Science.gov

Sample records for advective mass exchange

  1. The distribution of neodymium isotopes and concentrations in the Eastern Equatorial Pacific: Water mass advection versus particle exchange

    NASA Astrophysics Data System (ADS)

    Grasse, Patricia; Stichel, Torben; Stumpf, Roland; Stramma, Lothar; Frank, Martin

    2012-11-01

    The radiogenic isotope composition of the Rare Earth Element (REE) neodymium (Nd) is a powerful water mass proxy for present and past ocean circulation. The processes controlling the Nd budget of the global ocean are not quantitatively understood and in particular source and sink mechanisms are still under debate. In this study we present the first full water column data set of dissolved Nd isotope compositions and Nd concentrations for the Eastern Equatorial Pacific (EEP), where one of the globally largest Oxygen Minimum Zones (OMZ) is located. This region is of particular interest for understanding the biogeochemical cycling of REEs because anoxic conditions may lead to release of REEs from the shelf, whereas high particle densities and fluxes potentially remove the REEs from the water column. Data were obtained between 1°40‧N and 16°S along a nearshore and an offshore transect. Near surface zonal current bands, such as the Equatorial Undercurrent (EUC) and the Subsurface Countercurrent (SSCC), which are supplying oxygen-rich water to the OMZ are characterized by radiogenic Nd isotope signatures (εNd=-2). Surface waters in the northernmost part of the study area are even more radiogenic (εNd=+3), most likely due to release of Nd from volcanogenic material. Deep and bottom waters at the southernmost offshore station (14°S) are clearly controlled by advection of water masses with less radiogenic signatures (εNd=-7) originating from the Southern Ocean. Towards the equator, however, the deep waters show a clear trend towards more radiogenic values of up to εNd=-2. The northernmost station located in the Panama basin shows highly radiogenic Nd isotope signatures in the entire water column, which indicates that particle scavenging, downward transport and release processes play an important role. This is supported by relatively low Nd concentrations in deep waters (3000-6000 m) in the EEP (20 pmol/kg) compared to locations in the Northern and Central Pacific

  2. Efficient mass transport by optical advection

    NASA Astrophysics Data System (ADS)

    Kajorndejnukul, Veerachart; Sukhov, Sergey; Dogariu, Aristide

    2015-10-01

    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.

  3. 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

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

    NASA Astrophysics Data System (ADS)

    Solis, Kyle J.; Martin, James E.

    2012-11-01

    Isothermal magnetic advection (IMA) 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.

  5. 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)

  6. Heat and mass exchanger

    SciTech Connect

    Lowenstein, Andrew; Sibilia, Marc J.; Miller, Jeffrey A.; Tonon, Thomas

    2011-06-28

    A mass and heat exchanger includes at least one first substrate with a surface for supporting a continuous flow of a liquid thereon that either absorbs, desorbs, evaporates or condenses one or more gaseous species from or to a surrounding gas; and at least one second substrate operatively associated with the first substrate. The second substrate includes a surface for supporting the continuous flow of the liquid thereon and is adapted to carry a heat exchange fluid therethrough, wherein heat transfer occurs between the liquid and the heat exchange fluid.

  7. Heat and mass exchanger

    SciTech Connect

    Lowenstein, Andrew; Sibilia, Marc J.; Miller, Jeffrey A.; Tonon, Thomas

    2007-09-18

    A mass and heat exchanger includes at least one first substrate with a surface for supporting a continuous flow of a liquid thereon that either absorbs, desorbs, evaporates or condenses one or more gaseous species from or to a surrounding gas; and at least one second substrate operatively associated with the first substrate. The second substrate includes a surface for supporting the continuous flow of the liquid thereon and is adapted to carry a heat exchange fluid therethrough, wherein heat transfer occurs between the liquid and the heat exchange fluid.

  8. Advection and resulting CO2 exchange uncertainty in a tall forest in central Germany.

    PubMed

    Kutsch, Werner L; Kolle, Olaf; Rebmann, Corinna; Knohl, Alexander; Ziegler, Waldemar; Schulze, Ernst-Detlef

    2008-09-01

    Potential losses by advection were estimated at Hainich Forest, Thuringia, Germany, where the tower is located at a gentle slope. Three approaches were used: (1) comparing nighttime eddy covariance fluxes to an independent value of total ecosystem respiration by bottom-up modeling of the underlying processes, (2) direct measurements of a horizontal CO2 gradient and horizontal wind speed at 2 m height in order to calculate horizontal advection, and (3) direct measurements of a vertical CO2 gradient and a three-dimensional wind profile in order to calculate vertical advection. In the first approach, nighttime eddy covariance measurements were compared to independent values of total ecosystem respiration by means of bottom-up modeling of the underlying biological processes. Turbulent fluxes and storage term were normalized to the fluxes calculated by the bottom-up model. Below a u(*) threshold of 0.6 m/s the normalized turbulent fluxes decreased with decreasing u(*), but the flux to the storage increased only up to values less than 20% of the modeled flux at low turbulence. Horizontal advection was measured by a horizontal CO2 gradient over a distance of 130 m combined with horizontal wind speed measurements. Horizontal advection occurred at most of the evenings independently of friction velocity above the canopy. Nevertheless, horizontal advection was higher when u(*) was low. The peaks of horizontal advection correlated with changes in temperature. A full mass balance including turbulent fluxes, storage, and horizontal and vertical advection resulted in an increase of spikes and scatter but seemed to generally improve the results from the flux measurements. The comparison of flux data with independent bottom-up modeling results as well as the direct measurements resulted in strong indications that katabatic flows along the hill slope during evening and night reduces the measured apparent ecosystem respiration rate. In addition, anabatic flows may occur during the

  9. Modelling transport in media with heterogeneous advection properties and mass transfer with a Continuous Time Random Walk approach

    NASA Astrophysics Data System (ADS)

    Comolli, Alessandro; Moussey, Charlie; Dentz, Marco

    2016-04-01

    Transport processes in groundwater systems are strongly affected by the presence of heterogeneity. The heterogeneity leads to non-Fickian features, that manifest themselves in the heavy-tailed breakthrough curves, as well as in the non-linear growth of the mean squared displacement and in the non-Gaussian plumes of solute particles. The causes of non-Fickian transport can be the heterogeneity in the flow fields and the processes of mass exchange between mobile and immobile phases, such as sorption/desorption reactions and diffusive mass transfer. Here, we present a Continuous Time Random Walk (CTRW) model that describes the transport of solutes in d-dimensional systems by taking into account both heterogeneous advection and mobile-immobile mass transfer. In order to account for these processes in the CTRW, the heterogeneities are mapped onto a distribution of transition times, which can be decomposed into advective transition times and trapping times, the latter being treated as a compound Poisson process. While advective transition times are related to the Eulerian flow velocities and, thus, to the conductivity distribution, trapping times depend on the sorption/desorption time scale, in case of reactive problems, or on the distribution of diffusion times in the immobile zones. Since the trapping time scale is typically much larger than the advective time scale, we observe the existence of two temporal regimes. The pre-asymptotic regime is defined by a characteristic time scale at which the properties of transport are fully determined by the heterogeneity of the advective field. On the other hand, in the asymptotic regime both the heterogeneity and the mass exchange processes play a role in conditioning the behaviour of transport. We consider different scenarios to discuss the relative importance of the advective heterogeneity and the mass transfer for the occurrence of non-Fickian transport. For each case we calculate analytically the scalings of the breakthrough

  10. Warm-air advection, air mass transformation and fog causes rapid ice melt

    NASA Astrophysics Data System (ADS)

    Tjernström, Michael; Shupe, Matthew D.; Brooks, Ian M.; Persson, P. Ola G.; Prytherch, John; Salisbury, Dominic J.; Sedlar, Joseph; Achtert, Peggy; Brooks, Barbara J.; Johnston, Paul E.; Sotiropoulou, Georgia; Wolfe, Dan

    2015-07-01

    Direct observations during intense warm-air advection over the East Siberian Sea reveal a period of rapid sea-ice melt. A semistationary, high-pressure system north of the Bering Strait forced northward advection of warm, moist air from the continent. Air-mass transformation over melting sea ice formed a strong, surface-based temperature inversion in which dense fog formed. This induced a positive net longwave radiation at the surface while reducing net solar radiation only marginally; the inversion also resulted in downward turbulent heat flux. The sum of these processes enhanced the surface energy flux by an average of ~15 W m-2 for a week. Satellite images before and after the episode show sea-ice concentrations decreasing from > 90% to ~50% over a large area affected by the air-mass transformation. We argue that this rapid melt was triggered by the increased heat flux from the atmosphere due to the warm-air advection.

  11. The contribution of advective fluxes to net ecosystem exchange in a high-elevation, subalpine forest.

    PubMed

    Yi, Chuixiang; Anderson, Dean E; Turnipseed, Andrew A; Burns, Sean P; Sparks, Jed P; Stannard, David I; Monson, Russell K

    2008-09-01

    The eddy covariance technique, which is used in the determination of net ecosystem CO2 exchange (NEE), is subject to significant errors when advection that carries CO2 in the mean flow is ignored. We measured horizontal and vertical advective CO2 fluxes at the Niwot Ridge AmeriFlux site (Colorado, USA) using a measurement approach consisting of multiple towers. We observed relatively high rates of both horizontal (F(hadv)) and vertical (F(vadv)) advective fluxes at low surface friction velocities (u(*)) which were associated with downslope katabatic flows. We observed that F(hadv) was confined to a relatively thin layer (0-6 m thick) of subcanopy air that flowed beneath the eddy covariance sensors principally at night, carrying with it respired CO2 from the soil and lower parts of the canopy. The observed F(vadv) came from above the canopy and was presumably due to the convergence of drainage flows at the tower site. The magnitudes of both F(hadv) and F(vadv) were similar, of opposite sign, and increased with decreasing u(*), meaning that they most affected estimates of the total CO2 flux on calm nights with low wind speeds. The mathematical sign, temporal variation and dependence on u(*) of both F(hadv) and F(vadv) were determined by the unique terrain of the Niwot Ridge site. Therefore, the patterns we observed may not be broadly applicable to other sites. We evaluated the influence of advection on the cumulative annual and monthly estimates of the total CO2 flux (F(c)), which is often used as an estimate of NEE, over six years using the dependence of F(hadv) and F(vadv) on u(*). When the sum of F(hadv) and F(vadv) was used to correct monthly F(c), we observed values that were different from the monthly F(c) calculated using the traditional u(*)-filter correction by--16 to 20 g C x m(-2) x mo(-1); the mean percentage difference in monthly Fc for these two methods over the six-year period was 10%. When the sum of F(hadv) and F(vadv) was used to correct annual Fc

  12. 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.

  13. 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.

  14. Assessment of transient storage exchange and advection-dispersion mechanisms from concentration signatures along breakthrough curves

    NASA Astrophysics Data System (ADS)

    Zaramella, M.; Marion, A.; Lewandowski, J.; Nützmann, G.

    2016-07-01

    Solute transport in rivers is controlled by surface flow hydrodynamics and by transient storage in dead zones, pockets of vegetation and hyporheic sediments where mass exchange and retention are governed by complex mechanisms. The physics of these processes are generally investigated by optimization of transient storage models (TSMs) to experimental data often yielding inconsistent and equifinal parameter sets. Uncertainty on parameters estimation is found to depend not only on the rates of exchange between the stream and storage zones, the stream-water velocity and the stream reach length according to the experimental Damkohler number (DaI), but also on the relative significance between transient storage and longitudinal dispersion on breakthrough curves (BTCs). An optimization strategy was developed and applied to an experimental dataset obtained from tracer tests in a small lowland river, analyzing BTCs generated through tracer injections under different conditions. The method supplies a tool to estimate model parameters from observed data through the analysis of the relative parameter significance. To analyze model performance a double compartment TSM was optimized by a regular fit procedure based on simple root mean square error minimization and by a fit based on a relative significance analysis of mechanism signatures. As a result consistent longitudinal dispersion and transient storage parameters were obtained when the signature targeted optimization was used.

  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. Precipitation, dissolution, and ion exchange processes coupled with a lattice Boltzmann advection diffusion solver

    NASA Astrophysics Data System (ADS)

    Hiorth, A.; Jettestuen, E.; Cathles, L. M.; Madland, M. V.

    2013-03-01

    Pore water chemistry can dramatically affect the mechanical strength of chalk cores and the recovery of oil from them, but despite a great many core experiments, the mechanisms responsible remain unclear. This is in part because no single model is presently available that can address the changes in surface complexes and potential and mineral dissolution and precipitation that occur when fluids of different chemistry are injected. We report here the construction of a lattice Boltzmann model that includes non-linear dissolution-precipitation kinetics, surface complexation, and ion exchange. A link-based boundary condition which allows mineral boundaries to move and porosity to change is shown to converge to a correct representation of the macroscopic pore surface area. We show the chemical LB model developed predicts mineral dissolution and ion exchange similar to those predicted by PHREEQC for similar parameters, and we show how the methods developed can be applied to chalk core experiments where synthetic seawater is flooded through the core at 130 °C.

  17. Satellite formation flying control by mass exchange

    NASA Astrophysics Data System (ADS)

    Ivanov, Danil; Ovchinnikov, Michael; Shestakov, Sergey

    2014-09-01

    Novel approach for formation flying relative motion control is proposed and studied. It is based on a mass exchange between satellites. A certain mass is separated from one satellite in a given direction with a given velocity. It impacts absolutely inelastically another satellite to impart a pulse. The mass exchange causes desired change in a relative motion trajectory of both satellites. The feasibility of such a control approach is shown in the paper. The Hill-Clohessy-Wiltshire equations are used for relative motion representation. The resulting trajectory equations after mass exchange are analytically derived. The control approach is applied to formation reconfiguration, drift-stop and also to relative motion trajectory maintenance under perturbation effect J2. The mass exchange approach is verified by numerical simulations.

  18. 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

  19. 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.

  20. Aerosol composition and properties variation at the ground and over the column under different air masses advection in South Italy.

    PubMed

    Pavese, G; Lettino, A; Calvello, M; Esposito, F; Fiore, S

    2016-04-01

    Aerosol composition and properties variation under the advection of different air masses were investigated, as case studies, by contemporary measurements over the atmospheric column and at the ground in a semi-rural site in South Italy. The absence of local strong sources in this area allowed to characterize background aerosol and to compare particle mixing effects under various atmospheric circulation conditions. Aerosol optical depth (AOD) and Ǻngström parameters from radiometric measurements allowed the detection and identification of polluted, dust, and volcanic atmospheric conditions. AODs were the input for a suitable model to evaluate the columnar aerosol composition, according to six main atmospheric components (water-soluble, soot, sea salt accumulation, sea salt coarse, mineral dus,t and biological). Scanning electron microscope (SEM) analysis of particulate sampled with a 13-stage impactor at the ground showed not only fingerprints typical of the different air masses but also the effects of transport and aging on atmospheric particles, suggesting processes that changed their chemical and optical properties. Background columnar aerosol was characterized by 72% of water-soluble and soot, in agreement with ground-based findings that highlighted 60% of contribution from anthropogenic carbonate particles and soot. In general, a good agreement between ground-based and columnar results was observed. Under the advection of trans-boundary air masses, water-soluble and soot were always present in columnar aerosol, whereas, in variable percentages, sea salt and mineral particles characterized both dust and volcanic conditions. At the ground, sulfates characterized the amorphous matrix produced in finer stages by the evaporation of solutions of organic and inorganic aerosols. Sulfates were also one of the key players involved in heterogeneous chemical reactions, producing complex secondary aerosol, as such clay-sulfate internally mixed particle externally mixed

  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. 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

  5. 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

  6. 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.

  7. Reactive Transport in Porous Media: Pore-scale Mass Exchange between Aqueous Phase and Biofilms

    NASA Astrophysics Data System (ADS)

    Hassanizadeh, S.; Qin, C.

    2013-12-01

    In the presence of water and necessary nutrients, biofilms can grow on soil grain surfaces. They occupy void pore spaces blocking water flow. As a result, some hydrodynamic properties of porous media like porosity and permeability will be reduced. This ultimately leads to a condition known as bioclogging. Also, biofilms can degrade certain compounds. So, the features of bioclogging and biodegradation in porous media with biofilms have given rise to a broad range of environmental and engineering applications, such as bioremediation, biobarriers, microbial enhanced oil recovery, and protection of steel corrosion. To date, a number of macroscale and pore-scale models for describing biodegradation in porous media with biofilms are available in the literature. At the macro scale, to simplify numerical implementation, a ';one-equation' model is normally preferred. In this approach, only the solute concentration in aqueous phase is modeled associated with the consumption of solute in biofilms. Because the solute concentration in biofilms is different from that in aqueous phase, an effectiveness factor may be used in Monod kinetics for relating reaction rate within biofilms to the solute concentration in aqueous phase. Notice that this approach has its validity domains like local equilibrium and reaction-rate limited consumption. Another approach to modeling biodegradation is referred to as a ';two-equation' model, in which one needs to simultaneously track the solute concentrations in both aqueous phase and biofilms. In addition, the two concentrations may be related by a first-order kinetic mass exchange model. This first-rate exchange model is normally represented by a constant mas exchange coefficient multiplied by the concentration difference in the two domains. Here, one may question if complex advection-diffusion-reaction processes can be represented just by a constant mass exchange coefficient. In addition, the kinetic model of mass exchange between aqueous phase

  8. Hydrogen exchange and mass spectrometry: A historical perspective.

    PubMed

    Englander, S Walter

    2006-11-01

    Protein molecules naturally emit streams of information-rich signals in the language of hydrogen exchange concerning the intimate details of their stability, dynamics, function, changes therein, and effects thereon, all resolved to the level of their individual amino acids. The effort to measure protein hydrogen exchange behavior, understand the underlying chemistry and structural physics of hydrogen exchange processes, and use this information to learn about protein properties and function has continued for 50 years. Recent work uses mass spectrometric analysis together with an earlier proteolytic fragmentation method to extend the hydrogen exchange capability to large biologically interesting proteins. This article briefly reviews the advances that have led us to this point and the understanding that has so far been achieved. PMID:16876429

  9. 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%. PMID:22965280

  10. Hydromechanics and heat and mass exchange in weightlessness (Russian book): Table of contents

    NASA Technical Reports Server (NTRS)

    Avduyevskiy, V. S.; Poleshayev, V. I.

    1983-01-01

    The table of contents is given for a book on hydromechanics and heat and mass exchange in weightlessness. The book covers such subjects as hydromechanics, convection and heat and mass exchange, and technological experiments and complicated systems.

  11. Hydrogen exchange mass spectrometry: Are we out of the quicksand?

    PubMed Central

    Iacob, Roxana E.; Engen, John R.

    2012-01-01

    Although the use of hydrogen exchange (HX) mass spectrometry (MS) to study proteins and protein conformation is now over 20 years old, the perception lingers that it still has “issues”. Is this method, in fact, still in the quicksand with many remaining obstacles to overcome? We do not think so. This critical insight addresses the “issues” and explores several broad questions including: have the limitations of HX MS been surmounted and has HX MS achieved “indispensable” status in the pantheon of protein structural analysis tools. PMID:22476891

  12. VAC: Versatile Advection Code

    NASA Astrophysics Data System (ADS)

    Tóth, Gábor; Keppens, Rony

    2012-07-01

    The Versatile Advection Code (VAC) is a freely available general hydrodynamic and magnetohydrodynamic simulation software that works in 1, 2 or 3 dimensions on Cartesian and logically Cartesian grids. VAC runs on any Unix/Linux system with a Fortran 90 (or 77) compiler and Perl interpreter. VAC can run on parallel machines using either the Message Passing Interface (MPI) library or a High Performance Fortran (HPF) compiler.

  13. Analysis of carbohydrates by anion exchange chromatography and mass spectrometry.

    PubMed

    Bruggink, Cees; Maurer, Rolf; Herrmann, Heiko; Cavalli, Silvano; Hoefler, Frank

    2005-08-26

    A versatile liquid chromatographic platform has been developed for analysing underivatized carbohydrates using high performance anion exchange chromatography (HPAEC) followed by an inert PEEK splitter that splits the effluent to the integrated pulsed amperometric detector (IPAD) and to an on-line single quadrupole mass spectrometer (MS). Common eluents for HPAEC such as sodium hydroxide and sodium acetate are beneficial for the amperometric detection but not compatible with electrospray ionisation (ESI). Therefore a membrane-desalting device was installed after the splitter and prior to the ESI interface converting sodium hydroxide into water and sodium acetate into acetic acid. To enhance the sensitivity for the MS detection, 0.5 mmol/l lithium chloride was added after the membrane desalter to form lithium adducts of the carbohydrates. To compare sensitivity of IPAD and MS detection glucose, fructose, and sucrose were used as analytes. A calibration with external standards from 2.5 to 1000 pmole was performed showing a linear range over three orders of magnitude. Minimum detection limits (MDL) with IPAD were determined at 5 pmole levels for glucose to be 0.12 pmole, fructose 0.22 pmole and sucrose 0.11 pmole. With MS detection in the selected ion mode (SIM) the lithium adducts of the carbohydrates were detected obtaining MDL's for glucose of 1.49 pmole, fructose 1.19 pmole, and sucrose 0.36 pmole showing that under these conditions IPAD is 3-10 times more sensitive for those carbohydrates. The applicability of the method was demonstrated analysing carbohydrates in real world samples such as chicory inulin where polyfructans up to a molecular mass of 7000 g/mol were detected as quadrupoly charged lithium adducts. Furthermore mono-, di-, tri-, and oligosaccharides were detected in chicory coffee, honey and beer samples. PMID:16106855

  14. Hydrogen Exchange Mass Spectrometry of Proteins at Langmuir Monolayers.

    PubMed

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

    2015-07-21

    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 whether or not it is able to 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 the isolated use of either method. PMID:26134943

  15. 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.

  16. Recombinant Nepenthesin II for Hydrogen/Deuterium Exchange Mass Spectrometry.

    PubMed

    Yang, Menglin; Hoeppner, Morgan; Rey, Martial; Kadek, Alan; Man, Petr; Schriemer, David C

    2015-07-01

    The pitcher secretions of the Nepenthes genus of carnivorous plants contain a proteolytic activity that is very useful for hydrogen/deuterium exchange mass spectrometry (HX-MS). Our efforts to reconstitute pitcher fluid activity using recombinant nepenthesin I (one of two known aspartic proteases in the fluid) revealed a partial cleavage profile and reduced enzymatic stability in certain HX-MS applications. We produced and characterized recombinant nepenthesin II to determine if it complemented nepenthesin I in HX-MS applications. Nepenthesin II shares many properties with nepenthesin I, such as fast digestion at reduced temperature and pH, and broad cleavage specificity, but in addition, it cleaves C-terminal to tryptophan. Neither enzyme reproduces the C-terminal proline cleavage we observed in the natural extract. Nepenthesin II is considerably more resistant to chemical denaturants and reducing agents than nepenthesin I, and it possesses a stability profile that is similar to that of pepsin. Higher stability combined with the slightly broader cleavage specificity makes nepenthesin II a useful alternative to pepsin and a more complete replacement for pitcher fluid in HX-MS applications. PMID:25993527

  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. Concentration through large advection

    NASA Astrophysics Data System (ADS)

    Aleja, D.; López-Gómez, J.

    2014-11-01

    In this paper we extend the elegant results of Chen, Lam and Lou [6, Section 2], where a concentration phenomenon was established as the advection blows up, to a general class of adventive-diffusive generalized logistic equations of degenerate type. Our improvements are really sharp as we allow the carrying capacity of the species to vanish in some subdomain with non-empty interior. The main technical devices used in the derivation of the concentration phenomenon are Proposition 3.2 of Cano-Casanova and López-Gómez [5], Theorem 2.4 of Amann and López-Gómez [1] and the classical Harnack inequality. By the relevance of these results in spatial ecology, complete technical details seem imperative, because the proof of Theorem 2.2 of [6] contains some gaps originated by an “optimistic” use of Proposition 3.2 of [5]. Some of the general assumptions of [6] are substantially relaxed.

  19. 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...

  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. 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.

  2. Subzero temperature chromatography for reduced back-exchange and improved dynamic range in amide hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Venable, John D; Okach, Linda; Agarwalla, Sanjay; Brock, Ansgar

    2012-11-01

    Amide hydrogen/deuterium exchange is a commonly used technique for studying the dynamics of proteins and their interactions with other proteins or ligands. When coupled with liquid chromatography and mass spectrometry, hydrogen/deuterium exchange provides several unique advantages over other structural characterization techniques including very high sensitivity, the ability to analyze proteins in complex environments, and a large mass range. A fundamental limitation of the technique arises from the loss of the deuterium label (back-exchange) during the course of the analysis. A method to limit loss of the label during the separation stage of the analysis using subzero temperature reversed-phase chromatography is presented. The approach is facilitated by the use of buffer modifiers that prevent freezing. We evaluated ethylene glycol, dimethyl formamide, formamide, and methanol for their freezing point suppression capabilities, effects on peptide retention, and their compatibilities with electrospray ionization. Ethylene glycol was used extensively because of its good electrospray ionization compatibility; however, formamide has potential to be a superior modifier if detrimental effects on ionization can be overcome. It is demonstrated using suitable buffer modifiers that separations can be performed at temperatures as low as -30 °C with negligible loss of the deuterium label, even during long chromatographic separations. The reduction in back-exchange is shown to increase the dynamic range of hydrogen/deuterium exchange mass spectrometry in terms of mixture complexity and the magnitude with which changes in deuteration level can be quantified. PMID:23025328

  3. The relationship between seasonal variations of total-nitrogen and total-phosphorus in rainfall and air mass advection paths in Matsue, Japan

    NASA Astrophysics Data System (ADS)

    Yoshioka, Katsuhiro; Kamiya, Hiroshi; Kano, Yoshihiro; Saki, Yukiko; Yamamuro, Masumi; Ishitobi, Yu

    We collected rainwater samples from every rainfall in Matsue, Japan in order to study variations of nitrogen and phosphorus concentrations over time. The seasonal average concentration by magnitude order of Total Nitrogen (here after T-N) was highest in winter, then in spring, fall, and summer and that of Total Phosphorus (here after T-P) was highest in spring, then in winter, fall, and summer. These seasonal variations were examined in relation to the transportation paths of arrived air masses by using a backward trajectory and rainfall patterns from a surface synoptic weather chart. In winter, continental air masses frequently flow from China or Siberia and the resultant winter rainfall is on many occasions of a continental type. In summer, maritime air masses frequently arrive from the Pacific Ocean and this resultant rainfall therefore was often of maritime type. Looking at average concentrations of T-N and T-P for each rainfall type, continental types were high range and maritime types were low. It was therefore concluded that the monthly average concentration of T-N was affected by continental air masses from northern China in winter and by maritime ones from the Pacific Ocean in summer. The maximum deposition of T-N was caused by this concentration in winter and rainfall depth in summer. Seasonal variation of T-P showed a different fluctuation tendency from T-N, with a maximum concentration in spring, and minimum in summer and fall. T-P was susceptible to the yellow sand phenomenon which maximised T-P deposition in spring.

  4. Experiments in Advective and Turbulent Hyporheic Pumping

    NASA Astrophysics Data System (ADS)

    Mccluskey, A. H.; Grant, S.; Stewardson, M. J.

    2014-12-01

    Hyporheic exchange (HE) is the mixing of stream and subsurface waters beneath the sediment-water interface (SWI). At the patch and reach scales, HE is dominated by periodic upwelling and downwelling zones, induced by pressure variation and processes within the turbulent boundary layer (TBL). This can be caused by (1) the geometry of the stream, imposing a stationary wave at the SWI or (2) by a travelling wave associated with the propagation of turbulent pressure waves generated from the TBL. Case (1) has generally been the favoured model of hyporheic exchange and has been referred to as hyporheic 'pumping' by Elliott and Brooks, and subsequently others. Case (2) can be termed turbulent pumping, and has been proposed as a mechanism to model the combined effects of turbulent dispersion alongside steady-state advection. While this has been represented numerically and analytically, conjecture remains about the physical representation of these combined processes. We present initial results from experiments undertaken to classify the spatial and temporal characteristics of pressure variation at and beneath the SWI, with a periodic sinusoidal geometry of wavelength 0.28m and height 0.02m. As an initial characterisation, the advective flow profile has been examined using time-lapse photography of dyes released across the span of a periodic downwelling zone. These tracer tests confirmed delineation of isolated upwelling and downwelling cells as noted by previous authors in modelling studies. However, their distribution deviates from the typical pumping pattern with increased discharge and stream gradient. Empirical orthogonal function (EOF) analysis of high frequency (250Hz) pressure measurements, sampled at an array along the centroid of the flume underneath one wavelength gave further insight into the spatial distribution of turbulent signatures arising from roughness-generated turbulence. A turbulent frequency of 6-10Hz dominates, however the penetration depth appears to

  5. Vertical air mass exchange driven by the local circulation on the northern slope of Mount Everest

    NASA Astrophysics Data System (ADS)

    Zhou, Libo; Zou, Han; Ma, Shupo; Li, Peng; Zhu, Jinhuan; Huo, Cuiping

    2011-01-01

    To better understand vertical air mass exchange driven by local circulation in the Himalayas, the volume flux of air mass is estimated in the Rongbuk Valley on the northern slope of Mount Everest, based on a volume closure method and wind-profiler measurements during the HEST2006 campaign in June 2006. Vertical air mass exchange was found to be dominated by a strong downward mass transfer from the late morning to late night. The average vertical air volume flux was 0.09 m s-1, which could be equivalent to a daily ventilation of 30 times the enclosed valley volume. This vertical air mass exchange process was greatly affected by the evolution of the South Asian summer monsoon (SASM), with a strong downward transfer during the SASM break stage, and a weak transfer during the SASM active stage.

  6. Mass Dependence of Iron Isotope Fractionation in Fe(II)-Fe(III) Electron Exchange Equilibration

    NASA Astrophysics Data System (ADS)

    Fujii, Yasuhiko; Kim, Sang-Ho; Nomura, Masao; Kawakami, Fumiaki

    2013-02-01

    A one hundred meter long ion-exchange chromatograph was used to establish rigorously the mass effects in the iron isotope fractionation in the Fe(II)-Fe(III) electron exchange equilibration.We used a highly porous, strongly basic anion exchange resin packed in glass columns. The abundance ratios of all natural iron isotopes, 54Fe, 56Fe, 57Fe, and 58Fe, in the effluent at the iron adsorption band boundary were measured with a mass spectrometer. The enrichment correlations among these isotopes were analyzed by three-isotope plots. The results clearly showed that the isotope fractionation of Fe(II)-Fe(III) is governed by the normal mass effect; the iron isotope fractionation is not proportional to the nuclear size, but proportional to the reduced mass difference of the pair of iron isotopes.

  7. 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. PMID:25216897

  8. 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. PMID:26018631

  9. Hydrogen/deuterium exchange on aromatic rings during atmospheric pressure chemical ionization mass spectrometry.

    PubMed

    Davies, Noel W; Smith, Jason A; Molesworth, Peter P; Ross, John J

    2010-04-15

    It has been demonstrated that substituted indoles fully labelled with deuterium on the aromatic ring can undergo substantial exchange back to partial and even fully protonated forms during atmospheric pressure chemical ionisation (APCI) liquid chromatography/mass spectrometry (LC/MS). The degree of this exchange was strongly dependent on the absolute quantity of analyte, the APCI desolvation temperature, the nature of the mobile phase, the mobile phase flow rate and the instrument used. Hydrogen/deuterium (H/D) exchange on several other aromatic ring systems during APCI LC/MS was either undetectable (nitrobenzene, aniline) or extremely small (acetanilide) compared to the effect observed for substituted indoles. This observation has major implications for quantitative assays using deuterium-labelled internal standards and for the detection of deuterium-labelled products from isotopically labelled feeding experiments where there is a risk of back exchange to the protonated form during the analysis. PMID:20213724

  10. 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.

  11. 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.

  12. Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis.

    PubMed

    Kan, Zhong-Yuan; Walters, Benjamin T; Mayne, Leland; Englander, S Walter

    2013-10-01

    Hydrogen exchange technology provides a uniquely powerful instrument for measuring protein structural and biophysical properties, quantitatively and in a nonperturbing way, and determining how these properties are implemented to produce protein function. A developing hydrogen exchange-mass spectrometry method (HX MS) is able to analyze large biologically important protein systems while requiring only minuscule amounts of experimental material. The major remaining deficiency of the HX MS method is the inability to deconvolve HX results to individual amino acid residue resolution. To pursue this goal we used an iterative optimization program (HDsite) that integrates recent progress in multiple peptide acquisition together with previously unexamined isotopic envelope-shape information and a site-resolved back-exchange correction. To test this approach, residue-resolved HX rates computed from HX MS data were compared with extensive HX NMR measurements, and analogous comparisons were made in simulation trials. These tests found excellent agreement and revealed the important computational determinants. PMID:24019478

  13. 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.

  14. 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.

  15. Heat and mass transfer performances on plate fin and tube heat exchangers with dehumidification

    SciTech Connect

    Seshimo, Y.; Ogawa, K.; Marumoto, K.; Fujii, M. )

    1990-09-01

    The authors discuss how they conducted an experimental study on the air side performance of a single-row plate fin and tube heat exchanger in moist air where mass transfer exist under a relatively low driving potential. The results are as follows: The heat transfer with dehumidification is about 20% greater than that with only sensible heat transfer. Also the air side pressure drop is about 30-40% greater. The reason, as clarified by visual observations, comes from the condensate effect. To study how the condensate film affects performance, the presence of the stagnant condensate in the heat exchanger was modeled as an apparent change of the heat exchanger geometry, and the equivalent thickness of the condensate film was calculated from the increase in the air side pressure drop. As a result, if the presence of condensate in the heat exchanger is considered, then the heat transfer with dehumidification can be treated in the same way as with only sensible heat transfer. The analogy between heat and mass transfer does not strictly hold, the experimental results being closed to the Lewis Law.

  16. Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics.

    PubMed

    Rajabi, Khadijeh

    2015-01-01

    A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX. PMID:25318698

  17. 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.

  18. Time-Resolved Pulsed Hydrogen/Deuterium Exchange Mass Spectrometry Probes Gaseous Proteins Structural Kinetics

    NASA Astrophysics Data System (ADS)

    Rajabi, Khadijeh

    2015-01-01

    A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.

  19. Mass exchange between mobile fresh water and immobile saline water in the unsaturated zone

    NASA Astrophysics Data System (ADS)

    Gvirtzman, Haim; Paldor, Nathan; Magaritz, Mordeckai; Bachmat, Yehuda

    1988-10-01

    A profile of tritium concentrations measured in the unsaturated zone in loessial sediments in a semiarid area is interpreted in terms of mobile and immobile water domains, according to a nonequilibrium transport model. The mobile domain is represented by percolating freshwater from both rain and irrigation, and the immobile one is represented by isolated fossil saline water pockets. The two domains are connected by partially saturated narrow passages within dispersed clay minerals. The transport of the mobile water is described by convective-dispersive flow and by mass exchange between the two water domains. The relevant equations with the given initial and boundary conditions are solved numerically, and the simulated profile is adjusted to fit the measured one. In this study we concentrate on examination of the mass exchange law between the two domains. It was assumed that matrix characteristics vary in time due to the dispersion of clays at the interface between fresh and saline waters. Accordingly, a time-dependent mass exchange was adopted, which made it possible to obtain an adequate reconstruction of the measured tritium profile. By using a least squares optimization procedure it was found that the best fit between the simulated and measured profiles is attained when the fraction of mobile water is 30%, and the rate of mass exchange decreases from 0.60 to 0.01 year-1 in 26 years. The proposed model implies is that it is the immobile water domain which contains the memory of the "high tritium period" (thermonuclear tests period) of the 1960s.

  20. The gas exchange of hydrogen-adapted algae as followed by mass spectrometry.

    NASA Technical Reports Server (NTRS)

    Stuart, T. S.; Gaffron, H.

    1972-01-01

    The combination of a mass spectrometer inlet and an oxygen electrode in the same vessel permitted continuous recording of the gas exchange of hydrogenase-containing anaerobically adapted algae. In contrast to conventional manometry, the present method made it possible to discern the simultaneous course of reactions involving O2, CO2, and H2. The experiments strongly support the idea of a balance between the photoproduction and photoutilization of H2.

  1. 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.

  2. Hydrogen Exchange Mass Spectrometry of Functional Membrane-bound Chemotaxis Receptor Complexes

    PubMed Central

    Koshy, Seena S.; Eyles, Stephen J.; Weis, Robert M.; Thompson, Lynmarie K.

    2014-01-01

    The transmembrane signaling mechanism of bacterial chemotaxis receptors is thought to involve changes in receptor conformation and dynamics. The receptors function in ternary complexes with two other proteins, CheA and CheW, that form extended membrane-bound arrays. Previous studies have shown that attractant binding induces a small (~2 Å) piston displacement of one helix of the periplasmic and transmembrane domains towards the cytoplasm, but it is not clear how this signal propagates through the cytoplasmic domain to control the kinase activity of the CheA bound at the membrane-distal tip, nearly 200 Å away. The cytoplasmic domain has been shown to be highly dynamic, which raises the question of how a small piston motion could propagate through a dynamic domain to control CheA kinase activity. To address this, we have developed a method for measuring dynamics of the receptor cytoplasmic fragment (CF) in functional complexes with CheA and CheW. Hydrogen exchange mass spectrometry (HDX-MS) measurements of global exchange of CF demonstrate that CF exhibits significantly slower exchange in functional complexes than in solution. Since the exchange rates in functional complexes are comparable to that of other proteins of similar structure, the CF appears to be a well-structured protein within these complexes, which is compatible with its role in propagating a signal that appears to be a tiny conformational change in the periplasmic and transmembrane domains of the receptor. We also demonstrate the feasibility of this protocol for local exchange measurements, by incorporating a pepsin digest step to produce peptides with 87% sequence coverage and only 20% back exchange. This method extends HDX-MS to membrane-bound functional complexes without detergents that may perturb the stability or structure of the system. PMID:24274333

  3. 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.

  4. Electron capture in 163Ho, overlap plus exchange corrections and neutrino mass

    NASA Astrophysics Data System (ADS)

    Faessler, Amand; Gastaldo, Loredana; Šimkovic, F.

    2015-01-01

    Holmium 163 offers perhaps the best chance to determine the neutrino mass by electron capture (EC). This contribution treats the EC in 163Holmium completely relativistic for the overlap and exchange corrections and the description of the bolometer spectrum. The theoretical expressions are derived consistently in second quantization with the help of Wick's theorem assuming single Slater determinants for the initial Ho and the final Dy atoms with holes in the final n{{s}1/2} and n{{p}1/2} states. One needs no hand waving arguments to derive the exchange terms. It seems, that for the first time the multiplicity of electrons in the orbital overlaps are included in the numerical treatment. Electron capture {{e}-}+p\\to n+{{ν }e} is proportional to the probability to find the captured electron in the parent atom at the nucleus. Non-relativistically this is only possible for n{{s}1/2} electron states. Relativistically also {{p}1/2} electrons have a probability due to the lower part of the relativistic electron spinor, which does not disappear at the origin. Moreover relativistic effects increase by contraction the electron probability at the nucleus. Capture from other states are suppressed. However they can be allowed with smaller intensity due to finite nuclear size. These probabilities are at least three orders smaller than the EC from 3{{s}1/2} and 3{{p}1/2} states. The purpose of this work is to give a consistent relativistic formulation and treatment of the overlap and exchange corrections for EC in 67163Ho to excited atomic states in 66163Dy and to show the influence of the different configurations in the final Dy states. The overlap and exchange corrections are essential for the calorimetric spectrum of the de-excitation of the hole states in dysprosium. The slope of the upper end of the spectrum, which contains the information on the electron neutrino mass, is different. In addition the effect of the finite energy resolution on the spectrum and on the

  5. Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis

    PubMed Central

    Kan, Zhong-Yuan; Walters, Benjamin T.; Mayne, Leland; Englander, S. Walter

    2013-01-01

    Hydrogen exchange technology provides a uniquely powerful instrument for measuring protein structural and biophysical properties, quantitatively and in a nonperturbing way, and determining how these properties are implemented to produce protein function. A developing hydrogen exchange–mass spectrometry method (HX MS) is able to analyze large biologically important protein systems while requiring only minuscule amounts of experimental material. The major remaining deficiency of the HX MS method is the inability to deconvolve HX results to individual amino acid residue resolution. To pursue this goal we used an iterative optimization program (HDsite) that integrates recent progress in multiple peptide acquisition together with previously unexamined isotopic envelope-shape information and a site-resolved back-exchange correction. To test this approach, residue-resolved HX rates computed from HX MS data were compared with extensive HX NMR measurements, and analogous comparisons were made in simulation trials. These tests found excellent agreement and revealed the important computational determinants. PMID:24019478

  6. 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

  7. Analysis of overlapped and noisy hydrogen/deuterium exchange mass spectra.

    PubMed

    Guttman, Miklos; Weis, David D; Engen, John R; Lee, Kelly K

    2013-12-01

    Noisy and overlapped mass spectrometry data hinder the sequence coverage that can be obtained from hydrogen deuterium exchange analysis, and places a limit on the complexity of the samples that can be studied by this technique. Advances in instrumentation have addressed these limits, but as the complexity of the biological samples under investigation increases, these problems are re-encountered. Here we describe the use of binomial distribution fitting with asymmetric linear squares regression for calculating the accurate deuterium content for mass envelopes of low signal or that contain significant overlap. The approach is demonstrated with a test data set of HIV Env gp140 wherein inclusion of the new analysis regime resulted in obtaining exchange data for 42 additional peptides, improving the sequence coverage by 11%. At the same time, the precision of deuterium uptake measurements was improved for nearly every peptide examined. The improved processing algorithms also provide an efficient method for deconvolution of bimodal mass envelopes and EX1 kinetic signatures. All these functions and visualization tools have been implemented in the new version of the freely available software, HX-Express v2. PMID:24018862

  8. Analysis of Overlapped and Noisy Hydrogen/Deuterium Exchange Mass Spectra

    NASA Astrophysics Data System (ADS)

    Guttman, Miklos; Weis, David D.; Engen, John R.; Lee, Kelly K.

