Science.gov

Sample records for advective mass exchange

  1. 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.

  2. 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

  3. Advective-diffusive mass transfer in fractured porous media with variable rock matrix block size.

    PubMed

    Sharifi Haddad, Amin; Hassanzadeh, Hassan; Abedi, Jalal

    2012-05-15

    Traditional dual porosity models do not take into account the effect of matrix block size distribution on the mass transfer between matrix and fracture. In this study, we introduce the matrix block size distributions into an advective-diffusive solute transport model of a divergent radial system to evaluate the mass transfer shape factor, which is considered as a first-order exchange coefficient between the fracture and matrix. The results obtained lead to a better understanding of the advective-diffusive mass transport in fractured porous media by identifying two early and late time periods of mass transfer. Results show that fractured rock matrix block size distribution has a great impact on mass transfer during early time period. In addition, two dimensionless shape factors are obtained for the late time, which depend on the injection flow rate and the distance of the rock matrix from the injection point.

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

    USGS Publications Warehouse

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

    1986-01-01

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

  5. Heat and mass exchanger

    DOEpatents

    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.

  6. 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

  7. Hydrogen Exchange Mass Spectrometry.

    PubMed

    Mayne, Leland

    2016-01-01

    Hydrogen exchange (HX) methods can reveal much about the structure, energetics, and dynamics of proteins. The addition of mass spectrometry (MS) to an earlier fragmentation-separation HX analysis now extends HX studies to larger proteins at high structural resolution and can provide information not available before. This chapter discusses experimental aspects of HX labeling, especially with respect to the use of MS and the analysis of MS data.

  8. 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.

  9. 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

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

    NASA Astrophysics Data System (ADS)

    Schelenz, Sophie; Dietrich, Peter; Vienken, Thomas

    2016-04-01

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

  11. 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.

  12. Advection dispersion mass transport associated with a non-aqueous-phase liquid pool

    NASA Astrophysics Data System (ADS)

    Fyrillas, Marios M.

    2000-06-01

    The two-dimensional problem of advection dispersion associated with a non-aqueous-phase liquid (NAPL) pool is addressed using the boundary element method. The problem is appropriately posed with an inhomogeneous boundary condition taking into consideration the presence of the pool and the impermeable layer. We derive a Fredholm integral equation of the first kind for the concentration gradient along the pool location and compute the average mass transfer coefficient numerically using the boundary-element method. Numerical results are in agreement with asymptotic analytical solutions obtained for the cases of small and large Péclet number (Pex). The asymptotic solution for small Pex, which is obtained by applying a novel perturbation technique to the integral equation, is used to de-singularize the integral equation. Results predicted by this analysis are in good agreement with experimentally determined overall mass transfer coefficients.

  13. 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.

  14. Convection and interfacial mass exchange

    NASA Astrophysics Data System (ADS)

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

    2005-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Aktar, Ramiz; Das, Santabrata; Nandi, Anuj

    2015-11-01

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

  16. 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.

  17. 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

  18. Analytical Aspects of Hydrogen Exchange Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Engen, John R.; Wales, Thomas E.

    2015-07-01

    This article reviews the analytical aspects of measuring hydrogen exchange by mass spectrometry (HX MS). We describe the nature of analytical selectivity in hydrogen exchange, then review 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 HX MS 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 can 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.

  19. Translating metabolic exchange with imaging mass spectrometry

    PubMed Central

    Yang, Yu-Liang; Xu, Yuquan; Straight, Paul; Dorrestein, Pieter C.

    2009-01-01

    Metabolic exchange between an organism and the environment, including interactions with neighboring organisms, is important for processes of organismal development. Here we develop and use thin-layer agar natural product MALDI-TOF imaging mass spectrometry of intact bacterial colonies grown on top of the MALDI target plate to study an interaction between two species of bacteria and provide direct evidence that a Bacillus subtilis silences the defensive arsenal of Streptomyces coelicolor. PMID:19915536

  20. 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.

  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

    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.

  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. 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

  4. 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.

  5. Avian eggs: barriers to the exchange of heat and mass.

    PubMed

    Sotherland, P R; Spotila, J R; Paganelli, C V

    1987-01-01

    Measured boundary-layer conductance to heat exchange for bird eggs varies with egg mass to the 0.53 power. Calculations based on the Nusselt-Reynolds relationship for a sphere and the thermal properties of air indicate that the conductance of the boundary layer to heat and to mass at any wind speed other than still air should scale with mass to the 0.53 power. Although the boundary layer contributes little to the total barrier to mass flux between bird eggs and their environment, we show that it is the major barrier to the exchange of heat. From these observations we infer that birds incubating eggs in natural nests can alter only the gradient affecting mass flux between their eggs and the environment while having the capability to change both the gradient and conductance affecting heat flux.

  6. 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

  7. Radiocarbon detection by ion charge exchange mass spectrometry

    NASA Astrophysics Data System (ADS)

    Hotchkis, Michael; Wei, Tao

    2007-06-01

    A method for detection of radiocarbon at low levels is described and the results of tests are presented. We refer to this method as ion charge exchange mass spectrometry (ICE-MS). The ICE-MS instrument is a two stage mass spectrometer. In the first stage, molecular interferences which would otherwise affect radiocarbon detection at mass 14 are eliminated by producing high charge state ions directly in the ion source (charge state ⩾2). 14N interference is eliminated in the second stage by converting the beam to negative ions in a charge exchange cell. The beam is mass-analysed at each stage. We have built a test apparatus consisting of an electron cyclotron resonance ion source and a pair of analysing magnets with a charge exchange cell in between, followed by an electrostatic analyser to improve the signal to background ratio. With this apparatus we have measured charge exchange probabilities for (Cn+ → C-) from 4.5 to 40.5 keV (n = 1-3). We have studied the sources of background including assessment of limits for nitrogen interference by searching for negative ions from charge exchange of 14N ions. Our system has been used to detect 14C in enriched samples of CO2 gas with 14C/12C isotopic ratio down to the 10-9 level. Combined with a measured sample consumption rate of 4 ng/s, this corresponds to a capability to detect transient signals containing only a few μBq of 14C activity, such as may be obtained from chromatographic separation. The method will require further development to match the sensitivity of AMS with a gas ion source; however, even in its present state its sensitivity is well suited to tracer studies in biomedical research and drug development.

  8. Mass-resolving charge-exchange system on PDX

    SciTech Connect

    Davis, S.L.; Mueller, D.; Keane, C.J.

    1982-10-01

    The PDX charge-exchange system is comprised of four, ten channel, mass-resolved, charge-exchange analyzers. Each analyzer is constructed with parallel electric and magnetic fields and is calibrated over an energy range of 0.5 to 40 keV. The mass rejection between hydrogen and deuterium has been measured as better than 1000 to 1. For ohmic heated discharges the system can provide single shot radial ion temperature profiles (4 point) with 1 msec time resolution. For neutral beam heated discharges complete radial and temporal profiles can be obtained in 2 to 4 shots. The system is also equipped with a vertically aimed diagnostic neutral beam to allow local ion-energy distribution measurements. This report describes the analyzer system and its calibration, and presents results from ohmic and neutral beam heated discharges.

  9. A Warming Surface but a Cooling Top of Atmosphere Associated with Warm, Moist Air Mass Advection over the Ice and Snow Covered Arctic

    NASA Astrophysics Data System (ADS)

    Sedlar, J.

    2015-12-01

    Atmospheric advection of heat and moisture from lower latitudes to the high-latitude Arctic is a critical component of Earth's energy cycle. Large-scale advective events have been shown to make up a significant portion of the moist static energy budget of the Arctic atmosphere, even though such events are typically infrequent. The transport of heat and moisture over surfaces covered by ice and snow results in dynamic changes to the boundary layer structure, stability and turbulence, as well as to diabatic processes such as cloud distribution, microphysics and subsequent radiative effects. Recent studies have identified advection into the Arctic as a key mechanism for modulating the melt and freeze of snow and sea ice, via modification to all-sky longwave radiation. This paper examines the radiative impact during summer of such Arctic advective events at the top of the atmosphere (TOA), considering also the important role they play for the surface energy budget. Using infrared sounder measurements from the AIRS satellite, the summer frequency of significantly stable and moist advective events from 2003-2014 are characterized; justification of AIRS profiles over the Arctic are made using radiosoundings during a 3-month transect (ACSE) across the Eastern Arctic basin. One such event was observed within the East Siberian Sea in August 2014 during ACSE, providing in situ verification on the robustness and capability of AIRS to monitor advective cases. Results will highlight the important surface warming aspect of stable, moist instrusions. However a paradox emerges as such events also result in a cooling at the TOA evident on monthly mean TOA radiation. Thus such events have a climatic importance over ice and snow covered surfaces across the Arctic. ERA-Interim reanalyses are examined to provide a longer term perspective on the frequency of such events as well as providing capability to estimate meridional fluxes of moist static energy.

  10. HEMP advection model

    SciTech Connect

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

    1981-01-21

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

  11. Transport and mixing in the atmosphere: Anomalous diffusion and stratosphere-troposphere mass exchange

    NASA Astrophysics Data System (ADS)

    Seo, Kyong-Hwan

    2001-10-01

    Particle dispersion in the stratosphere and mass exchange between the stratosphere and troposphere are investigated in a Lagrangian framework using the United Kingdom Meteorological Office assimilated winds. In the winter stratosphere, isentropic dispersion can be characterized as chaotic advection. Parcel trajectories intermittently alternate between flying in jets and trapping in coherent quasi-stationary vortices. We show that these trajectories are described by a power-law probability density function (PDF) with a decay exponent of less than 3. For these PDFs mean square displacement per flight step is divergent and the trajectories correspond to Lévy flights (random walk processes with divergent second moment). The variance of the zonal displacement grows faster than linearly with time, corresponding to superdiffusive dispersion. The self- similarity in the trajectories is revealed by the convergence of the scaled PDFs of displacement and the saturation of the normalized third and fourth moments with time. Stratosphere-troposphere exchange (STE), calculated by a Lagrangian method, exhibits a pronounced annual cycle. The northern hemisphere net flux of stratospheric air into the troposphere across the extratropical tropopause has a primary peak in late spring or early summer, which is consistent with observation. The southern hemisphere net flux of stratospheric air into the troposphere shows a maximum in winter. The preferred locations for stratosphere-to-troposphere transport are identified as the regions with the highest frequency of Rossby wave breaking events and with the storm tracks. This suggests that tropopause folding and baroclinic eddy activity are a primary mechanism for STE. The greatest diabatic injection of tropospheric air into the tropical stratosphere takes place following the annual variation of the Hadley circulation. The tropical upward transport occurs in association with the monsoon anticyclones. The interannual change of total column

  12. 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

  13. 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.

  14. 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.

  15. Hydrogen exchange mass spectrometry of proteins at Langmuir monolayers

    PubMed Central

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

    2015-01-01

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

  16. 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. 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.

  18. Advection in geologic media

    NASA Astrophysics Data System (ADS)

    Moltyaner, G. L.

    1993-10-01

    In situ sensing technology, used in a series of natural-gradient tracer tests at the Chalk River Laboratories in Ontario, leads to the introduction of a conceptually new approach to the study of groundwater motion in porous media. As opposed to the conventional approach, based on the consideration of a fictitious fluid continuum with fluid properties distributed over both voids and solids, in the new approach the actual groundwater motion in the void space of a porous medium is considered and described at the local scale by the statistical characterization of the propagation of gamma-radiation energy associated with the moving water as a tracer. The essential feature of the new approach is that the mean free path of a gamma-energy photon instead of the porosity is used as a scaling factor in transferring information associated with pore-scale fluid motion to the local scale. This scaling factor is employed for reintroducing the familiar particle model of fluid motion but at the local scale. It is shown that when the local-scale dispersion is neglected, the evolution of local-scale fluid particles making up the tracer plume can be described by the advection equation; its equation of characteristics describes trajectories of local-scale particles. A simple analytical solution to the advection equation is then used to produce three-dimensional images of the spatial distribution of local-scale particles observed in the Twin Lake test. It is also shown that the spatial averaging procedure with regard to the weighting function for a spherical averaging volume of one mean free path radius may be used to introduce the three-dimensional field of local-scale concentration. The averaging procedure is then used to illustrate that the concept of the three-dimensional field of plume-scale concentration does not make physical sense and only the one-dimensional plume-scale concentration field may be introduced in shallow aquifers.

  19. On the tensorial nature of advective porosity

    NASA Astrophysics Data System (ADS)

    Neuman, Shlomo P.

    2005-02-01

    Field tracer tests indicate that advective porosity, the quantity relating advective velocity to Darcy flux, may exhibit directional dependence. Hydraulic anisotropy explains some but not all of the reported directional results. The present paper shows mathematically that directional variations in advective porosity may arise simply from incomplete mixing of an inert tracer between directional flow channels within a sampling (or support) volume ω of soil or rock that may be hydraulically isotropic or anisotropic. In the traditional fully homogenized case, our theory yields trivially a scalar advective porosity equal to the interconnected porosity ϕ, thus explaining neither the observed directional effects nor the widely reported experimental finding that advective porosity is generally smaller than ϕ. We consider incomplete mixing under conditions in which the characteristic time tD of longitudinal diffusion along channels across ω is much shorter than the characteristic time tH required for homogenization through transverse diffusion between channels. This may happen where flow takes place preferentially through relatively conductive channels and/or fractures of variable orientation separated by material that forms a partial barrier to diffusive transport. Our solution is valid for arbitrary channel Peclet numbers on a correspondingly wide range of time scales tD ⩽ t ≪ tH. It shows that the tracer center of mass is advected at a macroscopic velocity which is generally not collinear with the macroscopic Darcy flux and exceeds it in magnitude. These two vectors are related through a second-rank symmetric advective dispersivity tensor Φ. If the permeability k of ω is a symmetric positive-definite tensor, so is Φ. However, the principal directions and values of these two tensors are generally not the same; whereas those of k are a fixed property of the medium and the length-scale of ω, those of Φ depend additionally on the direction and magnitude of the

  20. 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...

  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. 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.

  3. 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.

  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. Intracellular water exchange for measuring the dry mass, water mass and changes in chemical composition of living cells.

