worms, human respiration, and some other processes. Human presence in the system in the form of "virtual human" that at regular intervals took part in the respirative gas exchange during the experiment. Experimental data demonstrated good oxygen/carbon dioxide balance, and the closure of the cycles of these gases was almost complete. The water cycle was nearly 100% closed. The main components in the water mass exchange were transpiration water and the watering solution with mineral elements. Human consumption of the edible plant biomass (grains and roots) was simulated by processing these products by a unique physicochemical method of oxidizing them to inorganic mineral compounds, which were then returned into the system and fully assimilated by the plants. The oxidation was achieved by "wet combustion" of organic biomass, using hydrogen peroxide following a special procedure, which does not require high temperature and pressure. Hydrogen peroxide is produced from the water inside the system. The closure of the cycle was estimated for individual elements and compounds. Stoichiometric proportions are given for the main components included in the experimental model of the system. Approaches to the mathematical modeling of the cycling processes are discussed, using the data of the experimental model. Nitrogen, as a representative of biogmic elements, shows an almost 100% closure of the cycle inside

  15. Toward a universal mass-momentum transfer relationship for predicting nutrient uptake and metabolite exchange in benthic reef communities

    NASA Astrophysics Data System (ADS)

    Falter, James L.; Lowe, Ryan J.; Zhang, Zhenlin

    2016-09-01

    Here we synthesize data from previous field and laboratory studies describing how rates of nutrient uptake and metabolite exchange (mass transfer) are related to form drag and bottom stresses (momentum transfer). Reanalysis of this data shows that rates of mass transfer are highly correlated (r2 ≥ 0.9) with the root of the bottom stress (τbot0.4) under both waves and currents and only slightly higher under waves (~10%). The amount of mass transfer that can occur per unit bottom stress (or form drag) is influenced by morphological features ranging anywhere from millimeters to meters in scale; however, surface-scale roughness (millimeters) appears to have little effect on actual nutrient uptake by living reef communities. Although field measurements of nutrient uptake by natural reef communities agree reasonably well with predictions based on existing mass-momentum transfer relationships, more work is needed to better constrain these relationships for more rugose and morphologically complex communities.

  16. Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry.

    PubMed

    Englander, Joan J; Del Mar, Charyl; Li, Will; Englander, S Walter; Kim, Jack S; Stranz, David D; Hamuro, Yoshitomo; Woods, Virgil L

    2003-06-10

    An automated high-throughput, high-resolution deuterium exchange HPLC-MS method (DXMS) was used to extend previous hydrogen exchange studies on the position and energetic role of regulatory structure changes in hemoglobin. The results match earlier highly accurate but much more limited tritium exchange results, extend the analysis to the entire sequence of both hemoglobin subunits, and identify some energetically important changes. Allosterically sensitive amide hydrogens located at near amino acid resolution help to confirm the reality of local unfolding reactions and their use to evaluate resolved structure changes in terms of allosteric free energy.

  17. Capillary deposition of advected floating particles

    NASA Astrophysics Data System (ADS)

    Dressaire, Emilie; Debaisieux, Aymeric; Gregori, Federico

    2016-11-01

    The deposition and aggregation of particles flowing through a confined environment can dramatically hinder the transport of suspensions. Yet, the mechanisms responsible for the deposition of particles in shear flow are not fully understood. Here, we use an experimental model system in which floating particles are advected on the surface of a water channel and deposited on fixed obstacles through attractive capillary effects. By varying the flow rate of the liquid, the wetting properties and size of the particles and obstacles, we can tune the magnitude of the capillary and hydrodynamic forces that determine the probability of deposition and the equilibrium position on the substrate. We show that arrays of obstacles can be designed to efficiently capture the floating particles advected by the flow.

  18. Distributed Parallel Particle Advection using Work Requesting

    SciTech Connect

    Muller, Cornelius; Camp, David; Hentschel, Bernd; Garth, Christoph

    2013-09-30

    Particle advection is an important vector field visualization technique that is difficult to apply to very large data sets in a distributed setting due to scalability limitations in existing algorithms. In this paper, we report on several experiments using work requesting dynamic scheduling which achieves balanced work distribution on arbitrary problems with minimal communication overhead. We present a corresponding prototype implementation, provide and analyze benchmark results, and compare our results to an existing algorithm.

  19. Circulation pattern and ice mass exchange for different water compositions in Lake Vostok, Antarctica

    NASA Astrophysics Data System (ADS)

    Mayer, C.; Grosfeld, K.; Siegert, M. J.

    2003-04-01

    Lake Vostok, Antarctica's largest known subglacial lake, isolated from direct exchange with the atmosphere or oceans for several million years due to its thick ice cover, provides a unique and so far inaccessible habitat. By implementing the newest available information about the lake geometry into a 3-dimensional fluid-dynamics model the lake circulation was investigated for different water compositions. In the case of fresh water, thermally driven circulation is predicted, as a result of the pressure-dependent melting point at the inclined ice-water interface, in agreement with other investigators. Ice pumping from north to south provides a steady supply of glacial water to the lake, whereby no unsusual geothermal conditions are required for maintaining the circulation and the melting/refreezing balance. The rather weak circulation is driven by very small, temperature determined, density contrasts between the resident lake water and the fresh melt water. The circulation pattern, however, is determined by the strongly structured trough geometry of the lake. For slightly saline water conditions, the circulation pattern is also influenced by the salinity impact on the equation of state and hence on the lake density. This results in a partly increased flow but influences the turnover time scale not significantly. Now, the freshwater flux due to melting of glacial ice stabilizes the stratification of the lake leading to a more pronounced temperature gradient over the water column. Colder water now overrides warmer water portions near bottom, which to a certain degree isolates the resident water mass from the circulation driven by meltig and freezing. In either saline or fresh water conditions approximately 200 m of refrozen ice accumulates beneath Vostok Station, which suggests either possibility is plausible under the current state of knowledge regarding the lake cavity and the hydrochemnistry. Our model results, however, show that the habitat of Lake Vostok will be

  20. High Order Semi-Lagrangian Advection Scheme

    NASA Astrophysics Data System (ADS)

    Malaga, Carlos; Mandujano, Francisco; Becerra, Julian

    2014-11-01

    In most fluid phenomena, advection plays an important roll. A numerical scheme capable of making quantitative predictions and simulations must compute correctly the advection terms appearing in the equations governing fluid flow. Here we present a high order forward semi-Lagrangian numerical scheme specifically tailored to compute material derivatives. The scheme relies on the geometrical interpretation of material derivatives to compute the time evolution of fields on grids that deform with the material fluid domain, an interpolating procedure of arbitrary order that preserves the moments of the interpolated distributions, and a nonlinear mapping strategy to perform interpolations between undeformed and deformed grids. Additionally, a discontinuity criterion was implemented to deal with discontinuous fields and shocks. Tests of pure advection, shock formation and nonlinear phenomena are presented to show performance and convergence of the scheme. The high computational cost is considerably reduced when implemented on massively parallel architectures found in graphic cards. The authors acknowledge funding from Fondo Sectorial CONACYT-SENER Grant Number 42536 (DGAJ-SPI-34-170412-217).

  1. Correlation Networks from Flows. The Case of Forced and Time-Dependent Advection-Diffusion Dynamics.

    PubMed

    Tupikina, Liubov; Molkenthin, Nora; López, Cristóbal; Hernández-García, Emilio; Marwan, Norbert; Kurths, Jürgen

    2016-01-01

    Complex network theory provides an elegant and powerful framework to statistically investigate different types of systems such as society, brain or the structure of local and long-range dynamical interrelationships in the climate system. Network links in climate networks typically imply information, mass or energy exchange. However, the specific connection between oceanic or atmospheric flows and the climate network's structure is still unclear. We propose a theoretical approach for verifying relations between the correlation matrix and the climate network measures, generalizing previous studies and overcoming the restriction to stationary flows. Our methods are developed for correlations of a scalar quantity (temperature, for example) which satisfies an advection-diffusion dynamics in the presence of forcing and dissipation. Our approach reveals that correlation networks are not sensitive to steady sources and sinks and the profound impact of the signal decay rate on the network topology. We illustrate our results with calculations of degree and clustering for a meandering flow resembling a geophysical ocean jet.

  2. Correlation Networks from Flows. The Case of Forced and Time-Dependent Advection-Diffusion Dynamics

    PubMed Central

    Tupikina, Liubov; Molkenthin, Nora; López, Cristóbal; Hernández-García, Emilio; Marwan, Norbert; Kurths, Jürgen

    2016-01-01

    Complex network theory provides an elegant and powerful framework to statistically investigate different types of systems such as society, brain or the structure of local and long-range dynamical interrelationships in the climate system. Network links in climate networks typically imply information, mass or energy exchange. However, the specific connection between oceanic or atmospheric flows and the climate network’s structure is still unclear. We propose a theoretical approach for verifying relations between the correlation matrix and the climate network measures, generalizing previous studies and overcoming the restriction to stationary flows. Our methods are developed for correlations of a scalar quantity (temperature, for example) which satisfies an advection-diffusion dynamics in the presence of forcing and dissipation. Our approach reveals that correlation networks are not sensitive to steady sources and sinks and the profound impact of the signal decay rate on the network topology. We illustrate our results with calculations of degree and clustering for a meandering flow resembling a geophysical ocean jet. PMID:27128846

  3. Determination of mu-oxo exchange rates in di-mu-oxo dimanganese complexes by electrospray ionization mass spectrometry.

    PubMed

    Tagore, Ranitendranath; Chen, Hongyu; Crabtree, Robert H; Brudvig, Gary W

    2006-07-26

    A time-resolved mass spectrometric technique has been used for the determination of rates of exchange of mu-O atoms with water for the complexes [(mes-terpy)2Mn2(III/IV)(mu-O)2(H2O)2](NO3)3 (1, mes-terpy = 4'-mesityl-2,2':6',2' '-terpyridine), [(bpy)4Mn2(III/IV)(mu-O)2](ClO4)3 (2, bpy = 2,2'-bipyridine), [(phen)4Mn2(III/IV)(mu-O)2](ClO4)3 (3, phen = 1,10-phenanthroline), [(bpea)2Mn2(III/IV)(mu-O)2(mu-OAc)](ClO4)2 (4, bpea = bis(2-pyridyl)ethylamine), [(bpea)2Mn2(IV/IV)(mu-O)2(mu-OAc)](ClO4)3 (4ox), [(terpy)4Mn4(IV/IV/IV/IV)(mu-O)5(H2O)2](ClO4)6 (5, terpy = 2,2':6',2''-terpyridine), and [(tacn)4Mn4(IV/IV/IV/IV)(mu-O)6]Br(3.5)(OH)0.5.6H2O (6, tacn = 1,4,7-triazacyclononane). The rate of exchange of mu-OAc bridges with free acetate in solution has been measured for complexes 4 and 4ox. These are the first measurements of rates of ligand exchange on biologically relevant high-valent Mn complexes. The data analysis method developed here is of general utility in the quantitation of isotope exchange processes by mass spectrometry. We find that the presence of labile coordination sites on Mn increases mu-O exchange rates, and that all-Mn(IV) states are more inert toward exchange than mixed Mn(III)-Mn(IV) states. The rates of mu-O exchange obtained in this work for a di-mu-oxo Mn2(III/IV) dimer with labile coordination sites are compared with the oxygen isotope incorporation rates from substrate water to evolved dioxygen measured in different S states of the oxygen evolving complex (OEC) of photosystem II (PSII). On the basis of this comparison, we propose that both substrate waters are not bound as mu-O bridges between Mn atoms in the S2 and S3 states of the OEC.

  4. Regulation of phenylalanine hydroxylase: conformational changes upon phenylalanine binding detected by hydrogen/deuterium exchange and mass spectrometry.

    PubMed

    Li, Jun; Dangott, Lawrence J; Fitzpatrick, Paul F

    2010-04-20

    Phenylalanine acts as an allosteric activator of the tetrahydropterin-dependent enzyme phenylalanine hydroxylase. Hydrogen/deuterium exchange monitored by mass spectrometry has been used to gain insight into local conformational changes accompanying activation of rat phenylalanine hydroxylase by phenylalanine. Peptides in the regulatory and catalytic domains that lie in the interface between these two domains show large increases in the extent of deuterium incorporation from solvent in the presence of phenylalanine. In contrast, the effects of phenylalanine on the exchange kinetics of a mutant enzyme lacking the regulatory domain are limited to peptides surrounding the binding site for the amino acid substrate. These results support a model in which the N-terminus of the protein acts as an inhibitory peptide, with phenylalanine binding causing a conformational change in the regulatory domain that alters the interaction between the catalytic and regulatory domains.

  5. U/Th dating by SHRIMP RG ion-microprobe mass spectrometry using single ion-exchange beads

    USGS Publications Warehouse

    Bischoff, J.L.; Wooden, J.; Murphy, F.; Williams, Ross W.

    2005-01-01

    We present a new analytical method for U-series isotopes using the SHRIMP RG (Sensitive High mass Resolution Ion MicroProbe) mass spectrometer that utilizes the preconcentration of the U-series isotopes from a sample onto a single ion-exchange bead. Ion-microprobe mass spectrometry is capable of producing Th ionization efficiencies in excess of 2%. Analytical precision is typically better than alpha spectroscopy, but not as good as thermal ionization mass spectroscopy (TIMS) and inductively coupled plasma multicollector mass spectrometry (ICP-MS). Like TIMS and ICP-MS the method allows analysis of small samples sizes, but also adds the advantage of rapidity of analysis. A major advantage of ion-microprobe analysis is that U and Th isotopes are analyzed in the same bead, simplifying the process of chemical separation. Analytical time on the instrument is ???60 min per sample, and a single instrument-loading can accommodate 15-20 samples to be analyzed in a 24-h day. An additional advantage is that the method allows multiple reanalyses of the same bead and that samples can be archived for reanalysis at a later time. Because the ion beam excavates a pit only a few ??m deep, the mount can later be repolished and reanalyzed numerous times. The method described of preconcentrating a low concentration sample onto a small conductive substrate to allow ion-microprobe mass spectrometry is potentially applicable to many other systems. Copyright ?? 2005 Elsevier Ltd.

  6. Modeling of Convective-Stratiform Precipitation Processes: Sensitivity to Partitioning Methods and Numerical Advection Schemes

    NASA Technical Reports Server (NTRS)

    Lang, Steve; Tao, W.-K.; Simpson, J.; Ferrier, B.; Einaudi, Franco (Technical Monitor)

    2001-01-01

    Six different convective-stratiform separation techniques, including a new technique that utilizes the ratio of vertical and terminal velocities, are compared and evaluated using two-dimensional numerical simulations of a tropical [Tropical Ocean Global Atmosphere Coupled Ocean-Atmosphere Response Experiment (TOGA COARE)] and midlatitude continental [Preliminary Regional Experiment for STORM-Central (PRESTORM)] squall line. The simulations are made using two different numerical advection schemes: 4th order and positive definite advection. Comparisons are made in terms of rainfall, cloud coverage, mass fluxes, apparent heating and moistening, mean hydrometeor profiles, CFADs (Contoured Frequency with Altitude Diagrams), microphysics, and latent heating retrieval. Overall, it was found that the different separation techniques produced results that qualitatively agreed. However, the quantitative differences were significant. Observational comparisons were unable to conclusively evaluate the performance of the techniques. Latent heating retrieval was shown to be sensitive to the use of separation technique mainly due to the stratiform region for methods that found very little stratiform rain. The midlatitude PRESTORM simulation was found to be nearly invariant with respect to advection type for most quantities while for TOGA COARE fourth order advection produced numerous shallow convective cores and positive definite advection fewer cells that were both broader and deeper penetrating above the freezing level.

  7. Deuterium Exchange in Ethyl Acetoacetate: An Undergraduate GC-MS [Gas Chromatography-Mass Spectroscopy] Experiment

    ERIC Educational Resources Information Center

    Heinson, C. D.; Williams, J. M.; Tinnerman, W. N.; Malloy, T. B.

    2005-01-01

    The role of ethanol O-d in nullifying the deuterolysis may be demonstrated by determining that transesterification of methyl acetoacetate of the ethyl ester occurs as well as deuterium exchange of the five acetoacetate hydrogens. The significant acidity of the methylene protons in the acetoacetate group, the efficacy of base catalysis, the role of…

  8. PEM (Proton exchange membrane) fuel cell stack heat and mass measurement

    SciTech Connect

    Vanderborgh, N.E.; Kimble, M.C.; Huff, J.R.; Hedstrom, J.C.

    1992-01-01

    PEM stacks are under evaluation as candidates for future space power technology. Results of long-term operation on a set of contemporary stacks fitted with different proton exchange membrane materials are given. Data on water balances show effects of membrane materials on stack performance. 15 refs.

  9. Characterization of IgG1 Conformation and Conformational Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry

    SciTech Connect

    Houde, Damian; Arndt, Joseph; Domeier, Wayne; Berkowitz, Steven; Engen, John R.

    2009-04-22

    Protein function is dictated by protein conformation. For the protein biopharmaceutical industry, therefore, it is important to have analytical tools that can detect changes in protein conformation rapidly, accurately, and with high sensitivity. In this paper we show that hydrogen/deuterium exchange mass spectrometry (H/DX-MS) can play an important role in fulfilling this need within the industry. H/DX-MS was used to assess both global and local conformational behavior of a recombinant monoclonal IgG1 antibody, a major class of biopharmaceuticals. Analysis of exchange into the intact, glycosylated IgG1 (and the Fab and Fc regions thereof) showed that the molecule was folded, highly stable, and highly amenable to analysis by this method using less than a nanomole of material. With improved chromatographic methods, peptide identification algorithms and data-processing steps, the analysis of deuterium levels in peptic peptides produced after labeling was accomplished in 1--2 days. On the basis of peptic peptide data, exchange was localized to specific regions of the antibody. Changes to IgG1 conformation as a result of deglycosylation were determined by comparing exchange into the glycosylated and deglycosylated forms of the antibody. Two regions of the IgG1 (residues 236-253 and 292-308) were found to have altered exchange properties upon deglycosylation. These results are consistent with previous findings concerning the role of glycosylation in the interaction of IgG1 with Fc receptors. Moreover, the data clearly illustrate how H/DX-MS can provide important characterization information on the higher order structure of antibodies and conformational changes that these molecules may experience upon modification.

  10. Regulation of phenylalanine hydroxylase: conformational changes upon phosphorylation detected by H/D exchange and mass spectrometry.

    PubMed

    Li, Jun; Fitzpatrick, Paul F

    2013-07-15

    The enzyme phenylalanine hydroxylase catalyzes the hydroxylation of excess phenylalanine in the liver to tyrosine. The enzyme is regulated allosterically by phenylalanine and by phosphorylation of Ser16. Hydrogen/deuterium exchange monitored by mass spectrometry has been used to gain insight into any structural change upon phosphorylation. Peptides in both the catalytic and regulatory domains show increased deuterium incorporation into the phosphorylated protein. Deuterium is incorporated into fewer peptides than when the enzyme is activated by phenylalanine, and the incorporation is slower. This establishes that the conformational change upon phosphorylation of phenylalanine hydroxylase is different from and less extensive than that upon phenylalanine activation.

  11. Characterization of Aggregation Propensity of a Human Fc-Fusion Protein Therapeutic by Hydrogen/Deuterium Exchange Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Huang, Richard Y.-C.; Iacob, Roxana E.; Krystek, Stanley R.; Jin, Mi; Wei, Hui; Tao, Li; Das, Tapan K.; Tymiak, Adrienne A.; Engen, John R.; Chen, Guodong

    2016-08-01

    Aggregation of protein therapeutics has long been a concern across different stages of manufacturing processes in the biopharmaceutical industry. It is often indicative of aberrant protein therapeutic higher-order structure. In this study, the aggregation propensity of a human Fc-fusion protein therapeutic was characterized. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) was applied to examine the conformational dynamics of dimers collected from a bioreactor. HDX-MS data combined with spatial aggregation propensity calculations revealed a potential aggregation interface in the Fc domain. This study provides a general strategy for the characterization of the aggregation propensity of Fc-fusion proteins at the molecular level.

  12. A computational method for sharp interface advection

    PubMed Central

    Bredmose, Henrik; Jasak, Hrvoje

    2016-01-01

    We devise a numerical method for passive advection of a surface, such as the interface between two incompressible fluids, across a computational mesh. The method is called isoAdvector, and is developed for general meshes consisting of arbitrary polyhedral cells. The algorithm is based on the volume of fluid (VOF) idea of calculating the volume of one of the fluids transported across the mesh faces during a time step. The novelty of the isoAdvector concept consists of two parts. First, we exploit an isosurface concept for modelling the interface inside cells in a geometric surface reconstruction step. Second, from the reconstructed surface, we model the motion of the face–interface intersection line for a general polygonal face to obtain the time evolution within a time step of the submerged face area. Integrating this submerged area over the time step leads to an accurate estimate for the total volume of fluid transported across the face. The method was tested on simple two-dimensional and three-dimensional interface advection problems on both structured and unstructured meshes. The results are very satisfactory in terms of volume conservation, boundedness, surface sharpness and efficiency. The isoAdvector method was implemented as an OpenFOAM® extension and is published as open source. PMID:28018619

  13. Striated populations in disordered environments with advection

    NASA Astrophysics Data System (ADS)

    Chotibut, Thiparat; Nelson, David R.; Succi, Sauro

    2017-01-01

    Growth in static and controlled environments such as a Petri dish can be used to study the spatial population dynamics of microorganisms. However, natural populations such as marine microbes experience fluid advection and often grow up in heterogeneous environments. We investigate a generalized Fisher-Kolmogorov-Petrovsky-Piscounov (FKPP) equation describing single species population subject to a constant flow field and quenched random spatially inhomogeneous growth rates with a fertile overall growth condition. We analytically and numerically demonstrate that the non-equilibrium steady-state population density develops a flow-driven striation pattern. The striations are highly asymmetric with a longitudinal correlation length that diverges linearly with the flow speed and a transverse correlation length that approaches a finite velocity-independent value. Linear response theory is developed to study the statistics of the steady states. Theoretical predictions show excellent agreement with the numerical steady states of the generalized FKPP equation obtained from Lattice Boltzmann simulations. These findings suggest that, although the growth disorder can be spatially uncorrelated, correlated population structures with striations emerge naturally at sufficiently strong advection.

  14. Waves, advection, and cloud patterns on Venus

    NASA Technical Reports Server (NTRS)

    Schinder, Paul J.; Gierasch, Peter J.; Leroy, Stephen S.; Smith, Michael D.

    1990-01-01

    The stable layers adjacent to the nearly neutral layer within the Venus clouds are found to be capable of supporting vertically trapped, horizontally propagating waves with horizontal wavelengths of about 10 km and speeds of a few meters per second relative to the mean wind in the neutral layer. These waves may possibly be excited by turbulence within the neutral layer. Here, the properties of the waves, and the patterns which they might produce within the visible clouds if excited near the subsolar point are examined. The patterns can be in agreement with many features in images. The waves are capable of transferring momentum latitudinally to help maintain the general atmospheric spin, but at present we are not able to evaluate wave amplitudes. We also examine an alternative possibility that the cloud patterns are produced by advection and shearing by the mean zonal and meridional flow of blobs formed near the equator. It is concluded that advection and shearing by the mean flow is the most likely explanation for the general pattern of small scale striations.

  15. Parallel algorithms for semi-lagrangian advection

    NASA Astrophysics Data System (ADS)

    Malevsky, A. V.; Thomas, S. J.

    1997-08-01

    Numerical time step limitations associated with the explicit treatment of advection-dominated problems in computational fluid dynamics are often relaxed by employing Eulerian-Lagrangian methods. These are also known as semi-Lagrangian methods in the atmospheric sciences. Such methods involve backward time integration of a characteristic equation to find the departure point of a fluid particle arriving at a Eulerian grid point. The value of the advected field at the departure point is obtained by interpolation. Both the trajectory integration and repeated interpolation influence accuracy. We compare the accuracy and performance of interpolation schemes based on piecewise cubic polynomials and cubic B-splines in the context of a distributed memory, parallel computing environment. The computational cost and interprocessor communication requirements for both methods are reported. Spline interpolation has better conservation properties but requires the solution of a global linear system, initially appearing to hinder a distributed memory implementation. The proposed parallel algorithm for multidimensional spline interpolation has almost the same communication overhead as local piecewise polynomial interpolation. We also compare various techniques for tracking trajectories given different values for the Courant number. Large Courant numbers require a high-order ODE solver involving multiple interpolations of the velocity field.

  16. Characterization of intact protein conjugates and biopharmaceuticals using ion-exchange chromatography with online detection by native electrospray ionization mass spectrometry and top-down tandem mass spectrometry.

    PubMed

    Muneeruddin, Khaja; Nazzaro, Mark; Kaltashov, Igor A

    2015-10-06

    Characterization of biopharmaceutical products is a challenging task, which needs to be carried out at several different levels (including both primary structure and conformation). An additional difficulty frequently arises due to the structural heterogeneity inherent to many protein-based therapeutics (e.g., extensive glycosylation or "designer" modifications such as chemical conjugation) or introduced postproduction as a result of stress (e.g., oxidation and deamidation). A combination of ion-exchange chromatography (IXC) with online detection by native electrospray ionization mass spectrometry (ESI MS) allows characterization of complex and heterogeneous therapeutic proteins and protein conjugates to be accomplished at a variety of levels without compromising their conformational integrity. The IXC/ESI MS measurements allow protein conjugates to be profiled by analyzing conjugation stoichiometry and the presence of multiple positional isomers, as well as to establish the effect of chemical modifications on the conformational integrity of each species. While mass profiling alone is not sufficient for identification of nonenzymatic post-translational modifications (PTMs) that result in a very small mass change of the eluting species (e.g., deamidation), this task can be completed using online top-down structural analysis, as demonstrated using stressed interferon-β as an example. The wealth of information that can be provided by IXC/native ESI MS and tandem mass spectrometry (MS/MS) on protein-based therapeutics will undoubtedly make it a very valuable addition to the experimental toolbox of biopharmaceutical analysis.

  17. Fluid flow through seamounts and implications for global mass fluxes

    NASA Astrophysics Data System (ADS)

    Harris, Robert N.; Fisher, Andrew T.; Chapman, David S.

    2004-08-01

    Seamounts contribute to globally significant hydrothermal fluxes, but the dynamics and impacts of fluid flow through these features are poorly understood. Numerical models of coupled heat and fluid flow illustrate how seamounts induce local convection in the oceanic crust. We consider idealized axisymmetric seamounts and calculate mass and heat fluxes by using a coupled heat- and fluid-flow model. By using P. Wessel's global database of ˜15,000 seamounts identified through satellite gravimetry, we estimate that the mass flux associated with seamounts is ˜1014 kg/yr, a number comparable to estimated regional mass fluxes through mid-ocean ridges and flanks. In addition, the seamount-generated advective heat flux may be locally significant well beyond the 65 Ma average age at which advective lithospheric heat loss on ridge flanks ends. These flows may be important for facilitating geochemical exchange between the crust and ocean and may affect subseafloor microbial ecosystems.

  18. Hydrogen Exchange Mass Spectrometry of Related Proteins with Divergent Sequences: A Comparative Study of HIV-1 Nef Allelic Variants

    NASA Astrophysics Data System (ADS)

    Wales, Thomas E.; Poe, Jerrod A.; Emert-Sedlak, Lori; Morgan, Christopher R.; Smithgall, Thomas E.; Engen, John R.

    2016-06-01

    Hydrogen exchange mass spectrometry can be used to compare the conformation and dynamics of proteins that are similar in tertiary structure. If relative deuterium levels are measured, differences in sequence, deuterium forward- and back-exchange, peptide retention time, and protease digestion patterns all complicate the data analysis. We illustrate what can be learned from such data sets by analyzing five variants (Consensus G2E, SF2, NL4-3, ELI, and LTNP4) of the HIV-1 Nef protein, both alone and when bound to the human Hck SH3 domain. Regions with similar sequence could be compared between variants. Although much of the hydrogen exchange features were preserved across the five proteins, the kinetics of Nef binding to Hck SH3 were not the same. These observations may be related to biological function, particularly for ELI Nef where we also observed an impaired ability to downregulate CD4 surface presentation. The data illustrate some of the caveats that must be considered for comparison experiments and provide a framework for investigations of other protein relatives, families, and superfamilies with HX MS.

  19. Inclusion of human mineralized exometabolites and fish wastes as a source of higher plant mineral nutrition in BTLSS mass exchange

    NASA Astrophysics Data System (ADS)

    Tikhomirova, Natalia; Tikhomirov, Alexander A.; Ushakova, Sofya; Anischenko, Olesya; Trifonov, Sergey V.

    Human exometabolites inclusion into an intrasystem mass exchange will allow increasing of a closure level of a biological-technical life support system (BTLSS). Previously at the IBP SB RAS it was shown that human mineralized exometabolites could be incorporated in the BTLSS mass exchange as a mineral nutrition source for higher plants. However, it is not known how that combined use of human mineralized exometabolites and fish wastes in the capacity of nutrient medium, being a part of the BTLSS consumer wastes, will affect the plant productivity. Several wheat vegetations were grown in an uneven-aged conveyor on a neutral substrate. A mixture of human mineralized exometabolites and fish wastes was used as a nutrient solution in the experiment treatment and human mineralized exometabolites were used in the control. Consequently, a high wheat yield in the experiment treatment practically equal to the control yield was obtained. Thus, mineralized fish wastes can be an additional source of macro-and micronutrients for plants, and use of such wastes for the plant mineral nutrition allows increasing of BTLSS closure level.

  20. A critical review of period analyses and implications for mass exchange in W UMa eclipsing binaries: Part 2

    NASA Astrophysics Data System (ADS)

    Nelson, R. H.; Terrell, D.; Milone, E. F.

    2015-12-01

    This is the second of a series of four papers, the goal of which is to identify the overcontact eclipsing binary star systems for which a solid case can be made for mass exchange. To reach this goal, it is necessary first to identify those systems for which there is a strong case for period change. We have identified 60 candidate systems; in the first paper (Nelson et al., 2014) we discussed 20 individual cases; this paper continues with the next 20. For each system, we present a detailed discussion and evaluation concerning the observational and interpretive material presented in the literature. An eclipse timing (ET) diagram (or diagrams), commonly referred to as an "O-C diagram", that includes the latest available data accompanies each discussion. In paper 4, we will discuss the mechanisms that can effect period change and which of the 60 systems can be reliably concluded to exhibit mass exchange; we will also provide a list of marginal and rejected cases suitable for future work.

  1. A critical review of period analyses and implications for mass exchange in W UMa eclipsing binaries: Paper 3

    NASA Astrophysics Data System (ADS)

    Nelson, R. H.; Terrell, D.; Milone, E. F.

    2016-02-01

    This is the third of a series of four papers, the goal of which is to identify the overcontact eclipsing binary star systems for which a solid case can be made for mass exchange. To reach this goal, it is necessary first to identify those systems for which there is a strong case for period change. We have identified 60 candidate systems; in the first two papers (Nelson et al. 2014, 2016) we discussed 40 individual cases; this paper continues with the last 20. For each system, we present a detailed discussion and evaluation concerning the observational and interpretive material presented in the literature. At least one eclipse timing (ET) diagram, commonly referred to as an "O-C diagram", that includes the latest available data, accompanies each discussion. In paper 4, we will discuss the mechanisms that can cause period change and which of the 60 systems can be reliably concluded to exhibit mass exchange; we will also provide a list of marginal and rejected cases - suitable for future work.

  2. Protein Structure-Function Correlation in Living Human Red Blood Cells Probed by Isotope Exchange-based Mass Spectrometry.

    PubMed

    Narayanan, Sreekala; Mitra, Gopa; Muralidharan, Monita; Mathew, Boby; Mandal, Amit K

    2015-12-01

    To gain insight into the underlying mechanisms of various biological events, it is important to study the structure-function correlation of proteins within cells. Structural probes used in spectroscopic tools to investigate protein conformation are similar across all proteins. Therefore, structural studies are restricted to purified proteins in vitro and these findings are extrapolated in cells to correlate their functions in vivo. However, due to cellular complexity, in vivo and in vitro environments are radically different. Here, we show a novel way to monitor the structural transition of human hemoglobin upon oxygen binding in living red blood cells (RBCs), using hydrogen/deuterium exchange-based mass spectrometry (H/DX-MS). Exploiting permeability of D2O across cell membrane, the isotope exchange of polypeptide backbone amide hydrogens of hemoglobin was carried out inside RBCs and monitored using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). To explore the conformational transition associated with oxygenation of hemoglobin in vivo, the isotope exchange kinetics was simplified using the method of initial rates. RBC might be considered as an in vivo system of pure hemoglobin. Thus, as a proof-of-concept, the observed results were correlated with structural transition of hemoglobin associated with its function established in vitro. This is the first report on structural changes of a protein upon ligand binding in its endogenous environment. The proposed method might be applicable to proteins in their native state, irrespective of location, concentration, and size. The present in-cell approach opens a new avenue to unravel a plethora of biological processes like ligand binding, folding, and post-translational modification of proteins in living cells.

  3. Modeling of water masses exchange between Brepolen and the main fjord in the Western Svalbard fjord - Hornsund

    NASA Astrophysics Data System (ADS)

    Jakacki, Jaromir; Przyborska, Anna; Sunfjord, Arild; Albertsen, Jon; Białoskórski, Michał; Pliszka, Bartosz

    2016-04-01

    Hornsund is the southernmost fjord of the Svalbard archipelago island - Spitsbergen. It is under the influence of two main currents - the coastal Sørkapp Current (SC) carrying fresher and colder water masses from the Barents Sea and the West Spitsbergen Current (WSC), which is the branch of the Norwegian Atlantic Current (NwAC) and carries warm and salty waters from the North Atlantic. The main local forcing, which is tidal motion, brings shelf waters into the central fjord basin and then the transformed masses are carried into the easternmost part of the fjord, Brepolen. For the purpose of studying circulation and water exchange in this area a three-dimensional hydrodynamic model has been implemented and validated. The model is based on MIKE by DHI product and covers the Hornsund fjord with the shelf area, which is the fjord foreground. It is sigma a coordinate model (in our case 35 vertical levels) with variable horizontal resolution (mesh grid). The smallest cell has a horizontal dimension less than one hundred meters and the largest cells about 5 km. In spite of model limitations, the model reproduces the main circulation and water pathways in the Brepolen area. Seasonal and annual volume, heat and salt exchanges have been also estimated. The influence of freshwater discharge on shelf-fjord exchange will be also analyzed. The model results allow to study full horizontal and vertical fields of physical parameters (temperature, salinity, sea level variations and currents). The model integration covers only years 2005-2010 and the presented results will be based on this simulation. The project has been financed from the funds of the Leading National Research Centre (KNOW) received by the Centre for Polar Studies for the period 2014-2018

  4. Fragmentation of mycosporine-like amino acids by hydrogen/deuterium exchange and electrospray ionisation tandem mass spectrometry.

    PubMed

    Cardozo, Karina H M; Carvalho, Valdemir M; Pinto, Ernani; Colepicolo, Pio

    2006-01-01

    The determination and identification of mycosporine-like amino acids (MAAs) from algae remain a major challenge due to the low concentration. Mass spectrometry (MS) can make an invaluable contribution in the search and identification of MAAs because of its high sensitivity, possibility of coupling with liquid chromatography, and the availability of powerful tandem mass spectrometric techniques. However, the unequivocal determination of the presence and location of important functional groups present on the basic skeleton of the MAAs is often elusive due to their inherent instability under MS conditions. In this study, the use of hydrogen/deuterium (H/D) exchange and electrospray ionisation tandem mass spectrometry (ESI-MS/MS) for characterisation of four MAAs (palythine, asterina, palythinol and shinorine) isolated from the macroalgae Gracilaria tenuistipitata Chang et Xia was investigated. The accurate-mass confirmation of the protonated molecules was performed on a Q-TOF instrument. We demonstrate that employing deuterium labelling in ESI-MS/MS analysis provides a convenient tool for the determination of new MAAs. Although the fragmentation patterns of MAAs were discussed earlier, to our knowledge, this is the first time that mechanisms are proposed.

  5. Fractures as Advective Conduits at the Earth Atmosphere Interface

    NASA Astrophysics Data System (ADS)

    Dragila, M. I.; Weisbrod, N.; Nachshon, U.; Kamai, T.

    2012-12-01

    Understanding gas exchange between the Earth's upper crust and the atmosphere is vital and necessary because this phenomenon controls to a large extent many important processes including, the water cycle, agricultural activities, greenhouse gas emissions and more. From a hydrological aspect, water vapor transport is an extremely important process related to Earth-atmosphere gas exchange because it affects above ground water vapor concentration, soil water content and soil salinity. Traditionally, diffusion was considered the main mechanism of gas exchange between the atmosphere and vadose zone, driven by gas concentration gradients. While this assumption may be correct for many porous media, our laboratory and field-scale studies have shown that advective gas transport mechanisms are governing these fluxes in fractured rocks and cracked soils. Convection driven by thermal gradients (free convection) and wind induced (forced convection) were explored and both were found to play a major role in Earth-atmosphere gas exchange. Long-term laboratory experiments using fracture simulators in a customized climate controlled laboratory have shown that thermal convection occurs when nighttime thermal conditions prevail. This convective venting significantly enhances evaporation and subsequently salt precipitation on the fracture walls. Experiment results were used to develop an empirical relationship between temperature gradients, fracture aperture and convective gas flux through the fracture. Theoretical calculations show that thermal convection is indeed likely to play a major role in evaporation from fractures and can explain enhanced salt accumulation observed in surface-exposed fractures. Long-term field measurements, carried out continuously for 5+ years in a single fracture in the Israeli Negev Desert, verified the development of air convection cycles of 10-18 hours duration on a daily basis, with a peak in both convective flux and duration during the winter. During

  6. BUOYANT ADVECTION OF GASES IN UNSATURATED SOIL

    PubMed Central

    Seely, Gregory E.; Falta, Ronald W.; Hunt, James R.

    2010-01-01

    In unsaturated soil, methane and volatile organic compounds can significantly alter the density of soil gas and induce buoyant gas flow. A series of laboratory experiments was conducted in a two-dimensional, homogeneous sand pack with gas permeabilities ranging from 110 to 3,000 darcy. Pure methane gas was injected horizontally into the sand and steady-state methane profiles were measured. Experimental results are in close agreement with a numerical model that represents the advective and diffusive components of methane transport. Comparison of simulations with and without gravitational acceleration permits identification of conditions where buoyancy dominates methane transport. Significant buoyant flow requires a Rayleigh number greater than 10 and an injected gas velocity sufficient to overcome dilution by molecular diffusion near the source. These criteria allow the extension of laboratory results to idealized field conditions for methane as well as denser-than-air vapors produced by volatilizing nonaqueous phase liquids trapped in unsaturated soil. PMID:20396624

  7. GEMS (Gravity Electro-Magnetism Strong) SU(5) Theory and The Prediction of Exchange Boson Masses

    NASA Astrophysics Data System (ADS)

    Brandenburg, John

    2012-10-01

    The GEMS SU(5) [1] theory includes short range Nuclear Forces in the GEM unification theory [2], where the importance of the square root of the proton-electron mass ratio: σ = 42.8503 was found. The creation of mass by a Higgs field coupling must, by the Equivalence Principle, be viewed in the context of General Relativity. This is done here using Kaluza-Klein theory in a Feynman-Hawkings path integral formalism. GEM theory, quantum concepts of virtual particles, and ZPF (Zero Point Fluctuation) allow understanding of the Strong Force and Weak forces as the extension of electrodynamics in the quantum limit. The Strong and Weak forces are found to be associated with EM models of the electron and proton as finite sized structures respectively. Higher order Mie resonances off the EM ``mass at a distance'' structures associated with the electron, proton and fifth dimension generate the quanta with masses of the pion mπ = 2 me /α 140.0 MeV and Z boson: mZ = 2σ mp = 80.4 GeV. The ηc meson mη = 2980 GeV is identified with the 5^th dimension compactification force mediated by the Radion field. Another particle associated with this mass inducing field is the ``Radion'' or Higgs scattering quanta off the fifth dimension with a mass σmη 128.6 GeV which is the Higgs Boson. A GEMS SU(5) Georgi-Glashow model, is proposed, where the unification energy is now the Planck energy.[0pt] [1] Brandenburg, J.E. (2012)., STAIF II Conference Albuquerque NM[0pt] [2] Brandenburg, J.E. (2007). IEEE Transactions On Plasma Science, Vol. 35, No. 4., p845.

  8. Plio-Pleistocene evolution of water mass exchange and erosional input at the Atlantic-Arctic gateway

    NASA Astrophysics Data System (ADS)

    Teschner, Claudia; Frank, Martin; Haley, Brian A.; Knies, Jochen

    2016-05-01

    Water mass exchange between the Arctic Ocean and the Norwegian-Greenland Seas has played an important role for the Atlantic thermohaline circulation and Northern Hemisphere climate. We reconstruct past water mass mixing and erosional inputs from the radiogenic isotope compositions of neodymium (Nd), lead (Pb), and strontium (Sr) at Ocean Drilling Program site 911 (leg 151) from 906 m water depth on Yermak Plateau in the Fram Strait over the past 5.2 Myr. The isotopic compositions of past bottom waters were extracted from authigenic oxyhydroxide coatings of the bulk sediments. Neodymium isotope signatures obtained from surface sediments agree well with present-day deepwater ɛNd signature of -11.0 ± 0.2. Prior to 2.7 Ma the Nd and Pb isotope compositions of the bottom waters only show small variations indicative of a consistent influence of Atlantic waters. Since the major intensification of the Northern Hemisphere Glaciation at 2.7 Ma the seawater Nd isotope composition has varied more pronouncedly due to changes in weathering inputs related to the waxing and waning of the ice sheets on Svalbard, the Barents Sea, and the Eurasian shelf, due to changes in water mass exchange and due to the increasing supply of ice-rafted debris (IRD) originating from the Arctic Ocean. The seawater Pb isotope record also exhibits a higher short-term variability after 2.7 Ma, but there is also a trend toward more radiogenic values, which reflects a combination of changes in input sources and enhanced incongruent weathering inputs of Pb released from freshly eroded old continental rocks.

  9. Carbon mass-balance modeling and carbon isotope exchange processes in the Curonian Lagoon

    NASA Astrophysics Data System (ADS)

    Barisevičiūtė, Rūta; Žilius, Mindaugas; Ertürk, Ali; Petkuvienė, Jolita

    2016-04-01

    The Curonian lagoon one of the largest coastal lagoons in Europe is located in the southeastern part of the Baltic Sea and lies along the Baltic coast of Lithuania and the Kaliningrad region of Russia. It is influenced by a discharge of the Nemunas and other smaller rivers and saline water of the Baltic Sea. The narrow (width 0.4 km, deep 8-14 m) Klaipėda Strait is the only way for fresh water run-off and brackish water intrusions. This research is focused on carbon isotope fractionations related with air - water exchange, primary production and organic carbon sedimentation, mineralization and uptake from both marine and terrestrial sources.

  10. [The study of the relationship between rates of carnitine exchange and fat mass in young swimmers].

    PubMed

    Ryloval, N v; Biktimiroval, A a; Sereda, A p; SamOylOv, A s

    2016-01-01

    The study of the state of carnitine metabolism is an actual problem for the specialists who are interested in the investigating of children's health, involved in sport. Indicators of carnitine metabolism reflect mitochondrial capacity and the state of energy of the cell, which in it's turn effect on the level of physical performance of athletes and their health status. The aim of our study was to identify the characteristics of carnitine metabolism in young athletes, as well as the establishment of correlation between carnitine metabolism and body fat mass. The study included 46 young athletes 12-17 years old involved in swimming. The average age of the athletes was 15.9 ± 0.2 years. Carnitine metabolism has been studied by gas chromatography-tandem mass spectrometry, the content of body fat mass has been established by bioimpedance. The free carnitine didn't significantly differ in males (36.3 ± 1.1 mmol/l) and females (36.3 ± 1.3 mmol/l). Content of related carnitine was higher in boys--17.4 ± 0.8 mmol/l (vs 14.0 ± 0.9 mmol/l in girls, p < 0.05). Value of related carnitine/free carnitine (AC/C0) was significantly 22.5% higher in boys (0.49 ± 0.03), because of higher content of related carnitine. The content of body fat mass in boys was 9.6 ± 0.87%, and in girls--22.24 ± 1.0%. There was found a significant correlation between indicators of carnitine metabolism and fat body mass. The findings may suggest a higher mitochondrial potential of girls engaged in swimming.

  11. Estimation of air-water gas exchange coefficient in a shallow lagoon based on 222Rn mass balance.

    PubMed

    Cockenpot, S; Claude, C; Radakovitch, O

    2015-05-01

    The radon-222 mass balance is now commonly used to quantify water fluxes due to Submarine Groundwater Discharge (SGD) in coastal areas. One of the main loss terms of this mass balance, the radon evasion to the atmosphere, is based on empirical equations. This term is generally estimated using one among the many empirical equations describing the gas transfer velocity as a function of wind speed that have been proposed in the literature. These equations were, however, mainly obtained from areas of deep water and may be less appropriate for shallow areas. Here, we calculate the radon mass balance for a windy shallow coastal lagoon (mean depth of 6m and surface area of 1.55*10(8) m(2)) and use these data to estimate the radon loss to the atmosphere and the corresponding gas transfer velocity. We present new equations, adapted to our shallow water body, to express the gas transfer velocity as a function of wind speed at 10 m height (wind range from 2 to 12.5 m/s). When compared with those from the literature, these equations fit particularly well with the one of Kremer et al. (2003). Finally, we emphasize that some gas transfer exchange may always occur, even for conditions without wind.

  12. Propagating of uncertainties due to human-induced surface-heterogeneities in regional estimation of energy and mass exchange from flux aggregation

    NASA Astrophysics Data System (ADS)

    Siqueira, M. B.

    2013-05-01

    and the horizontal advective scale. The advective scale, refers to how advective processes modify scalar fluxes of a given patch by its surrounding patches. The convective scales relates to processes that distort the equilibrium between the ABL and the underlying surface. In this study, I focus on the advective case, comparing the heterogeneity length scale to the downwind distance required by the local boundary layer to equilibrate with the surface (i.e. the statistics become virtually 1-dimensional). In order to do so, numerical simulations, using a Reynolds average closure models of the flow over a discontinuity on vegetation cover are performed aiming to establish the distance from the discontinuity at which the equilibrium with the new surface is re-establish. Comparing this length with a characteristic length scale of the heterogeneity will provide a framework to quantify uncertainties associated with regional exchange estimates from flux aggregation over heterogeneous landscape.

  13. Hydrophobic Peptides Affect Binding of Calmodulin and Ca2+ as Explored by H/D Amide Exchange and Mass Spectrometry

    PubMed Central

    Sperry, Justin B.; Huang, Richard Y-C.; Zhu, Mei M.; Rempel, Don L.; Gross, Michael L.

    2010-01-01

    Calmodulin (CaM), a ubiquitous intracellular sensor protein, binds Ca2+ and interacts with various targets as part of signal transduction. Using hydrogen/deuterium exchange (H/DX) and a high resolution PLIMSTEX (Protein-Ligand Interactions by Mass Spectrometry, Titration, and H/D Exchange) protocol, we examined five different states of calmodulin: calcium-free, calcium-loaded, and three states of calcium-loaded in the presence of either melittin, mastoparan, or skeletal myosin light-chain kinase (MLCK). When CaM binds Ca2+, the extent of HDX decreased, consistent with the protein becoming stabilized upon binding. Furthermore, Ca2+-saturated calmodulin exhibits increased protection when bound to the peptides, forming high affinity complexes. The protocol reveals significant changes in EF hands 1, 3, and 4 with saturating levels of Ca2+. Titration of the protein using PLIMSTEX provides the binding affinity of Ca2+ to calmodulin within previously reported values. The affinities of calmodulin to Ca2+ increase by factors of 300 and 1000 in the presence of melittin and mastoparan, respectively. A modified PLIMSTEX protocol whereby the protein is digested to component peptides gives a region-specific titration. The titration data taken in this way show a decrease in the root mean square fit of the residuals, indicating a better fit of the data. The global H/D exchange results and those obtained in a region-specific way provide new insight into the Ca2+-binding properties of this well-studied protein. PMID:21765646

  14. Structural dynamics of soluble chloride intracellular channel protein CLIC1 examined by amide hydrogen-deuterium exchange mass spectrometry.

    PubMed

    Stoychev, Stoyan H; Nathaniel, Christos; Fanucchi, Sylvia; Brock, Melissa; Li, Sheng; Asmus, Kyle; Woods, Virgil L; Dirr, Heini W

    2009-09-08

    Chloride intracellular channel protein 1 (CLIC1) functions as an anion channel in plasma and nuclear membranes when its soluble monomeric form converts to an integral-membrane form. The transmembrane region of CLIC1 is located in its thioredoxin-like domain 1, but the mechanism whereby the protein converts to its membrane conformation has yet to be determined. Since channel formation in membranes is enhanced at low pH (5 to 5.5), a condition that is found at the surface of membranes, the structural dynamics of soluble CLIC1 was studied at pH 7 and at pH 5.5 in the absence of membranes by amide hydrogen-deuterium exchange mass spectrometry (DXMS). Rapid hydrogen exchange data indicate that CLIC1 displays a similar core structure at these pH values. Domain 1 is less stable than the all-helical domain 2, and, while the structure of domain 1 remains intact, its conformational flexibility is further increased in an acidic environment (pH 5.5). In the absence of membrane, an acidic environment appears to prime the solution structure of CLIC1 by destabilizing domain 1 in order to lower the activation energy barrier for its conversion to the membrane-insertion conformation. The significantly enhanced H/D-exchange rates at pH 5.5 displayed by two segments (peptides 11-31 and 68-82) could be due to the protonation of acidic residues in salt bridges. One of these segments (peptide 11-31) includes part of the transmembrane region which, in the solution structure, consists of helix alpha1. This helix is intrinsically stable and is most likely retained in the membrane conformation. Strand beta2, another element of the transmembrane region, displays a propensity to form a helical structure and has putative N- and C-capping motifs, suggesting that it too most likely forms a helix in a lipid bilayer.

  15. Hydrothermal alteration and mass exchange in the hornblende latite porphyry, Rico, Colorado

    USGS Publications Warehouse

    Larson, P.B.; Cunningham, C.G.; Naeser, C.W.

    1994-01-01

    The Rico paleothermal anomaly, southwestern Colorado, records the effects of a large hydrothermal system that was active at 4 Ma. This hydrothermal system produced the deep Silver Creek stockwork Mo deposit, which formed above the anomaly's heat source, and shallower base and precious-metal vein and replacement deposits. A 65 Ma hornblende latite porphyry is present as widespread sills throughout the area and provided a homogenous material that recorded the effects of the hydrothermal system up to 8 km from the center. Hydrothermal alteration in the latite can be divided into a proximal facies which consists of two assemblages, quartz-illite-calcite and chlorite-epidote, and a distal facies which consists of a distinct propylitic assemblage. Temperatures were gradational vertically and laterally in the anomaly, and decreased away from the centra heat source. A convective hydrothermal plume, 3 km wide and at least 2 km high, was present above the stock-work molybdenum deposit and consisted of upwelling, high-temperature fluids that produced the proximal alteration facies. Distal facies alteration was produced by shallower cooler fluids. The most important shallow base and precious-metal vein deposits in the Rico district are at or close to the boundary of the thermal plume. Latite within the plume had a large loss of Na2O, large addition of CaO, and variable SiO2 exchante. Distal propylitized latite samples lost small amounts of Na2O and CaO and exchanged minor variable amounts of SiO2. The edge of the plume is marked by steep Na2O exchange gradients. Na2O exchange throughout the paleothermal anomaly was controlled by the reaction of the albite components in primary plagioclase and alkali feldspars. Initial feldspar alteration in the distal facies was dominated by reaction of the plagioclase, and the initial molar ratio of reactants (alkali feldspar albite component to plagioclase albite component) was 0.35. This ratio of the moles of plagioclase to alkali feldspar

  16. Experimental study of heat and mass transfer in a buoyant countercurrent exchange flow

    NASA Astrophysics Data System (ADS)

    Conover, Timothy Allan

    Buoyant Countercurrent Exchange Flow occurs in a vertical vent through which two miscible fluids communicate, the higher-density fluid, residing above the lower-density fluid, separated by the vented partition. The buoyancy- driven zero net volumetric flow through the vent transports any passive scalars, such as heat and toxic fumes, between the two compartments as the fluids seek thermodynamic and gravitational equilibrium. The plume rising from the vent into the top compartment resembles a pool fire plume. In some circumstances both countercurrent flows and pool fires can ``puff'' periodically, with distinct frequencies. One experimental test section containing fresh water in the top compartment and brine (NaCl solution) in the bottom compartment provided a convenient, idealized flow for study. This brine flow decayed in time as the concentrations approached equilibrium. A second test section contained fresh water that was cooled by heat exchangers above and heated by electrical elements below and operated steadily, allowing more time for data acquisition. Brine transport was reduced to a buoyancy- scaled flow coefficient, Q*, and heat transfer was reduced to an analogous coefficient, H*. Results for vent diameter D = 5.08 cm were consistent between test sections and with the literature. Some results for D = 2.54 cm were inconsistent, suggesting viscosity and/or molecular diffusion of heat become important at smaller scales. Laser Doppler Velocimetry was used to measure velocity fields in both test sections, and in thermal flow a small thermocouple measured temperature simultaneously with velocity. Measurement fields were restricted to the plume base region, above the vent proper. In baseline periodic flow, instantaneous velocity and temperature were ensemble averaged, producing a movie of the average variation of each measure during a puffing flow cycle. The temperature movie revealed the previously unknown cold core of the puff during its early development. The

  17. Determination of mercurial species in fish by inductively coupled plasma mass spectrometry with anion exchange chromatographic separation.

    PubMed

    Chen, Xiaopan; Han, Chao; Cheng, Heyong; Liu, Jinhua; Xu, Zigang; Yin, Xuefeng

    2013-09-24

    This work demonstrated the feasibility of mercury speciation analysis by anion exchange chromatographic separation with inductively coupled plasma mass spectrometry detection. For the first time, by complexing with the mobile phase containing 3-mercapto-1-propanesulfonate into negatively charged complexes, fast separation of inorganic mercury (Hg(2+)), monomethylmercury (MeHg), ethylmercury (EtHg) and phenylmercury (PhHg) was achieved within 5 min on a 12.5-mm strong anion exchange column. The detection limits for Hg(2+), MeHg, EtHg and PhHg were 0.008, 0.024, 0.029 and 0.034 μg L(-1), respectively. The relative standard deviations of peak height and peak area (5.0 μg L(-1) for each Hg species) were all below 3%. The determined contents of Hg(2+), MeHg and total Hg in a certified reference material of fish tissue by the proposed method were in good accordance with the certified values with satisfactory recoveries. The relative errors for determining MeHg and total mercury were -2.4% and -1.2%, respectively, with an acceptable range for spike recoveries of 94-101%. Mercury speciation in 11 fish samples were then analyzed after the pretreated procedure. The mercury contents in all fish samples analyzed were found compliant with the criteria of the National Standards of China.

  18. Modified ion exchange separation for tungsten isotopic measurements from kimberlite samples using multi-collector inductively coupled plasma mass spectrometry.

    PubMed

    Sahoo, Yu Vin; Nakai, Shun'ichi; Ali, Arshad

    2006-03-01

    Tungsten isotope composition of a sample of deep-seated rock can record the influence of core-mantle interaction of the parent magma. Samples of kimberlite, which is known as a carrier of diamond, from the deep mantle might exhibit effects of core-mantle interaction. Although tungsten isotope anomaly was reported for kimberlites from South Africa, a subsequent investigation did not verify the anomaly. The magnesium-rich and calcium-rich chemical composition of kimberlite might engender difficulty during chemical separation of tungsten for isotope analyses. This paper presents a simple, one-step anion exchange technique for precise and accurate determination of tungsten isotopes in kimberlites using multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS). Large quantities of Ca and Mg in kimberlite samples were precipitated and removed with aqueous H(2)SO(4). Highly pure fractions of tungsten for isotopic measurements were obtained following an anion exchange chromatographic procedure involving mixed acids. That procedure enabled efficient removal of high field strength elements (HFSE), such as Hf, Zr and Ti, which are small ions that carry strong charges and develop intense electrostatic fields. The tungsten yields were 85%-95%. Advantages of this system include less time and less use of reagents. Precise and accurate isotopic measurements are possible using fractions of tungsten that are obtained using this method. The accuracy and precision of these measurements were confirmed using various silicate standard rock samples, JB-2, JB-3 and AGV-1.

  19. Supercritical fluid chromatography coupled with in-source atmospheric pressure ionization hydrogen/deuterium exchange mass spectrometry for compound speciation.

    PubMed

    Cho, Yunju; Choi, Man-Ho; Kim, Byungjoo; Kim, Sunghwan

    2016-04-29

    An experimental setup for the speciation of compounds by hydrogen/deuterium exchange (HDX) with atmospheric pressure ionization while performing chromatographic separation is presented. The proposed experimental setup combines the high performance supercritical fluid chromatography (SFC) system that can be readily used as an inlet for mass spectrometry (MS) and atmospheric pressure photo ionization (APPI) or atmospheric pressure chemical ionization (APCI) HDX. This combination overcomes the limitation of an approach using conventional liquid chromatography (LC) by minimizing the amount of deuterium solvents used for separation. In the SFC separation, supercritical CO2 was used as a major component of the mobile phase, and methanol was used as a minor co-solvent. By using deuterated methanol (CH3OD), AP HDX was achieved during SFC separation. To prove the concept, thirty one nitrogen- and/or oxygen-containing standard compounds were analyzed by SFC-AP HDX MS. The compounds were successfully speciated from the obtained SFC-MS spectra. The exchange ions were observed with as low as 1% of CH3OD in the mobile phase, and separation could be performed within approximately 20min using approximately 0.24 mL of CH3OD. The results showed that SFC separation and APPI/APCI HDX could be successfully performed using the suggested method.