    2013-12-01

    Noisy and overlapped mass spectrometry data hinder the sequence coverage that can be obtained from hydrogen deuterium exchange analysis, and places a limit on the complexity of the samples that can be studied by this technique. Advances in instrumentation have addressed these limits, but as the complexity of the biological samples under investigation increases, these problems are re-encountered. Here we describe the use of binomial distribution fitting with asymmetric linear squares regression for calculating the accurate deuterium content for mass envelopes of low signal or that contain significant overlap. The approach is demonstrated with a test data set of HIV Env gp140 wherein inclusion of the new analysis regime resulted in obtaining exchange data for 42 additional peptides, improving the sequence coverage by 11 %. At the same time, the precision of deuterium uptake measurements was improved for nearly every peptide examined. The improved processing algorithms also provide an efficient method for deconvolution of bimodal mass envelopes and EX1 kinetic signatures. All these functions and visualization tools have been implemented in the new version of the freely available software, HX-Express v2.

  9. 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).

  10. 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.

  11. 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.

  12. Structural Analysis of Diheme Cytochrome c by Hydrogen–Deuterium Exchange Mass Spectrometry and Homology Modeling

    PubMed Central

    2015-01-01

    A lack of X-ray or nuclear magnetic resonance structures of proteins inhibits their further study and characterization, motivating the development of new ways of analyzing structural information without crystal structures. The combination of hydrogen–deuterium exchange mass spectrometry (HDX-MS) data in conjunction with homology modeling can provide improved structure and mechanistic predictions. Here a unique diheme cytochrome c (DHCC) protein from Heliobacterium modesticaldum is studied with both HDX and homology modeling to bring some definition of the structure of the protein and its role. Specifically, HDX data were used to guide the homology modeling to yield a more functionally relevant structural model of DHCC. PMID:25138816

  13. Ion Exchange Chromatography and Mass Spectrometric Methods for Analysis of Cadmium-Phytochelatin (II) Complexes

    PubMed Central

    Merlos Rodrigo, Miguel Angel; Cernei, Natalia; Kominkova, Marketa; Zitka, Ondrej; Beklova, Miroslava; Zehnalek, Josef; Kizek, Rene; Adam, Vojtech

    2013-01-01

    In this study, in vitro formed Cd-phytochelatin (PC2) complexes were characterized using ion exchange chromatography (IEC) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The ratio of both studied compounds as well as experimental conditions were optimized. The highest yield of the complex was observed under an applied concentration of 100 µg·mL−1 PC2 and 100 µg·mL−1 of CdCl2. The data obtained show that IEC in combination with MALDI-TOF is a reliable and fast method for the determination of these complexes. PMID:23538727

  14. Experimental studies of heat and mass exchange phenomena in the two-component heat pipe

    NASA Astrophysics Data System (ADS)

    Baum, J. M.; Ivanovskii, M. N.; Serbin, V. I.; Iurov, S. S.

    The results of the experimental studies of the two-component heat pipe performance are presented in this paper. The water/ethanol mixture was used as the working fluid. The qualitative mechanism of mass exchange in different sections of the heat pipe is suggested as a model. The value of the power transferred by the heat pipe, as well as the correlation of the evaporator, the condenser, and the transport section lengths practically do not influence the extent of separation of the components in the heat pipe.

  15. The influence of advection on the short term CO2-budget in and above a forest canopy

    NASA Astrophysics Data System (ADS)

    Feigenwinter, C.; Vogt, R.; Bernhofer, C.

    2003-04-01

    The investigation of advective effects in complex terrain requires an experimental setup, which is capable to precisely measure the horizontal concentration gradients of a property (i.e. CO2). For this purpose, the CARBOEUROFLUX site in Tharandt (Germany) was completed with additional measurements to account for the entire mass balance of CO2 in a soil-vegetation-atmosphere volume during the AFO 2000 VERTIKO MORE 1 campaign (Sep/Oct 2001) in close cooperation with IHM TU Dresden. Net Ecosystem Exchange is calculated by the conservation equation, in which the horizontal advection term is undoubtedly the less known and less investigated term. The large scatter of horizontal and vertical advection during 13 consecutive days of available 30-min values is supposed to be mainly natural and not due to measurement errors. The latter were minimized by measuring the horizontal CO2 concentration differences at the three edges of a prism volume at two heights (2 m and 26 m a.g.l.) with the same IRGA gas analyser additionally to the single profile measurements at 7 levels at each edge point. Wind vectors were simultaneously measured at two levels (0.5 m and 2.5 m) in the trunk space with carefully calibrated sonics. From these measurements profiles of the horizontal CO2 gradient (amount and direction) and of the mean horizontal wind vector are constructed. These profiles are supposed to be representative for the closer surroundings of the site. The horizontal advection in a certain layer depends essentially on the horizontal wind vector and CO2 gradient (amount and direction). It is very sensitive to smallest changes in input variables and thus, their derivation from profile measurements is actually the crucial task. It is shown that the direction of the horizontal concentration gradient as well as the horizontal wind vector is often height dependent. A minimum and a maximum scenario for the horizontal advection term gives gain of 10..30 g CO2 m-2 d-1 compared to a mean loss of

  16. Conformational changes in oxidatively stressed monoclonal antibodies studied by hydrogen exchange mass spectrometry

    PubMed Central

    Burkitt, William; Domann, Paula; O'Connor, Gavin

    2010-01-01

    Oxidation of methionine residues in biopharmaceuticals is a common and often unwanted modification that frequently occurs during their manufacture and storage. It often results in a lack of stability and biological function of the product, necessitating continuous testing for the modification throughout the product shelf life. A major class of biopharmaceutical products are monoclonal antibodies (mAbs), however, techniques for their detailed structural analysis have until recently been limited. Hydrogen/deuterium exchange mass spectrometry (HXMS) has recently been successfully applied to the analysis of mAbs. Here we used HXMS to identify and localise the structural changes that occurred in a mAb (IgG1) after accelerated oxidative stress. Structural alterations in a number of segments of the Fc region were observed and these related to oxidation of methionine residues. These included a large change in the hydrogen exchange profile of residues 247–253 of the heavy chain, while smaller changes in hydrogen exchange profile were identified for peptides that contained residues in the interface of the CH2 and CH3 domains. PMID:20162626

  17. Tag and Capture Flow Hydrogen Exchange Mass Spectrometry with a Fluorous-Immobilized Probe.

    PubMed

    Marcsisin, Sean R; Liptak, Cary; Marineau, Jason; Bradner, James E; Engen, John R

    2015-06-16

    Analysis of complex mixtures of proteins by hydrogen exchange (HX) mass spectrometry (MS) is limited by one's ability to resolve the protein(s) of interest from the proteins that are not of interest. One strategy for overcoming this problem is to tag the target protein(s) to allow for rapid removal from the mixture for subsequent analysis. Here we illustrate a new solution involving fluorous conjugation of a retrievable probe. The appended fluorous tag allows for facile immobilization on a fluorous surface. When a target protein is passed over the immobilized probe molecule, it can be efficiently captured and then exposed to a flowing stream of deuterated buffer for hydrogen exchange. The utility of this method is illustrated for a model system of the Elongin BC protein complex bound to a peptide from HIV Vif. Efficient capture is demonstrated, and deuteration when immobilized was identical to deuteration in conventional solution-phase hydrogen exchange MS. Protein captured from a crude bacterial cell lysate could also be deuterated without the need for separate purification steps before HX MS. The advantages and disadvantages of the method are discussed in light of miniaturization and automation. PMID:26023704

  18. 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.

  19. Many overlapping peptides for protein hydrogen exchange experiments by the fragment separation-mass spectrometry method.

    PubMed

    Mayne, Leland; Kan, Zhong-Yuan; Chetty, Palaniappan Sevugan; Ricciuti, Alec; Walters, Benjamin T; Englander, S Walter

    2011-11-01

    Measurement of the naturally occurring hydrogen exchange (HX) behavior of proteins can in principle provide highly resolved thermodynamic and kinetic information on protein structure, dynamics, and interactions. The HX fragment separation-mass spectrometry method (HX-MS) is able to measure hydrogen exchange in biologically important protein systems that are not accessible to NMR methods. In order to achieve high structural resolution in HX-MS experiments, it will be necessary to obtain many sequentially overlapping peptide fragments and be able to identify and analyze them efficiently and accurately by mass spectrometry. This paper describes operations which, when applied to four different proteins ranging in size from 140 to 908 residues, routinely provides hundreds of useful unique peptides, covering the entire protein length many times over. Coverage in terms of the average number of peptide fragments that span each amino acid exceeds 10. The ability to achieve these results required the integrated application of experimental methods that are described here and a computer analysis program, called ExMS, described in a following paper. PMID:21952777

  20. Exchange coupling between silicon donors: The crucial role of the central cell and mass anisotropy

    NASA Astrophysics Data System (ADS)

    Pica, G.; Lovett, B. W.; Bhatt, R. N.; Lyon, S. A.

    2014-06-01

    Donors in silicon are now demonstrated as one of the leading candidates for implementing qubits and quantum information processing. Single qubit operations, measurements, and long coherence times are firmly established, but progress on controlling two qubit interactions has been slower. One reason for this is that the interdonor exchange coupling has been predicted to oscillate with separation, making it hard to estimate in device designs. We present a multivalley effective mass theory of a donor pair in silicon, including both a central cell potential and the effective mass anisotropy intrinsic in the Si conduction band. We are able to accurately describe the single donor properties of valley-orbit coupling and the spatial extent of donor wave functions, highlighting the importance of fitting measured values of hyperfine coupling and the orbital energy of the 1s levels. Ours is a simple framework that can be applied flexibly to a range of experimental scenarios, but it is nonetheless able to provide fast and reliable predictions. We use it to estimate the exchange coupling between two donor electrons and we find a smoothing of its expected oscillations, and predict a monotonic dependence on separation if two donors are spaced precisely along the [100] direction.

  1. 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. PMID:11298444

  2. 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.

  3. 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.

  4. 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. PMID:27176431

  5. Advection, diffusion, and delivery over a network

    NASA Astrophysics Data System (ADS)

    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.

  6. Numerical simulation of life cycles of advection warm fog

    NASA Technical Reports Server (NTRS)

    Hung, R. J.; Vaughan, O. H.

    1977-01-01

    The formation, development and dissipation of advection warm fog is investigated. The equations employed in the model include the equation of continuity, momentum and energy for the descriptions of density, wind component and potential temperature, respectively, together with two diffusion equations for the modification of water-vapor mixing ratio and liquid-water mixing ratios. A description of the vertical turbulent transfer of heat, moisture and momentum has been taken into consideration. The turbulent exchange coefficients adopted in the model are based on empirical flux-gradient relations.

  7. 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

  8. 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

  9. Pulsed hydrogen/deuterium exchange mass spectrometry for time-resolved membrane protein folding studies.

    PubMed

    Khanal, Anil; Pan, Yan; Brown, Leonid S; Konermann, Lars

    2012-12-01

    Kinetic folding experiments by pulsed hydrogen/deuterium exchange (HDX) mass spectrometry (MS) are a well-established tool for water-soluble proteins. To the best of our knowledge, the current study is the first that applies this approach to an integral membrane protein. The native state of bacteriorhodopsin (BR) comprises seven transmembrane helices and a covalently bound retinal cofactor. BR exposure to sodium dodecyl sulfate (SDS) induces partial unfolding and retinal loss. We employ a custom-built three-stage mixing device for pulsed-HDX/MS investigations of BR refolding. The reaction is triggered by mixing SDS-denatured protein with bicelles. After a variable folding time (10 ms to 24 h), the protein is exposed to excess D(2) O buffer under rapid exchange conditions. The HDX pulse is terminated by acid quenching after 24 ms. Subsequent off-line analysis is performed by size exclusion chromatography and electrospray MS. These measurements yield the number of protected backbone N-H sites as a function of folding time, reflecting the recovery of secondary structure. Our results indicate that much of the BR secondary structure is formed quite late during the reaction, on a time scale of 10 s and beyond. It is hoped that in the future it will be possible to extend the pulsed-HDX/MS approach employed here to membrane proteins other than BR. PMID:23280751

  10. Isotopic exchange during derivatization of platelet activating factor for gas chromatography-mass spectrometry

    SciTech Connect

    Haroldsen, P.E.; Gaskell, S.J.; Weintraub, S.T.; Pinckard, R.N. )

    1991-04-01

    One approach to the quantitative analysis of platelet activating factor (PAF, 1-O-alkyl-2-acetyl-sn-glycerol-3-phosphocholine; also referred to as AGEPC, alkyl glyceryl ether phosphocholine) is hydrolytic removal of the phosphocholine group and conversion to an electron-capturing derivative for gas chromatography-negative ion mass spectrometry. (2H3)Acetyl-AGEPC has been commonly employed as an internal standard. When 1-hexadecyl-2-(2H3)acetyl glycerol (obtained by enzymatic hydrolysis of (2H3)-C16:0 AGEPC) is treated with pentafluorobenzoyl chloride at 120 degrees C, the resulting 3-pentafluorobenzoate derivative shows extensive loss of the deuterium label. This exchange is evidently acid-catalyzed since derivatization of 1-hexadecyl-2-acetyl glycerol under the same conditions in the presence of a trace of 2HCl results in the incorporation of up to three deuterium atoms. Isotope exchange can be avoided if the reaction is carried out at low temperature in the presence of base. Direct derivatization of (2H3)-C16:0 AGEPC by treatment with pentafluorobenzoyl chloride or heptafluorobutyric anhydride also results in loss of the deuterium label. The use of (13C2)-C16:0 AGEPC as an internal standard is recommended for rigorous quantitative analysis.

  11. 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.

  12. Hydrogen/Deuterium Exchange Mass Spectrometry Applied to IL-23 Interaction Characteristics: Potential Impact for Therapeutics

    PubMed Central

    Iacob, Roxana E.; Krystek, Stanley R.; Huang, Richard Y.-C.; Wei, Hui; Tao, Li; Lin, Zheng; Morin, Paul E.; Doyle, Michael L.; Tymiak, Adrienne A.; Engen, John R.

    2015-01-01

    Interleukin-23 (IL-23) is an important therapeutic target for the treatment of inflammatory diseases. Adnectins are targeted protein therapeutics that are derived from domain III of human fibronectin, and have similar protein scaffold to antibodies. A specific adnectin (Adnectin 2) was identified to bind to IL-23 and compete with IL-23/IL-23R interaction, being a potential protein therapeutic. Hydrogen/deuterium exchange mass spectrometry (HDX MS) and computational methods were applied to probe the binding interactions between IL-23 and Adnectin2 and to determine the correlation between the two orthogonal methods. This review article summarizes the current structural knowledge about Il-23 and it focuses on the applicability of HDX MS to investigate the higher order structure of proteins, which plays an important role for the discovery of new and improved biotherapeutics. PMID:25711416

  13. A mass balance method for non-intrusive measurements of surface-air trace gas exchange

    NASA Astrophysics Data System (ADS)

    Denmead, O. T.; Harper, L. A.; Freney, J. R.; Griffith, D. W. T.; Leuning, R.; Sharpe, R. R.

    A mass balance method is described for calculating gas production from a surface or volume source in a small test plot from measurements of differences in the horizontal fluxes of the gas across upwind and downwind boundaries. It employs a square plot, 24 m×24 m, with measurements of gas concentration at four heights (up to 3.5 m) along each of the four boundaries. Gas concentrations are multiplied by the appropriate vector winds to yield the horizontal fluxes at each height on each boundary. The difference between these fluxes integrated over downwind and upwind boundaries represents production. Illustrations of the method, which involve exchanges of methane and carbon dioxide, are drawn from experiments with landfills, pastures and grazing animals. Tests included calculation of recovery rates from known gas releases and comparisons with a conventional micrometeorological approach and a backward dispersion model. The method performed satisfactorily in all cases. Its sensitivity for measuring exchanges of CO 2, CH 4 and N 2O in various scenarios was examined. As employed by us, the mass balance method can suffer from errors arising from the large number of gas analyses required for a flux determination, and becomes unreliable when there are light winds and variable wind directions. On the other hand, it is non-disturbing, has a simple theoretical basis, is independent of atmospheric stability or the shape of the wind profile, and is appropriate for flux measurement in situations where conventional micrometeorological methods can not be used, e.g. for small plots, elevated point sources, and heterogeneous surface sources.

  14. Probing protein dynamics and function under native and mildly denaturing conditions with hydrogen exchange and mass spectrometry

    NASA Astrophysics Data System (ADS)

    Kaltashov, Igor A.

    2005-02-01

    A combination of hydrogen exchange and mass spectrometry emerged in recent years as a powerful experimental tool capable of probing both structural and dynamic features of proteins. Although its concept is very simple, the interpretation of experimental data is not always straightforward, as a combination of chemical reactions (isotope exchange) and dynamic processes within protein molecules give rise to convoluted exchange patterns. This paper provides a historical background of this technique, candid assessment of its current state and limitations and a discussion of promising recent developments that can result in tremendous improvements and a dramatic expansion of the scope of its applications.

  15. Measurement of advection of CO2 over grasslands in complex terrain in the Alps

    NASA Astrophysics Data System (ADS)

    Zhao, Peng; Hammerle, Albin; Wohlfahrt, Georg

    2015-04-01

    The role of advection is often ignored in the estimation of net ecosystem exchange (NEE) of CO2 in ecosystems. However, some studies reported that more realistic estimates of night-time NEE could be gathered if horizontal and vertical advections are included. While most of previous advection experiments have been conducted in forest ecosystems, grassland ecosystems have a great advantage as measurements of advection can be realised with smaller infrastructure and thus less experimental effort. In a preliminary simplified study, advection showed an important contribution to NEE during night time at a sub-alpine grassland site. This three-year program is focused on the role of advection for NEE of grassland ecosystems in complex terrain in the Alps. We are going to carry out field campaigns at four sites which cover a range of terrain types typical for mountains with varying degrees of complexity, including a valley-bottom site, a steep-slope site, a mixed-terrain site, and an undulating-terrain site. Observations will take place in a notional control volume with a length varying from 50 m to 5 m at each site in order to quantify the effects of horizontal spatial scale on advection estimates. The observations at each site include vertical flux of CO2 measured by eddy-covariance technique, horizontal and vertical advections of CO2 calculated from the measurement of wind components and CO2 gradients, and NEE measured by chambers. Among all, the measurement of the horizontal advection of CO2 needs many efforts because of small-scale variability in sources/sinks of CO2. We are going to use tubes with multiple inlets, which allows sampling at multiple positions across the faces at three heights of the control volume. Thus, we would be able to quantify the contribution of advection to NEE at different grassland sites situated in complex terrain in the Alps, and to quantify the effect of spatial scale of advection measurements with a given experimental setup and accuracy on

  16. Analysis of Amadori compounds by high-performance cation exchange chromatography coupled to tandem mass spectrometry.

    PubMed

    Davidek, Tomas; Kraehenbuehl, Karin; Devaud, Stéphanie; Robert, Fabien; Blank, Imre

    2005-01-01

    High-performance cation exchange chromatography coupled to tandem mass spectrometry or electrochemical detection was found to be an efficient tool for analyzing Amadori compounds derived from hexose and pentose sugars. The method allows rapid separation and identification of Amadori compounds, while benefiting from the well-known advantages of mass spectrometry, such as specificity and sensitivity. Glucose- and xylose-derived Amadori compounds of several amino acids, such as glycine, alanine, valine, leucine/isoleucine, methionine, proline, phenylalanine, and glutamic acid, were separated or discriminated using this new method. The method is suitable for the analysis of both model reaction mixtures and food products. Fructosylglutamate was found to be the major Amadori compound in dried tomatoes (approximately 1.5 g/100 g) and fructosylproline in dried apricots (approximately 0.2 g/100 g). Reaction of xylose and glycine at 90 degrees C (pH 6) for 2 h showed rapid formation of xylulosylglycine (approximately 12 mol %, 15 min) followed by slow decrease over time. Analysis of pentose-derived Amadori compounds is shown for the first time, which represents a major breakthrough in studying occurrence, formation, and decomposition of these labile Maillard intermediates. PMID:15623289

  17. Estimating groundwater exchange with lakes: 1. The stable isotope mass balance method

    USGS Publications Warehouse

    Krabbenhoft, David P.; Bowser, Carl J.; Anderson, Mary P.; Valley, John W.

    1990-01-01

    Groundwater inflow and outflow contributions to the hydrologic budget of lakes can be determined using a stable isotope (18O/16O) mass balance method. The stable isotope method provides a way of integrating the spatial and temporal complexities of the flow field around a lake, thereby offering an appealing alternative to the traditional time and labor intensive methods using seepage meters and an extensive piezometer network. In this paper the method is applied to a lake in northern Wisconsin, demonstrating that it can be successfully applied to lakes in the upper midwest where thousands of similar lakes exist. Inflow and outflow rates calculated for the Wisconsin lake using the isotope mass balance method are 29 and 54 cm/yr, respectively, which compare well to estimates, derived independently using a three-dimensional groundwater flow and solute transport model, of 20 and 50 cm/yr. Such a favorable comparison lends confidence to the use of the stable isotope method to estimate groundwater exchange with lakes. In addition, utilization of stable isotopes in studies of groundwater-lake systems lends insight into mixing processes occurring in the unsaturated zone and in the aquifer surrounding the lake and verifies assumed flow paths based on head measurements in piezometers.

  18. Modeling solute advection coupled with sorption kinetics in heterogeneous formations

    NASA Astrophysics Data System (ADS)

    Selroos, Jan-Olof; Cvetkovic, Vladimir

    1992-05-01

    A method for coupling sorption kinetics and solute advection in particle-tracking models is proposed; this method is efficient for the case where sorption rate coefficients can be assumed constant field scale parameters. A simulation example of reactive solute advection in two-dimensional heterogeneous porous media is presented. The effect of sorption kinetics on solute advection is investigated. Nonequilibrium effects are exhibited as enhanced tailing in the solute breakthrough. Because high variability in the hydraulic conductivity also yields enhanced tailing, the nonequilibrium effect is more pronounced for the case of low variability. Moreover, it may be difficult to distinguish cases of low variability with nonequilibrium sorption from cases of high variability with equilibrium sorption. A comparison of Monte Carlo ensemble results is made with an analytical model for the mass arrival of kinetically sorbing solute in heterogeneous porous media obtained using first-order perturbation. The comparison indicates that the analytical model provides reasonable approximations of the expected solute breakthrough if the variance of the natural logarithm of the hydraulic conductivity is smaller than 1.

  19. Laser speckle contrast imaging is sensitive to advective flux

    NASA Astrophysics Data System (ADS)

    Khaksari, Kosar; Kirkpatrick, Sean J.

    2016-07-01

    Unlike laser Doppler flowmetry, there has yet to be presented a clear description of the physical variables that laser speckle contrast imaging (LSCI) is sensitive to. Herein, we present a theoretical basis for demonstrating that LSCI is sensitive to total flux and, in particular, the summation of diffusive flux and advective flux. We view LSCI from the perspective of mass transport and briefly derive the diffusion with drift equation in terms of an LSCI experiment. This equation reveals the relative sensitivity of LSCI to both diffusive flux and advective flux and, thereby, to both concentration and the ordered velocity of the scattering particles. We demonstrate this dependence through a short series of flow experiments that yield relationships between the calculated speckle contrast and the concentration of the scatterers (manifesting as changes in scattering coefficient), between speckle contrast and the velocity of the scattering fluid, and ultimately between speckle contrast and advective flux. Finally, we argue that the diffusion with drift equation can be used to support both Lorentzian and Gaussian correlation models that relate observed contrast to the movement of the scattering particles and that a weighted linear combination of these two models is likely the most appropriate model for relating speckle contrast to particle motion.

  20. Hydrogen-deuterium exchange mass spectrometry for investigation of backbone dynamics of oxidized and reduced cytochrome P450cam.

    PubMed

    Hamuro, Yoshitomo; Molnar, Kathleen S; Coales, Stephen J; OuYang, Bo; Simorellis, Alana K; Pochapsky, Thomas C

    2008-02-01

    Backbone dynamics of the camphor monoxygenase cytochrome P450(cam) (CYP101) as a function of oxidation/ligation state of the heme iron were investigated via hydrogen/deuterium exchange (H/D exchange) as monitored by mass spectrometry. Main chain amide NH hydrogens can exchange readily with solvent and the rate of this exchange depends upon, among other things, dynamic fluctuations in local structural elements. A fluxional region of the polypeptide will exchange more quickly with solvent than one that is more constrained. In most regions of the enzyme, exchange rates were similar between oxidized high-spin camphor-bound and reduced camphor- and CO-bound CYP101 (CYP-S and CYP-S-CO, respectively). However, in regions of the protein that have previously been implicated in substrate access by structural and molecular dynamics investigations, the reduced enzyme shows significantly slower exchange rates than the oxidized CYP-S. This observation corresponds to increased flexibility of the oxidized enzyme relative to the reduced form. Structural features previously found to be perturbed in CYP-S-CO upon binding of the biologically relevant effector and reductant putidaredoxin (Pdx) as determined by nuclear magnetic resonance are also more protected from exchange in the reduced state. To our knowledge, this study represents the first experimental investigation of backbone dynamics within the P450 family using this methodology. PMID:18023482

  1. 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.

  2. Simultaneous reduction and digestion of proteins with disulfide bonds for hydrogen/deuterium exchange monitored by mass spectrometry.

    PubMed

    Zhang, Hui-Min; McLoughlin, Shaun M; Frausto, Stephen D; Tang, Hengli; Emmett, Mark R; Marshall, Alan G

    2010-02-15

    Proteolyzed peptides provide the basis for mass-analyzed hydrogen/deuterium exchange (HDX) for mapping solvent access to various segments of solution-phase proteins. Aspergillus saitoi protease type XIII and porcine pepsin can generate peptides of overlapping sequences and high sequence coverage. However, if disulfide bonds are present, proteolysis can be severely limited, particularly in the vicinity of the disulfide linkage(s). Disulfide bonds cannot be reduced before or during the H/D exchange reaction without affecting the protein higher-order structure. Here, we demonstrate simultaneous quench/digestion/reduction following H/D exchange, for subsequent mass analysis. Proteolysis is conducted in the presence of tris(2-carboxyethyl)phosphine hydrochloride (TCEP.HCl) and urea, and all other steps of the H/D exchange and analysis are maintained. This method yields dramatically increased sequence coverage and localization of solvent-exposed segments for mass-analyzed solution-phase H/D exchange of proteins containing disulfide bonds. PMID:20099838

  3. Advection fog formation in a polluted atmosphere

    SciTech Connect

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

    1981-01-01

    Large quantities of atmospheric aerosols with composition SO/sub 4//sup 2 -/, NO/sub 3//sup -/ and NH/sub 4//sup +/ have been detected in highly industrialized areas. The major portions of aerosol products are the results of energy related fuel combustion. Both microphysical and macrophysical processes are considered in investigating the time dependent evolution of the saturation spectra of condensation nuclei associated with both polluted and clean atmospheres during the time periods of advection fog formation. The results show that the condensation nuclei associated with a polluted atmosphere provide more favorable conditions than condensation nuclei associated with a clean atmosphere to produce dense advection fog, and that attaining a certain degree of supersaturation is not necessarily required for the formation of advection fog with condensation nuclei associated with a polluted atmosphere for monodisperse distribution.

  4. Antidiffusive velocities for multipass donor cell advection

    SciTech Connect

    Margolin, L.; Smolarkiewicz, P.K.

    1999-01-01

    Multidimensional positive definite advection transport algorithm (MPDATA) is an iterative process for approximating the advection equation, which uses a donor cell approximation to compensate for the truncation error of the originally specified donor cell scheme. This step may be repeated an arbitrary number of times, leading to successfully more accurate solutions to the advection equation. In this paper, the authors show how to sum the successive approximations analytically to find a single antidiffusive velocity that represents the effects of an arbitrary number of passes. The analysis is first done in one dimension to illustrate the method and then is repeated in two dimensions. The existence of cross terms in the truncation analysis of the two-dimensional equations introduces an extra complication into the calculation. The authors discuss the implementation of the antidiffusive velocities and provide some examples of applications, including a third-order accurate scheme.

  5. MAGNETIC ADVECTION DUE TO DIFFUSIVITY GRADIENTS

    NASA Astrophysics Data System (ADS)

    Zita, E. J.

    2009-12-01

    We derive and discuss an important source of advection of magnetic fields in plasmas, for a completely general case. Magnetic diffusivity is proportional to electrical resistivity: where the value this parameter is high, it is well known that magnetic fields can leak (or diffuse) rapidly into (or out) of the plasma. Magnetohydrodynamic lore has it that where gradients, or changes in space, of the value of the diffusivity are high, magnetic fields can have enhanced flow (or advection). We derive this phenomenon rigorously, compare our results to other work in the literature, and discuss its implications, especially for kinematic dynamos. As an extra mathematical bonus, we find that the magnetic advection due to diffusivity gradients can be expressed in terms of a diffusion equation within the induction equation, making its computational implementation especially simple.

  6. 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

  7. A numerical investigation of coherent structures and mass exchange processes in channel flow with two lateral submerged groynes

    NASA Astrophysics Data System (ADS)

    McCoy, Andrew; Constantinescu, George; Weber, Larry

    2007-05-01

    Large eddy simulation is used to investigate the dynamics of the main coherent structures present in the flow around two vertical submerged groynes situated in a long flatbed open channel. The mass exchange processes between the embayment region and the main channel are investigated by studying the ejection of a contaminant introduced instantaneously inside the embayment. The instantaneous and mean structure of the horseshoe vortex system forming at the base of the upstream groyne and the bed shear distributions that determine the evolution of the scour in the groyne region are investigated. It is found that the amplification of the bed shear stress in the accelerating region around the tip of the upstream groyne is around one order of magnitude larger relative to the mean bed shear stress in the incoming flow. Analysis of the instantaneous flow fields shows that the eddies that are shed inside the horizontal and vertical detached shear layers play an important role in controlling the mass exchange at the lateral and roof interfaces. It is found that most of the pollutant leaves the embayment through the roof and bottom lateral sections. The overall mass exchange process is qualitatively different and substantially accelerated compared to the case when the groynes are emerged. However, it is shown that similar to the emerged case, the decay of the mass of contaminant within the embayment cannot be characterized by a unique value of the exchange coefficient used in simple dead zone theory models.

  8. Nepenthesin from monkey cups for hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Rey, Martial; Yang, Menglin; Burns, Kyle M; Yu, Yaping; Lees-Miller, Susan P; Schriemer, David C

    2013-02-01

    Studies of protein dynamics, structure and interactions using hydrogen/deuterium exchange mass spectrometry (HDX-MS) have sharply increased over the past 5-10 years. The predominant technology requires fast digestion at pH 2-3 to retain deuterium label. Pepsin is used almost exclusively, but it provides relatively low efficiency under the constraints of the experiment, and a selectivity profile that renders poor coverage of intrinsically disordered regions. In this study we present nepenthesin-containing secretions of the pitcher plant Nepenthes, commonly called monkey cups, for use in HDX-MS. We show that nepenthesin is at least 1400-fold more efficient than pepsin under HDX-competent conditions, with a selectivity profile that mimics pepsin in part, but also includes efficient cleavage C-terminal to "forbidden" residues K, R, H, and P. High efficiency permits a solution-based analysis with no detectable autolysis, avoiding the complication of immobilized enzyme reactors. Relaxed selectivity promotes high coverage of disordered regions and the ability to "tune" the mass map for regions of interest. Nepenthesin-enriched secretions were applied to an analysis of protein complexes in the nonhomologous end-joining DNA repair pathway. The analysis of XRCC4 binding to the BRCT domains of Ligase IV points to secondary interactions between the disordered C-terminal tail of XRCC4 and remote regions of the BRCT domains, which could only be identified with a nepenthesin-based workflow. HDX data suggest that stalk-binding to XRCC4 primes a BRCT conformation in these remote regions to support tail interaction, an event which may be phosphoregulated. We conclude that nepenthesin is an effective alternative to pepsin for all HDX-MS applications, and especially for the analysis of structural transitions among intrinsically disordered proteins and their binding partners. PMID:23197791

  9. 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.

  10. Protein Folding-How and Why: By Hydrogen Exchange, Fragment Separation, and Mass Spectrometry.

    PubMed

    Englander, S Walter; Mayne, Leland; Kan, Zhong-Yuan; Hu, Wenbing

    2016-07-01

    Advanced hydrogen exchange (HX) methodology can now determine the structure of protein folding intermediates and their progression in folding pathways. Key developments over time include the HX pulse labeling method with nuclear magnetic resonance analysis, the fragment separation method, the addition to it of mass spectrometric (MS) analysis, and recent improvements in the HX MS technique and data analysis. Also, the discovery of protein foldons and their role supplies an essential interpretive link. Recent work using HX pulse labeling with MS analysis finds that a number of proteins fold by stepping through a reproducible sequence of native-like intermediates in an ordered pathway. The stepwise nature of the pathway is dictated by the cooperative foldon unit construction of the protein. The pathway order is determined by a sequential stabilization principle; prior native-like structure guides the formation of adjacent native-like structure. This view does not match the funneled energy landscape paradigm of a very large number of folding tracks, which was framed before foldons were known and is more appropriate for the unguided residue-level search to surmount an initial kinetic barrier rather than for the overall unfolded-state to native-state folding pathway. PMID:27145881

  11. Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry

    PubMed Central

    Hu, Wenbing; Walters, Benjamin T.; Kan, Zhong-Yuan; Mayne, Leland; Rosen, Laura E.; Marqusee, Susan; Englander, S. Walter

    2013-01-01

    The kinetic folding of ribonuclease H was studied by hydrogen exchange (HX) pulse labeling with analysis by an advanced fragment separation mass spectrometry technology. The results show that folding proceeds through distinct intermediates in a stepwise pathway that sequentially incorporates cooperative native-like structural elements to build the native protein. Each step is seen as a concerted transition of one or more segments from an HX-unprotected to an HX-protected state. Deconvolution of the data to near amino acid resolution shows that each step corresponds to the folding of a secondary structural element of the native protein, termed a “foldon.” Each folded segment is retained through subsequent steps of foldon addition, revealing a stepwise buildup of the native structure via a single dominant pathway. Analysis of the pertinent literature suggests that this model is consistent with experimental results for many proteins and some current theoretical results. Two biophysical principles appear to dictate this behavior. The principle of cooperativity determines the central role of native-like foldon units. An interaction principle termed “sequential stabilization” based on native-like interfoldon interactions orders the pathway. PMID:23603271

  12. Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry.

    PubMed

    Hu, Wenbing; Walters, Benjamin T; Kan, Zhong-Yuan; Mayne, Leland; Rosen, Laura E; Marqusee, Susan; Englander, S Walter

    2013-05-01

    The kinetic folding of ribonuclease H was studied by hydrogen exchange (HX) pulse labeling with analysis by an advanced fragment separation mass spectrometry technology. The results show that folding proceeds through distinct intermediates in a stepwise pathway that sequentially incorporates cooperative native-like structural elements to build the native protein. Each step is seen as a concerted transition of one or more segments from an HX-unprotected to an HX-protected state. Deconvolution of the data to near amino acid resolution shows that each step corresponds to the folding of a secondary structural element of the native protein, termed a "foldon." Each folded segment is retained through subsequent steps of foldon addition, revealing a stepwise buildup of the native structure via a single dominant pathway. Analysis of the pertinent literature suggests that this model is consistent with experimental results for many proteins and some current theoretical results. Two biophysical principles appear to dictate this behavior. The principle of cooperativity determines the central role of native-like foldon units. An interaction principle termed "sequential stabilization" based on native-like interfoldon interactions orders the pathway. PMID:23603271

  13. Helical structure and stability in human apolipoprotein A-I by hydrogen exchange and mass spectrometry.

    PubMed

    Chetty, Palaniappan Sevugan; Mayne, Leland; Lund-Katz, Sissel; Stranz, David; Englander, S Walter; Phillips, Michael C

    2009-11-10

    Apolipoprotein A-I (apoA-I) stabilizes anti-atherogenic high density lipoprotein particles (HDL) in the circulation and governs their biogenesis, metabolism, and functional interactions. To decipher these important structure-function relationships, it will be necessary to understand the structure, stability, and plasticity of the apoA-I molecule. Biophysical studies show that lipid-free apoA-I contains a large amount of alpha-helical structure but the location of this structure and its properties are not established. We used hydrogen-deuterium exchange coupled with a fragmentation-separation method and mass spectrometric analysis to study human lipid-free apoA-I in its physiologically pertinent monomeric form. The acquisition of approximately 100 overlapping peptide fragments that redundantly cover the 243-residue apoA-I polypeptide made it possible to define the positions and stabilities of helical segments and to draw inferences about their interactions and dynamic properties. Residues 7-44, 54-65, 70-78, 81-115, and 147-178 form alpha-helices, accounting for a helical content of 48 +/- 3%, in agreement with circular dichroism measurements (49%). At 3 to 5 kcal/mol in free energy of stabilization, the helices are far more stable than could be achieved in isolation, indicating mutually stabilizing helix bundle interactions. However the helical structure is dynamic, unfolding and refolding in seconds, allowing facile apoA-I reorganization during HDL particle formation and remodeling. PMID:19850866

  14. Mapping Protein Conformational Landscapes under Strongly Native Conditions with Hydrogen Exchange Mass Spectrometry.

    PubMed

    Witten, Jacob; Ruschak, Amy; Poterba, Timothy; Jaramillo, Alexis; Miranker, Andrew D; Jaswal, Sheila S

    2015-08-01

    The thermodynamic stability and kinetic barriers separating protein conformations under native conditions are critical for proper protein function and for understanding dysfunction in diseases of protein conformation. Traditional methods to probe protein unfolding and folding employ denaturants and highly non-native conditions, which may destabilize intermediate species or cause irreversible aggregation, especially at the high protein concentrations typically required. Hydrogen exchange (HX) is ideal for detecting conformational behavior under native conditions without the need for denaturants, but detection by NMR is limited to small highly soluble proteins. Mass spectrometry (MS) can, in principle, greatly extend the applicability of native-state HX to larger proteins and lower concentrations. However, quantitative analysis of HXMS profiles is currently limited by experimental and theoretical challenges. Here we address both limitations, by proposing an approach based on using standards to eliminate the systematic experimental artifacts in HXMS profiles, and developing the theoretical framework to describe HX behavior across all regimes based on the Linderstrøm-Lang formalism. We demonstrate proof of principle by a practical application to native-state HX of a globular protein. The framework and the practical tools developed advance the ability of HXMS to extract thermodynamic and kinetic conformational parameters of proteins under native conditions. PMID:26146955

  15. 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. PMID:24760958

  16. 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. PMID:25893550

  17. 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

  18. 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.

  19. Mass transport in gas diffusion layers of proton exchange membrane fuel cells

    NASA Astrophysics Data System (ADS)

    Martinez, Michael J.

    This dissertation describes fundamental properties of gas diffusion media (GDM) and their relationship to the mass transport in proton exchange membrane fuel cells (PEMFCs). First, the accuracy of solving the multi-component equations for PEMFC by using a computational fluid dynamics (CFD) technique is examined. This technique uses an approximated multi-component (AMC) model with a correction term that guarantees the overall mass balance. Accuracy is assessed by comparing the species concentrations computed with the Maxwell-Stefan and the AMC model. This comparison is important because the structure of some CFD programs does not permit the direct use of the Maxwell-Stefan equations. Here, it is shown that the maximum error between the two models is less than 5%. Second, the ratio of tortuosity to porosity, known as the MacMullin number, is reported for different carbon cloth and carbon paper GDM. This analysis show that only carbon cloths GDM follow the commonly accepted Bruggeman equation and that carbon paper GDM have a different relationship between the tortuosity and the porosity. These differences are discussed in terms of path length created by the orientation of fibers of each GDM. Third, data for the hydrophilic and hydrophobic pore size distributions (PSD) are presented for two types of GDM used in PEMFCs. The data were obtained by using two common measurement methods, intrusion porosimetry (IP) and the method of standard porosimetry (MSP). The use of multiple working fluids to access hydrophilic and hydrophobic pores is discussed as well as the limitations associated with structural changes of the GDM during the tests. The differences in interpretations of the data between the two methods for both GDM have significant implications relative to the distribution of hydrophilic and hydrophobic pores that control liquid water transport. Finally, a two-phase mass-transport-only model (MTOM) that incorporates the tortuosity and the PSD data described above is

  20. 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.

  1. 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.

  2. 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. PMID:22462957

  3. 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).