    PubMed

    Feijó Delgado, Francisco; Cermak, Nathan; Hecht, Vivian C; Son, Sungmin; Li, Yingzhong; Knudsen, Scott M; Olcum, Selim; Higgins, John M; Chen, Jianzhu; Grover, William H; Manalis, Scott R

    2013-01-01

    We present a method for direct non-optical quantification of dry mass, dry density and water mass of single living cells in suspension. Dry mass and dry density are obtained simultaneously by measuring a cell's buoyant mass sequentially in an H2O-based fluid and a D2O-based fluid. Rapid exchange of intracellular H2O for D2O renders the cell's water content neutrally buoyant in both measurements, and thus the paired measurements yield the mass and density of the cell's dry material alone. Utilizing this same property of rapid water exchange, we also demonstrate the quantification of intracellular water mass. In a population of E. coli, we paired these measurements to estimate the percent dry weight by mass and volume. We then focused on cellular dry density - the average density of all cellular biomolecules, weighted by their relative abundances. Given that densities vary across biomolecule types (RNA, DNA, protein), we investigated whether we could detect changes in biomolecular composition in bacteria, fungi, and mammalian cells. In E. coli, and S. cerevisiae, dry density increases from stationary to exponential phase, consistent with previously known increases in the RNA/protein ratio from up-regulated ribosome production. For mammalian cells, changes in growth conditions cause substantial shifts in dry density, suggesting concurrent changes in the protein, nucleic acid and lipid content of the cell.

  6. Advection of Sea-Ice Meltwater and Halocline Water Along the Siberian Continental Margin

    NASA Astrophysics Data System (ADS)

    Bauch, D.; Torres-Valdes, S.; Polyakov, I.; Chernyavskaya, E.; Novikhin, A.; Dmitrenko, I.; McKay, J. L.; Mix, A. C.

    2014-12-01

    Our study is based on hydrochemical and stable oxygen isotope data at the Laptev Sea continental slope from summers 2005-2009 and reveals a general pattern in water mass distribution and potential shelf-basin exchange. Despite considerable inter-annual variations, a frontal system can be inferred between shelf, continental slope and central Eurasian Basin waters in the upper 100 m of the water column along the continental slope. Net sea-ice melt is consistently found at the continental slope. However, the sea-ice meltwater signal is independent from the local retreat of the sea-ice edge and appears to be advected from upwind locations. In addition to the along-slope frontal system at the continental shelf break, a strong gradient is identified on the Laptev Sea shelf at ~122-126°E with an eastward increase of riverine and sea-ice related brine water contents. These waters cross the shelf break at ~140°E and feed the Low Salinity Halocline Water (LSHW, salinity S<33) in the upper 50 m of the water column. High silicate concentrations in Laptev Sea bottom waters may lead to speculation about a link to the local silicate maximum found within the salinity range of ~33 to 34.5, typical for the Lower Halocline Water (LHW) at the continental slope. However brine signatures and nutrient ratios from the central Laptev Sea differ from those observed at the continental slope. Similar to the advection of the sea-ice melt signal along the Laptev Sea continental slope the nutrient signal at 50-70 m water depth within the LHW might also be fed by advection parallel to the slope. Thus, our analyses suggest that advective processes from upstream locations play a significant role in the meltwater distribution and halocline formation in the northern Laptev Sea. Inter-annual variations within the properties of LHW are further investigated.

  7. Mapping Protein-Ligand Interactions with Proteolytic Fragmentation, Hydrogen/Deuterium Exchange-Mass Spectrometry.

    PubMed

    Gallagher, Elyssia S; Hudgens, Jeffrey W

    2016-01-01

    Biological processes are the result of noncovalent, protein-ligand interactions, where the ligands range from small organic and inorganic molecules to lipids, nucleic acids, peptides, and proteins. Amide groups within proteins constantly exchange protons with water. When immersed in heavy water (D2O), mass spectrometry (MS) can measure the change of mass associated with the hydrogen to deuterium exchange (HDX). Protein-ligand interactions modify the hydrogen exchange rates of amide protons, and the measurement of the amide exchange rates can provide rich information regarding the dynamical structure of the protein-ligand complex. This chapter describes a protocol for conducting bottom-up, continuous uptake, proteolytic fragmentation HDX-MS experiments that can help identify and map the interacting peptides of a protein-ligand interface. This tutorial outlines the fundamental theory governing hydrogen exchange; provides practical information regarding the preparation of protein samples and solutions; and describes the exchange reaction, reaction quenching, enzymatic digestion, chromatographic separation, and peptide analysis by MS. Tables list representative combinations of fluidic components used by HDX-MS researchers and summarize the available HDX-MS analysis software packages. Additionally, two HDX-MS case studies are used to illustrate protein-ligand interactions involving: (1) a continuous sequence of interacting residues and (2) a set of discontinuously numbered residues, residing spatially near each other.

  8. 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

  9. 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.

  10. Black Hole Advective Accretion Disks with Optical Depth Transition

    SciTech Connect

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

    2006-02-01

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

  11. 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. 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.

  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. 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.

  15. Boundary mass-exchange conditions in the form of the Newton and Dalton laws

    NASA Astrophysics Data System (ADS)

    Afanas'ev, A. M.; Siplivyi, B. N.

    2007-01-01

    It has been established that the linear boundary mass-exchange conditions in the form of the Newton law are unsuitable for description of the initial period of drying and the constant-rate period. The nonlinear boundary conditions of the third kind based on the Dalton evaporation law have been proposed. A numerical algorithm for investigation of the temperature and moisture-content fields up to the dropping-rate period has been developed.

  16. Advective coalescence in chaotic flows.

    PubMed

    Nishikawa, T; Toroczkai, Z; Grebogi, C

    2001-07-16

    We investigate the reaction kinetics of small spherical particles with inertia, obeying coalescence type of reaction, B+B-->B, and being advected by hydrodynamical flows with time-periodic forcing. In contrast to passive tracers, the particle dynamics is governed by the strongly nonlinear Maxey-Riley equations, which typically create chaos in the spatial component of the particle dynamics, appearing as filamental structures in the distribution of the reactants. Defining a stochastic description supported on the natural measure of the attractor, we show that, in the limit of slow reaction, the reaction kinetics assumes a universal behavior exhibiting a t(-1) decay in the amount of reagents, which become distributed on a subset of dimension D2, where D2 is the correlation dimension of the chaotic flow. PMID:11461595

  17. Chaotic advection of immiscible fluids

    NASA Astrophysics Data System (ADS)

    Vollmayr-Lee, Benjamin; Beller, Daniel; Yasuda, Sohei

    2012-02-01

    We consider a system of two immiscible fluids advected by a chaotic flow field. A nonequilibrium steady state arises from the competition between the coarsening of the immiscible fluids and the domain bursting caused by the chaotic flow. It has been established that the average domain size in this steady state scales as a inverse power of the Lyapunov exponent. We examine the issue of local structure and look for correlations between the local domain size and the finite-time Lyapunov exponent (FTLE) field. For a variety of chaotic flows, we consistently find the domains to be smallest in regions where the FTLE field is maximal. This raises the possibility of making universal predictions of steady-state characteristics based on Lyapunov analysis of the flow field.

  18. 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.

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

    PubMed Central

    Yi, Q.; Baker, D.

    1996-01-01

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

  20. 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

  1. Mass-transfer mechanisms for zeolite ion exchange in wastewater treatment

    SciTech Connect

    Robinson, S.M.; Arnold, W.D.; Byers, C.H. )

    1994-12-01

    In spite of the increasing commercial use of zeolites for binary and multicomponent ion exchange, understanding of the basic mass-transfer processes associated with multicomponent zeolite systems is quite limited. This study evaluates Na-Ca-Mg-Cs-Sr ion exchange from an aqueous solution using a chabazite zeolite. Mass-transfer coefficient are determined from experimental batch-reactor data for binary and multicomponent systems. The experimental data indicate that diffusion through the microporous zeolite crystals is the primary diffusional resistance. Macropore diffusion also significantly contributes to the mass-transfer resistance. Various mass-transfer models are compared with the experimental data to determine values for intraparticle diffusivities. Effective diffusivities obtained accurately predict experimental data sing a variety of models. Only the model accounting for micropore and macropore diffusion occurring in series accurately predict multicomponent data using diffusivities from the binary system. Liquid and surface diffusion both contribute to macropore diffusion. Surface and micropore diffusivities are concentration-dependent for the system of interest.

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

    PubMed Central

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

    2012-01-01

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

  3. High-resolution two dimensional advective transport

    USGS Publications Warehouse

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

    1989-01-01

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

  4. 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).

  5. Numerical experiments for advection equation

    SciTech Connect

    Sun, Wen-Yih )

    1993-10-01

    We propose to combine the Crowley fourth-order scheme and the Gadd scheme for solving the linear advection equation. Two new schemes will be presented: the first is to integrate the Crowley scheme and the Gadd scheme alternately (referred to as New1); the second is to integrate the Crowley scheme twice before we apply the Gadd scheme once (referred to as New2). The new schemes are designed such that no additional restriction is placed on the CFL criterion in an integration. The performance of the new schemes is better than that of the original Crowley or Gadd schemes. It is noted that the amplitude obtained from New2 is more accurate than that from New1 for long waves, but less accurate for short waves. The phase speed calculated from New2 is very close to the real phase speed in most cases tested here, but the phase speed of New 1 is faster than the real phase speed. Hence, New2 is a better choice, especially for a model that includes horizontal smoothing to dampen the short waves. 9 refs., 5 figs., 8 tabs.

  6. 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

  7. 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

  8. 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.

  9. 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

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

    NASA Technical Reports Server (NTRS)

    Hartley, Dana

    1995-01-01

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

  11. 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.

  12. Electrochemical reduction of disulfide-containing proteins for hydrogen/deuterium exchange monitored by mass spectrometry.

    PubMed

    Mysling, Simon; Salbo, Rune; Ploug, Michael; Jørgensen, Thomas J D

    2014-01-01

    Characterization of disulfide bond-containing proteins by hydrogen/deuterium exchange monitored by mass spectrometry (HDX-MS) requires reduction of the disulfide bonds under acidic and cold conditions, where the amide hydrogen exchange reaction is quenched (pH 2.5, 0 °C). The reduction typically requires a high concentration (>200 mM) of the chemical reducing agent Tris(2-carboxyethyl)phosphine (TCEP) as its reduction rate constant is decreased at low pH and temperature. Serious adverse effects on chromatographic and mass spectrometric performances have been reported when using high concentrations of TCEP. In the present study, we explore the feasibility of using electrochemical reduction as a substitute for TCEP in HDX-MS analyses. Our results demonstrate that efficient disulfide bond reduction is readily achieved by implementing an electrochemical cell into the HDX-MS workflow. We also identify some challenges in using electrochemical reduction in HDX-MS analyses and provide possible conditions to attenuate these limitations. For example, high salt concentrations hamper disulfide bond reduction, necessitating additional dilution of the sample with aqueous acidic solution at quench conditions. PMID:24251601

  13. Modeling the Channel/Floodplain Interface: The Influence of Riparian Vegetation on Mass and Momentum Exchange

    NASA Astrophysics Data System (ADS)

    Stone, M. C.

    2013-12-01

    The objective of this research was to improve understanding of the impacts of riparian vegetation on mass and momentum flux between the main channel and the floodplain. Numerical investigations were carried out on five sites within three rivers in New Mexico, USA. Vegetation characteristics were varied to represent different riparian scenarios ranging from no vegetation to dense understory. The sedimentation and river hydraulics in two dimensions (SRH-2D) model was applied to simulate hydrodynamic conditions. The model was modified to include two algorithms for simulating a dynamic hydraulic roughness in the riparian zone. Thus resistive forces were represented as a function of vegetation characteristics and hydrodynamic condition. The results provide insights into the processes of mass and momentum transfer at the channel/floodplain interface. As expected, an increase in vegetation density produced enhanced momentum exchange. However, a threshold was reached beyond which the momentum exchange peaked and then dropped. This threshold was the results of low floodplain velocities producing very little resistive force due to low drag. Future work will focus on unsteady investigations and laboratory and field verification studies.

  14. 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.

  15. 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.

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

    PubMed

    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.

  17. Conformational analysis of g protein-coupled receptor signaling by hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Li, Sheng; Lee, Su Youn; Chung, Ka Young

    2015-01-01

    Conformational change and protein-protein interactions are two major mechanisms of membrane protein signal transduction, including G protein-coupled receptors (GPCRs). Upon agonist binding, GPCRs change conformation, resulting in interaction with downstream signaling molecules such as G proteins. To understand the precise signaling mechanism, studies have investigated the structural mechanism of GPCR signaling using X-ray crystallography, nuclear magnetic resonance (NMR), or electron paramagnetic resonance. In addition to these techniques, hydrogen/deuterium exchange mass spectrometry (HDX-MS) has recently been used in GPCR studies. HDX-MS measures the rate at which peptide amide hydrogens exchange with deuterium in the solvent. Exposed or flexible regions have higher exchange rates and excluded or ordered regions have lower exchange rates. Therefore, HDX-MS is a useful tool for studying protein-protein interfaces and conformational changes after protein activation or protein-protein interactions. Although HDX-MS does not give high-resolution structures, it analyzes protein conformations that are difficult to study with X-ray crystallography or NMR. Furthermore, conformational information from HDX-MS can help in the crystallization of X-ray crystallography by suggesting highly flexible regions. Interactions between GPCRs and downstream signaling molecules are not easily analyzed by X-ray crystallography or NMR because of the large size of the GPCR-signaling molecule complexes, hydrophobicity, and flexibility of GPCRs. HDX-MS could be useful for analyzing the conformational mechanism of GPCR signaling. In this chapter, we discuss details of HDX-MS for analyzing GPCRs using the β2AR-G protein complex as a model system.

  18. 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.

  19. 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.

  20. 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

  1. Utilizing Kernelized Advection Schemes in Ocean Models

    NASA Astrophysics Data System (ADS)

    Zadeh, N.; Balaji, V.

    2008-12-01

    There has been a recent effort in the ocean model community to use a set of generic FORTRAN library routines for advection of scalar tracers in the ocean. In a collaborative project called Hybrid Ocean Model Environement (HOME), vastly different advection schemes (space-differencing schemes for advection equation) become available to modelers in the form of subroutine calls (kernels). In this talk we explore the possibility of utilizing ESMF data structures in wrapping these kernels so that they can be readily used in ESMF gridded components.

  2. 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.

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

    NASA Technical Reports Server (NTRS)

    Hartley, Dana

    1998-01-01

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

  4. Platform Dependencies in Bottom-up Hydrogen/Deuterium Exchange Mass Spectrometry*

    PubMed Central

    Burns, Kyle M.; Rey, Martial; Baker, Charles A. H.; Schriemer, David C.