  20. Speciation of trace elements in human serum by micro anion exchange chromatography coupled with inductively coupled plasma mass spectrometry.

    PubMed

    Malavolta, Marco; Piacenza, Francesco; Basso, Andrea; Giacconi, Robertina; Costarelli, Laura; Pierpaoli, Sara; Mocchegiani, Eugenio

    2012-02-01

    Speciation analysis of essential trace elements in human serum provides important information on nutritional status and homeostatic mechanisms regulating transport processes, acute phase reactions, and protection against oxidative damage. Anion exchange high-performance liquid chromatography (HPLC) combined with inductively coupled plasma mass spectrometry (ICP-MS) has proved to be a useful tool in speciation. Here we describe a fast method that can be applied to carry out the speciation of Fe, Cu, Zn, and Se in as little as 1 microl [corrected] of serum. The method employs monolithic anion exchange micro columns installed on a tandem HPLC system coupled on-line with an ICP-MS detector. The chromatographic separation is similar to those reported previously but with considerable gain in terms of time and sample requirement. Reproducibility is acceptable for most species. Using our method, we were able to find species-specific differences between different commercially available trace element reference materials. Because the method chosen to collect blood might interfere with speciation, the proposed methodology was used to compare heparinized plasma, ethylenediaminetetraacetic acid (EDTA) plasma, and serum from adult healthy volunteers. As expected, EDTA strongly affects speciation analysis (especially for Fe and Zn), whereas changes due to the use of lithium-heparin (Li-He) as anticoagulant appear to be minimized.

  1. Influence of domain interactions on conformational mobility of the progesterone receptor detected by hydrogen/deuterium exchange mass spectrometry

    PubMed Central

    Goswami, Devrishi; Callaway, Celetta; Pascal, Bruce D.; Kumar, Raj; Edwards, Dean P.; Griffin, Patrick R.

    2015-01-01

    Structural and functional details of the N-terminal activation function 1 (AF1) of most nuclear receptors are poorly understood due to the highly dynamic intrinsically disordered nature of this domain. A hydrogen/deuterium exchange (HDX) mass spectrometry based investigation of TATA box binding protein (TBP) interaction with various domains of progesterone receptor (PR) demonstrate that agonist bound PR interaction with TBP via AF1 impacts the mobility of the C-terminal AF2. Results from HDX and other biophysical studies involving agonist and antagonist bound full length PR and isolated PR domains reveals the molecular mechanism underlying synergistic transcriptional activation mediated by AF1 and AF2, dominance of PR-B isoform over PR-A, and the necessity of AF2 for full AF1-mediated transcriptional activity. These results provide a comprehensive picture elaborating the underlying mechanism of PR-TBP interactions as a model for studying NR-transcription factor functional interactions. PMID:24909783

  2. Fast Reversed-Phase Liquid Chromatography to Reduce Back Exchange and Increase Throughput in H/D Exchange Monitored by FT-ICR Mass Spectrometry

    PubMed Central

    Zhang, Hui-Min; Bou-Assaf, George M.; Emmett, Mark R.; Marshall, Alan G.

    2009-01-01

    In solution-phase hydrogen/deuterium exchange (HDX), it is essential to minimize the back exchange level of H for D after the exchange has been quenched, to accurately assign protein conformation and protein-protein or protein-ligand interactions. Reversed-phase HPLC is conducted at low pH and low temperature to desalt and separate proteolytic fragments. However, back exchange averages ∼30% due to long exposure to H2O in the mobile phase. In this paper, we first show that there is no significant backbone amide hydrogen back exchange during quenching and digestion; backbone exchange occurs primarily during subsequent LC separation. We then show that a rapid reversed-phase separation reduces back exchange for HDX by at least 25%, due to dramatically reduced retention time of the peptide fragments on the column. The influence of retention time on back exchange was also evaluated. The rapid separation coupled with high resolution FT-ICR MS at 14.5T provides high amino acid sequence coverage, high sample throughput, and high reproducibility and reliability. PMID:19095461

  3. An approximate calculation of advective gas-phase transport of 14C at Yucca Mountain, Nevada

    NASA Astrophysics Data System (ADS)

    Knapp, R. B.

    1990-01-01

    A quasilinear partial differential equation, which describes gas-phase transport of a 14C kinematic wave through a porous medium, is derived, its sensitivity to system variables is analyzed and it is applied to one possible release scenarion at the porposed Yucca Mountain, Nevada high-level radioactive waste repository. Advection, isotope exchange between CO 2 in a flowing gas phase and HCO 3- in a static aqueous phase, and radioactive decay are incorporated. The governing equation is solved analytically by the method of characteristics. The mass fraction of 14C in the gas phase,X 14g, is controlled by radioactive decay. The relatively long half-line of 14C, about 5720 years, and the relatively shallow proposed burial depth of the radioactive waste, about 350m, requires significant retardation of the 14C wave velocity for significant reduction in X 14g. 14C wave velocity is most sensitive to temperature and pH which control the distribution of total carbon between gas and liquid phase; the greater the partitioning of carbon into the liquid phase, the greater the retardation of the 14C wave velocity and the greater the ultimate reduction in X 14g from initial conditions. Partitioning of total carbon into the liquid phase is greatest at low temperatures, < 100° C, and high pH values, > 8. Increasing water saturation also tends to retard 14C wave velocity but to a lesser extent. The governing equation has been applied using conditions that may possibly occur at the proposed Yucca Mountain repository. Calculations indicate that the 14C wave takes about 5900 years to reach the surface with a X 14g equal to 25 ppm. Diffusion and dispersion are not of major importance for these conditions. These calculations are approximate due to the number of assumptions involved. Discharge of 14C into the gas before the selected time would accelerate wave arrival and increase the amount of 14C reaching the surface.

  4. Human recombinant [C22A] FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR.

    PubMed Central

    Zhang, Z.; Li, W.; Logan, T. M.; Li, M.; Marshall, A. G.

    1997-01-01

    Hydrogen/deuterium exchange behavior of human recombinant [C22A] FK506 binding protein (C22A FKBP) has been determined by protein fragmentation, combined with electrospray Fourier transform ion cyclotron resonance mass spectrometry (MS). After a specified period of H/D exchange in solution, C22A FKBP was digested by pepsin under slow exchange conditions (pH 2.4, 0 degree C), and then subjected to on-line HPLC/MS for deuterium analysis of each proteolytic peptide. The hydrogen exchange rate of each individual amide hydrogen was then determined independently by heteronuclear two-dimensional NMR on 15N-enriched C22A FKBP. A maximum entropy method (MEM) algorithm makes it possible to derive the distributions of hydrogen exchange rate constants from the MS-determined deuterium exchange-in curves in either the holoprotein or its proteolytic segments. The MEM-derived rate constant distributions of C22A FKBP and different segments of C22A FKBP are compared to the rate constants determined by NMR for individual amide protons. The rate constant distributions determined by both methods are consistent and complementary, thereby validating protein fragmentation/mass spectrometry as a reliable measure of hydrogen exchange in proteins. PMID:9336843

  5. Mass transfer limitations in protein separations using ion-exchange membranes.

    PubMed

    Sarfert, F T; Etzel, M R

    1997-03-07

    Sorption of bovine serum albumin to commercial 150-micron pore size membranes was measured in batch and flow experiments. For residence times of 2-40 min, early and broad breakthrough curves and broad asymmetric elution peaks were observed that depended strongly on flow-rate. System dispersion could not explain the flow-rate dependence. Breakthrough and elution curves were analyzed using new models that included Langmuir sorption, convection and diffusion. From the analysis, film mass transfer resistance was found to be the rate-limiting factor. The maximum allowable pore size that eliminates this limitation was calculated for different molecular weight solutes.

  6. Automated Hydrogen/Deuterium Exchange Electron Transfer Dissociation High Resolution Mass Spectrometry Measured at Single-Amide Resolution

    NASA Astrophysics Data System (ADS)

    Landgraf, Rachelle R.; Chalmers, Michael J.; Griffin, Patrick R.

    2012-02-01

    Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a well established method for the measurement of solution-phase deuterium incorporation into proteins, which can provide insight into protein conformational mobility. However, most HDX measurements are constrained to regions of the protein where pepsin proteolysis allows detection at peptide resolution. Recently, single-amide resolution deuterium incorporation has been achieved by limiting gas-phase scrambling in the mass spectrometer. This was accomplished by employing a combination of soft ionization and desolvation conditions coupled with the radical-driven fragmentation technique electron transfer dissociation (ETD). Here, a hybrid LTQ-Orbitrap XL is systematically evaluated for its utility in providing single-amide deuterium incorporation for differential HDX analysis of a nuclear receptor upon binding small molecule ligands. We are able to show that instrumental parameters can be optimized to minimize scrambling and can be incorporated into an established and fully automated HDX platform making differential single-amide HDX possible for bottom-up analysis of complex systems. We have applied this system to determine differential single amide resolution HDX data for the peroxizome proliferator activated receptor bound with two ligands of interest.

  7. Particulate export vs lateral advection in the Antarctic Polar Front (Southern Pacific Ocean)

    NASA Astrophysics Data System (ADS)

    Tesi, T.; Langone, L.; Ravaioli, M.; Capotondi, L.; Giglio, F.

    2012-04-01

    The overarching goal of our study was to describe and quantify the influence of lateral advection relative to the vertical export in the Antarctic Polar Front (Southern Pacific Ocean). In areas where lateral advection of particulate material is significant, budgets of bioactive elements can be inaccurate if fluxes through the water column and to the seabed are exclusively interpreted as passive sinking of particles. However, detailed information on the influence of lateral advection in the water column in the southern ocean is lacking. With this in mind, our study focused between the twilight zone (i.e. mesopelagic) and the benthic nepheloid layer to understand the relative importance of lateral flux with increasing water depth. Measurements were performed south of the Antarctic Polar Front for 1 year (January 10th 1999-January 3rd 2000) at 900, 1300, 2400, and 3700 m from the sea surface. The study was carried out using a 3.5 km long mooring line instrumented with sediment traps, current meters and sensors of temperature and conductivity. Sediment trap samples were characterized via several parameters including total mass flux, elemental composition (organic carbon, total nitrogen, biogenic silica, and calcium carbonate), concentration of metals (aluminum, iron, barium, and manganese), 210Pb activity, and foraminifera taxonomy. High fluxes of biogenic particles were observed in both summer 1999 and 2000 as a result of seasonal algal blooms associated with sea ice retreat and water column stratification. During no-productive periods, several high energy events occurred and resulted in advecting resuspended biogenic particles from flat-topped summits of the Pacific Antarctic Ridge. Whereas the distance between seabed and uppermost sediment traps was sufficient to avoid lateral advection processes, resuspension was significant in the lowermost sediment traps accounting for ~60 and ~90% of the material caught at 2400 and 3700 m, respectively. Samples collected during

  8. Advective removal of intraparticle uranium from contaminated vadose zone sediments, Hanford, U.S.

    PubMed

    Ilton, Eugene S; Qafoku, Nikolla P; Liu, Chongxuan; Moore, Dean A; Zachara, John M

    2008-03-01

    A column study on U(VI)-contaminated vadose zone sediments from the Hanford Site, WA, was performed to investigate U(VI) release kinetics with water advection and variable geochemical conditions. The sediments were collected from an area adjacent to and below tank BX-102 that was contaminated as a result of a radioactive tank waste overfill event. The primary reservoir for U(VI) in the sediments are micrometer-size precipitates composed of nanocrystallite aggregates of a Na-U-Silicate phase, most likely Na-boltwoodite, that nucleated and grew within microfractures of the plagioclase component of sand-sized granitic clasts. Two sediment samples, with different U(VI) concentrations and intraparticle mass transfer properties, were leached with advective flows of three different solutions. The influent solutions were all calcite-saturated and in equilibrium with atmospheric CO2. One solution was prepared from DI water, the second was a synthetic groundwater (SGW) with elevated Na that mimicked groundwater at the Hanford site, and the third was the same SGW but with both elevated Na and Si. The latter two solutions were employed, in part, to test the effect of saturation state on U(VI) release. For both sediments, and all three electrolytes, there was an initial rapid release of U(VI) to the advecting solution followed by slower near steady-state release. U(VI)aq concentrations increased during subsequent stop-flow events. The electrolytes with elevated Na and Si depressed U(VL)aq concentrations in effluent solutions. Effluent U(VI)aq concentrations for both sediments and all three electrolytes were simulated reasonably well by a three domain model (the advecting fluid, fractures, and matrix) that coupled U(VI) dissolution, intraparticle U(VI)aq diffusion, and interparticle advection, where diffusion and dissolution properties were parameterized in a previous batch study.

  9. Boundary Layer Vertical Exchange Processes and the Mass Budget of Ozone: Observations and Model Results

    SciTech Connect

    Berkowitz, Carl M.; Fast, Jerome D.; Easter, Richard C.

    2000-06-16

    An Eulerian chemical model is used to assess the relative importance of a variety of processes associated with producing high surface ozone episodes during selected periods of the NARSTO 1995 field campaign over the northeastern United States. A comparison of the observed and predicted hourly surface ozone mixing ratios showed that the model qualitatively reproduced the observed ozone trends over the northeastern U.S. The model, however, over-predicted the surface concentrations by 10 to 15 ppb. The simulated mass budget tendency terms are compared for days with low ozone values immediately followed by days with high values. The later days showed observed and simulated ozone mixing ratios aloft to be of order twice that found on preceding days, although the associated chemical mix appeared to have relatively little potential for the subsequent generation of "new" ozone. Under conditions of shallow mixing over urban regions, simulated surface ozone production rates were negative (a net loss) throughout much of the day with convective mixing bringing newly produced ozone from aloft to the surface. It is noted that surface ozone levels appeared to be relatively insensitive to mixing layer growth rates.

  10. Relativistic Dynamics and Mass Exchange in Binary Black Hole Mini-disks

    NASA Astrophysics Data System (ADS)

    Bowen, Dennis B.; Campanelli, Manuela; Krolik, Julian H.; Mewes, Vassilios; Noble, Scott C.

    2017-03-01

    We present the first exploration of gas dynamics in a relativistic binary black hole (BH) system in which an accretion disk (a “mini-disk”) orbits each BH. We focus on 2D hydrodynamical studies of comparable-mass, non-spinning systems. Relativistic effects alter the dynamics of gas in this environment in several ways. Because the gravitational potential between the two BHs becomes shallower than in the Newtonian regime, the mini-disks stretch toward the L1 point and the amount of gas passing back and forth between the mini disks increases sharply with decreasing binary separation. This “sloshing” is quasi-periodically modulated at 2 and 2.75 times the binary orbital frequency, corresponding to timescales of hours to days for supermassive binary black holes (SMBBHs). In addition, relativistic effects add an m = 1 component to the tidally driven spiral waves in the disks that are purely m = 2 in Newtonian gravity; this component becomes dominant when the separation is ≲100 gravitational radii. Both the sloshing and the spiral waves have the potential to create distinctive radiation features that may uniquely mark SMBBHs in the relativistic regime.

  11. Evaluation of advection-aridity complementary relations at the lab scale

    NASA Astrophysics Data System (ADS)

    Schymanski, Stanislaus J.; Aminzadeh, Milad; Roderick, Michael L.; Or, Dani

    2015-04-01

    A common view of evaporation from terrestrial surfaces considers limitations due to water supply in arid regions, and atmospheric demand (or energy) limitations to evaporation from wet surfaces in temperate regions. Evidence suggests that at large scales, energy and water limitations are not independent. While a surface dries and a larger fraction of the radiative energy is converted into sensible heat, that heat is injected into the air and altering its properties. This land-atmosphere feedback gives rise to the so-called complementary relationship (Bouchet 1963), referring to the simultaneous decrease in actual evaporation while potential evaporation increases as the surface dries. The effect of surface drying on atmospheric water demand is two-fold: an increase in air temperature and a decrease in water vapour content for fixed advective exchange rate across the system boundaries. To isolate the various mechanisms and improve understanding of the feedbacks, we designed an insulated wind tunnel, where wind speed, radiation, surface moisture and exchange rates of air and heat across the boundaries are controlled. Preliminary results show the magnitude of the feedbacks in terms of air and surface temperatures, and evaporation rates from drying and wet surfaces simultaneously. Experimental and associated simulation results provide a direct demonstration of the roles of advective exchange and the interplay between atmospheric boundary layer thickness and temporal variations in radiative energy input in determining the strength of surface-atmosphere feedbacks and the resulting phenomenon known as the complementary relationship.

  12. User's guide to PHREEQC, a computer program for speciation, reaction-path, advective-transport, and inverse geochemical calculations

    USGS Publications Warehouse

    Parkhurst, D.L.

    1995-01-01

    PHREEQC is a computer program written in the C pwgranuning language that is designed to perform a wide variety of aqueous geochemical calculations. PHREEQC is based on an ion-association aqueous model and has capabilities for (1) speciation and saturation-index calculations, (2) reaction-path and advective-transport calculations involving specified irreversible reactions, mixing of solutions, mineral and gas equilibria surface-complex-ation reactions, and ion-exchange reactions, and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for composition differences between waters, within specified compositional uncertainties. PHREEQC is derived from the Fortran program PHREEQE, but it has been completely rewritten in C with the addition many new capabilities. New features include the capabilities to use redox couples to distribute redox elements among their valence states in speciation calculations; to model ion-exchange and surface-compiexation reactions; to model reactions with a fixed-pressure, multicomponent gas phase (that is, a gas bubble); to calculate the mass of water in the aqueous phase during reaction and transport calculations; to keep track of the moles of minerals present in the solid phases and determine antomaticaHy the thermodynamically stable phase assemblage; to simulate advective transport in combination with PHREEQC's reaction-modeling capability; and to make inverse modeling calculations that allow for uncertainties in the analytical data. The user interface is improved through the use of a simplified approach to redox reactions, which includes explicit mole-balance equations for hydrogen and oxygen; the use of a revised input that is modular and completely free format; and the use of mineral names and standard chemical symbolism rather than index numbers. The use of (2 eliminates nearly all limitations on army sizes, including numbers of elements, aqueous species, solutions, phases, and lengths of character

  13. Hydrogen–Deuterium Exchange and Mass Spectrometry Reveal the pH-Dependent Conformational Changes of Diphtheria Toxin T Domain

    PubMed Central

    2015-01-01

    The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen–deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our “standard condition” (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W+-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8–9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8–9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain. PMID:25290210

  14. Analysis of ustiloxins in rice using polymer cation exchange cleanup followed by liquid chromatography-tandem mass spectrometry.

    PubMed

    Cao, Zhao-Yun; Sun, Li-Hua; Mou, Ren-Xiang; Lin, Xiao-Yan; Zhou, Rong; Ma, You-Ning; Chen, Ming-Xue

    2016-12-09

    Ustiloxins are cyclopeptide mycotoxins produced by the pathogenic fungus Ustilaginoidea virens of rice false smut. Quantification of ustiloxins is essential to assess the food safety of rice infected by rice false smut disease. This paper describes a sensitive method for the simultaneous quantification of ustiloxins A, B, C, D and F in rice grains using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Since notable matrix enhancement effects (21%-78%) occurred for all of the target analytes (except for ustiloxin A), several solid phase extraction materials were tested for their ability to retain ustiloxins from aqueous solutions prior to the LC-MS/MS analysis, including C18 sorbents, polymer anion exchange sorbents resin (PAX), and polymer cation exchange resin (PCX). The PCX resin was adopted due to its higher extraction capability and selectivity for all targets compared to others, and in this case, almost no matrix effects (-5% to 8%) were observed for all of the ustiloxins monitored. The developed method reached limits of quantification of 0.2-2ngg(-1), and linearity was statistically verified over two orders of magnitude with regression coefficients (R(2))>0.991. The mean recoveries were from 85% to 109%, and the inter-day precisions (n=11) were less than 16%, with intra-day precisions (n=6) within 12%. Analysis of samples showed that ustiloxin A was the dominant species, with the content ranging from 5.5 to 273.8ngg(-1), followed by ustiloxin B (≤88.7ngg(-1)), while concentrations of ustiloxins C, D and F were slightly lower (≤43.2ngg(-1)). To our knowledge, this is the first report on the determination and analysis of five ustiloxins simultaneously in a single analysis.

  15. Designing for chaos: applications of chaotic advection at the microscale.

    PubMed

    Stremler, Mark A; Haselton, F R; Aref, Hassan

    2004-05-15

    Chaotic advection can play an important role in efficient microfluidic mixers. We discuss a design paradigm that exploits chaotic advection and illustrate by two recent examples, namely enhancing gene expression profiling and constructing an in-line microfluidic mixing channel, how application of this paradigm has led to successful micromixers. We suggest that 'designing for chaos', that is, basing practical mixer design on chaotic advection analysis, is a promising approach to adopt in this developing field which otherwise has little to guide it and is constrained by issues of scale and manufacturability.

  16. MAST solution of advection problems in irrotational flow fields

    NASA Astrophysics Data System (ADS)

    Aricò, Costanza; Tucciarelli, Tullio

    2007-03-01

    A new numerical-analytical Eulerian procedure is proposed for the solution of convection-dominated problems in the case of existing scalar potential of the flow field. The methodology is based on the conservation inside each computational elements of the 0th and 1st order effective spatial moments of the advected variable. This leads to a set of small ODE systems solved sequentially, one element after the other over all the computational domain, according to a MArching in Space and Time technique. The proposed procedure shows the following advantages: (1) it guarantees the local and global mass balance; (2) it is unconditionally stable with respect to the Courant number, (3) the solution in each cell needs information only from the upstream cells and does not require wider and wider stencils as in most of the recently proposed higher-order methods; (4) it provides a monotone solution. Several 1D and 2D numerical test have been performed and results have been compared with analytical solutions, as well as with results provided by other recent numerical methods.

  17. Selection of greenery plants' group tolerant to mineralized human wastes for their inclusion into intrasystem mass exchange of BTLSS

    NASA Astrophysics Data System (ADS)

    Tikhomirova, Natalia; Tikhomirov, Alexander A.; Kalacheva, Galina; Ushakova, Sofya; Trifonov, Sergey V.; Pavlova, Anastasiya

    2016-07-01

    A possible way solving the inclusion problem of the human liquid wastes containing sodium chloride into intrasystem mass exchange of bio-technical life support system (BTLSS) is selection of such species of greenery plants that can utilize sodium chloride, be edible for a human and have rather a high productivity. Our previous works showed that salt-accumulating halophyte Salicornia europaea L. was a promising candidate for sodium chloride inclusion into BTLSS mass exchange. However, with the aim of creation of more various human diet possibilities a set of greenery plants cultivated by the water culture method was estimated. Based on preliminary experiments the plants Brassica juncea L., Nasturtium officinale R. Br., Lepidium sativum angustifolia L. and Salicornia europaea L. were chosen as the investigation objects. The nutrient solution for greenery plant's cultivation was obtained after harvesting the wheat plants grown on the solution with mineralized human wastes' addition. The results of the first stage of the investigations carried out showed that plants of Brassica juncea and Lepidium sativum angustifolia are unpromising for their inclusion into BTLSS because of a set of physiological characteristics. On the next stage of investigations, an experimental model of closed ecosystem was created. For that purpose the plants of Salicornia europaea and Nasturtium officinale were introduced in the phototroph unit structure. It was determined that there was deficiency of main macronutrients for Salicornia europaea and Nasturtium officinale including sodium for Salicornia europaea. The deficiency had an effect on plants productivity and on carry-over of sodium from solution by Salicornia europaea. Thus in the future experiment it is necessary to carry out desalinization of solution by Salicornia europaea plants. Nasturtium officinale, that is rich in essential fatty acids and contributes into variety of human vegetable diet is planned to be cultivated by the

  18. The effect of advection on the nutrient reservoir in the North Atlantic subtropical gyre.

    PubMed

    Palter, Jaime B; Lozier, M Susan; Barber, Richard T

    2005-09-29

    Though critically important in sustaining the ocean's biological pump, the cycling of nutrients in the subtropical gyres is poorly understood. The supply of nutrients to the sunlit surface layer of the ocean has traditionally been attributed solely to vertical processes. However, horizontal advection may also be important in establishing the availability of nutrients. Here we show that the production and advection of North Atlantic Subtropical Mode Water introduces spatial and temporal variability in the subsurface nutrient reservoir beneath the North Atlantic subtropical gyre. As the mode water is formed, its nutrients are depleted by biological utilization. When the depleted water mass is exported to the gyre, it injects a wedge of low-nutrient water into the upper layers of the ocean. Contrary to intuition, cold winters that promote deep convective mixing and vigorous mode water formation may diminish downstream primary productivity by altering the subsurface delivery of nutrients.

  19. Reaction-diffusion-advection approach to spatially localized treadmilling aggregates of molecular motors

    NASA Astrophysics Data System (ADS)

    Yochelis, Arik; Bar-On, Tomer; Gov, Nir S.

    2016-04-01

    Unconventional myosins belong to a class of molecular motors that walk processively inside cellular protrusions towards the tips, on top of actin filament. Surprisingly, in addition, they also form retrograde moving self-organized aggregates. The qualitative properties of these aggregates are recapitulated by a mass conserving reaction-diffusion-advection model and admit two distinct families of modes: traveling waves and pulse trains. Unlike the traveling waves that are generated by a linear instability, pulses are nonlinear structures that propagate on top of linearly stable uniform backgrounds. Asymptotic analysis of isolated pulses via a simplified reaction-diffusion-advection variant on large periodic domains, allows to draw qualitative trends for pulse properties, such as the amplitude, width, and propagation speed. The results agree well with numerical integrations and are related to available empirical observations.

  20. Anomalous scaling of a scalar field advected by turbulence

    SciTech Connect

    Kraichnan, R.H.

    1995-12-31

    Recent work leading to deduction of anomalous scaling exponents for the inertial range of an advected passive field from the equations of motion is reviewed. Implications for other turbulence problems are discussed.

  1. Constraints upon water advection in sediments of the Mariana Trough

    SciTech Connect

    Abbott, D.H.; Menke, W.; Morin, R.

    1983-02-10

    Thermal gradient measurements, consolidation tests, and pore water compositions from the Mariana Trough imply that water is moving through the sediments in areas with less than about 100 m of sediment cover. The maximum advection rates implied by the thermal measurements and consolidation tests may be as high as 10/sup -5/ cm s/sup -1/ but are most commonly in the range of 1 to 5 x 10/sup -6/ cm s/sup -1/. Theoretical calculations of the effect of the highest advection rates upon carbonate dissolution indicate that dissolution may be impeded or enhanced (depending upon the direction of flow) by a factor of 2 to 5 times the rate for diffusion alone. The average percentage of carbonate is consistently higher in two cores from the area with no advection or upward advection than the average percentage of carbonate in three cores from the area with downward advection. This increase in average amount of carbonate in cores with upward moving water or no movement cannot be attributed solely to differences in water depth or in amount of terrigenous dilution. If the sediment column acts as a passive boundary layer, then the water velocities necessary to affect chemical gradients of silica are in the range 10/sup -9/ to 10/sup -10/ cm s/sup -1/. However, if dissolution of silica occurs within the sediment column, then the advection velocities needed to affect chemical gradients are at least 3 x 10/sup -8/ cm s/sup -1/ and may be as high as 3 x 10/sup -6/ cm s/sup -1/. This order of magnitude increase in advection velocities when chemical reactions occur within the sediments is probably applicable to other cations in addition to silica. If so, then the advection velocities needed to affect heat flow (>10/sup -8/ cm s/sup -1/) and pore water chemical gradients are much nearer in magnitude than previously assumed.

  2. Advection around ventilated U-shaped burrows: A model study

    NASA Astrophysics Data System (ADS)

    Brand, Andreas; Lewandowski, JöRg; Hamann, Enrico; Nützmann, Gunnar

    2013-05-01

    Advective transport in the porous matrix of sediments surrounding burrows formed by fauna such as Chironomus plumosus has been generally neglected. A positron emission tomography study recently revealed that the pumping activity of the midge larvae can indeed induce fluid flow in the sediment. We present a numerical model study which explores the conditions at which advective transport in the sediment becomes relevant. A 0.15 m deep U-shaped burrow with a diameter of 0.002 m within the sediment was represented in a 3-D domain. Fluid flow in the burrow was calculated using the Navier-Stokes equation for incompressible laminar flow in the burrow, and flow in the sediment was described by Darcy's law. Nonreactive and reactive transport scenarios were simulated considering diffusion and advection. The pumping activity of the model larva results in considerable advective flow in the sediment at reasonable high permeabilities with flow velocities of up to 7.0 × 10-6 m s-1 close to the larva for a permeability of 3 × 10-12 m2. At permeabilities below 7 × 10-13 m2 advection is negligible compared to diffusion. Reactive transport simulations using first-order kinetics for oxygen revealed that advective flux into the sediment downstream of the pumping larva enhances sedimentary uptake, while the advective flux into the burrow upstream of the larvae inhibits diffusive sedimentary uptake. Despite the fact that both effects cancel each other with respect to total solute uptake, the advection-induced asymmetry in concentration distribution can lead to a heterogeneous solute and redox distribution in the sediment relevant to complex reaction networks.

  3. Mapping the interactions of selective biochemical probes of antibody conformation by hydrogen-deuterium exchange mass spectrometry.

    PubMed

    Leurs, Ulrike; Beck, Hermann; Bonnington, Lea; Lindner, Ingo; Pol, Ewa; Rand, Kasper Dyrberg

    2017-03-27

    Protein-based pharmaceuticals represent the fastest growing group of drugs in development in the pharmaceutical industry. One of the major challenges in the discovery, development and distribution of biopharmaceuticals is the assessment of changes in their higher-order structure due to chemical modifications. Here, we investigate the interactions of three different biochemical probes (Fabs) generated to detect conformational changes in a therapeutic IgG1 antibody (mAbX) by local hydrogen-deuterium exchange mass spectrometry (HDX-MS). We show that two of the probes target the Fc part of the antibody, while the third probe binds to the hinge region. Through HDX-ETD, we can distinguish specific binding patterns of the Fc-binding probes on mAbX at the single amino acid level. Preliminary surface plasmon resonance (SPR) experiments show that these domain-selective Fab probes are sensitive to conformational changes in distinct regions of a full-length therapeutic antibody upon oxidation.

  4. Hexicon 2: Automated Processing of Hydrogen-Deuterium Exchange Mass Spectrometry Data with Improved Deuteration Distribution Estimation

    NASA Astrophysics Data System (ADS)

    Lindner, Robert; Lou, Xinghua; Reinstein, Jochen; Shoeman, Robert L.; Hamprecht, Fred A.; Winkler, Andreas

    2014-06-01

    Hydrogen-deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.

  5. Design and experimental analysis of counter-flow heat and mass exchanger incorporating (M-cycle) for evaporative cooling

    NASA Astrophysics Data System (ADS)

    Khalid, Omar; Butt, Zubair; Tanveer, Waqas; Rao, Hasan Iqbal

    2016-09-01

    In this paper, the functioning of dew-point cooler is improved in terms of its thermal effectiveness. For this reason, a heat and mass exchanger has been designed by using a counter-flow pattern incorporating Maisotsenko cycle (M-cycle) having effective absorbing material called Kraft paper on wet channel side and improved width to height ratio. Experimentation has been performed under various inlet air working parameters such as humidity, velocity and temperature in addition with changing feed water temperature. The results from the experiments specify that the dew-point and the wet-bulb effectiveness is achieved between 67-87 % and 104-120 % respectively. Analysis is performed with temperature variation between 25 and 45 °C at different absolute humidity levels ranging from 14.4 to 18 g/kg, while the inlet air velocity is varied between 0.88 and 1.50 m/s. Thus, the working ability of the improved design has been found 5 % more effective in terms of wet bulb effectiveness as compared to previous counter-flow designs.

  6. Improvement of sugar analysis sensitivity using anion-exchange chromatography-electrospray ionization mass spectrometry with sheath liquid interface.

    PubMed

    Xu, Xian-Bing; Liu, Ding-Bo; Guo, Xiao Ming; Yu, Shu-Juan; Yu, Pei

    2014-10-31

    A novel interface that enables high-performance anion-exchange chromatography (HPAEC) to be coupled with electrospray ionization (ESI) mass spectrometry (MS) is reported. A sheath liquid consisting of 50mM NH4Ac in isopropanol with 0.05% acetic acid, infused at a flow rate of 3μL/min at the tip of the electrospray probe, requires less ESI source cleaning and promotes efficient ionization of mono- and di-carbohydrates. The results suggest that use of a sheath liquid interface rather than a T-joint allows volatile ammonium salts to replace non-volatile metal salts as modifiers for improving sugar ESI signals. The efficient ionization of mono- and di-carbohydrates in the ESI source is affected by the sheath liquid properties such as buffer concentration and type of organic solvent. HPAEC-ESI-MS was used for the analysis of monocarbohydrates in pectins, particularly co-eluted sugars, and the performance was evaluated. Addition of a make-up solution through the sheath liquid interface proved to be an efficient tool for enhancing the intensities of sugars analyzed using HPAEC-ESI-MS.

  7. High energy efficiency and high power density proton exchange membrane fuel cells: Electrode kinetics and mass transport

    NASA Technical Reports Server (NTRS)

    Srinivasan, Supramaniam; Velev, Omourtag A.; Parthasathy, Arvind; Manko, David J.; Appleby, A. John

    1991-01-01

    The development of proton exchange membrane (PEM) fuel cell power plants with high energy efficiencies and high power densities is gaining momentum because of the vital need of such high levels of performance for extraterrestrial (space, underwater) and terrestrial (power source for electric vehicles) applications. Since 1987, considerable progress has been made in achieving energy efficiencies of about 60 percent at a current density of 200 mA/sq cm and high power densities (greater than 1 W/sq cm) in PEM fuel cells with high (4 mg/sq cm) or low (0.4 mg/sq cm) platinum loadings in electrodes. The following areas are discussed: (1) methods to obtain these high levels of performance with low Pt loading electrodes - by proton conductor impregnation into electrodes, localization of Pt near front surface; (2) a novel microelectrode technique which yields electrode kinetic parameters for oxygen reduction and mass transport parameters; (3) demonstration of lack of water transport from anode to cathode; (4) modeling analysis of PEM fuel cell for comparison with experimental results and predicting further improvements in performance; and (5) recommendations of needed research and development for achieving the above goals.

  8. Quantification of genetically modified soya using strong anion exchange chromatography and time-of-flight mass spectrometry.

    PubMed

    Chang, Po-Chih; Reddy, P Muralidhar; Ho, Yen-Peng

    2014-09-01

    Stable-isotope dimethyl labeling was applied to the quantification of genetically modified (GM) soya. The herbicide-resistant gene-related protein 5-enolpyruvylshikimate-3-phosphate synthase (CP4 EPSPS) was labeled using a dimethyl labeling reagent, formaldehyde-H2 or -D2. The identification and quantification of CP4 EPSPS was performed using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The CP4 EPSPS protein was separated from high abundance proteins using strong anion exchange chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Then, the tryptic peptides from the samples and reference were labeled with formaldehyde-H2 and formaldehyde-D2, respectively. The two labeled pools were mixed and analyzed using MALDI-MS. The data showed a good correlation between the peak ratio of the H- and D-labeled peptides and the GM soya percentages at 0.5, 1, 3, and 5 %, with R (2) of 0.99. The labeling reagents are readily available. The labeling experiments and the detection procedures are simple. The approach is useful for the quantification of GM soya at a level as low as 0.5 %.

  9. Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling.

    PubMed

    Khakinejad, Mahdiar; Kondalaji, Samaneh Ghassabi; Donohoe, Gregory C; Valentine, Stephen J

    2016-03-01

    Ion mobility spectrometry (IMS) coupled with gas-phase hydrogen deuterium exchange (HDX)-mass spectrometry (MS) and molecular dynamic simulations (MDS) has been used for structural investigation of anions produced by electrospraying a sample containing a synthetic peptide having the sequence KKDDDDDIIKIIK. In these experiments the potential of the analytical method for locating charge sites on ions as well as for utilizing collision-induced dissociation (CID) to reveal the degree of deuterium uptake within specific amino acid residues has been assessed. For diffuse (i.e., more elongated) [M - 2H](2-) ions, decreased deuterium content along with MDS data suggest that the D4 and D6 residues are charge sites, whereas for the more diffuse [M - 3H](3-) ions, the data suggest that the D4, D7, and the C-terminus are deprotonated. Fragmentation of mobility-selected, diffuse [M - 2H](2-) ions to determine deuterium uptake at individual amino acid residues reveals a degree of deuterium retention at incorporation sites. Although the diffuse [M - 3H](3-) ions may show more HD scrambling, it is not possible to clearly distinguish HD scrambling from the expected deuterium uptake based on a hydrogen accessibility model. The capability of the IMS-HDX-MS/MS approach to provide relevant details about ion structure is discussed. Additionally, the ability to extend the approach for locating protonation sites on positively-charged ions is presented.

  10. Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling

    NASA Astrophysics Data System (ADS)

    Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Donohoe, Gregory C.; Valentine, Stephen J.

    2016-03-01

    Ion mobility spectrometry (IMS) coupled with gas-phase hydrogen deuterium exchange (HDX)-mass spectrometry (MS) and molecular dynamic simulations (MDS) has been used for structural investigation of anions produced by electrospraying a sample containing a synthetic peptide having the sequence KKDDDDDIIKIIK. In these experiments the potential of the analytical method for locating charge sites on ions as well as for utilizing collision-induced dissociation (CID) to reveal the degree of deuterium uptake within specific amino acid residues has been assessed. For diffuse (i.e., more elongated) [M - 2H]2- ions, decreased deuterium content along with MDS data suggest that the D4 and D6 residues are charge sites, whereas for the more diffuse [M - 3H]3- ions, the data suggest that the D4, D7, and the C-terminus are deprotonated. Fragmentation of mobility-selected, diffuse [M - 2H]2- ions to determine deuterium uptake at individual amino acid residues reveals a degree of deuterium retention at incorporation sites. Although the diffuse [M - 3H]3- ions may show more HD scrambling, it is not possible to clearly distinguish HD scrambling from the expected deuterium uptake based on a hydrogen accessibility model. The capability of the IMS-HDX-MS/MS approach to provide relevant details about ion structure is discussed. Additionally, the ability to extend the approach for locating protonation sites on positively-charged ions is presented.

  11. Pangolin v1.0, a conservative 2-D advection model towards large-scale parallel calculation

    NASA Astrophysics Data System (ADS)

    Praga, A.; Cariolle, D.; Giraud, L.

    2015-02-01

    To exploit the possibilities of parallel computers, we designed a large-scale bidimensional atmospheric advection model named Pangolin. As the basis for a future chemistry-transport model, a finite-volume approach for advection was chosen to ensure mass preservation and to ease parallelization. To overcome the pole restriction on time steps for a regular latitude-longitude grid, Pangolin uses a quasi-area-preserving reduced latitude-longitude grid. The features of the regular grid are exploited to reduce the memory footprint and enable effective parallel performances. In addition, a custom domain decomposition algorithm is presented. To assess the validity of the advection scheme, its results are compared with state-of-the-art models on algebraic test cases. Finally, parallel performances are shown in terms of strong scaling and confirm the efficient scalability up to a few hundred cores.

  12. Hydrogen exchange mass spectrometry of bacteriorhodopsin reveals light-induced changes in the structural dynamics of a biomolecular machine.

    PubMed

    Pan, Yan; Brown, Leonid; Konermann, Lars

    2011-12-21

    Many proteins act as molecular machines that are fuelled by a nonthermal energy source. Examples include transmembrane pumps and stator-rotor complexes. These systems undergo cyclic motions (CMs) that are being driven along a well-defined conformational trajectory. Superimposed on these CMs are thermal fluctuations (TFs) that are coupled to stochastic motions of the solvent. Here we explore whether the TFs of a molecular machine are affected by the occurrence of CMs. Bacteriorhodopsin (BR) is a light-driven proton pump that serves as a model system in this study. The function of BR is based on a photocycle that involves trans/cis isomerization of a retinal chromophore, as well as motions of transmembrane helices. Hydrogen/deuterium exchange (HDX) mass spectrometry was used to monitor the TFs of BR, focusing on the monomeric form of the protein. Comparative HDX studies were conducted under illumination and in the dark. The HDX kinetics of BR are dramatically accelerated in the presence of light. The isotope exchange rates and the number of backbone amides involved in EX2 opening transitions increase roughly 2-fold upon illumination. In contrast, light/dark control experiments on retinal-free protein produced no discernible differences. It can be concluded that the extent of TFs in BR strongly depends on photon-driven CMs. The light-induced differences in HDX behavior are ascribed to protein destabilization. Specifically, the thermodynamic stability of the dark-adapted protein is estimated to be 5.5 kJ mol(-1) under the conditions of our work. This value represents the free energy difference between the folded state F and a significantly unfolded conformer U. Illumination reduces the stability of F by 2.2 kJ mol(-1). Mechanical agitation caused by isomerization of the chromophore is transferred to the surrounding protein scaffold, and subsequently, the energy dissipates into the solvent. Light-induced retinal motions therefore act analogously to an internal heat

  13. Separation and characterisation of beta2-microglobulin folding conformers by ion-exchange liquid chromatography and ion-exchange liquid chromatography-mass spectrometry.

    PubMed

    Bertoletti, Laura; Regazzoni, Luca; Aldini, Giancarlo; Colombo, Raffaella; Abballe, Franco; Caccialanza, Gabriele; De Lorenzi, Ersilia

    2013-04-10

    In this work we present for the first time the use of ion-exchange liquid chromatography to separate the native form and a partially structured intermediate of the folding of the amyloidogenic protein beta2-microglobulin. Using a strong anion-exchange column that accounts for the differences in charge exposure of the two conformers, a LC-UV method is initially optimised in terms of mobile phase pH, composition and temperature. The preferred mobile phase conditions that afford useful information were found to be 35 mM ammonium formate, pH 7.4 at 25°C. The dynamic equilibrium of the two species is demonstrated upon increasing the concentration of acetonitrile in the protein sample. Then, the chromatographic method is transferred to MS detection and the respective charge state distributions of the separated conformers are identified. The LC-MS results demonstrate that one of the conformers is partially unfolded, compared with the native and more compact species. The correspondence with previous results obtained in free solution by capillary electrophoresis suggest that strong ion exchange LC-MS does not alter beta2-microglobulin conformation and maintains the dynamic equilibrium already observed between the native protein and its folding intermediate.

  14. Horizontal Advection and Mixing of Pollutants in the Urban Atmospheric Environment

    NASA Astrophysics Data System (ADS)

    Magnusson, S. P.; Entekhabi, D.; Britter, R.; Norford, L.; Fernando, H. J.

    2013-12-01

    Although urban air quality and its impacts on the public health have long been studied, the increasing urbanization is raising concerns on how to better control and mitigate these health impacts. A necessary element in predicting exposure levels is fundamental understanding of flow and dispersion in urban canyons. The complex topology of building structures and roads requires the resolution of turbulence phenomena within urban canyons. The use of dense and low porosity construction material can lead to rapid heating in response to direct solar exposure due to large thermal mass. Hence thermal and buoyancy effects may be as important as mechanically-forced or shear-induced flows. In this study, the transport of pollutants within the urban environment, as well as the thermal and advection effects, are investigated. The focus is on the horizontal transport or the advection effects within the urban environment. With increased urbanization and larger and more spread cities, concern about how the upstream air quality situation can affect downstream areas. The study also examines the release and the dispersion of hazardous material. Due to the variety and complexity of urban areas around the world, the urban environment is simplified into adjacent two-dimensional urban street canyons. Pollutants are released inside each canyon. Computational Fluid Dynamics (CFD) simulations are applied to evaluate and quantify the flow rate out of each canyon and also the exchange of pollutants between the canyons. Imagine a row of ten adjacent urban street canyons of aspect ratio 1 with horizontal flow perpendicular to it as shown in the attached figure. C is the concentration of pollutants. The first digit indicates in what canyon the pollutant is released and the second digit indicates the location of that pollutant. For example, C3,4 is the concentration of pollutant released inside canyon 3 measured in canyon 4. The same amount of pollution is released inside the ten street canyons

  15. Kinetic study of the concentration dependence of the mass transfer rate coefficient in anion-exchange chromatography of bovine serum albumin

    SciTech Connect

    Miyabe, Kanji; Guiochon, G. |

    1999-07-01

    The experimental results of a previous study of the mass transfer kinetics of bovine serum albumin (BSA) in ion-exchange chromatography under nonlinear conditions are reevaluated. The analysis of the concentration dependence of the lumped mass-transfer rate coefficient (k{sub m,L}) provides information on the kinetics of axial dispersion, fluid-to-particle mass transfer, intraparticle mass transfer, and adsorption/desorption. The new analysis shows that the contribution of intraparticle mass transfer is the dominant one. Similar to k{sub m,L}, the surface diffusivity (D{sub s}) of BSA increases with increasing concentration. The linear concentration dependence of k{sub m,L} seems to originate in a similar dependence of D{sub s}. The use of a heterogeneous-surface model for the anion-exchange resin provides an explanation of the positive concentration dependence of D{sub s}. This work illustrates how frontal analysis data can be used for a detailed investigation of the kinetics of mass transfer between the phases of a chromatographic column, in addition to its conventional use in the determination of the thermodynamic characteristics of the phase equilibrium.

  16. A computational Lagrangian-Eulerian advection remap for free surface flows

    NASA Astrophysics Data System (ADS)

    Ashgriz, Nasser; Barbat, Tiberiu; Wang, Gang

    2004-01-01

    A VOF-based algorithm for advecting free surfaces and interfaces across a 2-D unstructured grid is presented. This algorithm is based on a combination of a Computational Lagrangian-Eulerian Advection Remap and the Volume of the Fluid method (CLEAR-VOF). A set of geometric tools are used to remap the advected shape of the volume fraction from one cell onto the Eulerian fixed unstructured grid. The geometric remapping is used to compute the fluxes onto a group of neighbouring cells of the mesh. These fluxes are then redistributed and corrected to satisfy the conservation of mass. Here, we present methods for developing identification algorithms for surface cells and incorporating them with CLEAR-VOF. The CLEAR-VOF algorithm is then tested for translation of several geometries. It is also incorporated in a finite element based flow solver and tested in a laminar flow over a broad-crested weir and a turbulent flow over a semi-circular obstacle.

  17. An advection scheme based on the combination of particle mesh method and pure Lagrangian approach

    NASA Astrophysics Data System (ADS)

    Arsenic, Ilija; Mihailovic, Dragutin T.; Kapor, Darko

    2011-11-01

    Possibility of using pure Lagrangian approach in modeling transport phenomena is described in this paper. The application of pure Lagrangian approach in real atmospheric field induces highly irregular spatial distribution of grid points, after only a few time steps. In order to avoid problems caused by that irregularity, a quasi interpolation procedure is proposed. Proposed interpolation procedure is similar to the radial basis functions interpolation and does not impose any demands about spatial distribution of the grid points or about continuity and differentiability of the field that needs to be interpolated. Besides that, proposed procedure is explicitly mass conserving. Combination of particle mesh method and pure Lagrangian approach creates efficient transport scheme that does not produce any new local maxima and minima in advected field. In proposed advection scheme motion of points are performed in Lagrangian manner while spatial derivatives are evaluated on the basis of values interpolated onto regular grid. Applicability of proposed advection scheme in an unambiguous way is proved by performing "standard" numerical tests with (i) the slotted cylinder under solid body rotation, (ii) the test with Doswell's idealized cyclogenesis as well as (iii) integration of shallow water equations.

  18. Determination of propofol glucuronide from hair sample by using mixed mode anion exchange cartridge and liquid chromatography tandem mass spectrometry.

    PubMed

    Kwak, Jae-Hwan; Kim, Hye Kyung; Choe, Sanggil; In, Sangwhan; Pyo, Jae Sung

    2016-03-15

    The main objective of this study was to develop and validate a simpler and less time consuming analytical method for determination of propofol glucuronide from hair sample, by using mixed mode anion exchange cartridge and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The study uses propofol glucuronide, a major metabolite of propofol, as a marker for propofol abuse. The hair sample was digested in sodium hydroxide solution and loaded in mixed-mode anion cartridge for solid phase extraction. Water and ethyl acetate were used as washing solvents to remove interfering substances from the hair sample. Consequently, 2% formic acid in ethyl acetate was employed to elute propofol glucuronide from the sorbent of mixed-mode anion cartridge, and analyzed by LC-MS/MS. The method validation parameters such as selectivity, specificity, LOD, LLOQ, accuracy, precision, recovery, and matrix effect were also tested. The linearity of calibration curves showed good correlation, with correlation coefficient 0.998. The LOD and LLOQ of the propofol glucuronide were 0.2 pg/mg and 0.5 pg/mg, respectively. The intra and inter-day precision and accuracy were acceptable within 15%. The mean values of recovery and matrix effect were in the range of 91.7-98.7% and 87.5-90.3%, respectively, signifying that the sample preparation, washing and extraction procedure were efficient, and there was low significant hair matrix effect for the extraction of propofol glucuronide from hair sample on the mixed mode anion cartridge. To evaluate the suitability of method, the hair of propofol administered rat was successfully analyzed with this method.

  19. Effective application of bicelles for conformational analysis of G protein-coupled receptors by hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Duc, Nguyen Minh; Du, Yang; Thorsen, Thor S; Lee, Su Youn; Zhang, Cheng; Kato, Hideaki; Kobilka, Brian K; Chung, Ka Young

    2015-05-01

    G protein-coupled receptors (GPCRs) have important roles in physiology and pathology, and 40% of drugs currently on the market target GPCRs for the treatment of various diseases. Because of their therapeutic importance, the structural mechanism of GPCR signaling is of great interest in the field of drug discovery. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a useful tool for analyzing ligand binding sites, the protein-protein interaction interface, and conformational changes of proteins. However, its application to GPCRs has been limited for various reasons, including the hydrophobic nature of GPCRs and the use of detergents in their preparation. In the present study, we tested the application of bicelles as a means of solubilizing GPCRs for HDX-MS studies. GPCRs (e.g., β2-adrenergic receptor [β2AR], μ-opioid receptor, and protease-activated receptor 1) solubilized in bicelles produced better sequence coverage (greater than 90%) than GPCRs solubilized in n-dodecyl-β-D-maltopyranoside (DDM), suggesting that bicelles are a more effective method of solubilization for HDX-MS studies. The HDX-MS profile of β2AR in bicelles showed that transmembrane domains (TMs) undergo lower deuterium uptake than intracellular or extracellular regions, which is consistent with the fact that the TMs are highly ordered and embedded in bicelles. The overall HDX-MS profiles of β2AR solubilized in bicelles and in DDM were similar except for intracellular loop 3. Interestingly, we detected EX1 kinetics, an important phenomenon in protein dynamics, at the C-terminus of TM6 in β2AR. In conclusion, we suggest the application of bicelles as a useful method for solubilizing GPCRs for conformational analysis by HDX-MS.

  20. The membrane-associated conformation of HIV-1 Nef investigated with hydrogen exchange mass spectrometry at a Langmuir monolayer

    PubMed Central

    Pirrone, Gregory F.; Emert-Sedlak, Lori A.; Wales, Thomas E.; Smithgall, Thomas E.; Kent, Michael S.; Engen, John R.

    2015-01-01

    In the companion paper to this work, we have described development of a new type of hydrogen exchange (HX) mass spectrometry (MS) measurement that integrates Langmuir monolayers. With Langmuir monolayers, the lipid packing density can be reproducibly controlled and changed as desired. Analysis of HX in proteins that may undergo conformational changes as a function of lipid packing, for example conformational rearrangements after insertion into a lipid layer, are then possible. We previously used neutron reflection to characterize just such a conformational change in the myristoylated HIV-1 Nef protein (myrNef): at high lipid packing density, myrNef could not insert into the lipids and maintained a compact conformation adjacent to the monolayer whereas at lower lipid packing density, myrNef was able to insert N-terminal arm residues causing displacement of the core domain away from the monolayer. In order to locate where conformation may have been altered by lipid association, we applied the HX MS Langmuir monolayer method to myrNef associated with monolayers of packing densities identical to those used for the prior neutron reflection measurements. The results show that the N-terminal region and the C-terminal unstructured loop undergo conformational changes when associated with a low lipid density lipid monolayer. The results are not consistent with the hypothesis of myrNef dimerization upon membrane association in the absence of other myrNef binding partners. The HX MS Langmuir monolayer method provides new and meaningful information for myrNef that helps explain necessary conformational changes required for function at the membrane. PMID:26133569

  1. Evapotranspiration: A process driving mass transport and energy exchange in the soil-plant-atmosphere-climate system

    NASA Astrophysics Data System (ADS)

    Katul, Gabriel G.; Oren, Ram; Manzoni, Stefano; Higgins, Chad; Parlange, Marc B.

    2012-09-01

    The role of evapotranspiration (ET) in the global, continental, regional, and local water cycles is reviewed. Elevated atmospheric CO2, air temperature, vapor pressure deficit (D), turbulent transport, radiative transfer, and reduced soil moisture all impact biotic and abiotic processes controlling ET that must be extrapolated to large scales. Suggesting a blueprint to achieve this link is the main compass of this review. Leaf-scale transpiration (fe) as governed by the plant biochemical demand for CO2 is first considered. When this biochemical demand is combined with mass transfer formulations, the problem remains mathematically intractable, requiring additional assumptions. A mathematical "closure" that assumes stomatal aperture is autonomously regulated so as to maximize the leaf carbon gain while minimizing water loss is proposed, which leads to analytical expressions for leaf-scale transpiration. This formulation predicts well the effects of elevated atmospheric CO2 and increases in D on fe. The case of soil moisture stress is then considered using extensive gas exchange measurements collected in drought studies. Upscaling the fe to the canopy is then discussed at multiple time scales. The impact of limited soil water availability within the rooting zone on the upscaled ET as well as some plant strategies to cope with prolonged soil moisture stress are briefly presented. Moving further up in direction and scale, the soil-plant system is then embedded within the atmospheric boundary layer, where the influence of soil moisture on rainfall is outlined. The review concludes by discussing outstanding challenges and how to tackle them by means of novel theoretical, numerical, and experimental approaches.

  2. Assessing Gibberellins Oxidase Activity by Anion Exchange/Hydrophobic Polymer Monolithic Capillary Liquid Chromatography-Mass Spectrometry

    PubMed Central

    Liu, Jiu-Feng; Wu, Yan; Feng, Yu-Qi; Yuan, Bi-Feng

    2013-01-01

    Bioactive gibberellins (GAs) play a key regulatory role in plant growth and development. In the biosynthesis of GAs, GA3-oxidase catalyzes the final step to produce bioactive GAs. Thus, the evaluation of GA3-oxidase activity is critical for elucidating the regulation mechanism of plant growth controlled by GAs. However, assessing catalytic activity of endogenous GA3-oxidase remains challenging. In the current study, we developed a capillary liquid chromatography – mass spectrometry (cLC-MS) method for the sensitive assay of in-vitro recombinant or endogenous GA3-oxidase by analyzing the catalytic substrates and products of GA3-oxidase (GA1, GA4, GA9, GA20). An anion exchange/hydrophobic poly([2-(methacryloyloxy)ethyl]trimethylammonium-co-divinylbenzene-co-ethylene glycol dimethacrylate)(META-co-DVB-co-EDMA) monolithic column was successfully prepared for the separation of all target GAs. The limits of detection (LODs, Signal/Noise = 3) of GAs were in the range of 0.62–0.90 fmol. We determined the kinetic parameters (Km) of recombinant GA3-oxidase in Escherichia coli (E. coli) cell lysates, which is consistent with previous reports. Furthermore, by using isotope labeled substrates, we successfully evaluated the activity of endogenous GA3-oxidase that converts GA9 to GA4 in four types of plant samples, which is, to the best of our knowledge, the first report for the quantification of the activity of endogenous GA3-oxidase in plant. Taken together, the method developed here provides a good solution for the evaluation of endogenous GA3-oxidase activity in plant, which may promote the in-depth study of the growth regulation mechanism governed by GAs in plant physiology. PMID:23922762

  3. Differential isotopic enrichment to facilitate characterization of asymmetric multimeric proteins using hydrogen/deuterium exchange mass spectrometry

    PubMed Central

    Pascal, Bruce D.; Bauman, Joseph D.; Patel, Disha; Arnold, Eddy; Griffin, Patrick R.

    2015-01-01

    Hydrogen/deuterium exchange (HDX) coupled to mass spectrometry has emerged as a powerful tool for analyzing the conformational dynamics of protein-ligand and protein-protein interactions. Recent advances in instrumentation and methodology have expanded the utility of HDX for the analysis of large and complex proteins; however, asymmetric dimers with shared amino acid sequence present a unique challenge for HDX because assignment of peptides with identical sequence to their subunit of origin remains ambiguous. Here we report the use of differential isotopic labeling to facilitate HDX analysis of multimers using HIV-1 reverse transcriptase (RT) as a model. RT is an asymmetric heterodimer of 51 kDa (p51) and 66 kDa (p66) subunits. The first 440 residues of p51 and p66 are identical. In this study differentially labeled RT was reconstituted from isotopically enriched (15N-labeled) p51 and unlabeled p66. In order to enable detection of 15N-deuterated RT peptides, the software HDX Workbench was modified to follow a 100% 15N model. Our results demonstrated that 15N enrichment of p51 did not affect its conformational dynamics compared to unlabeled p51, but 15N-labeled p51 did show different conformational dynamics than p66 in the RT heterodimer. Differential HDX-MS of isotopically labeled RT in the presence of the nonnucleoside reverse transcriptase inhibitor (NNRTI) efavirenz (EFV) showed subunit-specific perturbation in the rate of HDX consistent with previously published results and the RT-EFV co-crystal structure. PMID:25763479

  4. Observational signatures of past mass-exchange episodes in massive binaries: The case of HD 149 404

    NASA Astrophysics Data System (ADS)

    Raucq, F.; Rauw, G.; Gosset, E.; Nazé, Y.; Mahy, L.; Hervé, A.; Martins, F.