  4. 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. PMID:22055831

  5. 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. PMID:25761782

  6. 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

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

    PubMed

    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

    2003-01-01

    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 worms, 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 biogenic elements, shows an almost 100% closure of the cycle inside

  8. 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

  9. Evolution of Advection Upstream Splitting Method Schemes

    NASA Technical Reports Server (NTRS)

    Liou, Meng-Sing

    2010-01-01

    This paper focuses on the evolution of advection upstream splitting method(AUSM) schemes. The main ingredients that have led to the development of modern computational fluid dynamics (CFD) methods have been reviewed, thus the ideas behind AUSM. First and foremost is the concept of upwinding. Second, the use of Riemann problem in constructing the numerical flux in the finite-volume setting. Third, the necessity of including all physical processes, as characterised by the linear (convection) and nonlinear (acoustic) fields. Fourth, the realisation of separating the flux into convection and pressure fluxes. The rest of this review briefly outlines the technical evolution of AUSM and more details can be found in the cited references. Keywords: Computational fluid dynamics methods, hyperbolic systems, advection upstream splitting method, conservation laws, upwinding, CFD

  10. Passive advection in a collisionless plasma

    NASA Astrophysics Data System (ADS)

    Kanekar, Anjor; Schekochihin, Alexander; Hammett, Greg; Dorland, William; Loureiro, Nuno

    2014-10-01

    We consider a simple kinetic model for the evolution of the particle distribution function in a magnetized turbulent plasma that includes both phase mixing (Landau damping) and advection by a stochastic velocity field: a ``kinetic passive scalar'' in the Batchelor regime. The advection due to stochastic velocity field allows for a stochastic version of the plasma echo by coupling the ``phase-mixing'' and the ``un-phase-mixing'' components of the free energy. We have developed a new analytical framework to diagnose the efficiency of such coupling. We have also developed a new GPU code named Gandalf that solves this kinetic model numerically. In this poster, we shall present numerical and analytical results related to this work.

  11. Antidiffusive velocities for multipass donor cell advection

    SciTech Connect

    Margolin, L.G. ); Smolarkiewicz, P.K. )

    1989-12-01

    Smolarkiewicz describes an iterative process for approximating the advection equation. Basically, he uses a donor cell approximation to correct for the truncation error of the originally specified donor cell scheme. This step may be repeated an arbitrary number of times leading to successively more accurate solutions to the advection equation. In this report, we show how to sum the successive approximations analytically to find a single antidiffusive velocity that represents the effects of an arbitrary number of passes. The analysis is first done dimension to illustrate the method. The analysis is then repeated in two dimensions. The existence of cross terms in the truncation analysis of the two-dimensional equations introduces an extra complication into the calculation. We discuss the implementation of our new antidiffusive velocities and provide some examples of applications. 6 refs., 5 figs., 4 tabs.

  12. CONTAMINANT TRANSPORT IN SEDIMENT UNDER THE INFLUENCE OF ADVECTIVE FLUX

    EPA Science Inventory

    Chemical flux across the sediment/water interface is controlled by a combination of diffusive, dispersive and advective processes. The advective process is a function of submarine groundwater discharge and tidal effects. In areas where surface water interacts with groundwater, ...

  13. Curves to determine the relative importance of advection and dispersion for solute and vapor transport

    USGS Publications Warehouse

    Garges, J.A.; Baehr, A.L.

    1998-01-01

    The relative importance of advection and dispersion for both solute and vapor transport can be determined from type curves or concentration, flux, or cumulative flux. The dimensionless form of the type curves provides a means to directly evaluate the importance of mass transport by advection relative to that of mass transport by diffusion and dispersion. Type curves based on an analytical solution to the advection-dispersion equation are plotted in terms of dimensionless time and Peclet number. Flux and cumulative flux type curves provide additional rationale for transport regime determination in addition to the traditional concentration type curves. The extension of type curves to include vapor transport with phase partitioning in the unsaturated zone is a new development. Type curves for negative Peclet numbers also are presented. A negative Peclet number characterizes a problem in which one direction of flow is toward the contamination source, and thereby diffusion and advection can act in opposite directions. Examples are the diffusion of solutes away from the downgradient edge of a pump-and-treat capture zone, the upward diffusion of vapors through the unsaturated zone with recharge, and the diffusion of solutes through a low hydraulic conductivity cutoff wall with an inward advective gradient.

  14. 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.

  15. 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).

  16. Energy and mass exchange between ocean and atmosphere in the area of winter polynya to the north of Svalbard

    NASA Astrophysics Data System (ADS)

    Ivanov, Boris; Wesman, Anna; Sviashchennikov, Pavel; Pavlov, Alexey

    2015-04-01

    The warm inflow of the West Spitsbergen Current keeps waters ice-free in winter to the north of Svalbard, an area also called the Whalers Bay. Here we present results of the winter expedition in the Arctic Ocean to the north of Svalbard on board a research vessel «Helmer Hanssen» in January 2012. The characteristics of the turbulent energy and mass exchange are calculated using an algorithm, which is based on semi-empirical theory of "Monin-Obukhov", adapted to the conditions of marine meteorological observations. The results are compared with the data obtained in this area in February 1986 on board Russian research icebreaker "Otto Schmidt". The features of energy-mass exchange are explained by synoptic and ice conditions in the study area. Intense heat and mass exchange in the area leads to enhanced convective mixing and, thus, upwelling of nutrients to surface waters that can contribute to higher biological activity in the area throughout the food web.

  17. 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. PMID:27128846

  18. 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

  19. Purely Lagrangian Simulation of Advection, Dispersion, Precipitation, and Dissolution

    NASA Astrophysics Data System (ADS)

    Benson, D.; Zhang, Y.; Reeves, D. M.

    2008-05-01

    We extend the advantages of Lagrangian random walk particle tracking (RWPT) methods that have long been used to simulate advection and dispersion in highly heterogeneous media. By formulating dissolution as a random, independent decay process, the classical continuum rate law is recovered. Formulating the random precipitation process requires a consideration of the probability that two nearby particles will coincide in a given time period. This depends on local mixing (as by diffusion) and the total domain particle number density, which are fixed and therefore easy to calculate. The result is that the classical law of mass action for equilibrium reactions can be reproduced in an ensemble sense. The same number of parameters for A+B ⇌ C are needed in a probabilistic versus continuum reaction simulation-- —one each for forward and backward probabilities that correspond to rates. The random nature of the simulations allows for significant disequilibrium in any given region at any time that is independent of the numerical details such as time stepping or particle density. This is exemplified by nearby or intermingled groups of reactants and little or no product--—a result that is often noted in the field that is difficult to reconcile with continuum methods or coarse-grained Eulerian models. Our results support recent results of perturbed advection-dispersion-reaction continuum models (Luo et al., WRR 44, 2008), and suggest that many different kinds of reactions can be easily added to existing RWPT codes.

  20. Advection and diffusion in shoreline change prediction

    NASA Astrophysics Data System (ADS)

    Anderson, T. R.; Frazer, L. N.

    2010-12-01

    We added longshore advection and diffusion to the simple cross-shore rate calculation method, as used widely by the USGS and others, to model historic shorelines and to predict future shoreline positions; and applied this to Hawaiian Island beach data. Aerial photographs, sporadically taken throughout the past century, yield usable, albeit limited, historic shoreline data. These photographs provide excellent spatial coverage, but poor temporal resolution, of the shoreline. Due to the sparse historic shoreline data, and the many natural and anthropogenic events influencing coastlines, we constructed a simplistic shoreline change model that can identify long-term behavior of a beach. Our new, two-dimensional model combines the simple rate method to accommodate for cross-shore sediment transport with the classic Pelnard-Considère model for diffusion, as well as a longshore advection speed term. Inverse methods identify cross-shore rate, longshore advection speed, and longshore diffusivity down a sandy coastline. A spatial averaging technique then identifies shoreline segments where one parameter can reasonably account for the cross-shore and longshore transport rates in that area. This produces model results with spatial resolution more appropriate to the temporal spacing of the data. Because changes in historic data can be accounted for by varying degrees of cross-shore and longshore sediment transport - for example, beach erosion can equally be explained by sand moving either off-shore or laterally - we tested several different model scenarios on the data: allowing only cross-shore sediment movement, only longshore movement, and a combination of the two. We used statistical information criteria to determine both the optimal spatial resolution and best-fitting scenario. Finally, we employed a voting method predicting the relaxed shoreline position over time.

  1. Metamorphism during temperature gradient with undersaturated advective airflow in a snow sample

    NASA Astrophysics Data System (ADS)

    Ebner, Pirmin Philipp; Schneebeli, Martin; Steinfeld, Aldo

    2016-04-01

    Snow at or close to the surface commonly undergoes temperature gradient metamorphism under advective flow, which alters its microstructure and physical properties. Time-lapse X-ray microtomography is applied to investigate the structural dynamics of temperature gradient snow metamorphism exposed to an advective airflow in controlled laboratory conditions. Cold saturated air at the inlet was blown into the snow samples and warmed up while flowing across the sample with a temperature gradient of around 50 K m-1. Changes of the porous ice structure were observed at mid-height of the snow sample. Sublimation occurred due to the slight undersaturation of the incoming air into the warmer ice matrix. Diffusion of water vapor opposite to the direction of the temperature gradient counteracted the mass transport of advection. Therefore, the total net ice change was negligible leading to a constant porosity profile. However, the strong recrystallization of water molecules in snow may impact its isotopic or chemical content.

  2. 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.

  3. Construction of the SILAM Eulerian atmospheric dispersion model based on the advection algorithm of Michael Galperin

    NASA Astrophysics Data System (ADS)

    Sofiev, M.; Vira, J.; Kouznetsov, R.; Prank, M.; Soares, J.; Genikhovich, E.

    2015-11-01

    The paper presents the transport module of the System for Integrated modeLling of Atmospheric coMposition SILAM v.5 based on the advection algorithm of Michael Galperin. This advection routine, so far weakly presented in the international literature, is positively defined, stable at any Courant number, and efficient computationally. We present the rigorous description of its original version, along with several updates that improve its monotonicity and shape preservation, allowing for applications to long-living species in conditions of complex atmospheric flows. The scheme is connected with other parts of the model in a way that preserves the sub-grid mass distribution information that is a cornerstone of the advection algorithm. The other parts include the previously developed vertical diffusion algorithm combined with dry deposition, a meteorological pre-processor, and chemical transformation modules. The quality of the advection routine is evaluated using a large set of tests. The original approach has been previously compared with several classic algorithms widely used in operational dispersion models. The basic tests were repeated for the updated scheme and extended with real-wind simulations and demanding global 2-D tests recently suggested in the literature, which allowed one to position the scheme with regard to sophisticated state-of-the-art approaches. The advection scheme performance was fully comparable with other algorithms, with a modest computational cost. This work was the last project of Dr. Sci. Michael Galperin, who passed away on 18 March 2008.

  4. Coupled ensemble flow line advection and analysis.

    PubMed

    Guo, Hanqi; Yuan, Xiaoru; Huang, Jian; Zhu, Xiaomin

    2013-12-01

    Ensemble run simulations are becoming increasingly widespread. In this work, we couple particle advection with pathline analysis to visualize and reveal the differences among the flow fields of ensemble runs. Our method first constructs a variation field using a Lagrangian-based distance metric. The variation field characterizes the variation between vector fields of the ensemble runs, by extracting and visualizing the variation of pathlines within ensemble. Parallelism in a MapReduce style is leveraged to handle data processing and computing at scale. Using our prototype system, we demonstrate how scientists can effectively explore and investigate differences within ensemble simulations. PMID:24051840

  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. 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…

  7. 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.

    1992-08-01

    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.

  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. Recombinant immobilized rhizopuspepsin as a new tool for protein digestion in hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Rey, Martial; Man, Petr; Brandolin, Gérard; Forest, Eric; Pelosi, Ludovic

    2009-11-01

    Hydrogen/deuterium (H/D) exchange coupled to mass spectrometry is nowadays routinely used to probe protein interactions or conformational changes. The method has many advantages, e.g. very low sample consumption, but offers limited spatial resolution. One way to higher resolution leads through the use of different proteases or their combinations. In the present work we describe recombinant production, purification and use of aspartic protease zymogen from Rhizopus chimensis, protease type XVIII (EC 3.4.23.6), commonly referred to as rhizopuspepsinogen (Rpg). The enzyme was expressed in Escherichia coli, refolded and purified to homogeneity. A typical yield was approximately 100 mg of pure enzyme per 1 L of original bacterial culture. The kinetics of protease activation, i.e. removal of the propeptide achieved by autolysis in an acidic environment, was followed by mass spectrometry. The digestion efficiency was tested for the protease in solution as well as for the immobilized enzyme. Apomyoglobin was successfully digested under all conditions tested and the protease displayed very low or no autodigestion. The results outperformed those obtained with commercial protease where the digestion of apomyoglobin was incomplete and accompanied by many contaminating peptides. Taken together, the recombinant protease type XVIII can be considered as a new and highly efficient tool for H/D exchange followed by mass spectrometry. PMID:19827048

  10. 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.

  11. Advective turbulent transport in the fluid plasma

    NASA Astrophysics Data System (ADS)

    Min, Byung-Hoon; An, Chan-Yong; Kim, Chang-Bae

    2013-10-01

    The Hasegawa-Wakatani model (HWM) has been employed in pedagogical analyses of the physics behind the behavior of the tokamak plasmas. In addition to the geometric simplicity HWM has an appealing feature of sustaining autonomous quasi-steady state, unstable modes providing the power that is being transported by the nonlinear interactions and is eventually dissipated by the collisional damping at small scales. Emergence of the zonal flow out of the turbulence is a main candidate to cause the transition from the low plasma confinement to the high mode. In the study of such LH transition with the HWM, the adiabaticity parameter has been shown to play an important role in forcing the zonal flow that results in the regulation of the drift-wave turbulence. Instead of concentrating on the physics of the feedback loop between the turbulence and the zonal flow the present study focuses on the presence of the advective transport of the energy. Numerical simulations of HWM are performed and the connections between the advective transport and the zonal flow will be presented. This work was supported by the Supercpmputing Center/Korea Institute of Science and Technology Information with supercomputing resources including technical support (KSC-2013-C1-009).

  12. Advection, diffusion and delivery over a network

    PubMed Central

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

    2014-01-01

    Many biological, geophysical and technological systems involve the transport of resource over a network. In this paper we present an algorithm for calculating the exact concentration of resource at any point in space or time, given that the resource in the network is lost or delivered out of the network at a given rate, while being subject to advection and diffusion. We consider the implications of advection, diffusion and delivery for simple models of glucose delivery through a vascular network, and conclude that in certain circumstances, increasing the volume of blood and the number of glucose transporters can actually decrease the total rate of glucose delivery. We also consider the case of empirically determined fungal networks, and analyze the distribution of resource that emerges as such networks grow over time. Fungal growth involves the expansion of fluid filled vessels, which necessarily involves the movement of fluid. In three empirically determined fungal networks we found that the minimum currents consistent with the observed growth would effectively transport resource throughout the network over the time-scale of growth. This suggests that in foraging fungi, the active transport mechanisms observed in the growing tips may not be required for long range transport. PMID:23005783

  13. 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.

  14. On-line cation exchange for suppression of adduct formation in negative-ion electrospray mass spectrometry of nucleic acids.

    PubMed

    Huber, C G; Buchmeiser, M R

    1998-12-15

    One major difficulty in the analysis of nucleic acids by electrospray mass spectrometry is represented by the affinity of the polyanionic sugar-phosphate backbone for nonvolatile cations, especially ubiquitous sodium and potassium ions. A simple on-line sample preparation system comprising a microflow pumping system and 45 x 0.8-mm-i.d. microcolumns packed with weak or strong cation-exchange resins is described for the efficient removal of cations from nucleic acid samples. Samples were analyzed by flow injection analysis at a 3-5 microL/min flow of 10 mM triethylamine in 50% water-50% acetonitrile. After on-line desalting, mass spectra of oligonucleotides revealed no significant sodium adduct peaks. Moreover, signal-to-noise ratios were greatly enhanced compared to direct injection of the samples. Electrospray mass spectrometry with on-line sample preparation allowed accurate molecular mass determinations of picomole amounts of crude oligonucleotide preparations ranging in size from 8 to 80 nucleotides within a few minutes. The good linearity of the calibration plot (R2 = 0.9988) over at least 2 orders of magnitude and a relative standard deviation in peak areas of less than 9% permitted the sensitive quantitative measurement of oligonucleotides in a concentration range of 0.2-20 microM with selected-ion monitoring. Finally, the on-line sample preparation system was evaluated for the mass spectrometric analysis of complex oligonucleotide mixtures. PMID:9868919

  15. 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

    2015-10-01

    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. PMID:26360183

  16. 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.

    2016-03-01

    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.

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

    PubMed

    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. Graphical Abstract ᅟ. PMID:27032648

  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. Modeling data from titration, amide H/D exchange, and mass spectrometry to obtain protein-ligand binding constants.

    PubMed

    Zhu, Mei M; Rempel, Don L; Gross, Michael L

    2004-03-01

    We recently reported a new method for quantification of protein-ligand interaction by mass spectrometry, titration and H/D exchange (PLIMSTEX) for determining the binding stoichiometry and affinity of a wide range of protein-ligand interactions. Here we describe the method for analyzing the PLIMSTEX titration curves and evaluate the effect of various models on the precision and accuracy for determining binding constants using H/D exchange and a titration. The titration data were fitted using a 1:n protein:ligand sequential binding model, where n is the number of binding sites for the same ligand. An ordinary differential equation was used for the first time in calculating the free ligand concentration from the total ligand concentration. A nonlinear least squares regression method was applied to minimize the error between the calculated and the experimentally measured deuterium shift by varying the unknown parameters. A resampling method and second-order statistics were used to evaluate the uncertainties of the fitting parameters. The interaction of intestinal fatty-acid-binding protein (IFABP) with a fatty-acid carboxylate and that of calmodulin with Ca(2+) are used as two tests. The modeling process described here not only is a new tool for analyzing H/D exchange data acquired by ESI-MS, but also possesses novel aspects in modeling experimental titration data to determine the affinity of ligand binding. PMID:14998541

  20. 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.

  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. Optimization and Application of APCI Hydrogen-Deuterium Exchange Mass Spectrometry (HDX MS) for the Speciation of Nitrogen Compounds

    NASA Astrophysics Data System (ADS)

    Acter, Thamina; Cho, Yunju; Kim, Sungji; Ahmed, Arif; Kim, Byungjoo; Kim, Sunghwan

    2015-09-01

    A systematic study was performed to investigate the utility of atmospheric pressure chemical ionization hydrogen-deuterium exchange mass spectrometry (APCI HDX MS) to identify the structures of nitrogen-containing aromatic compounds. First, experiments were performed to determine the optimized experimental conditions, with dichloromethane and CH3OD found to be good cosolvents for APCI HDX. In addition, a positive correlation between the heated capillary temperature and the observed HDX signal was observed, and it was suggested that the HDX reaction occurred when molecules were contained in the solvent cluster. Second, 20 standard nitrogen-containing compounds were analyzed to investigate whether speciation could be determined based on the different types of ions produced from nitrogen-containing compounds with various functional groups. The number of exchanges occurring within the compounds correlated well with the number of active hydrogen atoms attached to nitrogen, and it was confirmed that APCI HDX MS could be used to determine speciation. The results obtained by APCI HDX MS were combined with the subsequent investigation of the double bond equivalence distribution and indicated that resins of shale oil extract contained mostly pyridine type nitrogen compounds. This study confirmed that APCI HDX MS can be added to previously reported chemical ionization, electrospray ionization, and atmospheric pressure photo ionization-based HDX methods, which can be used for structural elucidation by mass spectrometry.

  3. Optimization and Application of APCI Hydrogen-Deuterium Exchange Mass Spectrometry (HDX MS) for the Speciation of Nitrogen Compounds.

    PubMed

    Acter, Thamina; Cho, Yunju; Kim, Sungji; Ahmed, Arif; Kim, Byungjoo; Kim, Sunghwan

    2015-09-01

    A systematic study was performed to investigate the utility of atmospheric pressure chemical ionization hydrogen-deuterium exchange mass spectrometry (APCI HDX MS) to identify the structures of nitrogen-containing aromatic compounds. First, experiments were performed to determine the optimized experimental conditions, with dichloromethane and CH(3)OD found to be good cosolvents for APCI HDX. In addition, a positive correlation between the heated capillary temperature and the observed HDX signal was observed, and it was suggested that the HDX reaction occurred when molecules were contained in the solvent cluster. Second, 20 standard nitrogen-containing compounds were analyzed to investigate whether speciation could be determined based on the different types of ions produced from nitrogen-containing compounds with various functional groups. The number of exchanges occurring within the compounds correlated well with the number of active hydrogen atoms attached to nitrogen, and it was confirmed that APCI HDX MS could be used to determine speciation. The results obtained by APCI HDX MS were combined with the subsequent investigation of the double bond equivalence distribution and indicated that resins of shale oil extract contained mostly pyridine type nitrogen compounds. This study confirmed that APCI HDX MS can be added to previously reported chemical ionization, electrospray ionization, and atmospheric pressure photo ionization-based HDX methods, which can be used for structural elucidation by mass spectrometry. PMID:26115964

  4. 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

  5. Imidazole C-2 Hydrogen/Deuterium Exchange Reaction at Histidine for Probing Protein Structure and Function with MALDI Mass Spectrometry

    PubMed Central

    Hayashi, Naoka; Kuyama, Hiroki; Nakajima, Chihiro; Kawahara, Kazuki; Miyagi, Masaru; Nishimura, Osamu; Matsuo, Hisayuki; Nakazawa, Takashi

    2015-01-01

    We present a mass spectrometric method for analyzing protein structure and function, based on the imidazole C-2 or histidine Cε1 hydrogen/deuterium (H/D) exchange reaction, which is intrinsically second order with respect to the concentrations of the imidazolium cation and OD− in D2O. The second-order rate constant (k2) of this reaction was calculated from the pH-dependency of the pseudo-first-order rate constant (kφ) obtained from the change of average mass ΔMr (0 ≤ ΔMr < 1) of a peptide fragment containing a defined histidine residue at incubation time (t) such that kφ = − [ln(1−ΔMr)]/t. We preferred using k2 rather than kφ because k2max (maximal value of k2) was empirically related to pKa as illustrated with a Brønsted plot: logk2max=-0.7pKa+α (α is an arbitrary constant), so that we could analyze the effect of structure on the H/D-exchange rate in terms of log(k2max/k2) representing the deviation of k2 from k2max. In the catalytic site of bovine ribonuclease A, His12 showed much larger change in log(k2max/k2) compared with His119 upon binding with cytidine 3′-monophosphate, as anticipated from the X-ray structures and the possible change in solvent accessibility. However, there is a need of considering the hydrogen bonds of the imidazole group with non-dissociable groups to interpret an extremely slow H/D exchange rate of His48 in partially solvent-exposed situation. PMID:24606199

  6. 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. PMID:26531244

  7. 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

  8. Optimization of heat and mass transfers in counterflow corrugated-plate liquid-gas exchangers used in a greenhouse dehumidifier

    NASA Astrophysics Data System (ADS)

    Bentounes, N.; Jaffrin, A.

    1998-09-01

    Heat and mass transfers occuring in a counterflow direct contact liquid-gas exchanger determine the performance of a new greenhouse air dehumidifier designed at INRA. This prototype uses triethylene glycol (TEG) as the desiccant fluid which extracts water vapor from the air. The regeneration of the TEG desiccant fluid is then performed by direct contact with combustion gas from a high efficiency boiler equipped with a condensor. The heat and mass transfers between the thin film of diluted TEG and the hot gas were simulated by a model which uses correlation formula from the literature specifically relevant to the present cross-corrugated plates geometry. A simple set of analytical solutions is first derived, which explains why some possible processes can clearly be far from optimal. Then, more exact numerical calculations confirm that some undesirable water recondensations on the upper part of the exchanger were limiting the performance of this prototype. More suitable conditions were defined for the process, which lead to a new design of the apparatus. In this second prototype, a gas-gas exchanger provides dryer and cooler gas to the basis of the regenerators, while a warmer TEG is fed on the top. A whole range of operating conditions was experimented and measured parameters were compared with numerical simulations of this new configuration: recondensation did not occur any more. As a consequence, this second prototype was able to concentrate the desiccant fluid at the desired rate of 20 kg H_{2O}/hour, under temperature and humidity conditions which correspond to the dehumidification of a 1000 m2 greenhouse heated at night during the winter season.

  9. Monitoring the Dynamics of Monomer Exchange Using Electrospray Mass Spectrometry: The Case of the Dimeric Glucosamine-6-Phosphate Synthase

    NASA Astrophysics Data System (ADS)

    Chevreux, Guillaume; Atmanene, Cédric; Lopez, Philippe; Ouazzani, Jamal; Van Dorsselaer, Alain; Badet, Bernard; Badet-Denisot, Marie-Ange; Sanglier-Cianférani, Sarah

    2011-03-01

    Escherichia coli glucosamine-6-phosphate synthase (GlmS) is a dimeric enzyme from the glutamine-dependent amidotransferases family, which catalyses the conversion of D-fructose-6-phosphate (Fru6P) and glutamine (Gln) into D-glucosamine-6-phosphate (GlcN6P) and glutamate, respectively. Extensive X-ray crystallography investigations have been reported, highlighting the importance of the dimeric association to form the sugar active site as well as significant conformational changes of the protein upon substrate and product binding. In the present work, an approach based on time-resolved noncovalent mass spectrometry has been developed to study the dynamics of GlmS subunit exchange. Using 14N versus 15N labeled proteins, the kinetics of GlmS subunit exchange was monitored with the wild-type enzyme in the presence of different substrates and products as well as with the protein bearing a key amino acid mutation specially designed to weaken the dimer interface. Determination of rate constants of subunit exchange revealed important modifications of the protein dynamics: while glutamine, glutamate, and K603A mutation accelerates subunit exchange, Fru6P and GlcN6P totally prevent it. These results are described in light of the available structural information, providing additional useful data for both the characterization of GlmS catalytic process and the design of new GlmS inhibitors. Finally, time-resolved noncovalent MS can be proposed as an additional biophysical technique for real-time monitoring of protein dynamics.

  10. Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis.

    PubMed

    Weis, David D; Wales, Thomas E; Engen, John R; Hotchko, Matthew; Ten Eyck, Lynn F

    2006-11-01

    Proteins that undergo cooperative unfolding events display EX1 kinetic signatures in hydrogen exchange mass spectra. The hallmark bimodal isotope pattern observed for EX1 kinetics is distinct from the binomial isotope pattern for uncorrelated exchange (EX2), the normal exchange regime for folded proteins. Detection and characterization of EX1 kinetics is simple when the cooperative unit is large enough that the isotopic envelopes in the bimodal pattern are resolved in the m/z scale but become complicated in cases where the unit is small or there is a mixture of EX1 and EX2 kinetics. Here we describe a data interpretation method involving peak width analysis that makes characterization of EX1 kinetics simple and rapid. The theoretical basis for EX1 and EX2 isotopic signatures and the effects each have on peak width are described. Modeling of EX2 widening and analysis of empirical data for proteins and peptides containing purely EX2 kinetics showed that the amount of widening attributable to stochastic forward- and back exchange in a typical experiment is small and can be quantified. Proteins and peptides with both obvious and less obvious EX1 kinetics were analyzed with the peak width method. Such analyses provide the half-life for the cooperative unfolding event and the relative number of residues involved. Automated analysis of peak width was performed with custom Excel macros and the DEX software package. Peak width analysis is robust, capable of automation, and provides quick interpretation of the key information contained in EX1 kinetic events. PMID:16875839

  11. A Combined Desorption Ionization by Charge Exchange (DICE) and Desorption Electrospray Ionization (DESI) Source for Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Chan, Chang-Ching; Bolgar, Mark S.; Miller, Scott A.; Attygalle, Athula B.

    2011-01-01

    A source that couples the desorption ionization by charge exchange (DICE) and desorption electrospray ionization (DESI) techniques together was demonstrated to broaden the range of compounds that can be analyzed in a single mass spectrometric experiment under ambient conditions. A tee union was used to mix the spray reagents into a partially immiscible blend before this mixture was passed through a conventional electrospray (ES) probe capillary. Using this technique, compounds that are ionized more efficiently by the DICE method and those that are ionized better with the DESI procedure could be analyzed simultaneously. For example, hydroquinone, which is not detected when subjected to DESI-MS in the positive-ion generation mode, or the sodium adduct of guaifenesin, which is not detected when examined by DICE-MS, could both be detected in one experiment when the two techniques were combined. The combined technique was able to generate the molecular ion, proton and metal adduct from the same compound. When coupled to a tandem mass spectrometer, the combined source enabled the generation of product ion spectra from the molecular ion and the [M + H]+ or [M + metal]+ ions of the same compound without the need to physically change the source from DICE to DESI. The ability to record CID spectra of both the molecular ion and adduct ions in a single mass spectrometric experiment adds a new dimension to the array of mass spectrometric methods available for structural studies.

  12. A combined desorption ionization by charge exchange (DICE) and desorption electrospray ionization (DESI) source for mass spectrometry.

    PubMed

    Chan, Chang-Ching; Bolgar, Mark S; Miller, Scott A; Attygalle, Athula B

    2011-01-01

    A source that couples the desorption ionization by charge exchange (DICE) and desorption electrospray ionization (DESI) techniques together was demonstrated to broaden the range of compounds that can be analyzed in a single mass spectrometric experiment under ambient conditions. A tee union was used to mix the spray reagents into a partially immiscible blend before this mixture was passed through a conventional electrospray (ES) probe capillary. Using this technique, compounds that are ionized more efficiently by the DICE method and those that are ionized better with the DESI procedure could be analyzed simultaneously. For example, hydroquinone, which is not detected when subjected to DESI-MS in the positive-ion generation mode, or the sodium adduct of guaifenesin, which is not detected when examined by DICE-MS, could both be detected in one experiment when the two techniques were combined. The combined technique was able to generate the molecular ion, proton and metal adduct from the same compound. When coupled to a tandem mass spectrometer, the combined source enabled the generation of product ion spectra from the molecular ion and the [M + H](+) or [M + metal](+) ions of the same compound without the need to physically change the source from DICE to DESI. The ability to record CID spectra of both the molecular ion and adduct ions in a single mass spectrometric experiment adds a new dimension to the array of mass spectrometric methods available for structural studies. PMID:21472555

  13. Pulsed hydrogen–deuterium exchange mass spectrometry probes conformational changes in amyloid beta (Aβ) peptide aggregation

    PubMed Central

    Zhang, Ying; Rempel, Don L.; Zhang, Jun; Sharma, Anuj K.; Mirica, Liviu M.; Gross, Michael L.

    2013-01-01

    Probing the conformational changes of amyloid beta (Aβ) peptide aggregation is challenging owing to the vast heterogeneity of the resulting soluble aggregates. To investigate the formation of these aggregates in solution, we designed an MS-based biophysical approach and applied it to the formation of soluble aggregates of the Aβ42 peptide, the proposed causative agent in Alzheimer’s disease. The approach incorporates pulsed hydrogen–deuterium exchange coupled with MS analysis. The combined approach provides evidence for a self-catalyzed aggregation with a lag phase, as observed previously by fluorescence methods. Unlike those approaches, pulsed hydrogen–deuterium exchange does not require modified Aβ42 (e.g., labeling with a fluorophore). Furthermore, the approach reveals that the center region of Aβ42 is first to aggregate, followed by the C and N termini. We also found that the lag phase in the aggregation of soluble species is affected by temperature and Cu2+ ions. This MS approach has sufficient structural resolution to allow interrogation of Aβ aggregation in physiologically relevant environments. This platform should be generally useful for investigating the aggregation of other amyloid-forming proteins and neurotoxic soluble peptide aggregates. PMID:23959898

  14. Probing Conserved Helical Modules of Portal Complexes by Mass Spectrometry based Hydrogen/deuterium Exchange

    PubMed Central

    Kang, Sebyung; Poliakov, Anton; Sexton, Jennifer; Renfrow, Matthew B.; Prevelige, Peter E.

    2008-01-01

    The dsDNA bacteriophage P22 has a ring shaped dodecameric complex composed of the 84 kDa portal protein subunit which forms the central channel of the phage’s DNA packaging motor. The overall morphology of the P22 portal complex is similar to that of the portal complexes of Phi29, SPP1, T3, T7 phages and herpes simplex virus. Secondary structure prediction of P22 portal protein and its threading onto the crystal structure of the Phi29 portal complexes suggested that P22 portal protein complex shares conserved helical modules which were found in the dodecameric interfaces of the Phi29 portal complex. To identify the amino acids involved in inter-subunit contacts in the P22 portal ring complexes and validate the threading model, we performed comparative hydrogen/deuterium exchange analysis of monomeric and in vitro assembled portal proteins of P22 and the dodecameric Phi29 portal. Hydrogen/deuterium exchange experiments provided evidence of inter-subunit interactions in the P22 portal complex similar to those in the Phi29 portal which map to the regions predicted to be conserved helical modules. PMID:18621389

  15. Evaluating two numerical advection schemes in HYCOM for eddy-resolving modelling of the Agulhas Current

    NASA Astrophysics Data System (ADS)

    Backeberg, B. C.; Bertino, L.; Johannessen, J. A.

    2009-06-01

    A 4th order advection scheme is applied in a nested eddy-resolving Hybrid Coordinate Ocean Model (HYCOM) of the greater Agulhas Current system for the purpose of testing advanced numerics as a means for improving the model simulation for eventual operational implementation. Model validation techniques comparing sea surface height variations, sea level skewness and variogram analyses to satellite altimetry measurements quantify that generally the 4th order advection scheme improves the realism of the model simulation. The most striking improvement over the standard 2nd order momentum advection scheme, is that the southern Agulhas Current is simulated as a well-defined meandering current, rather than a train of successive eddies. A better vertical structure and stronger poleward transports in the Agulhas Current core contribute toward a better southwestward penetration of the current, and its temperature field, implying a stronger Indo-Atlantic inter-ocean exchange. It is found that the transport, and hence this exchange, is sensitive to the occurrences of mesoscale features originating upstream in the Mozambique Channel and southern East Madagascar Current, and that the improved HYCOM simulation is well suited for further studies of these inter-actions.

  16. Evaluating two numerical advection schemes in HYCOM for eddy-resolving modelling of the Agulhas Current

    NASA Astrophysics Data System (ADS)

    Backeberg, B. C.; Bertino, L.; Johannessen, J. A.

    2009-02-01

    A 4th order advection scheme is applied in a nested eddy-resolving Hybrid Coordinate Ocean Model (HYCOM) of the greater Agulhas Current system for the purpose of testing advanced numerics as a means for improving the model simulation for eventual operational implementation. Model validation techniques comparing sea surface height variations, sea level skewness and variogram analyses to satellite altimetry measurements quantify that generally the 4th order advection scheme improves the realism of the model simulation. The most striking improvement over the standard 2nd order momentum advection scheme, is that the Southern Agulhas Current is simulated as a well-defined meandering current, rather than a train of successive eddies. A better vertical structure and stronger poleward transports in the Agulhas Current core contribute toward a better southwestward penetration of the current, and its temperature field, implying a stronger Indo-Atlantic inter-ocean exchange. It is found that the transport, and hence this exchange, is sensitive to the occurrences of mesoscale features originating upstream in the Mozambique Channel and Southern East Madagascar Current, and that the improved HYCOM simulation is well suited for further studies of these inter-actions.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Larson, Peter B.; Cunningham, Charles G.; Naeser, Charles W.

    1994-03-01

    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

  19. 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.

  20. Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Kazazic, Sasa; Zhang, Hui-Min; Schaub, Tanner M; Emmett, Mark R; Hendrickson, Christopher L; Blakney, Gregory T; Marshall, Alan G

    2010-04-01

    Mass analysis of proteolytic fragment peptides following hydrogen/deuterium exchange offers a general measure of solvent accessibility/hydrogen bonding (and thus conformation) of solution-phase proteins and their complexes. The primary problem in such mass analyses is reliable and rapid assignment of mass spectral peaks to the correct charge state and degree of deuteration of each fragment peptide, in the presence of substantial overlap between isotopic distributions of target peptides, autolysis products, and other interferant species. Here, we show that at sufficiently high mass resolving power (m/Delta m(50%) > or = 100,000), it becomes possible to resolve enough of those overlaps so that automated data reduction becomes possible, based on the actual elemental composition of each peptide without the need to deconvolve isotopic distributions. We demonstrate automated, rapid, reliable assignment of peptide masses from H/D exchange experiments, based on electrospray ionization FT-ICR mass spectra from H/D exchange of solution-phase myoglobin. Combined with previously demonstrated automated data acquisition for such experiments, the present data reduction algorithm enhances automation (and thus expands generality and applicability) for high-resolution mass spectrometry-based analysis of H/D exchange of solution-phase proteins. PMID:20116280

  1. Breakthrough curve moments scaling in hyporheic exchange

    NASA Astrophysics Data System (ADS)

    Bellin, A.; Tonina, D.; Marzadri, A.

    2015-02-01

    The interaction between stream flow and bed forms creates an uneven distribution of near-bed energy heads, which is the driving force of hyporheic exchange. Owing to the large disparity of advection characteristic times in the stream and within the hyporheic zone, solute mass exchange is often modeled by considering the latter as an immobile region. In a recent contribution Gónzalez-Pinzón et al. (2013) showed that existing models employing this hypothesis are structurally inconsistent with the scaling revealed by the analysis of 384 breakthrough curves collected in 44 streams across five continents. Motivated by this result, we analyze the scaling characteristics of a model that we recently developed by combining the analytical solution of the advective flow within the hyporheic zone with a Lagrangian solute transport model. Results show that similarly to the experimental data our model predicts breakthrough curves with a constant skewness, irrespective of the stream size, and that the scaling of the first three moments observed by Gónzalez-Pinzón et al. (2013) is also respected. Moreover, we propose regression curves that relate the first three moments of the residence time distribution with the alternate bar dimensionless depth (YBM*), a quantity that is easily measurable in the field. The connection between BTC moments and YBM* opens new possibilities for modeling transport processes at the catchment scale.

  2. Ammonium Ion Exchanged Zeolite for Laser Desorption/Ionization Mass Spectrometry of Phosphorylated Peptides

    PubMed Central

    Yang, Mengrui; Fujino, Tatsuya

    2015-01-01

    α-Cyano-4-hydroxycinnamic acid (CHCA), an organic matrix molecule for matrix-assisted laser desorption/ionization mass spectrometry, was adsorbed to NH4+-type zeolite surface, and this new matrix was used for the detection of low-molecular-weight compounds. It was found that this matrix could simplify the mass spectrum in the low-molecular-weight region and prevent interference from fragments and alkali metal ion adducted species. CHCA adsorbed to NH4+-type ZSM5 zeolite (CHCA/NH4ZSM5) was used to measure atropine and aconitine, two toxic alkaloids in plants. In addition, CHCA/NH4ZSM5 enabled us to detect phosphorylated peptides; peaks of the protonated peptides had higher intensities than the peaks observed using CHCA only. PMID:26448749

  3. Advective transport and decomposition of chain-forming planktonic diatoms in permeable sediments

    NASA Astrophysics Data System (ADS)

    Ehrenhauss, Sandra; Huettel, Markus

    2004-09-01

    In laboratory chamber experiments we demonstrate that permeable sediments (>7×10 -12 m 2) exposed to boundary flows filter chain-forming coastal bloom diatoms ( Skeletonema costatum and Thalassiosira rotula) from the water column, causing rapid transfer of fresh organic particulate matter into sediment layers as deep as 5 cm within 72 h. The penetration depth of the diatoms depends on the permeability of the bed and the length of the chains. Long chains were not transported as deep into the sediment as short chains or single cells. The fast advective transfer of phytoplankton cells into sandy sediments may be an important process facilitating organic matter uptake and preventing resuspension of deposited organic material in high-energy coastal environments. High advective flushing rates in medium- and coarse-grained sandy sediments enhanced the mineralisation of the trapped diatoms (2300 to 3200 μmol C m -2 d -1), stimulated benthic oxygen consumption (2300 to 3000 μmol O 2 m -2 d -1), as well as nitrification (up to 20 μmol NO 3- m -2 d -1), relative to sediment where diffusion dominated the solute exchange. Advective solute exchange rates that increase with increasing permeability prevent the accumulation of Si(OH) 4 near the dissolving frustules and in the pore water, leading to an effective recycling of dissolved silica to the production process in the water column (95 to 101 μmol Si(OH) 4 m -2 d -1). This process may also enhance dissolution rates of the deposited opal in coarse-grained sands by maintaining higher degrees of undersaturation than in fine-grained sediments. Our results suggest that advective filtration of planktonic diatoms into permeable sediments increases mineralisation and recycling of Si(OH) 4 and organic matter in high energetic shelf areas.

  4. Hourly and daily evapotranspiration of alfalfa under regional advection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Regional advection often affects the evapotranspiration rates of irrigated crops in the Southern High Plains. In 1998, during a 10-day period (13-22 June) of unusually strong advection, high evapotranspiration (ET) rates for unstressed, irrigated alfalfa (Medicago sativa) were measured with two prec...

  5. 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. PMID:16496054

  6. 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. PMID:27020885

  7. Study of the conformational change of adsorbed proteins on biomaterial surfaces using hydrogen-deuterium exchange with mass spectroscopy.