    2013-01-01

    Hydrogen-deuterium exchange mass spectrometry is an important method for protein structure-function analysis. The bottom-up approach uses protein digestion to localize deuteration to higher resolution, and the essential measurement involves centroid mass determinations on a very large set of peptides. In the course of evaluating systems for various projects, we established two (HDX-MS) platforms that consisted of a FT-MS and a high-resolution QTOF mass spectrometer, each with matched front-end fluidic systems. Digests of proteins spanning a 20–110 kDa range were deuterated to equilibrium, and figures-of-merit for a typical bottom-up (HDX-MS) experiment were compared for each platform. The Orbitrap Velos identified 64% more peptides than the 5600 QTOF, with a 42% overlap between the two systems, independent of protein size. Precision in deuterium measurements using the Orbitrap marginally exceeded that of the QTOF, depending on the Orbitrap resolution setting. However, the unique nature of FT-MS data generates situations where deuteration measurements can be inaccurate, because of destructive interference arising from mismatches in elemental mass defects. This is shown through the analysis of the peptides common to both platforms, where deuteration values can be as low as 35% of the expected values, depending on FT-MS resolution, peptide length and charge state. These findings are supported by simulations of Orbitrap transients, and highlight that caution should be exercised in deriving centroid mass values from FT transients that do not support baseline separation of the full isotopic composition. PMID:23197788

  5. 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

  6. Dual diffusion and finite mass exchange model for adsorption kinetics in activated carbon

    SciTech Connect

    Do, D.D.; Wang, K.

    1998-01-01

    A model allowing for the finite mass exchange between the two phases is proposed for the description of adsorption kinetics in activated carbon. This model based on Do`s earlier structural model for activated carbon involves three mass-transfer processes: pore diffusion, adsorbed phase diffusion, and finite mass interchange between the fluid and adsorbed phases. The solid phase is heterogeneous, which is characterized by the micropore size distribution. The interaction between the adsorbate molecule and the micropore is calculated from the Lennard-Jones potential theory. The model developed for nonpolar adsorbates is tested with the experimental data of seven adsorbates (paraffin gases, aromatics, carbon dioxide, and sulfur dioxide) on pellets of different shapes and sizes and at various operating conditions. The finite kinetics play an important role in the overall kinetics. Failure to account for this finite kinetics makes the model unable to describe correctly the desorption behavior, since under such conditions, the ability of the particle to release adsorbed molecules is dictated mostly by the resistance at the pore mouth of the micropore.

  7. Quantification of protein-ligand interactions by mass spectrometry, titration, and H/D exchange: PLIMSTEX.

    PubMed

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

    2003-05-01

    Protein-ligand binding and the concomitant conformational change in the protein are of crucial importance in biophysics and drug design. We report a novel method to quantify protein-ligand interactions in solution by mass spectrometry, titration, and H/D exchange (PLIMSTEX). The approach can determine the conformational change, binding stoichiometry, and affinity in protein-ligand interactions including those that involve small molecules, metal ions, and peptides. Binding constants obtained by PLIMSTEX for four model protein-ligand systems agree with K values measured by conventional methods. At higher protein concentration, the method can be used to determine quickly the binding stoichiometry and possibly the purity of proteins. Taking advantage of concentrating the protein on-column and desalting, we are able to use different concentrations of proteins, buffer systems, salts, and pH in the exchange protocol. High picomole quantities of proteins are sufficient, offering significantly better sensitivity than that of NMR and X-ray crystallography. Automation could make PLIMSTEX a high throughput method for library screening, drug discovery, and proteomics.

  8. Identifying Zn-bound histidine residues in metalloproteins using hydrogen-deuterium exchange mass spectrometry.

    PubMed

    Dong, Jia; Callahan, Katie L; Borotto, Nicholas B; Vachet, Richard W

    2014-01-01

    In this work, we have developed a method that uses hydrogen-deuterium exchange (HDX) of C2-hydrogens of histidines coupled with mass spectrometry (MS) to identify Zn-bound histidines in metalloproteins. This method relies on differences in HDX reaction rates of Zn-bound and Zn-free His residues. Using several model peptides and proteins, we find that all Zn-bound His residues have substantially lower HDX reaction rates in the presence of the metal. The vast majority of non-Zn-binding His residues undergo no significant changes in HDX reaction rates when their reactivity is compared in the presence and absence of Zn. Using this new approach, we then determined the Zn binding site of β-2-microglobulin, a protein associated with metal-induced amyloidosis. Together, these results suggest that HDX-MS of His C2-hydrogens is a promising new method for identifying Zn-bound histidines in metalloproteins.

  9. Hydrogen deuterium exchange mass spectrometry in biopharmaceutical discovery and development - A review.

    PubMed

    Deng, Bin; Lento, Cristina; Wilson, Derek J

    2016-10-12

    Protein therapeutics have emerged as a major class of biopharmaceuticals over the past several decades, a trend that has motivated the advancement of bioanalytical technologies for protein therapeutic characterization. Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful and sensitive technique that can probe the higher order structure of proteins and has been used in the assessment and development of monoclonal antibodies (mAbs), antibody-drug conjugates (ADCs) and biosimilar antibodies. It has also been used to quantify protein-ligand, protein-receptor and other protein-protein interactions involved in signaling pathways. In manufacturing and development, HDX-MS can validate storage formulations and manufacturing processes for various biotherapeutics. Currently, HDX-MS is being refined to provide additional coverage, sensitivity and structural specificity and implemented on the millisecond timescale to reveal residual structure and dynamics in disordered domains and intrinsically disordered proteins. PMID:27662755

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Mass-independent isotopic fractionation of tin in a chemical exchange reaction

    NASA Astrophysics Data System (ADS)

    Fujii, T.; Moynier, F.

    2008-12-01

    Tin isotopes were fractionated by the liquid-liquid extraction technique with a crown ether, dicyclohexano-18- crown-6 (DC18C6). Tin dichloride was dissolved in HCl to create solutions, 0.1 mol dm-3 (M) Sn(II) in various [HCl]. The organic phase was 0.1 M DC18C6 in 1,2-dichloroethane. A 5 cm3 aqueous solution and a 5 cm3 organic solution were mixed in a glass vial with a stirrer bar, and the glass vial was sealed. The two phases were stirred by a magnetic stirrer, and after the equilibrium, the two phases were separated by centrifugation. An aliquot of the upper aqueous solution was taken for analysis. These procedures were carried out at room temperature. The Sn concentration in the equilibrated aqueous phase was analyzed by ICP-AES. In order to avoid any matrix effect, possible trace of organic materials from DC18C6 was separated from the Sn on a micro-column anion-exchange resin in HBr/HNO3. An aliquot of the aqueous phase was once dried by heating and then dissolved into a HBr solution. Sn was strongly adsorbed while organic materials went through. Finally Sn was collected in a HNO3 solution. A solution containing 300 ppb of Sn in 0.05 M HNO3 was prepared for isotopic analysis. Isotopic ratios of Sn in all samples were analyzed with the MC-ICP-MS Nu plasma 500 HR at ENS Lyon coupled with a desolvating nebulizer Nu DSN-100 (with a typical precision of <100 ppm). The instrumental mass bias was controlled by bracketing each of the samples with standards. Because 120Sn is the most abundant isotopes, the isotope ratios have been measured as mSn/120Sn (m : 116, 117, 118, 119, 122, and 124). 114Sn and 115Sn were not analyzed due to their low abundances. Possible interferences with Cd on the masses 116, with Te on the mass 120, 122 and 124 were verified to be under the detection of the ICP-MS. Odd atomic mass isotopes (117Sn and 119Sn) showed deficits of enrichment comparing to the even atomic mass isotopes (116Sn, 118Sn, 122Sn, and 124Sn). This odd-even staggering

  17. 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

  18. Deuterium exchange of alpha-helices and beta-sheets as monitored by electrospray ionization mass spectrometry.

    PubMed Central

    Wagner, D. S.; Melton, L. G.; Yan, Y.; Erickson, B. W.; Anderegg, R. J.

    1994-01-01

    Deuterium exchange was monitored by electrospray ionization mass spectrometry (ESI-MS) to study the slowly exchanging (hydrogen bonded) peptide hydrogens of several alpha-helical peptides and beta-sheet proteins. Polypeptides were synthetically engineered to have mainly disordered, alpha-helical, or beta-sheet structure. For 3 isomeric 31-residue alpha-helical peptides, the number of slowly exchanging hydrogens as measured by ESI-MS in 50% CF3CD2OD (pD 9.5) provided estimates of their alpha-helicities (26%, 40%, 94%) that agreed well with the values (17%, 34%, 98%) measured by circular dichroic spectroscopy in the same nondeuterated solvent. For 3 betabellins containing a pair of beta-sheets and a related disordered peptide, their order of structural stability (12D > 12S > 14D > 14S) shown by their deuterium exchange rates in 10% CD3OD/0.5% CD3CO2D (pD 3.8) as measured by ESI-MS was the same as their order of structural stability to unfolding with increasing temperature or guanidinium chloride concentration as measured by circular dichroic spectroscopy in water. Compared to monitoring deuterium exchange by proton NMR spectrometry, monitoring deuterium exchange by ESI-MS requires much less sample (1-50 micrograms), much shorter analysis time (10-90 min), and no chemical quenching of the exchange reaction. PMID:7987225

  19. Analysis of isomeric polycyclic aromatic hydrocarbons by charge-exchange chemical ionization mass spectrometry

    SciTech Connect

    Simonsick, W.J. Jr.; Hites, R.A.

    1984-12-01

    Charge-exchange chemical ionization mass spectrometry (using a 15% mixture of methane in argon) yields abundant M/sup +/, M + H/sup +/, M + C/sub 2/H/sub 5//sup +/ ions of polycyclic aromatic hydrocarbons (PAH). On the basis of the relative intensities of the M + H/sup +/ ion to the M/sup +/ ion, this technique can differentiate, in a predictable manner, isomeric structures of PAH. The operating conditions were evaluated and optimized; the most significant contributions to the variations in the (M + H)/sup +//M/sup +/ ratios are the temperature, pressure, and condition of the ion source. The optimum ion source temperature (250/sup 0/C) and pressure (0.8 torr) are easily controlled and regulated. The variable contamination of the ion source is compensated by an internal standard 1,2,3,5-tetrafluorobenzene. The analyses of Standard Reference Materials 1648 and 1649 (air particulate samples) and a carbon black extract are reported. Triphenylene and chrysene, although not chromatographically resolved, can be quantitated by using this technique. The identification of acephenanthrylene based on the measurement of ratios and calculated ionization potentials is also presented.

  20. 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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

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

    PubMed Central

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

    2011-01-01

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

  4. Metal-complex formation in continuous-flow ligand-exchange reactors studied by electrospray mass spectrometry.

    PubMed

    Krabbe, J G; de Boer, A R; van der Zwan, G; Lingeman, H; Niessen, W M A; Irth, H

    2007-04-01

    Electrospray ionization mass spectrometry was used to investigate complex formation of different metal complexes in a continuous-flow ligand-exchange reactor. A computer program was developed based on normal equilibrium calculations to predict the formation of various metal-ligand complexes. Corresponding to these calculations, infusion electrospray mass spectrometric experiments were performed to investigate the actual complex formation in solution. The data clearly show good correlation between the theoretically calculated formation of metal-ligand complexes and the experimental mass spectrometric data. Moreover, the approach demonstrates that the influence of the pH can be investigated using a similar approach. Indirectly, these infusion experiments provide information on relative binding constants of different ligands towards a metal-ion. To demonstrate this, a continuous-flow ligand-exchange detection system with mass spectrometric detection was developed. Injection of ligands, with different affinity for the metal-ion, into the reactor shows good correlation between binding constants and the response in the ligand-exchange detection system. Additional information on the introduced ligand, and the complexes formed after introduction of the ligand, can be obtained from interpretation of the mass spectra.

  5. 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.

  6. 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.

  7. A cryogenic circulating advective multi-pass absorption cell

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

  8. 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).

  9. 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.

  10. Characterization of the N370S mutant of glucocerebrosidase by hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Tang, Liangjie; Coales, Stephen J; Morrow, Jeffrey A; Edmunds, Tim; Hamuro, Yoshitomo

    2012-10-15

    An asparagine-to-serine substitution at residue 370 (N370S) in glucocerebrosidase (GCase) is the most prevalent mutation leading to Gaucher's disease, the most common lysosomal storage disorder. Two types of hydrogen/deuterium exchange experiment coupled with proteolysis and liquid chromatography-mass spectrometry (HDX-MS) were used to investigate the dynamic properties and unfolding stability of wt, R495H, and N370S GCases in the presence and absence of ligands. R495H GCase is used for enzyme replacement therapy and is considered to be a wt surrogate, whereas N370S is the most prevalent mutation leading to Gaucher's disease. Time-course HDX experiments of the GCases were performed under near-physiological conditions to detect the protein's local unfolding motions at a submolecular level. In guanidine-titration experiments, HDX reactions were performed with various concentrations of a chemical denaturant to provide the global stability of the proteins. The two types of experiment showed that all three purified GCases, wt, R495H, and N370S, have virtually identical local unfolding motions and global stabilities in solution. Combined with previous X-ray crystallographic studies, which showed indistinguishable backbone conformations for N370S and R495H GCase mutants and very similar melting temperatures for the wt, R495H, and N370S mutants, all three GCases are likely to have virtually identical structural and dynamic properties in solution. The guanidine-titration experiments revealed that the pharmacological chaperone, isofagomine (IFG), interacts more weakly with the N370S mutant than with the R495H GCase; this is consistent with the higher IC(50) value of IFG against N370S than against R495H. The time-course experiments showed that IFG restricts the local unfolding motions of N370S in the same way as those of R495H when the ligand saturates the proteins.