    2016-04-01

    Context. Mass and momentum exchanges in close massive binaries play an important role in their evolution, and produce several observational signatures such as asynchronous rotation and altered chemical compositions, that remain after the stars detach again. Aims: We investigated these effects for the detached massive O-star binary HD 149 404 (O7.5 If + ON9.7 I, P = 9.81 days), which is thought to have experienced a past episode of case A Roche-lobe overflow (RLOF). Methods: Using phase-resolved spectroscopy, we performed the disentangling of the optical spectra of the two stars. The reconstructed primary and secondary spectra were then analysed with the CMFGEN model atmosphere code to determine stellar parameters, such as the effective temperatures and surface gravities, and to constrain the chemical composition of the components. We complemented the optical study with the study of IUE spectra, which we compare to the synthetic binary spectra. The properties of the stars were compared to evolutionary models. Results: We confirmed a strong overabundance in nitrogen ([N/C] ~ 150[N/C]⊙) for the secondary and a slight nitrogen overabundance ([N/C] ~ 5[N/C]⊙) for the primary star. Comparing the two stars, we found evidence for asynchronous rotation, with a rotational period ratio of 0.50 ± 0.11. Conclusions: The hypothesis of a past case A RLOF interaction in HD 149 404 is most plausible to explain its chemical abundances and rotational asynchronicity. Some of the observed properties, such as the abundance pattern, are clearly a challenge for current case A binary evolution models, however. Based on observations collected at the European Southern Observatory (La Silla, Chile) and with the International Ultraviolet Explorer.The reduced spectra are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/588/A10

  5. Effective Application of Bicelles for Conformational Analysis of G Protein-Coupled Receptors by Hydrogen/Deuterium Exchange Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Duc, Nguyen Minh; Du, Yang; Thorsen, Thor S.; Lee, Su Youn; Zhang, Cheng; Kato, Hideaki; Kobilka, Brian K.; Chung, Ka Young

    2015-05-01

    G protein-coupled receptors (GPCRs) have important roles in physiology and pathology, and 40% of drugs currently on the market target GPCRs for the treatment of various diseases. Because of their therapeutic importance, the structural mechanism of GPCR signaling is of great interest in the field of drug discovery. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a useful tool for analyzing ligand binding sites, the protein-protein interaction interface, and conformational changes of proteins. However, its application to GPCRs has been limited for various reasons, including the hydrophobic nature of GPCRs and the use of detergents in their preparation. In the present study, we tested the application of bicelles as a means of solubilizing GPCRs for HDX-MS studies. GPCRs (e.g., β2-adrenergic receptor [β2AR], μ-opioid receptor, and protease-activated receptor 1) solubilized in bicelles produced better sequence coverage (greater than 90%) than GPCRs solubilized in n-dodecyl-β-D-maltopyranoside (DDM), suggesting that bicelles are a more effective method of solubilization for HDX-MS studies. The HDX-MS profile of β2AR in bicelles showed that transmembrane domains (TMs) undergo lower deuterium uptake than intracellular or extracellular regions, which is consistent with the fact that the TMs are highly ordered and embedded in bicelles. The overall HDX-MS profiles of β2AR solubilized in bicelles and in DDM were similar except for intracellular loop 3. Interestingly, we detected EX1 kinetics, an important phenomenon in protein dynamics, at the C-terminus of TM6 in β2AR. In conclusion, we suggest the application of bicelles as a useful method for solubilizing GPCRs for conformational analysis by HDX-MS.

  6. Millennial-scale variability in Atlantic water advection to the Nordic Seas derived from Holocene coccolith concentration records

    NASA Astrophysics Data System (ADS)

    Giraudeau, J.; Grelaud, M.; Solignac, S.; Andrews, J. T.; Moros, M.; Jansen, E.

    2010-05-01

    Abundance patterns of coccolith species in two Holocene marine cores retrieved off Norway and northern Iceland are indicative of millennial-scale modulations in the flow of the main (Norwegian Atlantic Current) and secondary (North Iceland Irminger Current) branches of the North Atlantic Drift to the Nordic Seas. Long-term trends in coccolith abundance changes reflect major Holocene steps in Atlantic Water transfer to the Nordic Seas at orbital scale with important constraints on the convective activity of the Nordic Seas that leads to the formation of the precursor water mass of North Atlantic Deep Water. Millennial-scale Holocene episodes of increased advection of Atlantic waters off Norway are associated with enhanced winter precipitation over Scandinavia, increased sea-salt fluxes over Greenland, and strengthened wind over Iceland, thereby suggesting a common atmospheric forcing: the location and intensity of the westerlies and the associated changes in mid- to high-latitude pressure gradients. Our biotic data indicate an opposite pattern of Atlantic water inflow at suborbital scale between the western (Denmark) and eastern (Iceland-Scotland) straits of the northern Atlantic throughout the Holocene. This, as supported by present observational and simulated data, further highlights the role of atmospheric oscillations in the recent history of the North Atlantic-Nordic Seas water mass exchanges across the Greenland-Scotland Ridge. Such atmospheric processes are thought to explain the observed coupling between periods of excess export of arctic sea-ice to the Nordic Seas and intervals of maximum inflow of Atlantic water to the Norwegian Sea throughout the last 11 000 years.

  7. STANDING SHOCK INSTABILITY IN ADVECTION-DOMINATED ACCRETION FLOWS

    SciTech Connect

    Le, Truong; Wood, Kent S.; Wolff, Michael T.; Becker, Peter A.; Putney, Joy

    2016-03-10

    Depending on the values of the energy and angular momentum per unit mass in the gas supplied at large radii, inviscid advection-dominated accretion flows can display velocity profiles with either preshock deceleration or preshock acceleration. Nakayama has shown that these two types of flow configurations are expected to have different stability properties. By employing the Chevalier and Imamura linearization method and the Nakayama instability boundary conditions, we discover that there are regions of parameter space where disks/shocks with outflows can be stable or unstable. In regions of instability, we find that preshock deceleration is always unstable to the zeroth mode with zero frequency of oscillation, but is always stable to the fundamental mode and overtones. Furthermore, we also find that preshock acceleration is always unstable to the zeroth mode and that the fundamental mode and overtones become increasingly less stable as the shock location moves away from the horizon when the disk half-height expands above ∼12 gravitational radii at the shock radius. In regions of stability, we demonstrate the zeroth mode to be stable for the velocity profiles that exhibit preshock acceleration and deceleration. Moreover, for models that are linearly unstable, our model suggests the possible existence of quasi-periodic oscillations (QPOs) with ratios 2:3 and 3:5. These ratios are believed to occur in stellar and supermassive black hole candidates, for example, in GRS 1915+105 and Sgr A*, respectively. We expect that similar QPO ratios also exist in regions of stable shocks.

  8. Simultaneous determination of 13 carbohydrates using high-performance anion-exchange chromatography coupled with pulsed amperometric detection and mass spectrometry.

    PubMed

    Zhao, Dan; Feng, Feng; Yuan, Fei; Su, Jin; Cheng, Yan; Wu, Hanqiu; Song, Kun; Nie, Bo; Yu, Lian; Zhang, Feng

    2017-02-28

    A simple, accurate, and highly sensitive method was developed for the determination of 13 carbohydrates in polysaccharide of spirulina platensis based on high-performance anion-exchange chromatography coupled with pulsed amperometric detection and mass spectrometry. Samples were extracted with deionized water using ultrasonic-assisted extraction, and the ultrasound-assisted extraction conditions were optimized by Box-Behnken design. Then the extracted polysaccharide was hydrolyzed by adding 1 mol/L trifluoroacetic acid before determination by high-performance anion-exchange chromatography coupled with pulsed amperometric detection and confirmed by high-performance anion-exchange chromatography coupled with mass spectrometry. The high-performance anion-exchange chromatography coupled with pulsed amperometric detection method was performed on a CarboPac PA20 column by gradient elution using deionized water, 0.1 mol/L sodium hydroxide solution and 0.4 mol/L sodium acetate solution. Excellent linearity was observed in the range of 0.05-10 mg/L. The average recoveries ranged from 80.7 to 121.7%. The limits of detection and limits of quantification for 13 carbohydrates were 0.02-0.10 and 0.2-1.2  μg/kg, respectively. The developed method has been successfully applied to ambient samples, and the results indicated that high-performance anion-exchange chromatography coupled with pulsed amperometric detection and mass spectrometry could provide a rapid and accurate method for the simultaneous determination of carbohydrates.

  9. Mass-Action Expressions of Ion Exchange Applied to Ca2+, H+, K+, and Mg2+ Sorption on Isolated Cells Walls of Leaves from Brassica oleracea1

    PubMed Central

    Bush, Douglas Scott; McColl, John G.

    1987-01-01

    The cation exchange properties of cell walls isolated from collard (Bassica oleracea var acephala D.C.) leaves were investigated. Cation sorption on cell walls was described by mass-action expressions of ion exchange, rather than by the traditional Donnan equilibrium. The mass-action expressions enable the selectivity of the wall for one cation over another to be determined unambiguously from ion exchange isotherms. We found that: (a) the cation composition of the wall varied as a function of the solution cation concentration, solution cation composition, and pH in a way predicted by mass action; (b) the affinity of the wall for divalent cations increased as the equivalent fraction of divalent cation on the wall increased, and as the concentration of divalent cations in solution increased; (c) the selectivity of the wall for any metal cation pair was not altered by the concentration of H+ in solution or on the wall; (d) H+ sorption on the wall may be treated as a cation exchange reaction making it possible to calculate the relative affinity of the wall for metal cation pairs from H+-metal (Me) titration curves; and (e) the relative affinity of the wall for the cations we studied was: H+ ≫ (K+ ≥ Ca2+) > Mg2+. A cation-exchange model including surface complexes is consistent with observed cation selectivity. We conclude that metal cations interact with the wall to minimize or eliminate long-range electrostatic interactions and suggest that this may be due to the formation of site-specific cation-wall surface complexes. PMID:16665665

  10. Combined cation-exchange and extraction chromatographic method of preconcentration and concomitant separation of bismuth(III) with high molecular mass liquid cation exchanger.

    PubMed

    Mandal, Bhabatosh; Ghosh, Niladri

    2010-10-15

    A selective method has been developed for the extraction chromatographic separation of Bi(III) with Versatic 10 coated on silanized silica gel (SSG). Bi(III) has been quantitatively extracted from 0.1 M acetate buffer at the range of pH 5.0-5.5. The result showed that the solution pH, influent volume, flow-rate and solution temperature would affect the sorption of Bi(III). The sorbed Bi(III) was eluted with 0.1 M H(2)SO(4). The extractor system has got good values of exchange capacity (1.42 meq. of H(+) g(-1) of dry exchanger at 25 degrees C), break-through capacity (19.75 mg g(-1) at pH 5.5) and column efficiencies (300) with respect to Bi(III). The positive value of DeltaH (12.63 kJ mol(-1)) and DeltaS (0.271 kJ mol(-1) K(-1)) and negative value of DeltaG (-68.241 kJ mol(-1)) indicated that the sorption process was endothermic, entropy gaining and spontaneous in nature. P.F. has been optimized at 76.4+/-0.3 and the desorption constants K(desorption) (8x10(-3)) and K'(desorption) (1.4x10(-1)) have been determined. R(f) values and selectivity factors for diverse metal ions with respect to that of Bi(III) have been determined by ion-exchange paper chromatography. Bi(III) has been separated from synthetic mixtures containing its congeners and other metal ions associated with it in ores and alloy samples. The method was found effective for removal of Bi(III) from different water samples. A plausible mechanism for the extraction of Bi(III) has been suggested.

  11. Folding analysis of hormonal polypeptide calcitonins and the oxidized calcitonins using electrospray ionization mass spectrometry combined with H/D exchange.

    PubMed

    Nabuchi, Yoshiaki; Asoh, Yoshinori; Takayama, Mitsuo

    2004-11-01

    Conformational change of calcitonins has been examined by measuring the rate of hydrogen/deuterium (H/D) exchange in amino acids. Time dependent m/z shift caused by H/D exchange was monitored by electrospray ionization quadrupole ion trap mass spectrometry (ESI-QIT MS). The rate constants of H/D exchange were calculated from apparent first-order kinetics. The time course of H/D exchange exhibited two phases of faster and slower exchange. The smaller rate constant (k2) estimated from the slower H/D exchange was correlated with an alpha-helix content that reflected the folding state. The order of k2 values obtained for human calcitonin (hCT), porcine calcitonin (pCT), salmon calcitonin (sCT), and elcatonin (ECT) was hCT > pCT approximately sCT > ECT. Although the amino acid sequence of sCT is similar to that of ECT, their k2 values were considerably different. The results suggest that ECT is relatively rigid on the N-terminal side cyclic structure in the folded state. Further, the effect of methionine oxidation on k2 has been examined. In the oxidized pCT that possesses similar biological activity with the intact pCT, the k2 values obtained were nearly equal. The k2 of hCT increased via methionine oxidation, and the biological activity was weakened by oxidation. This suggested that methionine oxidation of hCT produced unfolding in the secondary structure and that oxidative unfolding of hCT led to the loss of biological activity. The results indicate that the H/D exchange rate constant may be used as an informative parameter to elucidate the relationship between the folded state and biological activity of polypeptides like calcitonins with secondary structure.

  12. Influence of phase transformations and heat and mass exchange on the course of the processes of pyrolysis of single high-ash-coal particles at elevated pressures

    SciTech Connect

    V.P. Patskov

    2007-03-15

    A comparative analysis of equilibrium and nonequilibrium models for calculation of the rates of phase transitions (evaporation and condensation) of pyrolysis products and the influence of convective heat and mass exchange with inert ash particles and the gas flow in pyrolysis of single particles of high-ash bituminous coals in the operation of technological units with a circulating fluidized bed under pressure is made.

  13. Advecting Procedural Textures for 2D Flow Animation

    NASA Technical Reports Server (NTRS)

    Kao, David; Pang, Alex; Moran, Pat (Technical Monitor)

    2001-01-01

    This paper proposes the use of specially generated 3D procedural textures for visualizing steady state 2D flow fields. We use the flow field to advect and animate the texture over time. However, using standard texture advection techniques and arbitrary textures will introduce some undesirable effects such as: (a) expanding texture from a critical source point, (b) streaking pattern from the boundary of the flowfield, (c) crowding of advected textures near an attracting spiral or sink, and (d) absent or lack of textures in some regions of the flow. This paper proposes a number of strategies to solve these problems. We demonstrate how the technique works using both synthetic data and computational fluid dynamics data.

  14. Concentration polarization, surface currents, and bulk advection in a microchannel

    NASA Astrophysics Data System (ADS)

    Nielsen, Christoffer P.; Bruus, Henrik

    2014-10-01

    We present a comprehensive analysis of salt transport and overlimiting currents in a microchannel during concentration polarization. We have carried out full numerical simulations of the coupled Poisson-Nernst-Planck-Stokes problem governing the transport and rationalized the behavior of the system. A remarkable outcome of the investigations is the discovery of strong couplings between bulk advection and the surface current; without a surface current, bulk advection is strongly suppressed. The numerical simulations are supplemented by analytical models valid in the long channel limit as well as in the limit of negligible surface charge. By including the effects of diffusion and advection in the diffuse part of the electric double layers, we extend a recently published analytical model of overlimiting current due to surface conduction.

  15. Mass

    SciTech Connect

    Quigg, Chris

    2007-12-05

    In the classical physics we inherited from Isaac Newton, mass does not arise, it simply is. The mass of a classical object is the sum of the masses of its parts. Albert Einstein showed that the mass of a body is a measure of its energy content, inviting us to consider the origins of mass. The protons we accelerate at Fermilab are prime examples of Einsteinian matter: nearly all of their mass arises from stored energy. Missing mass led to the discovery of the noble gases, and a new form of missing mass leads us to the notion of dark matter. Starting with a brief guided tour of the meanings of mass, the colloquium will explore the multiple origins of mass. We will see how far we have come toward understanding mass, and survey the issues that guide our research today.

  16. Optimal Stretching in Advection-Reaction-Diffusion Systems

    NASA Astrophysics Data System (ADS)

    Nevins, Thomas D.; Kelley, Douglas H.

    2016-10-01

    We investigate growth of the excitable Belousov-Zhabotinsky reaction in chaotic, time-varying flows. In slow flows, reacted regions tend to lie near vortex edges, whereas fast flows restrict reacted regions to vortex cores. We show that reacted regions travel toward vortex centers faster as flow speed increases, but nonreactive scalars do not. For either slow or fast flows, reaction is promoted by the same optimal range of the local advective stretching, but stronger stretching causes reaction blowout and can hinder reaction from spreading. We hypothesize that optimal stretching and blowout occur in many advection-diffusion-reaction systems, perhaps creating ecological niches for phytoplankton in the ocean.

  17. Optimal Stretching in Advection-Reaction-Diffusion Systems.

    PubMed

    Nevins, Thomas D; Kelley, Douglas H

    2016-10-14

    We investigate growth of the excitable Belousov-Zhabotinsky reaction in chaotic, time-varying flows. In slow flows, reacted regions tend to lie near vortex edges, whereas fast flows restrict reacted regions to vortex cores. We show that reacted regions travel toward vortex centers faster as flow speed increases, but nonreactive scalars do not. For either slow or fast flows, reaction is promoted by the same optimal range of the local advective stretching, but stronger stretching causes reaction blowout and can hinder reaction from spreading. We hypothesize that optimal stretching and blowout occur in many advection-diffusion-reaction systems, perhaps creating ecological niches for phytoplankton in the ocean.

  18. Jet Magnetically Accelerated from Advection Dominated Accretion Flow

    NASA Astrophysics Data System (ADS)

    Gong, Xiao-Long; Jiang, Zhi-Xiong

    2014-08-01

    A jet model for the jet power arising from a steady, optically thin, advection dominated accretion flow (ADAF) around a Kerr black hole (BH) is proposed. We investigate the typical numerical solutions of ADAF, and calculate the jet power from an ADAF using a general relativistic version of electronic circuit theory. It is shown that the jet power concentrates in the inner region of the accretion flow, and the higher the degree to which the flow advection-dominated is, the lower the jet power from the ADAF is.

  19. Fast multigrid solution of the advection problem with closed characteristics

    SciTech Connect

    Yavneh, I.; Venner, C.H.; Brandt, A.

    1996-12-31

    The numerical solution of the advection-diffusion problem in the inviscid limit with closed characteristics is studied as a prelude to an efficient high Reynolds-number flow solver. It is demonstrated by a heuristic analysis and numerical calculations that using upstream discretization with downstream relaxation-ordering and appropriate residual weighting in a simple multigrid V cycle produces an efficient solution process. We also derive upstream finite-difference approximations to the advection operator, whose truncation terms approximate {open_quotes}physical{close_quotes} (Laplacian) viscosity, thus avoiding spurious solutions to the homogeneous problem when the artificial diffusivity dominates the physical viscosity.

  20. Studies of aerosols advected to coastal areas

    NASA Astrophysics Data System (ADS)

    Zielinski, T.; Petelski, T.; Makuch, P.; Strzalkowska, A.; Ponczkowska, A.; Drozdowska, V.; Gutowska, D.; Kowalczyk, J.; Darecki, M.; Piskozub, J.

    2012-04-01

    Characterizing aerosols involves the specification of not only their spatial and temporal distributions but their multi-component composition, particle size distribution and physical properties as well. Due to their light attenuation and scattering properties, aerosols influence radiance measured by satellite for ocean color remote sensingmaking them highly relevant for the ocean color atmospheric correction. This paper presents the results of the studies of aerosol optical properties measured using lidars and sun photometers. We describe two case studies of the combined measurements made in two coastal zones, in Crete in 2006and in Rozewie on the Baltic Sea in 2009. The combination of lidar and sun photometer measurements provides comprehensive information on both the total aerosol optical thickness in the entire atmosphere as well as the vertical structure of aerosol optical properties. Combination of such information with air mass back-trajectories and data collected at stations located on the route of air masses provides complete picture of the aerosol variations in the study area both vertically and horizontally. We show that such combined studies are especially important in the coastal areas. Additionally, aerosol particle direct and indirect radiative effects have been identified as key uncertainties for the prediction of the future global climate. This research has been made within the framework of the NASA/AERONET Program and Polish National Grants 1276/B/P01/2010/38, PBW 1283/B/P01/2010/38, POLAR-AOD, NN 306315536 and Satellite Monitoring of the Baltic Sea Environment - SatBałtyk funded by the European Union through European Regional Development Fund contract no. POIG 01.01.02-22-011/09.

  1. Hygroscopic chemicals and the formation of advection warm fog: A numerical simulation

    NASA Technical Reports Server (NTRS)

    Hung, R. J.; Liaw, G. S.

    1978-01-01

    The formation of advection fog is closely associated with the characteristics of the aerosol particles, including the chemical composition, mass of the nuclei, particle size, and concentration. Both macrophysical and microphysical processes are considered. In the macrophysical model, the evolution of wind components, water vapor content, liquid water content and potential temperature under the influences of vertical turbulent diffusion, turbulent momentum, and turbulent energy transfers are taken into account. In the microphysical model, the supersaturation effect is incorporated with the surface tension and hygroscopic material solution.

  2. Structure and Dynamics of NBD1 from CFTR Characterized Using Crystallography and Hydrogen/Deuterium Exchange Mass Spectrometry

    SciTech Connect

    Lewis, H.A.; Wang, C.; Zhao, X.; Hamuro, Y.; Conners, K.; Kearins, M.C.; Lu, F.; Sauder, J.M.; Molnar, K.S.; Coales, S.J.; Maloney, P.C.; Guggino, W.B.; Wetmore, D.R.; Weber, P.C.; Hunt, J.F.

    2012-04-30

    The {Delta}F508 mutation in nucleotide-binding domain 1 (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) is the predominant cause of cystic fibrosis. Previous biophysical studies on human F508 and {Delta}F508 domains showed only local structural changes restricted to residues 509-511 and only minor differences in folding rate and stability. These results were remarkable because {Delta}F508 was widely assumed to perturb domain folding based on the fact that it prevents trafficking of CFTR out of the endoplasmic reticulum. However, the previously reported crystal structures did not come from matched F508 and {Delta}F508 constructs, and the {Delta}F508 structure contained additional mutations that were required to obtain sufficient protein solubility. In this article, we present additional biophysical studies of NBD1 designed to address these ambiguities. Mass spectral measurements of backbone amide {sup 1}H/{sup 2}H exchange rates in matched F508 and {Delta}F508 constructs reveal that {Delta}F508 increases backbone dynamics at residues 509-511 and the adjacent protein segments but not elsewhere in NBD1. These measurements also confirm a high level of flexibility in the protein segments exhibiting variable conformations in the crystal structures. We additionally present crystal structures of a broader set of human NBD1 constructs, including one harboring the native F508 residue and others harboring the {Delta}F508 mutation in the presence of fewer and different solubilizing mutations. The only consistent conformational difference is observed at residues 509-511. The side chain of residue V510 in this loop is mostly buried in all non-{Delta}F508 structures but completely solvent exposed in all {Delta}F508 structures. These results reinforce the importance of the perturbation {Delta}F508 causes in the surface topography of NBD1 in a region likely to mediate contact with the transmembrane domains of CFTR. However, they also suggest that increased

  3. Temperature- and body mass-related variation in cyclic gas exchange characteristics and metabolic rate of seven weevil species: Broader implications.

    PubMed

    Klok, C J; Chown, S L

    2005-07-01

    The influence of temperature on metabolic rate and characteristics of the gas exchange patterns of flightless, sub-Antarctic Ectemnorhinus-group species from Heard and Marion islands was investigated. All of the species showed cyclic gas exchange with no Flutter period, indicating that these species are not characterized by discontinuous gas exchange cycles. Metabolic rate estimates were substantially lower in this study than in a previous one of a subset of the species, demonstrating that open-system respirometry methods provide more representative estimates of standard metabolic rate than do many closed-system methods. We recommend that the latter, and especially constant-pressure methods, either be abandoned for estimates of standard metabolic rate in insects, or have their outputs subject to careful scrutiny, given the wide availability of the former. V(.)CO(2) increase with an increase in temperature (range: 0-15 degrees C) was modulated by an increase in cycle frequency, but typically not by an increase in burst volume. Previous investigations of temperature-related changes in cyclic gas exchange (both cyclic and discontinuous) in several other insect species were therefore substantiated. Interspecific mass-scaling of metabolic rate (ca. 0.466-0.573, excluding and including phylogenetic non-independence, respectively) produced an exponent lower than 0.75 (but not distinguishable from it or from 0.67). The increase of metabolic rate with mass was modulated by an increase in burst volume and not by a change in cycle frequency, in keeping with investigations of species showing discontinuous gas exchange. These findings are discussed in the context of the emerging macrophysiological metabolic theory of ecology.

  4. Carbon source/sink function of a subtropical, eutrophic lake determined from an overall mass balance and a gas exchange and carbon burial balance.

    PubMed

    Yang, Hong; Xing, Yangping; Xie, Ping; Ni, Leyi; Rong, Kewen

    2008-02-01

    Although studies on carbon burial in lake sediments have shown that lakes are disproportionately important carbon sinks, many studies on gaseous carbon exchange across the water-air interface have demonstrated that lakes are supersaturated with CO(2) and CH(4) causing a net release of CO(2) and CH(4) to the atmosphere. In order to more accurately estimate the net carbon source/sink function of lake ecosystems, a more comprehensive carbon budget is needed, especially for gaseous carbon exchange across the water-air interface. Using two methods, overall mass balance and gas exchange and carbon burial balance, we assessed the carbon source/sink function of Lake Donghu, a subtropical, eutrophic lake, from April 2003 to March 2004. With the overall mass balance calculations, total carbon input was 14 905 t, total carbon output was 4950 t, and net carbon budget was +9955 t, suggesting that Lake Donghu was a great carbon sink. For the gas exchange and carbon burial balance, gaseous carbon (CO(2) and CH(4)) emission across the water-air interface totaled 752 t while carbon burial in the lake sediment was 9477 t. The ratio of carbon emission into the atmosphere to carbon burial into the sediment was only 0.08. This low ratio indicates that Lake Donghu is a great carbon sink. Results showed good agreement between the two methods with both showing Lake Donghu to be a great carbon sink. This results from the high primary production of Lake Donghu, substantive allochthonous carbon inputs and intensive anthropogenic activity. Gaseous carbon emission accounted for about 15% of the total carbon output, indicating that the total output would be underestimated without including gaseous carbon exchange.

  5. Closure of mass exchange under use of a vegetable conveyer cultivated on a neutral and soil-like substrates as applied to BLSS

    NASA Astrophysics Data System (ADS)

    Velitchko, Vladimir; Tikhomirov, Alexander; Ushakova, Sofya

    To increase a closure level of mass exchange processes in bioregenerative life support systems (BLSS) including a human a technology of plants cultivation on a soil-like substrate (SLS) consisting in a gradual decomposition of inedible plants biomass under its addition in the SLS was developed at the Institute of Biophysics SB RAS (Russia). In the given work the effect of periodical introduction of inedible plant biomass in the SLS on plants photosynthetic productivity and on the closure of mass exchange has been analyzed. Thereupon CO2 gas exchange and the certain vegetables' productivity under their cultivation in a conveyor regime on the SLS and on a neutral substrate with reference to the closure of mass exchange processes in BLSS have been studied in this work. The vegetables Raphanus sativus L., Brassica caulorapa L. Daucus carota L. and Beta vulgaris L. being prospective plantsrepresentatives of the BLSS phototrophic unit were taken as the research objects. The SLS was taken as an experiment substrate and an expanded clay aggregate as the control. The changeable Knop solution was used for the control, and an irrigation solution with the SLS extract was used for the experiment. Rapidity dynamics of CO2 consumption showed sharp distinctions of the ‘plants-SLS' system from the ‘plantsexpanded clay aggregate' system connected with the oxidation processes coursing in the SLS. The intensity of CO2 evolution from the SLS on average was 70% of the total plants conveyor's respiration. Thus a balance between the system's respiration and photosynthesis was often determined by the processes coursing in the SLS. Here the sharp CO2 evolution was recorded after introduction of the plants inedible biomass in the SLS. That peak was gradually coming down during 10-14 days after the beginning of every cycle of plants cultivation that was connected with intensification of plants photosynthesis and drop of decomposition intensity of the biomass introduced. Comparative

  6. Single-relaxation-time lattice Boltzmann scheme for advection-diffusion problems with large diffusion-coefficient heterogeneities and high-advection transport.

    PubMed

    Perko, Janez; Patel, Ravi A

    2014-05-01

    The paper presents an approach that extends the flexibility of the standard lattice Boltzmann single relaxation time scheme in terms of spatial variation of dissipative terms (e.g., diffusion coefficient) and stability for high Péclet mass transfer problems. Spatial variability of diffusion coefficient in SRT is typically accommodated through the variation of relaxation time during the collision step. This method is effective but cannot deal with large diffusion coefficient variations, which can span over several orders of magnitude in some natural systems. The approach explores an alternative way of dealing with large diffusion coefficient variations in advection-diffusion transport systems by introducing so-called diffusion velocity. The diffusion velocity is essentially an additional convective term that replaces variations in diffusion coefficients vis-à-vis a chosen reference diffusion coefficient which defines the simulation time step. Special attention is paid to the main idea behind the diffusion velocity formulation and its implementation into the lattice Boltzmann framework. Finally, the performance, stability, and accuracy of the diffusion velocity formulation are discussed via several advection-diffusion transport benchmark examples. These examples demonstrate improved stability and flexibility of the proposed scheme with marginal consequences on the numerical performance.

  7. Determination of Equine Cytochrome c Backbone Amide Hydrogen/Deuterium Exchange Rates by Mass Spectrometry Using a Wider Time Window and Isotope Envelope

    NASA Astrophysics Data System (ADS)

    Hamuro, Yoshitomo

    2017-03-01

    A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism. Toward this goal, a typical HDX-MS protocol was modified in two aspects: measurement of a wider time window in HDX-MS experiments and deconvolution of isotope envelope of each peptide. Measurement of a wider time window enabled the observation of deuterium incorporation of most backbone amide hydrogens. Analysis of the isotope envelope instead of centroid value provides the deuterium distribution instead of the sum of deuteration levels in each peptide. A one-step, global-fitting algorithm optimized exchange rate and deuterium retention during the analysis of each amide hydrogen by fitting the deuterated isotope envelopes at all time points of all peptides in a region. Application of this strategy to cytochrome c yielded 97 out of 100 amide hydrogen exchange rates. A set of exchange rates determined by this approach is more appropriate for a patent or regulatory filing of a biopharmaceutical than a set of peptide deuteration levels obtained by a typical protocol. A wider time window of this method also eliminates false negatives in protein-ligand binding site identification.

  8. Determination of Equine Cytochrome c Backbone Amide Hydrogen/Deuterium Exchange Rates by Mass Spectrometry Using a Wider Time Window and Isotope Envelope.

    PubMed

    Hamuro, Yoshitomo

    2017-03-01

    A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism. Toward this goal, a typical HDX-MS protocol was modified in two aspects: measurement of a wider time window in HDX-MS experiments and deconvolution of isotope envelope of each peptide. Measurement of a wider time window enabled the observation of deuterium incorporation of most backbone amide hydrogens. Analysis of the isotope envelope instead of centroid value provides the deuterium distribution instead of the sum of deuteration levels in each peptide. A one-step, global-fitting algorithm optimized exchange rate and deuterium retention during the analysis of each amide hydrogen by fitting the deuterated isotope envelopes at all time points of all peptides in a region. Application of this strategy to cytochrome c yielded 97 out of 100 amide hydrogen exchange rates. A set of exchange rates determined by this approach is more appropriate for a patent or regulatory filing of a biopharmaceutical than a set of peptide deuteration levels obtained by a typical protocol. A wider time window of this method also eliminates false negatives in protein-ligand binding site identification. Graphical Abstract ᅟ.

  9. Determination of Equine Cytochrome c Backbone Amide Hydrogen/Deuterium Exchange Rates by Mass Spectrometry Using a Wider Time Window and Isotope Envelope

    NASA Astrophysics Data System (ADS)

    Hamuro, Yoshitomo

    2017-01-01

    A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism. Toward this goal, a typical HDX-MS protocol was modified in two aspects: measurement of a wider time window in HDX-MS experiments and deconvolution of isotope envelope of each peptide. Measurement of a wider time window enabled the observation of deuterium incorporation of most backbone amide hydrogens. Analysis of the isotope envelope instead of centroid value provides the deuterium distribution instead of the sum of deuteration levels in each peptide. A one-step, global-fitting algorithm optimized exchange rate and deuterium retention during the analysis of each amide hydrogen by fitting the deuterated isotope envelopes at all time points of all peptides in a region. Application of this strategy to cytochrome c yielded 97 out of 100 amide hydrogen exchange rates. A set of exchange rates determined by this approach is more appropriate for a patent or regulatory filing of a biopharmaceutical than a set of peptide deuteration levels obtained by a typical protocol. A wider time window of this method also eliminates false negatives in protein-ligand binding site identification.

  10. Changes in particulate matter physical properties during Saharan advections over Rome (Italy): a four-year study, 2001-2004

    NASA Astrophysics Data System (ADS)

    Gobbi, G. P.; Angelini, F.; Barnaba, F.; Costabile, F.; Baldasano, J. M.; Basart, S.; Sozzi, R.; Bolignano, A.

    2013-08-01

    Particulate matter mass concentrations measured in the city of Rome (Italy) in the period 2001-2004 have been cross-analysed with concurrent Saharan dust advection events to infer the impact these natural episodes bear on the standard air quality parameter PM10 observed at two city stations and at one regional background station. Natural events such as Saharan dust advections are associated with a definite health risk. At the same time, the Directive 2008/50/EC allows subtraction of PM exceedances caused by natural contributions from statistics used to determine air quality of EU sites. In this respect, it is important to detect and characterise such advections by means of reliable, operational techniques. To assess the PM10 increase we used both the "regional-background method" suggested by EC Guidelines and a "local background" method, demonstrated to be most suited to this central Mediterranean region. In terms of exceedances, the two approaches provided results within ~20% of each other at background sites, and at ~50% of each other in traffic conditions. The sequence of Saharan advections over the city has been either detected by Polarization Lidar (laser radar) observations or forecast by the operational numerical regional mineral dust model BSC-DREAM8b of the Barcelona Supercomputing Centre. Lidar observations were also employed to retrieve the average physical properties of the dust clouds as a function of height. Over the four-year period, Lidar measurements (703 evenly distributed days) revealed Saharan plumes transits over Rome on 28.6% of the days, with minimum occurrence in wintertime. Dust was observed to reach the ground on 17.5% of the days totalling 88 episodes. Most (90%) of these advections lasted up to 5 days, averaging to ~3 days. Median time lag between advections was 7 days. Typical altitude range of the dust plumes was 0-6 km, with the centre of mass at ~3 km a.g.l. BSC-DREAM8b model simulations (1461 days) predicted Lidar detectable (532 nm

  11. Gas chromatography mass spectrometry study of hydrogen deuterium exchange reactions of volatile hydrides of As, Sb, Bi, Ge and Sn in aqueous media

    NASA Astrophysics Data System (ADS)

    D'Ulivo, Alessandro; Mester, Zoltan; Meija, Juris; Sturgeon, Ralph E.

    2006-07-01

    The H-D exchange processes in MH n or MD n hydrides (M = As, Sb, Bi, n = 3; M = Ge, Sn, n = 4) taking place when they are in contact with H 2O or D 2O solution at different pH or pD values (interval of pH = [0,13]) have been investigated using gas chromatography-mass spectrometry (GC-MS). MH n or MD n compounds were injected into the headspace of reaction vials (4-12 ml) containing 1-2 ml of buffered solution maintained under stirring or shaking conditions. The isotopic composition of the gaseous phase hydrides/deuterides was determined at regular intervals in the range of time 0-15 min. The MH n or MD n compounds were synthesized in separate vials and their purity was checked separately before injection into the reaction vials. The mass spectra were deconvoluted in order to estimate the relative abundance of each species formed following the H-D exchange process (AsH nD 3- n , SbH nD 3- n, BiH nD 3- n, n = 0-3; GeH nD 4- n, SnH nD 4- n, n = 0-4) and the relative abundance of H and D. In the investigated pH (or pD) interval arsanes and stibanes undergo H-D exchange in alkaline media for pH > 7. No H-D exchange was detected for the other hydrides, where the prevailing process is their decomposition in the aqueous phase. A reaction model, based on the formation of protonated or deprotonated intermediates is proposed for H-D exchange of MH n or MD n compounds placed in contact with H 2O or D 2O at different pH or pD values. The H-D exchange in the already formed hydrides can be source of the interference in mechanistic studies on hydride formation performed using labeled reagents; no H-D exchange was detected within the following pH intervals that can be considered free from interference: arsanes pH = [0,7), stibanes pH = [0,7), bismuthanes, germanes and stannanes pH = [0,13].

  12. Invasions in heterogeneous habitats in the presence of advection.

    PubMed

    Vergni, Davide; Iannaccone, Sandro; Berti, Stefano; Cencini, Massimo

    2012-05-21

    We investigate invasions from a biological reservoir to an initially empty, heterogeneous habitat in the presence of advection. The habitat consists of a periodic alternation of favorable and unfavorable patches. In the latter the population dies at fixed rate. In the former it grows either with the logistic or with an Allee effect type dynamics, where the population has to overcome a threshold to grow. We study the conditions for successful invasions and the speed of the invasion process, which is numerically and analytically investigated in several limits. Generically advection enhances the downstream invasion speed but decreases the population size of the invading species, and can even inhibit the invasion process. Remarkably, however, the rate of population increase, which quantifies the invasion efficiency, is maximized by an optimal advection velocity. In models with Allee effect, differently from the logistic case, above a critical unfavorable patch size the population localizes in a favorable patch, being unable to invade the habitat. However, we show that advection, when intense enough, may activate the invasion process.

  13. Theory of advection-driven long range biotic transport

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We propose a simple mechanistic model to examine the effects of advective flow on the spread of fungal diseases spread by wind-blown spores. The model is defined by a set of two coupled non-linear partial differential equations for spore densities. One equation describes the long-distance advectiv...

  14. Evaluation of strong cation-exchange polymers for the determination of drugs by solid-phase extraction-liquid chromatography-tandem mass spectrometry.

    PubMed

    Fontanals, Núria; Miralles, Núria; Abdullah, Norhayati; Davies, Arlene; Gilart, Núria; Cormack, P A G

    2014-05-23

    This paper presents eight distinct strong cation-exchange resins, all of which were derived from precursor resins that had been synthesised using either precipitation polymerisation or non-aqueous dispersion polymerisation. The precursor resins were transformed into the corresponding strong cation-exchange resins by hypercrosslinking followed by polymer analogous reactions, to yield materials with high specific surface areas and strong cation-exchange character. These novel resins were then evaluated as strong cation-exchange (SCX) sorbents in the solid-phase extraction (SPE) of a group of drugs from aqueous samples. Following preliminary experiments, the two best-performing resins were then evaluated in solid-phase extraction-liquid chromatography-tandem mass spectrometry (SPE/LC-MS/MS) to determine a group of drugs from sewage samples. In general, use of these sorbents led to excellent recovery values (75-100%) for most of the target drugs and negligible matrix effects (ME) (<20% ion suppression/enhancement of the analyte signal), when 50mL and 25mL of effluent and influent sewage water samples, respectively, were percolated through the resins. Finally, a validated method based on SPE/LC-MS/MS was used to quantify the target drugs present in different sewage samples.

  15. Enhanced Digestion Efficiency, Peptide Ionization Efficiency, and Sequence Resolution for Protein Hydrogen/Deuterium Exchange Monitored by FT-ICR Mass Spectrometry

    PubMed Central

    Zhang, Hui-Min; Kazazic, Saša; Schaub, Tanner M.; Tipton, Jeremiah D.; Emmett, Mark R.; Marshall, Alan G.

    2009-01-01

    Solution-phase hydrogen/deuterium exchange (HDX) monitored by high-resolution FT-ICR mass spectrometry offers a rapid method to study protein conformations and protein-protein interactions. Pepsin is usually used to digest proteins in HDX and is known as lack of cleavage specificity. To improve digestion efficiency and specificity, we have optimized digestion conditions and cleavage preferences for pepsin and protease type XIII from Aspergillus saitoi. A dilution series of the proteases was used to determine the digestion efficiency for several test proteins. Protease type XIII prefers to cleave on the C-terminal end of basic amino acids and produced the highest number of fragments and the best sequence coverage compared to pepsin or protease type XVIII from Rhizhopus. Furthermore, protease type XIII exhibited much less self-digestion than pepsin, and thus is superior for HDX experiments. Many highly overlapped segments from protease type XIII and pepsin digestion, combined with high-resolution FT-ICR mass spectrometry, provide high sequence resolution (to as few as one or two amino acids) for the assignment of amide hydrogen exchange rate. Our H/D exchange results correlate well with the secondary and tertiary structure of myoglobin. Such assignments of highly overlapped fragments promise to greatly enhance the accuracy and sequence resolution for determining conformational differences resulting from ligand binding or protein-protein interactions. PMID:19551977

  16. Advective velocity and energy dissipation rate in an oscillatory flow.

    PubMed

    Haider, Ziaul; Hondzo, Miki; Porte-Agel, Fernando

    2005-07-01

    Characterizing the transport processes at the sediment-water interface along sloping boundaries in lakes and reservoirs is of fundamental interest in lake and reservoir water quality management. The turbulent bottom boundary layer (TBBL) along a slope, induced by the breaking of internal waves in a linearly stratified fluid, was investigated through laboratory measurements. Fast response micro-scale conductivity and temperature probes in conjunction with laser-Doppler velocimetry were used to measure the time series of salinity, temperature, and velocity along a sloping boundary. Turbulent energy spectra were computed from the velocity data using a time-dependent advective velocity and Taylor's hypothesis. The energy spectra were used to estimate the energy dissipation rate at different positions in the TBBL. The advective velocity in this near-zero mean shear flow is based on an integral time scale (T(int)). The integral time scale is related to the average frequency of the spectral energy density of the flow velocity. The energy dissipation rate estimated from the variable advective velocity with an averaging time window equal to the integral time scale (T=T(int)) was 43% higher than the energy dissipation rate estimated from a constant advective velocity. The estimated dissipation rates with T=T(int) were comparable to values obtained by curve-fitting a theoretical Batchelor spectrum for the temperature gradient spectra. This study proposes the integral time scale to be used for the oscillatory flows as (a) a time-averaging window to estimate the advective velocity and associated energy dissipation level, and (b) a normalizing parameter in the energy spectrum.

  17. Persistence of cluster synchronization under the influence of advection.

    PubMed

    Guirey, Emma; Bees, Martin; Martin, Adrian; Srokosz, Meric

    2010-05-01

    We present a study on the emergence of spatial structure in plankton dynamics under the influence of stirring and mixing. A distribution of plankton is represented as a lattice of nonidentical, interacting, oscillatory plankton populations. Each population evolves according to (i) the internal biological dynamics represented by an NPZ model with population-specific phytoplankton growth rate, (ii) sub-grid-cell stirring and mixing parameterized by a nearest-neighbor coupling, and (iii) explicit advection resulting from a constant horizontal shear. Using the methods of synchronization theory, the emergent spatial structure of the simulation is investigated as a function of the coupling strength and rate of advection. Previous work using similar methods has neglected the effects of explicit stirring (i.e., at scales larger than the grid cell), leaving as an open question the relevance of the work to real marine systems. Here, we show that persistent spatial structure emerges for a range of coupling strengths for all realistic levels of surface ocean shear. Spatially, this corresponds to the formation of temporally evolving clusters of local synchronization. Increasing shear alters the spatial characteristics of this clustering by stretching and narrowing patches of synchronized dynamics. These patches are not stretched into stripes of synchronized abundance aligned with the flow, as may be expected, but instead lie at an angle to the flow. This study shows that advection does not diminish the relevance of conclusions from previous studies of spatial structure in plankton simulations. In fact, the inclusion of advection adds characteristic filamental structure, as observed in real-world plankton distributions. The results also show that the ability of coupled oscillators to synchronize depends strongly on the spatial arrangement of oscillator natural frequencies; under the influence of advection, therefore, the impact of the coupling strength on the emergent spatial

  18. Vertical Advection Effects on Hyper-accretion Disks and Potential Link between Gamma-Ray Bursts and Kilonovae

    NASA Astrophysics Data System (ADS)

    Yi, Tuan; Gu, Wei-Min; Yuan, Feng; Liu, Tong; Mu, Hui-Jun

    2017-02-01

    Recent simulations on super-Eddington accretion flows have shown that, apart from the diffusion process, the vertical advection based on magnetic buoyancy can be a more efficient process to release the trapped photons in the optically thick disk. As a consequence, the radiative luminosity from the accretion disk can be far beyond the Eddington value. Following this spirit, we revisit the structure and radiation of hyper-accretion disks with mass accretion rates in the range of {10}-3∼ 10 {M}ȯ {{{s}}}-1. Our results show that, due to the strong cooling through the vertical advection, the disk temperature becomes lower than that in the classic model without the vertical advection process, and therefore the neutrino luminosity from the disk is lower. On the other hand, the gamma-ray photons released through the vertical advection can be extremely super-Eddington. We argue that the large amount of escaped gamma-ray photons may have more significant contribution to the primordial fireball than the neutrino annihilation, and may hint at a link between gamma-ray bursts and kilonovae in the black hole hyper-accretion scenario.

  19. Black Hole Event Horizons and Advection-Dominated Accretion

    NASA Technical Reports Server (NTRS)

    McClintock, Jeffrey; Mushotzky, Richard F. (Technical Monitor)

    2001-01-01

    The XMM data on black-hole X-ray novae are only now becoming available and they have so far not been included in any publications. This work is part of a larger project that makes use of both XMM and Chandra data. Our first publication on the Chandra results is the following: "New Evidence for Black Hole Event Horizons from Chandra" by M.R. Garcia, J.E. McClintock, R. Narayan, P. Callanan, D. Barret and S. Murray (2001, ApJ, 553, L47). Therein we present the luminosities of the two black-hole X-ray novae, GRO J0422+22 and 4U1 543-47, which were observed by Chandra. These results are combined with the luminosities of four additional black-hole X-ray novae, which were observed as part of a Chandra GTO program (PI: S. Murray). The very low, but nonzero, quiescent X-ray luminosities of these black hole binaries is very difficult to understand in the context of standard viscous accretion disk theory. The principal result of this work is that X-ray novae that contain black hole primaries are about 100 times fainter that X-ray novae that contain neutron star primaries. This result had been suggested in earlier work, but the present work very firmly establishes this large luminosity difference. The result is remarkable because the black-hole and the neutron-star systems are believed to be similar in many respects. Most importantly, the mass transfer rate from the secondary star is believed to be very comparable for the two kinds of systems for similar orbital periods. The advection-dominated accretion flow (ADAF) model provides a natural framework for understanding the extraordinarily low luminosities of the black hole systems and the hundred-fold greater luminosities of the neutron star systems. The chief feature of an ADAF is that the heat energy in the accreting gas is trapped in the gas and travels with it, rather than being radiated promptly. Thus the accreting gas reaches the central object with a huge amount of thermal energy. If the accretor is a black hole, the

  20. Qualitative and quantitative analysis of branches in dextran using high-performance anion exchange chromatography coupled to quadrupole time-of-flight mass spectrometry.

    PubMed

    Yi, Lin; Ouyang, Yilan; Sun, Xue; Xu, Naiyu; Linhardt, Robert J; Zhang, Zhenqing

    2015-12-04

    Dextran, a family of natural polysaccharides, consists of an α (1→6) linked-glucose main (backbone) chain having a number of branches. The determination of the types and the quantities of branches in dextran is important in understanding its various biological roles. In this study, a hyphenated method using high-performance anion exchange chromatography (HPAEC) in parallel with pulsed amperometric detection (PAD) and mass spectrometry (MS) was applied to qualitative and quantitative analysis of dextran branches. A rotary cation-exchange cartridge array desalter was used for removal of salt from the HPAEC eluent making it MS compatible. MS and MS/MS were used to provide structural information on the enzymatically prepared dextran oligosaccharides. PAD provides quantitative data on the ratio of enzyme-resistant, branched dextran oligosaccharides. Both the types and degree of branching found in a variety of dextrans could be simultaneously determined online using this method.

  1. An algorithm for the deconvolution of mass spectroscopic patterns in isotope labeling studies. Evaluation for the hydrogen-deuterium exchange reaction in ketones.

    PubMed

    Gruber, Christian C; Oberdorfer, Gustav; Voss, Constance V; Kremsner, Jennifer M; Kappe, C Oliver; Kroutil, Wolfgang

    2007-07-20

    An easy to use computerized algorithm for the determination of the amount of each labeled species differing in the number of incorporated isotope labels based on mass spectroscopic data is described and evaluated. Employing this algorithm, the microwave-assisted synthesis of various alpha-labeled deuterium ketones via hydrogen-deuterium exchange with deuterium oxide was optimized with respect to time, temperature, and degree of labeling. For thermally stable ketones the exchange of alpha-protons was achieved at 180 degrees C within 40-200 min. Compared to reflux conditions, the microwave-assisted protocol led to a reduction of the required reaction time from 75-94 h to 40-200 min. The alpha-labeled deuterium ketones were reduced by biocatalytic hydrogen transfer to the corresponding enantiopure chiral alcohols and the deconvolution algorithm validated by regression analysis of a mixture of labeled and unlabeled ketones/alcohols.

  2. Rapid Screening for Potential Epitopes Reactive with a Polycolonal Antibody by Solution-Phase H/D Exchange Monitored by FT-ICR Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Zhang, Qian; Noble, Kyle A.; Mao, Yuan; Young, Nicolas L.; Sathe, Shridhar K.; Roux, Kenneth H.; Marshall, Alan G.

    2013-07-01

    The potential epitopes of a recombinant food allergen protein, cashew Ana o 2, reactive to polyclonal antibodies, were mapped by solution-phase amide backbone H/D exchange (HDX) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Ana o 2 polyclonal antibodies were purified in the serum from a goat immunized with cashew nut extract. Antibodies were incubated with recombinant Ana o 2 (rAna o 2) to form antigen:polyclonal antibody (Ag:pAb) complexes. Complexed and uncomplexed (free) rAna o 2 were then subjected to HDX-MS analysis. Four regions protected from H/D exchange upon pAb binding are identified as potential epitopes and mapped onto a homologous model.

  3. Affinity capture of biotinylated proteins at acidic conditions to facilitate hydrogen/deuterium exchange mass spectrometry analysis of multimeric protein complexes.

    PubMed

    Jensen, Pernille Foged; Jørgensen, Thomas J D; Koefoed, Klaus; Nygaard, Frank; Sen, Jette Wagtberg

    2013-08-06

    Characterization of conformational and dynamic changes associated with protein interactions can be done by hydrogen/deuterium exchange mass spectrometry (HDX-MS) by comparing the deuterium uptake in the bound and unbound state of the proteins. Investigation of local hydrogen/deuterium exchange in heteromultimeric protein complexes poses a challenge for the method due to the increased complexity of the mixture of peptides originating from all interaction partners in the complex. Previously, interference of peptides from one interaction partner has been removed by immobilizing the intact protein on beads prior to the HDX-MS experiment. However, when studying protein complexes of more than two proteins, immobilization can possibly introduce steric limitations to the interactions. Here, we present a method based on the high affinity biotin-streptavidin interaction that allows selective capture of biotinylated proteins even under the extreme conditions for hydrogen/deuterium exchange quenching i.e. pH 2.5 and 0 °C. This biotin-streptavidin capture strategy allows hydrogen/deuterium exchange to occur in proteins in solution and enables characterization of specific proteins in heteromultimeric protein complexes without interference of peptides originating from other interaction partners in the complex. The biotin-streptavidin strategy has been successfully implemented in a model system with two recombinant monoclonal antibodies that target nonoverlapping epitopes on the human epidermal growth factor receptor (EGFR). We present a workflow for biotinylation and characterization of recombinant antibodies and demonstrate affinity capture of biotinylated antibodies under hydrogen/deuterium exchange quench conditions by the biotin-streptavidin strategy.

  4. Changes in particulate matter physical properties during Saharan advections over Rome (Italy): a four-year study, 2001-2004

    NASA Astrophysics Data System (ADS)

    Gobbi, G. P.; Angelini, F.; Barnaba, F.; Costabile, F.; Baldasano, J. M.; Basart, S.; Sozzi, R.; Bolignano, A.

    2013-02-01

    Particulate matter mass concentrations measured in the city of Rome (Italy) in the period 2001-2004 have been cross-analysed with concurrent Saharan dust advection events to infer the impact these natural episodes bear on the standard air quality parameter PM10 observed at two city stations and at one regional background station. Natural events as Saharan dust advections are associated to a definite health risk. At the same time, the Directive 2008/50/EC allows subtraction of PM exceedances caused by natural contributions from statistics used to determine air-quality of EU sites. In this respect, it is important to detect and characterize such advections by means of reliable, operational techniques. To assess the PM10 increase we used both the "regional-background method" suggested by EC Guidelines and a "local background" one, demonstrated to be most suited to this central Mediterranean region. The two approaches provided results within 20% from each other. The sequence of Saharan advections over the city has been either detected by Polarization Lidar (laser radar) observations or forecast by the operational numerical regional mineral dust model BSC-DREAM8b of the Barcelona Supercomputing Centre. Lidar observations were also employed to retrieve the average physical properties of the dust clouds as a function of height. Along the four-year period, Lidar measurements (703 evenly distributed days) revealed Saharan plumes transits over Rome on 28.6% of the days, with minimum occurrence in wintertime. Dust was observed to reach the ground on 17.5% of the days totalling 88 episodes. Most (90%) of these advections lasted up to 5 days, averaging to ~3 days. Median time lag between advections was 7 days. Typical altitude range of the dust plumes was 0-6 km, with centre of mass at ~3 km a.g.l. BSC-DREAM8b model simulations (1461 days) predicted Lidar detectable (532nm extinction coefficient >0.005 km-1) dust advections on 25.9% of the days, with ground contacts on 13% of

  5. The TFTR E Parallel B Spectrometer for Mass and Energy Resolved Multi-Ion Charge Exchange Diagnostics

    SciTech Connect

    A.L. Roquemore; S.S. Medley

    1998-01-01

    The Charge Exchange Neutral Analyzer diagnostic for the Tokamak Fusion Test Reactor was designed to measure the energy distributions of both the thermal ions and the supra thermal populations arising from neutral-beam injection and ion cyclotron radio-frequency heating. These measurements yield the plasma ion temperature, as well as several other plasma parameters necessary to provide an understanding of the plasma condition and the performance of the auxiliary heating methods. For this application, a novel charge-exchange spectrometer using a dee-shaped region of parallel electric and magnetic fields was developed at the Princeton Plasma Physics Laboratory. The design and performance of this spectrometer is described in detail, including the effects of exposure of the microchannel plate detector to magnetic fields, neutrons, and tritium.

  6. An evaluation and intercomparison of four new advection schemes for use in global chemistry models

    NASA Astrophysics Data System (ADS)

    Petersen, Arthur C.; Spee, Edwin J.; van Dop, Han; Hundsdorfer, Willem

    1998-08-01

    The need to use a higher spatial resolution and to include more chemical species in global atmospheric chemistry models has led to a demand for efficient advection schemes with high accuracy. We test four newly developed three-dimensional advection schemes named Mol-rg, Split-u, Split-us, and Split-rg. We compare the new schemes with the existing schemes Slopes and Second Moments, both implemented on a uniform grid. Mol-rg and Split-rg make use of a reduced grid. Split-us is an unconditionally stable scheme on a uniform grid. Two tests are performed with all schemes: a solid-body rotation test and a radon transport test. The radon transport test is performed with the off-line global tracer model TM2. The solid-body rotation test shows that none of the new schemes generates undershoot and overshoot and that all of them are mass conservative. Slopes and Second Moments both generate small undershoot and overshoot at all resolutions. The accuracy of the new and old schemes for rotation of a smooth profile is similar for the horizontal resolutions studied. Since the new schemes are slightly more diffusive than the old schemes, they perform worse for rotation of a cone. The radon test shows that the errors related to the numerical schemes are much smaller than other model errors. The main advantage of the new schemes is that they use 75% and 90% less memory than Slopes and Second Moments, respectively. At horizontal resolutions higher than 5° × 5° Split-us and Split-rg are the most efficient of the schemes in terms of cpu time. The new advection schemes are available through Internet.

  7. Mass transfer of single- and double-charged anions through an MA-41L anion-exchange membrane

    SciTech Connect

    Kulikova, O.M.; Sharkova, O.V.; Kulikov, S.M.

    1995-02-20

    Selective anion transfer through an MA-41L anion-exchange membrane in the Cl{sup -}-F{sup -}, Cl{sup -}-SO{sub 4}{sup 2-}, F{sup -}-SO{sub 4}{sup 2-}, and F{sup -}-CO{sub 3}{sup 2-} systems has been studied. The feasibility of partial anion separation in the chloride-sulfate system has been demonstrated. The separation of fluoride ions from accompanying anions was found to be practically impossible.

  8. Phase Segregation of Passive Advective Particles in an Active Medium

    NASA Astrophysics Data System (ADS)

    Das, Amit; Polley, Anirban; Rao, Madan

    2016-02-01

    Localized contractile configurations or asters spontaneously appear and disappear as emergent structures in the collective stochastic dynamics of active polar actomyosin filaments. Passive particles which (un)bind to the active filaments get advected into the asters, forming transient clusters. We study the phase segregation of such passive advective scalars in a medium of dynamic asters, as a function of the aster density and the ratio of the rates of aster remodeling to particle diffusion. The dynamics of coarsening shows a violation of Porod behavior; the growing domains have diffuse interfaces and low interfacial tension. The phase-segregated steady state shows strong macroscopic fluctuations characterized by multiscaling and intermittency, signifying rapid reorganization of macroscopic structures. We expect these unique nonequilibrium features to manifest in the actin-dependent molecular clustering at the cell surface.