    PubMed

    Kim, Jinku

    2016-05-01

    There is no doubt that protein adsorption plays a crucial role in determining biocompatibility of biomaterials. Despite the information of the identity and composition of blood plasma/serum proteins adsorbed on surfaces of biomaterials to understand which proteins are involved in blood/biomaterial interactions, it still does not provide information about the conformations and orientations of adsorbed protein, which are very important in determining biological responses to biomaterials. Therefore, our laboratory has developed an experimental technology to probe protein conformations on materials that is applicable to mixtures of proteins. Herein, the new application of hydrogen/deuterium (H/D) exchange combined with mass spectrometry was applied to determine conformational changes of adsorbed proteins at biomaterial surfaces. The results suggest that there may be a significant conformational change in adsorbed proteins at 'low' bulk concentrations that leads to a large change in the kinetics of H/D exchange as compared to 'high' bulk concentrations. This technique may eventually be useful for the study of the kinetics of protein conformational changes. PMID:26896658

  8. Label-Free, In-Solution Screening of Peptide Libraries for Binding to Protein Targets Using Hydrogen Exchange Mass Spectrometry.

    PubMed

    Maaty, Walid S; Weis, David D

    2016-02-01

    There is considerable interest in the discovery of peptide ligands that bind to protein targets. Discovery of such ligands is usually approached by screening large peptide libraries. However, the individual peptides must be tethered to a tag that preserves their individual identities (e.g., phage display or one-bead one-compound). To overcome this limitation, we have developed a method for screening libraries of label-free peptides for binding to a protein target in solution as a single batch. The screening is based on decreased amide hydrogen exchange by peptides that bind to the target. Hydrogen exchange is measured by mass spectrometry. We demonstrate the approach using a peptide library derived from the Escherichia coli proteome that contained 6664 identifiable features. The library was spiked separately with a peptide spanning the calmodulin binding domain of endothelial nitric oxide synthase (eNOS, 494-513) and a peptide spanning the N-terminal 20 residues of bovine ribonuclease A (S peptide). Human calmodulin and bovine ribonuclease S (RNase S) were screened against the library. Using a novel data analysis workflow, we identified the eNOS peptide as the only calmodulin binding peptide and S peptide as the only ribonuclease S binding peptide in the library. PMID:26741284

  9. Advective Mechanisms in Tree Island Formation

    NASA Astrophysics Data System (ADS)

    Stothoff, S.

    2002-05-01

    Tree islands are important landscape features in the Florida Everglades. Tres islands are formed of peat deposited on the shallow limestone bedrock, and have been stressed as the system has changed in response to anthropogenic activities due to the sensitivity of organic soils to hydrologic cycles. The plume shape aligned with flow direction for typical tree islands is characteristic of advective transport, despite the rather low flow velocities in the system. Hypothesized mechanisms for the plume shape include sediment transport downstream from the head of the island (often anchored by a bedrock rise), or nutrient transport downstream allowing plants to produce more sediments in situ. Understanding mechanisms controlling tree island shape will aid in understanding the response of tree islands to hydrologic management. An integrated system of field, laboratory, and modeling studies is underway, with the first effort aimed at bounding the importance of the simpler sediment transport processes before tackling more-complex nutrient transport processes. The numerical model integrating the field and laboratory efforts is a 3D finite volume model considering water flow in the shallow groundwater/surface-water system together with sediment transport. The model can account for variable vegetative resistance through the flow column, including the important case where a dense mat forms at the surface. Model components specific for this system and associated data requirements are presented.

  10. Towards entropy detection of anomalous mass and momentum exchange in incompressible fluid flow

    NASA Astrophysics Data System (ADS)

    Naterer, G. F.; Rinn, D.

    2002-08-01

    An entropy-based approach is presented for assessment of computational accuracy in incompressible flow problems. It is shown that computational entropy can serve as an effective parameter in detecting erroneous or anomalous predictions of mass and momentum transport in the flow field. In the present paper, the fluid flow equations and second law of thermodynamics are discretized by a Galerkin finite-element method with linear, isoparametric triangular elements. It is shown that a weighted entropy residual is closely related to truncation error; this relationship is examined in an application problem involving incompressible flow through a converging channel. In particular, regions exhibiting anomalous flow behaviour, such as under-predicted velocities, appear together with analogous trends in the weighted entropy residual. It is anticipated that entropy-based error detection can provide important steps towards improved accuracy in computational fluid flow. Copyright

  11. Two-step ion-exchange chromatographic purification combined with reversed-phase chromatography to isolate C-peptide for mass spectrometric analysis.

    PubMed

    Kabytaev, Kuanysh; Durairaj, Anita; Shin, Dmitriy; Rohlfing, Curt L; Connolly, Shawn; Little, Randie R; Stoyanov, Alexander V

    2016-02-01

    A liquid chromatography with mass spectrometry on-line platform that includes the orthogonal techniques of ion exchange and reversed phase chromatography is applied for C-peptide analysis. Additional improvement is achieved by the subsequent application of cation- and anion-exchange purification steps that allow for isolating components that have their isoelectric points in a narrow pH range before final reversed-phase mass spectrometry analysis. The utility of this approach for isolating fractions in the desired "pI window" for profiling complex mixtures is discussed. PMID:26717885

  12. 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

  13. 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.

  14. Slow histidine H/D exchange protocol for thermodynamic analysis of protein folding and stability using mass spectrometry.

    PubMed

    Tran, Duc T; Banerjee, Sambuddha; Alayash, Abdu I; Crumbliss, Alvin L; Fitzgerald, Michael C

    2012-02-01

    Described here is a mass spectrometry-based protocol to study the thermodynamic stability of proteins and protein-ligand complexes using the chemical denaturant dependence of the slow H/D exchange reaction of the imidazole C(2) proton in histidine side chains. The protocol is developed using several model protein systems including: ribonuclease (Rnase) A, myoglobin, bovine carbonic anhydrase (BCA) II, hemoglobin (Hb), and the hemoglobin-haptoglobin (Hb-Hp) protein complex. Folding free energies consistent with those previously determined by other more conventional techniques were obtained for the two-state folding proteins, Rnase A and myoglobin. The protocol successfully detected a previously observed partially unfolded intermediate stabilized in the BCA II folding/unfolding reaction, and it could be used to generate a K(d) value of 0.24 nM for the Hb-Hp complex. The compatibility of the protocol with conventional mass spectrometry-based proteomic sample preparation and analysis methods was also demonstrated in an experiment in which the protocol was used to detect the binding of zinc to superoxide dismutase in the yeast cell lysate sample. The yeast cell sample analyses also helped define the scope of the technique, which requires the presence of globally protected histidine residues in a protein's three-dimensional structure for successful application. PMID:22185579

  15. The Hornsund fjord - modeling of the general circulation, heat exchange and water masses transport.

    NASA Astrophysics Data System (ADS)

    Przyborska, Anna; Jakacki, Jaromir; Kosecki, Szymon; Sundfjord, Arild

    2015-04-01

    The MIKE3D hydrodynamic model has been implemented for diagnosis an ecosystem status in the most southern fjord of the Svalbard Archipelago. The model is based on MIKE 3 Flow Model FM that uses flexible mesh grid. The spatial discretization in solutions of equations is performed by the finite element method. The regional scale of the model implicated implementation of external data at the lateral boundary region. In our case Flather's boundary condition let us to force the model with combined information. At the same time tidal ordinate and barotropic component of velocity that reflects the West Spitsbergen Current are implemented. Also salinity and temperature were nested at the boundary area. The upper boundary conditions was also introduced. The data for the boundary were taken from Global Tide Model (all tidal components), an 800 m ROMS simulation of the Svalbard area made by the Norwegian Institute of Marine Research (bartoropic velocities, temperature and salinity), European Centre for Medium Weather Forecast (ECMWF) and also from Global Data Assimilation System (GDAS). Implemented model was validated and the mean circulation and its seasonal variability will be presented. Also influence of the shelf water masses on the fjord will be discussed. Fresh water transport from glaciers, run off and snow will be estimated. Results are based on 5 years simulation (2005-2010) This work was partially performed in the frame of the projects GAME (DEC-2012/04/A/NZ8/00661) and AWAKE2 (Pol-Nor/198675/17/2013)

  16. 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.

  17. On the theory of heat and mass exchange between contacting spherical particles

    NASA Astrophysics Data System (ADS)

    D'Yakonov, S. N.; Ryumshin, B. V.; Kotlyarova, L. V.

    2011-10-01

    The steady-state mass transfer of a chemically active impurity to the surface of a stationary dumbbell-shaped particle consisting of two solid contacting reacting spheres of different sizes is analyzed theoretically. The surrounding medium is at rest, and the numerical concentration of the reagent at a large distance from the aggregate of the spheres is maintained constant. The first-order chemical heterogeneous reaction occurs at a high finite rate and is assumed to be isothermal. The solution to the boundary-value diffusion problem is described by a Laplace axisymmetric equation in the system of tangential-spherical coordinates of revolution. A system of two second-order linear perturbed ordinary differential equations with variable coefficients are obtained using the zero-order integral Hankel transformation and its properties from the boundary conditions for transformed functions. Partial integrals and the mean auxiliary Sherwood numbers are obtained approximately. The solution to the formulated problem is used in various technological applications associated with combustion or chemical reactions at the interface between the continuous and discrete phases in the dispersed system, in meteorology, in analysis of problems associated with environmental pollution, etc.

  18. Vacuum fluctuation effects on the {rho}-meson mass and the one-{rho} exchange potential at finite temperature and density

    SciTech Connect

    Zhang, Yi-Jun; Gao, Song; Su, Ru-Keng Zhang, Yi-Jun Gao, Song Su, Ru-Keng

    1997-12-01

    Based on thermofield dynamics, the temperature- and density-dependent effective mass and screening mass of {rho} meson have been calculated. The effects of vacuum fluctuation corrections through effective nucleon mass are examined. We have shown that vacuum fluctuations give an important correction to the self-energy of the {rho} meson and lead to a reduction of the {rho}-meson mass in hot and dense matter. The temperature and density dependence of one-{rho}-meson exchange potential with vacuum fluctuation correction is also given. {copyright} {ital 1997} {ital The American Physical Society}

  19. 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.

  20. Chaotic advection, diffusion, and reactions in open flows

    SciTech Connect

    Tel, Tamas; Karolyi, Gyoergy; Pentek, Aron; Scheuring, Istvan; Toroczkai, Zoltan; Grebogi, Celso; Kadtke, James

    2000-03-01

    We review and generalize recent results on advection of particles in open time-periodic hydrodynamical flows. First, the problem of passive advection is considered, and its fractal and chaotic nature is pointed out. Next, we study the effect of weak molecular diffusion or randomness of the flow. Finally, we investigate the influence of passive advection on chemical or biological activity superimposed on open flows. The nondiffusive approach is shown to carry some features of a weak diffusion, due to the finiteness of the reaction range or reaction velocity. (c) 2000 American Institute of Physics.

  1. 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

  2. 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.

  3. The cause of advective slowdown of tracer pebbles in rivers: Implementation of Exner-Based Master Equation for coevolving streamwise and vertical dispersion

    NASA Astrophysics Data System (ADS)

    Pelosi, A.; Schumer, R.; Parker, G.; Ferguson, R. I.

    2016-03-01

    Tracer pebbles are often used to study bed load transport processes in gravel bed rivers. Models have been proposed for their downstream dispersion, and also for vertical dispersion, but not for the combined effects of downstream and vertical movement. Here we use the Exner-Based Master Equation to characterize the transient coevolution of streamwise and vertical advection-diffusion of tracer pebbles under equilibrium transport conditions (no net aggradation or degradation). The coevolution of streamwise and vertical dispersion gives rise to behavior that can differ markedly from that associated with purely streamwise processes with no vertical exchange. One example is streamwise advective slowdown. Particles that are advected downward into zones where the probability of reentrainment becomes asymptotically small are essentially trapped and can no longer participate in streamwise advection. As a result, the mean streamwise velocity of the tracer plume declines in time. Qualitative and quantitative comparisons with two field experiments show encouraging agreement despite the simplified boundary conditions in the model.

  4. 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

  5. Quantification of melamine in human urine using cation-exchange based high performance liquid chromatography tandem mass spectrometry.

    PubMed

    Panuwet, Parinya; Nguyen, Johnny V; Wade, Erin L; D'Souza, Priya E; Ryan, P Barry; Barr, Dana Boyd

    2012-03-01

    Melamine and cyanuric acid have been implicated as adulterants in baby formula in China and pet foods in North America. In China, the effect of melamine or melamine-cyanuric acid adulteration lead to kidney stone development and acute renal failure in thousands of Chinese infants. A selective and sensitive analytical method was developed to measure melamine in human urine in order to evaluate the extent of potential health implications resulting from the consumption of these types of adulterated products in the general US population. This method involves extracting melamine from human urine using cation-exchange solid-phase extraction, chromatographically separating it from its urinary matrix co-extractants on a silica-based, strong-cation exchange analytical column using high performance liquid chromatography, and analysis using positive mode electrospray ionization tandem mass spectrometry. Quantification was performed using modified, matrix-based isotope dilution calibration covering the concentration range of 0.50-100 ng/mL. The limit of detection, calculated using replicates of blank and low level spiked samples, was 0.66 ng/mL and the relative standard deviations were between 6.89 and 14.9%. The relative recovery of melamine was 101-106%. This method was tested for viability by analyzing samples collected from the general US population. Melamine was detected in 76% of the samples tested, with a geometric mean of 2.37 ng/mL, indicating that this method is suitable for reliably detecting background exposures to melamine or other chemicals from which it can be derived. PMID:22309774

  6. Burgers turbulence and passive random advection

    NASA Astrophysics Data System (ADS)

    Boldyrev, Stanislav Anatolievich

    1999-10-01

    , and the diffusivity is neglected. These considerations illustrate that even with simple statistics of the velocity field, the statistics of advected quantities are nontrivial due to nonlinear interactions of different spatial directions. The last Chapter 5 summarizes the results and discusses future directions of research.

  7. 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

  8. 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.

  9. Magnetic helicity transport in the advective gauge family

    SciTech Connect

    Candelaresi, Simon; Brandenburg, Axel; Hubbard, Alexander; Mitra, Dhrubaditya

    2011-01-15

    Magnetic helicity fluxes are investigated in a family of gauges in which the contribution from ideal magnetohydrodynamics takes the form of a purely advective flux. Numerical simulations of magnetohydrodynamic turbulence in this advective gauge family exhibit instabilities triggered by the build-up of unphysical irrotational contributions to the magnetic vector potential. As a remedy, the vector potential is evolved in a numerically well behaved gauge, from which the advective vector potential is obtained by a gauge transformation. In the kinematic regime, the magnetic helicity density evolves similarly to a passive scalar when resistivity is small and turbulent mixing is mild, i.e., when the fluid Reynolds number is not too large. In the dynamical regime, resistive contributions to the magnetic helicity flux in the advective gauge are found to be significant owing to the development of small length scales in the irrotational part of the magnetic vector potential.

  10. 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.

  11. 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.

  12. Adaptive domain decomposition methods for advection-diffusion problems

    SciTech Connect

    Carlenzoli, C.; Quarteroni, A.

    1995-12-31

    Domain decomposition methods can perform poorly on advection-diffusion equations if diffusion is dominated by advection. Indeed, the hyperpolic part of the equations could affect the behavior of iterative schemes among subdomains slowing down dramatically their rate of convergence. Taking into account the direction of the characteristic lines we introduce suitable adaptive algorithms which are stable with respect to the magnitude of the convective field in the equations and very effective on bear boundary value problems.

  13. A spatial SIS model in advective heterogeneous environments

    NASA Astrophysics Data System (ADS)

    Cui, Renhao; Lou, Yuan

    2016-09-01

    We study the effects of diffusion and advection for a susceptible-infected-susceptible epidemic reaction-diffusion model in heterogeneous environments. The definition of the basic reproduction number R0 is given. If R0 < 1, the unique disease-free equilibrium (DFE) is globally asymptotically stable. Asymptotic behaviors of R0 for advection rate and mobility of the infected individuals (denoted by dI) are established, and the existence of the endemic equilibrium when R0 > 1 is studied. The effects of diffusion and advection rates on the stability of the DFE are further investigated. Among other things, we find that if the habitat is a low-risk domain, there may exist one critical value for the advection rate, under which the DFE changes its stability at least twice as dI varies from zero to infinity, while the DFE is unstable for any dI when the advection rate is larger than the critical value. These results are in strong contrast with the case of no advection, where the DFE changes its stability at most once as dI varies from zero to infinity.

  14. Conformational Analysis of Proteins in Highly Concentrated Solutions by Dialysis-Coupled Hydrogen/Deuterium Exchange Mass Spectrometry.

    PubMed

    Houde, Damian; Nazari, Zeinab E; Bou-Assaf, George M; Weiskopf, Andrew S; Rand, Kasper D

    2016-04-01

    When highly concentrated, an antibody solution can exhibit unusual behaviors, which can lead to unwanted properties, such as increased levels of protein aggregation and unusually high viscosity. Molecular modeling, along with many indirect biophysical measurements, has suggested that the cause for these phenomena can be due to short range electrostatic and/or hydrophobic protein-protein interactions. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a useful tool for investigating protein conformation, dynamics, and interactions. However, "traditional" continuous dilution labeling HDX-MS experiments have limited utility for the direct analysis of solutions with high concentrations of protein. Here, we present a dialysis-based HDX-MS (di-HDX-MS) method as an alternative HDX-MS labeling format, which takes advantage of passive dialysis rather than the classic dilution workflow. We applied this approach to a highly concentrated antibody solution without dilution or significant sample manipulation, prior to analysis. Such a method could pave the way for a deeper understanding of the unusual behavior of proteins at high concentrations, which is highly relevant for development of biopharmaceuticals in industry. Graphical Abstract ᅟ. PMID:26860088

  15. 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. PMID:25246101

  16. Hexicon 2: automated processing of hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation.

    PubMed

    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. PMID:24676893

  17. 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.

  18. Characterization of Stress-Exposed Granulocyte Colony Stimulating Factor Using ELISA and Hydrogen/Deuterium Exchange Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Tsuchida, Daisuke; Yamazaki, Katsuyoshi; Akashi, Satoko

    2014-10-01

    Information on the higher-order structure is important in the development of biopharmaceutical drugs. Recently, hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) has been widely used as a tool to evaluate protein conformation, and unique automated systems for HDX-MS are now commercially available. To investigate the potential of this technique for the prediction of the activity of biopharmaceuticals, granulocyte colony stimulating factor (G-CSF), which had been subjected to three different stress types, was analyzed using HDX-MS and through comparison with receptor-binding activity. It was found that HDX-MS, in combination with ion mobility separation, was able to identify conformational changes in G-CSF induced by stress, and a good correlation with the receptor-binding activity was demonstrated, which cannot be completely determined by conventional peptide mapping alone. The direct evaluation of biological activity using bioassay is absolutely imperative in biopharmaceutical development, but HDX-MS can provide the alternative information in a short time on the extent and location of the structural damage caused by stresses. Furthermore, the present study suggests the possibility of this system being a versatile evaluation method for the preservation stability of biopharmaceuticals.

  19. Using Hydrogen/Deuterium Exchange Mass Spectrometry to Study Conformational Changes in Granulocyte Colony Stimulating Factor upon PEGylation

    PubMed Central

    Wei, Hui; Ahn, Joomi; Yu, Ying Qing; Tymiak, Adrienne; Engen, John R.; Chen, Guodong

    2012-01-01

    PEGylation is the covalent attachment of polyethylene glycol to proteins, and it can be used to alter immunogenicity, circulating half life and other properties of therapeutic proteins. To determine the impact of PEGylation on protein conformation, we applied hydrogen/deuterium exchange mass spectrometry (HDX MS) to analyze Granulocyte Colony Stimulating Factor (G-CSF) upon PEGylation as a model system. The combined use of HDX automation technology and data analysis software allowed reproducible and robust measurements of the deuterium incorporation levels for peptic peptides of both PEGylated and non-PEGylated G-CSF. The results indicated that significant differences in deuterium incorporation were induced by PEGylation of G-CSF, although the overall changes observed were quite small. PEGylation did not result in gross conformational rearrangement of G-CSF. The data complexity often encountered in HDX MS measurements was greatly reduced though a data processing and presentation format designed to facilitate the comparison process. This study demonstrates the practical utility of HDX MS for comparability studies, process monitoring and protein therapeutic characterization in the biopharmaceutical industry. PMID:22227798

  20. 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 %. PMID:24969465

  1. 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.

  2. Conformational Analysis of Proteins in Highly Concentrated Solutions by Dialysis-Coupled Hydrogen/Deuterium Exchange Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Houde, Damian; Nazari, Zeinab E.; Bou-Assaf, George M.; Weiskopf, Andrew S.; Rand, Kasper D.

    2016-04-01

    When highly concentrated, an antibody solution can exhibit unusual behaviors, which can lead to unwanted properties, such as increased levels of protein aggregation and unusually high viscosity. Molecular modeling, along with many indirect biophysical measurements, has suggested that the cause for these phenomena can be due to short range electrostatic and/or hydrophobic protein-protein interactions. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a useful tool for investigating protein conformation, dynamics, and interactions. However, "traditional" continuous dilution labeling HDX-MS experiments have limited utility for the direct analysis of solutions with high concentrations of protein. Here, we present a dialysis-based HDX-MS (di-HDX-MS) method as an alternative HDX-MS labeling format, which takes advantage of passive dialysis rather than the classic dilution workflow. We applied this approach to a highly concentrated antibody solution without dilution or significant sample manipulation, prior to analysis. Such a method could pave the way for a deeper understanding of the unusual behavior of proteins at high concentrations, which is highly relevant for development of biopharmaceuticals in industry.

  3. 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.

  4. Heat exchanger

    SciTech Connect

    Drury, C.R.

    1988-02-02

    A heat exchanger having primary and secondary conduits in heat-exchanging relationship is described comprising: at least one serpentine tube having parallel sections connected by reverse bends, the serpentine tube constituting one of the conduits; a group of open-ended tubes disposed adjacent to the parallel sections, the open-ended tubes constituting the other of the conduits, and forming a continuous mass of contacting tubes extending between and surrounding the serpentine tube sections; and means securing the mass of tubes together to form a predetermined cross-section of the entirety of the mass of open-ended tubes and tube sections.

  5. Measurements of Horizontal Advection of Carbon Dioxide Within a Forest Canopy

    NASA Astrophysics Data System (ADS)

    Schroeder, M.; Falk, M.; Paw U, K.

    2002-12-01

    We present methodology, data and analysis on the horizontal advection of Carbon Dioxide within the understory at the Wind River Canopy Crane AMERIFLUX site. The Crane is located in a Pacific Northwest Old-growth Forest with trees up to 500 years old and 65 meters tall. The forest structure is complex with seven gymnosperm and two angiosperm tree species in the 2.3 ha crane circle, large amounts of woody debris on the forest floor, and a diverse understory. Data presented was collected using a 3-dimensional CO2/H2O profile system using LiCor LI6262 and LI7000 closed-path InfraRed Gas Analyzers (IRGA) with a total of 15 intakes distributed on the tower and throughout the canopy. Additional data was acquired using permanent eddy covariance stations consisting of a Gill-Solent HS Research sonic anemometer and a LiCor LI6262 IRGA, which have been operated for over 4 years at a height of 2.5 meters to complement an identical system measuring total ecosystem exchange at a height of 70 meters. Supplementary micro-meteorological data was collected by a vertical profile of 8 stations. Advection of Carbon Dioxide was calculated using horizontal concentration differences and mean wind speed and direction for half-hour periods. The Net ecosystem carbon exchange (NEE) estimated by eddy-covariance ranges from a sink of 1.9 tC ha-1 yr-1 to a source of 0.5 tC ha-1 yr-1. The long-term understory eddy covariance data indicate the release of carbon from the soil to be as large as 11 tC ha-1 yr-1 with maximum values of 6 to 8 \\mu mol m-1 s-1. Preliminary data show that advection can account for 20% of Carbon Dioxide fluxes measured by eddy covariance.

  6. Modulated point-vortex pairs on a rotating sphere: Dynamics and chaotic advection

    NASA Astrophysics Data System (ADS)

    Drótos, Gábor; Tél, Tamás; Kovács, Gergely

    2013-06-01

    The dynamics of modulated point-vortex pairs is investigated on a rotating sphere, where modulation is chosen to reflect the conservation of angular momentum (potential vorticity). For sufficiently close vortices (dipoles) the trajectories of their center-of-mass are shown to correspond to those of a point particle moving freely on a rotating sphere. For finite size vortex pairs, a qualitative similarity to the geodesic dynamics is found. The advection dynamics generated by vortex pairs on a rotating sphere is found to be chaotic. In the short time dynamics we point out a transition from closed to open chaotic advection, which implies that the transport properties of the flow might drastically be altered by changing the initial conditions of the pair on the sphere. Due to spherical topology, for long times, even the open advection patterns are found to gradually cross over to that corresponding to a homogeneous closed mixing. This pattern extends along a zonal band, whereas short term closed mixing remains always bounded to the moving pair.

  7. Parallel simulation of particle transport in an advection field applied to volcanic explosive eruptions

    NASA Astrophysics Data System (ADS)

    Künzli, Pierre; Tsunematsu, Kae; Albuquerque, Paul; Falcone, Jean-Luc; Chopard, Bastien; Bonadonna, Costanza

    2016-04-01

    Volcanic ash transport and dispersal models typically describe particle motion via a turbulent velocity field. Particles are advected inside this field from the moment they leave the vent of the volcano until they deposit on the ground. Several techniques exist to simulate particles in an advection field such as finite difference Eulerian, Lagrangian-puff or pure Lagrangian techniques. In this paper, we present a new flexible simulation tool called TETRAS (TEphra TRAnsport Simulator) based on a hybrid Eulerian-Lagrangian model. This scheme offers the advantages of being numerically stable with no numerical diffusion and easily parallelizable. It also allows us to output particle atmospheric concentration or ground mass load at any given time. The model is validated using the advection-diffusion analytical equation. We also obtained a good agreement with field observations of the tephra deposit associated with the 2450 BP Pululagua (Ecuador) and the 1996 Ruapehu (New Zealand) eruptions. As this kind of model can lead to computationally intensive simulations, a parallelization on a distributed memory architecture was developed. A related performance model, taking into account load imbalance, is proposed and its accuracy tested.

  8. Modulated point-vortex pairs on a rotating sphere: dynamics and chaotic advection.

    PubMed

    Drótos, Gábor; Tél, Tamás; Kovács, Gergely

    2013-06-01

    The dynamics of modulated point-vortex pairs is investigated on a rotating sphere, where modulation is chosen to reflect the conservation of angular momentum (potential vorticity). For sufficiently close vortices (dipoles) the trajectories of their center-of-mass are shown to correspond to those of a point particle moving freely on a rotating sphere. For finite size vortex pairs, a qualitative similarity to the geodesic dynamics is found. The advection dynamics generated by vortex pairs on a rotating sphere is found to be chaotic. In the short time dynamics we point out a transition from closed to open chaotic advection, which implies that the transport properties of the flow might drastically be altered by changing the initial conditions of the pair on the sphere. Due to spherical topology, for long times, even the open advection patterns are found to gradually cross over to that corresponding to a homogeneous closed mixing. This pattern extends along a zonal band, whereas short term closed mixing remains always bounded to the moving pair. PMID:23848782

  9. A deterministic Lagrangian particle separation-based method for advective-diffusion problems

    NASA Astrophysics Data System (ADS)

    Wong, Ken T. M.; Lee, Joseph H. W.; Choi, K. W.

    2008-12-01

    A simple and robust Lagrangian particle scheme is proposed to solve the advective-diffusion transport problem. The scheme is based on relative diffusion concepts and simulates diffusion by regulating particle separation. This new approach generates a deterministic result and requires far less number of particles than the random walk method. For the advection process, particles are simply moved according to their velocity. The general scheme is mass conservative and is free from numerical diffusion. It can be applied to a wide variety of advective-diffusion problems, but is particularly suited for ecological and water quality modelling when definition of particle attributes (e.g., cell status for modelling algal blooms or red tides) is a necessity. The basic derivation, numerical stability and practical implementation of the NEighborhood Separation Technique (NEST) are presented. The accuracy of the method is demonstrated through a series of test cases which embrace realistic features of coastal environmental transport problems. Two field application examples on the tidal flushing of a fish farm and the dynamics of vertically migrating marine algae are also presented.

  10. The effects of advection solvers on the performance of air quality models

    SciTech Connect

    Tanrikulu, S.; Odman, M.T.

    1996-12-31

    The available numerical solvers for the advection term in the chemical species conservation equation have different properties, and consequently introduce different types of errors. These errors can affect the performance of air quality models and lead to biases in model results. In this study, a large number of advection solvers have been studied and six of them were identified as having potential for use in photochemical models. The identified solvers were evaluated extensively using various numerical tests that are relevant to air quality simulations. Among the solvers evaluated, three of them showed better performance in terms of accuracy and some other characteristics such as conservation of mass and positivity. They are the solvers by Bott, Yuamartino, and Dabdub and Seinfeld. These three solvers were incorporated into the SARMAP Air Quality Model (SAQM) and the August 3-6, 1990 ozone episode in the San Joaquin Valley of California was simulated with each. A model performance analysis was conducted for each simulation using the rich air quality database of the 1990 San Joaquin Valley Air Quality Study. The results of the simulations were compared with each other and the effects of advection solvers on the performance of the model are discussed.

  11. 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

  12. Membrane-Associated Conformation of HIV-1 Nef Investigated with Hydrogen Exchange Mass Spectrometry at a Langmuir Monolayer.

    PubMed

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

    2015-07-21

    In the companion paper to this work, we 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 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

  13. 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.

  14. 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

  15. 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. PMID:25740347

  16. 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.

  17. Assessing gibberellins oxidase activity by anion exchange/hydrophobic polymer monolithic capillary liquid chromatography-mass spectrometry.

    PubMed

    Chen, Ming-Luan; Su, Xin; Xiong, Wei; 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 (K m) 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

  18. Water mass exchanges between the Norwegian and Iceland seas over the Jan Mayen Ridge using in-situ current measurements

    NASA Astrophysics Data System (ADS)

    Mork, Kjell Arne; Drinkwater, Kenneth F.; Jónsson, Steingrímur; Valdimarsson, Héðinn; Ostrowski, Marek

    2014-11-01

    The Jan Mayen Ridge, with bottom depths of 1000 m and less, runs southwards from Jan Mayen and separates the warmer and saltier Atlantic Water in the Norwegian Sea from the colder and fresher Arctic water in the Iceland Sea. During the International Polar Year (IPY, 2007-2008), three current meter moorings were deployed with the purpose to investigate water mass exchanges between the Norwegian and Iceland seas over the Ridge and their forcing mechanisms. These are the first in-situ current measurements for this region. The results showed relatively weak currents on the Ridge that frequently shifted direction except near-bottom and at the western slope of the Ridge. All current measurements showed low eddy activity and tidal velocities (less than 0.05 ms- 1). Wind-forced near-inertial motion generated from transient atmospheric low pressure systems were observed in the mixed layer being strongest during autumn and winter when ocean velocities reached 0.7 ms- 1. Near surface currents on the Ridge are influenced by local winds on a time scale of 6 days and longer, but during the two-year deployment no pronounced seasonal variation was observed, mainly due to a lack of seasonality in the local winds. In a 2000 m deep channel that cuts the Ridge, there was pronounced seasonal variation in the currents at all depths below 40 m with stronger flow toward the Iceland Sea during winter compared to summer. The variability of the deep current was found to be influenced by the large-scale wind stress curl. There was a weak net flow with averaged velocities of ~ 0.01 ms- 1 over the Ridge that was directed westward in the upper layer, signifying a small net transport of modified Atlantic Water into the Iceland Sea.

  19. 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

  20. 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. PMID:26946424

  1. Conformational difference in human IgG2 disulfide isoforms revealed by hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Zhang, Aming; Fang, Jing; Chou, Robert Y-T; Bondarenko, Pavel V; Zhang, Zhongqi

    2015-03-17

    Both recombinant and natural human IgG2 antibodies have several different disulfide bond isoforms, which possess different global structures, thermal stabilities, and biological activities. A detailed mapping of the structural difference among IgG2 disulfide isoforms, however, has not been established. In this work, we employed hydrogen/deuterium exchange mass spectrometry to study the conformation of three major IgG2 disulfide isoforms known as IgG2-B, IgG2-A1, and IgG2-A2 in two recombinant human IgG2 monoclonal antibodies. By comparing the protection factors between amino acid residues in isoforms B and A1 (the classical form), we successfully identified several local regions in which the IgG2-B isoform showed more solvent protection than the IgG2-A1 isoform. On the basis of three-dimensional structural models of IgG2, these identified regions were located on the Fab domains, close to the hinge, centered on the side where the two Fab arms faced each other in spatial proximity. We speculated that in the more solvent-protected B isoform, the two Fab arms were brought into contact by the nonclassical disulfide bonds, resulting in a more compact global structure. Loss of Fab domain flexibility in IgG2-B could limit its ability to access cell-surface epitopes, leading to reduced antigen binding potency. The A2 isoform was previously found to have disulfide linkages similar to those of the classical A1 isoform, but with different biophysical behaviors. Our data indicated that, compared to IgG2-A1, IgG2-A2 had less solvent protection in some heavy-chain Fab regions close the hinge, suggesting that the A2 isoform had more flexible Fab domains. PMID:25730439

  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. Analysis of Local Dynamics of Human Insulin and a Rapid-acting Insulin Analog by Hydrogen Deuterium Exchange Mass Spectrometry

    PubMed Central

    Nakazawa, Shiori; Hashii, Noritaka; Hirose, Kenji; Kawasaki, Nana; Ahn, Joomi

    2013-01-01

    Human insulin, used by diabetics to regulate blood sugar, was first introduced as a recombinant therapeutic drug nearly 30 years ago. Human insulin and insulin lispro have identical primary structure, except for the transposition of two amino acids. Lispro is one of the rapid-acting insulin analogs, which has higher tendency to dissociate than human insulin. In this study, we present an analytical workflow to allow us to detect the difference in the oligomeric dynamics using Hydrogen Deuterium Exchange Mass Spectrometry (HDX MS). The HDX analysis on Insulin and Lispro peptides was conducted to identify the location where different deuterium uptakes were observed between human insulin and lispro. The detected areas were illustrated in various formats to help understand their flexibility associated with rapid dissociation of insulin oligomers. Drug products, human insulin (Humulin R) and lispro (Humalog), were reduced and digested online by pepsin. Deuterium labeling, quenching, and injection to on-line pepsin digestion were prepared using a robotic sample manager. Labeling experiments in 0, 0.5, 5, 10, 60, and 180 min interval were duplicated for both samples. The peptic digests were separated on a UPLC system at 0 °C. Q-TOF MS was used to measure the deuterium incorporation of identified peptides. The amount of deuterium was determined by automated HDX data processing software, DynamX 2.0. We obtained 98% of sequence coverage for both human insulin and lispro. From peptide HDX determination, two regions were revealed distinctive different values in deuterium uptakes between human insulin and lispro; the N terminus of chain A, and a region adjacent to the C terminus of chain B. We attributed this localized behavior to the relation of hexamerization and dimerization, respectively. Furthermore, characteristic profiles that showed different deuteration margins between two insulins were determined, which was also consistent with their involvement in hexamer and dimer

  4. Variability of Sub-Canopy Flow, Temperature, and Horizontal Advection in Moderately Complex Terrain

    NASA Astrophysics Data System (ADS)

    Thomas, Christoph K.

    2011-04-01

    We examine the space-time structure of the wind and temperature fields, as well as that of the resulting spatial temperature gradients and horizontal advection of sensible heat, in the sub-canopy of a forest with a dense overstorey in moderately complex terrain. Data were collected from a sensor network consisting of ten stations and subject to orthogonal decomposition using the multiresolution basis set and stochastic analyses including two-point correlations, dimensional structure functions, and various other bulk measures for space and time variability. Despite some similarities, fundamental differences were found in the space-time structure of the motions dominating the variability of the sub-canopy wind and temperature fields. The dominating motions occupy similar spatial, but different temporal, scales. A conceptual space-time diagram was constructed based on the stochastic analysis that includes the important end members of the spatial and temporal scales of the observed motions of both variables. Short-lived and small-scale motions govern the variability of the wind, while the diurnal temperature oscillation driven by the surface radiative transfer is the main determinant of the variability in the temperature signal, which occupies much larger time scales. This scale mismatch renders Taylor's hypothesis for sub-canopy flow invalid and aggravates the computation of meaningful estimates of horizontal advective fluxes without dense spatial information. It may further explain the ambiguous and inconclusive results reported in numerous energy and mass balance and advection studies evaluating the hypothesis that accounting for budget components other than the change in storage term and the vertical turbulent flux improves the budget closure when turbulent diffusion is suppressed in plant canopies. Estimates of spatial temperature gradients and advective fluxes were sensitive to the network geometry and the spatial interpolation method. The assumption of linear

  5. Mass

    SciTech Connect

    Chris Quigg

    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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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. PMID:15907926

  14. 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...

  15. Topology preserving advection of implicit interfaces on Cartesian grids

    NASA Astrophysics Data System (ADS)

    Qin, Zhipeng; Delaney, Keegan; Riaz, Amir; Balaras, Elias

    2015-06-01

    Accurate representation of implicit interface topology is important for the numerical computation of two phase flow on Cartesian grids. A new method is proposed for the construction of signed distance function by geometrically projecting interface topology onto the Cartesian grid using a multi-level projection framework. The method involves a stepwise improvement in the approximation to the signed distance function based on pointwise, piecewise and locally smooth reconstructions of the interface. We show that this approach provides accurate representation of the projected interface and its topology on the Cartesian grid, including the distance from the interface and the interface normal and curvature. The projected interface can be in the form of either a connected set of marker particles that evolve with Lagrangian advection, or a discrete set of points associated with an implicit interface that evolves with the advection of a scalar function. The signed distance function obtained with geometric projection is independent of the details of the scaler field, in contrast to the conventional approach where advection and reinitialization cannot be decoupled. As a result, errors introduced by reinitialization do not amplify advection errors, which leads to substantial improvement in both volume conservation and topology representation.

  16. Consistency problem with tracer advection in the Atmospheric Model GAMIL

    NASA Astrophysics Data System (ADS)

    Zhang, Kai; Wan, Hui; Wang, Bin; Zhang, Meigen

    2008-03-01

    The radon transport test, which is a widely used test case for atmospheric transport models, is carried out to evaluate the tracer advection schemes in the Grid-Point Atmospheric Model of IAP-LASG (GAMIL). Two of the three available schemes in the model are found to be associated with significant biases in the polar regions and in the upper part of the atmosphere, which implies potentially large errors in the simulation of ozone-like tracers. Theoretical analyses show that inconsistency exists between the advection schemes and the discrete continuity equation in the dynamical core of GAMIL and consequently leads to spurious sources and sinks in the tracer transport equation. The impact of this type of inconsistency is demonstrated by idealized tests and identified as the cause of the aforementioned biases. Other potential effects of this inconsistency are also discussed. Results of this study provide some hints for choosing suitable advection schemes in the GAMIL model. At least for the polar-region-concentrated atmospheric components and the closely correlated chemical species, the Flux-Form Semi-Lagrangian advection scheme produces more reasonable simulations of the large-scale transport processes without significantly increasing the computational expense.

  17. ADVECTION INFLUENCES ON EVAPOTRANSPIRATION OF ALFALFA IN A SEMIARID ENVIRONMENT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advective enhancement of crop evapotranspiration (ET) occurs when drier, hotter air is transported into the crop by wind and can be an important factor in the water balance of irrigated crops in a semiarid climate. Thirteen days of moderate to extremely high ET rates of irrigated alfalfa (Medicago ...

  18. The 'optimum' upwind advection on a triangular mesh

    NASA Technical Reports Server (NTRS)

    Roe, P. L.

    1990-01-01

    For advection schemes based on fluctuation splitting, a design criterion of optimizing the time step leads to linear schemes that coincide with those designed for least truncation error. A further stage of optimizing the time step using a nonlinear positivity criterion, leads to considerable further gains in resolution.

  19. Tidal variability of lateral advection in a coastal plain estuary

    NASA Astrophysics Data System (ADS)

    Basdurak, N. B.; Valle-Levinson, A.

    2013-07-01

    Tidal variability of lateral advection of momentum (vuy, where u and v are along-estuary and lateral flows, respectively, and the subindex indicates differentiation with respect to the cross-estuary direction) was investigated in a coastal plain estuary with observations at Hampton Roads, which is the transition between the James River and Chesapeake Bay. Towed current velocity profiles and hydrographic profiles were captured during 9 expeditions in 2004 and 2005, to determine the intratidal and spatial changes in lateral advection of momentum and its contribution to along-channel flow. Curvature effects and lateral density gradients were important in driving lateral circulation and in modifying intratidal lateral advection of momentum. Lateral advection had the same order of magnitude as the baroclinic pressure gradient. Its contribution to the along-channel momentum balance was greatest during or just after peak flood and weakest at the end of ebb. During peak flood and peak ebb, the spatial distribution of vuy was seaward at the southern (left) side near surface and at the northern side (right) near bed (looking up-estuary), and landward in the rest of the channel. During slack periods the vuy structures were mostly landward. Observations were in good agreement with analytical model results during peak ebb and flood, but inconsistent during slack periods. The discrepancies between model results and field measurements can be attributed to bathymetry-density gradient interactions, which enhanced ebb-to-flood asymmetries in the along-channel and lateral flow.

  20. The use of 18O-exchange and base-catalyzed N-dealkylation with liquid chromatography/tandem mass spectrometry to identify carbinolamide metabolites.