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

    PubMed

    Xiao, Yiming; Konermann, Lars

    2015-08-01

    Gas/water interfaces (such as air bubbles or foam) are detrimental to the stability of proteins, often causing aggregation. This represents a potential problem for industrial processes, for example, the production and handling of protein drugs. Proteins possess surfactant-like properties, resulting in a high affinity for gas/water interfaces. The tendency of previously buried nonpolar residues to maximize contact with the gas phase can cause significant structural distortion. Most earlier studies in this area employed spectroscopic tools that could only provide limited information. Here we use hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for probing the conformational dynamics of the model protein myoglobin (Mb) in the presence of N(2) bubbles. HDX/MS relies on the principle that unfolded and/or highly dynamic regions undergo faster deuteration than tightly folded segments. In bubble-free solution Mb displays EX2 behavior, reflecting the occurrence of short-lived excursions to partially unfolded conformers. A dramatically different behavior is seen in the presence of N(2) bubbles; EX2 dynamics still take place, but in addition the protein shows EX1 behavior. The latter results from interconversion of the native state with conformers that are globally unfolded and long-lived. These unfolded species likely correspond to Mb that is adsorbed to the surface of gas bubbles. N(2) sparging also induces aggregation. To explain the observed behavior we propose a simple model, that is, "semi-unfolded" ↔ "native" ↔ "globally unfolded" → "aggregated". This model quantitatively reproduces the experimentally observed kinetics. To the best of our knowledge, the current study marks the first exploration of surface denaturation phenomena by HDX/MS. PMID:25761782

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

    PubMed Central

    Xiao, Yiming; Konermann, Lars

    2015-01-01

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

  13. 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

  14. Investigation of mass transfer in the ion-exchange-membrane-partitioned free-flow IEF system for protein separation.

    PubMed

    Cheng, Jiu-Hua; Chung, Tai Shung; Neo, Sok Hong

    2009-08-01

    In this study, novel polysulfone-based cation-exchange membranes with strong mechanical strength have been developed and applied in ion-exchange-membrane-partitioned free-flow IEF (IEM-FFIEF) to replace the conventional immobiline membranes. A fundamental understanding of protein mass transfer in the IEM-FFIEF process has been revealed experimentally with the aid of membrane-based boundary effect model contributed by Ennis et al. we have proven experimentally the existence of a pH gradient across the membrane cross-section when an IEM-FFIEF system is in operation. The boundary effects on particle velocities are calculated based on the IEF assumption and various characterizations, and are compared with the experimental results. In the IEM-FFIEF experiments, a protein mixture (BSA and myoglobin (Mb)) and sulfonated polysulfone membranes with different ion-exchange capacities are applied. Experimental results show that the real velocity and real mobility (of Mb in this study) are comparable with the mathematic model developed by Ennis et al. This suggests that the equation proposed by Ennis et al., is sufficient to capture the mass transfer through membrane in the IEM-FFIEF system after considering the effects of pore size distribution and effects of disturbed electric field. The charge properties of the membrane surface play a dominant role on the separation performance of the membranes. The newly developed porous solid-phase ion-exchange membranes may potentially and effectively replace immobilines to perform the selective function for protein separation.

  15. 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.

  16. 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).

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  19. 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.

  20. Use of Cation Exchange Chromatography for Human C-peptide Isotope Dilution – Mass Spectrometric Assay

    PubMed Central

    Stoyanov, Alexander V.; Rohlfing, Curt L.; Connolly, Shawn; Roberts, Matthew L.; Nauser, Christopher L.; Little, Randie R.

    2016-01-01

    An application of ion exchange chromatography for C-peptide analysis is described here. At the stage of C-peptide isolation, a strong cation exchanger (SP HP or MonoS) was used to purify the analyte from ballast proteins and peptides. The conditions of ion-exchange chromatographic separations were optimized using theoretical modeling of the net surface electric charge of the peptide as a function of pH. The purified and concentrated sample was further subjected to LC-MS/MS. In order to improve the reliability of analysis, two fragment ions were monitored simultaneously both for native C-peptide and internal standard, isotopically labeled C-peptides analogues (fragments with m/z of 927.7 and 147.2). Using ion-exchange chromatography, it became possible to process larger sample volumes, important for testing patients with very low C peptide levels, compared to currently used solid phase extraction methods. PMID:22098929

  1. 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

  2. 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.

  3. Dense-gas dispersion advection-diffusion model

    SciTech Connect

    Ermak, D.L.

    1992-07-01

    A dense-gas version of the ADPIC particle-in-cell, advection- diffusion model was developed to simulate the atmospheric dispersion of denser-than-air releases. In developing the model, it was assumed that the dense-gas effects could be described in terms of the vertically-averaged thermodynamic properties and the local height of the cloud. The dense-gas effects were treated as a perturbation to the ambient thermodynamic properties (density and temperature), ground level heat flux, turbulence level (diffusivity), and windfield (gravity flow) within the local region of the dense-gas cloud. These perturbations were calculated from conservation of energy and conservation of momentum principles along with the ideal gas law equation of state for a mixture of gases. ADPIC, which is generally run in conjunction with a mass-conserving wind flow model to provide the advection field, contains all the dense-gas modifications within it. This feature provides the versatility of coupling the new dense-gas ADPIC with alternative wind flow models. The new dense-gas ADPIC has been used to simulate the atmospheric dispersion of ground-level, colder-than-ambient, denser-than-air releases and has compared favorably with the results of field-scale experiments.

  4. Effect of charge regulation on steric mass-action equilibrium for the ion-exchange adsorption of proteins.

    PubMed

    Shen, Hong; Frey, Douglas D

    2005-06-24

    A thermodynamic formalism is developed for incorporating the effects of charge regulation on the ion-exchange adsorption of proteins under mass-overloaded conditions as described by the steric mass-action (SMA) isotherm. To accomplish this, the pH titration behavior of a protein and the associated adsorption equilibrium of the various charged forms of a protein are incorporated into a model which also accounts for the steric hindrance of salt counterions caused by protein adsorption. For the case where the protein is dilute, the new model reduces to the protein adsorption model described recently by the authors which accounts for charge regulation. Similarly, the new model reduces to the steric mass-action isotherm developed by Brooks and Cramer which applies to mass-overloaded conditions for the case where charge regulation is ignored so that the protein has a fixed charge. Calculations using the new model were found to agree with experimental data for the adsorption of bovine serum albumin (BSA) on an anion-exchange column packing when using reasonable physical properties. The new model was also used to develop an improved theoretical criterion for determining the conditions required for an adsorbed species to displace a protein in displacement chromatography when the pH is near the protein pI.

  5. 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.

  6. 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.

  7. The effect of advection at luminosities close to Eddington: The ULX in M 31

    NASA Astrophysics Data System (ADS)

    Straub, O.; Done, C.; Middleton, M.

    2013-05-01

    The transient, ultra-luminous X-ray source CXOM31 J004253.1+411422 in the Andromeda galaxy is most likely a 10 solar mass black hole, with super-Eddington luminosity at its peak. The XMM-Newton spectra taken during the decline then trace luminosities of 0.86-0.27 LEdd. These spectra are all dominated by a hot disc component, which roughly follows a constant inner radius track in luminosity and temperature as the source declines. At the highest luminosity the disc structure should change due to advection of radiation through the disc. This advected flux can be partly released at lower radii thus modifying the spectral shape. To study the effect of advection at luminosities close to Eddington we employ a fully relativistic slim disc model, SLIMBH, that includes advective cooling and full radiative transfer through the photosphere based on tlusty. The model also incorporates relativistic photon ray-tracing from the proper location of the disc photosphere rather than the mid-plane as the slim disc is no longer geometrically thin. We find that these new models differ only slightly from the non-advective (standard) BHSPEC models even at the highest luminosities considered here. While both discs can fit the highest luminosity data, neither is a very good fit to the lower luminosities. This could indicate a missing physical process that acts in low luminosity discs and subsides as the disc luminosity approaches the Eddington limit.

  8. 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.

  9. 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.

  10. 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…

  11. 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.

  12. 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.

  13. 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).

  14. Methods in the Study of PTEN Structure: X-Ray Crystallography and Hydrogen Deuterium Exchange Mass Spectrometry.

    PubMed

    Masson, Glenn R; Burke, John E; Williams, Roger L

    2016-01-01

    Despite its small size and deceptively simple domain organization, PTEN remains a challenging structural target due to its N- and C-terminal intrinsically disordered segments, and the conformational heterogeneity caused by phosphorylation of its C terminus. Using hydrogen/deuterium exchange mass spectrometry (HDX-MS), it is possible to probe the conformational dynamics of the disordered termini, and also to determine how PTEN binds to lipid membranes. Here, we describe how to purify recombinant, homogenously dephosphorylated PTEN from a eukaryotic system for subsequent investigation with HDX-MS or crystallography. PMID:27033079

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  16. Effects of advection on the seasonal abundance patterns of three species of planktonic calanoid copepods in Dabob Bay, Washington

    NASA Astrophysics Data System (ADS)

    Osgood, Kenric E.; Frost, Bruce W.

    1996-08-01

    The copepodid stage abundances of Calanus marshallae, Calanus pacificus and Metridia pacifica in Dabob Bay, Washington were followed through two years. Based on the species' life histories, vertical distributions, abundances inside and outside the bay, and the hydrographic setting, times when advection was important were explored. During the first study-year, 1973, advection acted to keep the copepod concentrations inside and outside Dabob Bay similar through the early summer. During the summer, a period of very little advective exchange, the copepod concentrations diverged at the two stations. In the fall, when advection picked up again, the copepod concentrations at the two stations once again became similar. During the summer of the other study-year, 1982, flow of deep water into Dabob Bay occurred. This may have caused some of the differences observed in the abundances of the copepods during the summer of 1982 vs 1973. Due in part to the advective events, the seasonal abundance patterns of the copepods could not be predicted based upon their locally expressed life history patterns. The most striking example of this was C. pacificus. Its population decreased during the spring and increased during the fall, despite having its major reproductive peak in the spring. Advective effects clearly contributed to this.

  17. 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

  18. Effects of water mass exchange on bacterial communities in an aquaculture area during summer

    NASA Astrophysics Data System (ADS)

    Sakami, T.; Abo, K.; Takayanagi, K.; Toda, S.

    2003-01-01

    Bacterial abundance (BA) and bacterial production (BP) and their relations with chlorophyll a, dissolved organic carbon (DOC) and dissolved organic (DON) and dissolved inorganic nitrogen (DIN) concentrations, were measured in the eutrophic fish farming ground of the Hasama-ura inlet of Gokasho Bay in the summer of 1996. The BP in the aquaculture area was 172±154 μgC/l/day (mean±standard deviation; n=24) and was higher in the aquaculture area than in the mouth of the bay, especially at the lower chlorophyll a concentrations of the mid and bottom waters. It correlated well with the concentrations of DON, but not with chlorophyll a or DOC. The BP per unit chlorophyll a was higher in the aquaculture area than in the bay mouth, especially at the lower chlorophyll a concentrations of the middle and bottom waters. Our findings suggested that the allochthonous organic matter added by farmed fish supported the bacterial activity in the aquaculture area. An occasional water exchange by intrusion of oceanic water into the Hasama-ura inlet did not cause a significant reduction of BA or BP. However, the correlation coefficient between BP and the DON concentration increased significantly after the water exchange, indicating that the water exchange caused a change in the organic substrate supporting the bacterial community.

  19. 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.

  20. 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.

  1. Lateral advection of organic matter in cascading-dominated submarine canyons

    NASA Astrophysics Data System (ADS)

    Tesi, T.; Puig, P.; Palanques, A.; Goñi, M. A.

    2010-03-01

    In the Gulf of Lions (GoL), dense water overflowing off the shelf occurs seasonally and represents the main mechanism affecting the shelf-slope exchange of particulate organic matter (OM). Most of the dense water export takes place in the south-western GoL and in particular through Cap de Creus (CdC) submarine canyon. Here, benthic instruments were deployed to collect down-canyon particulate fluxes whereas surface sediments were taken after the cascading event along the sediment dispersal system on the shelf, in CdC canyon and in the nearby Lacaze-Duthiers (LD) canyon. The chemical composition of the suspended material and surface sediments were investigated using several proxies including organic and inorganic carbon, total nitrogen, biogenic silica, δ 13C, Δ 14C, and alkaline CuO oxidation products. Thermohaline anomalies and high current speed events were measured in CdC canyon since December 2004 until mid-April 2005 indicating a marked off-shelf export of dense water trough the canyon. During the cascading, mud and relatively coarse shelf and upper canyon sediments were the major component of the mass flux. Conversely, advection of fine material via nepheloid layers dominated down-slope fluxes during pre- and post-cascading. The resulting change in grain-size affected the flux of mineral-bound terrigenous OC, indicating that the down-canyon transport of land-derived OM did not occur as bulk but rather its composition is driven by sediment sorting associated with different transport mechanisms. Both surface sediments and sediment trap samples indicated that CdC canyon is well connected to the GoL terrigenous dispersal system. Conversely, our results suggest an overall limited influence of land-derived OM in LD canyon. In spite of the reduced fluvial nutrient supply, a significant pulsed input of modern marine OM was observed in April 2005 at the end of the cascading period. Both intense mixing and lack of strong water column stratification likely played a key

  2. A positive finite-difference advection scheme

    SciTech Connect

    Hundsdorfer, W.; Koren, B.; Loon, M. van

    1995-03-01

    This paper examines a class of explicit finite-difference advection schemes derived along the method of lines. An important application field is large-scale atmospheric transport. The paper therefore focuses on the demand of positivity. For the spatial discretization, attention is confined to conservative schemes using five points per direction. The fourth-order central scheme and the family of {kappa}-schemes, comprising the second-order central, the second-order upwind, and the third-order upwind biased, are studied. Positivity is enforced through flux limiting. It is concluded that the limited third-order upwind discretization is the best candidate from the four examined. For the time integration attention is confined to a number of explicit Runge-Kutta methods of orders two to four. With regard to the demand of positivity, these integration methods turn out to behave almost equally and no best method could be identified. 16 refs., 4 figs., 4 tabs.

  3. 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.

  4. Mass balance modeling of PAHs and PCBs in the Chesapeake Bay: Importance of atmospheric deposition and exchange

    SciTech Connect

    Baker, J.; Nelson, E.; Nakanishi, K.

    1995-12-31

    During the past three years, the authors have measured the concentrations of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyl (PCB) congeners in air, precipitation, surface waters and surficial sediments throughout the mainstem of the Chesapeake Bay. Contaminant concentrations in the water column and surficial sediments show strong decreasing north to south gradients, implying efficient trapping of particle-reactive, volatile contaminants above the estuarine turbidity maximum. Seasonal estimates of water column and surficial sediment contaminant inventories, coupled with estimates of riverine loadings, atmospheric wet and dry aerosol depositional fluxes, and gas exchange rates, allowed them to construct first order mass balances for these semivolatile, particle reactive contaminants. This analysis shows that PAH and PCB water column inventories are extremely small relative to air-water and sediment-water exchange rates, suggesting short residence times and highly variable water column concentrations. The relative importance of the atmosphere as a source of or, in the case of volatile compounds, a sink for contaminants will be addressed with these mass balances.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. Investigating the Interaction between the Neonatal Fc Receptor and Monoclonal Antibody Variants by Hydrogen/Deuterium Exchange Mass Spectrometry*

    PubMed Central

    Jensen, Pernille Foged; Larraillet, Vincent; Schlothauer, Tilman; Kettenberger, Hubert; Hilger, Maximiliane; Rand, Kasper D.