  9. Chaotic Advection in a Bounded 3-Dimensional Potential Flow

    NASA Astrophysics Data System (ADS)

    Metcalfe, Guy; Smith, Lachlan; Lester, Daniel

    2012-11-01

    3-dimensional potential, or Darcy flows, are central to understanding and designing laminar transport in porous media; however, chaotic advection in 3-dimensional, volume-preserving flows is still not well understood. We show results of advecting passive scalars in a transient 3-dimensional potential flow that consists of a steady dipole flow and periodic reorientation. Even for the most symmetric reorientation protocol, neither of the two invarients of the motion are conserved; however, one invarient is closely shadowed by a surface of revolution constructed from particle paths of the steady flow, creating in practice an adiabatic surface. A consequence is that chaotic regions cover 3-dimensional space, though tubular regular regions are still transport barriers. This appears to be a new mechanism generating 3-dimensional chaotic orbits. These results contast with the experimental and theoretical results for chaotic scalar transport in 2-dimensional Darcy flows. Wiggins, J. Fluid Mech. 654 (2010).

  10. Advective-diffusive contaminant migration in unsaturated sand and gravel

    SciTech Connect

    Rowe, R.K.; Badv, K.

    1996-12-01

    A method is presented for estimating the diffusion coefficients for chloride and sodium in unsaturated coarse sand and fine gravel based on parameters obtained from saturated diffusion tests conducted for similar material. The method is tested by comparing the observed and predicted diffusion profiles through unsaturated soil. The method is shown to work well for predicting the advective-diffusive migration of chloride and sodium through a two-layer soil system consisting of a compacted clayey silt underlain by an unsaturated fine gravel. Over the range of conditions examined, it is concluded that existing solute transport theory along with the proposed procedure for estimating the unsaturated diffusion coefficients can adequately predict chloride and sodium diffusion through both unsaturated coarse sand and fine gravel as well as predict advective-diffusive transport through a compacted clayey layer and underlying unsaturated fine gravel.

  11. Advection fog formation and aerosols produced by combustion-originated air pollution

    NASA Technical Reports Server (NTRS)

    Hung, R. J.; Liaw, G. S.; Vaughan, O. H., Jr.

    1980-01-01

    The way in which pollutants produced by the photochemical reaction of NO(X) and SO(X) affect the quality of the human environment through such phenomena as the formation of advection fog is considered. These pollutants provide the major source of condensation nuclei for the formation of fog in highways, airports and seaports. Results based on the monodisperse, multicomponent aerosol model show that: (1) condensation nuclei can grow and form a dense fog without the air having attained supersaturation; (2) the mass concentration range for NO(X) is one-third that of SO(X); and (3) the greater the mass concentration, the particle concentration, and the radius of condensation nuclei, the denser the fog that is formed.

  12. Spectral Theory of Advective Diffusion in the Ocean

    DTIC Science & Technology

    2013-09-19

    to study this enhancement of sea ice thermal conductivity and better understand temperature data collected during a 2007 Antarctic expedition. 15...conductivity and better understand temperature data collected during a 2007 Antarctic expedition. Activities and Findings: 1. Advection-enhanced...critically on the properties of this Hilbert space. More specifically, it is only on a special subset of this space that the random operator is Hermitian

  13. The LEM exponential integrator for advection-diffusion-reaction equations

    NASA Astrophysics Data System (ADS)

    Caliari, Marco; Vianello, Marco; Bergamaschi, Luca

    2007-12-01

    We implement a second-order exponential integrator for semidiscretized advection-diffusion-reaction equations, obtained by coupling exponential-like Euler and Midpoint integrators, and computing the relevant matrix exponentials by polynomial interpolation at Leja points. Numerical tests on 2D models discretized in space by finite differences or finite elements, show that the Leja-Euler-Midpoint (LEM) exponential integrator can be up to 5 times faster than a classical second-order implicit solver.

  14. Stability of explicit advection schemes. The balance point location rule

    NASA Astrophysics Data System (ADS)

    Leonard, B. P.

    2002-02-01

    This paper introduces the balance point location rule, providing specific necessary and sufficient conditions for constructing unconditionally stable explicit advection schemes, in both semi-Lagrangian and flux-form Eulerian formulations. The rule determines how the spatial stencil is placed on the computational grid. It requires the balance point (the center of the stencil in index space) to be located in the same patch as the departure point for semi-Lagrangian schemes or the same cell as the sweep point for Eulerian schemes. Centering the stencil in this way guarantees stability, regardless of the size of the time step. In contrast, the original Courant-Friedrichs-Lewy (CFL) condition requiring the stencil merely to include the departure (sweep) point, although necessary, is not sufficient for guaranteeing stability. The CFL condition is of limited practical value, whereas the balance point location rule always gives precise and easily implemented prescriptions for constructing stable algorithms. The rule is also helpful in correcting a number of misconceptions that have arisen concerning explicit advection schemes. In particular, explicit Eulerian schemes are widely believed to be inefficient because of stability constraints on the time step, dictated by a narrow interpretation of the CFL condition requiring the Courant number to be less than or equal to one. However, such constraints apply only to a particular class of advection schemes resulting for centering the stencil on the arrival point, when in fact the sole function of the stencil is to estimate the departure (sweep) point value - the arrival point has no relevance in determining the placement of the stencil. Unconditionally stable explicit Eulerian advection schemes are efficient and accurate, comparable in operation count to semi-Lagrangian schemes of the same order, but because of their flux-based formulation, they have the added advantage of being inherently conservative. Copyright

  15. STATE TRANSITIONS IN LOW-MASS X-RAY BINARIES

    SciTech Connect

    Bradley, Charles K.; Frank, Juhan

    2009-10-10

    We investigate the model of disk/coronal accretion into a black hole. We show that the inner regions of an accretion disk in X-ray binaries can transform from a cool standard disk to an advection-dominated flow through the known properties of Coulomb interaction in a two-temperature plasma, viscous heating, radiative processes, and thermal conduction. A hot, diffuse corona covering the disk is powered by accretion, but it exchanges mass with the underlying cold disk. If the accretion rate in the system is low enough, we show that the corona evaporates the disk away, leaving an advective flow to continue toward the hole. In the soft/hard transition commonly seen in X-ray binaries, we show that this advective flow can recondense back onto the underlying disk if the change in the system's accretion rate is slow enough due to thermal conduction. Unabsorbed spectra are produced to test against observations as well as prediction of the location of truncation radii of the accretion disk.

  16. Optimization and application of atmospheric pressure chemical and photoionization hydrogen-deuterium exchange mass spectrometry for speciation of oxygen-containing compounds.

    PubMed

    Acter, Thamina; Kim, Donghwi; Ahmed, Arif; Jin, Jang Mi; Yim, Un Hyuk; Shim, Won Joon; Kim, Young Hwan; Kim, Sunghwan

    2016-05-01

    This paper presents a detailed investigation of the feasibility of optimized positive and negative atmospheric pressure chemical ionization (APCI) mass spectrometry (MS) and atmospheric pressure photoionization (APPI) MS coupled to hydrogen-deuterium exchange (HDX) for structural assignment of diverse oxygen-containing compounds. The important parameters for optimization of HDX MS were characterized. The optimized techniques employed in the positive and negative modes showed satisfactory HDX product ions for the model compounds when dichloromethane and toluene were employed as a co-solvent in APCI- and APPI-HDX, respectively. The evaluation of the mass spectra obtained from 38 oxygen-containing compounds demonstrated that the extent of the HDX of the ions was structure-dependent. The combination of information provided by different ionization techniques could be used for better speciation of oxygen-containing compounds. For example, (+) APPI-HDX is sensitive to compounds with alcohol, ketone, or aldehyde substituents, while (-) APPI-HDX is sensitive to compounds with carboxylic functional groups. In addition, the compounds with alcohol can be distinguished from other compounds by the presence of exchanged peaks. The combined information was applied to study chemical compositions of degraded oils. The HDX pattern, double bond equivalent (DBE) distribution, and previously reported oxidation products were combined to predict structures of the compounds produced from oxidation of oil. Overall, this study shows that APCI- and APPI-HDX MS are useful experimental techniques that can be applied for the structural analysis of oxygen-containing compounds.

  17. Diurnal and annual exchanges of mass and energy between an aspen-hazelnut forest and the atmosphere: Testing the mathematical model Ecosys with data from the BOREAS experiment

    NASA Astrophysics Data System (ADS)

    Grant, R. F.; Black, T. A.; den Hartog, G.; Berry, J. A.; Neumann, H. H.; Blanken, P. D.; Yang, P. C.; Russell, C.; Nalder, I. A.

    1999-11-01

    There is much uncertainty about the net carbon (C) exchange of boreal forest ecosystems, although this exchange may be an important part of global C dynamics. To resolve this uncertainty, net C exchange has been measured at several sites in the boreal forest of Canada as part of the Boreal Ecosystem-Atmosphere Study (BOREAS). One of these sites is the Southern Old Aspen site at which diurnal CO2 and energy (radiation, latent, and sensible heat) fluxes were measured during 1994 using eddy correlation techniques at different positions within a mixed 70 year old aspen-hazelnut forest. These measurements were used to test a complex ecosystem model "ecosys" in which mass and energy exchanges between terrestrial ecosystems and the atmosphere are simulated hourly under diverse conditions of soil, management, and climate. These simulations explained between 70% and 80% of diurnal variation in ecosystem CO2 and energy fluxes measured during three 1 week intervals in late April, early June, and mid-July. Total annual CO2 fluxes indicated that during 1994, aspen was a net sink of 540 (modeled) versus 670 (measured) g C m-2 yr-1, while hazelnut plus soil were a net source of 472 (modeled) versus 540 (measured) g C m-2 yr-1. The aspen-hazelnut forest at the BOREAS site was therefore estimated to be a net sink of about 68 (modeled) versus 130 (measured) g C m-2 yr-1 during 1994. Long-term simulations indicated that this sink may be larger during cooler years and smaller during warmer years because C fixation in the model was less sensitive to temperature than respiration. These simulations also indicated that the magnitude of this sink declines with forest age because respiration increases with respect to fixation as standing phytomass grows. Confidence in the predictive capabilities of ecosystem models at decadal or centennial timescales is improved by well-constrained tests of these models at hourly timescales.

  18. Application of a Particle Method to the Advection-Diffusion-Reaction Equation

    NASA Astrophysics Data System (ADS)

    Paster, A.; Bolster, D.; Benson, D. A.

    2012-12-01

    A reaction between two chemical species can only happen if molecules collide and react. Thus, the mixing of a system can become a limiting factor in the onset of reaction. Solving for reaction rate in a well-mixed system is typically a straightforward task. However, when incomplete mixing kicks in, obtaining a solution becomes more challenging. Since reaction can only happen in regions where both reactants co-exist, the incomplete mixing may slow down the reaction rate, when compared to a well-mixed system. The effect of incomplete mixing upon reaction is a highly important aspect of various processes in natural and engineered systems, ranging from mineral precipitation in geological formations to groundwater remediation in aquifers. We study a relatively simple system with a bi-molecular irreversible kinetic reaction A+B → Ø where the underlying transport of reactants is governed by an advection-diffusion equation, and the initial concentrations are given in terms of an average and a perturbation. Such a system does not have an analytical solution to date, even for the zero advection case. We model the system by a Monte Carlo particle tracking method, where particles represent some reactant mass. In this method, diffusion is modeled by a random walk of the particles, and reaction is modeled by annihilation of particles. The probability of the annihilation is proportional to the reaction rate constant and the probability density associated with particle co-location. We study the numerical method in depth, characterizing typical numerical errors and time step restrictions. In particular, we show that the numerical method converges to the advection-diffusion-reaction equation at the limit Δt →0. We also rigorously derive the relationship between the initial number of particles in the system and the initial concentrations perturbations represented by that number. We then use the particle simulations of zero-advection system to demonstrate the well

  19. Effects of local advection on the spatial sensible heat flux variation on a mountain glacier

    NASA Astrophysics Data System (ADS)

    Sauter, Tobias; Galos, Stephan Peter

    2016-11-01

    Distributed mass balance models, which translate micrometeorological conditions into local melt rates, have proven deficient to reflect the energy flux variability on mountain glaciers. This deficiency is predominantly related to shortcomings in the representation of local processes in the forcing data. We found by means of idealized large-eddy simulations that heat advection, associated with local wind systems, causes small-scale sensible heat flux variations by up to 100 Wm-2 during clear sky conditions. Here we show that process understanding at a few observation sites is insufficient to infer the wind and temperature distributions across the glacier. The glacier-wide hourly averaged sensible heat fluxes are both over- and underestimated by up to 16 Wm-2 when using extrapolated temperature and wind fields. The sign and magnitude of the differences depend on the site selection, which is used for extrapolation as well as on the large-scale flow direction. Our results demonstrate how the shortcomings in the local sensible heat flux estimates are related to topographic effects and the insufficient characterization of the temperature advection process.

  20. A high order characteristic discontinuous Galerkin scheme for advection on unstructured meshes

    NASA Astrophysics Data System (ADS)

    Lee, D.; Lowrie, R.; Petersen, M.; Ringler, T.; Hecht, M.

    2016-11-01

    A new characteristic discontinuous Galerkin (CDG) advection scheme is presented. In contrast to standard discontinuous Galerkin schemes, the test functions themselves follow characteristics in order to ensure conservation and the edges of each element are also traced backwards along characteristics in order to create a swept region, which is integrated in order to determine the mass flux across the edge. Both the accuracy and performance of the scheme are greatly improved by the use of large Courant-Friedrichs-Lewy numbers for a shear flow test case and the scheme is shown to scale sublinearly with the number of tracers being advected, outperforming a standard flux corrected transport scheme for 10 or more tracers with a linear basis. Moreover the CDG scheme may be run to arbitrarily high order spatial accuracy and on unstructured grids, and is shown to give the correct order of error convergence for piecewise linear and quadratic bases on regular quadrilateral and hexahedral planar grids. Using a modal Taylor series basis, the scheme may be made monotone while preserving conservation with the use of a standard slope limiter, although this reduces the formal accuracy of the scheme to first order. The second order scheme is roughly as accurate as the incremental remap scheme with nonlocal gradient reconstruction at half the horizontal resolution. The scheme is being developed for implementation within the Model for Prediction Across Scales (MPAS) Ocean model, an unstructured grid finite volume ocean model.

  1. A Hybrid Advection Scheme for Conserving Angular Momentum on a Refined Cartesian Mesh

    NASA Astrophysics Data System (ADS)

    Byerly, Zachary D.; Adelstein-Lelbach, Bryce; Tohline, Joel E.; Marcello, Dominic C.

    2014-06-01

    We test a new "hybrid" scheme for simulating dynamical fluid flows in which cylindrical components of the momentum are advected across a rotating Cartesian coordinate mesh. This hybrid scheme allows us to conserve angular momentum to machine precision while capitalizing on the advantages offered by a Cartesian mesh, such as a straightforward implementation of mesh refinement. Our test focuses on measuring the real and imaginary parts of the eigenfrequency of unstable nonaxisymmetric modes that naturally arise in massless polytropic tori having a range of different aspect ratios and on quantifying the uncertainty in these measurements. Our measured eigenfrequencies show good agreement with the results obtained from the linear stability analysis of Kojima and from nonlinear hydrodynamic simulations performed on a cylindrical coordinate mesh by Woodward et al. When compared against results conducted with a traditional Cartesian advection scheme, the hybrid scheme achieves qualitative convergence at the same or, in some cases, much lower grid resolutions and conserves angular momentum to a much higher degree of precision. As a result, this hybrid scheme is much better suited for simulating astrophysical fluid flows such as accretion disks and mass-transferring binary systems.

  2. Pathogen and chemical transport in the karst limestone of the Biscayne aquifer: 2. Chemical retention from diffusion and slow advection

    USGS Publications Warehouse

    Shapiro, A.M.; Renken, R.A.; Harvey, R.W.; Zygnerski, M.R.; Metge, D.W.

    2008-01-01

    A tracer experiment, using a nonreactive tracer, was conducted as part of an investigation of the potential for chemical and pathogen migration to public supply wells that draw groundwater from the highly transmissive karst limestone of the Biscayne aquifer in southeastern Florida. The tracer was injected into the formation over approximately 1 h, and its recovery was monitored at a pumping well approximately 100 m from the injection well. The first detection of the tracer occurred after approximately 5 h, and the peak concentration occurred at about 8 h after the injection. The tracer was still detected in the production well more than 6 days after injection, and only 42% of the tracer mass was recovered. It is hypothesized that a combination of chemical diffusion and slow advection resulted in significant retention of the tracer in the formation, despite the high transmissivity of the karst limestone. The tail of the breakthrough curve exhibited a straight-line behavior with a slope of -2 on a log-log plot of concentration versus time. The -2 slope is hypothesized to be a function of slow advection, where the velocities of flow paths are hypothesized to range over several orders of magnitude. The flow paths having the slowest velocities result in a response similar to chemical diffusion. Chemical diffusion, due to chemical gradients, is still ongoing during the declining limb of the breakthrough curve, but this process is dwarfed by the magnitude of the mass flux by slow advection.

  3. Changes in water mass exchange between the NW shelf areas and the North Atlantic and their impact on nutrient/carbon cycling

    NASA Astrophysics Data System (ADS)

    Gröger, Matthias; Maier-Reimer, Ernst; Mikolajewicz, Uwe; Segschneider, Joachim; Sein, Dimitry

    2010-05-01

    Despite their comparatively small extension on a global scale, shelf areas are of interest for several economic reasons and climatic processes related to nutrient cycling, sea food supply, and biological productivity. Moreover, they constitute an important interface for nutrients, pollutants and freshwater on their pathway from the continents to the open ocean. This modelling study aims to investigate the spatial and temporal variability of water mass exchange between the North Atlantic and the NW European shelf and their impact on nutrient/carbon cycling and biological productivity. For this, a new modeling approach has been set up which bridges the gap between pure shelf models where water mass transports across the model domain too strongly depend on the formulation of open boundaries and global models suffering under their too coarse resolution in shelf regions. The new model consists of the global ocean and carbon cycle model MPIOM/HAMOCC with strongly increased resolution in the North Sea and the North Atlantic coupled to the regional atmosphere model REMO. The model takes the full luni-solar tides into account. It includes further a 12 layer sediment module with the relevant pore water chemistry. The main focus lies on the governing mechanisms of water mass exchange across the shelf break and the imprint on shelf biogeochemistry. For this, artificial tracers with a prescribed decay rate have been implemented to distinguish waters arriving from polar and shelf regions and those that originate from the tropics. Experiments were carried out for the years 1948 - 2007. The relationship to larger scale circulation patterns like the position and variability of the subtropical and subpolar gyres is analyzed. The water mass exchange is analyzed with respect to the nutrient concentration and productivity on the European shelf areas. The implementation of tides leads to an enhanced vertical mixing which causes lower sea surface temperatures compared to simulations

  4. Measuring dynamics in weakly structured regions of proteins using microfluidics-enabled subsecond H/D exchange mass spectrometry.

    PubMed

    Rob, Tamanna; Liuni, Peter; Gill, Preet Kamal; Zhu, Shaolong; Balachandran, Naresh; Berti, Paul J; Wilson, Derek J

    2012-04-17

    This work introduces an integrated microfluidic device for measuring rapid H/D exchange (HDX) in proteins. By monitoring backbone amide HDX on the millisecond to low second time scale, we are able to characterize conformational dynamics in weakly structured regions, such as loops and molten globule-like domains that are inaccessible in conventional HDX experiments. The device accommodates the entire MS-based HDX workflow on a single chip with residence times sufficiently small (ca. 8 s) that back-exchange is negligible (≤5%), even without cooling. Components include an adjustable position capillary mixer providing a variable-time labeling pulse, a static mixer for HDX quenching, a proteolytic microreactor for rapid protein digestion, and on-chip electrospray ionization (ESI). In the present work, we characterize device performance using three model systems, each illustrating a different application of 'time-resolved' HDX. Ubiquitin is used to illustrate a crude, high throughput structural analysis based on a single subsecond HDX time-point. In experiments using cytochrome c, we distinguish dynamic behavior in loops, establishing a link between flexibility and interactions with the heme prosthetic group. Finally, we localize an unusually high 'burst-phase' of HDX in the large tetrameric enzyme DAHP synthase to a 'molten globule-like' region surrounding the active site.

  5. Development of Online pH Gradient-Eluted Strong Cation Exchange Nanoelectrospray-Tandem Mass Spectrometry for Proteomic Analysis Facilitating Basic and Histidine-Containing Peptides Identification.

    PubMed

    Xu, Jingjing; Gao, Jing; Yu, Chengli; He, Han; Yang, Yiming; Figeys, Daniel; Zhou, Hu

    2016-01-05

    A novel one-dimensional online pH gradient-eluted strong cation exchange-nanoelectrospray ionization-tandem mass spectrometry (SCX-nano-ESI-MS/MS) method was developed for protein identification and tested with a mixture of six standard proteins, total lysate of HuH7 and N2a cells, as well as membrane fraction of N2a cells. This method utilized an online nanoflow SCX column in a nano-LC system coupled with a nanoelectrospray high-resolution mass spectrometer. Protein digests were separated on a nanoflow SCX column with a pH gradient and directly introduced into a mass spectrometer through nanoelectrospray ionization. More than five thousand unique peptides were identified in each 90 min LC-MS/MS run using 500 nanogram of protein digest either from total cell lysate or from membrane fraction. The unique peptide overlap between online strong cation exchange nano-ESI-MS/MS (SCXLC-MS/MS) and reverse phase nano-ESI-MS/MS (RPLC-MS/MS) is only ≤30%, which indicated these two methods were complementary to each other. The correlation coefficient of retention time and theoretical isoelectric point (pI) of identified peptides in SCXLC-MS/MS was higher than 0.4, which showed that peptides elution in SCXLC-MS/MS was dependent on their charge states. Furthermore, SCXLC-MS/MS showed identification capability for a higher proportion of basic peptides compared to the RPLC-MS/MS method, especially for histidine-containing peptides. Our SCXLC-MS/MS method is an excellent alternative method to the RPLC-MS/MS method for analysis of standard proteins, total cell and membrane proteomes.

  6. Preparation of Microvolume Anion-Exchange Cartridge for Inductively Coupled Plasma Mass Spectrometry-Based Determination of (237)Np Content in Spent Nuclear Fuel.

    PubMed

    Asai, Shiho; Hanzawa, Yukiko; Konda, Miki; Suzuki, Daisuke; Magara, Masaaki; Kimura, Takaumi; Ishihara, Ryo; Saito, Kyoichi; Yamada, Shinsuke; Hirota, Hideyuki

    2016-03-15

    Microvolume anion-exchange porous polymer disk-packed cartridges were prepared for Am/Np separation, which is required prior to the measurement of Neptunium-237 ((237)Np) with inductively coupled plasma mass spectrometry (ICPMS). Disks with a volume of 0.08 cm(3) were cut out from porous sheets having anion-exchange-group-containing polymer chains densely attached on the pore surface. Four different amine-based groups, N,N-dimethylaminoethyl methacrylate, trimethylammonium, diethylamine, and triethylenediamine (TEDA), were selected as the anion-exchange groups to be introduced into the porous sheets. The separation performances of Am/Np were evaluated using a standard solution of (243)Am, which had the same activity as its daughter nuclide (239)Np in secular equilibrium. (239)Np recovery of close to 100% with practically no contamination of (243)Am was achieved using the TEDA-introduced disk-packed cartridge. The time to elute (239)Np from the cartridge was approximately 40 s. The TEDA-introduced disk-packed cartridge was applied to the separation of Np from a spent nuclear fuel sample to confirm its separation performance. A known amount of (243)Am ((239)Np) was added to the spent nuclear fuel sample solution to monitor the chemical yield of Np. The chemical yield of Np calculated from a measured concentration of (239)Np was 90.4%. Am leakage in the Np-eluted solution was less than 1 ppt, corresponding to 0.001% of the original Am concentration in the sample. This indicates that no additional (239)Np was produced by the decay of the (243)Am remaining in the Np-eluted solution, thus providing a reliable chemical yield. U, which can cause a serious spectral interference involving the peak tail from the mass spectrum of (238)U, was thoroughly removed with the TEDA cartridge, providing interference-free measurement of (237)Np. The concentration of (237)Np obtained by ICPMS was 718 ± 12 ng/mg-U, which agrees well with the theoretically calculated value. Compared with

  7. Analyzing critical propagation in a reaction-diffusion-advection model using unstable slow waves.

    PubMed

    Kneer, Frederike; Obermayer, Klaus; Dahlem, Markus A

    2015-02-01

    The effect of advection on the propagation and in particular on the critical minimal speed of traveling waves in a reaction-diffusion model is studied. Previous theoretical studies estimated this effect on the velocity of stable fast waves and predicted the existence of a critical advection strength below which propagating waves are not supported anymore. In this paper, an analytical expression for the advection-velocity relation of the unstable slow wave is derived. In addition, the critical advection strength is calculated taking into account the unstable slow wave solution. We also analyze a two-variable reaction-diffusion-advection model numerically in a wide parameter range. Due to the new control parameter (advection) we can find stable wave propagation in the otherwise non-excitable parameter regime, if the advection strength exceeds a critical value. Comparing theoretical predictions to numerical results, we find that they are in good agreement. Theory provides an explanation for the observed behaviour.

  8. Dynamic typology of hydrothermal systems: competing effects of advection, dispersion and reactivity

    NASA Astrophysics Data System (ADS)

    Dolejs, David

    2016-04-01

    Genetic interpretation hydrothermal systems relies on recognition of (i) hydrothermal fluid source, (ii) fluid migration pathways, and (iii) deposition site identified by hydrothermal alteration and/or mineralization. Frequently, only the last object is of interest or accessible to direct observation, but constraints on the fluid source (volume) and pathways can be obtained from evaluation of the time-integrated fluid flux during hydrothermal event. Successful interpretation of the petrological record, that is, progress of alteration reactions, relies on identification of individual contributions arising from solute advection (to the deposition site), its lateral dispersion, and reaction efficiency. Although these terms are all applicable in a mass-conservation relationship within the framework of the transport theory, they are rarely considered simultaneously and their relative magnitudes evaluated. These phenomena operate on variable length and time scales, and may in turn provide insight into the system dynamics such as flow, diffusion and reaction rates, or continuous vs. episodic behavior of hydrothermal events. In addition, here we demonstrate that they also affect estimate of the net fluid flux, frequently by several orders of magnitude. The extent of alteration and mineralization reactions between the hydrothermal fluid and the host environment is determined by: (i) temperature, pressure or any other gradients across the mineralization site, (ii) magnitude of disequilibrium at inflow to the mineralization site, which is related to physico-chemical gradient between the fluid source and the mineralization site, and (iii) chemical redistribution (dispersion) within the mineralization site. We introduce quantitative mass-transport descriptors - Péclet and Damköhler II numbers - to introduce division into dispersion-dominated, advection-dominated and reaction-constrained systems. Dispersive systems are characterized by lateral solute redistribution, driven by

  9. Formation of metal-nicotianamine complexes as affected by pH, ligand exchange with citrate and metal exchange. A study by electrospray ionization time-of-flight mass spectrometry.

    PubMed

    Rellán-Alvarez, Rubén; Abadía, Javier; Alvarez-Fernández, Ana

    2008-05-01

    Nicotianamine (NA) is considered as a key element in plant metal homeostasis. This non-proteinogenic amino acid has an optimal structure for chelation of metal ions, with six functional groups that allow octahedral coordination. The ability to chelate metals by NA is largely dependent on the pK of the resulting complex and the pH of the solution, with most metals being chelated at neutral or basic pH values. In silico calculations using pKa and pK values have predicted the occurrence of metal-NA complexes in plant fluids, but the use of soft ionization techniques (e.g. electrospray), together with high-resolution mass spectrometers (e.g. time-of-flight mass detector), can offer direct and metal-specific information on the speciation of NA in solution. We have used direct infusion electrospray ionization mass spectrometry (time-of-flight) ESI-MS(TOF) to study the complexation of Mn, Fe(II), Fe(III), Ni, Cu by NA. The pH dependence of the metal-NA complexes in ESI-MS was compared to that predicted in silico. Possible exchange reactions that may occur between Fe-NA and other metal micronutrients as Zn and Cu, as well as between Fe-NA and citrate, another possible Fe ligand candidate in plants, were studied at pH 5.5 and 7.5, values typical of the plant xylem and phloem saps. Metal-NA complexes were generally observed in the ESI-MS experiments at a pH value approximately 1-2 units lower than that predicted in silico, and this difference could be only partially explained by the estimated error, approximately 0.3 pH units, associated with measuring pH in organic solvent-containing solutions. Iron-NA complexes are less likely to participate in ligand- and metal-exchange reactions at pH 7.5 than at pH 5.5. Results support that NA may be the ligand chelating Fe at pH values usually found in phloem sap, whereas in the xylem sap NA is not likely to be involved in Fe transport, conversely to what occurs with other metals such as Cu and Ni. Some considerations that need to be

  10. Chaotic advection in the restricted four-vortex problem on a sphere

    NASA Astrophysics Data System (ADS)

    Newton, Paul K.; Ross, Shane D.

    2006-11-01

    The chaotic advection of tracer particles in the field of a perturbed latitudinal ring of point vortices on a sphere is considered. We consider a restricted four-vortex problem where three vortices have equal strength, while the fourth has strength zero. The equal-strength vortices are initially spaced evenly on a ring of fixed latitude in the northern hemisphere. The equilateral triangle formed by the vortices is known to be a nonlinearly stable relative equilibrium configuration. When perturbed, the vortex motion induces chaotic particle advection analyzed by means of stroboscopic Poincaré maps as a function of the dimensionless energy of the system, which can be related to the size of the perturbation from equilibrium. A critical energy is identified which separates the vortex motion into two distinct dynamical regimes. For energies below critical, the vortices undergo periodic partner exchange while retaining their relative orientation. For values above critical, the relative orientation of the vortices changes throughout the periodic cycle. We consider how the streamline topologies bifurcate both as a function of the energy and during the course of their evolution, as well as the role that the evolution of instantaneous streamline structures plays in the mixing and transport of particles. The geometric extent of the mixing region on the full sphere is considered (measured as a percentage of the surface area of the sphere) and dynamical properties in the region, such as mixing and stretching rates as well as computational evidence of ergodicity, are obtained. Global mixing on the sphere does not seem to increase monotonically with energy, but appears to be maximized for values near critical.

  11. Visualizing Vector Fields Using Line Integral Convolution and Dye Advection

    NASA Technical Reports Server (NTRS)

    Shen, Han-Wei; Johnson, Christopher R.; Ma, Kwan-Liu

    1996-01-01

    We present local and global techniques to visualize three-dimensional vector field data. Using the Line Integral Convolution (LIC) method to image the global vector field, our new algorithm allows the user to introduce colored 'dye' into the vector field to highlight local flow features. A fast algorithm is proposed that quickly recomputes the dyed LIC images. In addition, we introduce volume rendering methods that can map the LIC texture on any contour surface and/or translucent region defined by additional scalar quantities, and can follow the advection of colored dye throughout the volume.

  12. Update on Advection-Diffusion Purge Flow Model

    NASA Technical Reports Server (NTRS)

    Brieda, Lubos

    2015-01-01

    Gaseous purge is commonly used in sensitive spacecraft optical or electronic instruments to prevent infiltration of contaminants and/or water vapor. Typically, purge is sized using simplistic zero-dimensional models that do not take into account instrument geometry, surface effects, and the dependence of diffusive flux on the concentration gradient. For this reason, an axisymmetric computational fluid dynamics (CFD) simulation was recently developed to model contaminant infiltration and removal by purge. The solver uses a combined Navier-Stokes and Advection-Diffusion approach. In this talk, we report on updates in the model, namely inclusion of a particulate transport model.

  13. Subsurface barrier design alternatives for confinement and controlled advection flow

    SciTech Connect

    Phillips, S.J.; Stewart, W.E.; Alexander, R.G.; Cantrell, K.J.; McLaughlin, T.J.

    1994-02-01

    Various technologies and designs are being considered to serve as subsurface barriers to confine or control contaminant migration from underground waste storage or disposal structures containing radioactive and hazardous wastes. Alternatives including direct-coupled flood and controlled advection designs are described as preconceptual examples. Prototype geotechnical equipment for testing and demonstration of these alternative designs tested at the Hanford Geotechnical Development and Test Facility and the Hanford Small-Tube Lysimeter Facility include mobile high-pressure injectors and pumps, mobile transport and pumping units, vibratory and impact pile drivers, and mobile batching systems. Preliminary laboratory testing of barrier materials and additive sequestering agents have been completed and are described.

  14. Is Chaotic Advection Inherent to Porous Media Flow?

    NASA Astrophysics Data System (ADS)

    Lester, Daniel; Metcalfe, Guy; Trefry, Mike

    2013-11-01

    All porous media, including granular and packed media, fractured and open networks, are typified by the inherent topological complexity of the pore-space. This topological complexity admits a large number density of stagnation points under steady Stokes flow, which in turn generates a 3D fluid mechanical analouge of the Bakers map, termed the Baker's flow. We demonstrate that via this mechanism, chaotic advection at the pore-scale is inherent to almost all porous media under reasonable conditions, and such dynamics have significant implications for a range of fluid-borne processes including transport and mixing, chemical reactions and biological activity.

  15. Vortex emission accompanies the advection of optical localized structures.

    PubMed

    Haudin, F; Rojas, R G; Bortolozzo, U; Clerc, M G; Residori, S

    2011-02-11

    We show that the advection of optical localized structures is accompanied by the emission of vortices, with phase singularities appearing in the wake of the drifting structure. Localized structures are obtained in a light-valve experiment and made to drift by a mirror tilt in the feedback loop. Pairs of oppositely charged vortices are detected for small drifts, whereas for large drifts a vortex array develops. Observations are supported by numerical simulations and linear stability analysis of the system equations and are expected to be generic for a large class of translated optical patterns.

  16. A convexity preserving scheme for conservative advection transport

    NASA Astrophysics Data System (ADS)

    Xiao, Feng; Peng, Xindong

    2004-08-01

    A simple and practical scheme for advection transport equation is presented. The scheme, namely piecewise rational method (PRM), is a variant of the existing piecewise parabolic method (PPM) of Colella and Woodward (1984). Instead of the parabolic function, a rational function is used for the reconstruction. Making use of the convexity preserving nature of the rational function enables us to obtain oscillation-less numerical solutions, but avoids the adjustments of the cell-interface values to enforce the monotonicity in PPM. The PRM is very simple and computationally efficient. Our numerical results show that PRM is competitive to the PPM in many aspects, such as numerical accuracy and shape-preserving property.

  17. Proteomic analysis with integrated multiple dimensional liquid chromatography/mass spectrometry based on elution of ion exchange column using pH steps.

    PubMed

    Dai, Jie; Shieh, Chia Hui; Sheng, Quan-Hu; Zhou, Hu; Zeng, Rong

    2005-09-15

    A novel integrated multidimensional liquid chromatography (IMDL) method is demonstrated for the separation of peptide mixtures by two-dimensional HPLC coupled with ion trap mass spectrometry. The method uses an integrated column, containing both strong cation exchange and reversed-phase sections for two-dimensional liquid chromatography. The peptide mixture was fractionated by a pH step using a series of pH buffers, followed by reversed-phase chromatography. Since no salt was used during separation, the integrated multidimensional liquid chromatography can be directly connected to mass spectrometry for peptide analysis. The pH buffers were injected from an autosampler, and the entire process can be carried out on a one-dimensional liquid chromatography system. In a single analysis, the IMDL system, coupled with linear ion trap mass spectrometry, identified more than 2000 proteins in mouse liver. The peptides were eluted according to their pI distribution. The resolution of the pH fractionation is approximately 0.5 pH unit. The method has low overlapping across pH fractions, good resolution of peptide mixture, and good correlation of peptide pIs with pH steps. This method provides a technique for large-scale protein identification using existing one-dimensional HPLC systems.

  18. Formation of the black-hole binary M33 X-7 through mass exchange in a tight massive system.

    PubMed

    Valsecchi, Francesca; Glebbeek, Evert; Farr, Will M; Fragos, Tassos; Willems, Bart; Orosz, Jerome A; Liu, Jifeng; Kalogera, Vassiliki

    2010-11-04

    The X-ray source M33 X-7 in the nearby galaxy Messier 33 is among the most massive X-ray binary stellar systems known, hosting a rapidly spinning, 15.65M(⊙) black hole orbiting an underluminous, 70M(⊙) main-sequence companion in a slightly eccentric 3.45-day orbit (M(⊙), solar mass). Although post-main-sequence mass transfer explains the masses and tight orbit, it leaves unexplained the observed X-ray luminosity, the star's underluminosity, the black hole's spin and the orbital eccentricity. A common envelope phase, or rotational mixing, could explain the orbit, but the former would lead to a merger and the latter to an overluminous companion. A merger would also ensue if mass transfer to the black hole were invoked for its spin-up. Here we report simulations of evolutionary tracks which reveal that if M33 X-7 started as a primary body of 85M(⊙)-99M(⊙) and a secondary body of 28M(⊙)-32M(⊙), in a 2.8-3.1-d orbit, its observed properties can be consistently explained. In this model, the main-sequence primary transfers part of its envelope to the secondary and loses the rest in a wind; it ends its life as a ∼16M(⊙) helium star with an iron-nickel core that collapses to a black hole (with or without an accompanying supernova). The release of binding energy, and possibly collapse asymmetries, 'kick' the nascent black hole into an eccentric orbit. Wind accretion explains the X-ray luminosity, and the black-hole spin can be natal.

  19. Second All-Union Seminar on Hydromechanics and Heat and Mass Exchange in Weightlessness, summaries of reports

    NASA Technical Reports Server (NTRS)

    Gershuni, G. Z. (Editor); Zhukhovitskiy, Y. M. (Editor)

    1984-01-01

    Abstracts of reports are given which were presented at the Second All Union Seminar on Hydromechanics and Heat-Mass Transfer in Weightlessness. Topics include: (1) features of crystallization of semiconductor materials under conditions of microacceleration; (2) experimental results of crystallization of solid solutions of CDTE-HGTE under conditions of weightlessness; (3) impurities in crystals cultivated under conditions of weightlessness; and (4) a numerical investigation of the distribution of impurities during guided crystallization of a melt.

  20. Direct analysis of ultra-trace semiconductor gas by inductively coupled plasma mass spectrometry coupled with gas to particle conversion-gas exchange technique.

    PubMed

    Ohata, Masaki; Sakurai, Hiromu; Nishiguchi, Kohei; Utani, Keisuke; Günther, Detlef

    2015-09-03

    An inductively coupled plasma mass spectrometry (ICPMS) coupled with gas to particle conversion-gas exchange technique was applied to the direct analysis of ultra-trace semiconductor gas in ambient air. The ultra-trace semiconductor gases such as arsine (AsH3) and phosphine (PH3) were converted to particles by reaction with ozone (O3) and ammonia (NH3) gases within a gas to particle conversion device (GPD). The converted particles were directly introduced and measured by ICPMS through a gas exchange device (GED), which could penetrate the particles as well as exchange to Ar from either non-reacted gases such as an air or remaining gases of O3 and NH3. The particle size distribution of converted particles was measured by scanning mobility particle sizer (SMPS) and the results supported the elucidation of particle agglomeration between the particle converted from semiconductor gas and the particle of ammonium nitrate (NH4NO3) which was produced as major particle in GPD. Stable time-resolved signals from AsH3 and PH3 in air were obtained by GPD-GED-ICPMS with continuous gas introduction; however, the slightly larger fluctuation, which could be due to the ionization fluctuation of particles in ICP, was observed compared to that of metal carbonyl gas in Ar introduced directly into ICPMS. The linear regression lines were obtained and the limits of detection (LODs) of 1.5 pL L(-1) and 2.4 nL L(-1) for AsH3 and PH3, respectively, were estimated. Since these LODs revealed sufficiently lower values than the measurement concentrations required from semiconductor industry such as 0.5 nL L(-1) and 30 nL L(-1) for AsH3 and PH3, respectively, the GPD-GED-ICPMS could be useful for direct and high sensitive analysis of ultra-trace semiconductor gas in air.

  1. An advective volume-balance model for flow in porous media

    NASA Astrophysics Data System (ADS)

    Malaga, Carlos; Mandujano, Francisco; Becerra, Julian

    2016-11-01

    Volume-balance models are used by petroleum engineers to simulate multiphase and multicomponent flow phenomena in porous media and the extraction process in oil reservoirs. In these models, mass conservation equations and Darcy's law are supplemented by a balance condition for the pore and fluid volumes. This provides a pressure equation suitable for simulating a compressible flow within a compressible solid matrix. Here we present an alternative interpretation of the volume-balance condition that includes the advective transport within a consolidated porous media. We obtain a modified equation for the time evolution of the pressure field. Preliminary numerical tests of phase separation due to gravity suggest the model reproduces qualitatively the physical phenomena. Fondo Sectorial CONACYT-SENER Grant Number 42536 (DGAJ-SPI-34-170412-217).

  2. Determination of self-exchange rate of alkanethiolates in self-assembled monolayers on gold using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

    PubMed

    Kang, Hyunook; Kim, Yongbin; Choi, Inseong; Chang, Rakwoo; Yeo, Woon-Seok

    2014-09-16

    In this paper, we describe a new method for determining the exchange rates of alkanethiolates in self-assembled monolayers (SAMs) on gold using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze the compositions of the alkanethiolate in SAMs rapidly and directly. In particular, to investigate the self-exchange of alkanethiols, we prepared a deuterated alkanethiol that has the same molecular properties as the non-deuterated alkanethiol but a different molecular weight. SAMs consisting of deuterated alkanethiolates were immersed in a solution of the non-deuterated alkanethiol, and the influences of the immersion time, temperature, concentration, and solvent on the self-exchange rates were investigated. Furthermore, we assessed the exchange rates among alkanethiols with different carbon chain lengths and different size of ethylene glycol units. In addition, we performed molecular dynamics simulations using a model SAM system in order to understand the molecular mechanism of the exchange process.

  3. A Residue Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions.

    PubMed

    Saltzberg, Daniel John; Broughton, Howard B; Pellarin, Riccardo; Chalmers, Michael J; Espada, Alfonso; Dodge, Jeffrey A; Pascal, Bruce D; Griffin, Patrick R; Humblet, Christine; Sali, Andrej

    2016-11-03

    Characterization of interactions between proteins and other molecules is crucial for understanding the mechanisms of action of biological systems and, thus, drug discovery. An increasingly useful approach to mapping these interactions is measurement of hydrogen/deuterium exchange (HDX) using mass spectrometry (HDX-MS), which measures the time-resolved deuterium incorporation of peptides obtained by enzymatic digestion of the protein. Comparison of exchange rates between apo- and ligand-bound conditions results in a mapping of the differential HDX (ΔHDX) of the ligand. Residue-level analysis of these data, however, must account for experimental error, sparseness and ambiguity due to overlapping peptides. Here, we propose a Bayesian method consisting of a forward model, noise model, prior probabilities, and a Monte Carlo sampling scheme. This method exploits a residue-resolved exponential rate model of HDX-MS data obtained from all peptides simultaneously, and explicitly models experimental error. The result is the best possible estimate of ΔHDX magnitude and significance for each residue given the data. We demonstrate the method by revealing richer structural interpretation of ΔHDX data on two nuclear receptors: vitamin D-receptor (VDR) and retinoic acid receptor gamma (RORγ). The method is implemented in HDX Workbench and as a standalone module of the open source Integrative Modeling Platform.

  4. Minimizing Carry-Over in an Online Pepsin Digestion System used for the H/D Exchange Mass Spectrometric Analysis of an IgG1 Monoclonal Antibody

    NASA Astrophysics Data System (ADS)

    Majumdar, Ranajoy; Manikwar, Prakash; Hickey, John M.; Arora, Jayant; Middaugh, C. Russell; Volkin, David B.; Weis, David D.

    2012-12-01

    Chromatographic carry-over can severely distort measurements of amide H/D exchange in proteins analyzed by LC/MS. In this work, we explored the origin of carry-over in the online digestion of an IgG1 monoclonal antibody using an immobilized pepsin column under quenched H/D exchange conditions (pH 2.5, 0 °C). From a consensus list of 169 different peptides consistently detected during digestion of this large, ~150 kDa protein, approximately 30 % of the peptic peptides exhibited carry-over. The majority of carry-over originates from the online digestion. Carry-over can be substantially decreased by washing the online digestion flow-path and pepsin column with two wash cocktails: [acetonitrile (5 %)/ isopropanol (5 %)/ acetic acid (20 %) in water] and [2 M guanidine hydrochloride in 100 mM phosphate buffer pH 2.5]. Extended use of this two-step washing procedure does not adversely affect the specificity or activity of the immobilized pepsin column. The results suggest that although the mechanism of carry-over appears to be chemical in nature, and not hydrodynamic, carry-over cannot be attributed to a single factor such as mass, abundance, pI, or hydrophobicity of the peptides.

  5. Determination of Histidine pKa Values in the Propeptides of Furin and Proprotein Convertase 1/3 Using Histidine Hydrogen-Deuterium Exchange Mass Spectrometry.

    PubMed

    Elferich, Johannes; Williamson, Danielle M; David, Larry L; Shinde, Ujwal

    2015-08-04

    Propeptides of proprotein convertases regulate activation of their protease domains by sensing the organellar pH within the secretory pathway. Earlier experimental work highlighted the importance of a conserved histidine residue within the propeptide of a widely studied member, furin. A subsequent evolutionary analysis found an increase in histidine content within propeptides of secreted eukaryotic proteases compared with their prokaryotic orthologs. However, furin activates in the trans-golgi network at a pH of 6.5 while a paralog, proprotein convertase 1/3, activates in secretory vesicles at a pH of 5.5. It is unclear how a conserved histidine can mediate activation at two different pH values. In this manuscript, we measured the pKa values of histidines within the propeptides of furin and proprotein convertase 1/3 using a histidine hydrogen-deuterium exchange mass spectrometry approach. The high density of histidine residues combined with an abundance of basic residues provided challenges for generation of peptide ions with unique histidine residues, which were overcome by employing ETD fragmentation. During this analysis, we found slow hydrogen-deuterium exchange in residues other than histidine at basic pH. Finally, we demonstrate that the pKa of the conserved histidine in proprotein convertase 1/3 is acid-shifted compared with furin and is consistent with its lower pH of activation.

  6. Interaction of arginine with protein during refolding process probed by amide H/D exchange mass spectrometry and isothermal titration calorimetry.

    PubMed

    Zhao, Dawei; Liu, Yongdong; Zhang, Guifeng; Zhang, Chun; Li, Xiunan; Wang, Qingqing; Shi, Hong; Su, Zhiguo

    2015-01-01

    Arginine has been widely used as low molecular weight additive to promote protein refolding by suppressing aggregate formation. However, methods to investigate the role of arginine in protein refolding are often limited on protein's global conformational properties. Here, hydrogen/deuterium exchange mass spectrometry (HDX-MS) was used to study the effects of arginine on recombinant human granulocyte colony-stimulating factor (rhG-CSF) refolding at the scale of peptide mapping. It was found that deuteration levels of rhG-CSF refolded with arginine was higher than that without arginine during the whole refolding process, but they became almost the same when the refolding reached equilibrium. This phenomenon indicated that arginine could protect some amide deuterium atoms from being exchanged with hydrogen, but the protection diminished gradually along with refolding proceeding. Enzymatic digestion revealed six particular peptides of 16-47, 72-84, 84-93, 114-124, 145-153 and 154-162 were mainly responsible for the deuteration, and all of them dominantly located in protein's α-helix domain. Furthermore, thermodynamics analysis by isothermal titration calorimetry provided direct evidence that arginine could only react with denatured and partially refolded rhG-CSF. Taking all of the results together, we suggest that arginine suppresses protein aggregation by a reversible combination. At the initial refolding stage, arginine could combine with the denatured protein mainly through hydrogen bonding. Subsequently, arginine is gradually excluded from protein with protein's native conformation recovering.

  7. Elucidation of the binding sites of sodium dodecyl sulfate to β-lactoglobulin using hydrogen/deuterium exchange mass spectrometry combined with docking simulation.

    PubMed

    Hu, Wenbing; Liu, Jianan; Luo, Qun; Han, Yumiao; Wu, Kui; Lv, Shuang; Xiong, Shaoxiang; Wang, Fuyi

    2011-05-30

    Hydrogen/deuterium exchange mass spectrometry (H/DX MS) has become a powerful tool to investigate protein-protein and protein-ligand interactions, but it is still challenging to localize the interaction regions/sites of ligands with pepsin-resistant proteins such as lipocalins. β-Lactoglobulin (BLG), a member of the lipocalin family, can bind a variety of small hydrophobic molecules including retinols, retinoic acids, and long linear fatty acids. However, whether the binding site of linear molecules locates in the external groove or internal cavity of BLG is controversial. In this study we used H/DX MS combined with docking simulation to localize the interaction sites of a tested ligand, sodium dodecyl sulfate (SDS), binding to BLG. H/DX MS results indicated that SDS can bind to both the external and the internal sites in BLG. However, neither of the sites is saturated with SDS, allowing a dynamic ligand exchange to occur between the sites at equilibrium state. Docking studies revealed that SDS forms H-bonds with Lys69 in the internal site and Lys138 and Lys141 in the external site in BLG via the sulfate group, and interacts with the hydrophobic residues valine, leucine, isoleucine and methionine within both of the sites via its hydrocarbon tail, stabilizing the BLG-SDS complex.

  8. Role of tentacles and protein loading on pore accessibility and mass transfer in cation exchange materials for proteins.

    PubMed

    Thomas, Helen; Coquebert de Neuville, Bertrand; Storti, Giuseppe; Morbidelli, Massimo; Joehnck, Matthias; Schulte, Michael

    2013-04-12

    In protein chromatography, the size of the protein determines which fraction of pores it can access within a resin and at which rate of diffusion. Moreover, in the presence of grafted polymers like in advanced materials, adsorbed proteins and electrolytes complicate the interaction pore-protein. In this study, we evaluated in a comparative way the behavior of Fractogel EMD SO3 (M) and (S), "tentacle"-type, strong cation exchangers, as well as a reference material without tentacles, all of which are commonly used for protein purification. ISEC experiments were carried out with a set of Dextran tracers of largely different molecular size covering the typical range of protein sizes. Experimental values of porosity (internal and external to the particles) as well as of pore diffusion coefficients have been measured at different NaCl concentrations and under protein loading. These results provide useful insights into the complex interplay among mentioned factors: first, the presence of tentacles induces size exclusion selectivity in the materials; second, the salt induces conformational changes of the tentacles, leading to porosities larger than expected in tentacle materials; third, protein adsorption mainly leads to a reduction of porosity due to pore space occupied by the protein and to a decrease of pore diffusion coefficient.

  9. Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 3. Estimating Surface Area Exposure by Deuterium Uptake.

    PubMed

    Khakinejad, Mahdiar; Kondalaji, Samaneh Ghassabi; Donohoe, Gregory C; Valentine, Stephen J

    2016-03-01

    Gas-phase hydrogen deuterium exchange (HDX), collision cross section (CCS) measurement, and molecular dynamics simulation (MDS) techniques were utilized to develop and compare three methods for estimating the relative surface area exposure of separate peptide chains within bovine insulin ions. Electrosprayed [M - 3H](3-) and [M - 5H](5-) insulin ions produced a single conformer type with respective collision cross sections of 528 ± 5 Å(2) and 808 ± 2 Å(2). [M - 4H](4-) ions were comprised of more compact (Ω = 676 ± 3 Å(2)) and diffuse (i.e., more elongated, Ω = 779 ± 3 Å(2)) ion conformer types. Ions were subjected to HDX in the drift tube using D2O as the reagent gas. Collision-induced dissociation was used to fragment mobility-selected, isotopically labeled [M - 4H](4-) and [M - 5H](5-) ions into the protein subchains. Deuterium uptake levels of each chain can be explained by limited inter-chain isotopic scrambling upon collisional activation. Using nominal ion structures from MDS and a hydrogen accessibility model, the deuterium uptake for each chain was correlated to its exposed surface area. In separate experiments, the per-residue deuterium content for the protonated and deprotonated ions of the synthetic peptide KKDDDDDIIKIIK were compared. The differences in deuterium content indicated the regional HDX accessibility for cations versus anions. Using ions of similar conformational type, this comparison highlights the complementary nature of HDX data obtained from positive- and negative-ion analysis.

  10. Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 3. Estimating Surface Area Exposure by Deuterium Uptake

    NASA Astrophysics Data System (ADS)

    Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Donohoe, Gregory C.; Valentine, Stephen J.

    2016-03-01

    Gas-phase hydrogen deuterium exchange (HDX), collision cross section (CCS) measurement, and molecular dynamics simulation (MDS) techniques were utilized to develop and compare three methods for estimating the relative surface area exposure of separate peptide chains within bovine insulin ions. Electrosprayed [M - 3H]3- and [M - 5H]5- insulin ions produced a single conformer type with respective collision cross sections of 528 ± 5 Å2 and 808 ± 2 Å2. [M - 4H]4- ions were comprised of more compact (Ω = 676 ± 3 Å2) and diffuse (i.e., more elongated, Ω = 779 ± 3 Å2) ion conformer types. Ions were subjected to HDX in the drift tube using D2O as the reagent gas. Collision-induced dissociation was used to fragment mobility-selected, isotopically labeled [M - 4H]4- and [M - 5H]5- ions into the protein subchains. Deuterium uptake levels of each chain can be explained by limited inter-chain isotopic scrambling upon collisional activation. Using nominal ion structures from MDS and a hydrogen accessibility model, the deuterium uptake for each chain was correlated to its exposed surface area. In separate experiments, the per-residue deuterium content for the protonated and deprotonated ions of the synthetic peptide KKDDDDDIIKIIK were compared. The differences in deuterium content indicated the regional HDX accessibility for cations versus anions. Using ions of similar conformational type, this comparison highlights the complementary nature of HDX data obtained from positive- and negative-ion analysis.

  11. Predicting protein aggregation during storage in lyophilized solids using solid state amide hydrogen/deuterium exchange with mass spectrometric analysis (ssHDX-MS).

    PubMed

    Moorthy, Balakrishnan S; Schultz, Steven G; Kim, Sherry G; Topp, Elizabeth M

    2014-06-02

    Solid state amide hydrogen/deuterium exchange with mass spectrometric analysis (ssHDX-MS) was used to assess the conformation of myoglobin (Mb) in lyophilized formulations, and the results correlated with the extent of aggregation during storage. Mb was colyophilized with sucrose (1:1 or 1:8 w/w), mannitol (1:1 w/w), or NaCl (1:1 w/w) or in the absence of excipients. Immediately after lyophilization, samples of each formulation were analyzed by ssHDX-MS and Fourier transform infrared spectroscopy (FTIR) to assess Mb conformation, and by dynamic light scattering (DLS) and size exclusion chromatography (SEC) to determine the extent of aggregation. The remaining samples were then placed on stability at 25 °C and 60% RH or 40 °C and 75% RH for up to 1 year, withdrawn at intervals, and analyzed for aggregate content by SEC and DLS. In ssHDX-MS of samples immediately after lyophilization (t = 0), Mb was less deuterated in solids containing sucrose (1:1 and 1:8 w/w) than in those containing mannitol (1:1 w/w), NaCl (1:1 w/w), or Mb alone. Deuterium uptake kinetics and peptide mass envelopes also indicated greater Mb structural perturbation in mannitol, NaCl, or Mb-alone samples at t = 0. The extent of deuterium incorporation and kinetic parameters related to rapidly and slowly exchanging amide pools (Nfast, Nslow), measured at t = 0, were highly correlated with the extent of aggregation on storage as measured by SEC. In contrast, the extent of aggregation was weakly correlated with FTIR band intensity and peak position measured at t = 0. The results support the use of ssHDX-MS as a formulation screening tool in developing lyophilized protein drug products.

  12. Horizontal advection, diffusion and plankton spectra at the sea surface.

    NASA Astrophysics Data System (ADS)

    Bracco, A.; Clayton, S.; Pasquero, C.

    2009-04-01

    Plankton patchiness is ubiquitous in the oceans, and various physical and biological processes have been proposed as its generating mechanisms. However, a coherent statement on the problem is missing, due to both a small number of suitable observations and to an incomplete understanding of the properties of reactive tracers in turbulent media. Abraham (1998) suggested that horizontal advection may be the dominant process behind the observed distributions of phytoplankton and zooplankton, acting to mix tracers with longer reaction times (Rt) down to smaller scales. Conversely, Mahadevan and Campbell (2002) attributed the relative distributions of sea surface temperature and phytoplankton to small scale upwelling, where tracers with longer Rt are able to homogenize more than those with shorter reaction times. Neither of the above mechanisms can explain simultaneously the (relative) spectral slopes of temperature, phytoplankton and zooplankton. Here, with a simple advection model and a large suite of numerical experiments, we concentrate on some of the physical processes influencing the relative distributions of tracers at the ocean surface, and we investigate: 1) the impact of the spatial scale of tracer supply; 2) the role played by coherent eddies on the distribution of tracers with different Rt; 3) the role of diffusion (so far neglected). We show that diffusion determines the distribution of temperature, regardless of the nature of the forcing. We also find that coherent structures together with differential diffusion of tracers with different Rt impact the tracer distributions. This may help in understanding the highly variable nature of observed plankton spectra.