    PubMed

    Bessire, Andrew J; Vaz, Alfin D N; Walker, Gregory S; Wang, Wei Wei; Sharma, Raman

    2010-07-30

    Oxidation of N-alkyl-substituted amides is a common transformation observed in metabolism studies of drugs and other chemicals. Metabolism at the alpha carbon atom can produce stable carbinolamide compounds, which may be abundant enough to require complete confidence in structural assignments. In a drug discovery setting, rapid structural elucidation of test compounds is critical to inform the compound selection process. Traditional approaches to the analysis of carbinolamides have relied upon the time-consuming synthesis of authentic standards or purification of large enough quantities for characterization by nuclear magnetic resonance (NMR). We describe a simple technique used in conjunction with liquid chromatography/tandem mass spectrometry (LC/MS/MS) which demonstrates the chemical identity of a carbinolamide by its distinctive ability to reversibly exchange [(18)O]water through an imine intermediate. A key advantage of the technique is that the chromatographic retention times of metabolites are preserved, allowing direct comparisons of mass chromatograms from non-treated and [(18)O]water-treated samples. Metabolites susceptible to the treatment are clearly indicated by the addition of 2 mass units to their original mass. An additional test which can be used in conjunction with (18)O-exchange is base-catalyzed N-dealkylation of N-(alpha-hydroxy)alkyl compounds. The use of the technique is described for carbinolamide metabolites of dirlotapide, loperamide, and a proprietary compound. PMID:20552706

  1. Feasibility of Measuring Mean Vertical Motion for Estimating Advection. Chapter 6

    NASA Technical Reports Server (NTRS)

    Vickers, Dean; Mahrt, L.

    2005-01-01

    Numerous recent studies calculate horizontal and vertical advection terms for budget studies of net ecosystem exchange of carbon. One potential uncertainty in such studies is the estimate of mean vertical motion. This work addresses the reliability of vertical advection estimates by contrasting the vertical motion obtained from the standard practise of measuring the vertical velocity and applying a tilt correction, to the vertical motion calculated from measurements of the horizontal divergence of the flow using a network of towers. Results are compared for three different tilt correction methods. Estimates of mean vertical motion are sensitive to the choice of tilt correction method. The short-term mean (10 to 60 minutes) vertical motion based on the horizontal divergence is more realistic compared to the estimates derived from the standard practise. The divergence shows long-term mean (days to months) sinking motion at the site, apparently due to the surface roughness change. Because all the tilt correction methods rely on the assumption that the long-term mean vertical motion is zero for a given wind direction, they fail to reproduce the vertical motion based on the divergence.

  2. 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

  3. Heat and mass transfer over slippery, superhydrophobic surfaces

    NASA Astrophysics Data System (ADS)

    Haase, A. Sander; Lammertink, Rob G. H.

    2016-04-01

    The classical Graetz-Nusselt problem is extended to describe heat and mass transfer over heterogeneously slippery, superhydrophobic surfaces. The cylindrical wall consists of segments with a constant temperature/concentration and areas that are insulating/impermeable. Only in the case of mass transport do the locations of hydrodynamic slip and mass exchange coincide. This makes advection near the mass exchanging wall segments larger than near the heat exchanging regions. Also the direction of radial fluid flow is reversed for heat and mass transport, which has an influence on the location where the concentration or temperature boundary layer is compressed or extended. As a result, mass transport is more efficient than heat transfer. Also the influence of axial diffusion on the Nusselt and Sherwood numbers is investigated for various Péclet numbers Pe. When Pe < 102, which is characteristic for heat transfer over superhydrophobic surfaces, axial conduction should be taken into account. For Pe ≥ 102, which are typical numbers for mass transport in microfluidic systems, axial diffusion can be neglected.

  4. Rapid screening for potential epitopes reactive with a polycolonal antibody by solution-phase H/D exchange monitored by FT-ICR mass spectrometry.

    PubMed

    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. PMID:23681851

  5. 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.

  6. Epitope mapping of 7S cashew antigen in complex with antibody by solution-phase H/D exchange monitored by FT-ICR mass spectrometry.

    PubMed

    Guan, Xiaoyan; Noble, Kyle A; Tao, Yeqing; Roux, Kenneth H; Sathe, Shridhar K; Young, Nicolas L; Marshall, Alan G

    2015-06-01

    The potential epitope of a recombinant food allergen protein, cashew Ana o 1, reactive to monoclonal antibody, mAb 2G4, has been mapped by solution-phase amide backbone H/D exchange (HDX) monitored by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Purified mAb 2G4 was incubated with recombinant Ana o 1 (rAna o 1) to form antigen:monoclonal antibody (Ag:mAb) complexes. Complexed and uncomplexed (free) rAna o 1 were then subjected to HDX-MS analysis. Five regions protected from H/D exchange upon mAb binding are identified as potential conformational epitope-contributing segments. PMID:26169135

  7. 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.

  8. Spiral defect chaos in an advection-reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Affan, H.; Friedrich, R.

    2014-06-01

    This paper comprises numerical and theoretical studies of spatiotemporal patterns in advection-reaction-diffusion systems in which the chemical species interact with the hydrodynamic fluid. Due to the interplay between the two, we obtained the spiral defect chaos in the activator-inhibitor-type model. We formulated the generalized Swift-Hohenberg-type model for this system. Then the evolution of fractal boundaries due to the effect of the strong nonlinearity at the interface of the two chemical species is studied numerically. The purpose of the present paper is to point out that spiral defect chaos, observed in model equations of the extended Swift-Hohenberg equation for low Prandtl number convection, may actually be obtained also in certain advection-reaction-diffusion systems.

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

    PubMed

    Das, Amit; Polley, Anirban; Rao, Madan

    2016-02-12

    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. PMID:26919022

  10. 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.

  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. Advective and diffusive cosmic ray transport in galactic haloes

    NASA Astrophysics Data System (ADS)

    Heesen, Volker; Dettmar, Ralf-Jürgen; Krause, Marita; Beck, Rainer; Stein, Yelena

    2016-05-01

    We present 1D cosmic ray transport models, numerically solving equations of pure advection and diffusion for the electrons and calculating synchrotron emission spectra. We find that for exponential halo magnetic field distributions advection leads to approximately exponential radio continuum intensity profiles, whereas diffusion leads to profiles that can be better approximated by a Gaussian function. Accordingly, the vertical radio spectral profiles for advection are approximately linear, whereas for diffusion they are of `parabolic' shape. We compare our models with deep Australia Telescope Compact Array observations of two edge-on galaxies, NGC 7090 and 7462, at λλ 22 and 6 cm. Our result is that the cosmic ray transport in NGC 7090 is advection dominated with V=150^{+80}_{-30} km s^{-1}, and that the one in NGC 7462 is diffusion dominated with D=3.0± 1.0 × 10^{28}E_GeV^{0.5} cm^2 s^{-1}. NGC 7090 has both a thin and thick radio disc with respective magnetic field scale heights of hB1 = 0.8 ± 0.1 kpc and hB2 = 4.7 ± 1.0 kpc. NGC 7462 has only a thick radio disc with hB2 = 3.8 ± 1.0 kpc. In both galaxies, the magnetic field scale heights are significantly smaller than what estimates from energy equipartition would suggest. A non-negligible fraction of cosmic ray electrons can escape from NGC 7090, so that this galaxy is not an electron calorimeter.

  13. Anomalous diffusion of a tracer advected by wave turbulence

    NASA Astrophysics Data System (ADS)

    Balk, Alexander M.

    2001-02-01

    We consider the advection of a passive tracer when the velocity field is a superposition of random waves. Green's function for the turbulent transport (turbulent diffusion and turbulent drift) is derived. This Green's function is shown to imply sub-diffusive or super-diffusive behavior of the tracer. For the analysis we introduce the statistical near-identity transformation. The results are confirmed by numerical simulations.

  14. Cellwise conservative unsplit advection for the volume of fluid method

    NASA Astrophysics Data System (ADS)

    Comminal, Raphaël; Spangenberg, Jon; Hattel, Jesper Henri

    2015-02-01

    We present a cellwise conservative unsplit (CCU) advection scheme for the volume of fluid method (VOF) in 2D. Contrary to other schemes based on explicit calculations of the flux balances, the CCU advection adopts a cellwise approach where the pre-images of the control volumes are traced backwards through the flow map. The donating regions of the fluxes are calculated via the streaklines of the grid intersections, represented as polygonal chains whose vertices are determined by backward tracing of particles injected in the flow at different times. High order accuracy is obtained from the fourth-order Runge-Kutta method, where intermediate velocities along pathlines are determined with quadratic temporal and bicubic spatial interpolations. The volumes of the donating regions are corrected in order to fulfill the discrete continuity of incompressible flows. Consequently, the calculation produces non-overlapping donating regions and pre-images with conforming edges to their neighbors, resulting in the conservativeness and the boundedness (liquid volume fraction inside the interval [ 0 , 1 ]) of the CCU advection scheme. Finally, the update of the liquid volume fractions is computed from the intersections of the pre-image polygons with the reconstructed interfaces. The CCU scheme is tested on several benchmark tests for the VOF advection, together with the standard piecewise linear interface calculation (PLIC). The geometrical errors of the CCU compare favorably with other unsplit VOF-PLIC schemes. Finally, potential improvements of the VOF method with the use of more precise interface representation techniques and the future extension of the CCU scheme to 3D are discussed.

  15. Heat and Mass Exchange of a Drop of a Solution Subjected to a Combined Energy Action Under Conditions of Deepening of the Evaporation Zone

    NASA Astrophysics Data System (ADS)

    Akulich, P. V.

    2016-05-01

    A model of the heat and mass exchange in the evaporation of drops moving in the carrying gas phase of a solution subjected to the combined energy action of a convective heat flow and electromagnetic infrared and microwave radiations under conditions where the size of the drops changes at the low-temperature stage of their evaporation and the evaporation zone deepens at the high-temperature stage of the evaporation process has been formulated. Kinetic dependences and features of the movement of the evaporation boundary in the process of dehydration of the indicated drops have been determined.

  16. Heat and Mass Exchange of a Drop of a Solution Subjected to a Combined Energy Action Under Conditions of Deepening of the Evaporation Zone

    NASA Astrophysics Data System (ADS)

    Akulich, P. V.

    2016-06-01

    A model of the heat and mass exchange in the evaporation of drops moving in the carrying gas phase of a solution subjected to the combined energy action of a convective heat flow and electromagnetic infrared and microwave radiations under conditions where the size of the drops changes at the low-temperature stage of their evaporation and the evaporation zone deepens at the high-temperature stage of the evaporation process has been formulated. Kinetic dependences and features of the movement of the evaporation boundary in the process of dehydration of the indicated drops have been determined.

  17. Difference in fibril core stability between two tau four-repeat domain proteins: a hydrogen-deuterium exchange coupled to mass spectrometry study.

    PubMed

    Ramachandran, Gayathri; Udgaonkar, Jayant B

    2013-12-10

    One of the signatures of Alzheimer's disease and tauopathies is fibrillization of the microtubule-associated protein tau. The purpose of this study was to compare the high-resolution structure of fibrils formed by two different tau four-repeat domain constructs, tau4RD and tauK18, using hydrogen-deuterium exchange coupled to mass spectrometry as a tool. While the two fibrils are found to be constructed on similar structural principles, the tauK18 fibril has a slightly more stable core. This difference in fibril core stability appears to be reflective of the mechanistic differences in the aggregation pathways of the two proteins. PMID:24256615

  18. A tube-by-tube reduction method for simultaneous heat and mass transfer characteristics for plain fin-and-tube heat exchangers in dehumidifying conditions

    NASA Astrophysics Data System (ADS)

    Pirompugd, Worachest; Wongwises, Somchai; Wang, Chi-Chuan

    2005-06-01

    This study proposed a new method, namely a tube-by-tube reduction method to analyze the performance of fin-and-tube heat exchangers having plain fin configuration under dehumidifying conditions. The mass transfer coefficients which seldom reported in the open literature, are also presented. For fully wet conditions, it is found that the reduced results for both sensible heat transfer performance and the mass transfer performance by the present method are insensitive to change of inlet humidity. Unlike those tested in fully dry condition, the sensible heat transfer performance under dehumidification is comparatively independent of fin pitch. The ratio of the heat transfer characteristic to mass transfer characteristic (hc,o/hd,o Cp,a) is in the range of 0.6~1.0, and the ratio is insensitive to change of fin spacing at low Reynolds number. However, a slight drop of the ratio of (hc,o/hd,o Cp,a) is seen with the decrease of fin spacing when the Reynolds number is sufficient high. This is associated with the more pronounced influence due to condensate removal by the vapor shear. Correlations are proposed to describe the heat and mass performance for the present plate fin configurations. These correlations can describe 89% of the Chilton Colburn j-factor of the heat transfer (jh) within 15% and can correlate 81% of the Chilton Colburn j-factor of the mass transfer (jm) within 20%.

  19. Super-diffusion versus competitive advection: a simulation

    NASA Astrophysics Data System (ADS)

    Del Moro, D.; Giannattasio, F.; Berrilli, F.; Consolini, G.; Lepreti, F.; Gošić, M.

    2015-04-01

    Context. Magnetic element tracking is often used to study the transport and diffusion of the magnetic field on the solar photosphere. From the analysis of the displacement spectrum of these tracers, it has recently been agreed that a regime of super-diffusivity dominates the solar surface. Quite habitually this result is discussed in the framework of fully developed turbulence. Aims: However, the debate whether the super-diffusivity is generated by a turbulent dispersion process, by the advection due to the convective pattern, or even by another process is still open, as is the question of the amount of diffusivity at the scales relevant to the local dynamo process. Methods: To understand how such peculiar diffusion in the solar atmosphere takes place, we compared the results from two different data sets (ground-based and space-borne) and developed a simulation of passive tracers advection by the deformation of a Voronoi network. Results: The displacement spectra of the magnetic elements obtained by the data sets are consistent in retrieving a super-diffusive regime for the solar photosphere, but the simulation also shows a super-diffusive displacement spectrum: its competitive advection process can reproduce the signature of super-diffusion. Conclusions: Therefore, it is not necessary to hypothesize a totally developed turbulence regime to explain the motion of the magnetic elements on the solar surface.

  20. Vertical Structure of Advection-dominated Accretion Flows

    NASA Astrophysics Data System (ADS)

    Zahra Zeraatgari, Fateme; Abbassi, Shahram

    2015-08-01

    We solve the set of hydrodynamic equations for optically thin advection-dominated accretion flows by assuming a radially self-similar spherical coordinate system (r,θ ,φ ). The disk is considered to be in steady state and axisymmetric. We define the boundary conditions at the pole and the equator of the disk and, to avoid singularity at the rotation axis, the disk is taken to be symmetric with respect to this axis. Moreover, only the {τ }rφ component of the viscous stress tensor is assumed, and we have set {v}θ =0. The main purpose of this study is to investigate the variation of dynamical quantities of the flow in the vertical direction by finding an analytical solution. As a consequence, we found that the advection parameter, {f}{adv}, varies along the θ direction and reaches its maximum near the rotation axis. Our results also show that, in terms of the no-outflow solution, thermal equilibrium still exists and consequently advection cooling can balance viscous heating.

  1. 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.

  2. Distinguishing resuspension and advection signals in a hypertidal estuary

    NASA Astrophysics Data System (ADS)

    Todd, David; Souza, Alex; Jago, Colin

    2015-04-01

    Terrestrial material is supplied to an estuary system by the river, while marine material is supplied by the sea. Whether the estuary acts as a trap or a bypass zone for SPM (suspended particulate matter) depends upon the properties and dynamics of both the estuary, including the tidal and residual behaviour of the currents, and the SPM, including particle sizes and settling velocities and concentration gradients, which together control the dynamics, such as the trapping efficiency, of the estuary. Whether an SPM signal is regarded as being one of resuspension or advection depends upon the area of interest, and therefore distinguishing between resuspension and advection can be complex. Material that is resuspended within the area of study is regarded as resuspension, while that which is resuspended outside, but passes through, the area of interest, is regarded as advection. The results of a measurement campaign undertaken in a hypertidal UK estuary during the pre-spring bloom February-March and post-spring bloom May-June are presented utilising a combination of acoustic and optical instruments, moorings, and CTD stations. A characteristic asymmetric "twin peak" signal is present during both time periods, implying the presence of both resuspension and advection. This is confirmed through the use of harmonic analysis. A seasonal variation in the relative importance of the resuspension and advection components is seen between the two observation periods, with the small (<122µm) and large (>122µm) particles displaying different behaviours and providing a strong indication of the presence of flocculation. Approximate point flux calculations showed a reduction in the horizontal gradient of concentration, and subsequently the flood dominance of sediment transport, between May-June and February-March. This has been attributed to changes in biological activity and atmospheric forcing between the two observational periods. Ebb-dominant concentrations brought about by the

  3. 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

  4. The nature and role of advection in advection-diffusion equations used for modelling bed load transport

    NASA Astrophysics Data System (ADS)

    Ancey, Christophe; Bohorquez, Patricio; Heyman, Joris

    2016-04-01

    The advection-diffusion equation arises quite often in the context of sediment transport, e.g., for describing time and space variations in the particle activity (the solid volume of particles in motion per unit streambed area). Stochastic models can also be used to derive this equation, with the significant advantage that they provide information on the statistical properties of particle activity. Stochastic models are quite useful when sediment transport exhibits large fluctuations (typically at low transport rates), making the measurement of mean values difficult. We develop an approach based on birth-death Markov processes, which involves monitoring the evolution of the number of particles moving within an array of cells of finite length. While the topic has been explored in detail for diffusion-reaction systems, the treatment of advection has received little attention. We show that particle advection produces nonlocal effects, which are more or less significant depending on the cell size and particle velocity. Albeit nonlocal, these effects look like (local) diffusion and add to the intrinsic particle diffusion (dispersal due to velocity fluctuations), with the important consequence that local measurements depend on both the intrinsic properties of particle displacement and the dimensions of the measurement system.

  5. Relativistic Outflows from Advection-dominated Accretion Disks around Black Holes

    NASA Astrophysics Data System (ADS)

    Subramanian, P.; Becker, P. A.

    1999-05-01

    Advection dominated accretion flows have been recently proposed as attractive models for explaining low luminosity black hole systems. However, the so-called ADAF models suffer from a serious drawback; namely, the accretion flow has a postive Bernoulli parameter, and is therefore gravitationally unbound. Blandford & Begelman (1999, MNRAS) recently proposed advection-dominated flows that incorporate an outflow that carries away an appreciable amount of mass, energy and angular momentum (ADIOS), thereby alleviating this problem. However, their solutions merely assume the existence of such outflows, and do not elaborate on the mechanisms that could drive them. Subramanian, Becker & Kazanas (1999, ApJ, astro-ph/9805044) have described a mechanism whereby particles are accelerated via collisions with magnetic scattering centers (kinks in the tangled magnetic field) embedded in the accreting plasma and form relativistic outflows. We examine the role of this mechanism in the context of Blandford & Begelman's ADIOS solutions with a view to elucidating the physical processes that drive the outflows, which in turn are a crucial component of the overall solution.

  6. An improved second moment method for solution of pure advection problems

    NASA Astrophysics Data System (ADS)

    Ghods, Abdolreza; Sobouti, Farhad; Arkani-Hamed, Jafar

    2000-04-01

    The second moment numerical method (SMM) of Egan and Mahoney [Numerical modeling of advection and diffusion of urban area source pollutant. Journal of Applied Meteorology 1972; 11: 312-322] is adapted to solve for the pure advection transport equation in a variety of flow fields. SMM eliminates numerical diffusion by employing a procedure that takes into account the first and second moments of mass distribution in each grid element. For pure translational flow fields, the method is conservative, positive definite and shape-preserving. In rotational and/or shear flows, the accuracy of SMM is significantly reduced. Two improvements are presented to make the SMM applicable to a wider range of flow problems. It is shown that the improved SMM (ISMM) is less diffusive and more shape-preserving than the SMM in rotational and/or deformational flows. The ISMM can also be used to solve for a color function in compressible flow fields. The computational efficiency of this method is compared with that of other methods and, for a given accuracy, it is shown that ISMM is a cost-effective, non-diffusive and shape-preserving method. Copyright

  7. 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.

  8. 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.

  9. On achieving element-wise species balance and enforcing non-negative constraint for advection-diffusion-reaction equations

    NASA Astrophysics Data System (ADS)

    Mudunuru, M. K.; Nakshatrala, K.

    2012-12-01

    Advection-Diffusion-Reaction (ADR) equations naturally arises in many physical phenomena, which include seepage of contaminants in heterogeneous porous media, transport of injected tracers due to the flow of oil in a petroleum reservoir, and degradation of a deformable solid due to diffusing chemical species. Vast literature exists on how to solve this equation in the cases when the medium is isotropic, velocity field being divergence free, and for advection-dominated problems. However, it is well know that many popular finite element formulations (e.g., the standard Galerkin formulation, stabilized methods, variational multi-scale methods, subgrid-scale methods, and primitive least-squares formulations) do not satisfy element-by-element mass/species balance and do not produce non-negative solutions on general computational grids. Various post-processing based methods were developed in order to recover some properties of computed numerical solutions. Most of these post-processing techniques are ad hoc, and are not variationally consistent. In this poster, we shall present a novel numerical methodology for ADR equations that satisfy discrete maximum principles, the non-negative constraint, and element-by-element mass/species balance. The methodology can handle general computational grids, no additional restrictions on time-step, and for heterogeneous anisotropic media. Several numerical results pertinent to advection-dominated ADR problems will be presented to illustrate the performance of the proposed numerical formulation.

  10. 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. PMID:26898203

  11. MT3DMS: A MODULAR THREE-DIMENSIONAL MULTISPECIES TRANSPORT MODEL FOR SIMULATION OF ADVECTION, DISPERSION, AND CHEMICAL REACTIONS OF CONTAMINANTS IN GROUNDWATER SYSTEMS: DOCUMENTATION AND USER'S GUIDE

    EPA Science Inventory

    This manual describes the next generation of the modular three-dimensional transport model, MT3D, with significantly expanded capabilities, including the addition of (a) a third-order total-variation-diminishing (TVD) scheme for solving the advection term that is mass conservativ...

  12. 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.

  13. A Binding Site on IL-17A for Inhibitory Macrocycles Revealed by Hydrogen/Deuterium Exchange Mass Spectrometry.

    PubMed

    Espada, Alfonso; Broughton, Howard; Jones, Spencer; Chalmers, Michael J; Dodge, Jeffrey A

    2016-03-10

    Computational assessment of the IL-17A structure identified two distinct binding pockets, the β-hairpin pocket and the α-helix pocket. The β-hairpin pocket was hypothesized to be the site of binding for peptide macrocycles. Support for this hypothesis was obtained using HDX-MS which revealed protection to exchange only within the β-hairpin pocket. This data represents the first direct structural evidence of a small molecule binding site on IL-17A that functions to disrupt the interaction with its receptor. PMID:26854023

  14. 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

  15. Measuring the hydrogen/deuterium exchange of proteins at high spatial resolution by mass spectrometry: overcoming gas-phase hydrogen/deuterium scrambling.

    PubMed

    Rand, Kasper D; Zehl, Martin; Jørgensen, Thomas J D

    2014-10-21

    Proteins are dynamic molecules that exhibit conformational flexibility to function properly. Well-known examples of this are allosteric regulation of protein activity and ligand-induced conformational changes in protein receptors. Detailed knowledge of the conformational properties of proteins is therefore pertinent to both basic and applied research, including drug development, since the majority of drugs target protein receptors and a growing number of drugs introduced to the market are therapeutic peptides or proteins. X-ray crystallography provides a static picture at atomic resolution of the lowest-energy structure of the native ensemble. There is a growing need for sensitive analytical tools to explore all of the significant molecular structures in the conformational landscape of proteins. Hydrogen/deuterium exchange monitored by mass spectrometry (HDX-MS) has recently emerged as a powerful method for characterizing protein conformational dynamics. The basis of this method is the fact that backbone amides in stable hydrogen-bonded structures (e.g., α-helices and β-sheets) are protected against exchange with the aqueous solvent. All protein structures are dynamic, however, and eventually all of the protecting hydrogen bonds will transiently break as the protein--according to thermodynamic principles--cycles through partially unfolded states that correspond to excited free energy levels. As a result, all of the backbone amides will eventually become temporarily solvent-exposed and exchange-competent over time. Consequently, a folded protein in D2O will gradually incorporate deuterium into its backbone amides, and the kinetics of the process can be readily monitored by mass spectrometry. The deuterium uptake kinetics for the intact protein (global exchange kinetics) represents the sum of the exchange kinetics for the individual backbone amides. Local exchange kinetics is typically achieved by using pepsin digestion under quench conditions (i.e., under cold

  16. 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

    2016-01-01

    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. PMID:26646553

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. Water mass exchange between the Nordic seas and the Arctic Ocean on millennial timescale during MIS 4-MIS 2

    NASA Astrophysics Data System (ADS)

    Rasmussen, Tine L.; Thomsen, Erik; Nielsen, Tove

    2014-03-01

    The climate of the last glaciation circa 65,000-25,000 years ago was interrupted by about 15 abrupt temperature fluctuations, the so-called Dansgaard-Oeschger events consisting of warm interstadials and cold stadials recorded in Greenland ice cores. The largest fluctuations occur in the North Atlantic region, but they have been registered over the most of the world. The events are linked to changes in deep water formation in the Nordic seas and North Atlantic, disrupting the thermohaline circulation. Yet, Dansgaard-Oeschger events have so far not been recorded north of the convection areas in the central Nordic seas, and it is not known if they affected the water exchange between the Nordic seas and the Arctic Ocean. In this study, we analyze core JM05-31GC from the northern Fram Strait at the very entrance to the Arctic Ocean. The core contains sediments from marine isotope stages (MISs) 4-2. The results show millennial timescale shifts in all the investigated proxies including the distribution of planktonic and benthic foraminifera, planktonic and benthic oxygen and carbon isotopes, and several sedimentological parameters. In JM05-31GC, the interstadials are characterized by relatively high surface and low bottom water temperatures, low content of ice-rafted debris, and well-ventilated bottom water. Stadials are characterized by the presence of icebergs and decreasing surface water and increasing bottom water temperatures due to increased inflow of Atlantic subsurface water. Ventilation decreased during Heinrich events and most stadials. The results show that the Dansgaard-Oeschger events strongly affected the water exchange between the Nordic seas and the Arctic Ocean.

  2. High-speed compressible flow and other advection-dominated problems of fluid dynamics

    NASA Technical Reports Server (NTRS)

    Zienkiewicz, O. C.; Lohner, R.; Morgan, K.; Peraire, J.

    1985-01-01

    Finite element methods are described for modeling high speed compressible flows with strong advection, problems important to aerodynamics. The situations are characterized by high pressure and temperature gradients, transients and the appearance of discontinuities, factors which require mesh refinement during computations. Techniques are developed for temporal and spatial discretization of a model problem. Several observations are made regarding the explicit and implicit features of the calculations, the use of the Lax-Wendroff scheme to produce a mass-matrix for obtaining accurate results for transients, methods of performing stability analyses, and simplification techniques. Examples are provided of solving the nonlinear shallow-water equations and describing compressible flows, particularly transonic flows. Domain splitting is defined for improving the calculations at each time step and in different parts of the flow regime while simultaneously advancing the calculations towards a solution.

  3. 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.

  4. 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

    2010-11-01

    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. PMID:20962778

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

    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, 15.65Msolar black hole orbiting an underluminous, 70Msolar main-sequence companion in a slightly eccentric 3.45-day orbit (Msolar, 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 85Msolar-99Msolar and a secondary body of 28Msolar-32Msolar, 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 ~16Msolar 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.

  6. Anaerobic, Nitrate-Dependent Fe(II) Oxidation Under Advective Flow

    NASA Astrophysics Data System (ADS)

    Weber, K. A.; Coates, J. D.

    2005-12-01

    Microbially-catalyzed nitrate-dependent Fe(II) oxidation has been identified as a ubiquitous biogeochemical process contributing to anaerobic iron redox cycling in sedimentary environments. Most probable number enumeration revealed nitrate-dependent Fe(II) oxidizing microbial communities in groundwater and subsurface sediments in the order of 0 - 2.04 x 103 cells mL-1 and 2.39 x 102 - 1.17 x 103 cells (g wet sediment)-1, respectively. The efficacy of nitrate-dependent Fe(II) oxidation under advective flow was evaluated in a meso-scale column reactor packed with sterile low iron sand amended with subsurface sediments collected from the NABIR FRC background field site (10% mass/mass). Continuous flow of minimal medium mimicked the natural groundwater. Periodic FeCl2 and nitrate injections over a period of 49 days resulted in the retention of 95% of the iron (290 mmol). Extraction of solid-phase Fe revealed a net increase in Fe(III) of 160 mmol above background Fe(III) content indicating that 55% of the injected Fe(II) was oxidized. Differential solubility analysis of 0.5M HCl-extractable Fe and 3M HCl-extractable Fe indicated that the oxidation product was crystalline in nature as only 20% was soluble in 0.5M HCl. This formation of crystalline biogenic Fe(III) oxides is consistent with previous studies. Periodic injections of nitrate and acetate did not result in significant changes in Fe(II) or Fe(III) throughout a control column. Together these results demonstrate that native subsurface sediments harbor microbial communities capable of nitrate-dependent Fe(II) oxidation under advective flow. The biogenic formation of reactive Fe(III) oxide minerals capable of immobilizing heavy metals and radionuclides presents a plausible bioremediative strategy for contaminated subsurface environments.

  7. 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. PMID:26356969

  8. 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.

  9. Moisture advection to the Arctic : forecasted, analysed and observed

    NASA Astrophysics Data System (ADS)

    Dufour, Ambroise; Zolina, Olga

    2015-04-01

    Besides its contribution to the Arctic hydrological budget, moisture imports from mid-latitudes are also influential on shorter time scales since water vapour advection tends to occur together with extratropical cyclones. Influx of moisture to the Arctic cause the formation of clouds that have an immediate impact on the surface energy budget especially in winter. In the long run, inaccuracies in the description of cloud cover and phase lead to temperature biases in CMIP5 models. The ECMWF workshop on polar prediction has highlighted moisture advection as one of the problematic physical processes limiting the quality of forecasts. Verifying the accuracy of medium-term forecasts is of interest beyond weather prediction : it points to the ability of models to bring adequate quantities of moisture to the Arctic when they are less constrained by observations than in analyses. In this study, we have compared forecasted moisture flux fields with analyses and observations over the period 2000-2010. ECMWF's ERA-Interim provided the forecasts, extending to ten days. For the analyses, in addition to ERA-Interim, we used the Arctic System Reanalysis whose forecast model is optimized for the polar regions and runs at high resolution (30 km). Finally, the Integrated Global Radiosonde Archive data over the Arctic allowed a validation by observations.

  10. Backward fractional advection dispersion model for contaminant source prediction

    NASA Astrophysics Data System (ADS)

    Zhang, Yong; Meerschaert, Mark M.; Neupauer, Roseanna M.

    2016-04-01

    The forward Fractional Advection Dispersion Equation (FADE) provides a useful model for non-Fickian transport in heterogeneous porous media. The space FADE captures the long leading tail, skewness, and fast spreading typically seen in concentration profiles from field data. This paper develops the corresponding backward FADE model, to identify source location and release time. The backward method is developed from the theory of inverse problems, and then explained from a stochastic point of view. The resultant backward FADE differs significantly from the traditional backward Advection Dispersion Equation (ADE) because the fractional derivative is not self-adjoint and the probability density function for backward locations is highly skewed. Finally, the method is validated using tracer data from a well-known field experiment, where the peak of the backward FADE curve predicts source release time, while the median or a range of percentiles can be used to determine the most likely source location for the observed plume. The backward ADE cannot reliably identify the source in this application, since the forward ADE does not provide an adequate fit to the concentration data.

  11. 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.

  12. SEPs Dropout Events Associated with Advected Interplanetary Magnetic Structures

    NASA Astrophysics Data System (ADS)

    Bruno, R.; Trenchi, L.; Telloni, D.; D'Amicis, R.; Marcucci, F.; Zurbuchen, T.; Weberg, M. J.

    2013-05-01

    The intensity profile of energetic particles from impulsive solar flares (SEP) often shows abrupt dropouts affecting all energies simultaneously, without time-dispersion. Part of the community thinks that these modulations are directly related to the presence of magnetic structures with a different magnetic topology advected by the wind, a sort of magnetic flux tubes. During the expansion, following the dynamical interaction between plasma regions travelling at different speed, these structures would be partially tangled up in a sort of spaghetti-like bundle. These flux tubes would be alternatively connected or not connected with the flare site and, consequently, they would be filled or devoid of SEPs. When the observer passes through them, he would observe clear particles dropout signatures. We will report about results from a detailed analysis of SEP events which showed several signatures in the local magnetic field and/or plasma parameters associated with SEP modulations. These findings corroborate the idea of a possible link between these particles events observed at the Earth's orbit and magnetic connection or disconnection of the ambient magnetic field with the flare region at the Sun. We will also discuss the advantages represented by future Solar Orbiter in-situ observations. As a matter of fact, Solar Orbiter, from its orbital vantage point during the quasi corotation phase, will be a priviledged observer of this kind of phenomenon since it will observe the advected structure of the solar wind not yet reprocessed by dynamical interaction due to wind expansion.

  13. Toward enhanced subsurface intervention methods using chaotic advection.

    PubMed

    Trefry, Michael G; Lester, Daniel R; Metcalfe, Guy; Ord, Alison; Regenauer-Lieb, Klaus

    2012-01-01

    Many intervention activities in the terrestrial subsurface involve the need to recover/emplace distributions of scalar quantities (e.g. dissolved phase concentrations or heat) from/in volumes of saturated porous media. These scalars can be targeted by pump-and-treat methods or by amendment technologies. Application examples include in-situ leaching for metals, recovery of dissolved contaminant plumes, or utilizing heat energy in geothermal reservoirs. While conventional pumping methods work reasonably well, costs associated with maintaining pumping schedules are high and improvements in efficiency would be welcome. In this paper we discuss how transient switching of the pressure at different wells can intimately control subsurface flow, generating a range of "programmed" flows with various beneficial characteristics. Some programs produce chaotic flows which accelerate mixing, while others create encapsulating flows which can isolate fluid zones for lengthy periods. In a simplified model of an aquifer subject to balanced pumping, chaotic flow topologies have been predicted theoretically and verified experimentally using Hele-Shaw cells. Here, a survey of the key characteristics of chaotic advection is presented. Mathematical methods are used to show how these characteristics may translate into practical situations involving regional flows and heterogeneity. The results are robust to perturbations, and withstand significant aquifer heterogeneity. It is proposed that chaotic advection may form the basis of new efficient technologies for groundwater interventions. PMID:21600670

  14. 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.

  15. Multiple anisotropic collisions for advection-diffusion Lattice Boltzmann schemes

    NASA Astrophysics Data System (ADS)

    Ginzburg, Irina

    2013-01-01

    This paper develops a symmetrized framework for the analysis of the anisotropic advection-diffusion Lattice Boltzmann schemes. Two main approaches build the anisotropic diffusion coefficients either from the anisotropic anti-symmetric collision matrix or from the anisotropic symmetric equilibrium distribution. We combine and extend existing approaches for all commonly used velocity sets, prescribe most general equilibrium and build the diffusion and numerical-diffusion forms, then derive and compare solvability conditions, examine available anisotropy and stable velocity magnitudes in the presence of advection. Besides the deterioration of accuracy, the numerical diffusion dictates the stable velocity range. Three techniques are proposed for its elimination: (i) velocity-dependent relaxation entries; (ii) their combination with the coordinate-link equilibrium correction; and (iii) equilibrium correction for all links. Two first techniques are also available for the minimal (coordinate) velocity sets. Even then, the two-relaxation-times model with the isotropic rates often gains in effective stability and accuracy. The key point is that the symmetric collision mode does not modify the modeled diffusion tensor but it controls the effective accuracy and stability, via eigenvalue combinations of the opposite parity eigenmodes. We propose to reduce the eigenvalue spectrum by properly combining different anisotropic collision elements. The stability role of the symmetric, multiple-relaxation-times component, is further investigated with the exact von Neumann stability analysis developed in diffusion-dominant limit.

  16. Chaotic Advection, Fluid Spreading, and Groundwater Contaminant Plumes

    NASA Astrophysics Data System (ADS)

    Neupauer, R. M.; Mays, D. C.

    2011-12-01

    In situ remediation of contaminated groundwater requires degradation reactions at the interface between the contaminant plume and an injected treatment solution containing chemical or biological amendments. Therefore a promising approach to accelerate in situ remediation is to elongate the interface between the contaminant plume and treatment solution through fluid spreading. The literature on chaotic advection describes how to accomplish spreading in laminar flows, which lack the turbulent eddies that provide spreading in streams or engineered reactors. A key result from the literature on chaotic advection is that spreading is inherent in the vicinity of certain periodic points, which are points to which fluid particles return in successive iterations of chaotic flows. Specifically, spreading is enhanced near the stable and unstable manifolds associated with hyperbolic periodic points. We investigate the transient flow created with a four-well system in which wells are operated sequentially as either injection wells or extraction wells. In particular, we identify the periodic points and demonstrate that fluid spreading occurs nearby. For appropriately designed injection and extraction sequences, the periodic points are located near the interface between the contaminant plume and treatment solution, leading to elongation of the interface, with expected benefits of enhanced reaction and accelerated remediation.

  17. 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.

  18. OBSERVATION OF MAGNETIC RECONNECTION DRIVEN BY GRANULAR SCALE ADVECTION

    SciTech Connect

    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 {approx} 4'' Multiplication-Sign 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 A) He I 10830 A and broadband (10 A) TiO 7057 A. Since He I 10830 A 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 ({approx}2 km s{sup -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 A 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.

  19. Effect of cation-exchange pretreatment of aqueous soil extracts on the gas chromatographic-mass spectrometric determination of nerve agent hydrolysis products after tert.-butyldimethylsilylation.

    PubMed

    Kataoka, M; Tsunoda, N; Ohta, H; Tsuge, K; Takesako, H; Seto, Y

    1998-10-23

    The efficiency of pretreatment of aqueous soil extracts using a cation-exchange resin has been investigated by gas chromatographic-mass spectrometric (GC-MS) determination of nerve agent hydrolysis products after tert.-butyldimethylsilyl (TBDMS) derivatization. An aqueous solution containing methylphosphonic acid (MPA) and its monoalkyl esters, ethyl methylphosphonic acid, isopropyl methylphosphonic acid and pinacolyl methylphosphonic acid, was dried, and these phosphonic acids were derivatized with N-methyl-N-(tert.-butyldimethylsilyl)trifluoro-acetamide and analyzed by GC-MS. The yields of TBDMS derivatives were significantly decreased by the addition of calcium and magnesium ions to an aqueous solution (approximately 0.5 mM) before derivatization. The extent of lowered yields was related to the hydrophilicity of phosphonic acids. MPA and its monoalkyl esters were spiked into soil samples (sand, alluvial soil and volcanic ash soil), extracted with distilled water, dried, silylated and applied to GC-MS. The yields of TBDMS derivatives of monoalkyl esters from soil samples were low (3-42%) and MPA derivative was scarcely detected (yield: < 0.7%). By desalting the aqueous soil extract by passage through a strong cation-exchange resin, the yields of TBDMS derivatives of monoalkyl esters were significantly improved (12-69%) and MPA derivative was detected (yield: 2-36%). The extent of improved yields was related to the concentrations of divalent metal cations in aqueous soil extracts. In combination with desalting by the cation-exchange resin, GC-MS after TBDMS derivatization enables detection of nerve agent hydrolysis products in soils at sub-ppm (0.2 microgram/g) concentrations. PMID:9818434

  20. Mass-spectrometric determination of O2 and CO 2 gas exchange in illuminated higher-plant cells : Evidence for light-inhibition of substrate decarboxylations.

    PubMed

    Avelange, M H; Thiéry, J M; Sarrey, F; Gans, P; Rébeillé, F

    1991-01-01

    In order to estimate photosynthetic and respiratory rates in illuminated photoautotrophic cells of carnation (Dianthus caryophyllus L.), simultaneous measurements of CO2 and O2 gas exchange were performed using (18)O2, (13)CO2 and a mass-spectrometry technique. This method allowed the determination, and thus the comparison, of unidirectional fluxes of O2 and CO2. In optimum photosynthetic conditions (i.e. in the presence of high light and a saturating level of CO2), the rate of CO2 influx represented 75±5% of the rate of gross O2 evolution. After a dark-to-light transition, the rate of CO2 efflux was inhibited by 50% whereas the O2-uptake rate was little affected. The effect of a recycling of respiratory CO2 through photosynthesis on the exchange of CO2 gas was investigated using a mathematical model. The confliction of the experimental data with the simulated gas-exchange rates strongly supported the view that CO2 recycling was a minor event in these cells and could not be responsible for the observed inhibition of CO2 efflux. On the basis of this assumption it was concluded that illumination of carnation cells resulted in a decrease of substrate decarboxylations, and that CO2 efflux and O2 uptake were not as tightly coupled in the light as in the dark. Furthermore, it could be calculated from the rate of gross photosynthesis that the chloroplastic electron-transport chain produced enough ATP in the light to account for the measured CO2-uptake rate without involving cyclic transfer of electrons around PS I or mitochondrial supplementation. PMID:24193614

  1. Analytical solutions to the fractional advection-diffusion equation with time-dependent pulses on the boundary

    NASA Astrophysics Data System (ADS)

    Rubbab, Qammar; Mirza, Itrat Abbas; Qureshi, M. Zubair Akbar

    2016-07-01

    The time-fractional advection-diffusion equation with Caputo-Fabrizio fractional derivatives (fractional derivatives without singular kernel) is considered under the time-dependent emissions on the boundary and the first order chemical reaction. The non-dimensional problem is formulated by using suitable dimensionless variables and the fundamental solutions to the Dirichlet problem for the fractional advection-diffusion equation are determined using the integral transforms technique. The fundamental solutions for the ordinary advection-diffusion equation, fractional and ordinary diffusion equation are obtained as limiting cases of the previous model. Using Duhamel's principle, the analytical solutions to the Dirichlet problem with time-dependent boundary pulses have been obtained. The influence of the fractional parameter and of the drift parameter on the solute concentration in various spatial positions was analyzed by numerical calculations. It is found that the variation of the fractional parameter has a significant effect on the solute concentration, namely, the memory effects lead to the retardation of the mass transport.