    2015-01-01

    The recycling of immunoglobulins by the neonatal Fc receptor (FcRn) is of crucial importance in the maintenance of antibody levels in plasma and is responsible for the long half-lives of endogenous and recombinant monoclonal antibodies. From a therapeutic point of view there is great interest in understanding and modulating the IgG–FcRn interaction to optimize antibody pharmacokinetics and ultimately improve efficacy and safety. Here we studied the interaction between a full-length human IgG1 and human FcRn via hydrogen/deuterium exchange mass spectrometry and targeted electron transfer dissociation to map sites perturbed by binding on both partners of the IgG–FcRn complex. Several regions in the antibody Fc region and the FcRn were protected from exchange upon complex formation, in good agreement with previous crystallographic studies of FcRn in complex with the Fc fragment. Interestingly, we found that several regions in the IgG Fab region also showed reduced deuterium uptake. Our findings indicate the presence of hitherto unknown FcRn interaction sites in the Fab region or a possible conformational link between the IgG Fc and Fab regions upon FcRn binding. Further, we investigated the role of IgG glycosylation in the conformational response of the IgG–FcRn interaction. Removal of antibody glycans increased the flexibility of the FcRn binding site in the Fc region. Consequently, FcRn binding did not induce a similar conformational stabilization of deglycosylated IgG as observed for the wild-type glycosylated IgG. Our results provide new molecular insight into the IgG–FcRn interaction and illustrate the capability of hydrogen/deuterium exchange mass spectrometry to advance structural proteomics by providing detailed information on the conformation and dynamics of large protein complexes in solution. PMID:25378534

  10. 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.

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

    PubMed

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

    2006-01-01

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

  13. Diapycnal advection by double diffusion and turbulence in the ocean

    NASA Astrophysics Data System (ADS)

    St. Laurent, Louis Christopher

    1999-11-01

    Observations of diapycnal mixing rates are examined and related to diapycnal advection for both double-diffusive and turbulent regimes. The role of double-diffusive mixing at the site of the North Atlantic Tracer Release Experiment is considered. The strength of salt-finger mixing is analyzed in terms of the stability parameters for shear and double- diffusive convection, and a nondimensional ratio of the thermal and energy dissipation rates. While the model for turbulence describes most dissipation occurring in high shear, dissipation in low shear is better described by the salt-finger model, and a method for estimating the salt-finger enhancement of the diapycnal haline diffusivity over the thermal diffusivity is proposed. Best agreement between tracer-inferred mixing rates and microstructure based estimates is achieved when the salt- finger enhancement of haline flux is taken into account. The role of turbulence occurring above rough bathymetry in the abyssal Brazil Basin is also considered. The mixing levels along sloping bathymetry exceed the levels observed on ridge crests and canyon floors. Additionally, mixing levels modulate in phase with the spring-neap tidal cycle. A model of the dissipation rate is derived and used to specify the turbulent mixing rate and constrain the diapycnal advection in an inverse model for the steady circulation. The inverse model solution reveals the presence of a secondary circulation with zonal character. These results suggest that mixing in abyssal canyons plays an important role in the mass budget of Antarctic Bottom Water. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

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

    NASA Astrophysics Data System (ADS)

    Brandenburg, John

    2012-10-01

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

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. Advection-Dominated Accretion Disks: Geometrically Slim or Thick?

    NASA Astrophysics Data System (ADS)

    Gu, Wei-Min; Xue, Li; Liu, Tong; Lu, Ju-Fu

    2009-12-01

    We revisit the vertical structure of black-hole accretion disks in spherical coordinates. By comparing the advective cooling with the viscous heating, we show that advection-dominated disks are geometrically thick, i.e., with a half-opening angle of Δθ > 2π/5, rather than being slim, as supposed previously in the literature.

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

    USGS Publications Warehouse

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

    1994-01-01

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

  2. Generalized Fourier Analyses of Semi-Discretizations of the Advection-Diffusion Equation

    SciTech Connect

    CHRISTON, MARK A.; VOTH, THOMAS E.; MARTINEZ, MARIO J.

    2002-11-01

    This report presents a detailed multi-methods comparison of the spatial errors associated with finite difference, finite element and finite volume semi-discretizations of the scalar advection-diffusion equation. The errors are reported in terms of non-dimensional phase and group speeds, discrete diffusivity, artificial diffusivity, and grid-induced anisotropy. It is demonstrated that Fourier analysis (aka von Neumann analysis) provides an automatic process for separating the spectral behavior of the discrete advective operator into its symmetric dissipative and skew-symmetric advective components. Further it is demonstrated that streamline upwind Petrov-Galerkin and its control-volume finite element analogue, streamline upwind control-volume, produce both an artificial diffusivity and an artificial phase speed in addition to the usual semi-discrete artifacts observed in the discrete phase speed, group speed and diffusivity. For each of the numerical methods considered, asymptotic truncation error and resolution estimates are presented for the limiting cases of pure advection and pure diffusion. The Galerkin finite element method and its streamline upwind derivatives are shown to exhibit super-convergent behavior in terms of phase and group speed when a consistent mass matrix is used in the formulation. In contrast, the CVFEM method and its streamline upwind derivatives yield strictly second-order behavior. While this work can only be considered a first step in a comprehensive multi-methods analysis and comparison, it serves to identify some of the relative strengths and weaknesses of multiple numerical methods in a common mathematical framework.

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

    PubMed

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

    2009-09-01

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

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

    PubMed Central

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

    2010-01-01

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

  5. 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

  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.

  7. 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.

  8. 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

  9. Characterization of phosphoantigens by high-performance anion-exchange chromatography-electrospray ionization ion trap mass spectrometry and nanoelectrospray ionization ion trap mass spectrometry.

    PubMed

    Pont, F; Luciani, B; Belmant, C; Fournié, J J

    2001-08-01

    New phosphorylated microbial metabolites referred to as phosphoantigens activate immune responses in humans. Although these molecules have leading applications in medical research, no direct method allows their rapid and unambiguous structural identification. Here, we interfaced online HPAEC (high performance anion-exchange chromatography) with ESI-ITMS (electrospray ionization ion trap mass spectrometry) to identify such pyrophosphorylated molecules. A self-regenerating anion suppressor located upstream of electrospray ionization enabled the simultaneous detection of pyrophosphoester by conductimetry, UV and MS. By HPAEC-ITMS and HPAEC-ITMS2, a single run permitted characterization of reference phosphoantigens and of related structures. Although all compounds were resolved by HPAEC, MS enabled their detection and identification by [M-H]- and fragment ions. Isobaric phosphoantigen analogues were also separated by HPAEC and distinguished by MS2. The relevance of this device was demonstrated for phosphoantigens analysis in human urine and plasma. Furthermore, identification of natural phosphoantigens by automatically generated 2D mass spectra from nano-ESI-ITMS is presented. This last technique permits the simultaneous performance of molecular screening of natural phosphoantigen extracts and their identification.

  10. An instrumented sample holder for time-lapse microtomography measurements of snow under advective airflow

    NASA Astrophysics Data System (ADS)

    Ebner, P. P.; Grimm, S. A.; Schneebeli, M.; Steinfeld, A.

    2014-09-01

    An instrumented sample holder was developed for time-lapse microtomography of snow samples to enable in situ nondestructive spatial and temporal measurements under controlled advective airflows, temperature gradients, and air humidities. The design was aided by computational fluid dynamics simulations to evaluate the airflow uniformity across the snow sample. Morphological and mass transport properties were evaluated during a 4-day test run. This instrument allows the experimental characterization of metamorphism of snow undergoing structural changes with time.

  11. Patch scale turbulence over dryland and irrigated surfaces in a semi-arid landscape under advective conditions during BEAREX08

    NASA Astrophysics Data System (ADS)

    Prueger, J. H.; Alfieri, J. G.; Hipps, L. E.; Kustas, W. P.; Chavez, J. L.; Evett, S. R.; Anderson, M. C.; French, A. N.; Neale, C. M. U.; McKee, L. G.; Hatfield, J. L.; Howell, T. A.; Agam, N.

    2012-12-01

    Quantifying turbulent fluxes of heat and water vapor over heterogeneous surfaces presents unique challenges. For example, in many arid and semi-arid regions, parcels of irrigated cropland are juxtaposed with hot, dry surfaces. Contrasting surface conditions can result in the advection of warm dry air over an irrigated crop surface where it increases the water vapor deficit and, thereby, atmospheric demand. If sufficient water is available, this can significantly enhance evaporative water loss from the irrigated field. The scale and frequency of turbulent eddies over an irrigated surface during periods of strong advection is not fully understood. High frequency (20 Hz) data were acquired over irrigated cotton, wheat stubble, and rangeland fields during the 2008 growing season as part of the Bushland Evapotranspiration and Agricultural Remote Sensing Experiment (BEAREX08). Spectral analysis of momentum and scalar quantities including heat and water vapor revealed low frequency features in the turbulence structure due to the penetration of the surface boundary layer by large-scale eddies during periods of unusually strong advection. Wavelet analysis was applied to assess specific events contributing to the spatial and temporal structure of turbulent flux eddies. The analysis showed that low frequency contributions were linked to both local and regional scale advective processes. These results clearly point to a need to better understand surface energy balance exchange for heterogeneous surfaces in arid and semi-arid regions under conditions of strong local and regional advection.

  12. Electrohydrodynamically Driven Chaotic Advection in Drops

    NASA Astrophysics Data System (ADS)

    Ward, Thomas; Homsy, G. M.

    2002-11-01

    When a liquid drop of given dielectric constant, resistivity and viscosity is translating in a liquid of different dielectric constant, resistivity and viscosity under Stokes flow conditions in the presence of an electric field, the resulting internal circulation is a superposition of the Hadamard-Rybcynski circulation and the circulation first described theoretically by G. I. Taylor. For sufficiently strong electric field strengths, the quadrapole structure of the Taylor circulation can cause an internal stagnation disk to occur. Our interest is in the situation where a modulation of the electric field causes the stagnation disk to modulate its position, potentially leading to chaotic flows within the drop. The dimensionless electric field strength is characterized by W = 4V(1+lambda)/U where V is the maximum interfacial velocity of the Taylor circulation, U the translational velocity, and lambda the viscosity ratio. The streamfunction for the flow is: 1) psi = (r4-r2) sin2)(theta + W(t) (r3 - r5) sin2 (theta) cos(theta) 2) W(t) = W1 + W2 cos ((epsilon)t) where epsilon is the dimensionless frequency, and W1, W2 are the amplitudes of the DC and AC components, respectively. We have found it useful to replace these parameters by a secondary set, epsilon, Wmax and delta = (1 / W1 - 1 / W2) - (1 / W1 + 1 / W2). As shown in Figure 1a, delta is the dimensionless distance the stagnation disk moves over one period of modulation. The advection equations corresponding to the flow were integrated by standard techniques, and it was found that the trajectories were chaotic over a wide range of parameters. Experiments were conducted to test the predictions of rapid mixing on convective time scales. Drops of silicon oil were suspended in a small 60 mm x 120 mm x 120 mm test cell filled with castor oil, and subject to time-modulated axial electric fields with a wave form corresponding to eq(2). The drops were typically 5 mm in diameter and settled with typical speeds of O(10-1 mm

  13. 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.

  14. 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

  15. 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.

  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. 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.

  18. Predicting salt advection in groundwater from saline aquaculture ponds

    NASA Astrophysics Data System (ADS)

    Verrall, D. P.; Read, W. W.; Narayan, K. A.

    2009-01-01

    SummaryThis paper predicts saltwater advection in groundwater from leaky aquaculture ponds. A closed form solution for the potential function, stream function and velocity field is derived via the series solutions method. Numerically integrating along different streamlines gives the location (or advection front) of saltwater throughout the domain for any predefined upper time limit. Extending this process produces a function which predicts advection front location against time. The models considered in this paper are easily modified given knowledge of the required physical parameters.

  19. 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

  20. Advective transport in heterogeneous aquifers: Are proxy models predictive?

    NASA Astrophysics Data System (ADS)

    Fiori, A.; Zarlenga, A.; Gotovac, H.; Jankovic, I.; Volpi, E.; Cvetkovic, V.; Dagan, G.

    2015-12-01

    We examine the prediction capability of two approximate models (Multi-Rate Mass Transfer (MRMT) and Continuous Time Random Walk (CTRW)) of non-Fickian transport, by comparison with accurate 2-D and 3-D numerical simulations. Both nonlocal in time approaches circumvent the need to solve the flow and transport equations by using proxy models to advection, providing the breakthrough curves (BTC) at control planes at any x, depending on a vector of five unknown parameters. Although underlain by different mechanisms, the two models have an identical structure in the Laplace Transform domain and have the Markovian property of independent transitions. We show that also the numerical BTCs enjoy the Markovian property. Following the procedure recommended in the literature, along a practitioner perspective, we first calibrate the parameters values by a best fit with the numerical BTC at a control plane at x1, close to the injection plane, and subsequently use it for prediction at further control planes for a few values of σY2≤8. Due to a similar structure and Markovian property, the two methods perform equally well in matching the numerical BTC. The identified parameters are generally not unique, making their identification somewhat arbitrary. The inverse Gaussian model and the recently developed Multi-Indicator Model (MIM), which does not require any fitting as it relates the BTC to the permeability structure, are also discussed. The application of the proxy models for prediction requires carrying out transport field tests of large plumes for a long duration.