  13. Advection-Based Sparse Data Management for Visualizing Unsteady Flow.

    PubMed

    Guo, Hanqi; Zhang, Jiang; Liu, Richen; Liu, Lu; Yuan, Xiaoru; Huang, Jian; Meng, Xiangfei; Pan, Jingshan

    2014-12-01

    When computing integral curves and integral surfaces for large-scale unsteady flow fields, a major bottleneck is the widening gap between data access demands and the available bandwidth (both I/O and in-memory). In this work, we explore a novel advection-based scheme to manage flow field data for both efficiency and scalability. The key is to first partition flow field into blocklets (e.g. cells or very fine-grained blocks of cells), and then (pre)fetch and manage blocklets on-demand using a parallel key-value store. The benefits are (1) greatly increasing the scale of local-range analysis (e.g. source-destination queries, streak surface generation) that can fit within any given limit of hardware resources; (2) improving memory and I/O bandwidth-efficiencies as well as the scalability of naive task-parallel particle advection. We demonstrate our method using a prototype system that works on workstation and also in supercomputing environments. Results show significantly reduced I/O overhead compared to accessing raw flow data, and also high scalability on a supercomputer for a variety of applications.

  14. Local and nonlocal advection of a passive scalar

    NASA Astrophysics Data System (ADS)

    Scott, R. K.

    2006-11-01

    Passive and active scalar mixing is examined in a simple one-parameter family of two-dimensional flows based on quasi-geostrophic dynamics, in which the active scalar, the quasi-geostrophic potential vorticity, is confined to a single horizontal surface (so-called surface quasi-geostrophic dynamics) and in which a passive scalar field is also advected by the (horizontal, two-dimensional) velocity field at a finite distance from the surface. At large distances from the surface the flow is determined by the largest horizontal scales, the flow is spectrally nonlocal, and a chaotic advection-type regime dominates. At small distances, z, scaling arguments suggest a transition wavenumber kc˜1/2z, where the slope of the passive scalar spectrum changes from k-5/3, determined by local dynamics, to k-1, determined by nonlocal dynamics, analogous to the transition to a k-1 slope in the Batchelor regime in three-dimensional turbulence. Direct numerical simulations reproduce the qualitative aspects of this transition. Other characteristics of the simulated scalar fields, such as the relative dominance of coherent or filamentary structures, are also shown to depend strongly on the degree of locality.

  15. THE ADVECTION OF SUPERGRANULES BY THE SUN'S AXISYMMETRIC FLOWS

    SciTech Connect

    Hathaway, David H.; Williams, Peter E.; Rosa, Kevin Dela; Cuntz, Manfred E-mail: peter.williams@nasa.go

    2010-12-10

    We show that the motions of supergranules are consistent with a model in which they are simply advected by the axisymmetric flows in the Sun's surface shear layer. We produce a 10 day series of simulated Doppler images at a 15 minute cadence that reproduces most spatial and temporal characteristics seen in the SOHO/MDI Doppler data. Our simulated data have a spectrum of cellular flows with just two components-a granule component that peaks at spherical wavenumbers of about 4000 and a supergranule component that peaks at wavenumbers of about 110. We include the advection of these cellular components by the axisymmetric flows-differential rotation and meridional flow-whose variations with latitude and depth (wavenumber) are consistent with observations. We mimic the evolution of the cellular pattern by introducing random variations to the phases of the spectral components at rates that reproduce the levels of cross-correlation as functions of time and latitude. Our simulated data do not include any wave-like characteristics for the supergranules yet can reproduce the rotation characteristics previously attributed to wave-like behavior. We find rotation rates which appear faster than the actual rotation rates and attribute this to projection effects. We find that the measured meridional flow does accurately represent the actual flow and that the observations indicate poleward flow to 65{sup 0}-70{sup 0} latitude with equatorward countercells in the polar regions.

  16. Space-fractional advection-diffusion and reflective boundary condition.

    PubMed

    Krepysheva, Natalia; Di Pietro, Liliana; Néel, Marie-Christine

    2006-02-01

    Anomalous diffusive transport arises in a large diversity of disordered media. Stochastic formulations in terms of continuous time random walks (CTRWs) with transition probability densities showing space- and/or time-diverging moments were developed to account for anomalous behaviors. A broad class of CTRWs was shown to correspond, on the macroscopic scale, to advection-diffusion equations involving derivatives of noninteger order. In particular, CTRWs with Lévy distribution of jumps and finite mean waiting time lead to a space-fractional equation that accounts for superdiffusion and involves a nonlocal integral-differential operator. Within this framework, we analyze the evolution of particles performing symmetric Lévy flights with respect to a fluid moving at uniform speed . The particles are restricted to a semi-infinite domain limited by a reflective barrier. We show that the introduction of the boundary condition induces a modification in the kernel of the nonlocal operator. Thus, the macroscopic space-fractional advection-diffusion equation obtained is different from that in an infinite medium.

  17. Effects of demographic stochasticity on population persistence in advective media.

    PubMed

    Kolpas, Allison; Nisbet, Roger M

    2010-07-01

    Many populations live and disperse in advective media. A fundamental question, known as the "drift paradox" in stream ecology, is how a closed population can survive when it is constantly being transported downstream by the flow. Recent population-level models have focused on the role of diffusive movement in balancing the effects of advection, predicting critical conditions for persistence. Here, we formulate an individual-based stochastic analog of the model described in (Lutscher et al., SIAM Rev. 47(4):749-772, 2005) to quantify the effects of demographic stochasticity on persistence. Population dynamics are modeled as a logistic growth process and dispersal as a position-jump process on a finite domain divided into patches. When there is no correlation in the interpatch movement of residents, stochasticity simply smooths the persistence-extinction boundary. However, when individuals disperse in "packets" from one patch to another and the flow field is memoryless on the timescale of packet transport, the probability of persistence is greatly enhanced. The latter transport mechanism may be characteristic of larval dispersal in the coastal ocean or wind-dispersed seed pods.

  18. Transient responses to spatial perturbations in advective systems.

    PubMed

    Anderson, Kurt E; Nisbet, Roger M; McCauley, Edward

    2008-07-01

    We study the transient dynamics, following a spatially-extended perturbation of models describing populations residing in advective media such as streams and rivers. Our analyses emphasize metrics that are independent of initial perturbations-resilience, reactivity, and the amplification envelope-and relate them to component spatial wavelengths of the perturbation using spatial Fourier transforms of the state variables. This approach offers a powerful way of understanding the influence of spatial scale on the initial dynamics of a population following a spatially variable environmental perturbation, an important property in determining the ecological implications of transient dynamics in advective systems. We find that asymptotically stable systems may exhibit transient amplification of perturbations (i.e., have positive reactivity) for some spatial wavelengths and not others. Furthermore, the degree and duration of amplification varies strongly with spatial wavelength. For two single-population models, there is a relationship between transient dynamics and the response length that characterizes the steady state response to spatial perturbations: a long response length implies that peak amplification of perturbations is small and occurs fast. This relationship holds less generally in a specialist consumer-resource model, likely due to the model's tendency for flow-induced instabilities at an alternative characteristic spatial scale.

  19. Observation of Magnetic Reconnection Driven by Granular Scale Advection

    NASA Astrophysics Data System (ADS)

    Zeng, Zhichen; Cao, W.; Ji, H.

    2013-07-01

    We report the first evidence of magnetic reconnection driven by advection in a rapidly developing large granule, using high spatial resolution observations of a small surge event (base size 4‧‧ by 4‧‧) with the 1.6 meter aperture New Solar Telescope (NST) at Big Bear Solar Observatory. The observations were carried out in narrow-band (0.5 Å) Helium I 10830 Å and broad-band (10 Å) TiO 7057 Å. Since He I 10830 Å triplet has very high excitation level and is optically thin, its filtergrams enable us to investigate the surge from the photosphere through the chromosphere into the lower corona. Simultaneous space data from Atmospheric Imaging Assembly (AIA) and Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO) were used in the analysis. It is shown that the surge is spatio-temporally associated with magnetic flux emergence in the rapidly developing large granule. During the development of the granule, its advecting flow ( 2 km/ s) squeezed the magnetic flux into an intergranular lane area, where a magnetic flux concentration was formed and the neighboring flux with opposite magnetic polarity was cancelled. During the cancellation, the surge was produced as absorption in He I 10830 Å filtergrams while simultaneous EUV brightening occurred at its base. The observations clearly indicate evidence of finest-scale reconnection process driven by the granule’s motion.

  20. Observation of Magnetic Reconnection Driven by Granular Scale Advection

    NASA Astrophysics Data System (ADS)

    Zeng, Zhicheng; Cao, Wenda; Ji, Haisheng

    2013-06-01

    We report the first evidence of magnetic reconnection driven by advection in a rapidly developing large granule using high spatial resolution observations of a small surge event (base size ~ 4'' × 4'') with the 1.6 m aperture New Solar Telescope at the Big Bear Solar Observatory. The observations were carried out in narrowband (0.5 Å) He I 10830 Å and broadband (10 Å) TiO 7057 Å. Since He I 10830 Å triplet has a very high excitation level and is optically thin, its filtergrams enable us to investigate the surge from the photosphere through the chromosphere into the lower corona. Simultaneous space data from the Atmospheric Imaging Assembly and Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory were used in the analysis. It is shown that the surge is spatio-temporally associated with magnetic flux emergence in the rapidly developing large granule. During the development of the granule, its advecting flow (~2 km s-1) squeezed the magnetic flux into an intergranular lane area, where a magnetic flux concentration was formed and the neighboring flux with opposite magnetic polarity was canceled. During the cancellation, the surge was produced as absorption in He I 10830 Å filtergrams while simultaneous EUV brightening occurred at its base. The observations clearly indicate evidence of a finest-scale reconnection process driven by the granule's motion.

  1. Positivity-preserving numerical schemes for multidimensional advection

    NASA Technical Reports Server (NTRS)

    Leonard, B. P.; Macvean, M. K.; Lock, A. P.

    1993-01-01

    This report describes the construction of an explicit, single time-step, conservative, finite-volume method for multidimensional advective flow, based on a uniformly third-order polynomial interpolation algorithm (UTOPIA). Particular attention is paid to the problem of flow-to-grid angle-dependent, anisotropic distortion typical of one-dimensional schemes used component-wise. The third-order multidimensional scheme automatically includes certain cross-difference terms that guarantee good isotropy (and stability). However, above first-order, polynomial-based advection schemes do not preserve positivity (the multidimensional analogue of monotonicity). For this reason, a multidimensional generalization of the first author's universal flux-limiter is sought. This is a very challenging problem. A simple flux-limiter can be found; but this introduces strong anisotropic distortion. A more sophisticated technique, limiting part of the flux and then restoring the isotropy-maintaining cross-terms afterwards, gives more satisfactory results. Test cases are confined to two dimensions; three-dimensional extensions are briefly discussed.

  2. Chaotic advection in 2D anisotropic porous media

    NASA Astrophysics Data System (ADS)

    Varghese, Stephen; Speetjens, Michel; Trieling, Ruben; Toschi, Federico

    2015-11-01

    Traditional methods for heat recovery from underground geothermal reservoirs employ a static system of injector-producer wells. Recent studies in literature have shown that using a well-devised pumping scheme, through actuation of multiple injector-producer wells, can dramatically enhance production rates due to the increased scalar / heat transport by means of chaotic advection. However the effect of reservoir anisotropy on kinematic mixing and heat transport is unknown and has to be incorporated and studied for practical deployment in the field. As a first step, we numerically investigate the effect of anisotropy (both magnitude and direction) on (chaotic) advection of passive tracers in a time-periodic Darcy flow within a 2D circular domain driven by periodically reoriented diametrically opposite source-sink pairs. Preliminary results indicate that anisotropy has a significant impact on the location, shape and size of coherent structures in the Poincare sections. This implies that the optimal operating parameters (well spacing, time period of well actuation) may vary strongly and must be carefully chosen so as to enhance subsurface transport. This work is part of the research program of the Foundation for Fundamental Research on Matter (FOM), which is part of Netherlands Organisation for Scientific Research (NWO). This research program is co-financed by Shell Global Solutions International B.V.

  3. Construction and operation of parallel electric and magnetic field spectrometers for mass/energy resolved multi-ion charge exchange diagnostics on the Tokamak Fusion Test Reactor

    NASA Astrophysics Data System (ADS)

    Medley, S. S.; Roquemore, A. L.

    1998-07-01

    A novel charge exchange spectrometer using a dee-shaped region of parallel electric and magnetic fields was developed at the Princeton Plasma Physics Laboratory for neutral particle diagnostics on the Tokamak Fusion Test Reactor (TFTR). The E∥B spectrometer has an energy range of 0.5⩽A (amu)E (keV)⩽600 and provides mass-resolved energy spectra of H+, D+, and T+ (or 3He+) ion species simultaneously during a single discharge. The detector plane exhibits parallel rows of analyzed ions, each row containing the energy dispersed ions of a given mass-to-charge ratio. The detector consists of a large area microchannel plate (MCP) which is provided with three rectangular, semicontinuous active area strips, one coinciding with each of the mass rows for detection of H+, D+, and T+ (or 3He+) and each mass row has 75 energy channels. To suppress spurious signals attending operation of the plate in the magnetic fringe field of the spectrometer, the MCP was housed in a double-walled iron shield with a wire mesh ion entrance window. Using an accelerator neutron generator, the MCP neutron detection efficiency was measured to be 1.7×10-3 and 6.4×10-3 counts/neutron/cm2 for 2.5 MeV-DD and 14 MeV-DT neutrons, respectively. The design and calibration of the spectrometer are described in detail, including the effect of MCP exposure to tritium, and results obtained during high performance D-D operation on TFTR are presented to illustrate the performance of the E∥B spectrometer. The spectrometers were not used during D-T plasma operation due to the cost of providing the required radiation shielding.

  4. Simultaneous measurement of proline and related compounds in oak leaves by high-performance ligand-exchange chromatography and electrospray ionization mass spectrometry for environmental stress studies.

    PubMed

    Oufir, Mouhssin; Schulz, Nadine; Sha Vallikhan, Patan Shaik; Wilhelm, Eva; Burg, Kornel; Hausman, Jean-Francois; Hoffmann, Lucien; Guignard, Cedric

    2009-02-13

    A mass spectrometer was coupled to high-performance ligand-exchange liquid chromatography (HPLEC) for simultaneous analysis of stress associated solutes such as proline, hydroxyproline, methylproline, glycine betaine and trigonelline extracted from leaves of drought stressed oaks and an internal standard namely N-acetylproline. Methanol/chloroform/water extracts were analyzed using an Aminex HPX-87C column and specifically quantified by the positive ion mode of an electrospray ionisation-mass spectrometry (ESI-MS) in single ion monitoring (SIM) mode. The recovery of N-acetyl proline added to oak leaf extracts ranged from 85.2 to 122.1% for an intra-day study. Standard calibration curves showed good linearity in the measured range from 0.3125 to 10micromolL(-1) with the lowest correlation coefficient of 0.99961 for trigonelline. The advantages of this alternative procedure, compared to previously published methods using fluorescence or amperometric detections, are the simultaneous and direct detection of osmoprotectants in a single chromatographic run, a minimal sample preparation, a good specificity and reduced limits of quantification, ranging from 0.1 to 0.6micromolL(-1). Fifty-six days of water deficit exposure resulted in increased foliar free proline levels (2.4-fold, P<0.001, 155micromolg(-1) FW) and glycine betaine contents (2.5-fold, P<0.05, 175micromolg(-1) FW) of drought stressed oak compared to control.

  5. Quaternized chitosan particles as ion exchange supports for label-free DNA detection using PNA probe and MALDI-TOF mass spectrometry.

    PubMed

    Meebungpraw, Jittima; Wiarachai, Oraphan; Vilaivan, Tirayut; Kiatkamjornwong, Suda; Hoven, Voravee P

    2015-10-20

    Quaternized chitosan particles are introduced as anion-exchanged captures to be used with a conformationally constrained pyrrolidinyl peptide nucleic acid (acpcPNA) and MALDI-TOF mass spectrometry for DNA sequence analysis. Methylated chitosan (MC) and methylated N-benzyl chitosan (MBzC) particles were obtained by heterogeneous chemical modification of ionically cross-linked chitosan particles via direct methylation and reductive benzylation/methylation, respectively. N,N,N-trimethylchitosan (TMC) and N-[(2-hydroxyl-3-trimethylammonium)propyl]chitosan chloride (HTACC) particles were prepared by ionic cross-linking of quaternized chitosan derivatives, homogeneously modified from chitosan, namely TMC and HTACC, respectively. The particles formed had a size in a sub-micrometer range and possessed positive charge. Investigation by MALDI-TOF mass spectrometry suggested that some quaternized particles in combination with acpcPNA were capable of detecting a single mismatched base out of 9-14 base DNA sequences. Potential application of this technique for the detection of wild-type and mutant K-ras DNA, a gene that mutation is associated with certain cancers, has also been demonstrated.

  6. Application of the shock layer theory to the determination of the mass transfer rate coefficient and its concentration dependence for proteins on anion exchange columns

    SciTech Connect

    Sajonz, P. ||; Guan-Sajonz, H.; Zhong, G.; Guiochon, G. |

    1997-03-01

    The extension of the shock layer theory to systems having a slow mass transfer kinetics and a concentration-dependent rate coefficient is discussed. Experiments were carried out with bovine serum albumin on two anion exchanges, TSK-GEL-DEAE-5PW and Resource-Q. The adsorption isotherm data, determined by single-step frontal analysis, could be fitted to simplified bi-Langmuir equations with vary small residuals. A lumped kinetic model (solid film linear driving force model, with rate coefficient k{sub f}) was used to account for the mass transfer kinetics. The profile of each breakthrough curve (BC) was fitted to the curve calculated with this transport model and the rate coefficient k{sub f} obtained by identification. A linear dependence of k{sub f} on the average concentration of the step of the BC was found. The shock layer thicknesses (SLT) calculated for different relative concentrations agreed very well with the experimental results. This justifies the use of the SLT for the direct determination of rate coefficients. 19 refs., 9 figs., 2 tabs.

  7. A finite-volume Eulerian-Lagrangian localized adjoint method for solution of the advection-dispersion equation

    USGS Publications Warehouse

    Healy, R.W.; Russell, T.F.

    1993-01-01

    Test results demonstrate that the finite-volume Eulerian-Lagrangian localized adjoint method (FVELLAM) outperforms standard finite-difference methods for solute transport problems that are dominated by advection. FVELLAM systematically conserves mass globally with all types of boundary conditions. Integrated finite differences, instead of finite elements, are used to approximate the governing equation. This approach, in conjunction with a forward tracking scheme, greatly facilitates mass conservation. The mass storage integral is numerically evaluated at the current time level, and quadrature points are then tracked forward in time to the next level. Forward tracking permits straightforward treatment of inflow boundaries, thus avoiding the inherent problem in backtracking of characteristic lines intersecting inflow boundaries. FVELLAM extends previous results by obtaining mass conservation locally on Lagrangian space-time elements. -from Authors

  8. Thermally driven advection for radioxenon transport from an underground nuclear explosion

    NASA Astrophysics Data System (ADS)

    Sun, Yunwei; Carrigan, Charles R.

    2016-05-01

    Barometric pumping is a ubiquitous process resulting in migration of gases in the subsurface that has been studied as the primary mechanism for noble gas transport from an underground nuclear explosion (UNE). However, at early times following a UNE, advection driven by explosion residual heat is relevant to noble gas transport. A rigorous measure is needed for demonstrating how, when, and where advection is important. In this paper three physical processes of uncertain magnitude (oscillatory advection, matrix diffusion, and thermally driven advection) are parameterized by using boundary conditions, system properties, and source term strength. Sobol' sensitivity analysis is conducted to evaluate the importance of all physical processes influencing the xenon signals. This study indicates that thermally driven advection plays a more important role in producing xenon signals than oscillatory advection and matrix diffusion at early times following a UNE, and xenon isotopic ratios are observed to have both time and spatial dependence.

  9. In situ measurements of advective solute transport in permeable shelf sands

    NASA Astrophysics Data System (ADS)

    Reimers, Clare E.; Stecher, Hilmar A.; Taghon, Gary L.; Fuller, Charlotte M.; Huettel, Markus; Rusch, Antje; Ryckelynck, Natacha; Wild, Christian

    2004-01-01

    Solute transport rates within the uppermost 2 cm of a rippled continental shelf sand deposit, with a mean grain size of 400-500 μm and permeabilities of 2.0-2.4×10 -11 m 2, have been measured in situ by detecting the breakthrough of a pulse of iodide after its injection into the bottom water. These tracer experiments were conducted on the USA Middle Atlantic Bight shelf at a water depth of ˜13 m using a small tethered tripod that carried a close-up video camera, acoustic current meter, motorized 1.5 liter "syringe", and a microprofiling system for positioning and operating a solid-state voltammetric microelectrode. When triggered on shipboard, the syringe delivered a 0.21 M solution of potassium iodide and red dye through five nozzles positioned around and above the buried tip of the voltammetric sensor for 0.65-5 min. Bottom turbulence rapidly mixed and dispersed the tracer, which then was carried into the bed by interfacial water flows associated with ripple topography. The advective downward transport to the sensor tip was timed by a sequence of repetitive voltammetric scans. The distance-averaged vertical velocity, expressed as the depth of the sensor tip in the sand divided by the time to iodide breakthrough, was found to vary from 6 to 53 cm h -1 and generally to decrease with sediment depth. Because of episodic pumping and dispersion associated with the greatest 5% of wave heights and current speeds recorded, some concentration vs. time responses showed evidence of uneven solute migration. For reasons of mass balance, the advective flow field in the surface layers of permeable beds includes regions of water intrusion, horizontal pore-water flow and upwelling which also may explain some of the observed uneven migration. Pore-water advection was also evident in oxygen profiles measured before and after tracer injection with the voltammetric sensor. These profiles showed irregular distributions and oxygen penetration depths of 4-4.5 cm. Sand cores from the

  10. Thermo-chemical convection in planetary mantles: advection methods and magma ocean overturn simulations

    NASA Astrophysics Data System (ADS)

    Plesa, A.-C.; Tosi, N.; Hüttig, C.

    2012-04-01

    Thermal and chemical convection in planetary mantles are the most dominant dynamical processes influencing the thermal and geological evolution of a planet. After the planetary formation, convection in the interior is one of the most prominent processes being responsible for the heat transport efficiency, the interior structure, the magnetic field generation and the geological structures at the surface of a planet such as volcanoes, rifts and others. The slow creep of the silicate materials that make up the mantle of terrestrial planets (i.e. Mercury, Venus, the Earth and Mars) is driven by a combination of thermal and compositional buoyancy. On the one hand, the primordial heat accumulated after accretion and core formation and the heat released by the decay of radiogenic isotopes are transported from the interior to the surface by thermal convection. This process involves the transfer of heat both via diffusion, which occurs mainly across thermal boundary layers, and advection due to fluid motion in the bulk of the mantle. On the other hand, density anomalies of non-thermal origin associated with chemical (i.e. compositional) heterogeneities provide an additional source of buoyancy that actively contributes to the transport of energy and mass. In the present work we discuss the modeling of active compositional fields in the framework of solid-state mantle convection using the 3D spherical/2D cylindrical code Gaia [1, 2]. Numerical methods for the advection of active compositional fields fall in two main categories [3, 4]. They are based either on a fixed computational grid (Eulerian methods) or on evolving grids or moving particles (Lagrangian methods). We compare an Eulerian method based on double-diffusive convection against a Lagrangian, particle-based method. Though straightforward, the first method generally suffers from non-negligible numerical diffusion and demands then the use of grids with a high resolution. Moreover, its accuracy can substantially

  11. 129I and its species in the East China Sea: level, distribution, sources and tracing water masses exchange and movement

    PubMed Central

    Liu, Dan; Hou, Xiaolin; Du, Jinzhou; Zhang, Luyuan; Zhou, Weijian

    2016-01-01

    Anthropogenic 129I as a long-lived radioisotope of iodine has been considered as an ideal oceanographic tracer due to its high residence time and conservative property in the ocean. Surface water samples collected from the East China Sea (ECS) in August 2013 were analyzed for 129I, 127I and their inorganic chemical species in the first time. The measured 129I/127I ratio is 1–3 orders of magnitude higher than the pre-nuclear level, indicating its dominantly anthropogenic sources. Relatively high 129I levels were observed in the Yangtze River and its estuary, as well as in the southern Yellow Sea, and 129I level in seawater declines towards the ECS shelf. In the open sea, 129I and 127I in surface water exists mainly as iodate, while in Yangtze River estuary and some locations, iodide is dominated. The results indicate that the Fukushima nuclear accident has no detectable effects in the ECS until August 2013. The obtained results are used for investigation of interaction of various water masses and water circulation in the ECS, as well as the marine environment in this region. Meanwhile this work provides essential data for evaluation of the possible influence of the increasing NPPs along the coast of the ECS in the future. PMID:27849026

  12. Analyzing slowly exchanging protein conformations by ion mobility mass spectrometry: study of the dynamic equilibrium of prolyl oligopeptidase.

    PubMed

    López, Abraham; Vilaseca, Marta; Madurga, Sergio; Varese, Monica; Tarragó, Teresa; Giralt, Ernest

    2016-07-01

    Ion mobility mass spectrometry (IMMS) is a biophysical technique that allows the separation of isobaric species on the basis of their size and shape. The high separation capacity, sensitivity and relatively fast time scale measurements confer IMMS great potential for the study of proteins in slow (µs-ms) conformational equilibrium in solution. However, the use of this technique for examining dynamic proteins is still not generalized. One of the major limitations is the instability of protein ions in the gas phase, which raises the question as to what extent the structures detected reflect those in solution. Here, we addressed this issue by analyzing the conformational landscape of prolyl oligopeptidase (POP) - a model of a large dynamic enzyme in the µs-ms range - by native IMMS and compared the results obtained in the gas phase with those obtained in solution. In order to interpret the experimental results, we used theoretical simulations. In addition, the stability of POP gaseous ions was explored by charge reduction and collision-induced unfolding experiments. Our experiments disclosed two species of POP in the gas phase, which correlated well with the open and closed conformations in equilibrium in solution; moreover, a gas-phase collapsed form of POP was also detected. Therefore, our findings not only support the potential of IMMS for the study of multiple co-existing conformations of large proteins in slow dynamic equilibrium in solution but also stress the need for careful data analysis to avoid artifacts. Copyright © 2016 John Wiley & Sons, Ltd.

  13. 129I and its species in the East China Sea: level, distribution, sources and tracing water masses exchange and movement

    NASA Astrophysics Data System (ADS)

    Liu, Dan; Hou, Xiaolin; Du, Jinzhou; Zhang, Luyuan; Zhou, Weijian

    2016-11-01

    Anthropogenic 129I as a long-lived radioisotope of iodine has been considered as an ideal oceanographic tracer due to its high residence time and conservative property in the ocean. Surface water samples collected from the East China Sea (ECS) in August 2013 were analyzed for 129I, 127I and their inorganic chemical species in the first time. The measured 129I/127I ratio is 1–3 orders of magnitude higher than the pre-nuclear level, indicating its dominantly anthropogenic sources. Relatively high 129I levels were observed in the Yangtze River and its estuary, as well as in the southern Yellow Sea, and 129I level in seawater declines towards the ECS shelf. In the open sea, 129I and 127I in surface water exists mainly as iodate, while in Yangtze River estuary and some locations, iodide is dominated. The results indicate that the Fukushima nuclear accident has no detectable effects in the ECS until August 2013. The obtained results are used for investigation of interaction of various water masses and water circulation in the ECS, as well as the marine environment in this region. Meanwhile this work provides essential data for evaluation of the possible influence of the increasing NPPs along the coast of the ECS in the future.

  14. Deciphering the Mode of Action of the Processive Polysaccharide Modifying Enzyme Dermatan Sulfate Epimerase 1 by Hydrogen–Deuterium Exchange Mass Spectrometry

    PubMed Central

    Tykesson, Emil; Mao, Yang; Maccarana, Marco; Pu, Yi; Gao, Jinshan; Lin, Cheng; Zaia, Joseph; Westergren-Thorsson, Gunilla; Ellervik, Ulf; Malmström, Lars; Malmström, Anders

    2015-01-01

    Distinct from template-directed biosynthesis of nucleic acids and proteins, the enzymatic synthesis of heterogeneous polysaccharides is a complex process that is difficult to study using common analytical tools. Therefore, the mode of action and processivity of those enzymes are largely unknown. Dermatan sulfate epimerase 1 (DS-epi1) is the predominant enzyme during the formation of iduronic acid residues in the glycosaminoglycan dermatan sulfate. Using recombinant DS-epi1 as a model enzyme, we describe a tandem mass spectrometry-based method to study the mode of action of polysaccharide processing enzymes. The enzyme action on the substrate was monitored by hydrogen-deuterium exchange mass spectrometry and the sequence information was then fed into mathematical models with two different assumptions of the mode of action for the enzyme: processive reducing end to non-reducing end, and processive non-reducing end to reducing end. Model data was scored by correlation to experimental data and it was found that DS-epi1 attacks its substrate on a random position, followed by a processive mode of modification towards the non-reducing end and that the substrate affinity of the enzyme is negatively affected by each additional epimerization event. It could also be shown that the smallest active substrate was the reducing end uronic acid in a tetrasaccharide and that octasaccharides and longer oligosaccharides were optimal substrates. The method of using tandem mass spectrometry to generate sequence information of the complex enzymatic products in combination with in silico modeling can be potentially applied to study the mode of action of other enzymes involved in polysaccharide biosynthesis. PMID:26900446

  15. Unification of some advection schemes in two dimensions

    NASA Technical Reports Server (NTRS)

    Sidilkover, D.; Roe, P. L.

    1995-01-01

    The relationship between two approaches towards construction of genuinely two-dimensional upwind advection schemes is established. One of these approaches is of the control volume type applicable on structured cartesian meshes. It resulted in the compact high resolution schemes capable of maintaining second order accuracy in both homogeneous and inhomogeneous cases. Another one is the fluctuation splitting approach, which is well suited for triangular (and possibly) unstructured meshes. Understanding the relationship between these two approaches allows us to formulate here a new fluctuation splitting high resolution (i.e. possible use of artificial compression, while maintaining positivity property) scheme. This scheme is shown to be linearity preserving in inhomogeneous as well as homogeneous cases.

  16. Mobile scintillometry to study heat advection over heterogeneous surfaces

    NASA Astrophysics Data System (ADS)

    Kleissl, J.

    2007-12-01

    Large Aperture Scintillometer (LAS) receivers measure the structure parameter of the refractive index from intensity fluctuations of the transmitter beam. Due to the spatial averaging over 1-4 km employed by this emerging technique the constraints for long temporal averaging (15-30 min) and associated uncertainties that have to be met by other flux measurement techniques do not apply for LASs. In this paper the constraints for temporal averaging of LASs will be examined as a function of environmental conditions and transect geometry. Moreover, analysis of data from a mobile LAS measurement across a surface gradient from rough and dry to smoother and wet will be presented. In this experiment the LAS was mounted on a pickup truck, allowing for quick redeployment of the transect after meaurement. The potential for the use of LAS to study local advection of heat in riparian or irrigated areas in the semi-arid southwest will be evaluated.

  17. Microscale chaotic advection enables robust convective DNA replication.

    PubMed

    Priye, Aashish; Hassan, Yassin A; Ugaz, Victor M

    2013-11-05

    The ability of chaotic advection under microscale confinement to direct chemical processes along accelerated kinetic pathways has been recognized for some time. However, practical applications have been slow to emerge because optimal results are often counterintuitively achieved in flows that appear to possess undesirably high disorder. Here we present a 3D time-resolved analysis of polymerase chain reaction (PCR)-mediated DNA replication across a broad ensemble of geometric states. The resulting parametric map reveals an unexpectedly wide operating regime where reaction rates remain constant over 2 orders of magnitude of the Rayleigh number, encompassing virtually any realistic PCR condition (temperature, volume, gravitational alignment), a level of robustness previously thought unattainable in the convective format.

  18. Dependence of advection-diffusion-reaction on flow coherent structures

    NASA Astrophysics Data System (ADS)

    Tang, Wenbo; Luna, Christopher

    2013-10-01

    A study on an advection-diffusion-reaction system is presented. Variability of the reaction process in such a system triggered by a highly localized source is quantified. It is found, for geophysically motivated parameter regimes, that the difference in bulk concentration subject to realizations of different source locations is highly correlated with the local flow topology of the source. Such flow topologies can be highlighted by Lagrangian coherent structures. Reaction is relatively enhanced in regions of strong stretching, and relatively suppressed in regions where vortices are present. In any case, the presence of a divergence-free background flow helps speed up the reaction process, especially when the flow is time-dependent. Probability density of various quantities characterizing the reaction processes is also obtained. This reveals the inherent complexity of the reaction-diffusion process subject to nonlinear background stirring.

  19. Studies of aerosols advected to coastal areas with the use of remote techniques

    NASA Astrophysics Data System (ADS)

    Zieliński, Tymon; Petelski, Tomasz; Makuch, Przemysław; Strzałkowska, Agata; Ponczkowska, Agnieszka; Markowicz, Krzysztof; Chourdakis, Georgius; Georgoussis, George; Kratzer, Susanne

    2012-10-01

    This paper presents the results of the studies of aerosol optical properties measured using lidars and sun photometers. We describe two case studies of the combined measurements made in two coastal zones in Crete in 2006 and in Rozewie on the Baltic Sea in 2009. The combination of lidar and sun photometer measurements provides comprehensive information on both the total aerosol optical thickness in the entire atmosphere as well as the vertical structure of aerosol optical properties. Combination of such information with air mass back-trajectories and data collected at stations located on the route of air masses provides complete picture of the aerosol variations in the study area both vertically and horizontally. We show that such combined studies are especially important in the coastal areas where depending on air mass advection directions and altitudes the influence of fine or coarse mode (in this case possibly sea-salt) particles on the vertical structure of aerosol optical properties is an important issue to consider.

  20. Examination of the evolution of radiation and advection fogs. Final report

    SciTech Connect

    Orgill, M.M.

    1993-01-01

    A literature study was done on radiation and advection fog evolution. For radiation fog, six stages of fog evolution have been identified -- (1) precursor, (2) sunset, (3) conditioning, (4) mature, (5) sunrise, and (6) dissipation. The evolution of advection fog models has been in parallel with radiation fog models, but no identified stages in the evolution of advection fog have been proposed: (1) precursor, (2) initiation, (3) mature, and (4) dissipation. Radiation and advection fog models will require greater sophistication in order to study fog spatial and temporal variability. Physical aspects that require further study are discussed.

  1. How Hydrate Saturation Anomalies are Diffusively Constructed and Advectively Smoothed

    NASA Astrophysics Data System (ADS)

    Rempel, A. W.; Irizarry, J. T.; VanderBeek, B. P.; Handwerger, A. L.

    2015-12-01

    The physical processes that control the bulk characteristics of hydrate reservoirs are captured reasonably well by long-established model formulations that are rooted in laboratory-verified phase equilibrium parameterizations and field-based estimates of in situ conditions. More detailed assessments of hydrate distribution, especially involving the occurrence of high-saturation hydrate anomalies have been more difficult to obtain. Spatial variations in sediment properties are of central importance for modifying the phase behavior and promoting focussed fluid flow. However, quantitative predictions of hydrate anomaly development cannot be made rigorously without also addressing the changes in phase behavior and mechanical balances that accompany changes in hydrate saturation level. We demonstrate how pore-scale geometrical controls on hydrate phase stability can be parameterized for incorporation in simulations of hydrate anomaly development along dipping coarse-grained layers embedded in a more fine-grained background that is less amenable to fluid transport. Model simulations demonstrate how hydrate anomaly growth along coarse-layer boundaries is promoted by diffusive gas transport from the adjacent fine-grained matrix, while advective transport favors more distributed growth within the coarse-grained material and so effectively limits the difference between saturation peaks and background levels. Further analysis demonstrates how sediment contacts are unloaded once hydrate saturation reaches sufficient levels to form a load-bearing skeleton that can evolve to produce segregated nodules and lenses. Decomposition of such growth forms poses a significant geohazard that is expected to be particularly sensitive to perturbations induced by gas extraction. The figure illustrates the predicted evolution of hydrate saturation Sh in a coarse-grained dipping layer showing how prominent bounding hydrate anomalies (spikes) supplied by diffusive gas transport at early times

  2. Smoothed particle hydrodynamics model for Landau-Lifshitz-Navier-Stokes and advection-diffusion equations.

    PubMed

    Kordilla, Jannes; Pan, Wenxiao; Tartakovsky, Alexandre

    2014-12-14

    We propose a novel smoothed particle hydrodynamics (SPH) discretization of the fully coupled Landau-Lifshitz-Navier-Stokes (LLNS) and stochastic advection-diffusion equations. The accuracy of the SPH solution of the LLNS equations is demonstrated by comparing the scaling of velocity variance and the self-diffusion coefficient with kinetic temperature and particle mass obtained from the SPH simulations and analytical solutions. The spatial covariance of pressure and velocity fluctuations is found to be in a good agreement with theoretical models. To validate the accuracy of the SPH method for coupled LLNS and advection-diffusion equations, we simulate the interface between two miscible fluids. We study formation of the so-called "giant fluctuations" of the front between light and heavy fluids with and without gravity, where the light fluid lies on the top of the heavy fluid. We find that the power spectra of the simulated concentration field are in good agreement with the experiments and analytical solutions. In the absence of gravity, the power spectra decay as the power -4 of the wavenumber-except for small wavenumbers that diverge from this power law behavior due to the effect of finite domain size. Gravity suppresses the fluctuations, resulting in much weaker dependence of the power spectra on the wavenumber. Finally, the model is used to study the effect of thermal fluctuation on the Rayleigh-Taylor instability, an unstable dynamics of the front between a heavy fluid overlaying a light fluid. The front dynamics is shown to agree well with the analytical solutions.

  3. Smoothed particle hydrodynamics model for Landau-Lifshitz-Navier-Stokes and advection-diffusion equations

    SciTech Connect

    Kordilla, Jannes; Pan, Wenxiao Tartakovsky, Alexandre

    2014-12-14

    We propose a novel smoothed particle hydrodynamics (SPH) discretization of the fully coupled Landau-Lifshitz-Navier-Stokes (LLNS) and stochastic advection-diffusion equations. The accuracy of the SPH solution of the LLNS equations is demonstrated by comparing the scaling of velocity variance and the self-diffusion coefficient with kinetic temperature and particle mass obtained from the SPH simulations and analytical solutions. The spatial covariance of pressure and velocity fluctuations is found to be in a good agreement with theoretical models. To validate the accuracy of the SPH method for coupled LLNS and advection-diffusion equations, we simulate the interface between two miscible fluids. We study formation of the so-called “giant fluctuations” of the front between light and heavy fluids with and without gravity, where the light fluid lies on the top of the heavy fluid. We find that the power spectra of the simulated concentration field are in good agreement with the experiments and analytical solutions. In the absence of gravity, the power spectra decay as the power −4 of the wavenumber—except for small wavenumbers that diverge from this power law behavior due to the effect of finite domain size. Gravity suppresses the fluctuations, resulting in much weaker dependence of the power spectra on the wavenumber. Finally, the model is used to study the effect of thermal fluctuation on the Rayleigh-Taylor instability, an unstable dynamics of the front between a heavy fluid overlaying a light fluid. The front dynamics is shown to agree well with the analytical solutions.

  4. Smoothed particle hydrodynamics model for Landau-Lifshitz Navier-Stokes and advection-diffusion equations

    SciTech Connect

    Kordilla, Jannes; Pan, Wenxiao; Tartakovsky, Alexandre M.

    2014-12-14

    We propose a novel Smoothed Particle Hydrodynamics (SPH) discretization of the fully-coupled Landau-Lifshitz-Navier-Stokes (LLNS) and advection-diffusion equations. The accuracy of the SPH solution of the LLNS equations is demonstrated by comparing the scaling of velocity variance and self-diffusion coefficient with kinetic temperature and particle mass obtained from the SPH simulations and analytical solutions. The spatial covariance of pressure and velocity fluctuations are found to be in a good agreement with theoretical models. To validate the accuracy of the SPH method for the coupled LLNS and advection-diffusion equations, we simulate the interface between two miscible fluids. We study the formation of the so-called giant fluctuations of the front between light and heavy fluids with and without gravity, where the light fluid lays on the top of the heavy fluid. We find that the power spectra of the simulated concentration field is in good agreement with the experiments and analytical solutions. In the absence of gravity the the power spectra decays as the power -4 of the wave number except for small wave numbers which diverge from this power law behavior due to the effect of finite domain size. Gravity suppresses the fluctuations resulting in the much weaker dependence of the power spectra on the wave number. Finally the model is used to study the effect of thermal fluctuation on the Rayleigh-Taylor instability, an unstable dynamics of the front between a heavy fluid overlying a light fluid. The front dynamics is shown to agree well with the analytical solutions.

  5. Hybrid Multiscale Finite Volume Method for Advection-Diffusion Equations Subject to Heterogeneous Reactive Boundary Conditions

    SciTech Connect

    Barajas-Solano, David A.; Tartakovsky, A. M.

    2016-10-13

    We present a hybrid scheme for the coupling of macro and microscale continuum models for reactive contaminant transport in fractured and porous media. The transport model considered is the advection-dispersion equation, subject to linear heterogeneous reactive boundary conditions. The Multiscale Finite Volume method (MsFV) is employed to define an approximation to the microscale concentration field defined in terms of macroscopic or \\emph{global} degrees of freedom, together with local interpolator and corrector functions capturing microscopic spatial variability. The macroscopic mass balance relations for the MsFV global degrees of freedom are coupled with the macroscopic model, resulting in a global problem for the simultaneous time-stepping of all macroscopic degrees of freedom throughout the domain. In order to perform the hybrid coupling, the micro and macroscale models are applied over overlapping subdomains of the simulation domain, with the overlap denoted as the handshake subdomain $\\Omega^{hs}$, over which continuity of concentration and transport fluxes between models is enforced. Continuity of concentration is enforced by posing a restriction relation between models over $\\Omega^{hs}$. Continuity of fluxes is enforced by prolongating the macroscopic model fluxes across the boundary of $\\Omega^{hs}$ to microscopic resolution. The microscopic interpolator and corrector functions are solutions to local microscopic advection-diffusion problems decoupled from the global degrees of freedom and from each other by virtue of the MsFV decoupling ansatz. The error introduced by the decoupling ansatz is reduced iteratively by the preconditioned GMRES algorithm, with the hybrid MsFV operator serving as the preconditioner.

  6. Comparison of estimated surface energy fluxes using METRIC and two-source algorithms for Advective Conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Surface energy fluxes have long been recognized as playing an important role in determining exchanges of energy and mass between the hydrosphere, atmosphere, and biosphere. In this study, we applied the METRIC (Mapping ET at high Resolutions with Internal Calibration) algorithm to derive daily surfa...

  7. Strong anion exchange liquid chromatographic separation of protein amino acids for natural 13C-abundance determination by isotope ratio mass spectrometry.

    PubMed

    Abaye, Daniel A; Morrison, Douglas J; Preston, Tom

    2011-02-15

    Amino acids are the building blocks of proteins and the analysis of their (13)C abundances is greatly simplified by the use of liquid chromatography (LC) systems coupled with isotope ratio mass spectrometry (IRMS) compared with gas chromatography (GC)-based methods. To date, various cation exchange chromatography columns have been employed for amino acid separation. Here, we report strong anion exchange chromatography (SAX) coupled to IRMS with a Liquiface interface for amino acid δ(13)C determination. Mixtures of underivatised amino acids (0.1-0.5 mM) and hydrolysates of representative proteins (prawns and bovine serum albumin) were resolved by LC/IRMS using a SAX column and inorganic eluents. Background inorganic carbon content was minimised through careful preparation of alkaline reagents and use of a pre-injector on-line carbonate removal device. SAX chromatography completely resolved 11 of the 16 expected protein amino acids following acid hydrolysis in underivatised form. Basic and neutral amino acids were resolved with 35 mM NaOH in isocratic mode. Elution of the aromatic and acidic amino acids required a higher hydroxide concentration (180 mM) and a counterion (NO 3-, 5-25 mM). The total run time was 70 min. The average δ(13)C precision of baseline-resolved peaks was 0.75‰ (range 0.04 to 1.06‰). SAX is a viable alternative to cation chromatography, especially where analysis of basic amino acids is important. The technology shows promise for (13)C amino acid analysis in ecology, archaeology, forensic science, nutrition and protein metabolism.

  8. Hydrogen exchange mass spectrometry reveals protein interfaces and distant dynamic coupling effects during the reversible self-association of an IgG1 monoclonal antibody

    PubMed Central

    Arora, Jayant; Hickey, John M; Majumdar, Ranajoy; Esfandiary, Reza; Bishop, Steven M; Samra, Hardeep S; Middaugh, C Russell; Weis, David D; Volkin, David B

    2015-01-01

    There is a need for new analytical approaches to better characterize the nature of the concentration-dependent, reversible self-association (RSA) of monoclonal antibodies (mAbs) directly, and with high resolution, when these proteins are formulated as highly concentrated solutions. In the work reported here, hydrogen exchange mass spectrometry (HX-MS) was used to define the concentration-dependent RSA interface, and to characterize the effects of association on the backbone dynamics of an IgG1 mAb (mAb-C). Dynamic light scattering, chemical cross-linking, and solution viscosity measurements were used to determine conditions that caused the RSA of mAb-C. A novel HX-MS experimental approach was then applied to directly monitor differences in local flexibility of mAb-C due to RSA at different protein concentrations in deuterated buffers. First, a stable formulation containing lyoprotectants that permitted freeze-drying of mAb-C at both 5 and 60 mg/mL was identified. Upon reconstitution with RSA-promoting deuterated solutions, the low vs. high protein concentration samples displayed different levels of solution viscosity (i.e., approx. 1 to 75 mPa.s). The reconstituted mAb-C samples were then analyzed by HX-MS. Two specific sequences covering complementarity-determining regions CDR2H and CDR2L (in the variable heavy and light chains, respectively) showed significant protection against deuterium uptake (i.e., decreased hydrogen exchange). These results define the major protein-protein interfaces associated with the concentration-dependent RSA of mAb-C. Surprisingly, certain peptide segments in the VH domain, the constant domain (CH2), and the hinge region (CH1-CH2 interface) concomitantly showed significant increases in local flexibility at high vs. low protein concentrations. These results indicate the presence of longer-range, distant dynamic coupling effects within mAb-C occurring upon RSA. PMID:25875351

  9. Eulerian-Lagrangian numerical scheme for simulating advection, dispersion, and transient storage in streams and a comparison of numerical methods

    USGS Publications Warehouse

    Cox, T.J.; Runkel, R.L.

    2008-01-01

    Past applications of one-dimensional advection, dispersion, and transient storage zone models have almost exclusively relied on a central differencing, Eulerian numerical approximation to the nonconservative form of the fundamental equation. However, there are scenarios where this approach generates unacceptable error. A new numerical scheme for this type of modeling is presented here that is based on tracking Lagrangian control volumes across a fixed (Eulerian) grid. Numerical tests are used to provide a direct comparison of the new scheme versus nonconservative Eulerian numerical methods, in terms of both accuracy and mass conservation. Key characteristics of systems for which the Lagrangian scheme performs better than the Eulerian scheme include: nonuniform flow fields, steep gradient plume fronts, and pulse and steady point source loadings in advection-dominated systems. A new analytical derivation is presented that provides insight into the loss of mass conservation in the nonconservative Eulerian scheme. This derivation shows that loss of mass conservation in the vicinity of spatial flow changes is directly proportional to the lateral inflow rate and the change in stream concentration due to the inflow. While the nonconservative Eulerian scheme has clearly worked well for past published applications, it is important for users to be aware of the scheme's limitations. ?? 2008 ASCE.

  10. Mass-dependent dynamics of the luminescent exchange reactions C+(2P), P+(3P) + H2, D2, HD

    NASA Astrophysics Data System (ADS)

    Glenewinkel-Meyer, Th; Hoppe, U.; Kowalski, A.; Ottinger, Ch; Rabenda, D.

    1995-06-01

    Chemiluminescent ion/molecule reactions of ground state C+ and P+ ions with H2, D2 and HD have been studied in an ion beam/target gas cell arrangement. Emission spectra of CH+, CD+ (A 1II) and of PH+, PD+ (A 2[Delta]) were observed with up to 1 Å FWHM resolution and at collision energies from threshold ([approximate] 3 eV) to 8 eVc.m. (centre-of-mass) and 15eVc.m., respectively. Very detailed computer simulations of the spectral contours were done, including ab initio transition moments and, in the case of PH+/PD+, the effects of predissociation. In simulating the spectra obtained with HD, the overlapped hydride and deuteride product ion spectra could be isolated by varying the respective weighting factors to achieve an optimum overall fit. In the case of C+ + HD, the two components were found to have very similar rovibrational distributions as with the products from C+ + H2 and C+ + D2. In the P+ case, however, the rotational, although not the vibrational, distributions were found to be significantly different for the isotopically mixed and the pure reactions. The cross-sections showed an intermolecular isotope effect only for C+ + H2 vs. C+ + D2 at high energies. However, both with C+ + HD and P+ + HD, a very strong intramolecular isotope effect, i.e. an energy-dependent branching ratio, was observed: at low energies deuteride formation prevails, at high energies hydride. This behaviour is discussed in terms of an impulsive collision model, assuming the "pairwise" relative kinetic energy between the reacting atoms to be the determining factor. On the basis of the measured cross-section curves for the H2 and D2 reactions, the energy-dependent hydride/deuteride ratio in the HD reaction can then be predicted. The agreement with the experimental results is excellent in the P+ case, but only moderate for the C+ reactions. Even the P+ reaction, however, does not occur via the spectator stripping mechanisms. The spectra show an energy-independent vibrational excitation

  11. Evidence for o-atom exchange in the O(1D) + N2O reaction as the source of mass-independent isotopic fractionation in atmospheric N2O.

    SciTech Connect

    Miller, Charles E.; Liang, Mao-Chang; Blake, Geoffrey A.; Muller, Richard Partain; Yung, Yuk L.

    2004-07-01

    Recent experiments have shown that in the oxygen isotopic exchange reaction for O({sup 1}D) + CO{sub 2} the elastic channel is approximately 50% that of the inelastic channel [Perri et al., 2003]. We propose an analogous oxygen atom exchange reaction for the isoelectronic O({sup 1}D) + N{sub 2}O system to explain the mass-independent isotopic fractionation (MIF) in atmospheric N{sub 2}O. We apply quantum chemical methods to compute the energetics of the potential energy surfaces on which the O({sup 1}D) + N{sub 2}O reaction occurs. Preliminary modeling results indicate that oxygen isotopic exchange via O({sup 1}D) + N{sub 2}O can account for the MIF oxygen anomaly if the oxygen atom isotopic exchange rate is 30-50% that of the total rate for the reactive channels.

  12. Cross-Shelf Exchange.

    PubMed

    Brink, K H

    2016-01-01

    Cross-shelf exchange dominates the pathways and rates by which nutrients, biota, and materials on the continental shelf are delivered and removed. This follows because cross-shelf gradients of most properties are usually far greater than those in the alongshore direction. The resulting transports are limited by Earth's rotation, which inhibits flow from crossing isobaths. Thus, cross-shelf flows are generally weak compared with alongshore flows, and this leads to interesting observational issues. Cross-shelf flows are enabled by turbulent mixing processes, nonlinear processes (such as momentum advection), and time dependence. Thus, there is a wide range of possible effects that can allow these critical transports, and different natural settings are often governed by different combinations of processes. This review discusses examples of representative transport mechanisms and explores possible observational and theoretical paths to future progress.

  13. Hydrogen/deuterium exchange and mass spectrometric analysis of a protein containing multiple disulfide bonds: Solution structure of recombinant macrophage colony stimulating factor-beta (rhM-CSFbeta).

    PubMed

    Yan, Xuguang; Zhang, Heidi; Watson, Jeffrey; Schimerlik, Michael I; Deinzer, Max L

    2002-09-01

    Studies with the homodimeric recombinant human macrophage colony-stimulating factor beta (rhM-CSFbeta), show for the first time that a large number (9) of disulfide linkages can be reduced after amide hydrogen/deuterium (H/D) exchange, and the protein digested and analyzed successfully for the isotopic composition by electrospray mass spectrometry. Analysis of amide H/D after exchange-in shows that in solution the conserved four-helix bundle of (rhM-CSFbeta) has fast and moderately fast exchangeable sections of amide hydrogens in the alphaA helix, and mostly slow exchanging sections of amide hydrogens in the alphaB, alphaC, and alphaD helices. Most of the amide hydrogens in the loop between the beta1 and beta4 sheets exhibited fast or moderately fast exchange, whereas in the amino acid 63-67 loop, located at the interface of the two subunits, the exchange was slow. Solvent accessibility as measured by H/D exchange showed a better correlation with the average depth of amide residues calculated from reported X-ray crystallographic data for rhM-CSFalpha than with the average B-factor. The rates of H/D exchange in rhM-CSFbeta appear to correlate well with the exposed surface calculated for each amino acid residue in the crystal structure except for the alphaD helix. Fast hydrogen isotope exchange throughout the segment amino acids 150-221 present in rhM-CSFbeta, but not rhM-CSFalpha, provides evidence that the carboxy-terminal region is unstructured. It is, therefore, proposed that the anomalous behavior of the alphaD helix is due to interaction of the carboxy-terminal tail with this helical segment.

  14. Acyl-biotinyl exchange chemistry and mass spectrometry-based analysis of palmitoylation sites of in vitro palmitoylated rat brain tubulin.

    PubMed

    Zhao, Zhiqiang; Hou, Junjie; Xie, Zhensheng; Deng, Jianwei; Wang, Xiaoming; Chen, Danfang; Yang, Fuquan; Gong, Weimin

    2010-11-01

    Research has shown that the palmitoyl group of α-tubulin mediates the hydrophobic interaction between microtubules and intracellular membranes and that palmitoylated tubulin plays a role in signal transduction. There are 20 cysteine residues per α/β tubulin heterodimer. C376 of α-tubulin was reported to be predominantly palmitoylated and C20, C213 and C305 of α-tubulin were palmitoylated at lower levels. The previous method used for the analysis of the palmitoylation sites on α-tubulin was based on ³H-labeling, enzymolysis, purification and sequencing. This approach, although efficient, is laborious. Mass spectrometry (MS), especially tandem MS, has been shown to be a successful method for identification of various post-translational modifications of proteins. We report here a convenient MS-based method to comprehensively analyze the palmitoylation sites of the α/β tubulin heterodimer. Acyl-biotinyl exchange chemistry and streptavidin agarose affinity purification were applied to enrich palmitoylated peptides from tubulin. After nano-LC-MS/MS analysis, database searching and manual analysis of the spectra revealed that 11 cysteine residues of the α/β tubulin heterodimer were palmitoylated.

  15. Load-dependent destabilization of the γ-rotor shaft in FOF1 ATP synthase revealed by hydrogen/deuterium-exchange mass spectrometry

    PubMed Central

    Vahidi, Siavash; Bi, Yumin; Dunn, Stanley D.; Konermann, Lars

    2016-01-01

    FoF1 is a membrane-bound molecular motor that uses proton-motive force (PMF) to drive the synthesis of ATP from ADP and Pi. Reverse operation generates PMF via ATP hydrolysis. Catalysis in either direction involves rotation of the γε shaft that connects the α3β3 head and the membrane-anchored cn ring. X-ray crystallography and other techniques have provided insights into the structure and function of FoF1 subcomplexes. However, interrogating the conformational dynamics of intact membrane-bound FoF1 during rotational catalysis has proven to be difficult. Here, we use hydrogen/deuterium exchange mass spectrometry to probe the inner workings of FoF1 in its natural membrane-bound state. A pronounced destabilization of the γ C-terminal helix during hydrolysis-driven rotation was observed. This behavior is attributed to torsional stress in γ, arising from γ⋅⋅⋅α3β3 interactions that cause resistance during γ rotation within the apical bearing. Intriguingly, we find that destabilization of γ occurs only when FoF1 operates against a PMF-induced torque; the effect disappears when PMF is eliminated by an uncoupler. This behavior resembles the properties of automotive engines, where bearings inflict greater forces on the crankshaft when operated under load than during idling. PMID:26884184

  16. Simultaneous detection of perchlorate and bromate using rapid high-performance ion exchange chromatography-tandem mass spectrometry and perchlorate removal in drinking water.

    PubMed

    West, Danielle M; Mu, Ruipu; Gamagedara, Sanjeewa; Ma, Yinfa; Adams, Craig; Eichholz, Todd; Burken, Joel G; Shi, Honglan

    2015-06-01

    Perchlorate and bromate occurrence in drinking water causes health concerns due to their effects on thyroid function and carcinogenicity, respectively. The purpose of this study was threefold: (1) to advance a sensitive method for simultaneous rapid detection of perchlorate and bromate in drinking water system, (2) to systematically study the occurrence of these two contaminants in Missouri drinking water treatment systems, and (3) to examine effective sorbents for minimizing perchlorate in drinking water. A rapid high-performance ion exchange chromatography-tandem mass spectrometry (HPIC-MS/MS) method was advanced for simultaneous detection of perchlorate and bromate in drinking water. The HPIC-MS/MS method was rapid, required no preconcentration of the water samples, and had detection limits for perchlorate and bromate of 0.04 and 0.01 μg/L, respectively. The method was applied to determine perchlorate and bromate concentrations in total of 23 selected Missouri drinking water treatment systems during differing seasons. The water systems selected include different source waters: groundwater, lake water, river water, and groundwater influenced by surface water. The concentrations of perchlorate and bromate were lower than or near to method detection limits in most of the drinking water samples monitored. The removal of perchlorate by various adsorbents was studied. A cationic organoclay (TC-99) exhibited effective removal of perchlorate from drinking water matrices.

  17. Structure-dependent degradation of polar compounds in weathered oils observed by atmospheric pressure photo-ionization hydrogen/deuterium exchange ultrahigh resolution mass spectrometry.