  2. 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. PMID:26620531

  3. 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.

  4. Mixed-mode anion-cation exchange/hydrophilic interaction liquid chromatography-electrospray mass spectrometry as an alternative to reversed phase for small molecule drug discovery

    PubMed

    Strege; Stevenson; Lawrence

    2000-10-01

    Within pharmaceutical drug discovery, significant needs currently exist for the analysis and purification of structurally diverse samples prior to or immediately following high-throughput screening. These processes are required to facilitate rapid and accurate biological profiling, structural determination, and resupply of new drug candidates. Reversed-phase high-performance liquid chromatography (RP-HPLC) coupled with electrospray ionization mass spectrometry (ESI-MS) for both analytical and preparative applications has become the small molecule separation/detection tool of choice for meeting many of these needs. However, the separation selectivity provided by RP-HPLC has been limited to the hydrophobicity-based resolution of relatively nonpolar sample components, and for high-throughput drug discovery applications, no sufficient alternative procedures have been identified. In this investigation, a mixed-mode anion-cation exchange/hydrophilic interaction chromatography (ACE-HILIC) method has been developed to provide both direct compatibility with ESI-MS and evaporative light-scattering detection (ELSD) and separation selectivity highly orthogonal to RP-HPLC. The technique employed silica-based small-pore weak ion exchange resins eluted with a combined aqueous and pH gradient. A diverse set of dipeptide probes was employed for the elucidation of the relative contributions of three retention mechanisms. ACE-HILIC-ESI-MS-ELSD should prove useful for the analysis and purification of compounds from both biological (e.g., natural products) and synthetic (e.g., combinatorial chemistry) sources of molecular diversity. PMID:11028621

  5. 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.

  6. Effect of detergent binding on cytochrome P450 2B4 structure as analyzed by X-ray crystallography and deuterium-exchange mass spectrometry.

    PubMed

    Shah, Manish B; Jang, Hyun-Hee; Wilderman, P Ross; Lee, David; Li, Sheng; Zhang, Qinghai; Stout, C David; Halpert, James R

    2016-09-01

    Multiple crystal structures of CYP2B4 have demonstrated the binding of the detergent 5-cyclohexyl-1-pentyl-β-D-maltoside (CYMAL-5) in a peripheral pocket located adjacent to the active site. To explore the consequences of detergent binding, X-ray crystal structures of the peripheral pocket mutant CYP2B4 F202W were solved in the presence of hexaethylene glycol monooctyl ether (C8E6) and CYMAL-5. The structure in the presence of CYMAL-5 illustrated a closed conformation indistinguishable from the previously solved wild-type. In contrast, the F202W structure in the presence of C8E6 revealed a detergent molecule that coordinated the heme-iron and extended to the protein surface through the substrate access channel 2f. Despite the overall structural similarity of these detergent complexes, remarkable differences were observed in the A, A', and H helices, the F-G cassette, the C-D and β4 loop region. Hydrogen-deuterium exchange mass spectrometry (DXMS) was employed to probe these differences and to test the effect of detergents in solution. The presence of either detergent increased the H/D exchange rate across the plastic regions, and the results obtained by DXMS in solution were consistent in general with the relevant structural snapshots. The study provides insight into effect of detergent binding and the interpretation of associated conformational dynamics of CYP2B4. PMID:27280734

  7. Exploring the ester-exchange reactions of diester-diterpenoid alkaloids in the aconite decoction process by electrospray ionization tandem mass spectrometry.

    PubMed

    Wang, Yong; Shi, Lei; Song, Fengrui; Liu, Zhiqiang; Liu, Shuying

    2003-01-01

    The chemical components in the decoctions of Chinese herbal medicines are not always the same as those in the crude herbs because of the insolubility or instability of some compounds. In this work electrospray ionization tandem mass spectrometry was used to explore the ester-exchange reactions for aconitine-type diester-diterpenoid alkaloids occurring during the process of decocting aconite root. The aconitines were screened in a diverse range of samples, including crude aconite, decoction of crude aconite, residues from decoction of crude aconite, prepared aconite, decoction of prepared aconite, decoction of prepared aconite with added palmitic acid, and decoction of a mixture of mesaconitine and hypaconitine standards with liquorice root. It was found that diester-diterpenoid aconitines were converted into lipo-alkaloids as well as monoester alkaloids by the decoction of aconite. PMID:12569436

  8. Oxygen isotopic transport and exchange during fluid flow: One-dimensional models and applications

    SciTech Connect

    Bowman, J.R. ); Willett, S.D. ); Cook, S.J. Environ Corp., Houston, TX )

    1994-01-01

    In this work the authors investigate the consequences of fluid flow and fluid-rock interaction to the isotopic evolution of fluids and rock with one-dimensional transport models of fluid flow and oxygen isotope exchange. Transport models dealing with stable isotopes are well established in recent geochemical literature. The authors extend previous treatments by presenting the derivation of both analytical and numerical solutions to the transport equations incorporating simultaneously advection, diffusion and hydrodynamic dispersion, and kinetics of isotopic exchange. The increased generality of numerical solutions allows the incorporation of other effects which control the spatial patterns of [delta][sup 18]O values developed in rocks and fluids including multiple reactive species and temperature gradients. The authors discuss the effects of flow parameters, conditions of isotopic exchange, and temperature gradients on the spatial patterns of isotopic shifts produced in rock sequences subjected to fluid flow, and on conventionally calculated W/R ratios for these rock sequences. Finally, the authors examine the implications of oxygen isotope transport for two natural systems where isotopic shifts or gradients could be interpreted in terms of unidirectional fluid infiltration. Solutions of one-dimensional transport equations including the mechanisms of advection, diffusion, hydrodynamic dispersion, and non-equilibrium exchange between water and rock indicate that the time-space evolution of oxygen isotopic compositions of rock and infiltrating fluid is dependent on (1) the rate of fluid infiltration, (2) the diffusive and dispersive properties of the rock matrix, (3) the rate of isotopic exchange, and (4) the rock-water mass oxygen ratio in a unit volume of water-saturated, porous rock. 56 refs., 18 figs., 2 tabs.

  9. Characterisation of legumes by enzymatic hydrolysis, microdialysis sampling, and micro-high-performance anion-exchange chromatography with electrospray ionisation mass spectrometry.

    PubMed

    Okatch, Harriet; Torto, Nelson; Armateifio, Joan

    2003-04-11

    An assay based on enzymatic hydrolysisand microdialysis sampling, micro-high-performance anion-exchange chromatography (micro-HPAEC) with electrospray ionisation mass spectrometry (ESI-MS) for the characterisation of legumes is presented. Characterisation of two bean varieties; Phaseolus mungo and P. acutifilous was based upon enzymatic hydrolysis using an endo-beta-mannanase from Aspergillus niger with subsequent analysis of the hydrolysates with HPAEC-MS. The hydrolysates were detected in the positive ionisation mode after desalting the chromatographic effluent, employing a cation-exchange membrane desalting device with water as the regenerating liquid. Mass chromatograms, acquiredafter hydrolysis of both bean samples for 12 h, showed two different profiles of hydrolysates. The P. mungo bean hydrolysate showed the presence of saccharides with a degree of polymerisation (DP) in the range of 2-6, whereas that of P. acutifilous showed only DPs of 2-5. Both bean samples had one type of DP 2, but showed different types of DPs 3, 4 and 5. Only the P. mungo sample showed the presence of DP 6. The most abundant fraction for P. mungo was DP 4, whereas that for P. acutifilous was DP 5. Tandem MS of the hydrolysates showed that the DP 2 hydrolysates observed for the samples were of the same type, having a 1,6 linkage. Also tandem MS data for DPs 3, 4, and 5 showed that similar hydrolysates were present within the same sample as well as among the two samples. The data also showed the existence of 1,6 linkages for DP 3, 4, and 5 hydrolysates. The single enzymatic hydrolysis in combination with microdialysis and HPAEC with ESI-MS proved to be sufficient and reproducible for profiling and showing the difference between the two bean samples. PMID:12735463

  10. Use of the time fractional advection dispersion equation for push-pull tests at the Macrodispersion Experiment (MADE) site

    NASA Astrophysics Data System (ADS)

    Dean, A. M.; Benson, D. A.; Major, E.

    2010-12-01

    By adding a fractional-in-time term to the traditional advection dispersion equation, a model is able to simulate a late-time heavy-tailed contaminant breakthrough curve. This heavy-tailed breakthrough curve is observed in data collected during a conservative tracer “push-pull” test at the Macrodispersion Experiment (MADE) site. A time fractional advection dispersion equation (fADE) is able to predict power law tailing of conservative solutes by accounting for solutes transferring between the mobile and relatively immobile phases. Solutes can become trapped in a low permeability zone where the transport is controlled by diffusion instead of advection. It has been observed that the late-time heavy-tailed breakthrough curve may follow a power law due to the movement into these low flow zones. By solving the time fADE in a particle tracking program (SLIM-FAST) the model accounts for mass transfer between various phases and produces the same power law tail as observed in field data. For the implementation of the time fADE, in SLIM-FAST, the particles move based on a random-walk motion but have the ability to transition into a relatively immobile phase after (exponentially) random mobile times. Following a period in the immobile phase, the particle re-enters the mobile phase to be moved by advection and Fickian dispersion. To test the fADE approach, a recent single-well push-pull tracer test at the MADE site is reproduced using a groundwater flow code (ParFlow) and a particle tracking code (SLIM-FAST) using various immobile residence-time distributions.

  11. 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

    SciTech Connect

    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{parallel}B spectrometer has an energy range of 0.5{le}Athinsp(amu)Ethinsp(keV){le}600 and provides mass-resolved energy spectra of H{sup +}, D{sup +}, and T{sup +} (or {sup 3}He{sup +}) 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{sup +}, D{sup +}, and T{sup +} (or {sup 3}He{sup +}) 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{times}10{sup {minus}3} and 6.4{times}10{sup {minus}3}thinspcounts/neutron/cm{sup 2} 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{endash}D operation on TFTR are presented to illustrate the performance of the E{parallel}B spectrometer. The spectrometers were not used during D{endash}T plasma operation due to the cost of providing the required radiation shielding. {copyright} {ital 1998 American Institute of Physics.}

  12. Mass, temperature and metabolic effects on discontinuous gas exchange cycles in eucalyptus-boring beetles (Coleoptera: cerambycidae).

    PubMed

    Chappell, M A; Rogowitz, G L

    2000-12-01

    Ventilatory accommodation of changing metabolic rates is a relatively little-studied aspect of the discontinuous gas exchange cycles (DGCs) that occur in a wide variety of terrestrial arthropods. We used correlation analysis of resting metabolic rate (RMR, measured as the rate of CO(2) emission; V(CO2)) and several components of the DGC to examine accommodation to both temperature-induced changes and individual variation in RMR in two wood-boring beetles (Phorocantha recurva and P. semipunctata; Coleoptera: Cerambycidae). At low to moderate ambient temperatures (T(a); 10-20 degrees C), Phorocantha spp. displayed a characteristic DGC with relatively brief but pronounced open (O) phase bursts of CO(2) emission separated by longer periods of low V(CO2), the flutter (F) phase. However, the V(CO2) never fell to zero, and we could not reliably differentiate a typical closed (C) phase from the F phase. Accordingly, we pooled the C and F phases for analysis as the C+F phase. At higher T(a) (30 degrees C), the duration of the combined C+F phase was greatly reduced. There were no differences between the two species or between males and females in either RMR or characteristics of the DGC. We found large variation in the major DGC components (cycle frequency, durations and emission volumes of the O and C+F phases); much of this variation was significantly repeatable. Accommodation of temperature-induced RMR changes was almost entirely due to changes in frequency (primarily in the C+F phase), as has been found in several other discontinuously ventilating arthropods. Frequency changes also contributed to accommodation at constant T(a), but modulation of emission volumes (during both O and C+F phases) played a larger role in this case. The DGC is often viewed as a water conservation mechanism, on the basis that respiratory evaporation is minimal during the C and F phases. This hypothesis assumes that the F phase is primarily convective (because of a reduction in tracheal P(O2

  13. Evolution with time of hydrophobicity and microrelief of a cation-exchange membrane surface and its impact on overlimiting mass transfer.

    PubMed

    Pismenskaya, Natalia D; Nikonenko, Victor V; Melnik, Nadezhda A; Shevtsova, Kseniya A; Belova, Elena I; Pourcelly, Gérald; Cot, Didier; Dammak, Lasâad; Larchet, Christian

    2012-02-23

    Surface properties were measured together with electrochemical characteristics of a CMX (Neosepta, Tokuyama Corp.) cation-exchange membrane. Relative hydrophobicity was controlled by the contact angle; XPS and SEM were used for characterizing chemical composition and microrelief of the surface, respectively. Voltammetry, chronopotentiometry, and mass transfer rate measurements were made as well. A "fresh" membrane and samples after 10, 25, 100, and 150 h of operation in an electrodialysis cell at an overlimiting current equal to 3 theoretical limiting currents, in a 0.02 M NaCl solution, were characterized. Some electrochemical properties were also measured for a Neosepta cation-exchange membrane, aged 2 years, in an industrial food process. It was found that the hydrophobicity of the CMX membrane has increased after the first 10 h of operation; more and more cavities of the dimension of the order of 1 μm have appeared with time testifying electrochemical erosion of the surface. The limiting current density (i(lim)) and the overlimiting transfer rate through the CMX membrane increased with time of its operation under overlimiting current. In the case of new CMX, i(lim) was very close to the theoretical value i(lim)(theor) calculated by the Lévêque equation. After 10 h of operation, i(lim) increased by 5%, and after 25, 100, and 150 h, the increase was by 30%, 70%, and 100%, respectively. Similarly, the mass transfer rate was found to increase up to 5 times (when desalting 0.005 M NaCl under 3 V) in comparison with the theoretical value. The ensemble of data was explained by the hypothesis that the passage of intensive current produces erosion of the ion-exchange polymer forming a continuous phase in CMX. This erosion results in exposure at the surface of the other constituent of CMX: small (about 100 nm) particles of relatively hydrophobic polyvinylchloride. Increasing surface hydrophobicity facilitates the slip of electroconvective vortexes along the surface

  14. A boundary exchange influence on deglacial neodymium isotope records from the deep western Indian Ocean

    NASA Astrophysics Data System (ADS)

    Wilson, David J.; Piotrowski, Alexander M.; Galy, Albert; McCave, I. Nicholas

    2012-08-01

    The use of neodymium (Nd) isotopes to reconstruct past water mass mixing relies upon the quasi-conservative behaviour of this tracer, whereas recent studies in the modern oceans have suggested that boundary exchange, involving the addition of Nd from ocean margin sediments, may be an important process in the Nd cycle. Here we suggest that the relative importance of water mass advection versus boundary exchange can be assessed where the deep western boundary current in the Indian Ocean flows past the Madagascan continental margin; a potential source of highly unradiogenic Nd. Foraminiferal coatings and bulk sediment reductive leachates are used to reconstruct bottom water Nd isotopic composition (εNd) in 8 Holocene age coretops, with excellent agreement between the two methods. These data record spatial variability of ∼4 εNd units along the flow path of Circumpolar Deep Water; εNd≈-8.8 in the deep southern inflow upstream of Madagascar, which evolves towards εNd≈-11.5 offshore northern Madagascar, whereas εNd≈-7.3 where deep water re-circulates in the eastern Mascarene Basin. This variability is attributed to boundary exchange and, together with measurements of detrital sediment εNd, an isotope mass balance suggests a deep water residence time for Nd of ≤400 yr along the Madagascan margin. Considering deglacial changes, a core in the deep inflow upstream of Madagascar records εNd changes that agree with previous reconstructions of the Circumpolar Deep Water composition in the Southern Ocean, consistent with a control by water mass advection and perhaps indicating a longer residence time for Nd in the open ocean away from local sediment inputs. In contrast, sites along the Madagascan margin record offset εNd values and reduced glacial-interglacial variability, underlining the importance of detecting boundary exchange before inferring water mass source changes from Nd isotope records. The extent of Madagascan boundary exchange appears to be unchanged

  15. Experimental studies of heat and mass exchange in parallel-passage rotary desiccant dehumidifiers for solar cooling applications

    NASA Astrophysics Data System (ADS)

    Bharathan, D.; Parsons, J. M.; Maclaine-Cross, I. L.

    1987-11-01

    This report presents results of work done to experimentally characterize the performance of rotary desiccant dehumidifiers and to develop and validate analytical methods for evaluating their performance in air-conditioning systems. A facility, the Cyclic Test Facility, and a test-and-analysis procedure were developed to evaluate the performance of the rotary dehumidifiers. Experiments were performed to develop a basic understanding of the simultaneous heat- and mass-transfer processes in the dehumidifiers. Two test articles were tested under cyclic operation to characterize their performance. Detailed accounts of the Cyclic Test Facility, its hardware and instrumentation, the two test articles, and data reduction and analysis methods are provided. The data provide an engineering data base for evaluating rotary desiccant dehumidifiers for cooling applications.

  16. 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

  17. 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.

  18. Missing-Mass Spectroscopy of the 4-Neutron System by Exothermic Double-Charge Exchange Reaction 4He(8He,8Be)4n

    NASA Astrophysics Data System (ADS)

    Kisamori, Keiichi; Shimoura, Susumu; Miya, Hiroyuki; Assie, Marlene; Baba, Hidetada; Baba, Tatsuo; Beaumel, Didier; Dozono, Masanori; Fujii, Toshihiko; Fukuda, Naoki; Go, Shintaro; Hammache, Fariouz; Ideguchi, Eiji; Inabe, Naohiro; Itoh, Masatoshi; Kameda, Daisuke; Kawase, Shoichiro; Kawabata, Takahiro; Kobayashi, Motoki; Kondo, Yosuke; Kubo, Toshiyuki; Kubota, Yuki; Kurata-Nishimura, Mizuki; Lee, CheongSoo; Maeda, Yukie; Matsubara, Hiroaki; Michimasa, Shin'ichiro; Miki, Kenjiro; Nishi, Takahiro; Noji, Shumpei; Ota, Shinsuke; Sakaguchi, Satoshi; Sakai, Hideyuki; Sasamoto, Yoshiko; Sasano, Masaki; Sato, Hiromi; Shimizu, Yohei; Stolz, Andreas; Suzuki, Hiroshi; Takaki, Motonobu; Takeda, Hiroyuki; Takeuchi, Satoshi; Tamii, Atsushi; Tang, Leung; Tokieda, Hiroshi; Tsumura, Miho; Uesaka, Tomohiro; Yako, Kentaro; Yanagisawa, Yoshiyuki; Yokoyama, Rin

    A possible existence of the tetra-neutron system as a resonance state is still an open and fascinating question, while theoretical papers using ab-initio calculation suggests that the bound tetra-neutron does not exist. We have performed a missing-mass spectroscopy of the 4n system via the exothermic double-charge exchange reaction 4He(8He,8Be)4n. The experiment was carried out at the RIBF at RIKEN using the SHARAQ spectrometer. Since the secondary beam, 8He at 190 A MeV, has a large internal energy, it is possible to produce the 4n system with small momentum transfers of less than 20 MeV/c. In the present analysis, a new analytical framework to treat multi-particles under high beam rate condition (2 MHz) was developed for good statistics. At the SHARAQ spectrometer, 8Be can be identified by measuring the invariant mass of the coincident two alpha particles with a good signal-to-noise ratio. About several tens of candidate events are obtained above the 4n threshold.

  19. Determination of trace phosphorus in high purity tantalum materials by inductively coupled plasma mass spectrometry subsequent to matrix separation with on-line anion exchange/coprecipitation.

    PubMed

    Kozono, Shuji; Takahashi, Shigeto; Haraguchi, Hiroki

    2002-02-01

    An on-line matrix separation/inductively coupled plasma mass spectrometry (ICP-MS) method is proposed for the determination of trace amounts of phosphorus in high purity tantalum metal, tantalum (V) oxide, and tantalum pentaethoxide. In the present method, the matrix tantalum in the sample solution was adsorbed on the anion exchange resin, and phosphorus (phosphate ion) was eluted with the carrier solution of HF and HNO3 mixture. Then, the effluent solution was subsequently mixed with bismuth solution and aqueous ammonia solution to coprecipitate phosphate together with bismuth hydroxide. The precipitate formed was collected on the in-line membrane filter to wash out nitric acid with pure water, and then dissolved with hydrochloric acid. The obtained phosphorus sample solution was introduced directly into the nebulizer of ICP-MS for the determination of phosphorus. Phosphorus was determined at the molecular ion signal of 31P16O+ (m/z 47). The detection limit (3sigma) of phosphorus in the present method was 1.3 ng mL(-1) as the sample solution basis, and the relative standard deviation for 30 ng mL(-1) of phosphorus in the standard solution was 4.3% in the replicate measurements (n=11). The present method was applied to the analysis of high purity tantalum materials. The concentrations of phosphorus in tantalum samples were in fairly good agreement with those obtained by glow discharge mass spectrometry (GDMS). PMID:11939629

  20. Rapid and sensitive quantification of levoglucosan in aerosols by high-performance anion-exchange chromatography with positive electrospray ionization mass spectrometry (HPAEC-positive ESI-MS)

    NASA Astrophysics Data System (ADS)

    Asakawa, Daichi; Furuichi, Yuko; Yamamoto, Atsushi; Oku, Yuichiro; Funasaka, Kunihiro

    2015-12-01

    A convenient quantification method for underivatized levoglucosan, which is a tracer for biomass burning influenced particulate matter (PM), has been established using high-performance anion-exchange chromatography (HPAEC) coupled to positive electrospray ionization mass spectrometry ((+)ESI-MS). Levoglucosan was chromatographically separated from its isomers (mannosan and galactosan) and detected selectively with positive ESI-MS. Limits of detection and quantification for this method were 0.40 and 1.3 ng mL-1, respectively. A comparison of simultaneous measurements by this method and conventional derivatization gas chromatography/mass spectrometry showed a good linearity with a slope of 1.008 and a determination coefficient of 0.9932. The developed method was applied to ambient suspended particulate matter hourly collected by continuous particulate monitors at 10 stations. The hourly concentration of levoglucosan during August 9-11, 2011, was 1.7-918 ng m-3 and its distribution indicated the transportation of biomass burning aerosols of a forest fire. This is the first report of horizontal distribution of the hourly levoglucosan concentration in Japan.

  1. 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.

  2. Deconvolved spectra of Two Component Advective Flow including jet

    NASA Astrophysics Data System (ADS)

    Mondal, Santanu; Debnath, Dipak; Chakrabarti, Sandip Kumar

    2016-07-01

    Outflows and winds are produced when the accretion flows have positive specific energy. Two Component Advective Flow (TCAF) model suggests that the centrifugal pressure supported region of the flow outside the black hole horizon, acts as the base of this outflow. We study the spectral properties of the TCAF which includes a jet component. We consider the jet as a conical in shape which also up-scatters the soft photons from the Keplerian disc. We see that due to the presence of jet component, spectrum become harder as the jet itself behaves like an another Compton cloud above the inner hot corona. We also see how the jet spectra depends on the flow rates. This gives the direct link in timing properties of the X-rays in CENBOL component and the radiation emitted in the jet component.

  3. Carbon dioxide degassing by advective flow from Usu volcano, Japan.

    PubMed

    Hernández, P A; Notsu, K; Salazar, J M; Mori, T; Natale, G; Okada, H; Virgili, G; Shimoike, Y; Sato, M; Pérez, N M

    2001-04-01

    Magmatic carbon dioxide (CO2) degassing has been documented before the 31 March 2000 eruption of Usu volcano, Hokkaido, Japan. Six months before the eruption, an increase in CO2 flux was detected on the summit caldera, from 120 (September 1998) to 340 metric tons per day (September 1999), followed by a sudden decrease to 39 metric tons per day in June 2000, 3 months after the eruption. The change in CO2 flux and seismic observations suggests that before the eruption, advective processes controlled gas migration toward the surface. The decrease in flux after the eruption at the summit caldera could be due to a rapid release of CO2 during the eruption from ascending dacitic dikes spreading away from the magma chamber beneath the caldera. PMID:11292867

  4. 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.

  5. 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

  6. Frictional drag reduction by wavy advection of deformable bubbles

    NASA Astrophysics Data System (ADS)

    Oishi, Yoshihiko; Murai, Yuichi; Tasaka, Yuji; Yasushi, Takeda

    2009-02-01

    Bubbles can reduce frictional drag in wall turbulence, and its effect is expected to use for ships and pipelines to save their power consumptions. A number of basic experiments have been carried out to date for finding out the best condition for enhancing the drag reduction. One issue that remains at present is the difference of the performance between steady and unsteady status in terms of bubble concentration. All the experiments in the past deal with the steady effect, i.e., the drag reduction is evaluated as a function of mean void fraction or given gas flow rate of continuous injection. Despite to this, the actual phenomena highly depend on local interaction between two phases upon unsteady manner. We focus on this point and elucidate the influence of time-fluctuating void fraction on the total response to the drag reduction. This view is in fact important to estimate the persistency of the bubble-based drag reduction in the flow direction since bubbles formulate wavy advection during their migration. Our experiments are designed to measure the above-mentioned effect from laminar, transitional, and turbulent flows in a horizontal channel. For avoiding the contamination effect that worsens the reproducibility of the experiment, Silicone oil is used as carrier fluid. The oil also simulates the high Weber number bubble condition because of low surface tension. The unsteady interaction between the wavy advection of bubbles and the local skin friction, a synchronized system is constructed to connect the high-speed camera with the shear transducer, which can evaluate the interaction at 1000 fps. From the results, we confirm that the drag reduction is provided at Re>3000 in the turbulent flow regime, and also the total drag reduction is enhanced by the presence of the waves.

  7. Multirate Runge-Kutta schemes for advection equations

    NASA Astrophysics Data System (ADS)

    Schlegel, Martin; Knoth, Oswald; Arnold, Martin; Wolke, Ralf

    2009-04-01

    Explicit time integration methods can be employed to simulate a broad spectrum of physical phenomena. The wide range of scales encountered lead to the problem that the fastest cell of the simulation dictates the global time step. Multirate time integration methods can be employed to alter the time step locally so that slower components take longer and fewer time steps, resulting in a moderate to substantial reduction of the computational cost, depending on the scenario to simulate [S. Osher, R. Sanders, Numerical approximations to nonlinear conservation laws with locally varying time and space grids, Math. Comput. 41 (1983) 321-336; H. Tang, G. Warnecke, A class of high resolution schemes for hyperbolic conservation laws and convection-diffusion equations with varying time and pace grids, SIAM J. Sci. Comput. 26 (4) (2005) 1415-1431; E. Constantinescu, A. Sandu, Multirate timestepping methods for hyperbolic conservation laws, SIAM J. Sci. Comput. 33 (3) (2007) 239-278]. In air pollution modeling the advection part is usually integrated explicitly in time, where the time step is constrained by a locally varying Courant-Friedrichs-Lewy (CFL) number. Multirate schemes are a useful tool to decouple different physical regions so that this constraint becomes a local instead of a global restriction. Therefore it is of major interest to apply multirate schemes to the advection equation. We introduce a generic recursive multirate Runge-Kutta scheme that can be easily adapted to an arbitrary number of refinement levels. It preserves the linear invariants of the system and is of third order accuracy when applied to certain explicit Runge-Kutta methods as base method.

  8. 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. PMID:27434808

  9. 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.

  10. 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.

  11. Smoothed particle hydrodynamics model for Landau-Lifshitz-Navier-Stokes and advection-diffusion equations

    NASA Astrophysics Data System (ADS)

    Kordilla, Jannes; Pan, Wenxiao; Tartakovsky, Alexandre

    2014-12-01

    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.

  12. 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.

  13. Weak cation exchange magnetic beads coupled with matrix-assisted laser desorption ionization-time of flight-mass spectrometry in screening serum protein markers in osteopenia.

    PubMed

    He, Wei-Tao; Liang, Bo-Cheng; Shi, Zhen-Yu; Li, Xu-Yun; Li, Chun-Wen; Shi, Xiao-Lin

    2016-01-01

    The present study aimed at investigating the weak cation magnetic separation technology and matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) in screening serum protein markers of osteopenia from ten postmenopausal women and ten postmenopausal women without osteopenia as control group, to find a new method for screening biomarkers and establishing a diagnostic model for primary type I osteoporosis. Serum samples were collected from postmenopausal women with osteopenia and postmenopausal women with normal bone mass. Proteins were extracted from serum samples by weak cation exchange magnetic beads technology, and mass spectra acquisition was done by MALDI-TOF-MS. The visualization and comparison of data sets, statistical peak evaluation, model recognition, and discovery of biomarker candidates were handled by the proteinchip data analysis system software(ZJU-PDAS). The diagnostic models were established using genetic arithmetic based support vector machine (SVM). The SVM result with the highest Youden Index was selected as the model. Combinatorial Peaks having the highest accuracy in distinguishing different samples were selected as potential biomarker. From the two group serum samples, a total of 133 differential features were selected. Ten features with significant intensity differences were screened. In the pair-wise comparisons, processing of MALDI-TOF spectra resulted in the identification of ten differential features between postmenopausal women with osteopenia and postmenopausal women with normal bone mass. The difference of features by Youden index showed that the highest features had a mass to charge ratio of 1699 and 3038 Da. A diagnosis model was established with these two peaks as the candidate marker, and the specificity of the model is 100 %, the sensitivity was 90 % by leave-one-out cross validation test. The two groups of specimens in SVM results on the scatter plot could be clearly distinguished. The peak

  14. Solution of the advection-dispersion equation by a finite-volume eulerian-lagrangian local adjoint method

    USGS Publications Warehouse

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

    1992-01-01

    A finite-volume Eulerian-Lagrangian local adjoint method for solution of the advection-dispersion equation is developed and discussed. The method is mass conservative and can solve advection-dominated ground-water solute-transport problems accurately and efficiently. An integrated finite-difference approach is used in the method. A key component of the method is that the integral representing the mass-storage term is evaluated numerically at the current time level. Integration points, and the mass associated with these points, are then forward tracked up to the next time level. The number of integration points required to reach a specified level of accuracy is problem dependent and increases as the sharpness of the simulated solute front increases. Integration points are generally equally spaced within each grid cell. For problems involving variable coefficients it has been found to be advantageous to include additional integration points at strategic locations in each well. These locations are determined by backtracking. Forward tracking of boundary fluxes by the method alleviates problems that are encountered in the backtracking approaches of most characteristic methods. A test problem is used to illustrate that the new method offers substantial advantages over other numerical methods for a wide range of problems.

  15. 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.

  16. 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...

  17. Large-scale advection and dispersion in the tidal Hudson River derived from a deliberate tracer release experiment

    NASA Astrophysics Data System (ADS)

    Ho, D. T.; Schlosser, P.; Schlosser, P.; Schlosser, P.; Caplow, T.; Garrison, M. R.

    2001-12-01

    In recent years, deliberate tracer release experiments have been used in the ocean, rivers, lakes, and groundwater flow systems to study advection, mixing, air-water gas exchange, and exchanges between subsystems. Here we report results from a recent deliberate tracer release experiment conducted in the tidal Hudson River. On July 25, 2001, ca. 3.3 moles of the inert gas SF6 were injected into the Hudson River near Newburgh, NY at a depth of about 6 m. Subsequently, the SF6 was monitored from a boat (Riverkeeper) by pumping water (from 2 m depth) via a submersed pump mounted on the front of the boat, through a gas extraction unit, followed by measurement using an onboard gas chromatograph. The measurement interval was about 2 minutes and the maximum speed of the boat was about 15 km h-1. This allowed us to obtain detailed surveys of the temporal evolution of the tracer plume for 14 days. Initial results from the experiment show that during July/August 2001, there was virtually no net downward advection of the water body originally tagged with SF6. Instead, we observed rapid mixing of the tracer-tagged water up- and down-river. After one week, the tracer-tagged water could be detected over a stretch of 70 km along the axis of the river channel. At this time, the stretch of river labeled with concentrations >50% of the peak value was about 14 km. After two weeks, the tracer-tagged water had extended to over 90 km, while 28 km had SF6 concentrations >50% of the peak value. Vertical mixing into depressions on the bottom of the river reaching more than 175 feet seemed to be rapid. Dispersion coefficients and vertical turbulent exchange coefficients will be discussed.

  18. 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

  19. Mass spectrometric determination of O2 gas exchange during a dark-to-light transition in higher-plant cells : Evidence for two individual O2-uptake components.

    PubMed

    Avelange, M H; Rébeillé, F

    1991-01-01

    The exchange of O2 and CO2 by photoautotrophic cells of Euphorbia characias L. was measured using a mass-spectrometry technique. During a dark-tolight transition the O2 uptake rate was little affected whereas CO2 efflux was decreased by 40%. In order to differentiate eventual superimposed O2-uptake processes, the kinetics of O2 exchange resulting from brief illuminations were measured with a highly sensitive device. When the cells were exposed to a saturating light for short periods, the rate of O2 uptake passed through a series of transients: there was first a stimulation occurring 2-3 s after the appearance of O2 from water-splitting, followed 30 s later by an inhibition. These two transients were reduced 80% by 3-(3',4'-dichlorophenyl)1, 1-dimethylurea (DCMU), indicating that they relied on the linear transport of electrons in the chloroplasts. The first transient (stimulation of an O2 uptake) was little affected by mitochondrial inhibitors such as antimycin A and oligomycin or the uncoupler carbonylcyanide m-chlorophenylhydrazone (CCCP) but was increased in presence of KCN. When spaced flashes (2 us duration; 100-ms intervals) were used instead of continuous light, this transient was almost suppressed indicating that it was dependent on the saturation of some component of the chloroplastic chain. The second transient (inhibition of O2 uptake) was present when spaced flashes were used instead of continuous light. It was markedly decreased by addition of CCCP and mitochondrial inhibitors (antimycin A, oligomycin, KCN) which strongly indicates that it relied on mitochondrial respiration. It is concluded from these experiments that illumination of the cells resulted in an inhibition of mitochondrial respiration, but the resulting inhibition of O2 uptake was hidden by the appearance of an O2-uptake process of extramitochondrial origin, presumably located in the chloroplast. PMID:24193615

  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

    2015-09-01

    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. PMID:26388365

  1. Conformational changes of the glucocorticoid receptor ligand binding domain induced by ligand and cofactor binding, and the location of cofactor binding sites determined by hydrogen/deuterium exchange mass spectrometry

    PubMed Central

    Frego, Lee; Davidson, Walter

    2006-01-01

    HXMS (hydrogen/deuterium exchange mass spectrometry) of the glucocorticoid receptor ligand-binding domain (GR LBD) complexed with the agonist dexamethasone and the antagonist RU-486 is described. Variations in the rates of exchange were observed in regions consistent with the published crystal structures of GR LBD complexed with RU-486 when compared with the GR dexamethasone complex. We also report the HXMS results for agonist-bound GR LBD with the coactivator transcriptional intermediary factor 2 (TIF2) and anatagonist-bound GR LBD with nuclear receptor corepressor (NCoR). Alterations in exchange rates observed for agonist-bound GR LBD with TIF2 present were consistent with the published crystal structural contacts for the complex. Alterations in exchange rates observed for antagonist-bound GR LBD with NCoR were a subset of those observed with TIF2 binding, suggesting a common or overlapping binding site for coactivator and corepressor. PMID:16600964

  2. Particulate export and lateral advection in the Antarctic Polar Front (Southern Pacific Ocean): One-year mooring deployment

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    An instrumented mooring line with sediment traps, current meters and recorders of temperature and conductivity was deployed just south of the Antarctic Polar Front (63° 26‧ S, 178° 03‧E; water depth 4400 m) from January 9th 1999 to January 10th 2000. Sediment traps at 900 and 3700 m had a single large cup to collect particulate material throughout the 1-year study whereas time-series sediment traps were used to characterize the temporal variability at 1300 and 2400 m. 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 identification. High vertical 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 autumn and winter, 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. Although resuspended material showed an elemental composition relatively similar to vertical summer fluxes, samples collected during high energy events contained benthic foraminifera and exhibited significantly higher 210Pb activity indicating a longer residence time in the water column. In addition, during quiescent periods characterized by low mass fluxes, the content of lithogenic particles increased at the expense of phytodetritus indicating the influence of material advected through the benthic nepheloid layer. Organic matter content was particularly high during these periods and showed

  3. Effects of thinning on transpiration by riparian buffer trees in response to advection and solar radiation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advective energy occurring in edge environments may increase tree water use (e.g., latent heat loss, LE > net radiation, Rn). In humid agricultural landscapes, advection-enhanced transpiration in riparian buffers may provide hydrologic regulation and flood control benefits; however, research in humi...

  4. Fractional Advective-Dispersive Equation as a Model of Solute Transport in Porous Media

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding and modeling transport of solutes in porous media is a critical issue in the environmental protection. The common model is the advective-dispersive equation (ADE) describing the superposition of the advective transport and the Brownian motion in water-filled pore space. Deviations from...

  5. Effects of thinning on transpiration by riparian buffer trees in response to advection and solar radiation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advective energy occurring in edge environments may increase tree water use. In humid agricultural landscapes, advection-enhanced transpiration in riparian buffers may provide hydrologic regulation; however, research in humid environments is lacking. The objectives of this study were to determine ho...

  6. 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...

  7. Direct aqueous determination of glyphosate and related compounds by liquid chromatography/tandem mass spectrometry using reversed-phase and weak anion-exchange mixed-mode column.

    PubMed

    Hao, Chunyan; Morse, David; Morra, Franca; Zhao, Xiaoming; Yang, Paul; Nunn, Brian

    2011-08-19

    Analysis of the broad-spectrum herbicide glyphosate and its related compounds is quite challenging. Tedious and time-consuming derivatization is often required for these substances due to their high polarity, high water solubility, low volatility and molecular structure which lacks either a chromophore or fluorophore. A novel liquid chromatography/tandem mass spectrometry (LC/MS-MS) method has been developed for the determination of glyphosate, aminomethylphosphonic acid (AMPA) and glufosinate using a reversed-phase and weak anion-exchange mixed-mode Acclaim® WAX-1 column. Aqueous environmental samples are directly injected and analyzed in 12 min with no sample concentration or derivatization steps. Two multiple reaction monitoring (MRM) channels are monitored in the method for each target compound to achieve true positive identification, and ¹³C, ¹⁵N-glyphosate is used as an internal standard to carry out isotope dilution mass spectrometric (IDMS) measurement for glyphosate. The instrument detection limits (IDLs) for glyphosate, AMPA and glufosinate are 1, 2 and 0.9 μg/L, respectively. Linearity of the detector response with a minimum coefficient of determination (R² value (R² > 0.995) was demonstrated in the range of ∼10 to 10³ μg/L for each analytes. Spiked drinking water, surface water and groundwater samples were analyzed using this method and the average recoveries of analytes in three matrices ranged from 77.0 to 102%, 62.1 to 101%, 66.1 to 93.7% while relative standard deviation ranged from 6.3 to 10.2%, 2.7 to 14.8%, 2.9 to 10.7%, respectively. Factors that may affect method performance, such as metal ions, sample preservation, and storage time, are also discussed. PMID:21752384

  8. Online determination of levoglucosan in ambient aerosols with Particle-into-Liquid Sampler - High-Performance Anion-Exchange Chromatography - Mass Spectrometry (PILS-HPAEC-MS)

    NASA Astrophysics Data System (ADS)

    Saarnio, K.; Teinilä, K.; Saarikoski, S.; Carbone, S.; Gilardoni, S.; Timonen, H.; Aurela, M.; Hillamo, R.

    2013-06-01

    Biomass burning, such as domestic heating, agricultural, and wild open-land fires, has a significant influence on the atmosphere at the global and, especially, at the local scale. Levoglucosan has been shown to be a good tracer for biomass burning emissions in atmospheric particulate matter and several analytical techniques have been presented for the determination of levoglucosan from filter samples. In this paper, a novel combination of a Particle-into-Liquid Sampler (PILS) to a high-performance anion-exchange chromatograph (HPAEC) with the detection by a mass spectrometer (MS) is presented for the online analysis of levoglucosan in ambient particles. The PILS-HPAEC-MS technique enables a fast online analysis of levoglucosan from the particulate samples. The method was tested at an urban background station in Helsinki, Finland, in winter 2011. A comparison with simultaneous levoglucosan measurements from filter samples by the HPAEC-MS was performed and it showed a good agreement between the online and offline methods. Additionally, the online levoglucosan data were compared with the biomass burning tracer fragments measured by a High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS). As there were no local biomass burning sources close to the measurement station, online levoglucosan measurements revealed that most of the particles from biomass burning were either regionally distributed or long-range transported in the urban background of Helsinki. The average levoglucosan concentrations were relatively low (average 0.083 μg m-3) during the measurement campaign. The highest concentration peak measured for levoglucosan (1.4 μg m-3) seemed to originate from biomass burning in Eastern Europe, likely in Estonia, that was transported to Helsinki.