  1. 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

  2. Discovery of novel cyclophilin A ligands using an H/D exchange- and mass spectrometry-based strategy.

    PubMed

    Dearmond, Patrick D; West, Graham M; Anbalagan, Victor; Campa, Michael J; Patz, Edward F; Fitzgerald, Michael C

    2010-10-01

    Cyclophilin A (CypA) is an overexpressed protein in lung cancer tumors and as a result is a potential therapeutic and diagnostic target. Described here is use of an H/D exchange- and a matrix assisted laser desorption/ionization (MALDI) mass spectrometry-based assay, termed single-point SUPREX (Stability of Unpurified Proteins from Rates of H/D Exchange), to screen 2 chemical libraries, including the 1280-compound LOPAC library and the 9600-compound DIVERSet library, for binding to CypA. This work represents the first application of single-point SUPREX using a pooled ligand approach, which is demonstrated here to yield screening rates as fast as 6 s/ligand. The false-positive and false-negative rates determined in the current work using a set of control samples were 0% and 9%, respectively. A false-positive rate of 20% was found in screening the actual libraries. Eight novel ligands to CypA were discovered, including 2-(α-naphthoyl)ethyltrimethyl-ammonium iodide, (E)-3-(4-t-Butylphenylsulfonyl)-2-propenenitrile, 3-(N-benzyl-N-isopropyl)amino-1-(naphthalen-2-yl)propan-1-one, cis-diammineplatinum (II) chloride, 1-(3,5-dichlorophenyl)-1H-pyrrole-2,5-dione, N-(3-chloro-1, 4-dioxo-1,4-dihydro-2-naphthalenyl)-N-cyclohexylacetamide, 1-[2-(3,4-dimethoxyphenyl)ethyl]-1H-pyrrole-2,5-dione, and 4-(2-methoxy-4-nitrophenyl)-1-methyl-10-oxa-4-azatricyclo[5.2.1.0~2,6~]dec-8-ene-3,5-dione. These compounds, which had moderate binding affinities to CypA (i.e., K(d) values in the low micromolar range), provide new molecular scaffolds that might be useful in the development of CypA-targeted diagnostic imaging or therapeutic agents for lung cancer.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Effects of Glucose Feeding on Respiration and Photosynthesis in Photoautotrophic Dianthus caryophyllus Cells: Mass Spectrometric Determination of Gas Exchange.

    PubMed

    Avelange, M H; Sarrey, F; Rébillé, F

    1990-11-01

    When glucose (20 millimolar) was added to photoautotrophic cell suspension cultures of Dianthus caryophyllus, there was during the first 10 hours an accumulation of carbohydrates and phosphorylated compounds. These biochemical changes were accompanied by a progressive decrease of net photosynthesis and a twofold increase of the dark respiratory rate. The rise of respiration was associated with a rise of fumarase and cytochrome c oxidase activities, two mitochondrial markers. Gas exchange of illuminated cells were performed with a mass spectrometry technique and clearly established that during the first hours of glucose feeding, the decrease of net photosynthesis was essentially due to an increase of respiration in light, whereas the photosynthetic processes (gross O(2) evolution and gross CO(2) fixation) were almost not affected. However, after 24 hours of experiment, O(2) evolution and CO(2) fixation started to decline in turn. While ribulose-1,5-bisphosphate carboxylase activity was little affected during the first 48 hours of the experiment, the maximal light-induced phosphoribulokinase activity dramatically decreased with time and represented after 48 hours only 30% of its initial activity. It is postulated that the decrease in phosphoribulokinase activity was at least partially responsible for the decrease of CO(2) fixation and the metabolic events involved in this regulation are discussed.

  10. Tidal mass exchange between a submersed aquatic vegetation bed and the main channel of the Potomac River

    USGS Publications Warehouse

    Jenter, Harry L.; Rybicki, Nancy B.; Baltzer, Robert A.; Carter, Virginia; ,

    1991-01-01

    Tidal mass exchange between a submersed aquatic vegetation (SAV) bed and the main channel of the Potomac River was investigated. Water levels were recorded at 5 minute intervals from August (when plants were present) through December (when plants were absent). Velocities were measured during individual tidal cycles both in the presence and absence of plants. Flow patterns were found to be altered significantly when plants were present. SAV impeded flow onto the shoal causing a water level phase lag between the bed and the channel, a reduction in flow speed and a change in flow direction. The phase lag was enhanced when the low frequency (subtidal) water level in the channel was below normal. The phase lag was further enhanced during spring tides. Ebb flow in the presence of plants was perpendicular to the edge of the SAV bed in the direction of the pressure gradient established by the lagging water level. Flood flow did not follow such a predictable pattern despite the strongest pressure gradients occurring during flood tides. In the absence of plants the flow speed increased by nearly an order of magnitude and the water-level phase lag disappeared.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  13. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  16. 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.

  17. Using hydrogen/deuterium exchange mass spectrometry to study conformational changes in granulocyte colony stimulating factor upon PEGylation.

    PubMed

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

    2012-03-01

    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 through 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.

  18. 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.

  19. Ion-exchange-membrane-based enzyme micro-reactor coupled online with liquid chromatography-mass spectrometry for protein analysis.

    PubMed

    Zhou, Zhigui; Yang, Youyou; Zhang, Jialing; Zhang, Zhengxiang; Bai, Yu; Liao, Yiping; Liu, Huwei

    2012-04-01

    In this article, we developed a membrane-based enzyme micro-reactor by directly using commercial polystyrene-divinylbenzene cation-exchange membrane as the support for trypsin immobilization via electrostatic and hydrophobic interactions and successfully applied it for protein digestion. The construction of the reactor can be simply achieved by continuously pumping trypsin solution through the reactor for only 2 min, which was much faster than the other enzyme immobilization methods. In addition, the membrane reactor could be rapidly regenerated within 35 min, resulting in a "new" reactor for the digestion of every protein sample, completely eliminating the cross-interference of different protein samples. The amount and the activity of immobilized trypsin were measured, and the repeatability of the reactor was tested, with an RSD of 3.2% for the sequence coverage of cytochrome c in ten digestion replicates. An integrated platform for protein analysis, including online protein digestion and peptide separation and detection, was established by coupling the membrane enzyme reactor with liquid chromatography-quadrupole time-of-flight mass spectrometry. The performance of the platform was evaluated using cytochrome c, myoglobin, and bovine serum albumin, showing that even in the short digestion time of several seconds the obtained sequence coverages was comparable to or higher than that with in-solution digestion. The system was also successfully used for the analysis of proteins from yeast cell lysate.

  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 %.

  1. 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.

  2. A finite element-boundary element method for advection-diffusion problems with variable advective fields and infinite domains

    SciTech Connect

    Driessen, B.J.; Dohner, J.L.

    1998-08-01

    In this paper a hybrid, finite element--boundary element method which can be used to solve for particle advection-diffusion in infinite domains with variable advective fields is presented. In previous work either boundary element, finite element, or difference methods have been used to solve for particle motion in advective-diffusive domains. These methods have a number of limitations. Due to the complexity of computing spatially dependent Green`s functions, the boundary element method is limited to domains containing only constant advective fields, and due to their inherent formulation, finite element and finite difference methods are limited to only domains of finite spatial extent. Thus, finite element and finite difference methods are limited to finite space problems for which the boundary element method is not, and the boundary element method is limited to constant advection field problems for which finite element and finite difference methods are not. In this paper it is proposed to split a domain into two sub-domains, and for each of these sub domains, apply the appropriate solution method; thereby, producing a method for the total infinite space, variable advective field domain.

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

    PubMed

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

    2013-04-10

    In this work we present for the first time the use of ion-exchange liquid chromatography to separate the native form and a partially structured intermediate of the folding of the amyloidogenic protein beta2-microglobulin. Using a strong anion-exchange column that accounts for the differences in charge exposure of the two conformers, a LC-UV method is initially optimised in terms of mobile phase pH, composition and temperature. The preferred mobile phase conditions that afford useful information were found to be 35 mM ammonium formate, pH 7.4 at 25°C. The dynamic equilibrium of the two species is demonstrated upon increasing the concentration of acetonitrile in the protein sample. Then, the chromatographic method is transferred to MS detection and the respective charge state distributions of the separated conformers are identified. The LC-MS results demonstrate that one of the conformers is partially unfolded, compared with the native and more compact species. The correspondence with previous results obtained in free solution by capillary electrophoresis suggest that strong ion exchange LC-MS does not alter beta2-microglobulin conformation and maintains the dynamic equilibrium already observed between the native protein and its folding intermediate. PMID:23522119

  4. Tomography-based observation of sublimation and snow metamorphism under temperature gradient and advective flow

    NASA Astrophysics Data System (ADS)

    Ebner, P. P.; Schneebeli, M.; Steinfeld, A.

    2015-09-01

    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 micro-tomography is applied to investigate the structural dynamics of temperature gradient snow metamorphism exposed to an advective airflow in controlled laboratory conditions. The sublimation of water vapor for saturated air flowing across the snow sample was experimentally determined via variations of the porous ice structure. The results showed that the exothermic gas-to-solid phase change is favorable vis-a-vis the endothermic solid-to-gas phase change, thus leading to more ice deposition than ice sublimation. Sublimation has a marked effect on the structural change of the ice matrix but diffusion of water vapor in 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 reposition process of water molecules on the ice grains is relevant for atmospheric chemistry.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry.

    PubMed

    Slebos, Robbert J C; Brock, Jonathan W C; Winters, Nancy F; Stuart, Sarah R; Martinez, Misti A; Li, Ming; Chambers, Mathew C; Zimmerman, Lisa J; Ham, Amy J; Tabb, David L; Liebler, Daniel C

    2008-12-01

    Shotgun proteome analysis platforms based on multidimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS) provide a powerful means to discover biomarker candidates in tissue specimens. Analysis platforms must balance sensitivity for peptide detection, reproducibility of detected peptide inventories and analytical throughput for protein amounts commonly present in tissue biospecimens (< 100 microg), such that platform stability is sufficient to detect modest changes in complex proteomes. We compared shotgun proteomics platforms by analyzing tryptic digests of whole cell and tissue proteomes using strong cation exchange (SCX) and isoelectric focusing (IEF) separations of peptides prior to LC-MS/MS analysis on a LTQ-Orbitrap hybrid instrument. IEF separations provided superior reproducibility and resolution for peptide fractionation from samples corresponding to both large (100 microg) and small (10 microg) protein inputs. SCX generated more peptide and protein identifications than did IEF with small (10 microg) samples, whereas the two platforms yielded similar numbers of identifications with large (100 microg) samples. In nine replicate analyses of tryptic peptides from 50 microg colon adenocarcinoma protein, overlap in protein detection by the two platforms was 77% of all proteins detected by both methods combined. IEF more quickly approached maximal detection, with 90% of IEF-detectable medium abundance proteins (those detected with a total of 3-4 peptides) detected within three replicate analyses. In contrast, the SCX platform required six replicates to detect 90% of SCX-detectable medium abundance proteins. High reproducibility and efficient resolution of IEF peptide separations make the IEF platform superior to the SCX platform for biomarker discovery via shotgun proteomic analyses of tissue specimens.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

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

    PubMed

    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. PMID:25375606

  19. Coupling of active motion and advection shapes intracellular cargo transport.

    PubMed

    Khuc Trong, Philipp; Guck, Jochen; Goldstein, Raymond E

    2012-07-13

    Intracellular cargo transport can arise from passive diffusion, active motor-driven transport along cytoskeletal filament networks, and passive advection by fluid flows entrained by such cargo-motor motion. Active and advective transport are thus intrinsically coupled as related, yet different representations of the same underlying network structure. A reaction-advection-diffusion system is used here to show that this coupling affects the transport and localization of a passive tracer in a confined geometry. For sufficiently low diffusion, cargo localization to a target zone is optimized either by low reaction kinetics and decoupling of bound and unbound states, or by a mostly disordered cytoskeletal network with only weak directional bias. These generic results may help to rationalize subtle features of cytoskeletal networks, for example as observed for microtubules in fly oocytes.

  20. 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.

  1. 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.

  2. Mass

    SciTech Connect

    Quigg, Chris

    2007-12-05

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

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

    PubMed

    Perko, Janez; Patel, Ravi A

    2014-05-01

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

  4. 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

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

    NASA Astrophysics Data System (ADS)

    Velitchko, Vladimir; Tikhomirov, Alexander; Ushakova, Sofya

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

  6. 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...

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

    PubMed

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

    2012-05-21

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

  8. Metabolite identification of artemether by data-dependent accurate mass spectrometric analysis using an LTQ-Orbitrap hybrid mass spectrometer in combination with the online hydrogen/deuterium exchange technique.

    PubMed

    Liu, Tian; Du, Fuying; Zhu, Fanping; Xing, Jie

    2011-11-15

    Artemether (ARM), the O-methyl ether prodrug of dihydroartemisinin (DHA), is a first-line antimalarial drug used in areas of multi-drug resistance. Artemisinin drugs can be metabolized extensively in vivo and this seems related to their autoinduction pharmacokinetics. In the present study, the metabolite identification of ARM was performed by the generic data-dependent accurate mass spectrometric analysis, using high-resolution (HR) liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) and tandem mass spectrometry (MS/MS) LTQ-Orbitrap hybrid mass spectrometer in conjunction with online hydrogen (H)/deuterium (D) exchange for rapid structural characterization. The LC separation was improved allowing the separation of ARM parent drugs and their metabolites from their diastereomers. A total of 77 phase I metabolites of ARM were identified in rat liver microsomal incubates and rat urine, including dihydroartemisinin and artemisinin. In rat bile, 12 phase II metabolites were found. Accurate mass data were obtained in both full scan and HR-MS/MS mode to support assignments of metabolite structures. Online H/D exchange LC/HR-ESI-MS experiments provided additional evidence in differentiating dihydroxylated deoxy-ARM from mono-hydroxylated ARM. The results showed the main phase I metabolites of artemether are hydroxylated, dehydro, demethylated and deoxy products, and they will undergo subsequent phase II glucuronidation processes. Most metabolites were reported for the first time. This study also demonstrated the effectiveness of high-resolution mass spectrometry in combination with an online H/D exchange LC/HR-MS(n) technique in rapid identification of drug metabolites. PMID:22006394

  9. 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.

  10. 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

  11. Gaining a Better Understanding of Surface-Subsurface Reactive Transport using a High-Order Advection Approach

    NASA Astrophysics Data System (ADS)

    Beisman, J. J., III; Maxwell, R. M.; Navarre-Sitchler, A.; Steefel, C. I.

    2014-12-01

    Understanding the interactions between physical, geochemical, and biological processes in the shallow subsurface is prerequisite to the development of effective contamination remediation techniques, or the accurate quantification of nutrient fluxes and biogeochemical cycling. Here we present recent developments to the massively parallel reactive transport code ParCrunchFlow. This model, previously applicable only to steady-state, saturated subsurface flows, has been extended to transient, surface-subsurface systems. Proof-of-concept simulations detailing reactive transport processes in hillslope and floodplain settings will be presented. In order to reduce the numerical dispersion inherent in grid based advection schemes, which can lead to an over prediction of reaction rates, a weighted, essentially non-oscillatory (WENO) advection scheme has been implemented, providing formal fifth-order spatial and third-order temporal accuracy. We use a mass-conservative, positivity-preserving flux limiter while advecting solute concentrations to prevent non-physical solutions. The effects of advection schemes and their associated numerical dispersion on reaction rates are evaluated by comparing our scheme to a monotonic lower order scheme in a transverse mixing scenario. The work presented here allows a better understanding of nutrient cycling dynamics in watershed systems.