    PubMed

    Islam, Ananna; Kim, Donghwi; Yim, Un Hyuk; Shim, Won Joon; Kim, Sunghwan

    2015-10-15

    The resin fractions of fresh mixtures of three oils spilled during the M/V Hebei Spirit oil spill, as well as weathered oils collected at weathering stages II and IV from the oil spill site were analyzed and compared by atmospheric pressure photo-ionization hydrogen/deuterium exchange mass spectrometry (HDX MS). The significantly decreased abundance of N(+) and [N-H+D](+) ions suggested that secondary and tertiary amine-containing compounds were preferentially degraded during the early stage of weathering. [N+H](+) and [N+D](+) ions previously attributed to pyridine-type compounds degraded more slowly than secondary and tertiary amine-containing compounds. The preferential degradation of nitrogen-containing compounds was confirmed by photo-degradation experiments using 15 standard compounds. In addition, significant increases of [S1O1+H](+) and [S1O1+D](+) ions with higher DBE values were observed from fresh oil mixtures as compared to stages II and IV samples, and that could be linked with the decrease of higher DBE compounds of the S1 class. This study presented convincing arguments and evidence demonstrating that secondary and tertiary amines were more vulnerable to photo-degradation than compounds containing pyridine, and hence, preferential degradation depending on chemical structures must be considered in the production of hazardous or toxic components.

  18. Conformational Dynamics of the Bovine Mitochondrial ADP/ATP Carrier Isoform 1 Revealed by Hydrogen/Deuterium Exchange Coupled to Mass Spectrometry*

    PubMed Central

    Rey, Martial; Man, Petr; Clémençon, Benjamin; Trézéguet, Véronique; Brandolin, Gérard; Forest, Eric; Pelosi, Ludovic

    2010-01-01

    The mitochondrial adenine nucleotide carrier (Ancp) catalyzes the transport of ADP and ATP across the mitochondrial inner membrane, thus playing an essential role in cellular energy metabolism. During the transport mechanism the carrier switches between two different conformations that can be blocked by two toxins: carboxyatractyloside (CATR) and bongkrekic acid. Therefore, our understanding of the nucleotide transport mechanism can be improved by analyzing structural differences of the individual inhibited states. We have solved the three-dimensional structure of bovine carrier isoform 1 (bAnc1p) in a complex with CATR, but the structure of the carrier-bongkrekic acid complex, and thus, the detailed mechanism of transport remains unknown. Improvements in sample processing in the hydrogen/deuterium exchange technique coupled to mass spectrometry (HDX-MS) have allowed us to gain novel insights into the conformational changes undergone by bAnc1p. This paper describes the first study of bAnc1p using HDX-MS. Results obtained with the CATR-bAnc1p complex were fully in agreement with published results, thus, validating our approach. On the other hand, the HDX kinetics of the two complexes displays marked differences. The bongkrekic acid-bAnc1p complex exhibits greater accessibility to the solvent on the matrix side, whereas the CATR-bAnc1p complex is more accessible on the intermembrane side. These results are discussed with respect to the structural and biochemical data available on Ancp. PMID:20805227

  19. Quantitative determination of corticosteroids in bovine milk using mixed-mode polymeric strong cation exchange solid-phase extraction and liquid chromatography-tandem mass spectrometry.

    PubMed

    Tölgyesi, Adám; Tölgyesi, László; Sharma, Virender K; Sohn, Mary; Fekete, Jeno

    2010-12-01

    A new method was developed to identify and quantify corticosteroids (prednisolone, methylprednisone, flumetasone, dexamethasone, and methylprednisolone) in raw bovine milk by liquid chromatography-tandem mass spectrometry (LC-MS/MS) utilizing mixed-mode polymeric strong cation exchange and reversed-phase (MCX) solid-phase extraction (SPE) to reduce ion effects in a multimode ion (MMI) source. The main advantage of this method over other commonly used methods includes the use of a single SPE cartridge with a low volume for sample preparation and fast separation on the HPLC system with reduced ion suppression. This study is the first to report the determination of methylprednisone, a metabolite of methylprednisolone, in bovine milk. This method was validated in accordance with the European Union (EU) Commission Decision 2002/657/EC. The recoveries vary between 90% and 105%. The within-laboratory reproducibility (precision) is less than 30%. The decision limits and detection capabilities were calculated along with LODs, which ranged from 0.02 to 0.07 microg/kg. The method was further enhanced by its successful adaptation to other LC-MS/MS systems equipped with the newly developed ion source, Agilent Jet Stream (AJS). After optimization of the AJS ion source and MS parameters, even lower LOD values were achieved (0.001-0.006 microg/kg) for the corticosteroids. Analytical results obtained with the AJS were characterized by an enhanced area response and similar noise level comparable to those obtained with conventional orthogonal atmospheric ionization (API).

  20. Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIβ with Rab11.

    PubMed

    Fowler, Melissa L; McPhail, Jacob A; Jenkins, Meredith L; Masson, Glenn R; Rutaganira, Florentine U; Shokat, Kevan M; Williams, Roger L; Burke, John E

    2016-04-01

    The ability of proteins to bind and interact with protein partners plays fundamental roles in many cellular contexts. X-ray crystallography has been a powerful approach to understand protein-protein interactions; however, a challenge in the crystallization of proteins and their complexes is the presence of intrinsically disordered regions. In this article, we describe an application of hydrogen deuterium exchange mass spectrometry (HDX-MS) to identify dynamic regions within type III phosphatidylinositol 4 kinase beta (PI4KIIIβ) in complex with the GTPase Rab11. This information was then used to design deletions that allowed for the production of diffraction quality crystals. Importantly, we also used HDX-MS to verify that the new construct was properly folded, consistent with it being catalytically and functionally active. Structures of PI4KIIIβ in an Apo state and bound to the potent inhibitor BQR695 in complex with both GTPγS and GDP loaded Rab11 were determined. This hybrid HDX-MS/crystallographic strategy revealed novel aspects of the PI4KIIIβ-Rab11 complex, as well as the molecular mechanism of potency of a PI4K specific inhibitor (BQR695). This approach is widely applicable to protein-protein complexes, and is an excellent strategy to optimize constructs for high-resolution structural approaches.

  1. Dynamics of disk galaxies under eccentric perturbations and the effect of radiative thermal exchange on the rotation of lower mass protostars

    NASA Astrophysics Data System (ADS)

    Zhang, Linchu

    2000-09-01

    In the first part of this dissertation, the dynamics of disk galaxies are treated using a representation in a number of circular rings*. The rings are assumed to be rigid and oscillate in a plane. Motion of matter within each ring is taken into account. Eccentric perturbations are studied. First the axisymmetric equilibrium configuration of the galaxy is discussed. After that eccentric perturbations are described. The ring representation is then applied and relevant equations of motion derived. Various formulas involving coefficients of terms in the equations of motion are derived. Angular momentum transport is then discussed with the results of numerical solutions of the equations of motion. Besides the disk, two other components: the galactic bulge, and the dark matter halo are also included, but only as passive sources of gravity. The central region of the disk is handled separately; it may contain a black hole. The second part of this dissertation treats protostars. It is shown that radiative thermal exchange can significantly reduce the angular momentum of a rapidly spinning protostar. The mechanism is especially important for high temperature and large surface area. Also, it is expected that the mechanism is most relevant to lower mass protostars, since they may be embedded inside H II regions which have high temperatures. *This first part of the dissertation is related to [15] (Lovelace, R. V. E., Zhang, L., Kornreich, D. A., & Haynes, M. P. 1999, THE ASTROPHYSICAL JOURNAL, 524, 634, published by the University of Chicago Press,© 1999.The American Astronomical Society. All rights reserved).

  2. Analysis of amphetamine-type stimulants and their metabolites in plasma, urine and bile by liquid chromatography with a strong cation-exchange column-tandem mass spectrometry.

    PubMed

    Kuwayama, Kenji; Inoue, Hiroyuki; Kanamori, Tatsuyuki; Tsujikawa, Kenji; Miyaguchi, Hajime; Iwata, Yuko T; Miyauchi, Seiji; Kamo, Naoki

    2008-05-01

    The aim of this work was to develop and validate a method for analysing amphetamine-type stimulants (ATSs) and their metabolites in plasma, urine and bile by liquid chromatography with a strong cation-exchange column-tandem mass spectrometry, and to apply it to the pharmacokinetic study of ATSs. 3,4-Methylenedioxymethamphetamine, methamphetamine, ketamine and their main metabolites, 4-hydroxy-3-methoxymethamphetamine, 3,4-methylenedioxyamphetamine, p-hydroxymethamphetamine, amphetamine and norketamine, were simultaneously quantified by the new method (50-5000 ng/ml). The coefficients of variation and the percent deviations for the eight compounds were in the range of 0.2 to 5.3% and -9.4 to +12.8%, respectively. The recoveries were over 90% in all biological samples tested. This method was effective for the separation and the identification of ATSs and their main metabolites having amine moieties in plasma, urine and bile, and was applicable to pharmacokinetic analysis of methamphetamine, ketamine and their main metabolites in biological samples. This analytical method should be useful for the pharmacokinetic analysis of ATSs.

  3. Mechanism and kinetics of tyrosinase inhibition by glycolic acid: a study using conventional spectroscopy methods and hydrogen/deuterium exchange coupling with mass spectrometry.

    PubMed

    Ma, Da; Tu, Zong-Cai; Wang, Hui; Zhang, Lu; He, Na; McClements, David Julian

    2017-01-25

    Tyrosinase is an enzyme that promotes enzymatic browning of fruits and vegetables, thereby reducing product quality. A variety of analytical tools were used to characterize the interactions between tyrosinase and a natural tyrosinase inhibitor (glycolic acid). Hydrogen/deuterium exchange coupling with mass spectrometry (HDX-MS) was used to elucidate the interaction mechanism between glycolic acid and tyrosinase. UV-visible, fluorescence and circular dichroism spectroscopy analysis indicated that glycolic acid inhibited tyrosinase activity in a mixed-type manner with an IC50 of 83 ± 14 μM. The results of these techniques suggested that glycolic acid bound to tyrosinase through hydrophobic attraction, and this interaction led to a pronounced conformational change of the enzyme molecules. HDX-MS analysis showed that the activity of tyrosinase was primarily inhibited by a structural perturbation of its active site (His 263). This study provides a comprehensive understanding of the interaction between glycolic acid and tyrosinase, which could lead to new approaches to control tyrosinase activity in foods and other products.

  4. Survey of inorganic arsenic in marine animals and marine certified reference materials by anion exchange high-performance liquid chromatography-inductively coupled plasma mass spectrometry.

    PubMed

    Sloth, Jens J; Larsen, Erik H; Julshamn, Kåre

    2005-07-27

    A method for the determination of inorganic arsenic in seafood samples using high-performance liquid chromatography-inductively coupled plasma mass spectrometry is described. The principle of the method relied on microwave-assisted alkaline dissolution of the sample, which at the same time oxidized arsenite [As(III)] to arsenate [As(V)], whereby inorganic arsenic could be determined as the single species As(V). Anion exchange chromatography using isocratic elution with aqueous ammonium carbonate as the mobile phase was used for the separation of As(V) from other coextracted organoarsenic compounds, including arsenobetaine. The stability of organoarsenic compounds during the sample pretreatment was investigated, and no degradation/conversion to inorganic arsenic was detected. The method was employed for the determination of inorganic arsenic in a variety of seafood samples including fish, crustaceans, bivalves, and marine mammals as well as a range of marine certified reference materials, and the results were compared to values published in the literature. For fish and marine mammals, the results were in most cases below the limit of detection. For other sample types, inorganic arsenic concentrations up to 0.060 mg kg(-)(1) were found. In all samples, the inorganic arsenic content constituted less than 1% of the total arsenic content.

  5. Analytical solution for the advection-dispersion transport equation in layered media

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The advection-dispersion transport equation with first-order decay was solved analytically for multi-layered media using the classic integral transform technique (CITT). The solution procedure used an associated non-self-adjoint advection-diffusion eigenvalue problem that had the same form and coef...

  6. The role of advection and dispersion in the rock matrix on the transport of leaking CO2-saturated brine along a fractured zone

    NASA Astrophysics Data System (ADS)

    Ahmad, Nawaz; Wörman, Anders; Sanchez-Vila, Xavier; Bottacin-Busolin, Andrea

    2016-12-01

    CO2 that is injected into a geological storage reservoir can leak in dissolved form because of brine displacement from the reservoir, which is caused by large-scale groundwater motion. Simulations of the reactive transport of leaking CO2aq along a conducting fracture in a clay-rich caprock are conducted to analyze the effect of various physical and geochemical processes. Whilst several modeling transport studies along rock fractures have considered diffusion as the only transport process in the surrounding rock matrix (diffusive transport), this study analyzes the combined role of advection and dispersion in the rock matrix in addition to diffusion (advection-dominated transport) on the migration of CO2aq along a leakage pathway and its conversion in geochemical reactions. A sensitivity analysis is performed to quantify the effect of fluid velocity and dispersivity. Variations in the porosity and permeability of the medium are found in response to calcite dissolution and precipitation along the leakage pathway. We observe that advection and dispersion in the rock matrix play a significant role in the overall transport process. For the parameters that were used in this study, advection-dominated transport increased the leakage of CO2aq from the reservoir by nearly 305%, caused faster transport and increased the mass conversion of CO2aq in geochemical reactions along the transport pathway by approximately 12.20% compared to diffusive transport.

  7. Analytical solution of advection-diffusion equation in heterogeneous infinite medium using Green's function method

    NASA Astrophysics Data System (ADS)

    Sanskrityayn, Abhishek; Kumar, Naveen

    2016-12-01

    Some analytical solutions of one-dimensional advection-diffusion equation (ADE) with variable dispersion coefficient and velocity are obtained using Green's function method (GFM). The variability attributes to the heterogeneity of hydro-geological media like river bed or aquifer in more general ways than that in the previous works. Dispersion coefficient is considered temporally dependent, while velocity is considered spatially and temporally dependent. The spatial dependence is considered to be linear and temporal dependence is considered to be of linear, exponential and asymptotic. The spatio-temporal dependence of velocity is considered in three ways. Results of previous works are also derived validating the results of the present work. To use GFM, a moving coordinate transformation is developed through which this ADE is reduced into a form, whose analytical solution is already known. Analytical solutions are obtained for the pollutant's mass dispersion from an instantaneous point source as well as from a continuous point source in a heterogeneous medium. The effect of such dependence on the mass transport is explained through the illustrations of the analytical solutions.

  8. The 8th-10 th January 2009 snowfalls: a case of Mediterranean warm advection event

    NASA Astrophysics Data System (ADS)

    Aguado, F.; Ayensa, E.; Barriga, M.; Del Hoyo, J.; Fernández, A.; Garrido, N.; Martín, A.; Martín, F.; Roa, I. Martínez, A.; Pascual, R.

    2009-09-01

    From 8 th to 10 th of January 2009, significant snowfalls were reported in many areas of the Iberian Peninsula and the Balearic Islands. This relevant event was very important from the meteorological and social impact point of views. The snow affected many zones, especially the regions of Madrid, Castilla & León and Castilla-La Mancha (Spanish central plateau) with the persistence and thickness of solid precipitation. Up to twenty-five centimetres of snow were reported in some places. On 9th of January the snowfalls caused great social and media impact due to the fact that they took place in the early hours in the Madrid metropolitan areas, affecting both air traffic and land transport. The "Madrid-Barajas" airport was closed and the city was collapsed during several hours. A study of this situation appears in the poster. The snowstorm was characterized by the previous irruption of an European continental polar air mass, that subsequently interacted with a wet and warm air mass of Mediterranean origin, all preceded by low level easterly flows. This type of snowfall is called "warm advection". These winter situations are very efficient from precipitation point of view, generating significant snowfalls and affecting a lot of areas.

  9. Self-organization and advective transport in the cell polarity formation for asymmetric cell division.

    PubMed

    Seirin Lee, Sungrim; Shibata, Tatsuo

    2015-10-07

    Anterior-Posterior (AP) polarity formation of cell membrane proteins plays a crucial role in determining cell asymmetry, which depends not only on the several genetic process but also biochemical and biophysical interactions. The mechanism of AP formation of Caenorhabditis elegans embryo is characterized into the three processes: (i) membrane association and dissociation of posterior and anterior proteins, (ii) diffusion into the membrane and cytosol, and (iii) active cortical and cytoplasmic flows induced by the contraction of the acto-myosin cortex. We explored the mechanism of symmetry breaking and AP polarity formation using self-recruitment model of posterior proteins. We found that the AP polarity pattern is established over wide range in the total mass of polarity proteins and the diffusion ratio in the cytosol to the membrane. We also showed that the advective transport in both membrane and cytosol during the establishment phase affects optimal time interval of establishment and positioning of the posterior domain, and plays a role to increase the robustness in the AP polarity formation by reducing the number of posterior domains for the sensitivity of initial conditions. We also demonstrated that a proper ratio of the total mass to cell size robustly regulate the length scale of the posterior domain.

  10. Structural characterization of in vitro rat liver microsomal metabolites of antihistamine desloratadine using LTQ-Orbitrap hybrid mass spectrometer in combination with online hydrogen/deuterium exchange HR-LC/MS.

    PubMed

    Chen, Guodong; Daaro, Ibrahim; Pramanik, Birendra N; Piwinski, John J

    2009-02-01

    In vitro drug metabolism study is an integral part of drug discovery process. In this report, we have described the application of LTQ-Orbitrap hybrid mass spectrometer in conjunction with online hydrogen (H)/deuterium (D) exchange high resolution (HR)-LC/MS for structural characterization of in vitro rat liver microsomal metabolites of antihistamine desloratadine. Five metabolites M1--M5 have been identified, including three hydroxylated metabolites M1--M3, one N-oxide M4 and one uncommon aromatized N-oxide M5. Accurate mass data have been obtained in both full scan and MSn mode support assignments of metabolite structures with reported mass errors less than 3 ppm. Online H/D exchange HR-LC/MS experiments provide additional evidence in differentiating hydroxylated metabolites from N-oxides. This study demonstrates the effectiveness of this approach in structural characterization of drug metabolites.

  11. Advective excess Ba transport as shown from sediment and trap geochemical signatures

    SciTech Connect

    Fagel, N.; Andre, L.; Dehairs, F.

    1999-08-01

    The authors report the results of a geochemical study of sediment and trap material. Major and trace elements (Zr, Ba, rare earth elements, and Th) were analyzed on bulk sedimentary material collected along the NE Atlantic margin. The aim is to test the widespread use of Ba-barite as a proxy for paleoproductivity in a continental margin area. This environment is of great interest because atmospheric-oceanic exchanges are important. In sediments, the geochemical signatures remain close to an upper crust reference, with flat shale-normalized rare earth elements patterns and constant elementary ratios. The calculated biogenic fraction of Ba or excess Ba (20--45%) remains lower than the excess Ba record in trap material (80--99%). The evolution of the geochemical signature along the margin reflects variable dilution of a detrital Post Archean Australian Shale-like component by a biogenic carbonaceous seawater-derived component. The trap material displays a wide range of variation in its trace element content (e.g., Ba {approximately}150--3,000 ppm, Zr {approximately}2--100 ppm), except for the abyssal site, which is characterized by constant signature. In the two other sites, all of the trace element contents increase with water depth and present pronounced seasonal changes at each sampled water depth. The amount of excess Ba also increases in the deepest traps, and its evolution throughout the year mimics the change of the other analyzed trace elements. In contrast, its relationships with particulate organic carbon are not obvious. In terms of fluxes, two periods of enhanced excess Ba fluxes are observed: (1) excess Ba flux increases with the detrital-like elements like Th especially during winter, and (2) excess Ba flux is enhanced without any change for the other trace elements during spring. To explain the first case, a supply through lateral advection is proposed. Such transient input of significant excess Ba flux will have a great impact on the yearly averaged

  12. Modeling velocity in gradient flows with coupled-map lattices with advection.

    PubMed

    Lind, Pedro G; Corte-Real, João; Gallas, Jason A C

    2002-07-01

    We introduce a simple model to investigate large scale behavior of gradient flows based on a lattice of coupled maps which, in addition to the usual diffusive term, incorporates advection, as an asymmetry in the coupling between nearest neighbors. This diffusive-advective model predicts traveling patterns to have velocities obeying the same scaling as wind velocities in the atmosphere, regarding the advective parameter as a sort of geostrophic wind. In addition, the velocity and wavelength of traveling wave solutions are studied. In general, due to the presence of advection, two regimes are identified: for strong diffusion the velocity varies linearly with advection, while for weak diffusion a power law is found with a characteristic exponent proportional to the diffusion.

  13. A three-dimensional volume-of-fluid method for reconstructing and advecting three-material interfaces forming contact lines

    NASA Astrophysics Data System (ADS)

    Pathak, Ashish; Raessi, Mehdi

    2016-02-01

    We introduce a piecewise-linear, volume-of-fluid method for reconstructing and advecting three-dimensional interfaces and contact lines formed by three materials. The new method employs a set of geometric constructs that can be used in conjunction with any volume-tracking scheme. In this work, we used the mass-conserving scheme of Youngs to handle two-material cells, perform interface reconstruction in three-material cells, and resolve the contact line. The only information required by the method is the available volume fraction field. Although the proposed method is order dependent and requires a priori information on material ordering, it is suitable for typical contact line applications, where the material representing the contact surface is always known. Following the reconstruction of the contact surface, to compute the interface orientation in a three-material cell, the proposed method minimizes an error function that is based on volume fraction distribution around that cell. As an option, the minimization procedure also allows the user to impose a contact angle. Performance of the proposed method is assessed via both static and advection test cases. The tests show that the new method preserves the accuracy and mass-conserving property of the Youngs method in volume-tracking three materials.

  14. Population persistence under advection-diffusion in river networks.

    PubMed

    Ramirez, Jorge M

    2012-11-01

    An integro-differential equation on a tree graph is used to model the time evolution and spatial distribution of a population of organisms in a river network. Individual organisms become mobile at a constant rate, and disperse according to an advection-diffusion process with coefficients that are constant on the edges of the graph. Appropriate boundary conditions are imposed at the outlet and upstream nodes of the river network. The local rates of population growth/decay and that by which the organisms become mobile, are assumed constant in time and space. Imminent extinction of the population is understood as the situation whereby the zero solution to the integro-differential equation is stable. Lower and upper bounds for the eigenvalues of the dispersion operator, and related Sturm-Liouville problems are found. The analysis yields sufficient conditions for imminent extinction and/or persistence in terms of the values of water velocity, channel length, cross-sectional area and diffusivity throughout the river network.

  15. Sea breezes and advective effects in southwest James Bay

    NASA Technical Reports Server (NTRS)

    Mckendry, Ian; Roulet, Nigel

    1994-01-01

    Observations from a transect extending 100 km inland during the Northern Wetlands Study (NOWES) in 1990 show that the sea breeze develops on approximately 25% of days during summer and may penetrate up to 100 km inland on occasions. The sea breeze exhibits a marked diurnal clockwise rotation as a result of the Coriolis effect along the unobstructed coastline. The marine advective effect is shown to depend on gradient wind direction. With northwesterly upper level flow the sea breeze tends to be northeasterly in direction and is associated with decreased temperatures and vapor pressure deficits (VPD). With southwesterly upper level flow the sea breeze tends to have a southeasterly direction and less effect on temperatures and VPD. This is attributed to shorter residence times of air parcels over water. For two cases, Colorado State University mesoscale model simulations show good agreement with surface wind observations and suggest that under northwesterly gradient flow, Bowen ratios are increased in the onshore flow along western James Bay, while during southwesterly gradient flow these effects are negligible. These results have implications for the interpretation of local climate, ecology, and hydrology as well as land-based and airborne turbulent flux measurements made during NOWES.

  16. Time Acceleration Methods for Advection on the Cubed Sphere

    SciTech Connect

    Archibald, Richard K; Evans, Katherine J; White III, James B; Drake, John B

    2009-01-01

    Climate simulation will not grow to the ultrascale without new algorithms to overcome the scalability barriers blocking existing implementations. Until recently, climate simulations concentrated on the question of whether the climate is changing. The emphasis is now shifting to impact assessments, mitigation and adaptation strategies, and regional details. Such studies will require significant increases in spatial resolution and model complexity while maintaining adequate throughput. The barrier to progress is the resulting decrease in time step without increasing single-thread performance. In this paper we demonstrate how to overcome this time barrier for the first standard test defined for the shallow-water equations on a sphere. This paper explains how combining a multiwavelet discontinuous Galerkin method with exact linear part time-evolution schemes can overcome the time barrier for advection equations on a sphere. The discontinuous Galerkin method is a high-order method that is conservative, flexible, and scalable. The addition of multiwavelets to discontinuous Galerkin provides a hierarchical scale structure that can be exploited to improve computational efficiency in both the spatial and temporal dimensions. Exact linear part time-evolution schemes are explicit schemes that remain stable for implicit-size time steps.

  17. Authalic parameterization of general surfaces using Lie advection.

    PubMed

    Zou, Guangyu; Hu, Jiaxi; Gu, Xianfeng; Hua, Jing

    2011-12-01

    Parameterization of complex surfaces constitutes a major means of visualizing highly convoluted geometric structures as well as other properties associated with the surface. It also enables users with the ability to navigate, orient, and focus on regions of interest within a global view and overcome the occlusions to inner concavities. In this paper, we propose a novel area-preserving surface parameterization method which is rigorous in theory, moderate in computation, yet easily extendable to surfaces of non-disc and closed-boundary topologies. Starting from the distortion induced by an initial parameterization, an area restoring diffeomorphic flow is constructed as a Lie advection of differential 2-forms along the manifold, which yields equality of the area elements between the domain and the original surface at its final state. Existence and uniqueness of result are assured through an analytical derivation. Based upon a triangulated surface representation, we also present an efficient algorithm in line with discrete differential modeling. As an exemplar application, the utilization of this method for the effective visualization of brain cortical imaging modalities is presented. Compared with conformal methods, our method can reveal more subtle surface patterns in a quantitative manner. It, therefore, provides a competitive alternative to the existing parameterization techniques for better surface-based analysis in various scenarios.

  18. Diffusion related isotopic fractionation effects with one-dimensional advective-dispersive transport.

    PubMed

    Xu, Bruce S; Lollar, Barbara Sherwood; Passeport, Elodie; Sleep, Brent E

    2016-04-15

    Aqueous phase diffusion-related isotope fractionation (DRIF) for carbon isotopes was investigated for common groundwater contaminants in systems in which transport could be considered to be one-dimensional. This paper focuses not only on theoretically observable DRIF effects in these systems but introduces the important concept of constraining "observable" DRIF based on constraints imposed by the scale of measurements in the field, and on standard limits of detection and analytical uncertainty. Specifically, constraints for the detection of DRIF were determined in terms of the diffusive fractionation factor, the initial concentration of contaminants (C0), the method detection limit (MDL) for isotopic analysis, the transport time, and the ratio of the longitudinal mechanical dispersion coefficient to effective molecular diffusion coefficient (Dmech/Deff). The results allow a determination of field conditions under which DRIF may be an important factor in the use of stable carbon isotope measurements for evaluation of contaminant transport and transformation for one-dimensional advective-dispersive transport. This study demonstrates that for diffusion-dominated transport of BTEX, MTBE, and chlorinated ethenes, DRIF effects are only detectable for the smaller molar mass compounds such as vinyl chloride for C0/MDL ratios of 50 or higher. Much larger C0/MDL ratios, corresponding to higher source concentrations or lower detection limits, are necessary for DRIF to be detectable for the higher molar mass compounds. The distance over which DRIF is observable for VC is small (less than 1m) for a relatively young diffusive plume (<100years), and DRIF will not easily be detected by using the conventional sampling approach with "typical" well spacing (at least several meters). With contaminant transport by advection, mechanical dispersion, and molecular diffusion this study suggests that in field sites where Dmech/Deff is larger than 10, DRIF effects will likely not be

  19. One-dimensional advection diffusion modeling of upwelled hyporheic stream temperature along Deer Creek, Vina, California

    NASA Astrophysics Data System (ADS)

    Butler, N. L.; Hunt, J. R.; Tompkins, M. R.

    2011-12-01

    Hyporheic exchange can locally mitigate thermal stress caused by high water temperatures by upwelling water cooler than ambient stream temperatures and thus providing thermal refuge for critical cold water organisms like salmonids. Ten hyporheic exchange locations were identified by dye tracer experiments along a 16 km stretch of Deer Creek near Vina, California. Four months of continuous temperature measurements were made in the late summer of 2005 at each downwelling and upwelling location and revealed upwelled temperatures that were lagged in time and damped in amplitude. Upwelling hyporheic temperatures that could provide thermal refuge were observed in seven of the ten temperature records. This data was modeled by an analytical one-dimensional advection-diffusion equation solution using subsurface water velocity and the hydrodynamic dispersivity fitting parameters. At each location variations in upwelling temperature are explained by changing subsurface water velocities and flow pathways. The lag time in hyporheic heat flow ranged from a few hours to 44 hours over distances of 15 to 76 meters. The daily stream temperature variation was on the order of 10°C, which was reduced to 1 to 8°C in the upwelling hyporheic flow. At four locations, there was evidence that changes in stream flow produced changes in the amplitude and phase of the upwelling hyporheic water temperature by altering both the subsurface water velocity and hydrodynamic dispersivity. At two locations, additional cold water refuge was created by decreases in surface water flow because it reduced the estimated subsurface water velocity increasing the lag time between the peak surface water and subsurface water temperatures. Increases in surface water flow increased the dispersivity at three locations providing more cold water refuge by reducing the amplitude of the upwelling hyporheic temperature. Such changes alter thermal refuge for salmonids placing a new emphasis on managing surface water

  20. A high-altitude balloon platform for determining exchange of carbon dioxide over agricultural landscapes

    NASA Astrophysics Data System (ADS)

    Bouche, Angie; Beck-Winchatz, Bernhard; Potosnak, Mark J.

    2016-11-01

    The exchange of carbon dioxide between the terrestrial biosphere and the atmosphere is a key process in the global carbon cycle. Given emissions from fossil fuel combustion and the appropriation of net primary productivity by human activities, understanding the carbon dioxide exchange of cropland agroecosystems is critical for evaluating future trajectories of climate change. In addition, human manipulation of agroecosystems has been proposed as a technique of removing carbon dioxide from the atmosphere via practices such as no-tillage and cover crops. We propose a novel method of measuring the exchange of carbon dioxide over croplands using a high-altitude balloon (HAB) platform. The HAB methodology measures two sequential vertical profiles of carbon dioxide mixing ratio, and the surface exchange is calculated using a fixed-mass column approach. This methodology is relatively inexpensive, does not rely on any assumptions besides spatial homogeneity (no horizontal advection) and provides data over a spatial scale between stationary flux towers and satellite-based inversion calculations. The HAB methodology was employed during the 2014 and 2015 growing seasons in central Illinois, and the results are compared to satellite-based NDVI values and a flux tower located relatively near the launch site in Bondville, Illinois. These initial favorable results demonstrate the utility of the methodology for providing carbon dioxide exchange data over a large (10-100 km) spatial area. One drawback is its relatively limited temporal coverage. While recruiting citizen scientists to perform the launches could provide a more extensive dataset, the HAB methodology is not appropriate for providing estimates of net annual carbon dioxide exchange. Instead, a HAB dataset could provide an important check for upscaling flux tower results and verifying satellite-derived exchange estimates.

  1. Terrestrial Fe-oxide Concretions and Mars Blueberries: Comparisons of Similar Advective and Diffusive Chemical Infiltration Reaction Mechanisms

    NASA Astrophysics Data System (ADS)

    Park, A. J.; Chan, M. A.

    2006-12-01

    Abundant iron oxide concretions occurring in Navajo Sandstone of southern Utah and those discovered at Meridiani Planum, Mars share many common observable physical traits such as their spheriodal shapes, occurrence, and distribution patterns in sediments. Terrestrial concretions are products of interaction between oxygen-rich aquifer water and basin-derived reducing (iron-rich) water. Water-rock interaction simulations show that diffusion of oxygen and iron supplied by slow-moving water is a reasonable mechanism for producing observed concretion patterns. In short, southern Utah iron oxide concretions are results of Liesegang-type diffusive infiltration reactions in sediments. We propose that the formation of blueberry hematite concretions in Mars sediments followed a similar diagenetic mechanism where iron was derived from the alteration of volcanic substrate and oxygen was provided by the early Martian atmosphere. Although the terrestrial analog differs in the original host rock composition, both the terrestrial and Mars iron-oxide precipitation mechanisms utilize iron and oxygen interactions in sedimentary host rock with diffusive infiltration of solutes from two opposite sources. For the terrestrial model, slow advection of iron-rich water is an important factor that allowed pervasive and in places massive precipitation of iron-oxide concretions. In Mars, evaporative flux of water at the top of the sediment column may have produced a slow advective mass-transfer mechanism that provided a steady source and the right quantity of iron. The similarities of the terrestrial and Martian systems are demonstrated using a water-rock interaction simulator Sym.8, initially in one-dimensional systems. Boundary conditions such as oxygen content of water, partial pressure of oxygen, and supply rate of iron were varied. The results demonstrate the importance of slow advection of water and diffusive processes for producing diagenetic iron oxide concretions.

  2. Tomography-based characterization of ice-air interface dynamics of temperature gradient snow metamorphism under advective conditions

    NASA Astrophysics Data System (ADS)

    Ebner, Pirmin Philipp; Andreoli, Christian; Schneebeli, Martin; Steinfeld, Aldo

    2015-12-01

    Snow at or close to the surface commonly undergoes temperature gradient metamorphism under advective flow, which alters its microstructure and physical properties. A functional understanding of this process is essential for many disciplines, from modeling the effects of snow on regional and global climate to assessing avalanche formation. Time-lapse X-ray microtomography was applied to investigate the structural dynamics of temperature gradient snow metamorphism exposed to an advective airflow in controlled laboratory conditions. Experiments specifically analyzed sublimation and deposition of water vapor on the ice structure. In addition, an analysis of the ice-air interface dynamics was carried out using a macroscopic equivalent model of heat and water vapor transport through a snow layer. The results indicate that sublimation of the ice matrix dominated for flow rates < 10-6 m3 s-1 while during increased mass flow rates the water vapor deposition supplied by the advective flow counteracted sublimation. A flow rate dependence of water vapor deposition at the ice interface was observed, asymptotically approaching an average estimated maximum deposition rate on the whole sample of 1.05 · 10-4 kg m-3 s-1. The growth of microsized whisker-like crystals on larger ice crystals was detected on microscope photographs, leading to an increase of the specific surface area and thus suggest a change of the physical and optical properties of the snow. The estimated values of the curvature effect of the ice crystals and the interface kinetic coefficient are in good agreement with previously published values.

  3. Differentiating transpiration from evaporation in seasonal agricultural wetlands and the link to advective fluxes in the root zone

    USGS Publications Warehouse

    Bachand, P.A.M.; S. Bachand,; Fleck, Jacob A.; Anderson, Frank E.; Windham-Myers, Lisamarie

    2014-01-01

    The current state of science and engineering related to analyzing wetlands overlooks the importance of transpiration and risks data misinterpretation. In response, we developed hydrologic and mass budgets for agricultural wetlands using electrical conductivity (EC) as a natural conservative tracer. We developed simple differential equations that quantify evaporation and transpiration rates using flowrates and tracer concentrations atwetland inflows and outflows. We used two ideal reactormodel solutions, a continuous flowstirred tank reactor (CFSTR) and a plug flow reactor (PFR), to bracket real non-ideal systems. From those models, estimated transpiration ranged from 55% (CFSTR) to 74% (PFR) of total evapotranspiration (ET) rates, consistent with published values using standard methods and direct measurements. The PFR model more appropriately represents these nonideal agricultural wetlands in which check ponds are in series. Using a fluxmodel, we also developed an equation delineating the root zone depth at which diffusive dominated fluxes transition to advective dominated fluxes. This relationship is similar to the Peclet number that identifies the dominance of advective or diffusive fluxes in surface and groundwater transport. Using diffusion coefficients for inorganic mercury (Hg) and methylmercury (MeHg) we calculated that during high ET periods typical of summer, advective fluxes dominate root zone transport except in the top millimeters below the sediment–water interface. The transition depth has diel and seasonal trends, tracking those of ET. Neglecting this pathway has profound implications: misallocating loads along different hydrologic pathways; misinterpreting seasonal and diel water quality trends; confounding Fick's First Law calculations when determining diffusion fluxes using pore water concentration data; and misinterpreting biogeochemicalmechanisms affecting dissolved constituent cycling in the root zone. In addition,our understanding of internal

  4. Heat advection processes leading to El Niño events as depicted by an ensemble of ocean assimilation products

    NASA Astrophysics Data System (ADS)

    Ballester, Joan; Bordoni, Simona; Petrova, Desislava; Rodó, Xavier

    2016-06-01

    The oscillatory nature of El Niño-Southern Oscillation results from an intricate superposition of near-equilibrium balances and out-of-phase disequilibrium processes between the ocean and the atmosphere. The main objective of the present work is to perform an exhaustive spatiotemporal analysis of the upper ocean heat budget in an ensemble of state-of-the-art ocean assimilation products. We put specific emphasis on the ocean heat advection mechanisms, and their representation in individual ensemble members and in the different stages of the ENSO oscillation leading to EN events. Our analyses consistently show that the initial subsurface warming in the western equatorial Pacific is advected to the central Pacific by the equatorial undercurrent, which, together with the equatorward advection associated with anomalies in both the meridional temperature gradient and circulation at the level of the thermocline, explains the heat buildup in the central Pacific during the recharge phase. We also find that the recharge phase is characterized by an increase of meridional tilting of the thermocline, as well as a southward upper-ocean cross-equatorial mass transport resulting from Ekman-induced anomalous vertical motion in the off-equatorial regions. Although differences between data sets are generally small, and anomalies tend to have the same sign, the differences in the magnitude of the meridional term are seen to be key for explaining the different propagation speed of the subsurface warming tendency along the thermocline. The only exception is GECCO, which does not produce the patterns of meridional surface Ekman divergence (subsurface Sverdrup convergence) in the western and central equatorial Pacific.

  5. Differentiating transpiration from evaporation in seasonal agricultural wetlands and the link to advective fluxes in the root zone.

    PubMed

    Bachand, P A M; Bachand, S; Fleck, J; Anderson, F; Windham-Myers, L

    2014-06-15

    The current state of science and engineering related to analyzing wetlands overlooks the importance of transpiration and risks data misinterpretation. In response, we developed hydrologic and mass budgets for agricultural wetlands using electrical conductivity (EC) as a natural conservative tracer. We developed simple differential equations that quantify evaporation and transpiration rates using flow rates and tracer concentrations at wetland inflows and outflows. We used two ideal reactor model solutions, a continuous flow stirred tank reactor (CFSTR) and a plug flow reactor (PFR), to bracket real non-ideal systems. From those models, estimated transpiration ranged from 55% (CFSTR) to 74% (PFR) of total evapotranspiration (ET) rates, consistent with published values using standard methods and direct measurements. The PFR model more appropriately represents these non-ideal agricultural wetlands in which check ponds are in series. Using a flux model, we also developed an equation delineating the root zone depth at which diffusive dominated fluxes transition to advective dominated fluxes. This relationship is similar to the Peclet number that identifies the dominance of advective or diffusive fluxes in surface and groundwater transport. Using diffusion coefficients for inorganic mercury (Hg) and methylmercury (MeHg) we calculated that during high ET periods typical of summer, advective fluxes dominate root zone transport except in the top millimeters below the sediment-water interface. The transition depth has diel and seasonal trends, tracking those of ET. Neglecting this pathway has profound implications: misallocating loads along different hydrologic pathways; misinterpreting seasonal and diel water quality trends; confounding Fick's First Law calculations when determining diffusion fluxes using pore water concentration data; and misinterpreting biogeochemical mechanisms affecting dissolved constituent cycling in the root zone. In addition, our understanding of

  6. Verification of Advective Bar Elements Implemented in the Aria Thermal Response Code.

    SciTech Connect

    Mills, Brantley

    2016-01-01

    A verification effort was undertaken to evaluate the implementation of the new advective bar capability in the Aria thermal response code. Several approaches to the verification process were taken : a mesh refinement study to demonstrate solution convergence in the fluid and the solid, visually examining the mapping of the advective bar element nodes to the surrounding surfaces, and a comparison of solutions produced using the advective bars for simple geometries with solutions from commercial CFD software . The mesh refinement study has shown solution convergence for simple pipe flow in both temperature and velocity . Guidelines were provided to achieve appropriate meshes between the advective bar elements and the surrounding volume. Simulations of pipe flow using advective bars elements in Aria have been compared to simulations using the commercial CFD software ANSYS Fluent (r) and provided comparable solutions in temperature and velocity supporting proper implementation of the new capability. Verification of Advective Bar Elements iv Acknowledgements A special thanks goes to Dean Dobranich for his guidance and expertise through all stages of this effort . His advice and feedback was instrumental to its completion. Thanks also goes to Sam Subia and Tolu Okusanya for helping to plan many of the verification activities performed in this document. Thank you to Sam, Justin Lamb and Victor Brunini for their assistance in resolving issues encountered with running the advective bar element model. Finally, thanks goes to Dean, Sam, and Adam Hetzler for reviewing the document and providing very valuable comments.

  7. An operator splitting algorithm for the three-dimensional advection-diffusion equation

    NASA Astrophysics Data System (ADS)

    Khan, Liaqat Ali; Liu, Philip L.-F.

    1998-09-01

    Operator splitting algorithms are frequently used for solving the advection-diffusion equation, especially to deal with advection dominated transport problems. In this paper an operator splitting algorithm for the three-dimensional advection-diffusion equation is presented. The algorithm represents a second-order-accurate adaptation of the Holly and Preissmann scheme for three-dimensional problems. The governing equation is split into an advection equation and a diffusion equation, and they are solved by a backward method of characteristics and a finite element method, respectively. The Hermite interpolation function is used for interpolation of concentration in the advection step. The spatial gradients of concentration in the Hermite interpolation are obtained by solving equations for concentration gradients in the advection step. To make the composite algorithm efficient, only three equations for first-order concentration derivatives are solved in the diffusion step of computation. The higher-order spatial concentration gradients, necessary to advance the solution in a computational cycle, are obtained by numerical differentiations based on the available information. The simulation characteristics and accuracy of the proposed algorithm are demonstrated by several advection dominated transport problems.

  8. Numerical simulation of advection fog formation on multi-disperse aerosols due to combustion-related pollutants

    NASA Technical Reports Server (NTRS)

    Hung, R. J.; Liaw, G. S.

    1980-01-01

    The effects of multi-disperse distribution of the aerosol population are presented. Single component and multi-component aerosol species on the condensation/nucleation processes which affect the reduction in visibility are described. The aerosol population with a high particle concentration provided more favorable conditions for the formation of a denser fog than the aerosol population with a greater particle size distribution when the value of the mass concentration of the aerosols was kept constant. The results were used as numerical predictions of fog formation. Two dimensional observations in horizontal and vertical coordinates, together with time-dependent measurements were needed as initial values for the following physical parameters: (1)wind profiles; (2) temperature profiles; (3) humidity profiles; (4) mass concentration of aerosol particles; (5) particle size distribution of aerosols; and (6) chemical composition of aerosols. Formation and dissipation of advection fog, thus, can be forecasted numerically by introducing initial values obtained from the observations.

  9. Ion-exchange solid-phase extraction combined with liquid chromatography-tandem mass spectrometry for the determination of veterinary drugs in organic fertilizers.

    PubMed

    Zhao, Zhiyong; Zhang, Yanmei; Xuan, Yanfang; Song, Wei; Si, Wenshuai; Zhao, Zhihui; Rao, Qinxiong

    2016-06-01

    The analysis of veterinary drugs in organic fertilizers is crucial for an assessment of potential risks to soil microbial communities and human health. We develop a robust and sensitive method to quantitatively determine 19 veterinary drugs (amantadine, sulfonamides and fluoroquinolones) in organic fertilizers. The method involved a simple solid-liquid extraction step using the combination of acetonitrile and McIlvaine buffer as extraction solvent, followed by cleanup with a solid-phase extraction cartridge containing polymeric mixed-mode anion-exchange sorbents. Ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) was used to separate and detect target analytes. We particularly focused on the optimization of sample clean-up step: different diluents and dilution factors were tested. The developed method was validated in terms of linearity, recovery, precision, sensitivity and specificity. The recoveries of all the drugs ranged from 70.9% to 112.7% at three concentration levels, with the intra-day and inter-day relative standard deviation lower than 15.7%. The limits of quantification were between 1.0 and 10.0μg/kg for all the drugs. Matrix effect was minimized by matrix-matched calibration curves. The analytical method was successfully applied for the survey of veterinary drugs contamination in 20 compost samples. The results indicated that fluoroquinolones had higher incidence rate and mean concentration levels ranging from 31.9 to 308.7μg/kg compared with other drugs. We expect the method will provide the basis for risk assessment of veterinary drugs in organic fertilizers.

  10. On-line two-dimensional capillary strong anion exchange/reversed phase liquid chromatography-tandem mass spectrometry for comprehensive lipid analysis.

    PubMed

    Bang, Dae Young; Moon, Myeong Hee

    2013-10-04

    An on-line two-dimensional liquid chromatography method was developed for comprehensive lipid profiling by coupling strong anion exchange (SAX) and nanoflow reversed-phase liquid chromatography (nRPLC) prior to electrospray ionization-tandem mass spectrometry (2D-SAX/nRPLC-ESI-MS/MS). Lipids can be classified into four different types according to the electrical propensities of the lipids: anionic, weak anionic, neutral polar, and special lipids. In 2D-SAX/nRPLC, various lipids can be fractionated in the first dimension (SAX: 5 μm to 100 Å, 5.0 cm × 75 μm i.d.) by step elution (methanol and salt solution), followed by the molecular separation of lipids in the second dimension (RP: 3 μm to 100 Å, 7.0 cm × 75 μm i.d.) with binary gradient LC. Since the elution of lipids from SAX can be achieved with a very small volume of eluent delivered from an autosampler, it can be simply implemented with an LC-ESI-MS instrument for full automation, and the salt step elution, including the two-step injection procedure, can be used for the selective analysis of the desired lipid fraction. For nRPLC-ESI-MS/MS run in either positive or negative ion mode, a common ionization modifier (0.05% ammonium hydroxide with 5mM ammonium formate) was introduced into the binary mobile phase solutions so that 2D-LC-MS could be operated in both ion modes without changing the mobile phase solutions. The developed on-line 2D-SAX/nRPLC-ESI-MS/MS was evaluated with 22 different standard lipids for the optimization of the salt step elution and was applied to a healthy human plasma lipid extract, resulting in the identification of a total of 303 plasma lipids, including 14 different classes.

  11. Epitope mapping of inhibitory antibodies targeting the C2 domain of coagulation factor VIII by hydrogen-deuterium exchange mass spectrometry

    PubMed Central

    Sevy, Alexander M.; Healey, John F.; Deng, Wei; Spiegel, P. Clint; Meeks, Shannon L.; Li, Renhao

    2014-01-01

    Summary Background The development of anti-factor VIII (fVIII) antibodies (inhibitors) is a significant complication in the management of patients with hemophilia A, leading to significant increases in morbidity and treatment cost. Using a panel of anti-fVIII monoclonal antibodies (MAbs) to different epitopes on fVIII, we recently have shown that epitope specificity, inhibitor kinetics, and time to maximum inhibition are more important than inhibitor titer in predicting response to fVIII and the combination of fVIII and recombinant factor VIIa. In particular, a subset of high-titer inhibitors responded to high dose fVIII, which would not be predicted based on their inhibitor titer alone. Thus the ability to quickly map the epitope spectrum of patient plasma using a clinically feasible assay may fundamentally change how clinicians approach the treatment of high-titer inhibitor patients. Objectives To map the epitopes of anti-fVIII MAbs, of which 3 are classical inhibitors and one non-classical, using hydrogen-deuterium exchange coupled with liquid chromatography-mass spectrometry (HDX-MS). Methods Binding epitopes of 4 MAbs targeting fVIII C2 domain were mapped using HDX-MS. Results The epitopes determined by HDX-MS are consistent with those obtained earlier through structural characterization and antibody competition assays. In addition classical and non-classical inhibitor epitopes could be distinguished using a limited subset of C2-derived peptic fragments. Conclusion Our results demonstrate the effectiveness and robustness of the HDX-MS method for epitope mapping and suggest a potential role of rapid mapping of fVIII inhibitor epitopes in facilitating individualized treatment of inhibitor patients. PMID:24152306

  12. Detection of Lipid Induced Structural Changes of the Marburg Virus Matrix Protein VP40 Using Hydrogen/Deuterium Exchange Mass Spectrometry.

    PubMed

    Wijesinghe, Kaveesha J; Urata, Sarah; Bhattarai, Nisha; Kooijman, Edgar E; Gerstman, Bernard S; Chapagain, Prem P; Li, Sheng; Stahelin, Robert V

    2017-02-06

    Marburg virus (MARV) is a lipid-enveloped virus from the Filoviridae family containing a negative sense RNA genome. One of the seven MARV genes encodes the matrix protein VP40, which forms a matrix layer beneath the plasma membrane inner leaflet to facilitate budding from the host cell. MARV VP40 (mVP40) has been shown to be a dimeric peripheral protein with a broad and flat basic surface that can associate with anionic phospholipids such as phosphatidylserine. While a number of mVP40 cationic residues have been shown to facilitate binding to membranes containing anionic lipids, much less is known on how mVP40 assembles to form the matrix layer following membrane binding. Here we have used hydrogen-deuterium exchange (H/DX) mass spectrometry to determine the solvent accessibility of mVP40 residues in the absence and presence of phosphatidylserine and phosphatidylinositol-4,5-bisphosphate. H/DX analysis demonstrates two basic loops in the mVP40 C-terminal domain make important contributions to anionic membrane binding and also revealed a potential oligomerization interface in the C-terminal domain as well as a conserved oligomerization interface in the mVP40 N-terminal domain. Lipid binding assays confirm the role of the two basic patches elucidated with HD/X measurements while molecular dynamics simulations and membrane insertion measurements complement these studies to demonstrate mVP40 doesn't appreciably insert into the hydrocarbon region of anionic membranes in contrast to the matrix protein from Ebola virus. Taken together, we propose a model by which association of the mVP40 dimer with the anionic plasma membrane facilitates assembly of mVP40 oligomers.

  13. Two-Site Evaluation of the Repeatability and Precision of an Automated Dual-Column Hydrogen/Deuterium Exchange Mass Spectrometry Platform.

    PubMed

    Cummins, David J; Espada, Alfonso; Novick, Scott J; Molina-Martin, Manuel; Stites, Ryan E; Espinosa, Juan Felix; Broughton, Howard; Goswami, Devrishi; Pascal, Bruce D; Dodge, Jeffrey A; Chalmers, Michael J; Griffin, Patrick R

    2016-06-21

    Hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) is an information-rich biophysical method for the characterization of protein dynamics. Successful applications of differential HDX-MS include the characterization of protein-ligand binding. A single differential HDX-MS data set (protein ± ligand) is often comprised of more than 40 individual HDX-MS experiments. To eliminate laborious manual processing of samples, and to minimize random and gross errors, automated systems for HDX-MS analysis have become routine in many laboratories. However, an automated system, while less prone to random errors introduced by human operators, may have systematic errors that go unnoticed without proper detection. Although the application of automated (and manual) HDX-MS has become common, there are only a handful of studies reporting the systematic evaluation of the performance of HDX-MS experiments, and no reports have been published describing a cross-site comparison of HDX-MS experiments. Here, we describe an automated HDX-MS platform that operates with a parallel, two-trap, two-column configuration that has been installed in two remote laboratories. To understand the performance of the system both within and between laboratories, we have designed and completed a test-retest repeatability study for differential HDX-MS experiments implemented at each of two laboratories, one in Florida and the other in Spain. This study provided sufficient data to do both within and between laboratory variability assessments. Initial results revealed a systematic run-order effect within one of the two systems. Therefore, the study was repeated, and this time the conclusion was that the experimental conditions were successfully replicated with minimal systematic error.

  14. Conformational analysis of large and highly disulfide-stabilized proteins by integrating online electrochemical reduction into an optimized H/D exchange mass spectrometry workflow.

    PubMed

    Trabjerg, Esben; Jakobsen, Rasmus U; Mysling, Simon; Christensen, Søren; Jørgensen, Thomas J D; Rand, Kasper D

    2015-09-01

    Analysis of disulfide-bonded proteins by hydrogen/deuterium exchange mass spectrometry (HDX-MS) requires effective and rapid reduction of disulfide bonds before enzymatic digestion in order to increase sequence coverage. In a conventional HDX-MS workflow, disulfide bonds are reduced chemically by addition of a reducing agent to the quench solution (e.g., tris(2-carboxyethyl)phosphine (TCEP)). The chemical reduction, however, is severely limited under quenched conditions due to a narrow time window as well as low pH and temperature. Here, we demonstrate the real-world applicability of integrating electrochemical reduction into an online HDX-MS workflow. We have optimized the electrochemical reduction efficiency during HDX-MS analysis of two particularly challenging disulfide stabilized proteins: a therapeutic IgG1-antibody and nerve growth factor-β (NGF). Several different parameters (flow rate and applied square wave potential, as well as the type of labeling and quench buffer) were investigated, and the optimized workflow increased the sequence coverage of NGF from 46% with chemical reduction to 99%, when electrochemical reduction was applied. Additionally, the optimized workflow also enabled a similar high sequence coverage of 96% and 87% for the heavy and light chain of the IgG1-antibody, respectively. The presented results demonstrate the successful electrochemical reduction during HDX-MS analysis of both a small exceptional tightly disulfide-bonded protein (NGF) as well as the largest protein attempted to date (IgG1-antibody). We envision that online electrochemical reduction is poised to decrease the complexity of sample handling and increase the versatility of the HDX-MS technique.

  15. A biological method of including mineralized human liquid and solid wastes into the mass exchange of bio-technical life support systems

    NASA Astrophysics Data System (ADS)

    Ushakova, S. A.; Tikhomirov, A. A.; Tikhomirova, N. A.; Kudenko, Yu. A.; Litovka, Yu. A.; Anishchenko, O. V.

    2012-10-01

    The main obstacle to using mineralized human solid and liquid wastes as a source of mineral elements for plants cultivated in bio-technical life support systems (BLSS) is that they contain NaCl. The purpose of this study is to determine whether mineralized human wastes can be used to prepare the nutrient solution for long-duration conveyor cultivation of uneven-aged wheat and Salicornia europaea L. plant community. Human solid and liquid wastes were mineralized by the method of "wet incineration" developed by Yu. Kudenko. They served as a basis for preparing the solutions that were used for conveyor-type cultivation of wheat community represented by 5 age groups, planted with a time interval of 14 days. Wheat was cultivated hydroponically on expanded clay particles. To reduce salt content of the nutrient solution, every two weeks, after wheat was harvested, 12 L of solution was removed from the wheat irrigation tank and used for Salicornia europaea cultivation in water culture in a conveyor mode. The Salicornia community was represented by 2 age groups, planted with a time interval of 14 days. As some portion of the nutrient solution used for wheat cultivation was regularly removed, sodium concentration in the wheat irrigation solution did not exceed 400 mg/L, and mineral elements contained in the removed portion were used for Salicornia cultivation. The experiment lasted 4 months. The total wheat biomass productivity averaged 30.1 g · m-2 · day-1, and the harvest index amounted to 36.8%. The average productivity of Salicornia edible biomass on a dry weight basis was 39.3 g · m-2 · day-1, and its aboveground mass contained at least 20% of NaCl. Thus, the proposed technology of cultivation of wheat and halophyte plant community enables using mineralized human wastes as a basis for preparing nutrient solutions and including NaCl in the mass exchange of the BLSS; moreover, humans are supplied with additional amounts of leafy vegetables.

  16. The distortion of the level set gradient under advection

    NASA Astrophysics Data System (ADS)

    Trujillo, Mario F.; Anumolu, Lakshman; Ryddner, Doug

    2017-04-01

    The practice of periodically reinitializing the level set function is well established in two-phase flow applications as a way of controlling the growth of anomalies and/or numerical errors. In the present work, the underlying roots of this anomalous growth are studied, where it is established that the augmentation of the magnitude of the level set gradient (| ∇ϕ |) is directly connected to the nature of the flow field; hence, it is not necessarily the result of some type of numerical error. More specifically, for a general flow field advecting the level set function, it is shown that the eigenpairs of the strain rate tensor are responsible for the rate of change of | ∇ϕ | along a fluid particle trajectory. This straining action not only affects the magnitude of | ∇ϕ |, but the general character of ϕ, and consequently contributes to the growth in numerical error. These numerical consequences are examined by adopting the Gradient Augmented Level Set method. Specifically, it is shown that the local error for ϕ is directly connected to the size of | ∇ϕ | and to the magnitude of the second and fourth order derivatives of ϕ. These analytical findings are subsequently supported by various examples. The role of reinitialization is discussed, where it is shown that in cases where the zero level set contour has a local radius of curvature that is below the local grid resolution, reinitialization exacerbates rather than diminishes the degree of error. For other cases, where the interface is well resolved, reinitialization helps stabilize the error as intended.

  17. Critical time scales for advection-diffusion-reaction processes

    NASA Astrophysics Data System (ADS)

    Ellery, Adam J.; Simpson, Matthew J.; McCue, Scott W.; Baker, Ruth E.