  9. Online determination of levoglucosan in ambient aerosols with particle-into-liquid sampler - high-performance anion-exchange chromatography - mass spectrometry (PILS-HPAEC-MS)

    NASA Astrophysics Data System (ADS)

    Saarnio, K.; Teinilä, K.; Saarikoski, S.; Carbone, S.; Gilardoni, S.; Timonen, H.; Aurela, M.; Hillamo, R.

    2013-10-01

    Biomass burning, such as domestic heating, agricultural, and wild open-land fires, has a significant influence on the atmosphere at the global and, especially, at the local scale. Levoglucosan has been shown to be a good tracer for biomass burning emissions in atmospheric particulate matter, and several analytical techniques have been presented for the determination of levoglucosan from filter samples. In this paper, a novel combination of a particle-into-liquid sampler (PILS) to a high-performance anion-exchange chromatograph (HPAEC) with the detection by a mass spectrometer (MS) is presented for the online analysis of levoglucosan in ambient particles. The PILS-HPAEC-MS technique enables a fast online analysis of levoglucosan from the particulate samples. The method was tested at an urban background station in Helsinki, Finland, in winter 2011. A comparison with simultaneous levoglucosan measurements from filter samples by the HPAEC-MS was performed and it showed a good agreement between the online and offline methods. Additionally, the online levoglucosan data were compared with the biomass burning tracer fragments measured by a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS). As there were no local biomass burning sources close to the measurement station, online levoglucosan measurements revealed that most of the particles from biomass burning were either regionally distributed or long-range transported in the urban background of Helsinki. The average levoglucosan concentrations were relatively low (average 0.083 μg m-3) during the measurement campaign. The highest concentration peak measured for levoglucosan (1.4 μg m-3) seemed to originate from biomass burning in the Baltic countries, likely in Estonia, that was transported to Helsinki.

  10. 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. PMID:26747520

  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. Probing the Conformational and Functional Consequences of Disulfide Bond Engineering in Growth Hormone by Hydrogen-Deuterium Exchange Mass Spectrometry Coupled to Electron Transfer Dissociation.

    PubMed

    Seger, Signe T; Breinholt, Jens; Faber, Johan H; Andersen, Mette D; Wiberg, Charlotte; Schjødt, Christine B; Rand, Kasper D

    2015-06-16

    Human growth hormone (hGH), and its receptor interaction, is essential for cell growth. To stabilize a flexible loop between helices 3 and 4, while retaining affinity for the hGH receptor, we have engineered a new hGH variant (Q84C/Y143C). Here, we employ hydrogen-deuterium exchange mass spectrometry (HDX-MS) to map the impact of the new disulfide bond on the conformational dynamics of this new hGH variant. Compared to wild type hGH, the variant exhibits reduced loop dynamics, indicating a stabilizing effect of the introduced disulfide bond. Furthermore, the disulfide bond exhibits longer ranging effects, stabilizing a short α-helix quite distant from the mutation sites, but also rendering a part of the α-helical hGH core slightly more dynamic. In the regions where the hGH variant exhibits a different deuterium uptake than the wild type protein, electron transfer dissociation (ETD) fragmentation has been used to pinpoint the residues responsible for the observed differences (HDX-ETD). Finally, by use of surface plasmon resonance (SPR) measurements, we show that the new disulfide bond does not compromise receptor affinity. Our work highlight the analytical potential of HDX-ETD combined with functional assays to guide protein engineering. PMID:25978680

  13. 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).

  14. Effects of the Iowa and Milano mutations on apolipoprotein A-I structure and dynamics determined by hydrogen exchange and mass spectrometry.

    PubMed

    Chetty, Palaniappan Sevugan; Ohshiro, Maki; Saito, Hiroyuki; Dhanasekaran, Padmaja; Lund-Katz, Sissel; Mayne, Leland; Englander, Walter; Phillips, Michael C

    2012-11-01

    The Iowa point mutation in apolipoprotein A-I (G26R) leads to a systemic amyloidosis condition, and the Milano mutation (R173C) is associated with hypoalphalipoproteinemia, a reduced plasma level of high-density lipoprotein. To probe the structural effects that lead to these outcomes, we used amide hydrogen-deuterium exchange coupled with a fragment separation/mass spectrometry analysis (HX MS). The Iowa mutation inserts an arginine residue into the nonpolar face of an α-helix that spans residues 7-44 and causes changes in structure and structural dynamics. This helix unfolds, and other helices in the N-terminal helix bundle domain are destabilized. The segment encompassing residues 116-158, largely unstructured in wild-type apolipoprotein A-I, becomes helical. The helix spanning residues 81-115 is destabilized by 2 kcal/mol, increasing the small fraction of time it is transiently unfolded to ≥1%, which allows proteolysis at residue 83 in vivo over time, releasing an amyloid-forming peptide. The Milano mutation situated on the polar face of the helix spanning residues 147-178 destabilizes the helix bundle domain only moderately, but enough to allow cysteine-mediated dimerization that leads to the altered functionality of this variant. These results show how the HX MS approach can provide a powerful means of monitoring, in a nonperturbing way and at close to amino acid resolution, the structural, dynamic, and energetic consequences of biologically interesting point mutations. PMID:23066790

  15. Nucleotide-induced conformational changes of tetradecameric GroEL mapped by H/D exchange monitored by FT-ICR mass spectrometry

    PubMed Central

    Zhang, Qian; Chen, Jin; Kuwajima, Kunihiro; Zhang, Hui-Min; Xian, Feng; Young, Nicolas L.; Marshall, Alan G.

    2013-01-01

    Here we employ hydrogen/deuterium exchange mass spectrometry (HDX-MS) to access E. coli chaperonin GroEL conformation. The ~800 kDa tetradecameric GroEL plays an essential role in the proper folding of many proteins. Previous studies of the structural dynamics of GroEL upon ATP binding have been inconsistent, showing either minimal or major allosteric changes. Our results, based on the native, non-mutated, protein under physiological conditions in solution demonstrate substantial changes in conformation and/or flexibility upon ATP binding. We capture the pivotal step in its functional cycle by use of a non-hydrolyzable ATP analog, ATPγS, to mimic the ATP-bound GroEL state. Comparison of HDX-MS results for apo GroEL and GroEL-ATPγS enables the characterization of the nucleotide-regulated conformational changes throughout the entire protein with high sequence resolution. The 14-mer GroEL complex is the largest protein assembly yet accessed by HDX-MS, with sequence resolution of segments of as few as five amino acids. PMID:23409238

  16. Hydrogen-deuterium exchange mass spectrometry reveals the interaction of Fenna-Matthews-Olson protein and chlorosome CsmA protein

    PubMed Central

    Huang, Richard Y-C.; Wen, Jianzhong; Blankenship, Robert E.; Gross, Michael L.

    2011-01-01

    In green-sulfur bacterial photosynthesis, excitation energy absorbed by a peripheral antenna structure known as the chlorosome is sequentially transferred through a baseplate protein to the Fenna-Matthews-Olson (FMO) antenna protein and into the reaction center, which is embedded in the cytoplasmic membrane. The molecular details of the optimized photosystem architecture required for efficient energy transfer are only partially understood. We address here the question of how the baseplate interacts with the FMO protein by applying hydrogen/deuterium exchange coupled with enzymatic digestion and mass spectrometry analysis to reveal the binding interface of the FMO antenna protein and the CsmA baseplate protein. Several regions on the FMO protein, represented by peptides consisting of 123-129, 140-149, 150-162, 191-208 and 224-232, show significant decreases of deuterium uptake after CsmA binding. The results indicate that the CsmA protein interacts with the Bchl a #1 side of the FMO protein. A global picture including peptide-level details for the architecture of the photosystem from green sulfur bacteria can now be drawn. PMID:22142245

  17. Quantitative determination of 22 primary aromatic amines by cation-exchange solid-phase extraction and liquid chromatography-mass spectrometry.

    PubMed

    Aznar, Margarita; Canellas, Elena; Nerín, Cristina

    2009-07-01

    Primary aromatic amines (PAAs) have been broadly studied due to their high toxicity. In this work a method for the analysis of 22 PAAs in aqueous simulants has been developed. The method is based on a solid-phase extraction step using cation-exchange cartridges and the subsequent analysis of the extracts by ultra-high-performance liquid chromatography with mass spectrometric detection. The recoveries obtained for all the amines analyzed ranged between 81 and 109%, linear range was between 0.03 and 75 microg L(-1), with the RSD values between 4.5 and 13.4% and an average value of 7.5% and limits of detection at microg L(-1) level. The method has been applied to two real samples obtained from migration experiments of polyurethane based laminates to simulant B (water with 3% (w/v) acetic acid) which represents the worst case for the migration of aromatic amines. The main amines found in both samples were methylenedianiline isomers, obtained from the corresponding residual diisocyanates used during polyurethane adhesive polymerization. The total amine concentration found was 26 and 6.3 microg of aniline equivalents per kg of food simulant. PMID:19464690

  18. Conformational dynamics of human FXR-LBD ligand interactions studied by hydrogen/deuterium exchange mass spectrometry: insights into the antagonism of the hypolipidemic agent Z-guggulsterone.

    PubMed

    Yang, Liping; Broderick, David; Jiang, Yuan; Hsu, Victor; Maier, Claudia S

    2014-09-01

    Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of transcription factors that plays a key role in the regulation of bile acids, lipid and glucose metabolisms. The regulative function of FXR is governed by conformational changes of the ligand binding domain (LBD) upon ligand binding. Although FXR is a highly researched potential therapeutic target, only a limited number of FXR-agonist complexes have been successfully crystallized and subsequently yielded high resolution structures. There is currently no structural information of any FXR-antagonist complexes publically available. We therefore explored the use of amide hydrogen/deuterium exchange (HDX) coupled with mass spectrometry for characterizing conformational changes in the FXR-LBD upon ligand binding. Ligand-specific deuterium incorporation profiles were obtained for three FXR ligand chemotypes: GW4064, a synthetic non-steroidal high affinity agonist; the bile acid chenodeoxycholic acid (CDCA), the endogenous low affinity agonist of FXR; and Z-guggulsterone (GG), an in vitro antagonist of the steroid chemotype. A comparison of the HDX profiles of their ligand-bound FXR-LBD complexes revealed a unique mode of interaction for GG. The conformational features of the FXR-LBD-antagonist interaction are discussed. PMID:24953769

  19. 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

  20. Load-dependent destabilization of the γ-rotor shaft in FOF1 ATP synthase revealed by hydrogen/deuterium-exchange mass spectrometry.

    PubMed

    Vahidi, Siavash; Bi, Yumin; Dunn, Stanley D; Konermann, Lars

    2016-03-01

    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

  1. Different conformational dynamics of PDZ1 and PDZ2 in full-length EBP50 analyzed by hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Park, Ji Young; Duc, Nguyen Minh; Kim, Dong Kyun; Lee, Su Youn; Li, Sheng; Seo, Min-Duk; Woods, Virgil L; Chung, Ka Young

    2015-08-01

    Ezrin-radixin-moesin-binding protein 50 (EBP50) is a scaffolding protein expressed in polarized epithelial cells in various organs, including the liver, kidney, and small intestine, in which it regulates the trafficking and targeting cellular proteins. EBP50 contains two postsynaptic density-95/disk-large/ZO-1 homology (PDZ) domains (e.g., PDZ1 and PDZ2) and an ezrin/radixin/moesin-binding (EB) domain. PDZ domains are one of the major scaffolding domains regulating protein-protein interactions with critical biological roles in cell polarity, migration, proliferation, recognition, and cell-cell interaction. PDZ1 and PDZ2 in EBP50 have different ligand selectivity, although several high-resolution structural studies of isolated PDZ1 and PDZ2 showed similar structures. We studied the conformations of full-length EBP50 and isolated PDZ1 and PDZ2 using hydrogen/deuterium exchange mass spectrometry (HDX-MS). The deuterium uptake profiles of isolated PDZ1 and PDZ2 were similar to those of full-length EBP50. Interestingly, PDZ1 was more dynamic than PDZ2, and these PDZ domains underwent different conformational changes upon ligand binding. These results might explain the differences in ligand-selectivity between PDZ1 and PDZ2. PMID:25789870

  2. Sites Involved in Intra- and Interdomain Allostery Associated with the Activation of Factor VIIa Pinpointed by Hydrogen-Deuterium Exchange and Electron Transfer Dissociation Mass Spectrometry*

    PubMed Central

    Song, Hongjian; Olsen, Ole H.; Persson, Egon; Rand, Kasper D.

    2014-01-01

    Factor VIIa (FVIIa) is a trypsin-like protease that plays an important role in initiating blood coagulation. Very limited structural information is available for the free, inactive form of FVIIa that circulates in the blood prior to vascular injury and the molecular details of its activity enhancement remain elusive. Here we have applied hydrogen/deuterium exchange mass spectrometry coupled to electron transfer dissociation to pinpoint individual residues in the heavy chain of FVIIa whose conformation and/or local interaction pattern changes when the enzyme transitions to the active form, as induced either by its cofactor tissue factor or a covalent active site inhibitor. Identified regulatory residues are situated at key sites across one continuous surface of the protease domain spanning the TF-binding helix across the activation pocket to the calcium binding site and are embedded in elements of secondary structure and at the base of flexible loops. Thus these residues are optimally positioned to mediate crosstalk between functional sites in FVIIa, particularly the cofactor binding site and the active site. Our results unambiguously show that the conformational allosteric activation signal extends to the EGF1 domain in the light chain of FVIIa, underscoring a remarkable intra- and interdomain allosteric regulation of this trypsin-like protease. PMID:25344622

  3. Identification of pharmacological chaperones for Gaucher disease and characterization of their effects on beta-glucocerebrosidase by hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Tropak, Michael B; Kornhaber, Gregory J; Rigat, Brigitte A; Maegawa, Gustavo H; Buttner, Justin D; Blanchard, Jan E; Murphy, Cecilia; Tuske, Steven J; Coales, Stephen J; Hamuro, Yoshitomo; Brown, Eric D; Mahuran, Don J

    2008-11-01

    Point mutations in beta-glucocerebrosidase (GCase) can result in a deficiency of both GCase activity and protein in lysosomes thereby causing Gaucher Disease (GD). Enzyme inhibitors such as isofagomine, acting as pharmacological chaperones (PCs), increase these levels by binding and stabilizing the native form of the enzyme in the endoplasmic reticulum (ER), and allow increased lysosomal transport of the enzyme. A high-throughput screen of the 50,000-compound Maybridge library identified two, non-carbohydrate-based inhibitory molecules, a 2,4-diamino-5-substituted quinazoline (IC(50) 5 microM) and a 5-substituted pyridinyl-2-furamide (IC(50) 8 microM). They raised the levels of functional GCase 1.5-2.5-fold in N370S or F213I GD fibroblasts. Immunofluorescence confirmed that treated GD fibroblasts had decreased levels of GCase in their ER and increased levels in lysosomes. Changes in protein dynamics, monitored by hydrogen/deuterium-exchange mass spectrometry, identified a domain III active-site loop (residues 243-249) as being significantly stabilized upon binding of isofagomine or either of these two new compounds; this suggests a common mechanism for PC enhancement of intracellular transport. PMID:18972510

  4. Identification of Pharmacological Chaperones for Gaucher Disease and Characterization of Their Effects on β-Glucocerebrosidase by Hydrogen/Deuterium Exchange Mass Spectrometry

    PubMed Central

    Tropak, Michael B.; Kornhaber, Gregory J.; Rigat, Brigitte A.; Maegawa, Gustavo H.; Buttner, Justin D.; Blanchard, Jan E.; Murphy, Cecilia; Tuske, Steven J.; Coales, Stephen J.; Hamuro, Yoshitomo; Brown, Eric D.

    2010-01-01

    Point mutations in β-glucocerebrosidase (GCase) can result in a deficiency of both GCase activity and protein in lysosomes thereby causing Gaucher Disease (GD). Enzyme inhibitors such as isofagomine, acting as pharmacological chaperones (PCs), increase these levels by binding and stabilizing the native form of the enzyme in the endoplasmic reticulum (ER), and allow increased lysosomal transport of the enzyme. A high-throughput screen of the 50 000-compound Maybridge library identified two, non-carbohydrate-based inhibitory molecules, a 2,4-diamino-5-substituted quinazoline (IC50 5 μM) and a 5-substituted pyridinyl-2-furamide (IC50 8 μM). They raised the levels of functional GCase 1.5–2.5-fold in N370S or F213I GD fibroblasts. Immunofluorescence confirmed that treated GD fibroblasts had decreased levels of GCase in their ER and increased levels in lysosomes. Changes in protein dynamics, monitored by hydrogen/deuterium-exchange mass spectrometry, identified a domain III active-site loop (residues 243–249) as being significantly stabilized upon binding of isofagomine or either of these two new compounds; this suggests a common mechanism for PC enhancement of intracellular transport. PMID:18972510

  5. Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIβ with Rab11

    PubMed Central

    Fowler, Melissa L.; McPhail, Jacob A.; Jenkins, Meredith L.; Masson, Glenn R.; Rutaganira, Florentine U.; Shokat, Kevan M.; Williams, Roger L.

    2016-01-01

    Abstract 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. PMID:26756197

  6. R-subunit Isoform Specificity in Protein Kinase A: Distinct Features of Protein Interfaces in PKA Types I and II by Amide H/2H exchange Mass Spectrometry

    PubMed Central

    Anand, Ganesh S.; Hotchko, Matthew; Brown, Simon H.J.; Ten Eyck, Lynn F.; Komives, Elizabeth A.; Taylor, Susan S.

    2009-01-01

    The two isoforms (RI and RII) of the regulatory (R) subunit of cAMP-dependent protein kinase or protein kinase A (PKA) are similar in sequence yet have different biochemical properties and physiological functions. To further understand the molecular basis for R-isoform-specificity, the interactions of the RIIβ isoform with the PKA catalytic (C) subunit were analyzed by amide H/2H exchange mass spectrometry to compare solvent accessibility of RIIβ and the C subunit in their free and complexed states. Direct mapping of the RIIβ-C interface revealed important differences between the intersubunit interfaces in the type I and type II holoenzyme complexes. These differences are seen in both the R-subunits as well as the C-subunit. Unlike the type I isoform, the type II isoform complexes require both cAMP-binding domains, and ATP is not obligatory for high affinity interactions with the C-subunit. Surprisingly, the C-subunit mediates distinct, overlapping surfaces of interaction with the two R-isoforms despite a strong homology in sequence and similarity in domain organization. Identification of a remote allosteric site on the C-subunit that is essential for interactions with RII, but not RI subunits, further highlights the considerable diversity in interfaces found in higher order protein complexes mediated by the C-subunit of PKA. PMID:17942118

  7. 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.

  8. Sediment transport in a surface-advected estuarine plume

    NASA Astrophysics Data System (ADS)

    Yao, H. Y.; Leonardi, N.; Li, J. F.; Fagherazzi, S.

    2016-03-01

    The interplay between suspended-sediment transport and plume hydrodynamics in a surface-advected estuarine plume is studied using a three-dimensional numerical model. Our analysis focuses on the formation of a sediment-rich alongshore current and on the effect of sediments on the structure of the recirculating freshwater bulge. We introduce the ratio Y between the traveling time of sediment along the bulge edge and the settling timescale. When Y <1, suspended sediments enter the alongshore coastal current. When Y >1 the sediments are deposited within the bulge. We find that a critical range of settling velocities exist above which no transport in the costal current is allowed. Critical settling-velocity values increase with river discharge. Therefore, low magnitude and long-lasting floods promote sediment sorting in the continental shelf. We further find that, for a given flood duration, intermediate flood magnitudes at the limit between subcritical and supercritical flow maximize the alongshore sediment transport. Similarly, for a fixed input of water and sediments, intermediate discharge durations maximize alongshore sediment transport.

  9. Implementation of two-component advective flow solution in XSPEC

    NASA Astrophysics Data System (ADS)

    Debnath, Dipak; Chakrabarti, Sandip K.; Mondal, Santanu

    2014-05-01

    Spectral and temporal properties of black hole candidates can be explained reasonably well using Chakrabarti-Titarchuk solution of two-component advective flow (TCAF). This model requires two accretion rates, namely the Keplerian disc accretion rate and the halo accretion rate, the latter being composed of a sub-Keplerian, low-angular-momentum flow which may or may not develop a shock. In this solution, the relevant parameter is the relative importance of the halo (which creates the Compton cloud region) rate with respect to the Keplerian disc rate (soft photon source). Though this model has been used earlier to manually fit data of several black hole candidates quite satisfactorily, for the first time, we made it user friendly by implementing it into XSPEC software of Goddard Space Flight Center (GSFC)/NASA. This enables any user to extract physical parameters of the accretion flows, such as two accretion rates, the shock location, the shock strength, etc., for any black hole candidate. We provide some examples of fitting a few cases using this model. Most importantly, unlike any other model, we show that TCAF is capable of predicting timing properties from the spectral fits, since in TCAF, a shock is responsible for deciding spectral slopes as well as quasi-periodic oscillation frequencies. L86

  10. Revisiting the Rossby Haurwitz wave test case with contour advection

    NASA Astrophysics Data System (ADS)

    Smith, Robert K.; Dritschel, David G.

    2006-09-01

    This paper re-examines a basic test case used for spherical shallow-water numerical models, and underscores the need for accurate, high resolution models of atmospheric and ocean dynamics. The Rossby-Haurwitz test case, first proposed by Williamson et al. [D.L. Williamson, J.B. Drake, J.J. Hack, R. Jakob, P.N. Swarztrauber, A standard test set for numerical approximations to the shallow-water equations on the sphere, J. Comput. Phys. (1992) 221-224], has been examined using a wide variety of shallow-water models in previous papers. Here, two contour-advective semi-Lagrangian (CASL) models are considered, and results are compared with previous test results. We go further by modifying this test case in a simple way to initiate a rapid breakdown of the basic wave state. This breakdown is accompanied by the formation of sharp potential vorticity gradients (fronts), placing far greater demands on the numerics than the original test case does. We also go further by examining other dynamical fields besides the height and potential vorticity, to assess how well the models deal with gravity waves. Such waves are sensitive to the presence or not of sharp potential vorticity gradients, as well as to numerical parameter settings. In particular, large time steps (convenient for semi-Lagrangian schemes) can seriously affect gravity waves but can also have an adverse impact on the primary fields of height and velocity. These problems are exacerbated by a poor resolution of potential vorticity gradients.

  11. Compact heat and mass exchangers of the plate fin type in thermal sorption systems: Application in an absorption heat pump with the working pair CH3OH-LiBr/ZnBr2

    NASA Astrophysics Data System (ADS)

    Becker, Harry

    The possible application of Compact Heat and Mass Exchangers (CHME) in a gas fired Absorption Heat Pump (AHP) for domestic heating is studied. The above mentioned heat and mass exchangers are of the plate type. The space between the parallel and plain plates is filled up with corrugated plates of a certain height. The plain and finned plates are stacked and welded together. This gives a heat and mass exchanger which is very compact, expressed by a high area density (m2/m3). This leads to heat and mass transfer processes with small temperature and concentration differences. For testing purposes a pilot plant was built using the above type of components in order to test their heat and/or mass transfer performance. Only the generator is of the Shell And Tube (SAT) type. As the working pair, CH3OH - LiBr/ ZnBr2 was chosen, with the alcohol as the solvent and the salt mixture as the absorbent. This leads to sub atmospheric working pressures with only solvent in the vapor phase. Three series of experiments have been carried out, during which the input parameters were varied over a certain range. It is concluded that the plate fin CHMES are very suitable for application in an AHP for domestic heating purposes.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. Effects of chaotic advection on the timescales of cooling and crystallization of magma bodies at mid crustal levels

    NASA Astrophysics Data System (ADS)

    Petrelli, Maurizio; El Omari, Kamal; Le Guer, Yves; Perugini, Diego

    2016-02-01

    We numerically define the thermochemical evolution of a subduction-related crystal-bearing magmatic mass at mid crustal levels (0.7 GPa, 20-25 km). Two main dynamic mechanisms are considered: (1) a pure buoyancy-driven system where the convective flow is induced by density changes during magma cooling; (2) a buoyancy-driven convective system governed by chaotic advection. The non-Newtonian rheology of natural magmas is taken into account linking the Herschel-Bulkley formulation with the results of fractional crystallization experiments of magmas with the same composition and at the same conditions of temperature and pressure of the studied system. The latent heat of crystallization is also considered in order to address the thermal release in the system induced by the crystallization. Results indicate that the development of chaotic advection generates a complex thermochemical evolution of the system speeding up the crystallization process and the timing required to reach the jamming condition relative to the pure buoyancy-driven convective system (nearly 2 times faster). Our results have important implications for both the rheological history of the magmatic body and the refilling of shallower magmatic systems. In particular, (1) a time-dependent composition ranging from basalt to andesite can be extracted from an initial basaltic magmatic batch; (2) at the attainment of the maximum packing fraction (i.e., just before the jamming condition), homogeneous andesitic melts can be potentially extracted from the system; and (3) the development of chaotic advection within the system allows for the extraction of andesitic melt in shorter times compared to a buoyancy-dominated system.

  19. Round window membrane intracochlear drug delivery enhanced by induced advection.

    PubMed

    Borkholder, David A; Zhu, Xiaoxia; Frisina, Robert D

    2014-01-28

    Delivery of therapeutic compounds to the inner ear via absorption through the round window membrane (RWM) has advantages over direct intracochlear infusions; specifically, minimizing impact upon functional hearing measures. However, previous reports show that significant basal-to-apical concentration gradients occur, with the potential to impact treatment efficacy. Here we present a new approach to inner ear drug delivery with induced advection aiding distribution of compounds throughout the inner ear in the murine cochlea. Polyimide microtubing was placed near the RWM niche through a bullaostomy into the middle ear cavity allowing directed delivery of compounds to the RWM. We hypothesized that a posterior semicircular canalostomy would induce apical flow from the patent cochlear aqueduct to the canalostomy due to influx of cerebral spinal fluid. To test this hypothesis, young adult CBA/CaJ mice were divided into two groups: bullaostomy approach only (BA) and bullaostomy+canalostomy (B+C). Cochlear function was evaluated by distortion product otoacoustic emission (DPOAE) and auditory brainstem response (ABR) thresholds during and after middle ear infusion of salicylate in artificial perilymph (AP), applied near the RWM. The mice recovered for 1week, and were re-tested. The results demonstrate there was no significant impact on auditory function utilizing the RWM surgical procedure with or without the canalostomy, and DPOAE thresholds were elevated reversibly during the salicylate infusion. Comparing the threshold shifts for both methods, the B+C approach had more of a physiological effect than the BA approach, including at lower frequencies representing more apical cochlear locations. Unlike mouse cochleostomies, there was no deleterious auditory functional impact after 1week recovery from surgery. The B+C approach had more drug efficacy at lower frequencies, underscoring potential benefits for more precise control of delivery of inner ear therapeutic compounds

  20. Round Window Membrane Intracochlear Drug Delivery Enhanced by Induced Advection

    PubMed Central

    Borkholder, David A.; Zhu, Xiaoxia; Frisina, Robert D.

    2014-01-01

    Delivery of therapeutic compounds to the inner ear via absorption through the round window membrane (RWM) has advantages over direct intracochlear infusions; specifically, minimizing impact upon functional hearing measures. However, previous reports show that significant basal-to-apical concentration gradients occur, with the potential to impact treatment efficacy. Here we present a new approach to inner ear drug delivery with induced advection aiding distribution of compounds throughout the inner ear in the murine cochlea. Polyimide microtubing was placed near the RWM niche through a bullaostomy into the middle ear cavity allowing directed delivery of compounds to the RWM. We hypothesized that a posterior semicircular canalostomy would induce apical flow from the patent cochlear aqueduct to the canalostomy due to influx of cerebral spinal fluid. To test this hypothesis, young adult CBA/CaJ mice were divided into two groups: bullaostomy approach only (BA) and bullaostomy + canalostomy (B+C). Cochlear function was evaluated by distortion product otoacoustic emission (DPOAE) and auditory brainstem response (ABR) thresholds during and after middle ear infusion of salicylate in artificial perilymph (AP), applied near the RWM. The mice recovered for 1 week, and were re-tested. The results demonstrate there was no significant impact on auditory function utilizing the RWM surgical procedure with or without the canalostomy, and DPOAE thresholds were elevated reversibly during the salicylate infusion. Comparing the threshold shifts for both methods, the B+C approach had more of a physiological effect than the BA approach, including at lower frequencies representing more apical cochlear locations. Unlike mouse cochleostomies, there was no deleterious auditory functional impact after 1 week recovery from surgery. The B+C approach had more drug efficacy at lower frequencies, underscoring potential benefits for more precise control of delivery of inner ear therapeutic compounds

  1. Evaporation of traffic-generated nanoparticles during advection from source

    NASA Astrophysics Data System (ADS)

    Harrison, Roy M.; Jones, Alan M.; Beddows, David C. S.; Dall'Osto, Manuel; Nikolova, Irina

    2016-01-01

    Earlier work has demonstrated the potential for volatilisation of nanoparticles emitted by road traffic as these are advected downwind from the source of emissions, but there have been few studies and the processes have yet to be elucidated in detail. Using a dataset collected at paired sampling sites located respectively in a street canyon and in a nearby park, an in depth analysis of particle number size distributions has been conducted in order to better understand the size reduction of the semi-volatile nanoparticles. By sorting the size distributions according to wind direction and fitting log normal modes, it can be seen that the mode peaking at around 22 nm at the street canyon site is on average shrinking to 6.2 nm diameter at the park site which indicates a mean shrinkage rate for these particles of 0.13 nm s-1 with temperatures within the range 12-18 °C. The diurnal variation of the shrunken mode in the park reflects the diurnal pattern of particle concentrations at the street canyon site taken as the main source area. An analysis of peak diameter for the smallest mode at the downwind park site shows an inverse relationship to wind speed suggesting that dilution rather than travel time is the main determinant of the particle shrinkage rate. An evaluation of previously collected C10 to C35 n-alkane data from a different urban location shows a good fit to Pankow partitioning theory reflecting the semi-volatility of compounds believed to be representative of the composition of diesel exhaust nanoparticles, hence confirming the feasibility of an evaporative mechanism for particle shrinkage.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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. PMID:27131104

  7. Apolipoprotein A-I helical structure and stability in discoidal high-density lipoprotein (HDL) particles by hydrogen exchange and mass spectrometry.

    PubMed

    Sevugan Chetty, Palaniappan; Mayne, Leland; Kan, Zhong-Yuan; Lund-Katz, Sissel; Englander, S Walter; Phillips, Michael C

    2012-07-17

    To understand high-density lipoprotein (HDL) structure at the molecular level, the location and stability of α-helical segments in human apolipoprotein (apo) A-I in large (9.6 nm) and small (7.8 nm) discoidal HDL particles were determined by hydrogen-deuterium exchange (HX) and mass spectrometry methods. The measured HX kinetics of some 100 apoA-I peptides specify, at close to amino acid resolution, the structural condition of segments throughout the protein sequence and changes in structure and stability that occur on incorporation into lipoprotein particles. When incorporated into the large HDL particle, the nonhelical regions in lipid-free apoA-I (residues 45-53, 66-69, 116-146, and 179-236) change conformation from random coil to α-helix so that nearly the entire apoA-I molecule adopts helical structure (except for the terminal residues 1-6 and 237-243). The amphipathic α-helices have relatively low stability, in the range 3-5 kcal/mol, indicating high flexibility and dynamic unfolding and refolding in seconds or less. A segment encompassed by residues 125-158 exhibits bimodal HX labeling indicating co-existing helical and disordered loop conformations that interchange on a time scale of minutes. When incorporated around the edge of the smaller HDL particle, the increase in packing density of the two apoA-I molecules forces about 20% more residues out of direct contact with the phospholipid molecules to form disordered loops, and these are the same segments that form loops in the lipid-free state. The region of disc-associated apoA-I that binds the lecithin-cholesterol acyltransferase enzyme is well structured and not a protruding unstructured loop as reported by others. PMID:22745166

  8. 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. PMID:27224086

  9. Microvascular fluid exchange following thermal skin injury in the rat: changes in extravascular colloid osmotic pressure, albumin mass, and water content.

    PubMed

    Lund, T; Reed, R K

    1986-01-01

    Microvascular fluid exchange was studied in rats subjected to 0, 10, and 40% body surface area (BSA) full-thickness cutaneous burns without providing fluid substitution. The total amounts of water and of albumin entering the entire burned skin area following 10% BSA burns were similar to that in 40% BSA burns. Colloid osmotic pressure in interstitial fluid (COPi) was around 10 mmHg and did not change in the control group or in burned skin from the 40% BSA burn group. COPi after 10% burns increased to 15 mmHg in injured skin, while plasma COP fell from 16 to 12.5 mmHg. Preburn, the interstitial albumin mass (Qalb) was 14.9 mg/g dry tissue weight (DW) and increased to 42 and 20 mg/g DW in injured skin after 10 and 40% burns, respectively. Extravasation of radiolabeled albumin (Ealb) estimated as plasma equivalents per 30 min increased from 6.0 to 321 microliters/g DW at 30-60 min postburn (PB) in injured skin following 10% BSA burns. At 90-120 and 150-180 min PB Ealb in this group was reduced to approximately 120 microliters/g DW. These levels of Ealb were roughly 6 times higher than those after 40% BSA burns. Total tissue water (TTW) was 1.78 ml/g DW preburn and increased to 3.0 and 2.0 ml X g-1 DW PB in the 10 and 40% burn groups, respectively. TTW and Qalb did not change beyond 60 min PB. PMID:3779907

  10. Simultaneous separation and determination of six arsenic species in rice by anion-exchange chromatography with inductively coupled plasma mass spectrometry.

    PubMed

    Ma, Li; Yang, Zhaoguang; Tang, Jie; Wang, Lin

    2016-06-01

    The simultaneous separation and determination of arsenite As(III), arsenate As(V), monomethylarsonic acid (MMA), dimethylarsinic acid (DMA), arsenobetaine (AsB), and arsenocholine (AsC) in rice samples have been carried out in one single anion-exchange column run by high-performance liquid chromatography with inductively coupled plasma mass spectrometry. To estimate the effect of variables on arsenic (As) speciation, the chromatographic conditions including type of competing anion, ionic strength, pH of elution buffer, and flow rate of mobile phase have been investigated by a univariate approach. Under the optimum chromatographic conditions, baseline separation of six As species has been achieved within 10 min by gradient elution program using 4 mM NH4 HCO3 at pH 8.6 as mobile phase A and 4 mM NH4 HCO3 , 40 mM NH4 NO3 at pH 8.6 as mobile phase B. The method detection limits for As(III), As(V), MMA, DMA, AsB, and AsC were 0.4, 0.9, 0.2, 0.4, 0.5, and 0.3 μg/kg, respectively. The proposed method has been applied to separation and quantification of As species in real rice samples collected from Hunan Province, China. The main As species detected in all samples were As(III), As(V) and DMA, with inorganic As accounting for over 80% of total As in these samples. PMID:27062347

  11. Structural basis of specific interactions of Lp-PLA2 with HDL revealed by hydrogen deuterium exchange mass spectrometry[S

    PubMed Central

    Cao, Jian; Hsu, Yuan-Hao; Li, Sheng; Woods, Virgil L.; Dennis, Edward A.

    2013-01-01

    Lipoprotein-associated phospholipase A2 (Lp-PLA2), specifically Group VIIA PLA2, is a member of the phospholipase A2 superfamily and is found mainly associated with LDL and HDL in human plasma. Lp-PLA2 is considered as a risk factor, a potential biomarker, a target for therapy in the treatment of cardiovascular disease, and evidence suggests that the level of Lp-PLA2 in plasma is associated with the risk of future cardiovascular and stroke events. The differential location of the enzyme in LDL/HDL lipoproteins has been suggested to affect Lp-PLA2 function and/or its physiological role and an abnormal distribution of the enzyme may correlate with diseases. Although a mutagenesis study suggested that a surface helix (residues 362–369) mediates the association between Lp-PLA2 and HDL, the molecular details and mechanism of association has remained unknown. We have now employed hydrogen deuterium exchange mass spectrometry to characterize the interaction between recombinant human Lp-PLA2 and human HDL. We have found that specific residues 113–120, 192–204, and 360–368 likely mediate HDL binding. In a previous study, we showed that residues 113–120 are important for Lp-PLA2-liposome interactions. We now find that residues 192–204 show a decreased deuteration level when Lp-PLA2 is exposed to apoA-I, but not apoA-II, the most abundant apoproteins in HDL, and additionally, residues 360–368 are only affected by HDL.The results suggest that apoA-I and phospholipid membranes play crucial roles in Lp-PLA2 localization to HDL. PMID:23089916

  12. Interwoven Four-Compartment Capillary Membrane Technology for Three-Dimensional Perfusion with Decentralized Mass Exchange to Scale Up Embryonic Stem Cell Culture

    PubMed Central

    Gerlach, Jörg C.; Lübberstedt, Marc; Edsbagge, Josefina; Ring, Alexander; Hout, Mariah; Baun, Matt; Rossberg, Ingrid; Knöspel, Fanny; Peters, Grant; Eckert, Klaus; Wulf-Goldenberg, Annika; Björquist, Petter; Stachelscheid, Harald; Urbaniak, Thomas; Schatten, Gerald; Miki, Toshio; Schmelzer, Eva; Zeilinger, Katrin

    2010-01-01

    We describe hollow fiber-based three-dimensional (3D) dynamic perfusion bioreactor technology for embryonic stem cells (ESC) which is scalable for laboratory and potentially clinical translation applications. We added 2 more compartments to the typical 2-compartment devices, namely an additional media capillary compartment for countercurrent ‘arteriovenous’ flow and an oxygenation capillary compartment. Each capillary membrane compartment can be perfused independently. Interweaving the 3 capillary systems to form repetitive units allows bioreactor scalability by multiplying the capillary units and provides decentralized media perfusion while enhancing mass exchange and reducing gradient distances from decimeters to more physiologic lengths of <1 mm. The exterior of the resulting membrane network, the cell compartment, is used as a physically active scaffold for cell aggregation; adjusting intercapillary distances enables control of the size of cell aggregates. To demonstrate the technology, mouse ESC (mESC) were cultured in 8- or 800-ml cell compartment bioreactors. We were able to confirm the hypothesis that this bioreactor enables mESC expansion qualitatively comparable to that obtained with Petri dishes, but on a larger scale. To test this, we compared the growth of 129/SVEV mESC in static two-dimensional Petri dishes with that in 3D perfusion bioreactors. We then tested the feasibility of scaling up the culture. In an 800-ml prototype, we cultured approximately 5 × 109 cells, replacing up to 800 conventional 100-mm Petri dishes. Teratoma formation studies in mice confirmed protein expression and gene expression results with regard to maintaining ‘stemness’ markers during cell expansion. PMID:20197653

  13. 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.

  14. 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.

  15. 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...

  16. Advection and Diffusion of Substances in Biological Tissues With Complex Vascular Networks

    PubMed Central

    Beard, Daniel A.; Bassingthwaighte, James B.

    2010-01-01

    For highly diffusive solutes the kinetics of blood–tissue exchange is only poorly represented by a model consisting of sets of independent parallel capillary–tissue units. We constructed a more realistic multicapillary network model conforming statistically to morphometric data. Flows through the tortuous paths in the network were calculated based on constant resistance per unit length throughout the network and the resulting advective intracapillary velocity field was used as a framework for describing the extravascular diffusion of a substance for which there is no barrier or permeability limitation. Simulated impulse responses from the system, analogous to tracer water outflow dilution curves, showed flow-limited behavior over a range of flows from about 2 to 5 ml min−1 g−1, as is observed for water in the heart in vivo. The present model serves as a reference standard against which to evaluate computationally simpler, less physically realistic models. The simulated outflow curves from the network model, like experimental water curves, were matched to outflow curves from the commonly used axially distributed models only by setting the capillary wall permeability–surface area (PS) to a value so artifactually low that it is incompatible with the experimental observations that transport is flow limited. However, simple axially distributed models with appropriately high PSs will fit water outflow dilution curves if axial diffusion coefficients are set at high enough values to account for enhanced dispersion due to the complex geometry of the capillary network. Without incorporating this enhanced dispersion, when applied to experimental curves over a range of flows, the simpler models give a false inference that there is recruitment of capillary surface area with increasing flow. Thus distributed models must account for diffusional as well as permeation processes to provide physiologically appropriate parameter estimates. PMID:10784090

  17. 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.

  18. 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...

  19. 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...