  12. An instrumented sample holder for time-lapse micro-tomography measurements of snow under advective airflow

    NASA Astrophysics Data System (ADS)

    Ebner, P. P.; Grimm, S. A.; Schneebeli, M.; Steinfeld, A.

    2014-06-01

    An instrumented sample holder was developed for time-lapse micro-tomography of snow samples to enable in-situ nondestructive spatial and temporal measurements under controlled advective airflows, temperature gradients, and air humidities. The design was aided by computational fluid dynamics simulations to evaluate the airflow uniformity across the snow sample. Morphological and mass transport properties were evaluated during a 4 day test run. This instrument allows the experimental characterization of metamorphism of snow undergoing structural changes with time.

  13. 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.

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

    PubMed

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

    2015-12-01

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

  15. 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

  16. Sorption-induced effects of humic substances on mass transfer of organic pollutants through aqueous diffusion boundary layers: the example of water/air exchange.

    PubMed

    Ramus, Ksenia; Kopinke, Frank-Dieter; Georgi, Anett

    2012-02-21

    This study examines the effect of dissolved humic substances (DHS) on the rate of water-gas exchange of organic compounds under conditions where diffusion through the aqueous boundary layer is rate-determining. A synthetic surfactant was applied for comparison. Mass-transfer coefficients were determined from the rate of depletion of the model compounds by means of an apparatus containing a stirred aqueous solution with continuous purging of the headspace above the solution. In addition, experiments with continuous passive dosing of analytes into the water phase were conducted to simulate a system where thermodynamic activity of the chemical in the aqueous phase is identical in the presence and absence of DHS. The experimental results show that DHS and surfactants can affect water-gas exchange rates by the superposition of two mechanisms: (1) hydrodynamic effects due to surface film formation ("surface smoothing"), and (2) sorption-induced effects. Whether sorption accelerates or retards mass transfer depends on its effect on the thermodynamic activity of the pollutant in the aqueous phase. Mass transfer will be retarded if the activity (or freely dissolved concentration) of the pollutant is decreased due to sorption. If it remains unchanged (e.g., due to fast equilibration with a sediment acting as a large source phase), then DHS and surfactant micelles can act as an additional shuttle for the pollutants, enhancing the flux through the boundary layer.

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

    PubMed

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

    2013-08-01

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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. Drift by drift: effective population size is limited by advection

    PubMed Central

    2008-01-01

    Background Genetic estimates of effective population size often generate surprising results, including dramatically low ratios of effective population size to census size. This is particularly true for many marine species, and this effect has been associated with hypotheses of "sweepstakes" reproduction and selective hitchhiking. Results Here we show that in advective environments such as oceans and rivers, the mean asymmetric transport of passively dispersed reproductive propagules will act to limit the effective population size in species with a drifting developmental stage. As advection increases, effective population size becomes decoupled from census size as the persistence of novel genetic lineages is restricted to those that arise in a small upstream portion of the species domain. Conclusion This result leads to predictions about the maintenance of diversity in advective systems, and complements the "sweepstakes" hypothesis and other hypotheses proposed to explain cases of low allelic diversity in species with high fecundity. We describe the spatial extent of the species domain in which novel allelic diversity will be retained, thus determining how large an appropriately placed marine reserve must be to allow the persistence of endemic allelic diversity. PMID:18710549

  3. 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.

  4. Evaluation of recombinant human interferon alpha-2b structure and stability by in-gel tryptic digestion, H/D exchange and mass spectrometry.

    PubMed

    Cindrić, Mario; Galić, Nives; Vuletić, Marko; Klarić, Mia; Drevenkar, Vlasta

    2006-02-24

    Stability and structure of recombinant interferon alpha-2b (rHuINF alpha-2b) was studied by mass spectrometry (MALDI-TOF and Q-TOF MS), chromatography (LC-UV-FLD-DAD, LC-MS) and CD spectroscopy. Besides analysis of the substance according to Ph. Eur. methods, two additional mass spectrometric methods were developed. The aim of both methods was to estimate structure-stability relationship connected to methionine oxidation or protein degradation. Preservation or degradation of protein structure was confirmed by H/D exchange in four separate experiments. Kinetics of deuterium incorporation into macromolecule was monitored over 2670 min. Isoforms of rHuINF alpha-2b were separated by 2D gel electrophoresis. In-gel digestion with trypsin and mass spectrometric analysis, performed on four separated isoforms at the mass corresponding to the mass of rHuINF alpha-2b with oxidized methionines, confirmed oxidation of all methionines to a different extent. Another four isoforms observed in 2D gel are most likely dimers of the same macromolecules with scrambled disulphide bridges. Oxidation and dimerisation are consequences of protein interaction with oxidizing reagents in polyacrilamide gel.

  5. 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

  6. 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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  9. Time-Lapse Micro-Tomography Measurements and Determination of Effective Transport Properties of Snow Metamorphism Under Advective Conditions

    NASA Astrophysics Data System (ADS)

    Ebner, P. P.; Grimm, S.; Steen-Larsen, H. C.; Schneebeli, M.; Steinfeld, A.

    2014-12-01

    The metamorphism of snow under advective air flow, with and without temperature gradient, was never experimentally investigated. We developed a new sample holder where metamorphism under advective conditions can be observed and measured using time-lapse micro-tomography [1]. Long-term experiments were performed and direct pore-level simulation (DPLS) [2,3] was directly applied on the extracted 3D digital geometry of the snow to calculate the effective transport properties by solving the governing fluid flow equations. The results showed no effect of isothermal advection, compared to rates typical for isothermal metamorphism. Appling a temperature gradient, the results showed increased snow metamorphism compared to rates typical for temperature gradient metamorphism. However, for both cases a change in the isotopic composition in the air as well as in the snow sample could be observed. These measurements could be influential to better understand snow-air exchange processes relevant for atmospheric chemistry and isotopic composition. REFERENCES[1] Ebner P. P., Grimm S., Schneebeli M., and Steinfeld A.: An instrumented sample holder for time-lapse micro-tomography measurements of snow under advective airflow. Geoscientific Instrumentation, Methods and Data Systems 4(2014), 353-373. [2] Zermatten E., Haussener S., Schneebeli M., and Steinfeld A.: Tomography-based determination of permeability and Dupuit-Forchheimer coefficient of characteristic snow samples. Journal of Glaciology 57(2011), 811-816. [3] Zermatten E., Schneebeli M., Arakawa H., and Steinfeld A.: Tomography-based determination of porosity, specific area and permeability of snow and comparison with measurements. Cold Regions Science and Technology 97 (2014), 33-40. Fig. 1: 3-D surface rendering of a refrozen wet snow sample with fluid flow streamline.

  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.

  11. 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

  12. 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.

  13. 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.

  14. Offshore advection of particles within the Cape Blanc filament, Mauritania: Results from observational and modelling studies

    NASA Astrophysics Data System (ADS)

    Fischer, G.; Reuter, C.; Karakas, G.; Nowald, N.; Wefer, G.

    2009-12-01

    This article will review major features of the ‘giant’ Cape Blanc filament off Mauritania with regard to the transport of chlorophyll and organic carbon from the shelf to the open ocean. Within the filament, chlorophyll is transported about 400 km offshore. Modelled particle distributions along a zonal transect at 21°N showed that particles with a sinking velocity of 5 m d -1 are advected offshore by up to 600 km in subsurface particle clouds generally located between 400 m and 800 m water depth, forming an Intermediate Nepheloid Layer (INL). It corresponds to the depth of the oxygen minimum zone. Heavier particles with a sinking velocity of 30 m d -1 are transported from the shelf within the Bottom Layer (BL) of more than 1000 m thickness, largely following the topography of the bottom slope. The particles advected within the BL contribute to the enhanced winter-spring mass fluxes collected at the open-ocean mesotrophic sediment trap site CB-13 (∼200 nm offshore), due to a long distance advection in deeper waters. The lateral contribution to the deep sediment trap in winter-spring is estimated to be 63% and 72% for organic carbon and total mass, respectively, whereas the lateral input for both components on an annual basis is estimated to be in the order of 15%. Biogenic opal increases almost fivefold from the upper to the lower mesotrophic CB-13 trap, also pointing to an additional source for biogenic silica from eutrophic coastal waters. Blooms obviously sink in smaller, probably mesoscale-sized patches with variable settling rates, depending on the type of aggregated particles and their ballast content. Generally, particle sinking rates are exceptionally high off NW Africa. Very high chlorophyll values and a large size of the Cape Blanc filament in 1998-1999 are also documented in enhanced total mass and organic carbon fluxes. An increasing trend in satellite chlorophyll concentrations and the size of the Cape Blanc filament between 1997 and 2008 as

  15. 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

  16. 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

  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. Two tools for applying chromatographic retention data to the mass-based identification of peptides during hydrogen/deuterium exchange experiments by nano-liquid chromatography/matrix-assisted laser desorption/ionization mass spectrometry.

    PubMed

    Gershon, P D

    2010-12-15

    Two tools are described for integrating LC elution position with mass-based data in hydrogen-deuterium exchange (HDX) experiments by nano-liquid chromatography/matrix-assisted laser desorption/ionization mass spectrometry (nanoLC/MALDI-MS, a novel approach to HDX-MS). The first of these, 'TOF2H-Z Comparator', highlights peptides in HDX experiments that are potentially misidentified on the basis of mass alone. The program first calculates normalized values for the organic solvent concentration responsible for the elution of ions in nanoLC/MALDI HDX experiments. It then allows the solvent gradients for the multiple experiments contributing to an MS/MS-confirmed peptic peptide library to be brought into mutual alignment by iteratively re-modeling variables among LC parameters such as gradient shape, solvent species, fraction duration and LC dead time. Finally, using the program, high-probability chromatographic outliers can be flagged within HDX experimental data. The role of the second tool, 'TOF2H-XIC Comparator', is to normalize the LC chromatograms corresponding to all deuteration timepoints of all HDX experiments of a project, to a common reference. Accurate normalization facilitates the verification of chromatographic consistency between all ions whose spectral segments contribute to particular deuterium uptake plots. Gradient normalization in this manner revealed chromatographic inconsistencies between ions whose masses were either indistinguishable or separated by precise isotopic increments.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. A Dynamic and Spatial Scaling Approach to Advection Forecasting.

    NASA Astrophysics Data System (ADS)

    Seed, A. W.

    2003-03-01

    Quantitative nowcasts of rainfall are frequently based on the advection of rain fields observed by weather radar. Spectral Prognosis (S-PROG) is an advection-based nowcasting system that uses the observations that rain fields commonly exhibit both spatial and dynamic scaling properties, that is, the lifetime of a feature in the field is dependent on the scale of the feature (large features evolve more slowly than small features), and that features at all scales between the outer and inner observed scales are present in the field. The logarithm of the radar reflectivity field is disaggregated into a set or cascade of fields, in which each field in the set (or level in the cascade) represents the features of the original field over a limited range of scales. The Lagrangian temporal evolution of each level in the cascade is modeled using a simple autoregressive (lag 2) model, which automatically causes the forecast field to become smooth as the structures at the various scales evolve through their life cycles, or can be used to generate conditional simulations if the noise term is included. This paper describes the model and presents preliminary results.

  5. Numerical modeling of DNA-chip hybridization with chaotic advection

    PubMed Central

    Raynal, Florence; Beuf, Aurélien; Carrière, Philippe

    2013-01-01

    We present numerical simulations of DNA-chip hybridization, both in the “static” and “dynamical” cases. In the static case, transport of free targets is limited by molecular diffusion; in the dynamical case, an efficient mixing is achieved by chaotic advection, with a periodic protocol using pumps in a rectangular chamber. This protocol has been shown to achieve rapid and homogeneous mixing. We suppose in our model that all free targets are identical; the chip has different spots on which the probes are fixed, also all identical, and complementary to the targets. The reaction model is an infinite sink potential of width dh, i.e., a target is captured as soon as it comes close enough to a probe, at a distance lower than dh. Our results prove that mixing with chaotic advection enables much more rapid hybridization than the static case. We show and explain why the potential width dh does not play an important role in the final results, and we discuss the role of molecular diffusion. We also recover realistic reaction rates in the static case. PMID:24404027

  6. 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.

  7. Toward enhanced subsurface intervention methods using chaotic advection

    NASA Astrophysics Data System (ADS)

    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.

  8. 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.

  9. 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.

  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. 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

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

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

    PubMed

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

    2015-01-01

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

  18. 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.

  19. Determination of ethephon residues in water by gas chromatography with cubic mass spectrometry after ion-exchange purification and derivatisation with N-(tert-butyldimethylsilyl)-N-methyltrifluoroacetamide.

    PubMed

    Royer, A; Laporte, F; Bouchonnet, S; Communal, P-Y

    2006-03-01

    An analytical method has been developed for the determination of residues of ethephon (2-chloroethyl phosphonic acid) in drinking and surface water. The procedure is based on de-ionisation with an anion/cation-exchange resin, solid phase extraction by means of anion-exchange polystyrene-divinylbenzene extraction disks, elution with a mixture of methanol and 10 M hydrochloric acid (98/2, v/v), redisolution into acetonitrile after evaporation and silylation with N-(tert-butyldimethylsilyl)-N-methyltrifluoroacetamide (MTBSTFA). Quantification is performed by gas chromatography with ion-trap cubic mass spectrometric detection in the electron impact mode (GC-EI-MS3). Method validation was conducted using samples of mineral, tap, and river water that were fortified with ethephon at concentration levels ranging from 0.1 to 1.0 microg/L. The mean recovery from all the fortified samples (n = 36) amounted to 88% with a relative standard deviation of 17%. The method, therefore, was shown to allow accurate determination of ethephon residues in drinking and surface water with a limit of quantification of 0.1 microg/L. PMID:16443233

  20. 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

  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. Capture and release zones of permeable reactive barriers under the influence of advective-dispersive transport in the aquifer

    NASA Astrophysics Data System (ADS)

    Klammler, Harald; Hatfield, Kirk; Mohamed, Mohamed M.; Perminova, Irina V.; Perlmutter, Mike

    2014-07-01

    The problem of permeable reactive barrier (PRB) capture and release behavior is investigated by means of an approximate analytical approach exploring the invariance of steady-state solutions of the advection-dispersion equation to conformal mapping. PRB configurations considered are doubly-symmetric funnel-and-gate as well as less frequent drain-and-gate systems. The effect of aquifer heterogeneity on contaminant plume spreading is hereby incorporated through an effective transverse macro-dispersion coefficient, which has to be known. Results are normalized and graphically represented in terms of a relative capture efficiency M of contaminant mass or groundwater passing a control plane (transect) at a sufficient distance up-stream of a PRB as to comply with underlying assumptions. Factors of safety FS are given as the ratios of required capture width under advective-dispersive and purely advective transport for achieving equal capture efficiency M. It is found that M also applies to the release behavior down-stream of a PRB, i.e., it describes the spreading and dilution of PRB treated groundwater possibly containing incompletely remediated contamination and/or remediation reaction products. Hypothetical examples are given to demonstrate results.