    2012-04-01

    The concept of local accumulation time (LAT) was introduced by Berezhkovskii and co-workers to give a finite measure of the time required for the transient solution of a reaction-diffusion equation to approach the steady-state solution [A. M. Berezhkovskii, C. Sample, and S. Y. Shvartsman, Biophys. J.BIOJAU0006-349510.1016/j.bpj.2010.07.045 99, L59 (2010); A. M. Berezhkovskii, C. Sample, and S. Y. Shvartsman, Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.83.051906 83, 051906 (2011)]. Such a measure is referred to as a critical time. Here, we show that LAT is, in fact, identical to the concept of mean action time (MAT) that was first introduced by McNabb [A. McNabb and G. C. Wake, IMA J. Appl. Math.IJAMDM0272-496010.1093/imamat/47.2.193 47, 193 (1991)]. Although McNabb's initial argument was motivated by considering the mean particle lifetime (MPLT) for a linear death process, he applied the ideas to study diffusion. We extend the work of these authors by deriving expressions for the MAT for a general one-dimensional linear advection-diffusion-reaction problem. Using a combination of continuum and discrete approaches, we show that MAT and MPLT are equivalent for certain uniform-to-uniform transitions; these results provide a practical interpretation for MAT by directly linking the stochastic microscopic processes to a meaningful macroscopic time scale. We find that for more general transitions, the equivalence between MAT and MPLT does not hold. Unlike other critical time definitions, we show that it is possible to evaluate the MAT without solving the underlying partial differential equation (pde). This makes MAT a simple and attractive quantity for practical situations. Finally, our work explores the accuracy of certain approximations derived using MAT, showing that useful approximations for nonlinear kinetic processes can be obtained, again without treating the governing pde directly.

  18. Broadband Spectral Energy Distributions of Active Galactic Nuclei from an Accretion Disk with Advective Coronal Flow

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Toshihiro; Shimura, Toshiya; Mineshige, Shin

    2001-01-01

    Recent multiwaveband observations of Seyfert nuclei and QSOs established significant deviations in the spectral shape of the big blue bump from a blackbody spectral shape; soft X-ray excess has a spectral index α (Fν~ν-α) of 1.6 and hard X-ray tail with α of ~0.7. We construct a disk-corona model which accounts for such broadband spectral properties. We study the emission spectrum emerging from a vertical disk-corona structure composed of two-temperature plasma by solving hydrostatic equilibrium and radiative transfer self-consistently. A fraction f of viscous heating due to mass accretion is assumed to be dissipated in a corona with a Thomson optical depth of τc, where advective cooling is also included, and a remaining fraction, 1-f, dissipates within a main body of the disk. Our model can nicely reproduce the soft X-ray excess with a power-law shape and the hard tail extending to ~50 keV. The different spectral slopes (α~1.5 below 2 keV and ~0.5 above) are the results of different emission mechanisms and different sites; the former slope is due to unsaturated Comptonization from the innermost zone, and the latter is due to a combination of the Comptonization, bremsstrahlung, and a reflection of the coronal radiation at the disk-corona boundary from the inner to surrounding zone (<=300 Schwarzschild radii). The emergent optical spectrum is redder (α~0.3) than that of the standard disk (α~-0.3), being consistent with observations, due to the different efficiencies of spectral hardening of disk emission at different radii. Further, we find that the cutoff frequency of the hard X-ray (~coronal electron temperature) and broadband spectral shape are insensitive to the black hole mass, while the peak frequency of the big blue bump is sensitive to the mass as the peak frequency ~M-1/4BH.

  19. The contiguous domains of Arctic Ocean advection: Trails of life and death

    NASA Astrophysics Data System (ADS)

    Wassmann, P.; Kosobokova, K. N.; Slagstad, D.; Drinkwater, K. F.; Hopcroft, R. R.; Moore, S. E.; Ellingsen, I.; Nelson, R. J.; Carmack, E.; Popova, E.; Berge, J.

    2015-12-01

    The central Arctic Ocean is not isolated, but tightly connected to the northern Pacific and Atlantic Oceans. Advection of nutrient-, detritus- and plankton-rich waters into the Arctic Ocean forms lengthy contiguous domains that connect subarctic with the arctic biota, supporting both primary production and higher trophic level consumers. In turn, the Arctic influences the physical, chemical and biological oceanography of adjacent subarctic waters through southward fluxes. However, exports of biomass out of the Arctic Ocean into both the Pacific and Atlantic Oceans are thought to be far smaller than the northward influx. Thus, Arctic Ocean ecosystems are net biomass beneficiaries through advection. The biotic impact of Atlantic- and Pacific-origin taxa in arctic waters depends on the total supply of allochthonously-produced biomass, their ability to survive as adults and their (unsuccessful) reproduction in the new environment. Thus, advective transport can be thought of as trails of life and death in the Arctic Ocean. Through direct and indirect (mammal stomachs, models) observations this overview presents information about the advection and fate of zooplankton in the Arctic Ocean, now and in the future. The main zooplankton organisms subjected to advection into and inside the Arctic Ocean are (a) oceanic expatriates of boreal Atlantic and Pacific origin, (b) oceanic Arctic residents and (c) neritic Arctic expatriates. As compared to the Pacific gateway the advective supply of zooplankton biomass through the Atlantic gateways is 2-3 times higher. Advection characterises how the main planktonic organisms interact along the contiguous domains and shows how the subarctic production regimes fuel life in the Arctic Ocean. The main differences in the advective regimes through the Pacific and Atlantic gateways are presented. The Arctic Ocean is, at least in some regions, a net heterotrophic ocean that - during the foreseeable global warming trend - will more and more rely

  20. Determination of longitudinal dispersion coefficient and net advection in the tidal hudson river with a large-scale, high resolution SF6 tracer release experiment.

    PubMed

    Ho, David T; Schlosser, Peter; Caplow, Theodore

    2002-08-01

    Physical processes such as advection, dispersion, and air-water gas exchange play important roles in determining the movement and change in concentration of contaminants discharged into rivers. In the following, we report results from a large-scale SF6 tracer release experiment conducted in the tidal Hudson Riverto examine longitudinal dispersion and net advection. SF6 was injected into the Hudson River near Newburgh, NY, and surveyed for 13 days using a new, fully automated, high-resolution SF6 sampling and analysis system. Net down river advection of the water body originally tagged with SF6 was slow, averaging mean displacement rates of about 0.5 +/- 0.2 km d(-1). In contrast, spreading of the tracer was driven by tidal movement, causing rapid mixing of the water up and down river. By examining the change in the second moment of the tracer distribution with time, we determined the mean longitudinal dispersion coefficient to be 70.1 +/- 4.3 m2 s(-1). Temporal evolution of the SF6 inventory indicates an average gas transfer velocity over the period of the experiment of 6.5 +/- 0.5 cm h(-1) (1.56 +/- 0.12 m d(-1)). Vertical profiles show that mixing into the bottom layers of the river, in places reaching more than 53 m, seemed to be rapid.

  1. SEBAL-A: A remote sensing ET algorithm that accounts for advection with limited data. Part II: Test for transferability

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Because the Surface Energy Balance Algorithm for Land (SEBAL) tends to underestimate ET under conditions of advection, the model was modified by incorporating an advection component as part of the energy usable for crop evapotranspiration (ET). The modification involved the estimation of advected en...

  2. Removing volatile contaminants from the unsaturated zone by inducing advective air-phase transport

    USGS Publications Warehouse

    Baehr, A.L.; Hoag, G.E.; Marley, M.C.

    1989-01-01

    Organic liquids inadvertently spilled and then distributed in the unsaturated zone can pose a long-term threat to ground water. Many of these substances have significant volatility, and thereby establish a premise for contaminant removal from the unsaturated zone by inducing advective air-phase transport with wells screened in the unsaturated zone. In order to focus attention on the rates of mass transfer from liquid to vapour phases, sand columns were partially saturated with gasoline and vented under steady air-flow conditions. The ability of an equilibrium-based transport model to predict the hydrocarbon vapor flux from the columns implies an efficient rate of local phase transfer for reasonably high air-phase velocities. Thus the success of venting remediations will depend primarily on the ability to induce an air-flow field in a heterogeneous unsaturated zone that will intersect the distributed contaminant. To analyze this aspect of the technique, a mathematical model was developed to predict radially symmetric air flow induced by venting from a single well. This model allows for in-situ determinations of air-phase permeability, which is the fundamental design parameter, and for the analysis of the limitations of a single well design. A successful application of the technique at a site once contaminated by gasoline supports the optimism derived from the experimental and modeliing phases of this study, and illustrates the well construction and field methods used to document the volatile contaminant recovery. ?? 1989.

  3. A validated 2-D diffusion-advection model for prediction of drift from ground boom sprayers

    NASA Astrophysics Data System (ADS)

    Baetens, K.; Ho, Q. T.; Nuyttens, D.; De Schampheleire, M.; Melese Endalew, A.; Hertog, M. L. A. T. M.; Nicolaï, B.; Ramon, H.; Verboven, P.

    Correct field drift prediction is a key element in environmental risk assessment of spraying applications. A reduced order drift prediction model based on the diffusion-advection equation is presented. It allows fast assessment of the drift potential of specific ground boom applications under specific environmental wind conditions that obey the logarithmic wind profile. The model was calibrated based on simulations with a validated Computational Fluid Dynamics (CFD) model. Validation of both models against 38 carefully conducted field experiments is successfully performed for distances up to 20 m from the field edge, for spraying on flat pasture land. The reduced order model succeeded in correct drift predictions for different nozzle types, wind velocities, boom heights and spray pressures. It used 4 parameters representing the physical aspects of the drift cloud; the height of the cloud at the field edge, the mass flux crossing the field edge, the settling velocity of the droplets and the turbulence. For the parameter set and range considered, it is demonstrated for the first time that the effect of the droplet diameter distribution of the different nozzle types on the amount of deposition spray drift can be evaluated by a single parameter, i.e., the volume fraction of droplets with a diameter smaller than 191 μm. The reduced order model can be solved more than 4 orders of magnitude faster than the comprehensive CFD model.

  4. Advective loss of overwintering Calanus finmarchicus from the Faroe-Shetland Channel

    NASA Astrophysics Data System (ADS)

    Rullyanto, Arief; Jónasdóttir, Sigrún H.; Visser, André W.

    2015-04-01

    The flow of deep water from the Norwegian Sea to the North Atlantic via the Faroe-Shetland Channel is one of the critical bottlenecks in the meridional overturn circulation. It is also a flow that potentially carries with it a large number of the overwintering copepod, Calanus finmarchicus, a regionally important secondary producer. Using a high resolution hydrodynamic model, MIKE 3 FM, we simulate the overflow of deep water and estimate the associated loss rate of C. finmarchicus as a function of the water depth strata within which they reside. We estimate a net advective loss from the Norwegian Sea population of 80±10 kt carbon bound in lipids of C. finmarchicus biomass per year, a number that constitutes about 50% of the total overwintering population. Estimates of water mass characteristics and particle tracking suggest that the fate of individuals transported in the overflowing water is to be entrained into warmer waters of the North Atlantic Basin, a habitat that appears to be unsuitable for successful overwintering.

  5. On the potential importance of transient air flow in advective radon entry into buildings

    SciTech Connect

    Narasimhan, T.N.; Tsang, Y.W.; Holman, H.Y. )

    1990-05-01

    The authors have investigated, using a mathematical model, the temporal variations of air flux within the soil mass surrounding a basement in the presence of time dependent periodic variations of barometric pressure and a persistent under-pressure at the basement. The results of transient air flow show that for a homogeneous soil medium, the effects of barometric fluctuations are most significant in the cases where soil permeability to air is low and the fluctuation frequency is high. In these cases, the barometric fluctuation can greatly enhance the magnitude of fluxes as well as introduce flow direction reversals from surrounding soil into the basement. These large fluxes with direction reversals have strong implications in regard to advective transport of radon. The results suggest that the transient oscillations have to be accounted for in quantifying radon entry into buildings. In the actual field set up, the transient behavior will be further influenced by soil permeability heterogeneity, by soil moisture variations, and by the effects of multiple periodic components in the barometric pressure fluctuations.

  6. Modeling surfzone to inner-shelf tracer exchange

    NASA Astrophysics Data System (ADS)

    Hally-Rosendahl, Kai; Feddersen, Falk

    2016-06-01

    A near-shoreline, continuous dye release at an approximately alongshore-uniform beach (IB09 experiment) is simulated with the wave-resolving Boussinesq model funwaveC. The model generates surfzone eddies and transient rip currents but does not resolve inner-shelf vertical variation or stratification. The funwaveC model reproduces well the observed surfzone and inner-shelf dye observations over roughly 350 m cross-shore and 2 km alongshore. Dye is advected alongshore by wave- and wind-driven currents similarly in the observations and model. Near-shoreline mean dye concentration decays downstream as a power law with similar observed (-0.33) and modeled (-0.38) exponents. Observed and modeled cross-shore mean dye profiles are similar, though modeled inner-shelf dye is somewhat elevated. Observed and modeled alongshore dye transports agree, though with compensating surfzone and inner-shelf errors later in the release. For times <3.5 h (before observed and modeled dye advects beyond the model alongshore domain), observed and modeled dye budgets are similar to each other and close to within 10%, and half the observed and modeled dye is exported to the inner-shelf. Later in the release, surfzone and inner-shelf dye masses are under and overpredicted, respectively. Model-data differences may be due to the model's lack of vertical variation, stratification, or tide. The good overall model-data agreement indicates that nearshore tracer transport and dispersion are realistically simulated over 5 h and 2 km alongshore, and that the model transient rip currents accurately induce cross-shore exchange between the surfzone and inner-shelf.

  7. Clay with Desiccation Cracks is an Advection Dominated Environment

    NASA Astrophysics Data System (ADS)

    Baram, S.; Kurtzman, D.; Sher, Y.; Ronen, Z.; Dahan, O.

    2012-04-01

    , indicating deep soil evaporation. Daily fluctuation of the air temperature in the desiccation cracks supported thermally induced air convection within the cracks void and could explain the deep soil salinization process. Combination of all the abovementioned observations demonstrated that the formation of desiccation cracks network in dispersive clay sediments generates a bulk advection dominated environment for both air and water flow, and that the reference to clay sediments as "hydrologically safe" should to be reconsidered.

  8. Rigorous upper bounds for fluid and plasma transport due to passive advection

    SciTech Connect

    Krommes, J.A.; Smith, R.A.; Kim, C.B.

    1987-07-01

    The formulation of variational principles for transport due to passive advection is described. A detailed account of the work has been published elsewhere. In the present paper, the motivations, philosophy, and implications of the method are briefly discussed. 15 refs.

  9. AN EULERIAN-LAGRANGIAN LOCALIZED ADJOINT METHOD FOR THE ADVECTION-DIFFUSION EQUATION

    EPA Science Inventory

    Many numerical methods use characteristic analysis to accommodate the advective component of transport. Such characteristic methods include Eulerian-Lagrangian methods (ELM), modified method of characteristics (MMOC), and operator splitting methods. A generalization of characteri...

  10. Simulation of Helical Flow Hydrodynamics in Meanders and Advection-Turbulent Diffusion Using Smoothed Particle Hydrodynamics

    NASA Astrophysics Data System (ADS)

    Gusti, T. P.; Hertanti, D. R.; Bahsan, E.; Soeryantono, H.

    2013-12-01

    Particle-based numerical methods, such as Smoothed Particle Hydrodynamics (SPH), may be able to simulate some hydrodynamic and morphodynamic behaviors better than grid-based numerical methods. This study simulates hydrodynamics in meanders and advection and turbulent diffusion in straight river channels using Microsoft Excel and Visual Basic. The simulators generate three-dimensional data for hydrodynamics and one-dimensional data for advection-turbulent diffusion. Fluid at rest, sloshing, and helical flow are simulated in the river meanders. Spill loading and step loading are done to simulate concentration patterns associated with advection-turbulent diffusion. Results indicate that helical flow is formed due to disturbance in morphology and particle velocity in the stream and the number of particles does not have a significant effect on the pattern of advection-turbulent diffusion concentration.

  11. A Quasi-Conservative Adaptive Semi-Lagrangian Advection-Diffusion Scheme

    NASA Astrophysics Data System (ADS)

    Behrens, Joern

    2014-05-01

    Many processes in atmospheric or oceanic tracer transport are conveniently represented by advection-diffusion type equations. Depending on the magnitudes of both components, the mathematical representation and consequently the discretization is a non-trivial problem. We will focus on advection-dominated situations and will introduce a semi-Lagrangian scheme with adaptive mesh refinement for high local resolution. This scheme is well suited for pollutant transport from point sources, or transport processes featuring fine filamentation with corresponding local concentration maxima. In order to achieve stability, accuracy and conservation, we combine an adaptive mesh refinement quasi-conservative semi-Lagrangian scheme, based on an integral formulation of the underlying advective conservation law (Behrens, 2006), with an advection diffusion scheme as described by Spiegelman and Katz (2006). The resulting scheme proves to be conservative and stable, while maintaining high computational efficiency and accuracy.

  12. AN EXACT PEAK CAPTURING AND OSCILLATION-FREE SCHEME TO SOLVE ADVECTION-DISPERSION TRANSPORT EQUATIONS

    EPA Science Inventory

    An exact peak capturing and essentially oscillation-free (EPCOF) algorithm, consisting of advection-dispersion decoupling, backward method of characteristics, forward node tracking, and adaptive local grid refinement, is developed to solve transport equations. This algorithm repr...

  13. The impact of advection on stratification and chlorophyll variability in the equatorial Pacific

    NASA Astrophysics Data System (ADS)

    Dave, Apurva C.; Lozier, M. Susan

    2015-06-01

    Previously reported global-scale correlations between interannual variability in upper ocean stratification and chlorophyll a (a proxy for phytoplankton biomass) have been shown to be driven by strong associations between the two properties in the central and western equatorial Pacific. Herein, we present evidence that these correlations are not causal but instead result from the advection of heat, salt, and nutrients in the region. Specifically, we demonstrate that stratification and chlorophyll are simultaneously influenced by shifts in the horizontal advective inputs of cold/saline/nutrient-rich waters from upwelling regions to the east and warm/fresh/nutrient-poor waters to the west. We find that horizontal advection contributes substantially to the annual surface layer nutrient budget and, together with vertical advection, significantly impacts interannual variability in chlorophyll. These results highlight the importance of a three-dimensional framework for examining nutrient supply in the upper ocean—a crucial requirement for assessing future marine ecosystem responses to a changing climate.

  14. Advection-Induced Spectrotemporal Defects in a Free-Electron Laser

    SciTech Connect

    Bielawski, S.; Szwaj, C.; Bruni, C.; Garzella, D.; Orlandi, G.L.; Couprie, M.E.

    2005-07-15

    We evidence numerically and experimentally that advection can induce spectrotemporal defects in a system presenting a localized structure. Those defects in the spectrum are associated with the breakings induced by the drift of the localized solution. The results are based on simulations and experiments performed on the super-ACO free-electron laser. However, we show that this instability can be generalized using a real Ginzburg-Landau equation with (i) advection and (ii) a finite-size supercritical region.

  15. Exploration of POD-Galerkin Techniques for Developing Reduced Order Models of Reaction-Advection Equations

    DTIC Science & Technology

    2014-04-01

    downstream boundary (when needed) is obtained by extrapolation, taking into account the hyperbolic character of the equation . By separating the...for Developing Reduced Order Models of Reaction-Advection Equations 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT...advection scalar equation is used as a representative equation to investigate the overall approach. Both linear and nonlinear model equations are

  16. Advection and dispersion heat transport mechanisms in the quantification of shallow geothermal resources and associated environmental impacts.

    PubMed

    Alcaraz, Mar; García-Gil, Alejandro; Vázquez-Suñé, Enric; Velasco, Violeta

    2016-02-01

    Borehole Heat Exchangers (BHEs) are increasingly being used to exploit shallow geothermal energy. This paper presents a new methodology to provide a response to the need for a regional quantification of the geothermal potential that can be extracted by BHEs and the associated environmental impacts. A set of analytical solutions facilitates accurate calculation of the heat exchange of BHEs with the ground and its environmental impacts. For the first time, advection and dispersion heat transport mechanisms and the temporal evolution from the start of operation of the BHE are taken into account in the regional estimation of shallow geothermal resources. This methodology is integrated in a GIS environment, which facilitates the management of input and output data at a regional scale. An example of the methodology's application is presented for Barcelona, in Spain. As a result of the application, it is possible to show the strengths and improvements of this methodology in the development of potential maps of low temperature geothermal energy as well as maps of environmental impacts. The minimum and maximum energy potential values for the study site are 50 and 1800 W/m(2) for a drilled depth of 100 m, proportionally to Darcy velocity. Regarding to thermal impacts, the higher the groundwater velocity and the energy potential, the higher the size of the thermal plume after 6 months of exploitation, whose length ranges from 10 to 27 m long. A sensitivity analysis was carried out in the calculation of heat exchange rate and its impacts for different scenarios and for a wide range of Darcy velocities. The results of this analysis lead to the conclusion that the consideration of dispersion effects and temporal evolution of the exploitation prevent significant differences up to a factor 2.5 in the heat exchange rate accuracy and up to several orders of magnitude in the impacts generated.

  17. Different conformational dynamics of β-arrestin1 and β-arrestin2 analyzed by hydrogen/deuterium exchange mass spectrometry

    SciTech Connect

    Yun, Youngjoo; Kim, Dong Kyun; Seo, Min-Duk; Kim, Kyeong-Man; Chung, Ka Young

    2015-01-30

    Highlights: • The conformational dynamics of β-arrestin1 or β-arrestin2 were analyzed by HDX-MS. • β-Strands II through IV were more dynamic in β-arrestin2 than in β-arrestin1. • The middle loop was less dynamic in β-arrestin2 than in β-arrestin1. • Upon pre-activation by the R169E mutation, β-arrestins became more dynamic. • Pre-activation affected a wider region of β-arrestin1 compared to β-arrestin2. - Abstract: Arrestins have important roles in G protein-coupled receptor (GPCR) signaling including desensitization of GPCRs and G protein-independent signaling. There have been four arrestins identified: arrestin1, arrestin2 (e.g. β-arrestin1), arrestin3 (e.g. β-arrestin2), and arrestin4. β-Arrestin1 and β-arrestin2 are ubiquitously expressed and regulate a broad range of GPCRs, while arrestin1 and arrestin4 are expressed in the visual system. Although the functions of β-arrestin1 and β-arrestin2 widely overlap, β-arrestin2 has broader receptor selectivity, and a few studies have suggested that β-arrestin1 and β-arrestin2 have distinct cellular functions. Here, we compared the conformational dynamics of β-arrestin1 and β-arrestin2 by hydrogen/deuterium exchange mass spectrometry (HDX-MS). We also used the R169E mutant as a pre-activation model system. HDX-MS data revealed that β-strands II through IV were more dynamic in β-arrestin2 in the basal state, while the middle loop was more dynamic in β-arrestin1. With pre-activation, both β-arrestin1 and β-arrestin2 became more flexible, but broader regions of β-arrestin1 became flexible compared to β-arrestin2. The conformational differences between β-arrestin1 and β-arrestin2 in both the basal and pre-activated states might determine their different receptor selectivities and different cellular functions.

  18. Sensitivity of solute advective travel time to porosities of hydrogeologic units.

    PubMed

    Zhu, Jianting; Pohlmann, Karl F; Chapman, Jenny B; Russell, Charles E; Carroll, Rosemary W H; Shafer, David S

    2010-01-01

    An integral approach is proposed to quantify uncertainty and sensitivity of advective travel time to the effective porosities of hydrogeologic units (HGUs) along groundwater flow paths. The approach is applicable in situations where a groundwater flow model exists, but a full solute transport model is not available. The approach can be used to: (1) determine HGUs whose porosities are influential to the solute advective travel time; and (2) apportion uncertainties of solute advective travel times to the uncertainty contributions from individual HGU porosities. A simple one-dimensional steady-state flow example is used to illustrate the approach. Advective travel times of solutes are obtained based on the one-dimensional steady-state flow results in conjunction with the HGU porosities. The approach can be easily applicable to more complex multi-dimensional cases where advective solute travel time can be calculated based on simulated flow results from groundwater flow models. This approach is particularly valuable for optimizing limited resources when designing field characterization programs for uncertainty reduction by identifying HGUs that contribute most to the estimation uncertainty of advective travel times of solutes.

  19. Optimization of Heat Exchangers

    SciTech Connect

    Ivan Catton

    2010-10-01

    The objective of this research is to develop tools to design and optimize heat exchangers (HE) and compact heat exchangers (CHE) for intermediate loop heat transport systems found in the very high temperature reator (VHTR) and other Generation IV designs by addressing heat transfer surface augmentation and conjugate modeling. To optimize heat exchanger, a fast running model must be created that will allow for multiple designs to be compared quickly. To model a heat exchanger, volume averaging theory, VAT, is used. VAT allows for the conservation of mass, momentum and energy to be solved for point by point in a 3 dimensional computer model of a heat exchanger. The end product of this project is a computer code that can predict an optimal configuration for a heat exchanger given only a few constraints (input fluids, size, cost, etc.). As VAT computer code can be used to model characteristics )pumping power, temperatures, and cost) of heat exchangers more quickly than traditional CFD or experiment, optimization of every geometric parameter simultaneously can be made. Using design of experiment, DOE and genetric algorithms, GE, to optimize the results of the computer code will improve heat exchanger disign.

  20. "Best match" model and effect of Na+/H+ exchange on anion attachment to peptides and stability of formed adducts in negative ion electrospray mass spectrometry.

    PubMed

    Liu, Xiaohua; Cole, Richard B

    2014-02-01

    The "Best Match" model has been extended to account for the role that Na(+)/H(+) exchange plays on anion attachment in negative ion electrospray. Without any Na(+)/H(+) exchange on (Glu) fibrinopeptide B, the higher basicity anions F(-) and CH3COO(-) can hardly form observable adducts; however, after multiple Na(+)/H(+) exchanges, adduct formation is enabled. Moreover, dissociation pathways of CF3COO(-) adducts with singly deprotonated peptides that have undergone 0 to 3 Na(+)/H(+) exchanges exhibit a shift in CID product ions from losing predominately CF3COOH (case of 0 Na(+)/H(+) exchanges) to losing predominately CF3COO(-) (case of 3 Na(+)/H(+) exchanges). These phenomena can be rationalized by considering that Na(+) cations exchange at, and serve to "block", the most acidic sites, thereby forcing implicated anions to attach to lower acidity protons. In addition to forming ion pairs with carboxylate groups, Na(+) also participates in formation of tri-atomic ions of the form ANaA(-) during adduct dissociation. The fact that low gas-phase basicity (GB) anions preferentially form ANaA(-) species, even though high GB anions form more stable tri-atomic species, indicates that the monatomic ions were not in close contact in the initial adduct. The propensity for formation of stable anionic adducts is dependent on the degree of matching between anion GBs and GBapp of deprotonated sites on the peptide. The GBapp is raised dramatically as the charge state of the peptide increases via a through-space effect. The presence of Na(+) on carboxylate sites substantially decreases the GBapp by neutralizing these sites, while slightly increasing the intrinsic GBs by an inductive effect.

  1. Advection and evolution of river basins in mountain ranges.

    NASA Astrophysics Data System (ADS)

    Castelltort, S.; Simpson, G.; Willett, S.

    2009-04-01

    Simpson (2006) have proposed a mechanism which involves (1) the idea that river networks in the lowland plains are incorporated in the orogen as it widens, and (2) that they do not change after their incorporation, thus "importing" a geometry acquired outside of the range independently of the tectonic and climatic influences acting inside the uplifting zone. This mechanisms implies rather a "static" view of river networks which serves as an alternative to models in which river networks continuously reorganize inside uplifting topography in such a way as to maintain a statistical geometry dictated solely by geomorphic processes. In the present work our approach to this problem is to measure and compare the form of river basins in the lowlands and in the uplands of the Himalayas, New-Zealand, Taiwan, the European Alps, the Pyrenees and the Apennines. We first present the method we employ to measure the shape of river basins and the data used. Second, we analyse and discuss our results which show a correlation between the shape of networks developed in the pro-lowlands of active orogens and their upland counterparts whereas such a correlation does not exist on the retro-side of the considered orogens. Our results thus support (1) the horizontal advection of river basins from the pro-lowlands to the pro-uplands, (2) a certain amount of reorganization by widening of basin boundaries, and (3) the existence of a different mechanism of drainage network evolution in the retro-side of the orogens. Castelltort, S., and Simpson, G., 2006, Basin Research, 18: 267-276. Hallet, B. and Molnar, P., 2001. J. Geophys. Res, 106: 13697-13709. Hovius, N., 1996, Basin Research, 8: 29-44.

  2. Enumeration of non-labile oxygen atoms in dissolved organic matter by use of ¹⁶O/ ¹⁸O exchange and Fourier transform ion-cyclotron resonance mass spectrometry.

    PubMed

    Kostyukevich, Yury; Kononikhin, Alexey; Zherebker, Alexander; Popov, Igor; Perminova, Irina; Nikolaev, Eugene

    2014-10-01

    We report a simple approach for enumeration of non-labile oxygen atoms in individual molecules of dissolved organic matter (DOM), using acid-catalyzed (16)O/(18)O exchange and ultrahigh-resolution Fourier-transform ion-cyclotron-resonance mass spectrometry (FTICR-MS). We found that by dissolving DOM in H2 (18)O at 95 °C for 20 days it is possible to replace all oxygen atoms of DOM molecules (excluding oxygen from ether groups) with (18)O. The number of exchanges in each molecule can be determined using high-resolution FTICR. Using the proposed method we identified the number of non-labile oxygen atoms in 231 molecules composing DOM. Also, using a previously developed hydrogen-deuterium (H/D)-exchange approach we identified the number of labile hydrogen atoms in 450 individual molecular formulas. In addition, we observed that several backbone hydrogen atoms can be exchanged for deuterium under acidic conditions. The method can be used for structural and chemical characterization of individual DOM molecules, comparing different DOM samples, and investigation of biological pathways of DOM in the environment.

  3. Developing a 3D constrained variational analysis method to obtain accurate gridded atmospheric vertical velocity and horizontal advections

    NASA Astrophysics Data System (ADS)

    Tang, S.; Zhang, M.

    2013-12-01

    Based on the constrained variational analysis (CVA) algorithm developed by Zhang and Lin (1997), a 3-dimensional (3D) version of CVA is developed. The new algorithm used gridded surface and TOA observations as constraints to adjust atmospheric state variables in each grid point to satisfy column-integrated mass, moisture and static energy conservation. From the process of adjustment a set of high-quality 3D large-scale forcing data (vertical velocity and horizontal advections) can be derived to drive Single-Column models (SCM), Cloud-Resolving Models (CRM) and Large-Eddy Simulations (LES) to evaluate and improve parameterizations. Since the 3D CVA can adjust gridded state variables from any data source with observed precipitation, radiation and surface fluxes, it also gives a potential possibility to use this algorithm in data assimilation system to assimilate precipitation and radiation data.

  4. New Automated and High-Throughput Quantitative Analysis of Urinary Ketones by Multifiber Exchange-Solid Phase Microextraction Coupled to Fast Gas Chromatography/Negative Chemical-Electron Ionization/Mass Spectrometry

    PubMed Central

    Pacenti, Marco; Dugheri, Stefano; Traldi, Pietro; Degli Esposti, Filippo; Perchiazzi, Nicola; Franchi, Elena; Calamante, Massimo; Kikic, Ireneo; Alessi, Paolo; Bonacchi, Alice; Salvadori, Edoardo; Arcangeli, Giulio; Cupelli, Vincenzo

    2010-01-01

    The present research is focused on automation, miniaturization, and system interaction with high throughput for multiple and specific Direct Immersion-Solid Phase Microextraction/Fast Gas Chromatography analysis of the urinary ketones. The specific Mass Spectrometry instrumentation, capable of supporting such the automated changeover from Negative Chemical to Electron Ionization mode, as well as the automation of the preparation procedure by new device called MultiFiber Exchange, through change of the fibers, allowed a friendly use of mass spectrometry apparatus with a number of advantages including reduced analyst time and greater reproducibility (2.01–5.32%). The detection limits for the seven ketones were less than 0.004 mg/L. For an innovative powerful meaning in high-throughput routine, the generality of the structurally informative Mass Spectrometry fragmentation patterns together with the chromatographic separation and software automation are also investigated. PMID:20628512

  5. Combined cation-exchange and extraction chromatographic method of pre-concentration and concomitant separation of Cu(II) with high molecular mass liquid cation exchanger after its online detection.

    PubMed

    Mandal, B; Roy, U S; Datta, D; Ghosh, N

    2011-08-19

    A selective method has been developed for the extraction chromatographic trace level separation of Cu(II) with Versatic 10 (liquid cation exchanger) coated on silanised silica gel (SSG-V10). Cu(II) has been extracted from 0.1M acetate buffer at the range of pH 4.0-5.5. The effects of foreign ions, pH, flow-rate, stripping agents on extraction and elution have been investigated. Exchange capacity of the prepared exchanger at different temperatures with respect to Cu(II) has been determined. The extraction equilibrium constant (K(ex)) and different standard thermodynamic parameters have also been calculated by temperature variation method. Positive value of ΔH (7.98 kJ mol⁻¹) and ΔS (0.1916 kJ mol⁻¹) and negative value of ΔG (-49.16 kJ mol⁻¹) indicated that the process was endothermic, entropy gaining and spontaneous. Preconcentration factor was optimized at 74.7 ± 0.2 and the desorption constants K(desorption)¹(1.4 × 10⁻²) and K(desorption)²(9.8 × 10⁻²) were determined. The effect of pH on R(f) values in ion exchange paper chromatography has been investigated. In order to investigate the sorption isotherm, two equilibrium models, the Freundlich and Langmuir isotherms, were analyzed. Cu(II) has been separated from synthetic binary and multi-component mixtures containing various metal ions associated with it in ores and alloy samples. The method effectively permits sequential separation of Cu(II) from synthetic quaternary mixture containing its congeners Bi(III), Sn(II), Hg(II) and Cu(II), Cd(II), Pb(II) of same analytical group. The method was found effective for the selective detection, removal and recovery of Cu(II) from industrial waste and standard alloy samples following its preconcentration on the column. A plausible mechanism for the extraction of Cu(II) has been suggested.

  6. Laboratory-Scale Column Testing Using IONSIV IE-911 for Removing Cesium from Acidic Tank Waste Simulant. 2: Determination of Cesium Exchange Capacity and Effective Mass Transfer Coefficient from a 500-cm3 Column Experiement

    SciTech Connect

    T.J. Tranter; R.D. Tillotson; T.A. Todd

    2005-04-01

    A semi-scale column test was performed using a commercial form of crystalline silicotitanate (CST) for removing radio-cesium from a surrogate acidic tank solution, which represents liquid waste stored at the Idaho National Engineering and Environmental Laboratory (INEEL). The engineered form of CST ion exchanger, known as IONSIVtmIE-911 (UOP, Mt. Laurel,NJ, USA), was tested in a 500-cm3 column to obtain a cesium breakthrough curve. The cesium exchange capacity of this column matched that obtained from previous testing with a 15-mc3 column. A numerical algorithm using implicit finite difference approximations was developed to solve the governing mass transport equations for the CST columns. An effective mass transfer coefficient was derived from solving these equations for previously reported 15 cm3 tests. The effective mass transfer coefficient was then used to predict the cesium breakthrough curve for the 500-cm3 column and compared to the experimental data reported in this paper. The calculated breakthrough curve showed excellent agreement with the data from the 500-cm3 column even though the interstitial velocity was a factor of two greater. Thus, this approach should provide a reasonable method for scale up to larger columns for treating actual tank waste.

  7. Estimation of the advection effects induced by surface heterogeneities in the surface energy budget

    NASA Astrophysics Data System (ADS)

    Cuxart, Joan; Wrenger, Burkhard; Martínez-Villagrasa, Daniel; Reuder, Joachim; Jonassen, Marius O.; Jiménez, Maria A.; Lothon, Marie; Lohou, Fabienne; Hartogensis, Oscar; Dünnermann, Jens; Conangla, Laura; Garai, Anirban

    2016-07-01

    The effect of terrain heterogeneities in one-point measurements is a continuous subject of discussion. Here we focus on the order of magnitude of the advection term in the equation of the evolution of temperature as generated by documented terrain heterogeneities and we estimate its importance as a term in the surface energy budget (SEB), for which the turbulent fluxes are computed using the eddy-correlation method. The heterogeneities are estimated from satellite and model fields for scales near 1 km or broader, while the smaller scales are estimated through direct measurements with remotely piloted aircraft and thermal cameras and also by high-resolution modelling. The variability of the surface temperature fields is not found to decrease clearly with increasing resolution, and consequently the advection term becomes more important as the scales become finer. The advection term provides non-significant values to the SEB at scales larger than a few kilometres. In contrast, surface heterogeneities at the metre scale yield large values of the advection, which are probably only significant in the first centimetres above the ground. The motions that seem to contribute significantly to the advection term in the SEB equation in our case are roughly those around the hectometre scales.

  8. Local and nonlocal advected invariants and helicities in magnetohydrodynamics and gas dynamics I: Lie dragging approach

    NASA Astrophysics Data System (ADS)

    Webb, G. M.; Dasgupta, B.; McKenzie, J. F.; Hu, Q.; Zank, G. P.

    2014-03-01

    In this paper advected invariants and conservation laws in ideal magnetohydrodynamics (MHD) and gas dynamics are obtained using Lie dragging techniques. There are different classes of invariants that are advected or Lie dragged with the flow. Simple examples are the advection of the entropy S (a 0-form), and the conservation of magnetic flux (an invariant 2-form advected with the flow). The magnetic flux conservation law is equivalent to Faraday's equation. The gauge condition for the magnetic helicity to be advected with the flow is determined. Different variants of the helicity in ideal fluid dynamics and MHD including: fluid helicity, cross helicity and magnetic helicity are investigated. The fluid helicity conservation law and the cross-helicity conservation law in MHD are derived for the case of a barotropic gas. If the magnetic field lies in the constant entropy surface, then the gas pressure can depend on both the entropy and the density. In these cases the conservation laws are local conservation laws. For non-barotropic gases, we obtain nonlocal conservation laws for fluid helicity and cross helicity by using Clebsch variables. These nonlocal conservation laws are the main new results of the paper. Ertel's theorem and potential vorticity, the Hollman invariant, and the Godbillon-Vey invariant for special flows for which the magnetic helicity is zero are also discussed.

  9. Solving the advection-diffusion equations in biological contexts using the cellular Potts model

    NASA Astrophysics Data System (ADS)

    Dan, Debasis; Mueller, Chris; Chen, Kun; Glazier, James A.

    2005-10-01

    The cellular Potts model (CPM) is a robust, cell-level methodology for simulation of biological tissues and morphogenesis. Both tissue physiology and morphogenesis depend on diffusion of chemical morphogens in the extra-cellular fluid or matrix (ECM). Standard diffusion solvers applied to the cellular potts model use finite difference methods on the underlying CPM lattice. However, these methods produce a diffusing field tied to the underlying lattice, which is inaccurate in many biological situations in which cell or ECM movement causes advection rapid compared to diffusion. Finite difference schemes suffer numerical instabilities solving the resulting advection-diffusion equations. To circumvent these problems we simulate advection diffusion within the framework of the CPM using off-lattice finite-difference methods. We define a set of generalized fluid particles which detach advection and diffusion from the lattice. Diffusion occurs between neighboring fluid particles by local averaging rules which approximate the Laplacian. Directed spin flips in the CPM handle the advective movement of the fluid particles. A constraint on relative velocities in the fluid explicitly accounts for fluid viscosity. We use the CPM to solve various diffusion examples including multiple instantaneous sources, continuous sources, moving sources, and different boundary geometries and conditions to validate our approximation against analytical and established numerical solutions. We also verify the CPM results for Poiseuille flow and Taylor-Aris dispersion.

  10. Quantification of Art v 1 and Act c 1 being major allergens of mugwort pollen and kiwi fruit extracts in mass-units by ion-exchange HPLC-UV method.

    PubMed

    Blanusa, Milan; Perovic, Iva; Popovic, Milica; Polovic, Natalija; Burazer, Lidija; Milovanovic, Mina; Gavrovic-Jankulovic, Marija; Jankov, Ratko; Cirkovic Velickovic, Tanja

    2007-10-01

    A simple ion-exchange HPLC-UV method was developed for determination of major allergens from mugwort pollen and kiwi fruit extracts in mass-units. The separation of Art v 1 and Act c 1 from other components in the extracts was achieved in one step. The extinction coefficients used in the study were theoretically determined and compared to the extinction coefficients determined by gravimetry. We also reported a close correlation of the major allergen contents with the overall allergenic potency of the extracts determined by inhibition ELISA. This method could be a useful tool for standardization of allergenic extracts for clinical use.

  11. Scaling hyporheic exchange and its influence on biogeochemical reactions in aquatic ecosystems

    USGS Publications Warehouse

    O'Connor, B.L.; Harvey, J.W.

    2008-01-01

    Hyporheic exchange and biogeochemical reactions are difficult to quantify because of the range in fluid-flow and sediment conditions inherent to streams, wetlands, and nearshore marine ecosystems. Field measurements of biogeochemical reactions in aquatic systems are impeded by the difficulty of measuring hyporheic flow simultaneously with chemical gradients in sediments. Simplified models of hyporheic exchange have been developed using Darcy's law generated by flow and bed topography at the sediment-water interface. However, many modes of transport are potentially involved (molecular diffusion, bioturbation, advection, shear, bed mobility, and turbulence) with even simple models being difficult to apply in complex natural systems characterized by variable sediment sizes and irregular bed geometries. In this study, we synthesize information from published hyporheic exchange investigations to develop a scaling relationship for estimating mass transfer in near-surface sediments across a range in fluid-flow and sediment conditions. Net hyporheic exchange was quantified using an effective diffusion coefficient (De) that integrates all of the various transport processes that occur simultaneously in sediments, and dimensional analysis was used to scale De to shear stress velocity, roughness height, and permeability that describe fluid-flow and sediment characteristics. We demonstrated the value of the derived scaling relationship by using it to quantify dissolved oxygen (DO) uptake rates on the basis of DO profiles in sediments and compared them to independent flux measurements. The results support a broad application of the De scaling relationship for quantifying coupled hyporheic exchange and biogeochemical reaction rates in streams and other aquatic ecosystems characterized by complex fluid-flow and sediment conditions.

  12. First-Order Hyperbolic System Method for Time-Dependent Advection-Diffusion Problems

    NASA Technical Reports Server (NTRS)

    Mazaheri, Alireza; Nishikawa, Hiroaki

    2014-01-01

    A time-dependent extension of the first-order hyperbolic system method for advection-diffusion problems is introduced. Diffusive/viscous terms are written and discretized as a hyperbolic system, which recovers the original equation in the steady state. The resulting scheme offers advantages over traditional schemes: a dramatic simplification in the discretization, high-order accuracy in the solution gradients, and orders-of-magnitude convergence acceleration. The hyperbolic advection-diffusion system is discretized by the second-order upwind residual-distribution scheme in a unified manner, and the system of implicit-residual-equations is solved by Newton's method over every physical time step. The numerical results are presented for linear and nonlinear advection-diffusion problems, demonstrating solutions and gradients produced to the same order of accuracy, with rapid convergence over each physical time step, typically less than five Newton iterations.

  13. Tomography-based monitoring of isothermal snow metamorphism under advective conditions

    NASA Astrophysics Data System (ADS)

    Ebner, P. P.; Schneebeli, M.; Steinfeld, A.

    2015-07-01

    Time-lapse X-ray microtomography was used to investigate the structural dynamics of isothermal snow metamorphism exposed to an advective airflow. The effect of diffusion and advection across the snow pores on the snow microstructure were analysed in controlled laboratory experiments and possible effects on natural snowpacks discussed. The 3-D digital geometry obtained by tomographic scans was used in direct pore-level numerical simulations to determine the effective permeability. The results showed that isothermal advection with saturated air have no influence on the coarsening rate that is typical for isothermal snow metamorphism. Isothermal snow metamorphism is driven by sublimation deposition caused by the Kelvin effect and is the limiting factor independently of the transport regime in the pores.

  14. Variational optimization analysis of temperature and moisture advection in a severe storm environment

    NASA Technical Reports Server (NTRS)

    Mcfarland, M. J.

    1975-01-01

    Horizontal wind components, potential temperature, and mixing ratio fields associated with a severe storm environment in the south central U.S. were analyzed from synoptic upper air observations with a nonhomogeneous, anisotropic weighting function. Each data field was filtered with variational optimization analysis techniques. Variational optimization analysis was also performed on the vertical motion field and was used to produce advective forecasts of the potential temperature and mixing ratio fields. Results show that the dry intrusion is characterized by warm air, the advection of which produces a well-defined upward motion pattern. A corresponding downward motion pattern comprising a deep vertical circulation in the warm air sector of the low pressure system was detected. The axes alignment of maximum dry and warm advection with the axis of the tornado-producing squall line also resulted.

  15. Small-scale particle advection, manipulation and mixing: beyond the hydrodynamic scale.

    PubMed

    Straube, Arthur V

    2011-05-11

    In this paper we discuss the problems of particle advection, manipulation and mixing at small scales. We start by considering reaction-advection-diffusion systems with the focus on mixing. We show how mixing advection affects the processes of reaction-diffusion and discuss mixing-induced instabilities. Further, we consider the problem of particle manipulation and discuss collective effects in systems comprising solid and compressible particles. We particularly discuss mechanisms of particle entrapment, the role of compressibility in the dynamics of bubbly liquids and nonequilibrium colloidal explosion. Finally, we address two issues related to the problem of wetting. First, we study the role of contact line motion for a sessile droplet (or a bubble) on an oscillating substrate. Second, we discuss an instability of a thin film leading to the formation of a fractal structure of droplets.

  16. Advective transport observations with MODPATH-OBS--documentation of the MODPATH observation process

    USGS Publications Warehouse

    Hanson, R.T.; Kauffman, L.K.; Hill, M.C.; Dickinson, J.E.; Mehl, S.W.

    2013-01-01

    The MODPATH-OBS computer program described in this report is designed to calculate simulated equivalents for observations related to advective groundwater transport that can be represented in a quantitative way by using simulated particle-tracking data. The simulated equivalents supported by MODPATH-OBS are (1) distance from a source location at a defined time, or proximity to an observed location; (2) time of travel from an initial location to defined locations, areas, or volumes of the simulated system; (3) concentrations used to simulate groundwater age; and (4) percentages of water derived from contributing source areas. Although particle tracking only simulates the advective component of conservative transport, effects of non-conservative processes such as retardation can be approximated through manipulation of the effective-porosity value used to calculate velocity based on the properties of selected conservative tracers. This program can also account for simple decay or production, but it cannot account for diffusion. Dispersion can be represented through direct simulation of subsurface heterogeneity and the use of many particles. MODPATH-OBS acts as a postprocessor to MODPATH, so that the sequence of model runs generally required is MODFLOW, MODPATH, and MODPATH-OBS. The version of MODFLOW and MODPATH that support the version of MODPATH-OBS presented in this report are MODFLOW-2005 or MODFLOW-LGR, and MODPATH-LGR. MODFLOW-LGR is derived from MODFLOW-2005, MODPATH 5, and MODPATH 6 and supports local grid refinement. MODPATH-LGR is derived from MODPATH 5. It supports the forward and backward tracking of particles through locally refined grids and provides the output needed for MODPATH_OBS. For a single grid and no observations, MODPATH-LGR results are equivalent to MODPATH 5. MODPATH-LGR and MODPATH-OBS simulations can use nearly all of the capabilities of MODFLOW-2005 and MODFLOW-LGR; for example, simulations may be steady-state, transient, or a combination

  17. Ocean-shelf exchange through the Berau barrier reef, Indonesia

    NASA Astrophysics Data System (ADS)

    Tarya, A.; Hoitink, A.; Van Der Vegt, M.

    2011-12-01

    The present study investigates the freshwater spreading on the Berau Continental Shelf, Indonesia, including the ocean-shelf exchange through a barrier reef located at the shelf edge. Moored and shipboard measurements on currents and turbulence were taken as part of the multidisciplinary East Kalimantan Research Programme. These measurements, and collected data on sea levels, currents, wind speed and bathymetry, were used to setup and calibrate a three-dimensional hydrodynamic model in the ECOMSED environment, which is derived from the Princeton Ocean Model. The data and model results were first used to study the tidal propagation and mean circulation patterns on the entire Berau Shelf. The diurnal and semidiurnal tides propagate across the isobaths towards the coast, where amplitudes increase. Tide-induced mean currents dominate over monsoon-driven currents, and feature a southward transport pattern close to the coast and a northward transport patterns at 10 to 20 meters depth. Next, the river plume behaviour is studied. Key factors controlling the river plume behavior include advection of stratified waters by the subtidal motion and mixing, which inhibits the stratified region to extend beyond the reef region. The tides drive freshwater in northeastern direction, towards the reef area. The model is subsequently refined and used to study the freshwater transport and exchange of water via the reef gaps and over the reef flats in detail. Moored ADCP data reveal extremely large roughness heights in the reef passages and reef flats. These limit the exchange of tidal energy to some degree, acting as a control on sealevel gradients over the reefs. The spatial structure of velocity exhibits tidal eddies generated by irregularities of reef gaps. The flow in the center of the reef passage is often opposed to the flow near the reef boundaries. The mean mass transport in the passages that were studied were found to be caused by Eulerian residual currents generated by

  18. Large-eddy Advection in Evapotranspiration Estimates from an Array of Eddy Covariance Towers

    NASA Astrophysics Data System (ADS)

    Lin, X.; Evett, S. R.; Gowda, P. H.; Colaizzi, P. D.; Aiken, R.

    2014-12-01

    Evapotranspiration was continuously measured by an array of eddy covariance systems and large weighting lysimeter in a sorghum in Bushland, Texas in 2014. The advective divergence from both horizontal and vertical directions were measured through profile measurements above canopy. All storage terms were integrated from the depth of soil heat flux plate to the height of eddy covariance measurement. Therefore, a comparison between the eddy covariance system and large weighing lysimeter was conducted on hourly and daily basis. The results for the discrepancy between eddy covariance towers and the lysimeter will be discussed in terms of advection and storage contributions in time domain and frequency domain.

  19. An extension of Prandtl-Batchelor theory and consequences for chaotic advection

    NASA Astrophysics Data System (ADS)

    Mezic, Igor

    2002-09-01

    We extend the Prandtl-Batchelor theory of steady laminar motion at large Reynolds number to derive conditions that steady three-dimensional Navier-Stokes flows have to satisfy. We combine these results with ergodic theory to show that flows with strong Beltrami property (e.g., ABC flows) cannot be a paradigm for chaotic advection in inertia-dominated boundary-driven three-dimensional flows. Our results indicate that viscous forces are responsible for chaotic advection in steady, three-dimensional boundary-driven Navier-Stokes flows at large Reynolds numbers.

  20. Kull ALE: I. Unstructured Mesh Advection, Interface Capturing, and Multiphase 2T RHD with Material Interfaces

    SciTech Connect

    Anninos, P

    2002-02-11

    Several advection algorithms are presented within the remap framework for unstructured mesh ALE codes. The methods discussed include a generic advection scheme based on a finite volume approach, and three groups of algorithms for the treatment of material boundary interfaces. The interface capturing algorithms belong to the Volume of Fluid (VoF) class of methods to approximate material interfaces from the local fractional volume of fluid distribution in arbitrary unstructured polyhedral meshes appropriate for the Kull code. Also presented are several schemes for extending single material radiation diffusion solvers to account for multi-material interfaces.

  1. Horizontal turbulent carbon dioxide flux divergence and energy balance closure: loose ends from an advection experiment in a Douglas-fir forest on a gentle slope

    NASA Astrophysics Data System (ADS)

    Leitch, A. S.; Nesic, Z.; Christen, A.; Black, T. A.

    2010-12-01

    An observational study was conducted during an eight-week period in the summer of 2009 at a forested site in British Columbia (“DF49”) to measure advective carbon dioxide (CO2) fluxes. The site is situated in a 35-m tall Douglas-fir forest on a 5-10 degree slope. Wind vector and CO2 concentration measurements were made at heights of 1, 2.6, 8, 20 and 42 m on the main flux tower, while CO2 concentration measurements were made 73.5 m upslope from the tower at heights of 1, 2.6, 8 and 20 m, creating a two-dimensional transect. Wind vector measurement was made with sonic anemometers. Eight thermostated LI-COR Inc. infrared gas analyzers (IRGAs) were paired using a solenoid valve switching system, creating four differential analyzers. The switching system, combined with a twice-daily polynomial IRGA calibration, enabled measurement of CO2 concentration differences at the four subcanopy measurement heights to an accuracy of 0.5 µmol mol-1 (horizontal) and 1 µmol mol-1 (vertical). The system also recorded semi-continuous CO2 and H2O traces at all sample points. Horizontal advective fluxes, averaged over the main measurement period (August 2 - 25), reached 5 µmol m-2 s-1 at night and 10 µmol m-2 s-1 in the afternoon (a net source to the atmosphere) and -2 µmol m-2 s-1 during the morning (net sink). Vertical advective fluxes averaged around zero during the night, 5 µmol m-2 s-1 during the morning and -5 µmol m-2 s-1 during the afternoon. A cumulative sum of advective flux-corrected net ecosystem exchange (NEE) over the main measurement period (-57 g C m-2) was close to that of the friction velocity-corrected NEE (-60 g C m-2), both predicting less carbon uptake by the Douglas-fir forest than the storage flux-corrected NEE (-86 g C m-2). Additional CO2 difference measurements made after the main sampling period along the 73.5-m transect demonstrated that horizontal CO2 differences increased monotonically down slope (on average) at the 2.6-m height, despite an

  2. Assessment of the possibility of establishing material cycling in an experimental model of the bio-technical life support system with plant and human wastes included in mass exchange

    NASA Astrophysics Data System (ADS)

    Tikhomirov, A. A.; Ushakova, S. A.; Velichko, V. V.; Tikhomirova, N. A.; Kudenko, Yu. A.; Gribovskaya, I. V.; Gros, J.-B.; Lasseur, Ch.

    2011-05-01

    A pilot model of a bio-technical life support system (BTLSS) including human and plant wastes has been developed at the Institute of Biophysics SB RAS (Krasnoyarsk, Russia). This paper describes the structure of the photosynthesizing unit of the system, which includes wheat, chufa and vegetables. The study substantiates the simultaneous use of neutral and biological substrates for cultivating plants. A novel physicochemical method for the involvement of human wastes in the cycling has been employed, which enables the use of recycled products as nutrients for plants. Inedible plant biomass was subjected to biological combustion in the soil-like substrate (SLS) and was thus involved in the system mass exchange; NaCl contained in native urine was returned to the human through the consumption of Salicornia europaea, an edible salt-concentrating plant. Mass transfer processes in the studied BLSS have been examined for different chemical components.

  3. Comparative estimation of use potentialities of salt-accumulating and salt-eliminating halophytes for inclusion of NaCl contained in human mineralized urine in BLSS's mass exchange

    NASA Astrophysics Data System (ADS)

    Tikhomirova, Natalia; Ushakova, Sofya; Kudenko, Yurii; Griboskaya, Illiada; Shklavtsova, Ekaterina; Balnokin, Yurii; Popova, Larissa; Myasoedov, Nikolay; Gros, Jean-Bernard; Lasseur, Christophe

    Comparative potentialities of different halophytes' cultivation on a human mineralized urine containing NaCl with the aim of this salt inclusion into the intrasystem BLSS mass exchange were investigated. Two halophyte species were studied namely, salt-accumulating (Salicornia europaea) and salt-eliminating (Limonium gmelinii). During the first two vegetation weeks the plants had been grown on the Knop solution; then a daily norm of the human mineralized urine was gradually added in the experiment solutions. During vegetation the model solutions simulating the urine mineral composition were gradually added in the control solutions. The NaCl concentration in the experiment and control solutions of the first treatment was 9 g/l and that of the second treatment was 20 g/l. The mineralized human urine exposed some inhibitory action on Salicornia europaea and Limonium gmelinii plants. The experiment plants' productivity was lower in comparison with the control. As far as Limonium gmelinii appears to be a perennial plant the growth rate and productivity of this halophyte species was signifi- cantly lower in comparison with Salicornia europaea. Na content in Salicornia europaea plants was higher in comparison with sodium amount emitted by Limonium gmelinii. Consequently Salicornia europaea appears to be a more perspective halophyte for its further use in BLSS aiming at involvement of sodium chloride contained in human liquid wastes in intrasystem mass exchange.

  4. Charge variants characterization of a monoclonal antibody by ion exchange chromatography coupled on-line to native mass spectrometry: Case study after a long-term storage at +5°C.

    PubMed

    Leblanc, Y; Ramon, C; Bihoreau, N; Chevreux, G

    2017-03-24

    Numerous putative post-translational modifications may induce variations of monoclonal antibodies charge distribution that can potentially affect their biological activity. The characterization and the monitoring of these charge variants are critical quality requirements to ensure stability and process consistency. Charge variants are usually characterized by preparative ion exchange chromatography, collection of fractions and subsequent reverse-phase liquid chromatography with mass spectrometry analysis. While this process can be automatized by on-line two-dimensional chromatography, it remains often complex and time consuming. For this reason, a straightforward on-line charge variant analysis method is highly desirable and analytical laboratories are actively pursuing efforts to overcome this challenge. In this study, a mixed mode ion exchange chromatographic method using volatile salts and coupled on-line to native mass spectrometry was developed in association with a middle-up approach for a detailed characterization of monoclonal antibodies charge variants. An aged monoclonal antibody, presenting a complex charge variant profile was successfully investigated by this methodology as a case study. Results demonstrate that deamidation of the heavy chain was the major degradation pathway after long-term storage at 5°C while oxidation was rather low. The method was also very useful to identify all the clipped forms of the antibody.

  5. High-throughput sequential injection method for simultaneous determination of plutonium and neptunium in environmental solids using macroporous anion-exchange chromatography, followed by inductively coupled plasma mass spectrometric detection.