  20. Fast Coherent Particle Advection through Time-Varying Unstructured Flow Datasets.

    PubMed

    Chen, Mingcheng; Shadden, Shawn C; Hart, John C

    2016-08-01

    Tracing the paths of collections of particles through a flow field is a key step for many flow visualization and analysis methods. When a flow field is interpolated from the nodes of an unstructured mesh, the process of advecting a particle must first find which cell in the unstructured mesh contains the particle. Since the paths of nearby particles often diverge, the parallelization of particle advection quickly leads to incoherent memory accesses of the unstructured mesh. We have developed a new block advection GPU approach that reorganizes particles into spatially coherent bundles as they follow their advection paths, which greatly improves memory coherence and thus shared-memory GPU performance. This approach works best for flows that meet the CFL criterion on unstructured meshes of uniformly sized elements, small enough to fit at least two timesteps in GPU memory. PMID:26353375

  1. Finite element approximation of large air pollution problems. I. Advection. Technical report, January-March 1995

    SciTech Connect

    Giraldo, F.X.; Neta, B.

    1995-04-21

    An Eulerian and semi-Lagrangian finite element methods for the solution of the two dimensional advection equation were developed. Bilinear rectangular elements were used. Linear stability analysis of the method is given.

  2. Sensitivity of Gcm Inm Ras To The Change of Humidity Advection Scheme

    NASA Astrophysics Data System (ADS)

    Kostrykin, S. V.

    We study the influence of change the numerical scheme used for humidity advection in the GCM INM RAS on the model results. The previously used advection scheme of the second order ­ leap-frog was changed on the semi-lagrangian cip scheme of the third order. It has shown that the last scheme has excelent numerical properties among other common semi-lagrangian schemes dealing with precise advection of sharp gra- dients. The numerical expriments with GCM has shown that the main changes in the humidity and temperature fields has happend near tropopause. More closeness of the model fields obtained with new advection of humidity to the NCAR/NCEP reanalyses fields are shown.

  3. 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. uch characteristic methods include Eulerian-Lagrangian methods (ELM), modified method of characteristics (MMOC), and operator splitting methods. eneralization of characteristic...

  4. 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.

  5. Comparison of thermal advection measurements by clear-air radar and radiosonde techniques

    SciTech Connect

    Crochet, M.; Rougier, G.; Bazile, G. Meteorologie Nationale, Trappes )

    1990-10-01

    Vertical profiles of the horizontal wind have been measured every 4 min by a clear-air radar (stratospheric-troposphere radar), and vertical profiles of temperature have been obtained every 2 hours by three radiosonde soundings in the same zone in Brittany during the Mesoscale Frontal Dynamics Project FRONTS 87 campaign. Radar thermal advection is deduced from the thermal wind equation using the measured real horizontal wind instead of the geostrophic wind. Radiosonde thermal advection is determined directly from the sounding station data sets of temperature gradients and also approximately from the thermodynamic equation by the temperature tendency. These approximations, applied during a frontal passage, show the same general features and magnitude of the thermal advection, giving a preliminary but encouraging conclusion for a possible real-time utilization of clear-air radars to monitor thermal advection and to identify its characteristic features. 6 refs.

  6. 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.

  7. 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.

  8. A fully implicit method for 3D quasi-steady state magnetic advection-diffusion.

    SciTech Connect

    Siefert, Christopher; Robinson, Allen Conrad

    2009-09-01

    We describe the implementation of a prototype fully implicit method for solving three-dimensional quasi-steady state magnetic advection-diffusion problems. This method allows us to solve the magnetic advection diffusion equations in an Eulerian frame with a fixed, user-prescribed velocity field. We have verified the correctness of method and implementation on two standard verification problems, the Solberg-White magnetic shear problem and the Perry-Jones-White rotating cylinder problem.

  9. 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.

  10. Spectral approximation to advection-diffusion problems by the fictitious interface method

    NASA Astrophysics Data System (ADS)

    Frati, A.; Pasquarelli, F.; Quarteroni, A.

    1993-08-01

    The algorithmic aspects of the 'fictitious interface' method used in numerical approximations of convection-dominated flows are discussed. The solution algorithm presented alternates the advection-equation solution with that of the advection-diffusion equation within complementary subdomains. For the problems presently considered, spatial discretization is obtained by the spectral collocation method via Legendre-Gaussian modes. Attention is given to the the fictitious interface method's application to the Burgers equation.

  11. NONMETHANE ORGANIC CARBON CONCENTRATIONS IN AIR MASSES ADVECTED INTO URBAN AREAS IN THE UNITED STATES

    EPA Science Inventory

    The report describes recent aircraft sampling programs to measure nonmethane organic carbon (NMOC) levels aloft in the upwind vicinity of several U.S. cities during the morning period of 0600 - 0900 A.M. The cities studied included Dallas-Ft. Worth, Tulsa, Atlanta, Birmingham, Ph...

  12. 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. PMID:26605833

  13. 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.

  14. Clinical relevance of the discrepancy in phenylalanine concentrations analyzed using tandem mass spectrometry compared with ion-exchange chromatography in phenylketonuria

    PubMed Central

    Stroup, Bridget M.; Held, Patrice K.; Williams, Phillip; Clayton, Murray K.; Murali, Sangita G.; Rice, Gregory M.; Ney, Denise M.

    2016-01-01

    Introduction Metabolic control of phenylketonuria (PKU) and compliance with the low-phenylalanine (phe) diet are frequently assessed by measuring blood phe concentrations in dried blood spots (DBS) collected by patients instead of plasma phe concentrations. Objective Our objective was to investigate the difference in blood phe concentrations in DBS collected by subjects and analyzed using either a validated newborn screening tandem mass spectrometry (MS/MS) protocol or ion-exchange chromatography (IEC) compared to plasma phe concentrations obtained simultaneously and analyzed using IEC. Design Three to four fasting blood samples were obtained from 29 subjects with PKU, ages 15–49 years. Capillary blood was spotted on filter paper by each subject and the DBS analyzed using both MS/MS and IEC. Plasma was isolated from venous blood and analyzed using IEC. Results Blood phe concentrations in DBS analyzed using MS/MS are 28% ± 1% (n = 110, p < 0.0001) lower than plasma phe concentrations analyzed using IEC resulting in a blood phe concentration of 514 ± 23 μmol/L and a plasma phe concentration of 731 ± 32 μmol/L (mean ± SEM). This discrepancy is larger when plasma phe is > 600 μmol/L. Due to the large variability across subjects of 13.2%, a calibration factor to adjust blood phe concentrations is not recommended. Analysis of DBS using IEC reduced the discrepancy to 15 ± 2% lower phe concentrations compared to plasma analyzed using IEC (n = 38, p = 0.0001). This suggests that a major contributor to the discrepancy in phe concentrations is the analytical method. Conclusion Use of DBS analyzed using MS/MS to monitor blood phe concentrations in individuals with PKU yields significantly lower phe levels compared to plasma phe levels analyzed using IEC. Optimization of current testing methodologies for measuring phe in DBS, along with patient education regarding the appropriate technique for spotting blood on filter paper is needed to improve

  15. Microtube strip heat exchanger

    SciTech Connect

    Doty, F.D.

    1991-10-16

    This progress report is for the September--October 1991 quarter. 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.

  16. Solution of the advection-dispersion equation in two dimensions by a finite-volume Eulerian-Lagrangian localized adjoint method

    USGS Publications Warehouse

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

    1998-01-01

    We extend the finite-volume Eulerian-Lagrangian localized adjoint method (FVELLAM) for solution of the advection-dispersion equation to two dimensions. The method can conserve mass globally and is not limited by restrictions on the size of the grid Peclet or Courant number. Therefore, it is well suited for solution of advection-dominated ground-water solute transport problems. In test problem comparisons with standard finite differences, FVELLAM is able to attain accurate solutions on much coarser space and time grids. On fine grids, the accuracy of the two methods is comparable. A critical aspect of FVELLAM (and all other ELLAMs) is evaluation of the mass storage integral from the preceding time level. In FVELLAM this may be accomplished with either a forward or backtracking approach. The forward tracking approach conserves mass globally and is the preferred approach. The backtracking approach is less computationally intensive, but not globally mass conservative. Boundary terms are systematically represented as integrals in space and time which are evaluated by a common integration scheme in conjunction with forward tracking through time. Unlike the one-dimensional case, local mass conservation cannot be guaranteed, so slight oscillations in concentration can develop, particularly in the vicinity of inflow or outflow boundaries. Published by Elsevier Science Ltd.

  17. "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

    NASA Astrophysics Data System (ADS)

    Liu, Xiaohua; Cole, Richard B.

    2013-12-01

    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.

  18. Nocturnal Respiration: Can we use the Temporal Dynamics of Advection to Derive an Alternative to the u*-Threshold Filtering Technique?

    NASA Astrophysics Data System (ADS)

    van Gorsel, E.; Leuning, R.; Delpierre, N.; Haverd, V.; Davy, R.; Cleugh, H.

    2007-12-01

    Even moderately complex topography can lead to significant horizontal and vertical advection and a consequent underestimation of nocturnal CO2 fluxes derived from eddy covariance measurements on a single tower. The presence of advective transport is identified using the time series of CO2 concentrations. Given a continuous input of carbon (soil-, wood- and leaf respiration) into a control volume (CV) we expect concentrations in that control volume to increase through time if there is no flux through the upper lid and no advective transport. Time series measurements usually show a strong increase in carbon concentration once the atmosphere is stably stratified, but after this initially strong increase the temporal build-up of concentrations is slower and may even remain relatively constant. As this steady-state situation is not associated with fluxes through the top of the CV we can assume that advection is draining CO2 away. We have analysed data from 24 Fluxnet sites where turbulent flux (Fc) and change of storage (Sc) of CO2 are routinely measured. Analysis of Sc confirms the observation by Aubinet et al. [1] that a common feature in canopy flows is that a maximum rate of change of CO2 occurs in the early evening. This suggests that after this maximum, the advection terms in the mass balance become non negligible. Based on this observation we have developed an alternative to the u*-threshold filtering technique [2]. We have shown that applying this alternative approach leads to good agreement between eddy covariance derived estimates of respiration and independent chamber measurements on a study site in a medium dense Eucalyptus forest in south-east Australia. In this contribution we discuss the applicability of this approach for several sites ranging from the tropics to subpolar latitudes and located in terrain that varies from almost ideally flat to very complex. We compare results from three different estimates of respiration and discuss differences between

  19. Influence of porewater advection on denitrification in carbonate sands: Evidence from repacked sediment column experiments

    NASA Astrophysics Data System (ADS)

    Santos, Isaac R.; Eyre, Bradley D.; Glud, Ronnie N.

    2012-11-01

    Porewater flow enhances mineralization rates in organic-poor permeable sands. Here, a series of sediment column experiments were undertaken to assess the potential effect of advective porewater transport on denitrification in permeable carbonate sands collected from Heron Island (Great Barrier Reef). Experimental conditions (flow path length, advection rate, and temperature) were manipulated to represent conditions similar to near shore tropical environments. HgCl2-poisoned controls were used to assess whether reactions were microbially mediated. Overall, significant correlations were found between oxygen consumption and N2 production. The N:O2 slope of 0.114 implied that about 75% of all the nitrogen mineralized was denitrified. A 4-fold increase in sediment column length (from 10 to 40 cm) resulted in an overall increase in oxygen consumption (1.6-fold), TCO2 production (1.8-fold), and denitrification (1.9-fold). Oxic respiration increased quickly until advection reached 80 L m-2 h-1 and then plateaued at higher advection rates. Interestingly, denitrification peaked (up to 336 μmol N2 m-2 h-1) at intermediate advection rates (30-80 L m-2 h-1). We speculate that intermediate advection rates enhance the development of microniches (i.e., steep oxygen gradients) within porous carbonate sands, perhaps providing optimum conditions for denitrification. The denitrification peak fell within the broad range of advection rates (often on scales of 1-100 L m-2 h-1) typically found on continental shelves implying that carbonate sands may play a major, but as yet unquantified, role in oceanic nitrogen budgets.

  20. 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.

  1. Lagrangian Model of a Surface Advected River Plume in Marginal and Enclosed Seas

    NASA Astrophysics Data System (ADS)

    Osadchiev, A.; Zavialov, P.

    2012-04-01

    Freshwater discharges represent an important constituent in the mass, momentum, and vorticity budgets of the inland and enclosed seas. They are also a major pathway for nutrients and pollutants into the seas. Therefore, it is important to elaborate means for predicting the behavior of the plume under specific forcing conditions. We developed a Lagrangian particle tracking model that simulates a distribution of a surface advected river plume. The model combines deterministic and stochastic approaches for representing convection-diffusion and turbulent processes and is computationally unpretentious. Further, we applied the model to simulate the plumes at different spatial scales. The simulation results under idealized external forcing were verified against the findings from previous studies. The model runs with realistic shore lines, winds and discharge configurations for the Mzymta River plume at the eastern part of the Black Sea coast, with the area smaller than 50 km2, as well as the extensive Ob-Yenisey plume in the Kara Sea, whose area is of order 10000 km2. The simulated variability of the both plumes at the scales from synoptic to seasonal showed good agreement with the in-situ measurements and satellite images. Using the model, we also studied the general aspects of the plume dynamics. The dependence of the spatial extent of a plume of small size river on the wind stress and Coriollis parameter was investigated. We identified three distinctive regimes of the plume evolution depending on the wind direction with respect to the shoreline and the river mouth geometry. The dependence on the Coriollis parameter exhibited a characteristic "M-shaped" pattern indicating that under otherwise equal conditions, the plumes are best developed in the tropical regions. This dependence, however, is largely offset by a much stronger dependence on the wind stress.

  2. A Novel Electrical Model for Advection-Diffusion-Based Molecular Communication in Nanonetworks.

    PubMed

    Azadi, Mehdi; Abouei, Jamshid

    2016-04-01

    In this paper, we propose an end-to-end electrical model to characterize the communication between two nanomachines via advection-diffusion motion along the conventional pipe medium. For this modeling, we consider three modules consisting of transmitter, advection-diffusion propagation and receiver. The modulation scheme and releasing molecules through the conventional pipe medium from the transmitter nanomachine is represented in the transmitter module. The advection-diffusion propagation of molecules along the flow-induced path is shown in advection-diffusion propagation module, and the demodulation scheme of bounded particles at the receiver nanomachine is characterized in the receiver module. Our objective is to find an electrical model of each module under the zero initial condition which enables us to represent the electrical circuit related to each module. The transmitter and the signal propagation models are built on the basis of the molecular advection-diffusion physics, whereas the receiver model is interpreted by stemming from the theory of the ligand-receptor binding chemical process. In addition, we employ the transfer function of modules to derive the normalized gain and the delay of each module. Supported by numerical results, we analyze the effect of physical parameters of the pipe medium on the total normalized gain and delay of molecular communications. PMID:27046879

  3. 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.

  4. 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. PMID:21764063

  5. Rapid isolation of plutonium in environmental solid samples using sequential injection anion exchange chromatography followed by detection with inductively coupled plasma mass spectrometry.

    PubMed

    Qiao, Jixin; Hou, Xiaolin; Roos, Per; Miró, Manuel

    2011-01-31

    This paper reports an automated analytical method for rapid determination of plutonium isotopes ((239)Pu and (240)Pu) in environmental solid extracts. Anion exchange chromatographic columns were incorporated in a sequential injection (SI) system to undertake the automated separation of plutonium from matrix and interfering elements. The analytical results most distinctly demonstrated that the crosslinkage of the anion exchanger is a key parameter controlling the separation efficiency. AG 1-×4 type resin was selected as the most suitable sorbent material for analyte separation. Investigation of column size effect upon the separation efficiency revealed that small-sized (2 mL) columns sufficed to handle up to 50 g of environmental soil samples. Under the optimum conditions, chemical yields of plutonium exceeded 90% and the decontamination factors for uranium, thorium and lead ranged from 10(3) to 10(4). The determination of plutonium isotopes in three standard/certified reference materials (IAEA-375 soil, IAEA-135 sediment and NIST-4359 seaweed) and two reference samples (Irish Sea sediment and Danish soil) revealed a good agreement with reference/certified values. The SI column-separation method is straightforward and less labor intensive as compared with batch-wise anion exchange chromatographic procedures. Besides, the automated method features low consumption of ion-exchanger and reagents for column washing and elution, with the consequent decrease in the generation of acidic waste, thus bearing green chemical credentials. PMID:21168558

  6. Modelling of Thermal Advective Reactive Flow in Hydrothermal Mineral Systems Using an Implicit Time-stepped Finite Element Method.

    NASA Astrophysics Data System (ADS)

    Hornby, P. G.

    2005-12-01

    Understanding chemical and thermal processes taking place in hydrothermal mineral deposition systems could well be a key to unlocking new mineral reserves through improved targeting of exploration efforts. To aid in this understanding it is very helpful to be able to model such processes with sufficient fidelity to test process hypotheses. To gain understanding, it is often sufficient to obtain semi-quantitative results that model the broad aspects of the complex set of thermal and chemical effects taking place in hydrothermal systems. For example, it is often sufficient to gain an understanding of where thermal, geometric and chemical factors converge to precipitate gold (say) without being perfectly precise about how much gold is precipitated. The traditional approach is to use incompressible Darcy flow together with the Boussinesq approximation. From the flow field, the heat equation is used to advect-conduct the heat. The flow field is also used to transport solutes by solving an advection-dispersion-diffusion equation. The reactions in the fluid and between fluid and rock act as source terms for these advection-dispersion equations. Many existing modelling systems that are used for simulating such systems use explicit time marching schemes and finite differences. The disadvantage of this approach is the need to work on rectilinear grids and the number of time steps required by the Courant condition in the solute transport step. The second factor can be particularly significant if the chemical system is complex, requiring (at a minimum) an equilibrium calculation at each grid point at each time step. In the approach we describe, we use finite elements rather than finite differences, and the pressure, heat and advection-dispersion equations are solved implicitly. The general idea is to put unconditional numerical stability of the time integration first, and let accuracy assume a secondary role. It is in this sense that the method is semi-quantiative. However

  7. Advection of methane in the hydrate zone: model, analysis and examples

    NASA Astrophysics Data System (ADS)

    Peszynska, Malgorzata; Showalter, Ralph E.; Webster, Justin T.

    2015-12-01

    A two-phase two-component model is formulated for the advective-diffusive transport of methane in liquid phase through sediment with the accompanying formation and dissolution of methane hydrate. This free-boundary problem has a unique generalized solution in $L^1$; the proof combines analysis of the stationary semilinear elliptic Dirichlet problem with the nonlinear semigroup theory in Banach space for an m-accretive multi-valued operator. Additional estimates of maximum principle type are obtained, and these permit appropriate maximal extensions of the phase-change relations. An example with pure advection indicates the limitations of these estimates and of the model developed here. We also consider and analyze the coupled pressure equation that determines the advective flux in the transport model.

  8. 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.

  9. Power law breakthrough curve tailing in a fracture: The role of advection

    NASA Astrophysics Data System (ADS)

    Fiori, Aldo; Becker, Matthew W.

    2015-06-01

    We offer an explanation of the strongly tailed solute breakthrough curve typically observed when a tracer test is conducted in fractured bedrock. In this example, we limit the model to a single planar fracture of varying aperture. Flow heterogeneity derives from variable fracture aperture, which implies variable transmissivity (T). The analysis employs a physically based model well-suited to strong heterogeneity and relies only upon advective transport. The purely advective model is able to explain a power-law trend of magnitude -2 to -3 in the breakthrough curve tail; a range that has been found in field tracer experiments. The principle cause of this trend is the comparatively slow transport in zones of small transmissivity (tight aperture). Slow advection occurs when either heterogeneity (variance of lnT) is strong or when the assumed heterogeneity distribution is non-Gaussian. Thus, we link breakthrough tailing to the statistical parameters for the transmissivity field.

  10. Altimetric lagrangian advection to reconstruct Pacific Ocean fine scale surface tracer fields

    NASA Astrophysics Data System (ADS)

    Rogé, Marine; Morrow, Rosemary; Dencausse, Guillaume

    2015-04-01

    In past studies, lagrangian stirring of surface tracer fields by altimetric surface geostrophic currents has been performed in different mid to high-latitude regions, showing good results in reconstructing finer-scale tracer patterns. Here we apply the technique to three different regions in the eastern and western tropical Pacific, and in the subtropical southwest Pacific. Initial conditions are derived from weekly gridded temperature and salinity fields, based on hydrographic data and Argo. Validation of the improved fine-scale surface tracer fields is performed using satellite AMSRE SST data, and high-resolution ship thermosalinograph data. We test two kinds of lagrangian advection. The standard one-way advection is shown to introduce an increased tracer bias as the advection time increases. Indeed, since we only use passive stirring, a bias is introduced from the missing physics, such as air-sea fluxes or mixing. A second "backward-forward" advection technique is shown to reduce the seasonal bias, but more data is lost around coasts and islands, a strong handicap in the tropical Pacific with many small islands. In the subtropical Pacific Ocean, the mesoscale temperature and salinity fronts are well represented by the one-way advection over a 10-day advection time, including westward propagating features not apparent in the initial fields. In the tropics, the results are less clear. The validation is hampered by the complex vertical stratification, and the technique is limited by the lack of accurate surface currents for the stirring - the gridded altimetric fields poorly represent the meridional currents, and are not detecting the fast tropical instability waves, nor the wind-driven circulation. We suggest that the passive lateral stirring technique is efficient in regions with moderate the high mesoscale energy and correlated mesoscale surface temperature and surface height. In other regions, more complex dynamical processes may need to be included.

  11. Altimetric Lagrangian advection to reconstruct Pacific Ocean fine-scale surface tracer fields

    NASA Astrophysics Data System (ADS)

    Rogé, Marine; Morrow, Rosemary A.; Dencausse, Guillaume

    2015-09-01

    In past studies, Lagrangian stirring of surface tracer fields by altimetric surface geostrophic currents has been performed in different mid- to high-latitude regions, showing good results in reconstructing finer scale tracer patterns. Here, we explore the pertinence of the technique in the western equatorial Pacific and in the subtropical southwest Pacific. Initial conditions are derived from weekly gridded low-resolution temperature and salinity fields based on in situ hydrographic data. Validation of the reconstructed fine-scale surface tracer fields is performed using satellite AMSRE Sea Surface Temperature data and high-resolution ship thermosalinograph data. We test two kinds of Lagrangian advection. The standard one-way advection leads to an increased error as the advection time increases, due to the missing physics, such as air-sea fluxes or non-geostrophic dynamics. A second "backward-forward" advection technique is explored to reduce this bias in the tracer field, with improved results. In the subtropical southwest Pacific Ocean, the mesoscale temperature and salinity fronts are well represented by both Lagrangian advection techniques over a short 7- to 14-day advection time, including westward-propagating features not apparent in the initial fields. In the tropics, the results are less clear. The validation is hampered by the complex vertical stratification, and the lateral stirring technique is limited by the pertinence of using geostrophic surface current fields in the tropics. We suggest that the passive lateral stirring technique is efficient in regions with moderate to high mesoscale energy, where mesoscale surface tracer and surface height fields are correlated. In other regions, more complex dynamical processes may need to be included.

  12. Toward a Unified Parameterization of the Boundary Layer and Moist Convection. Part 2; Lateral Mass Exchanges and Subplume-Scale Fluxes

    NASA Technical Reports Server (NTRS)

    Lappan, Cara-Lyn; Randall, David A.

    2001-01-01

    The dissipation parameterizations developed for higher-order closure are used to parameterize lateral entrainment and detrainment in a mass-flux model. In addition, a subplume-scale turbulence scheme is included to represent fluxes not captured in the conventional mass-flux framework. These new parameterizations are tested by simulating trade wind cumulus from the Barbados Oceanographic and Meteorological Experiment (BOMEX).

  13. 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

  14. 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.

  15. 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.

  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. General solution of a fractional diffusion-advection equation for solar cosmic-ray transport

    NASA Astrophysics Data System (ADS)

    Rocca, M. C.; Plastino, A. R.; Plastino, A.; Ferri, G. L.; de Paoli, A.

    2016-04-01

    In this effort we exactly solve the fractional diffusion-advection equation for solar cosmic-ray transport and give its general solution in terms of hypergeometric distributions. Numerical analysis of this equation shows that its solutions resemble power-laws.

  18. Contributions of advective and diffusive oxygen transport through multilayer composite caps over mine waste.

    PubMed

    Kim, Hong; Benson, Craig H

    2004-07-01

    The relative contributions of four mechanisms of oxygen transport in multilayer composite (MLC) caps placed over oxygen-consuming mine waste were evaluated using numerical and analytical methods. MLC caps are defined here as caps consisting of earthen and geosynthetic (polymeric) components where a composite barrier layer consisting of a geomembrane (1-2 mm thick polymeric sheet) overlying a clay layer is the primary barrier to transport. The transport mechanisms that were considered are gas-phase advective transport, gas-phase diffusive transport, liquid-phase advective transport via infiltrating precipitation and liquid-phase diffusive transport. A numerical model was developed to simulate gas-phase advective-diffusive transport of oxygen through a multilayer cap containing seven layers. This model was also used to simulate oxygen diffusion in the liquid phase. An approximate analytical method was used to compute the advective flux of oxygen in the liquid phase. The numerical model was verified for limiting cases using an analytical solution. Comparisons were also made between model predictions and field data for earthen caps reported by others. Results of the analysis show that the dominant mechanism for oxygen transport through MLC caps is gas-phase diffusion. For the cases that were considered, the gas-phase diffusive flux typically comprises at least 99% of the total oxygen flux. Thus, designers of MLC caps should focus on design elements and features that will limit diffusion of gas-phase oxygen. PMID:15145567

  19. An objective method for computing advective surface velocities from sequential infrared satellite images

    NASA Astrophysics Data System (ADS)

    Emery, W. J.; Thomas, A. C.; Collins, M. J.; Crawford, W. R.; Mackas, D. L.

    1986-11-01

    Using cross correlations between sequential infrared satellite images, an objective technique is developed to compute advective sea surface velocities. Cross correlations are computed in 32 × 32 pixel search (second image) and 22 × 22 template (first image) windows from gradients of sea surface temperature computed from the satellite images. Velocity vectors, computed from sequential images of the British Columbia coastal ocean, generally appear coherent and consistent with the seasonal surface current in the region. During periods of strong wind forcing, as indicated by maps of sea level pressure, the image advective velocities are stronger and more coherent spatially and appear to cross surface temperature gradients; when winds are weaker, the advective velocities correspond better with the infrared temperature patterns, suggesting the increased contribution of the geostrophic current to the surface flow. Velocities determined from coincident, near-surface drogued (5-10 m) buoys, positioned every half hour by internal LORAN-C units in mid-June, show excellent agreement with the image advective velocities. In addition, conductivity, temperature, and depth (CTD) measurements (taken during the buoy tracking) confirm the homogeneity of the upper 10 m, and CTD-derived geostrophic currents are consistent with both buoy and sequential image displacement velocities.

  20. 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.

  1. 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...

  2. 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...

  3. 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.

  4. 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.

  5. ADVECTION, EDGE, AND OASIS EFFECTS ON SPATIAL MOISTURE AND FLUX FIELDS FROM LIDAR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Relatively narrow forest stands such as the riparian Tamarisk bordering the Rio Grande are subject to dry air advection from the adjacent semi-desert environment. The transport of warm dry air into the canopy has a profound effect upon the spatial properties of the moisture field and associated lat...

  6. 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

  7. 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.

  8. 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.

  9. 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. PMID:21121695

  10. 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...

  11. Analytical solution of the advection-diffusion transport equation using a change-of-variable and integral transform technique

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This paper presents a formal exact solution of the linear advection-diffusion transport equation with constant coefficients for both transient and steady-state regimes. A classical mathematical substitution transforms the original advection-diffusion equation into an exclusively diffusive equation. ...

  12. 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...

  13. 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

  14. 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

  15. 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.

  16. 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)

  17. Intraseasonal variations in the surface layer heat balance of the central equatorial Indian Ocean: The importance of zonal advection and vertical mixing

    NASA Astrophysics Data System (ADS)

    McPhaden, M. J.; Foltz, G. R.

    2013-06-01

    examine the ocean mixed layer response to intraseasonal atmospheric forcing using moored time series data in the central equatorial Indian Ocean for October 2004 to March 2005, a period coincident with two active phases of the Madden-Julian Oscillation (MJO). Both MJO events were accompanied by a sea surface temperature decrease that was partially the consequence of reduced net surface heat flux. In addition, during the first event in October-November 2004, advection by an enhanced Wyrtki Jet contributed substantial cooling, while during the second event in December 2004 to January 2005, vertical processes, most likely related to entrainment mixing, were pronounced. Heavy rainfall at the mooring location during the first event may have contributed to the formation of a 30-40 m thick barrier layer that limited turbulent vertical transfers between the mixed layer and the thermocline. There was no barrier layer present during the second event, which presumably allowed for much freer vertical turbulent exchanges.

  18. [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). PMID:25518559

  19. Hydraulic transmissivity and heat exchange efficiency of open fractures: a model based on lowpass filtered apertures

    NASA Astrophysics Data System (ADS)

    Neuville, Amélie; Toussaint, Renaud; Schmittbuhl, Jean

    2011-09-01

    Natural open joints in rocks commonly present multiscale self-affine apertures. This geometrical complexity affects fluid transport and heat exchange between the flowing fluid and the surrounding rock. In particular, long range correlations of self-affine apertures induce strong channelling of the flow which influences both mass and heat advection. A key question is to find a geometrical model of the complex aperture that describes at best the macroscopic properties (hydraulic conductivity, heat exchange) with the smallest number of parameters. Solving numerically the Stokes and heat equations with a lubrication approximation, we show that a low pass filtering of the aperture geometry provides efficient estimates of the effective hydraulic and thermal properties (apertures). A detailed study of the influence of the bandwidth of the lowpass filtering on these transport properties is also performed. For instance, keeping the information of amplitude only of the largest Fourier length scales allows us to reach already an accuracy of 9 per cent on the hydraulic and the thermal apertures.

  20. Surfzone to inner-shelf exchange estimated from dye tracer balances

    NASA Astrophysics Data System (ADS)

    Hally-Rosendahl, Kai; Feddersen, Falk; Clark, David B.; Guza, R. T.

    2015-09-01

    Surfzone and inner-shelf tracer dispersion are observed at an approximately alongshore-uniform beach. Fluorescent Rhodamine WT dye, released near the shoreline continuously for 6.5 h, is advected alongshore by breaking-wave- and wind-driven currents, and ejected offshore from the surfzone to the inner-shelf by transient rip currents. Novel aerial-based multispectral dye concentration images and in situ measurements of dye, waves, and currents provide tracer transport and dilution observations spanning about 350 m cross-shore and 3 km alongshore. Downstream dilution of near-shoreline dye follows power law decay with exponent -0.33, implying that a tenfold increase in alongshore distance reduces the concentration about 50%. Coupled surfzone and inner-shelf dye mass balances close, and in 5 h, roughly half of the surfzone-released dye is transported offshore to the inner-shelf. Observed cross-shore transports are parameterized well (r2=0.85, best fit slope 0.7) using a bulk exchange velocity and mean surfzone to inner-shelf dye concentration difference. The best fit cross-shore exchange velocity u*=1.2×10-2 m s-1 is similar to a temperature-derived exchange velocity on another day with similar wave conditions. The u* magnitude and observed inner-shelf dye length scales, time scales, and vertical structure indicate the dominance of transient rip currents in surfzone to inner-shelf cross-shore exchange during moderate waves at this alongshore-uniform beach.

  1. A balancing domain decomposition method by constraints for advection-diffusion problems

    SciTech Connect

    Tu, Xuemin; Li, Jing

    2008-12-10

    The balancing domain decomposition methods by constraints are extended to solving nonsymmetric, positive definite linear systems resulting from the finite element discretization of advection-diffusion equations. A pre-conditioned GMRES iteration is used to solve a Schur complement system of equations for the subdomain interface variables. In the preconditioning step of each iteration, a partially sub-assembled finite element problem is solved. A convergence rate estimate for the GMRES iteration is established, under the condition that the diameters of subdomains are small enough. It is independent of the number of subdomains and grows only slowly with the subdomain problem size. Numerical experiments for several two-dimensional advection-diffusion problems illustrate the fast convergence of the proposed algorithm.

  2. Perturbation analysis of steady and unsteady electrohydrodynamic chaotic advection inside translating drops

    NASA Astrophysics Data System (ADS)

    Wu, Fan; Vainchtein, Dmitri; Ward, Thomas

    2015-08-01

    A drop translating in the presence of an electric field is studied analytically. The flow is a combination of a Hadamard-Rybczynski and a Taylor circulation due to the translation and electric field, respectively. We consider chaotic advection that is generated by (1) tilting and (2) time-dependent modulation of the electric field. For the analysis we consider small perturbations in time and space to what is otherwise an integrable flow. By using a robust analytical technique we find an adiabatic invariant (AI) for the system by averaging the equations of motion. The chaotic advection is due to quasirandom jumps of the AI after crossing the separatrix of the unperturbed flow. We demonstrate that the asymptotic analysis leads to a set of criteria that can be used to optimize stirring in these systems.

  3. 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.

  4. 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.

  5. On Vortex Genesis. An Heuristic Model of Convection-Advection Linkages

    NASA Astrophysics Data System (ADS)

    Bouali, S.

    2003-04-01

    We connect to a model of convection roll an appropriate feedback loop (i.e., the advection retroaction) which unfolds a wide range of vorticity behavior. The 3D numerical computations display the conservative aerologic flows of waterspouts and tropical cyclones. Moreover, several simulations exhibit the singular topology of the structure of cyclones eventually trapped in period-2 orbit. On the other hand, additional advection linkages provide our dynamical system with an explicative proof of the tornadogenesis. These amendements modify the model. The airflows are now dissipatives and we investigate the kinematics of these short life span phenomena. The extended model leads the trajectories of air pockets to one or more vortices. The downbursts and microbursts described in the Fujita classification are also simulated. Our heuristic dynamical system lays the foundation of an unified modelisation of vortices. Theory and Direct Numerical Simulation of the vortex genesis are associated in a new perspective.

  6. A study of turbulent transport of an advective nature in a fluid plasma

    NASA Astrophysics Data System (ADS)

    Min, Byunghoon; An, Chan-Yong; Kim, Chang-Bae

    2014-08-01

    The advective nature of the electrostatic turbulent flux of plasma energy in Fourier space is studied numerically in a nearly adiabatic state. Such a state is represented by the Hasegawa-Mima equation, which is driven by a noise that may model the destabilization due to the phase mismatch of the plasma density and the electric potential. The noise is assumed to be Gaussian and not to be invariant under reflection along a direction ŝ. The flux density induced by such noise is found to be anisotropic: While it is random along ŝ, it is not along the perpendicular direction ŝ ⊥, and the flux is not diffusive. The renormalized response may be approximated as advective, with the velocity being proportional to ( kρ s )2, in the Fourier space.

  7. DPDC (double-pass donor cell): A second-order monotone scheme for advection

    SciTech Connect

    Beason, C W; Margolin, L G

    1988-09-26

    We are developing a new, second-order, monotone scheme for advection. DPDC (i.e., double-pass donor cell) is based on Smolarkiewicz' simple, positive definite method. Both schemes are multipass methods in which upstream approximations to the truncation error are subtracted from the equations. We describe two significant improvements to Smolarkiewicz' method. First, we use a local gauge transformation to convert the method from being positive definite to the stronger condition of being monotone. Second, we analytically approximate the sum of the corrections of all the passes to use in a single corrective pass. This increases the accuracy of the method, but does not increase the order of accuracy. We compare DPDC with van Leer's method for advection of several different pulses in a constant velocity field. 5 refs., 4 figs.

  8. Multi-moment advection scheme in three dimension for Vlasov simulations of magnetized plasma

    SciTech Connect

    Minoshima, Takashi; Matsumoto, Yosuke; Amano, Takanobu

    2013-03-01

    We present an extension of the multi-moment advection scheme [T. Minoshima, Y. Matsumoto, T. Amano, Multi-moment advection scheme for Vlasov simulations, Journal of Computational Physics 230 (2011) 6800–6823] to the three-dimensional case, for full electromagnetic Vlasov simulations of magnetized plasma. The scheme treats not only point values of a profile but also its zeroth to second order piecewise moments as dependent variables, and advances them on the basis of their governing equations. Similar to the two-dimensional scheme, the three-dimensional scheme can accurately solve the solid body rotation problem of a gaussian profile with little numerical dispersion or diffusion. This is a very important property for Vlasov simulations of magnetized plasma. We apply the scheme to electromagnetic Vlasov simulations. Propagation of linear waves and nonlinear evolution of the electron temperature anisotropy instability are successfully simulated with a good accuracy of the energy conservation.

  9. A traceable physical calibration of the vertical advection-diffusion equation for modeling ocean heat uptake

    NASA Astrophysics Data System (ADS)

    Huber, Markus; Tailleux, Remi; Ferreira, David; Kuhlbrodt, Till; Gregory, Jonathan

    2015-04-01

    The classic vertical advection-diffusion (VAD) balance is a central concept in studying the ocean heat budget, in particular in simple climate models (SCMs). Here we present a new framework to calibrate the parameters of the VAD equation to the vertical ocean heat balance of two fully-coupled climate models that is traceable to the models' circulation as well as to vertical mixing and diffusion processes. Based on temperature diagnostics, we derive an effective vertical velocity w∗ and turbulent diffusivity kν∗ for each individual physical process. In steady state, we find that the residual vertical velocity and diffusivity change sign in middepth, highlighting the different regional contributions of isopycnal and diapycnal diffusion in balancing the models' residual advection and vertical mixing. We quantify the impacts of the time evolution of the effective quantities under a transient 1% CO2 simulation and make the link to the parameters of currently employed SCMs.

  10. Numerical advection algorithms and their role in atmospheric transport and chemistry models

    NASA Technical Reports Server (NTRS)

    Rood, Richard B.

    1987-01-01

    During the last 35 years, well over 100 algorithms for modeling advection processes have been described and tested. This review summarizes the development and improvements that have taken place. The nature of the errors caused by numerical approximation to the advection equation are highlighted. Then the particular devices that have been proposed to remedy these errors are discussed. The extensive literature comparing transport algorithms is reviewed. Although there is no clear cut 'best' algorithm, several conclusions can be made. Spectral and pseudospectral techniques consistently provide the highest degree of accuracy, but expense and difficulties assuring positive mixing ratios are serious drawbacks. Schemes which consider fluid slabs bounded by grid points (volume schemes), rather than the simple specification of constituent values at the grid points, provide accurate positive definite results.

  11. 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.

  12. Sasaki's variational optimization analysis of temperature and moisture advection in a severe storm environment

    NASA Technical Reports Server (NTRS)

    Mcfarland, M. J.

    1975-01-01

    Temperature and moisture advection patterns of dry air intrusion were analyzed by a variational optimization method to relate mesoscale advection to a severe thunderstorm environment. The analysis results presented here were obtained from a case study, May 26, 1973, when a tornado squall line developed in Oklahoma in conjunction with a clearly delineated dry air intrusion. Observations from the synoptic upper air network were used for inputs of horizontal wind components, potential temperature, and mixing ratio at each 50 mb increment from 950 to 100 mb. An objective analysis was performed to assign values of the variables to grid points of a 15 x 14 horizontal grid with approximate 125 km grid spacing at each pressure level. After the analysis the data fields were smoothed using a variational formalism.

  13. CDF Solutions of Advection-Reaction equations with uncertain parameters (Invited)

    NASA Astrophysics Data System (ADS)

    Boso, F.; Tartakovsky, D. M.

    2013-12-01

    Flow and transport models are affected by parametric uncertainty. Quantitative forecasting of such processes in natural porous media are especially prone to uncertainty because of the inaccessibility and multi-scale nature of the subsurface. We consider a reduced-complexity stochastic transport system which takes into account advection and nonlinear reactions in advection-reaction equations (AREs) with uncertain (random) velocity and reaction parameters. We derive a deterministic equation that governs the evolution of cumulative distribution function (CDF) of a solution of the underlying ARE. Although requiring closure, this differential equation benefits from uniquely defined boundary and initial conditions and can be solved with classic techniques. Here we analyze the accuracy and robustness of the large-eddy-diffusivity closure by comparison with Monte Carlo simulations for different correlation structures and parameters.

  14. Increasing productivity for the analysis of trace contaminants in food by gas chromatography-mass spectrometry using automated liner exchange, backflushing and heart-cutting.

    PubMed

    David, Frank; Tienpont, Bart; Devos, Christophe; Lerch, Oliver; Sandra, Pat

    2013-10-25

    Laboratories focusing on residue analysis in food are continuously seeking to increase sample throughput by minimizing sample preparation. Generic sample extraction methods such as QuEChERS lack selectivity and consequently extracts are not free from non-volatile material that contaminates the analytical system. Co-extracted matrix constituents interfere with target analytes, even if highly sensitive and selective GC-MS/MS is used. A number of GC approaches are described that can be used to increase laboratory productivity. These techniques include automated inlet liner exchange and column backflushing for preservation of the performance of the analytical system and heart-cutting two-dimensional GC for increasing sensitivity and selectivity. The application of these tools is illustrated by the analysis of pesticides in vegetables and fruits, PCBs in milk powder and coplanar PCBs in fish. It is demonstrated that considerable increase in productivity can be achieved by decreasing instrument down-time, while analytical performance is equal or better compared to conventional trace contaminant analysis. PMID:23891373

  15. Direct analysis of un-derivatized asymmetric dimethylarginine (ADMA) and L-arginine from plasma using mixed-mode ion-exchange liquid chromatography-tandem mass spectrometry.

    PubMed

    Bishop, Michael J; Crow, Brian; Norton, Dean; Paliakov, Ekaterina; George, Joe; Bralley, J A

    2007-11-15

    A