    PubMed

    Qiao, Jixin; Hou, Xiaolin; Roos, Per; Miró, Manuel

    2011-01-01

    This paper reports an automated analytical method for rapid and simultaneous determination of plutonium and neptunium in soil, sediment, and seaweed, with detection via inductively coupled plasma mass spectrometry (ICP-MS). A chromatographic column packed with a macroporous anion exchanger (AG MP-1 M) was incorporated in a sequential injection (SI) system for the efficient retrieval of plutonium, along with neptunium, from matrix elements and potential interfering nuclides. The sorption and elution behavior of plutonium and neptunium onto AG MP-1 M resin was compared with a commonly utilized AG 1-gel-type anion exchanger. Experimental results reveal that the pore structure of the anion exchanger plays a pivotal role in ensuring similar separation behavior of plutonium and neptunium along the separation protocol. It is proven that plutonium-242 ((242)Pu) performs well as a tracer for monitoring the chemical yield of neptunium when using AG MP-1 M resin, whereby the difficulties in obtaining a reliable and practicable isotopic neptunium tracer are overcome. An important asset of the SI setup is the feasibility of processing up to 100 g of solid substrates using a small-sized (ca. 2 mL) column with chemical yields of neptunium and plutonium being ≥79%. Analytical results of three certified/standard reference materials and two solid samples from intercomparison exercises are in good agreement with the reference values at the 0.05 significance level. The overall on-column separation can be completed within 3.5 h for 10 g of soil samples. Most importantly, the anion-exchange mini-column suffices to be reused up to 10-fold with satisfactory chemical yields (>70%), as demanded in environmental monitoring and emergency scenarios, making the proposed automated assembly well-suited for unattended and high-throughput analysis.

  6. Black Hole Event Horizons and Advection-Dominated Accretion

    NASA Technical Reports Server (NTRS)

    McClintock, Jeffrey; Mushotzky, Richard F. (Technical Monitor)

    2002-01-01

    The work supported in part by this grant is part of a larger program on the detection of black hole event horizons, which is also partially supported by NASA grant GO0-1105A. This work has been carried out primarily in collaboration with Dr. M. Garcia and Prof. R. Narayan at the Harvard-Smithsonian Center for Astrophysics and with D. Barret and J. Hameury at Centre d'Etude Spoliate des Rayonnements, France. Our purpose is to confirm the existence of black-hole event horizons by comparing accreting black holes to secreting neutron stars in quiescent X-ray novae. Such a comparison is feasible because black holes and neutron stars are both present in similar environments in X-ray novae. Our second purpose is to assess the nature of accretion flows onto black holes at very low mass transfer rates. Observations of some XMM targets are still pending, whereas most of the Chandra observations have been completed. We anticipate further publications on this work in the future.

  7. Microtube strip heat exchanger

    SciTech Connect

    Doty, F.D.

    1992-07-09

    The purpose of this contract has been to explore the limits of miniaturization of heat exchangers with the goals of (1) improving the theoretical understanding of laminar heat exchangers, (2) evaluating various manufacturing difficulties, and (3) identifying major applications for the technology. A low-cost, ultra-compact heat exchanger could have an enormous impact on industry in the areas of cryocoolers and energy conversion. Compact cryocoolers based on the reverse Brayton cycle (RBC) would become practical with the availability of compact heat exchangers. Many experts believe that hardware advances in personal computer technology will rapidly slow down in four to six years unless lowcost, portable cryocoolers suitable for the desktop supercomputer can be developed. Compact refrigeration systems would permit dramatic advances in high-performance computer work stations with conventional'' microprocessors operating at 150 K, and especially with low-cost cryocoolers below 77 K. NASA has also expressed strong interest in our MTS exchanger for space-based RBC cryocoolers for sensor cooling. We have demonstrated feasibility of higher specific conductance by a factor of five than any other work in high-temperature gas-to-gas exchangers. These laminar-flow, microtube exchangers exhibit extremely low pressure drop compared to alternative compact designs under similar conditions because of their much shorter flow length and larger total flow area for lower flow velocities. The design appears to be amenable to mass production techniques, but considerable process development remains. The reduction in materials usage and the improved heat exchanger performance promise to be of enormous significance in advanced engine designs and in cryogenics.

  8. Vertical and horizontal soil CO2 transport and its exchanges with the atmosphere

    NASA Astrophysics Data System (ADS)

    Sánchez-Cañete, Enrique P.; Serrano-Ortíz, Penélope; Kowalski, Andrew S.; Curiel Yuste, Jorge; Domingo, Francisco; Oyonarte, Cecilio

    2015-04-01

    The CO2 efflux from soils to the atmosphere constitutes one of the major fluxes of the terrestrial carbon cycle and is a key determinant for sources and sinks of CO2 in land-atmosphere exchanges. Because of their large global magnitude, even small changes in soil CO2 effluxes directly affect the atmospheric CO2 content. Despite much research, models of soil CO2 efflux rates are highly uncertain, with the positive or negative feedbacks between underground carbon pools and fluxes and their temperature sensitivities in future climate scenarios largely unknown. Now it is necessary to change the point of view regarding CO2 exchange studies from an inappropriately conceived static system in which all respired CO2 is directly emitted by molecular processes to the atmosphere, to a dynamic system with gas transport by three different processes: convection, advection and molecular diffusion. Here we study the effects of wind-induced advection on the soil CO2 molar fraction during two years in a shrubland plateau situated in the Southeast of Spain. A borehole and two subterranean profiles (vertical and horizontal) were installed to study CO2 transport in the soil. Exchanges with the atmosphere were measured by an eddy covariance tower. In the vertical profile, two CO2 sensors (GMP-343, Vaisala) were installed at 0.15m and 1.5m along with soil temperature and humidity probes. The horizontal profile was designed to measure horizontal movements in the soil CO2 molar fraction due to down-gradient CO2 from the plant, where the majority CO2 is produced, towards bare soil. Three CO2 sensors (GMM-222, Vaisala) were installed, the first below plant (under-plant), the second in bare soil separated 25 cm from the first sensor (near-plant) and the third in bare soil at 25 cm from the second sensor (bare soil). The results show how the wind induces the movement of subterranean air masses both horizontally and vertically, affecting atmospheric CO2 exchanges. The eddy covariance tower

  9. Exact analytical solutions for contaminant transport in rivers 1. The equilibrium advection-dispersion equation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analytical solutions of the advection-dispersion equation and related models are indispensable for predicting or analyzing contaminant transport processes in streams and rivers, as well as in other surface water bodies. Many useful analytical solutions originated in disciplines other than surface-w...

  10. Alteration of chaotic advection in blood flow around partial blockage zone: Role of hematocrit concentration

    NASA Astrophysics Data System (ADS)

    Maiti, Soumyabrata; Chaudhury, Kaustav; DasGupta, Debabrata; Chakraborty, Suman

    2013-01-01

    Spatial distributions of particles carried by blood exhibit complex filamentary pattern under the combined effects of geometrical irregularities of the blood vessels and pulsating pumping by the heart. This signifies the existence of so called chaotic advection. In the present article, we argue that the understanding of such pathologically triggered chaotic advection is incomplete without giving due consideration to a major constituent of blood: abundant presence of red blood cells quantified by the hematocrit (HCT) concentration. We show that the hematocrit concentration in blood cells can alter the filamentary structures of the spatial distribution of advected particles in an intriguing manner. Our results reveal that there primarily are two major impacts of HCT concentrations towards dictating the chaotic dynamics of blood flow: changing the zone of influence of chaotic mixing and determining the enhancement of residence time of the advected particles away from the wall. This, in turn, may alter the extent of activation of platelets or other reactive biological entities, bearing immense consequence towards dictating the biophysical mechanisms behind possible life-threatening diseases originating in the circulatory system.

  11. Wind tunnel measurement of turbulent and advective scalar fluxes: a case study on intersection ventilation.

    PubMed

    Kukačka, Libor; Nosek, Štĕpán; Kellnerová, Radka; Jurčáková, Klára; Jaňour, Zbyněk

    2012-01-01

    The objective of this study is to determine processes of pollution ventilation in the X-shaped street intersection in an idealized symmetric urban area for the changing approach flow direction. A unique experimental setup for simultaneous wind tunnel measurement of the flow velocity and the tracer gas concentration in a high temporal resolution is assembled. Advective horizontal and vertical scalar fluxes are computed from averaged measured velocity and concentration data within the street intersection. Vertical advective and turbulent scalar fluxes are computed from synchronized velocity and concentration signals measured in the plane above the intersection. All the results are obtained for five approach flow directions. The influence of the approach flow on the advective and turbulent fluxes is determined. The contribution of the advective and turbulent flux to the ventilation is discussed. Wind direction with the best dispersive conditions in the area is found. The quadrant analysis is applied to the synchronized signals of velocity and concentration fluctuation to determine events with the dominant contribution to the momentum flux and turbulent scalar flux.

  12. MECHANISM OF OUTFLOWS IN ACCRETION SYSTEM: ADVECTIVE COOLING CANNOT BALANCE VISCOUS HEATING?

    SciTech Connect

    Gu, Wei-Min

    2015-01-20

    Based on the no-outflow assumption, we investigate steady-state, axisymmetric, optically thin accretion flows in spherical coordinates. By comparing the vertically integrated advective cooling rate with the viscous heating rate, we find that the former is generally less than 30% of the latter, which indicates that the advective cooling itself cannot balance the viscous heating. As a consequence, for radiatively inefficient flows with low accretion rates such as M-dot ≲10{sup −3} M-dot {sub Edd}, where M-dot {sub Edd} is the Eddington accretion rate, the viscous heating rate will be larger than the sum of the advective cooling rate and the radiative cooling one. Thus, no thermal equilibrium can be established under the no-outflow assumption. We therefore argue that in such cases outflows ought to occur and take away more than 70% of the thermal energy generated by viscous dissipation. Similarly, for optically thick flows with extremely large accretion rates such as M-dot ≳10 M-dot {sub Edd}, outflows should also occur owing to the limited advection and the low efficiency of radiative cooling. Our results may help to understand the mechanism of outflows found in observations and numerical simulations.

  13. Satellite-advection based solar forecasting: lessons learned and progress towards probabalistic solar forecasting

    NASA Astrophysics Data System (ADS)

    Rogers, M. A.

    2015-12-01

    Using satellite observations from GOES-E and GOES-W platforms in concert with GFS-derived cloud-level winds and a standalone radiative transfer model, an advection-derived forecast for surface GHI over the continental United States, with intercomparison between forecasts for four zones over the CONUS and Central Pacific with SURFRAD results. Primary sources for error in advection-based forecasts, primarily driven by false- or mistimed ramp events are discussed, with identification of error sources quantified along with techniques used to improve advection-based forecasts to approximately 10% MAE for designated surface locations. Development of a blended steering wind product utilizing NWP output combined with satellite-derived winds from AMV techniques to improve 0-1 hour advection forecasts will be discussed. Additionally, the use of two years' of solar forecast observations in the development of a prototype probablistic forecast for ramp events will be shown, with the intent of increasing the use of satellite-derived forecasts for grid operators and optimizing integration of renewable resources into the power grid. Elements of the work were developed under the 'Public-Private-Academic Partnership to Advance Solar Power Forecasting' project spearheaded by the National Center for Atmospheric Research.

  14. An enriched finite element method to fractional advection-diffusion equation

    NASA Astrophysics Data System (ADS)

    Luan, Shengzhi; Lian, Yanping; Ying, Yuping; Tang, Shaoqiang; Wagner, Gregory J.; Liu, Wing Kam

    2017-03-01

    In this paper, an enriched finite element method with fractional basis [ 1,x^{α }] for spatial fractional partial differential equations is proposed to obtain more stable and accurate numerical solutions. For pure fractional diffusion equation without advection, the enriched Galerkin finite element method formulation is demonstrated to simulate the exact solution successfully without any numerical oscillation, which is advantageous compared to the traditional Galerkin finite element method with integer basis [ 1,x] . For fractional advection-diffusion equation, the oscillatory behavior becomes complex due to the introduction of the advection term which can be characterized by a fractional element Peclet number. For the purpose of addressing the more complex numerical oscillation, an enriched Petrov-Galerkin finite element method is developed by using a dimensionless fractional stabilization parameter, which is formulated through a minimization of the residual of the nodal solution. The effectiveness and accuracy of the enriched finite element method are demonstrated by a series of numerical examples of fractional diffusion equation and fractional advection-diffusion equation, including both one-dimensional and two-dimensional, steady-state and time-dependent cases.

  15. DEVELOPMENT AND DEMONSTRATION OF A BIDIRECTIONAL ADVECTIVE FLUX METER FOR SEDIMENT-WATER INTERFACE

    EPA Science Inventory

    A bidirectional advective flux meter for measuring water transport across the sediment-water interface has been successfully developed and field tested. The flow sensor employs a heat-pulse technique combined with a flow collection funnel for the flow measurement. Because the dir...

  16. A global spectral element model for poisson equations and advective flow over a sphere

    NASA Astrophysics Data System (ADS)

    Mei, Huan; Wang, Faming; Zeng, Zhong; Qiu, Zhouhua; Yin, Linmao; Li, Liang

    2016-03-01

    A global spherical Fourier-Legendre spectral element method is proposed to solve Poisson equations and advective flow over a sphere. In the meridional direction, Legendre polynomials are used and the region is divided into several elements. In order to avoid coordinate singularities at the north and south poles in the meridional direction, Legendre-Gauss-Radau points are chosen at the elements involving the two poles. Fourier polynomials are applied in the zonal direction for its periodicity, with only one element. Then, the partial differential equations are solved on the longitude-latitude meshes without coordinate transformation between spherical and Cartesian coordinates. For verification of the proposed method, a few Poisson equations and advective flows are tested. Firstly, the method is found to be valid for test cases with smooth solution. The results of the Poisson equations demonstrate that the present method exhibits high accuracy and exponential convergence. Highprecision solutions are also obtained with near negligible numerical diffusion during the time evolution for advective flow with smooth shape. Secondly, the results of advective flow with non-smooth shape and deformational flow are also shown to be reasonable and effective. As a result, the present method is proved to be capable of solving flow through different types of elements, and thereby a desirable method with reliability and high accuracy for solving partial differential equations over a sphere.

  17. Wind Tunnel Measurement of Turbulent and Advective Scalar Fluxes: A Case Study on Intersection Ventilation

    PubMed Central

    Kukačka, Libor; Nosek, Štĕpán; Kellnerová, Radka; Jurčáková, Klára; Jaňour, Zbyněk

    2012-01-01

    The objective of this study is to determine processes of pollution ventilation in the X-shaped street intersection in an idealized symmetric urban area for the changing approach flow direction. A unique experimental setup for simultaneous wind tunnel measurement of the flow velocity and the tracer gas concentration in a high temporal resolution is assembled. Advective horizontal and vertical scalar fluxes are computed from averaged measured velocity and concentration data within the street intersection. Vertical advective and turbulent scalar fluxes are computed from synchronized velocity and concentration signals measured in the plane above the intersection. All the results are obtained for five approach flow directions. The influence of the approach flow on the advective and turbulent fluxes is determined. The contribution of the advective and turbulent flux to the ventilation is discussed. Wind direction with the best dispersive conditions in the area is found. The quadrant analysis is applied to the synchronized signals of velocity and concentration fluctuation to determine events with the dominant contribution to the momentum flux and turbulent scalar flux. PMID:22649290

  18. A Study of the Physical Processes of an Advection Fog Boundary Layer

    NASA Astrophysics Data System (ADS)

    Liu, Duan Yang; Yan, Wen Lian; Yang, Jun; Pu, Mei Juan; Niu, Sheng Jie; Li, Zi Hua

    2016-01-01

    A large quantity of advection fog appeared in the Yangtze River delta region between 1 and 2 December 2009. Here, we detail the fog formation and dissipation processes and the background weather conditions. The fog boundary layer and its formation and dissipation mechanisms have also been analyzed using field data recorded in a northern suburb of Nanjing. The results showed the following: (1) This advection fog was generated by interaction between advection of a north-east cold ground layer and a south-east warm upper layer. The double-inversion structure generated by this interaction between the cold and warm advections and steady south-east vapour transport was the main cause of this long-lasting fog. The double-inversion structure provided good thermal conditions for the thick fog, and the south-east vapour transport was not only conducive to maintaining the thickness of the fog but also sustained its long duration. (2) The fog-top altitude was over 600 m for most of the time, and the fog reduced visibility to less than 100 m for approximately 12 h. (3) The low-level jet near the lower inversion layer also played a role in maintaining the thick fog system by promoting heat, momentum and south-east vapour transport.

  19. The connection of standard thin disk with advection-dominated accretion flow

    NASA Astrophysics Data System (ADS)

    Lin, Yi-qing; Lu, Ju-fu; G. U., Wei-min

    2005-04-01

    Using the standard Runge-Kutta method, a global solution of the basic equations describing black hole accretion flows is derived. It is proved that transition from a standard thin disk to an advection-dominated accretion flow is realizable in case of high viscosity, without introducing any additional mechanism of energy transfer or specifying any ad hoc outer boundary condition.

  20. Exchange Network

    EPA Pesticide Factsheets

    The Environmental Information Exchange Network (EIEN) is an Internet-based system used by state, tribal and territorial partners to securely share environmental and health information with one another and EPA.

  1. Gas exchange

    MedlinePlus Videos and Cool Tools

    ... during exhalation. Gas exchange is the delivery of oxygen from the lungs to the bloodstream, and the ... share a membrane with the capillaries in which oxygen and carbon dioxide move freely between the respiratory ...

  2. HEAT EXCHANGER

    DOEpatents

    Fox, T.H. III; Richey, T. Jr.; Winders, G.R.

    1962-10-23

    A heat exchanger is designed for use in the transfer of heat between a radioactive fiuid and a non-radioactive fiuid. The exchanger employs a removable section containing the non-hazardous fluid extending into the section designed to contain the radioactive fluid. The removable section is provided with a construction to cancel out thermal stresses. The stationary section is pressurized to prevent leakage of the radioactive fiuid and to maintain a safe, desirable level for this fiuid. (AEC)

  3. Modeling the advection of discontinuous quantities in Geophysical flows using Particle Level Sets

    NASA Astrophysics Data System (ADS)

    Aleksandrov, V.; Samuel, H.; Evonuk, M.

    2010-12-01

    Advection is one of the major processes that commonly acts on various scales in nature (core formation, mantle convective stirring, multi-phase flows in magma chambers, salt diapirism ...). While this process can be modeled numerically by solving conservation equations, various geodynamic scenarios involve advection of quantities with sharp discontinuities. Unfortunately, in these cases modeling numerically pure advection becomes very challenging, in particular because sharp discontinuities lead to numerical instabilities, which prevent the local use of high order numerical schemes. Several approaches have been used in computational geodynamics in order to overcome this difficulty, with variable amounts of success. Despite the use of correcting filters or non-oscillatory, shock-preserving schemes, Eulerian (fixed grid) techniques generally suffer from artificial numerical diffusion. Lagrangian approaches (dynamic grids or particles) tend to be more popular in computational geodynamics because they are not prone to excessive numerical diffusion. However, these approaches are generally computationally expensive, especially in 3D, and can suffer from spurious statistical noise. As an alternative to these aforementioned approaches, we have applied a relatively recent Particle Level set method [Enright et al., 2002] for modeling advection of quantities with the presence of sharp discontinuities. We have tested this improved method, which combines the best of Eulerian and Lagrangian approaches, against well known benchmarks and classical Geodynamic flows. In each case the Particle Level Set method accuracy equals or is better than other Eulerian and Lagrangian methods, and leads to significantly smaller computational cost, in particular in three-dimensional flows, where the reduction of computational time for modeling advection processes is most needed.

  4. Fast and accurate advection of sharp discontinuities in Geophysical flows using hybrid implicit surfaces

    NASA Astrophysics Data System (ADS)

    Samuel, Henri

    2010-05-01

    Advection is one of the major processes that commonly acts on various scales in nature (core formation, mantle convective stirring, multi-phase flows in magma chambers, salt diapirism ...). While this process can be modeled numerically by solving conservation equations, various geodynamic scenarios involve advection of quantities with sharp discontinuities. Unfortunately, in these cases modeling numerically pure advection becomes very challenging, in particular because sharp discontinuities lead to numerical instabilities, which prevent the local use of high order numerical schemes. Several approaches have been used in computational geodynamics in order to overcome this difficulty, with variable amounts of success. Despite the use of correcting filters or non-oscillatory, shock-preserving schemes, Eulerian (fixed grid) techniques generally suffer from artificial numerical diffusion. Lagrangian approaches (dynamic grids or particles) tend to be more popular in computational geodynamics because they are not prone to excessive numerical diffusion. However, these approaches are generally computationally expensive, especially in 3D, and can suffer from spurious statistical noise. As an alternative to these aforementioned approaches, I have applied a relatively recent Particle Level set method [Enright et al., 2002] for modeling advection of quantities with the presence of sharp discontinuities. I have adapted this improved method, which combines the best of Eulerian and Lagrangian approaches, and I have tested it against well known benchmarks and classical Geodynamic flows. In each case the Particle Level Set method accuracy equals or is better than other Eulerian and Lagrangian methods, and leads to significantly smaller computational cost, in particular in three-dimensional flows, where the reduction of computational time for modeling advection processes is most needed.

  5. High-resolution stochastic downscaling of climate models: simulating wind advection, cloud cover and precipitation

    NASA Astrophysics Data System (ADS)

    Peleg, Nadav; Fatichi, Simone; Burlando, Paolo

    2015-04-01

    A new stochastic approach to generate wind advection, cloud cover and precipitation fields is presented with the aim of formulating a space-time weather generator characterized by fields with high spatial and temporal resolution (e.g., 1 km x 1 km and 5 min). Its use is suitable for stochastic downscaling of climate scenarios in the context of hydrological, ecological and geomorphological applications. The approach is based on concepts from the Advanced WEather GENerator (AWE-GEN) presented by Fatichi et al. (2011, Adv. Water Resour.), the Space-Time Realizations of Areal Precipitation model (STREAP) introduced by Paschalis et al. (2013, Water Resour. Res.), and the High-Resolution Synoptically conditioned Weather Generator (HiReS-WG) presented by Peleg and Morin (2014, Water Resour. Res.). Advection fields are generated on the basis of the 500 hPa u and v wind direction variables derived from global or regional climate models. The advection velocity and direction are parameterized using Kappa and von Mises distributions respectively. A random Gaussian fields is generated using a fast Fourier transform to preserve the spatial correlation of advection. The cloud cover area, total precipitation area and mean advection of the field are coupled using a multi-autoregressive model. The approach is relatively parsimonious in terms of computational demand and, in the context of climate change, allows generating many stochastic realizations of current and projected climate in a fast and efficient way. A preliminary test of the approach is presented with reference to a case study in a complex orography terrain in the Swiss Alps.

  6. Quantification of numerical diffusivity due to TVD schemes in the advection equation

    NASA Astrophysics Data System (ADS)

    Bidadi, Shreyas; Rani, Sarma L.

    2014-03-01

    In this study, the numerical diffusivity νnum inherent to the Roe-MUSCL scheme has been quantified for the scalar advection equation. The Roe-MUSCL scheme employed is a combination of: (1) the standard extension of the original Roe's formulation to the advection equation, and (2) van Leer's Monotone Upwind Scheme for Conservation Laws (MUSCL) technique that applies a linear variable reconstruction in a cell along with a scaled limiter function. An explicit expression is derived for the numerical diffusivity in terms of the limiter function, the distance between the cell centers on either side of a face, and the face-normal velocity. The numerical diffusivity formulation shows that a scaled limiter function is more appropriate for MUSCL in order to consistently recover the central-differenced flux at the maximum value of the limiter. The significance of the scaling factor is revealed when the Roe-MUSCL scheme, originally developed for 1-D scenarios, is applied to 2-D scalar advection problems. It is seen that without the scaling factor, the MUSCL scheme may not necessarily be monotonic in multi-dimensional scenarios. Numerical diffusivities of the minmod, superbee, van Leer and Barth-Jesperson TVD limiters were quantified for four problems: 1-D advection of a step function profile, and 2-D advection of step, sinusoidal, and double-step profiles. For all the cases, it is shown that the superbee scheme provides the lowest numerical diffusivity that is also most confined to the vicinity of the discontinuity. The minmod scheme is the most diffusive, as well as active in regions away from high gradients. As expected, the grid resolution study demonstrates that the magnitude and the spatial extent of the numerical diffusivity decrease with increasing resolution.

  7. A novel method for analytically solving a radial advection-dispersion equation

    NASA Astrophysics Data System (ADS)

    Lai, Keng-Hsin; Liu, Chen-Wuing; Liang, Ching-Ping; Chen, Jui-Sheng; Sie, Bing-Ruei

    2016-11-01

    An analytical solution for solute transport in a radial flow field has a variety of practical applications in the study of the transport in push-pull/divergent/convergent flow tracer tests, aquifer remediation by pumping and aquifer storage and recovery. However, an analytical solution for radial advective-dispersive transport has been proven very difficult to develop and relatively few in subsurface hydrology have made efforts to do so, because variable coefficients in the governing partial differential equations. Most of the solutions for radial advective-dispersive transport presented in the literature have generally been solved semi-analytically with the final concentration values being obtained with the help of a numerical Laplace inversion. This study presents a novel solution strategy for analytically solving the radial advective-dispersive transport problem. A Laplace transform with respect to the time variable and a generalized integral transform technique with respect to the spatial variable are first performed to convert the transient governing partial differential equations into an algebraic equation. Subsequently, the algebraic equation is solved using simple algebraic manipulations, easily yielding the solution in the transformed domain. The solution in the original domain is ultimately obtained by successive applications of the Laplace and corresponding generalized integral transform inversions. A convergent flow tracer test is used to demonstrate the robustness of the proposed method for deriving an exact analytical solution to the radial advective-dispersive transport problem. The developed analytical solution is verified against a semi-analytical solution taken from the literature. The results show perfect agreement between our exact analytical solution and the semi-analytical solution. The solution method presented in this study can be applied to create more comprehensive analytical models for a great variety of radial advective

  8. Improving estimates of ecosystem metabolism by reducing effects of tidal advection on dissolved oxygen time series-Abstract

    EPA Science Inventory

    Continuous time series of dissolved oxygen (DO) have been used to compute estimates of metabolism in aquatic ecosystems. Central to this open water or "Odum" method is the assumption that the DO time is not strongly affected by advection and that effects due to advection or mixin...

  9. Analytical solutions of the one-dimensional advection-dispersion solute transport equation subject to time-dependent boundary conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analytical solutions of the advection-dispersion solute transport equation remain useful for a large number of applications in science and engineering. In this paper we extend the Duhamel theorem, originally established for diffusion type problems, to the case of advective-dispersive transport subj...

  10. Development of anion-exchange/reversed-phase high performance liquid chromatography-inductively coupled plasma-mass spectrometry methods for the speciation of bio-available iodine and bromine from edible seaweed.

    PubMed

    Romarís-Hortas, Vanessa; Bermejo-Barrera, Pilar; Moreda-Piñeiro, Antonio

    2012-05-04

    Anion exchange high performance liquid chromatography hyphenated with inductively coupled plasma-mass spectrometry has been novelly applied to assess inorganic (iodide and iodate) and organic (3-iodotyrosine - MIT, and 3,5-diiodotyrosine - DIT) iodine species in a single chromatographic run. The optimized operating conditions (Dionex IonPac AS7, gradient elution with 175 mM ammonium nitrate plus 15% (v/v) methanol, pH 3.8, as a mobile phase and flow rates within the 0.5-1.5 mL min(-1) range) have also been used to perform inorganic bromine speciation analysis (bromide and bromate). The developed method has been applied for determining the bio-available contents of iodine and bromine species in dialyzates from edible seaweed. Reverse phase high performance liquid chromatography (Zorbax Eclipse XDB-C8, gradient elution with 0.2% (m/m) acetic acid, and 0.2% (m/m) acetic acid in methanol, as mobile phases, and a constant flow rate of 0.75 mL min(-1)) also hyphenated with inductively coupled plasma-mass spectrometry was used to confirm the presence of organic iodine species (MIT and DIT) in the dialyzates. The verification of the presence of iodinated amino acids (MIT and DIT) in the extracts was also performed by reverse phase high performance liquid chromatography-electrospray ionization-mass spectrometry (LTQ Orbitrap). The developed methods have provided good repeatability (RSD values lower than 10% for both anion exchange and reverse phase separations) and analytical recoveries within the 90-105% range for all cases. The in vitro bio-availability method consisted of a simulated gastric and an intestinal digestion/dialysis (10 kDa molecular weight cut-off - MWCO) two-stage procedure. Iodide and MIT were the main bio-available species quantified, whereas bromide was the major bromine species found in the extracts.

  11. Surface Layer Flux Processes During Cloud Intermittency and Advection above a Middle Rio Grande Riparian Forest, New Mexico

    NASA Astrophysics Data System (ADS)

    Cleverly, J. R.; Prueger, J.; Cooper, D. I.; Hipps, L.; Eichinger, W.

    2002-12-01

    An intensive field campaign was undertaken to bring together state-of-the-art methodologies for investigating surface layer physical characteristics over a desert riparian forest. Three-dimensional sonic eddy covariance (3SEC), LIDAR, SODAR, Radiosonde, one-dimensional propeller eddy covariance (1PEC), heat dissipation sap flux, and leaf gas exchange were simultaneously in use 13 -- 21 June 1999 at Bosque del Apache National Wildlife Refuge (NWR) in New Mexico. A one hour period of intense advection was identified by /line{v} >> 0 and /line{u} = 0, indicating that wind direction was transverse to the riparian corridor. The period of highest /line{v} was 1400 h on 20 June; this hour experienced intermittent cloud cover and enhanced mesoscale forcing of surface fluxes. High-frequency (20 Hz) time series of u, v, w, q, θ , and T were collected for spectral, cospectral, and wavelet analyses. These time series analyses illustrate scales at which processes co-occur. At high frequencies (> 0.015 Hz), /line{T' q'} > 0, and (KH)/ (KW) = 1. At low frequencies, however, /line{T' q'} < 0, and (KH)/(KW) !=q 1. Under these transient conditions, frequencies below 0.015 Hz are associated with advection. While power cospectra are useful in associating processes at certain frequencies, further analysis must be performed to determine whether such examples of aphasia are localized to transient events or constant through time. Continuous wavelet transformation (CWT) sacrifices localization in frequency space for localization in time. Mother wavelets were evaluated, and Daubechies order 10 wavelet was found to reduce red noise and leakage near the spectral gap. The spectral gap is a frequency domain between synoptic and turbulent scales. Low frequency turbulent structures near the spectral gap in the time series of /line{T' q'}, /line{w' T'}, and /line{w' q'} followed a perturbation--relaxation pattern to cloud cover. Further cloud cover in the same hour did not produce the low

  12. GAS EXCHANGE WITH MASS CULTURES OF ALGAE. I. EFFECTS OF LIGHT INTENSITY AND RATE OF CARBON DIOXIDE INPUT ON OXYGEN PRODUCTION.

    PubMed

    HANNAN, P J; PATOUILLET, C

    1963-09-01

    The performance of a small photosynthetic gas exchanger is described in which simultaneous measurements of suspension density, O(2) production, and CO(2) absorption are readily accomplished. The volume of suspension was 6200 ml. With the Sorokin strain of Chlorella pyrenoidosa 7-11-05, this unit produced 4500 cc of O(2) per hr at a light intensity of 34,000 ft-c from each of six Quartzline lamps. At any given light intensity, the O(2) production was proportional to the rate of CO(2) input up to a maximum. The impetus for this study was the consideration of the algal system as a means of oxygen generation in a submarine. Based on the performance of this unit, the power requirement per man for a system having the geometry described would be 52 kw, but reasons are given for the hope that this may be reduced to less than 5 kw.

  13. Characteristics of mineral nutrition of plants in the bio-technical life support system with human wastes included in mass exchange

    NASA Astrophysics Data System (ADS)

    Tikhomirova, Natalia; Ushakova, Sofya; Kalacheva, Galina; Tikhomirov, Alexander

    2016-09-01

    The study addresses the effectiveness of using ion exchange substrates (IES) to optimize mineral nutrition of plants grown in the nutrient solutions containing oxidized human wastes for application in bio-technical life support systems. The study shows that the addition of IES to the root-inhabited substrate is favorable for the growth of wheat vegetative organs but causes a decrease in the grain yield. By contrast, the addition of IES to the nutrient solution does not influence the growth of vegetative organs but favors normal development of wheat reproductive organs. Thus, to choose the proper method of adjusting the solution with IES, one should take into account specific parameters of plant growth and development and the possibility of multiple recycling of IES based on the liquid products of mineralization of human wastes.

  14. Implications of rate-limited mass transfer for aquifer storage and recovery.

    PubMed

    Culkin, Sean L; Singha, Kamini; Day-Lewis, Frederick D

    2008-01-01

    Pressure to decrease reliance on surface water storage has led to increased interest in aquifer storage and recovery (ASR) systems. Recovery efficiency, which is the ratio of the volume of recovered water that meets a predefined standard to total volume of injected fluid, is a common criterion of ASR viability. Recovery efficiency can be degraded by a number of physical and geochemical processes, including rate-limited mass transfer (RLMT), which describes the exchange of solutes between mobile and immobile pore fluids. RLMT may control transport behavior that cannot be explained by advection and dispersion. We present data from a pilot-scale ASR study in Charleston, South Carolina, and develop a three-dimensional finite-difference model to evaluate the impact of RLMT processes on ASR efficiency. The modeling shows that RLMT can explain a rebound in salinity during fresh water storage in a brackish aquifer. Multicycle model results show low efficiencies over one to three ASR cycles due to RLMT degrading water quality during storage; efficiencies can evolve and improve markedly, however, over multiple cycles, even exceeding efficiencies generated by advection-dispersion only models. For an idealized ASR model where RLMT is active, our simulations show a discrete range of diffusive length scales over which the viability of ASR schemes in brackish aquifers would be hindered.

  15. Numerical Experiments on Advective Transport in Large Three-Dimensional Discrete Fracture Networks

    NASA Astrophysics Data System (ADS)

    Makedonska, N.; Painter, S. L.; Karra, S.; Gable, C. W.

    2013-12-01

    Modeling of flow and solute transport in discrete fracture networks is an important approach for understanding the migration of contaminants in impermeable hard rocks such as granite, where fractures provide dominant flow and transport pathways. The discrete fracture network (DFN) model attempts to mimic discrete pathways for fluid flow through a fractured low-permeable rock mass, and may be combined with particle tracking simulations to address solute transport. However, experience has shown that it is challenging to obtain accurate transport results in three-dimensional DFNs because of the high computational burden and difficulty in constructing a high-quality unstructured computational mesh on simulated fractures. An integrated DFN meshing [1], flow, and particle tracking [2] simulation capability that enables accurate flow and particle tracking simulation on large DFNs has recently been developed. The new capability has been used in numerical experiments on advective transport in large DFNs with tens of thousands of fractures and millions of computational cells. The modeling procedure starts from the fracture network generation using a stochastic model derived from site data. A high-quality computational mesh is then generated [1]. Flow is then solved using the highly parallel PFLOTRAN [3] code. PFLOTRAN uses the finite volume approach, which is locally mass conserving and thus eliminates mass balance problems during particle tracking. The flow solver provides the scalar fluxes on each control volume face. From the obtained fluxes the Darcy velocity is reconstructed for each node in the network [4]. Velocities can then be continuously interpolated to any point in the domain of interest, thus enabling random walk particle tracking. In order to describe the flow field on fractures intersections, the control volume cells on intersections are split into four planar polygons, where each polygon corresponds to a piece of a fracture near the intersection line. Thus

  16. [Energy and mass exchange and the productivity of the main ecosystems of Siberia (from eddy covariance measurements). 1. Heat balance structure in the vegetation season].

    PubMed

    Chebakova, N M; Vygodskaia, N N; Arnet, A; Belelli Markezini, L; Kolle, O; Kurbatova, Iu A; Parfenova, E I; Valentini, R; Vaganov, E A; Shul'tse, E D

    2013-01-01

    Direct measurements of heat balance (turbulent heat transfer and evaporation heat consumption) by the method of turbulent pulsations in 1998-2000 and 2002-2004 were used to obtain information on the daily, seasonal, and annual dynamics of energy fluxes and mass transfer between the atmosphere and the typical ecosystems of Siberia (middle-taiga pine forest and raised bog, true four-grass steppe, with the use of data for typical tundra) along the Yenisei meridian (90 degrees E).

  17. Trace enrichment and characterization of polyphenols in Bistort Rhizoma using weak anion-exchange solid phase extraction and high performance liquid chromatography-quadrupole time-of-flight mass spectrometry.

    PubMed

    Wang, Shao-Teng; Yang, Hua; Gao, Wen; Li, Hui-Jun; Li, Ping

    2016-02-05

    The analysis of trace constituents in herbal medicines has always been a challenge due to complex matrices and structural diversities. In this work, a pH-sensitive solid phase extraction (SPE) procedure capable of enriching trace polyphenols in Bistort Rhizoma (BR) was proposed and preliminary chemical characterization was accomplished by high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (HPLC-QTOF MS). A weak anion-exchange SPE column packed with divinylbenzene/vinylpyrrolidone bonding quaternary amine group was employed for anionic extraction, and the target fraction was obtained by eluting with acidic methanol (apparent pH 1.9). On the other hand, the MS/MS fragmentation rules of four reference polyphenols in negative ion mode were outlined. Using these rules, a total of 31 polyphenols including 20 benzoyl derivatives and 11 caffeoyl derivatives were screened out from BR extract, of which 26 trace members were found for the first time in this herb. Those findings demonstrated that the anion-exchange SPE could enhance the detection capability and selectivity for plant polyphenols in the LC-MS analysis and the strategy for deducing structures could be applied for analysis of polyphenols in BR and other herbal medicines.

  18. [Separation and identification of beta-casein from Chinese human milk by ion exchange chromatography-matrix-assisted laser desorption/ionization time of flight/time of flight mass spectrometry].

    PubMed

    Huang, Yu; Ren, Haowei; Liu, Biao; Liu, Ning; Li, Meng; Wang, Dongmao

    2013-05-01

    The selective precipitation of whole casein from skimmed milk was achieved by the addition of calcium salt under acidic pH. The effects of pH, centrifugal force and final concentration of CaCl2 on the separation of casein were studied by measuring the purity of final products using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The results showed that casein with the highest purity could be obtained with the pH of 4.3, the centrifugal force of 10 400 g and the final concentration of CaCl2 of 60 mmol/L. The casein was processed with DEAE anion exchange chromatography and three peaks were obtained. Then the third peak (peak III) was identified with Western-Blot method and matrix-assisted laser desorption/ionization time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS). The identification of Western-Blot showed that peak III can combine with the specificity of human milk beta-casein antibody, and it is proved to be human milk beta-casein. The fingerprints of peak III were nalyzed by Mascot searching, and the sequence coverage was 50%, further supporting it is human milk beta-casein. In conclusion, an effective method to obtain human milk beta-casein from milk samples through DEAE anion exchange chromatography was established, and it is suitable for the proteomics research requirements of the beta-casein from human milk.

  19. Real-time HD Exchange Kinetics of Proteins from Buffered Aqueous Solution with Electrothermal Supercharging and Top-Down Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Going, Catherine C.; Xia, Zijie; Williams, Evan R.

    2016-06-01

    Electrothermal supercharging (ETS) with electrospray ionization produces highly charged protein ions from buffered aqueous solutions in which proteins have native folded structures. ETS increases the charge of ribonuclease A by 34%, whereas only a 6% increase in charge occurs for a reduced-alkylated form of this protein, which is unfolded and its structure is ~66% random coil in this solution. These results indicate that protein denaturation that occurs in the ESI droplets is the primary mechanism for ETS. ETS does not affect the extent of solution-phase hydrogen-deuterium exchange (HDX) that occurs for four proteins that have significantly different structures in solution, consistent with a droplet lifetime that is considerably shorter than observable rates of HDX. Rate constants for HDX of ubiquitin are obtained with a spatial resolution of ~1.3 residues with ETS and electron transfer dissociation of the 10+ charge-state using a single capillary containing a few μL of protein solution in which HDX continuously occurs. HDX protection at individual residues with ETS HDX is similar to that with reagent supercharging HDX and with solution-phase NMR, indicating that the high spray potentials required to induce ETS do not lead to HD scrambling.

  20. Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC/ESI-MS/MS) Study for the Identification and Characterization of In Vivo Metabolites of Cisplatin in Rat Kidney Cancer Tissues: Online Hydrogen/Deuterium (H/D) Exchange Study.

    PubMed

    Bandu, Raju; Ahn, Hyun Soo; Lee, Joon Won; Kim, Yong Woo; Choi, Seon Hee; Kim, Hak Jin; Kim, Kwang Pyo

    2015-01-01

    In vivo rat kidney tissue metabolites of an anticancer drug, cisplatin (cis-diamminedichloroplatinum [II]) (CP) which is used for the treatment of testicular, ovarian, bladder, cervical, esophageal, small cell lung, head and neck cancers, have been identified and characterized by using liquid chromatography positive ion electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) in combination with on line hydrogen/deuterium exchange (HDX) experiments. To identify in vivo metabolites, kidney tissues were collected after intravenous administration of CP to adult male Sprague-Dawley rats (n = 3 per group). The tissue samples were homogenized and extracted using newly optimized metabolite extraction procedure which involves liquid extraction with phosphate buffer containing ethyl acetate and protein precipitation with mixed solvents of methanol-water-chloroform followed by solid-phase clean-up procedure on Oasis HLB 3cc cartridges and then subjected to LC/ESI-HRMS analysis. A total of thirty one unknown in vivo metabolites have been identified and the structures of metabolites were elucidated using LC-MS/MS experiments combined with accurate mass measurements. Online HDX experiments have been used to further support the structural characterization of metabolites. The results showed that CP undergoes a series of ligand exchange biotransformation reactions with water and other nucleophiles like thio groups of methionine, cysteine, acetylcysteine, glutathione and thioether. This is the first research approach focused on the structure elucidation of biotransformation products of CP in rats, and the identification of metabolites provides essential information for further pharmacological and clinical studies of CP, and may also be useful to develop various effective new anticancer agents.

  1. "TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis

    PubMed Central

    Nikamanon, Pornpat; Pun, Elroy; Chou, Wayne; Koter, Marek D; Gershon, Paul D

    2008-01-01

    Background Protein-amide proton hydrogen-deuterium exchange (HDX) is used to investigate protein conformation, conformational changes and surface binding sites for other molecules. To our knowledge, software tools to automate data processing and analysis from sample fractionating (LC-MALDI) mass-spectrometry-based HDX workflows are not publicly available. Results An integrated data pipeline (Solvent Explorer/TOF2H) has been developed for the processing of LC-MALDI-derived HDX data. Based on an experiment-wide template, and taking an ab initio approach to chromatographic and spectral peak finding, initial data processing is based on accurate mass-matching to fully deisotoped peaklists accommodating, in MS/MS-confirmed peptide library searches, ambiguous mass-hits to non-target proteins. Isotope-shift re-interrogation of library search results allows quick assessment of the extent of deuteration from peaklist data alone. During raw spectrum editing, each spectral segment is validated in real time, consistent with the manageable spectral numbers resulting from LC-MALDI experiments. A semi-automated spectral-segment editor includes a semi-automated or automated assessment of the quality of all spectral segments as they are pooled across an XIC peak for summing, centroid mass determination, building of rates plots on-the-fly, and automated back exchange correction. The resulting deuterium uptake rates plots from various experiments can be averaged, subtracted, re-scaled, error-barred, and/or scatter-plotted from individual spectral segment centroids, compared to solvent exposure and hydrogen bonding predictions and receive a color suggestion for 3D visualization. This software lends itself to a "divorced" HDX approach in which MS/MS-confirmed peptide libraries are built via nano or standard ESI without source modification, and HDX is performed via LC-MALDI using a standard MALDI-TOF. The complete TOF2H package includes additional (eg LC analysis) modules. Conclusion

  2. Estimation and correction of advection effects with single and multiple, conventional and Doppler radars

    NASA Technical Reports Server (NTRS)

    Gal-Chen, T.

    1981-01-01

    The laws of fluid motion are invariant under a Gallilean transformation. For a perfect observing system, the data analysis should, therefore, also be invariant under a Gallilean transformation. This invariance is often not preserved in practical observing systems. In this connection, it is often advisable to perform mesoscale analysis in a frame moving with respect to the earth's surface. In the present investigation the velocity of such a frame is referred to as an advection velocity. The investigation is concerned with remaining problems regarding the Gallilean transformation. The establishment of a frame of reference for the achievement of maximum coherence is considered, taking into account the case of given nonsimultaneous observations of scalars or Cartesian vectors. It is found that advection speed can be estimated objectively if a scalar or Cartesian vector can be observed directly and if, in addition, the time and position of each observation is approximately known.

  3. Scalar variance decay in chaotic advection and Batchelor-regime turbulence

    NASA Astrophysics Data System (ADS)

    Fereday, D. R.; Haynes, P. H.; Wonhas, A.; Vassilicos, J. C.

    2002-03-01

    The decay of the variance of a diffusive scalar in chaotic advection flow (or equivalently Batchelor-regime turbulence) is analyzed using a model in which the advection is represented by an inhomogeneous baker's map on the unit square. The variance decays exponentially at large times, with a rate that has a finite limit as the diffusivity κ tends to zero and is determined by the action of the inhomogeneous map on the gravest Fourier modes in the scalar field. The decay rate predicted by recent theoretical work that follows scalar evolution in linear flow and then averages over all stretching histories is shown to be incorrect. The exponentially decaying scalar field is shown to have a spatial power spectrum of the form P(k)~k-σ at wave numbers small enough for diffusion to be neglected, with σ<1.

  4. Analytic radiative-advective equilibrium as a model for high-latitude climate

    NASA Astrophysics Data System (ADS)

    Cronin, Timothy W.; Jansen, Malte F.

    2016-01-01

    We propose radiative-advective equilibrium as a basic-state model for the high-latitude atmosphere. Temperature profiles are determined by a competition between stabilization by atmospheric shortwave absorption and advective heat flux convergence, and destabilization by surface shortwave absorption. We derive analytic expressions for temperature profiles, assuming power law atmospheric heating profiles as a function of pressure and two-stream windowed-gray longwave radiative transfer. We discuss example profiles with and without an atmospheric window and show that the sensitivity of surface temperature to forcing depends on the nature of the forcing, with greatest sensitivity to radiative forcing by increased optical thickness and least sensitivity to increased atmospheric heat transport. These differences in sensitivity of surface temperature to forcing can be explained in terms of a forcing-dependent lapse-rate feedback.

  5. Advective-diffusive motion on large scales from small-scale dynamics with an internal symmetry

    NASA Astrophysics Data System (ADS)

    Marino, Raffaele; Aurell, Erik

    2016-06-01

    We consider coupled diffusions in n -dimensional space and on a compact manifold and the resulting effective advective-diffusive motion on large scales in space. The effective drift (advection) and effective diffusion are determined as a solvability conditions in a multiscale analysis. As an example, we consider coupled diffusions in three-dimensional space and on the group manifold SO(3) of proper rotations, generalizing results obtained by H. Brenner [J. Colloid Interface Sci. 80, 548 (1981), 10.1016/0021-9797(81)90214-9]. We show in detail how the analysis can be conveniently carried out using local charts and invariance arguments. As a further example, we consider coupled diffusions in two-dimensional complex space and on the group manifold SU(2). We show that although the local operators may be the same as for SO(3), due to the global nature of the solvability conditions the resulting diffusion will differ and generally be more isotropic.

  6. Comparison of Nonlinear and Linear Stabilization Schemes for Advection-Diffusion Equations

    NASA Astrophysics Data System (ADS)

    Grove, R. R.; Heister, T.

    2015-12-01

    Accurately solving advection-diffusion equations that appear in the finite element discretization of a mantle convection simulation is an important computational issue to the computational geoscience community. This is because it allows for users studying mantle convection to create reliable simulations for something as small and simple as a 2D simulation on their personal laptop to something as complex as a massively parallel 3D simulation on their university supercomputer. Standard finite element discretizations of advection-diffusion equations introduce unphysical oscillations around steep gradients. Therefore, stabilization must be added to the discrete formulation to obtain correct solutions. Using the open source scientific library ASPECT, the SUPG and Entropy Viscosity schemes are compared using stationary and non-stationary test equations. Differences in maximum overshoot and undershoot, smear, and convergence orders are compared to see if improvements can be made to the existing numerical method existing in ASPECT.

  7. Two-dimensional atmospheric transport and chemistry model - Numerical experiments with a new advection algorithm

    NASA Technical Reports Server (NTRS)

    Shia, Run-Lie; Ha, Yuk Lung; Wen, Jun-Shan; Yung, Yuk L.

    1990-01-01

    Extensive testing of the advective scheme proposed by Prather (1986) has been carried out in support of the California Institute of Technology-Jet Propulsion Laboratory two-dimensional model of the middle atmosphere. The original scheme is generalized to include higher-order moments. In addition, it is shown how well the scheme works in the presence of chemistry as well as eddy diffusion. Six types of numerical experiments including simple clock motion and pure advection in two dimensions have been investigated in detail. By comparison with analytic solutions, it is shown that the new algorithm can faithfully preserve concentration profiles, has essentially no numerical diffusion, and is superior to a typical fourth-order finite difference scheme.

  8. Oxygen Advection and Diffusion in a Three Dimensional Vascular Anatomical Network

    PubMed Central

    Fang, Qianqian; Sakadžić, Sava; Ruvinskaya, Lana; Devor, Anna; Dale, Anders M.; Boas, David A.

    2008-01-01

    There is an increasing need for quantitative and computationally affordable models for analyzing tissue metabolism and hemodynamics in microvascular networks. In this work, we develop a hybrid model to solve for the time-varying oxygen advection-diffusion equation in the vessels and tissue. To obtain a three-dimensional temporal evolution of tissue oxygen concentration for realistic complex vessel networks, we used a graph-based advection model combined with a finite-element based diffusion model and an implicit time-advancing scheme. We validated this algorithm for both static and dynamic conditions. We also applied it to a complex vascular network obtained from a rodent somatosensory cortex. Qualitative agreement was found with in-vivo experiments. PMID:18958033

  9. Advection and the Efficiency of Spectral Energy Transfer in Two-Dimensional Turbulence.

    PubMed

    Fang, Lei; Ouellette, Nicholas T

    2016-09-02

    We report measurements of the geometric alignment of the small-scale turbulent stress and the large-scale rate of strain that together lead to the net flux of energy from small scales to large scales in two-dimensional turbulence. We find that the instantaneous alignment between these two tensors is weak and, thus, that the spectral transport of energy is inefficient. We show, however, that the strain rate is much better aligned with the stress at times in the past, suggesting that the differential advection of the two is responsible for the inefficient spectral transfer. We provide evidence for this conjecture by measuring the alignment statistics conditioned on weakly changing stress history. Our results give new insight into the relationship between scale-to-scale energy transfer, geometric alignment, and advection in turbulent flows.

  10. Estimating ground-water exchange with lakes using water-budget and chemical mass-balance approaches for ten lakes in ridge areas of Polk and Highlands counties, Florida

    USGS Publications Warehouse

    Sacks, L.A.; Swancar, Amy; Lee, T.M.

    1998-01-01

    Water budget and chemical mass-balance approaches were used to estimate ground-water exchange with 10 lakes in ridge areas of Polk and Highlands Counties, Florida. At each lake, heads were monitored in the surficial aquifer system and deeper Upper Floridan aquifer, lake stage and rainfall were measured continuously, and lakes and wells were sampled three times between October 1995 and December 1996. The water-budget approach computes net ground-water flow (ground-water inflow minus outflow) as the residual of the monthly waterbudget equation. Net ground-water flow varied seasonally at each of the 10 lakes, and was notably different between lakes, illustrating short-term differences in ground-water fluxes. Monthly patterns in net ground-water flow were related to monthly patterns of other hydrologic variables such as rainfall, ground-water flow patterns, and head differences between the lake and the Upper Floridan aquifer. The chemical mass-balance approach combines the water budget and solute or isotope mass-balance equations, and assumes steady-state conditions. Naturally occurring tracers that were analyzed for include calcium, magnesium, sodium, potassium, chloride, and bromide, the isotopes deuterium and oxygen-18. Chloride and sodium were the most successful solute tracers; however, their concentrations in ground water typically varied spatially, and in places were similar to that in lake water, limiting their sensitivity as tracers. In contrast, the isotopes were more robust tracers because the isotopic composition of ground water was relatively uniform and was distinctly different from the lake water. Groundwater inflow computed using the chemical massbalance method varied significantly between lakes, and ranged from less than 10 to more than 150 inches per year. Both water-budget and chemical mass-balance approaches had limitations, but the multiple lines of evidence gained using both approaches improved the understanding of the role of ground water in the

  11. Estimating Advective Near-surface Currents from Ocean Color Satellite Images

    DTIC Science & Technology

    2015-01-01

    RESPONSIBLE PERSON 19b. TELEPHONE NUMBER (Include area code) 01/23/2015 Journal Article Estimating advective near-surface currents from ocean color ...currents from the sequential ocean color imagery provided by multiple newer generations of satellite sensors on hourly scales in the Yellow Sea and the...optical properties are discussed regarding the performances of various color products on the retrieval of currents. Similarities of velocity

  12. A family of compact high order coupled time-space unconditionally stable vertical advection schemes

    NASA Astrophysics Data System (ADS)

    Lemarié, Florian; Debreu, Laurent

    2016-04-01

    Recent papers by Shchepetkin (2015) and Lemarié et al. (2015) have emphasized that the time-step of an oceanic model with an Eulerian vertical coordinate and an explicit time-stepping scheme is very often restricted by vertical advection in a few hot spots (i.e. most of the grid points are integrated with small Courant numbers, compared to the Courant-Friedrichs-Lewy (CFL) condition, except just few spots where numerical instability of the explicit scheme occurs first). The consequence is that the numerics for vertical advection must have good stability properties while being robust to changes in Courant number in terms of accuracy. An other constraint for oceanic models is the strict control of numerical mixing imposed by the highly adiabatic nature of the oceanic interior (i.e. mixing must be very small in the vertical direction below the boundary layer). We examine in this talk the possibility of mitigating vertical Courant-Friedrichs-Lewy (CFL) restriction, while avoiding numerical inaccuracies associated with standard implicit advection schemes (i.e. large sensitivity of the solution on Courant number, large phase delay, and possibly excess of numerical damping with unphysical orientation). Most regional oceanic models have been successfully using fourth order compact schemes for vertical advection. In this talk we present a new general framework to derive generic expressions for (one-step) coupled time and space high order compact schemes (see Daru & Tenaud (2004) for a thorough description of coupled time and space schemes). Among other properties, we show that those schemes are unconditionally stable and have very good accuracy properties even for large Courant numbers while having a very reasonable computational cost.

  13. Statistical evaluation of thermal advection and stratification effects in scatterometer observations

    NASA Technical Reports Server (NTRS)

    Levy, Gad; Tiu, F. S.

    1991-01-01

    The effects of thermal advection and atmospheric stratification are statistically evaluated using Seasat scatterometer observations as a data base. The results indicate that, whenever the surface winds or wind stress are related to the atmospheric pressure field, the appropriate stratification and baroclinic corrections should be applied. Without such corrections, errors of 15-25 percent are likely to arise in the surface fluxes computed from model low-level winds or pressure measurements.

  14. An advection-based model to increase the temporal resolution of PIV time series.

    PubMed

    Scarano, Fulvio; Moore, Peter

    A numerical implementation of the advection equation is proposed to increase the temporal resolution of PIV time series. The method is based on the principle that velocity fluctuations are transported passively, similar to Taylor's hypothesis of frozen turbulence. In the present work, the advection model is extended to unsteady three-dimensional flows. The main objective of the method is that of lowering the requirement on the PIV repetition rate from the Eulerian frequency toward the Lagrangian one. The local trajectory of the fluid parcel is obtained by forward projection of the instantaneous velocity at the preceding time instant and backward projection from the subsequent time step. The trajectories are approximated by the instantaneous streamlines, which yields accurate results when the amplitude of velocity fluctuations is small with respect to the convective motion. The verification is performed with two experiments conducted at temporal resolutions significantly higher than that dictated by Nyquist criterion. The flow past the trailing edge of a NACA0012 airfoil closely approximates frozen turbulence, where the largest ratio between the Lagrangian and Eulerian temporal scales is expected. An order of magnitude reduction of the needed acquisition frequency is demonstrated by the velocity spectra of super-sampled series. The application to three-dimensional data is made with time-resolved tomographic PIV measurements of a transitional jet. Here, the 3D advection equation is implemented to estimate the fluid trajectories. The reduction in the minimum sampling rate by the use of super-sampling in this case is less, due to the fact that vortices occurring in the jet shear layer are not well approximated by sole advection at large time separation. Both cases reveal that the current requirements for time-resolved PIV experiments can be revised when information is poured from space to time. An additional favorable effect is observed by the analysis in the frequency

  15. Approximate Solution of Time-Fractional Advection-Dispersion Equation via Fractional Variational Iteration Method

    PubMed Central

    İbiş, Birol

    2014-01-01

    This paper aims to obtain the approximate solution of time-fractional advection-dispersion equation (FADE) involving Jumarie's modification of Riemann-Liouville derivative by the fractional variational iteration method (FVIM). FVIM provides an analytical approximate solution in the form of a convergent series. Some examples are given and the results indicate that the FVIM is of high accuracy, more efficient, and more convenient for solving time FADEs. PMID:24578662

  16. Noise Prevents Infinite Stretching of the Passive Field in a Stochastic Vector Advection Equation

    NASA Astrophysics Data System (ADS)

    Flandoli, Franco; Maurelli, Mario; Neklyudov, Mikhail

    2014-09-01

    A linear stochastic vector advection equation is considered; the equation may model a passive magnetic field in a random fluid. When the driving velocity field is rough but deterministic, in particular just Hölder continuous and bounded, one can construct examples of infinite stretching of the passive field, arising from smooth initial conditions. The purpose of the paper is to prove that infinite stretching is prevented if the driving velocity field contains in addition a white noise component.

  17. New Solution of Diffusion-Ad