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

    PubMed

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

    2014-06-01

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

  4. 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

  5. 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

  6. 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

  7. 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

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

    NASA Astrophysics Data System (ADS)

    Sun, Yunwei; Carrigan, Charles R.

    2016-05-01

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

  9. 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

  10. Wind-driven gas networks and star formation in galaxies: reaction-advection hydrodynamic simulations

    NASA Astrophysics Data System (ADS)

    Chappell, David; Scalo, John

    2001-07-01

    The effects of wind-driven star formation feedback on the spatio-temporal organization of stars and gas in galaxies is studied using two-dimensional intermediate-representational quasi-hydrodynamical simulations. The model retains only a reduced subset of the physics, including mass and momentum conservation, fully non-linear fluid advection, inelastic macroscopic interactions, threshold star formation, and momentum forcing by winds from young star clusters on the surrounding gas. Expanding shells of swept-up gas evolve through the action of fluid advection to form a `turbulent' network of interacting shell fragments which have the overall appearance of a web of filaments (in two dimensions). A new star cluster is formed whenever the column density through a filament exceeds a critical threshold based on the gravitational instability criterion for an expanding shell, which then generates a new expanding shell after some time delay. A filament-finding algorithm is developed to locate the potential sites of new star formation. The major result is the dominance of multiple interactions between advectively distorted shells in controlling the gas and star morphology, gas velocity distribution and mass spectrum of high mass density peaks, and the global star formation history. The gas morphology strongly resembles the model envisioned by Norman & Silk, and observations of gas in the Large Magellanic Cloud (LMC)Q1 and local molecular clouds. The dependence of the frequency distribution of present-to-past average global star formation rate on a number of parameters is investigated. Bursts of star formation only occur when the time-averaged star formation rate per unit area is low, or the system is small. Percolation does not play a role. The broad distribution observed in late-type galaxies can be understood as a result of either small size or small metallicity, resulting in larger shell column densities required for gravitational instability. The star formation rate

  11. Finite amplitude gravity waves: Harmonics, advective steepening, breaking and saturation

    NASA Technical Reports Server (NTRS)

    Weinstock, J.

    1985-01-01

    A simple theory is presented which determines details of the breaking and saturation of a gravity wave as it propagates upward in the atmosphere. Breaking and saturation are here due to nonlinear advection analogous to the breaching of a surface wave and to the breaking of a planetary wave. Much simplification is obtained by the assumption that in a wave packet consisting of a primary wave and its harmonics, the primary wave remains dominant. This assumption, referred to a quasi-monochromatic approximation, is suggested by observations. Determined by this approximate theory are: a detailed picture of the waveform as it steepens and breaks; harmonics of the wave; the turbulence generation; and an underlying relationship between superadiabatic lapse rate and saturation by wave-wave interactions.

  12. 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.

  13. Anomalous transport and chaotic advection in homogeneous porous media.

    PubMed

    Lester, D R; Metcalfe, G; Trefry, M G

    2014-12-01

    The topological complexity inherent to all porous media imparts persistent chaotic advection under steady flow conditions, which, in concert with the no-slip boundary condition, generates anomalous transport. We explore the impact of this mechanism upon longitudinal dispersion via a model random porous network and develop a continuous-time random walk that predicts both preasymptotic and asymptotic transport. In the absence of diffusion, the ergodicity of chaotic fluid orbits acts to suppress longitudinal dispersion from ballistic to superdiffusive transport, with asymptotic variance scaling as σ(L)(2)(t)∼t(2)/(ln t)(3). These results demonstrate that anomalous transport is inherent to homogeneous porous media and has significant implications for macrodispersion.

  14. Magnetic field advection in two interpenetrating plasma streams

    SciTech Connect

    Ryutov, D. D.; Kugland, N. L.; Levy, M. C.; Plechaty, C.; Ross, J. S.; Park, H. S.

    2013-03-15

    Laser-generated colliding plasma streams can serve as a test-bed for the study of various astrophysical phenomena and the general physics of self-organization. For streams of a sufficiently high kinetic energy, collisions between the ions of one stream with the ions of the other stream are negligible, and the streams can penetrate through each other. On the other hand, the intra-stream collisions for high-Mach-number flows can still be very frequent, so that each stream can be described hydrodynamically. This paper presents an analytical study of the effects that these interpenetrating streams have on large-scale magnetic fields either introduced by external coils or generated in the plasma near the laser targets. Specifically, a problem of the frozen-in constraint is assessed and paradoxical features of the field advection in this system are revealed. A possibility of using this system for studies of magnetic reconnection is mentioned.

  15. Anomalous transport and chaotic advection in homogeneous porous media.

    PubMed

    Lester, D R; Metcalfe, G; Trefry, M G

    2014-12-01

    The topological complexity inherent to all porous media imparts persistent chaotic advection under steady flow conditions, which, in concert with the no-slip boundary condition, generates anomalous transport. We explore the impact of this mechanism upon longitudinal dispersion via a model random porous network and develop a continuous-time random walk that predicts both preasymptotic and asymptotic transport. In the absence of diffusion, the ergodicity of chaotic fluid orbits acts to suppress longitudinal dispersion from ballistic to superdiffusive transport, with asymptotic variance scaling as σ(L)(2)(t)∼t(2)/(ln t)(3). These results demonstrate that anomalous transport is inherent to homogeneous porous media and has significant implications for macrodispersion. PMID:25615192

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

    Kordilla, Jannes; Pan, Wenxiao; Tartakovsky, Alexandre

    2014-12-14

    We propose a novel smoothed particle hydrodynamics (SPH) discretization of the fully coupled Landau-Lifshitz-Navier-Stokes (LLNS) and stochastic advection-diffusion equations. The accuracy of the SPH solution of the LLNS equations is demonstrated by comparing the scaling of velocity variance and the self-diffusion coefficient with kinetic temperature and particle mass obtained from the SPH simulations and analytical solutions. The spatial covariance of pressure and velocity fluctuations is found to be in a good agreement with theoretical models. To validate the accuracy of the SPH method for coupled LLNS and advection-diffusion equations, we simulate the interface between two miscible fluids. We study formation of the so-called "giant fluctuations" of the front between light and heavy fluids with and without gravity, where the light fluid lies on the top of the heavy fluid. We find that the power spectra of the simulated concentration field are in good agreement with the experiments and analytical solutions. In the absence of gravity, the power spectra decay as the power -4 of the wavenumber-except for small wavenumbers that diverge from this power law behavior due to the effect of finite domain size. Gravity suppresses the fluctuations, resulting in much weaker dependence of the power spectra on the wavenumber. Finally, the model is used to study the effect of thermal fluctuation on the Rayleigh-Taylor instability, an unstable dynamics of the front between a heavy fluid overlaying a light fluid. The front dynamics is shown to agree well with the analytical solutions.

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

    SciTech Connect

    Kordilla, Jannes; Pan, Wenxiao; Tartakovsky, Alexandre 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.

  4. 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.

  5. 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.

  6. Synthesis of model humic substances: a mechanistic study using controllable H/D exchange and Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Zherebker, Alexander Ya; Airapetyan, David; Konstantinov, Andrey I; Kostyukevich, Yury I; Kononikhin, Alexey S; Popov, Igor A; Zaitsev, Kirill V; Nikolaev, Eugene N; Perminova, Irina V

    2015-07-01

    The products of the oxidative coupling of phenols are frequently used as synthetic analogues to natural humic substances (HS) for biomedical research. However, their molecular compositions and exact structures remain largely unknown. The objective of this study was to develop a novel approach for the molecular-level analysis of phenolic polymerisates that is capable of inventorying molecular constituents and resolving their distinct structural formulas. For this purpose, we have synthesized the model HS using the oxidative coupling of a specifically designed phenylpropanoic monomer, 3-(4-hydroxy-3-methoxyphenyl)-3-oxopropionic acid, to hydroquinone. We have characterized the synthesized model HS using high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS), (1)H NMR spectroscopy, and controllable hydrogen/deuterium (H/D) exchange. We succeeded in the molecular inventory of the model HS. The assigned molecular formulas occupied the substantial space of CHO compositions in the Van Krevelen diagram with a maximum density found in the regions of tannins and lignins, resembling those of natural HS. To identify the exact structural formulas of the individual constituents in the model HS, we have applied selective H/D exchange of non-labile backbone protons by a choice of basic or acidic catalytic conditions followed by FTICR MS. The determined formulas allowed us to verify the proposed pathways of hydroxylation and carboxylation in the course of the phenolic coupling and to identify the acetylation of aromatic rings as an important side reaction. We conclude that the proposed analytical approach may be used to identify the molecular carriers of biological activity within the phenolic polymerisates and eventually within natural HS.

  7. 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

  8. The calcium-modulated structures of calmodulin and S100b proteins are useful to monitor hydrogen/deuterium exchange efficiency using matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

    PubMed

    Pingerelli, Peter L; Ozols, Victor V; Saleem, Haroon; Anderson, Carly R; Burns, Richard S

    2009-01-01

    Hydrogen/deuterium exchange (HDX) using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) is a sensitive, salt-tolerant and high-throughput method useful to probe protein conformation and molecular interactions. However, a drawback of the MALDI HDX technique is that sample preparation methods can typically result in higher levels of artificial deuterium in-exchange and/or hydrogen back- exchange just prior to or during mass analysis; this may impair data reproducibility and impede structural and kinetic data interpretation. While methods to minimize effects of back-exchange during protein analyte deposition on MALDI plates have been reported, this study presents a readily available, highly sensitive protein control set to facilitate rapid MALDI HDX protocol workup. The Ca(2+)-induced solvent accessible surface area (ASA) changes of calmodulin (CaM) and S100 proteins were employed to monitor and optimize HDX protocol efficiency. Under non- stringent room temperature conditions, the Ca(2+)-induced deuterium exchange of CaM, DeltaD(ca2+ -apo), MH(+) shifts -17 to -24 Da, while S100 DeltaD(ca2+ -apo) MH(+) shifts +8 to +12 Da. By comparing the divergent CaM and S100 Ca(2+)-induced deuterium mass shift differences, HDX sample workup and MALDI plate spotting conditions can easily be monitored. PMID:19940340

  9. Structural Dynamics of Soluble Chloride Intracellular Channel Protein CLIC1 Examined by Amide Hydrogen-Deuterium Exchange Mass Spectrometry (DXMS)†

    PubMed Central

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

    2009-01-01

    Chloride intracellular channel protein 1 (CLIC1) functions as an anion channel in plasma and nuclear membranes when its soluble monomeric form converts to an integral-membrane form. The transmembrane region of CLIC1 is located in its thioredoxin-like domain 1 but the mechanism whereby the protein converts to its membrane conformation has yet to be determined. Since channel formation in membranes is enhanced at low pH (5 to 5.5), a condition that is found at the surface of membranes, the structural dynamics of soluble CLIC1 was studied at pH 7 and at pH 5.5 in the absence of membranes by amide hydrogen-deuterium exchange mass spectrometry (DXMS). Rapid hydrogen exchange data indicate that CLIC1 displays a similar core structure at these pH values. Domain 1 is less stable than the all-helical domain 2 and, while the structure of domain 1 remains intact, its conformational flexibility is further increased in an acidic environment (pH 5.5). In the absence of membrane, an acidic environment appears to prime the solution structure of CLIC1 by destabilising domain 1 in order to lower the activation energy barrier for its conversion to the membrane-insertion conformation. The significantly enhanced H/D-exchange rates at pH 5.5 displayed by two segments (peptides 11-31 and 68-82) could be due to the protonation of acidic residues in salt bridges. One of these segments (peptide 11-31) includes part of the transmembrane region which, in the solution structure, consists of helix α1. This helix is intrinsically stable and is most likely retained in the membrane conformation. Strand β2, another element of the transmembrane region, displays a propensity to form a helical structure and has putative N- and C-capping motifs, suggesting that it too most likely forms a helix in a lipid bilayer. PMID:19650640

  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.

  11. 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

  12. 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...

  13. Analytical solution for one-dimensional advection-dispersion transport equation with distance-dependent coefficients

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mathematical models describing contaminant transport in heterogeneous porous media are often formulated as an advection-dispersion transport equation with distance-dependent transport coefficients. In this work, a general analytical solution is presented for the linear, one-dimensional advection-di...

  14. Turing-Hopf instabilities through a combination of diffusion, advection, and finite size effects.

    PubMed

    Galhotra, Sainyam; Bhattacharjee, J K; Agarwalla, Bijay Kumar

    2014-01-14

    We show that in a reaction diffusion system on a two-dimensional substrate with advection in the confined direction, the drift (advection) induced instability occurs through a Hopf bifurcation, which can become a double Hopf bifurcation. The box size in the direction of the drift is a vital parameter. Our analysis involves reduction to a low dimensional dynamical system and constructing amplitude equations.

  15. 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...

  16. Self-organization and advective transport in the cell polarity formation for asymmetric cell division.

    PubMed

    Seirin Lee, Sungrim; Shibata, Tatsuo

    2015-10-01

    Anterior-Posterior (AP) polarity formation of cell membrane proteins plays a crucial role in determining cell asymmetry, which depends not only on the several genetic process but also biochemical and biophysical interactions. The mechanism of AP formation of Caenorhabditis elegans embryo is characterized into the three processes: (i) membrane association and dissociation of posterior and anterior proteins, (ii) diffusion into the membrane and cytosol, and (iii) active cortical and cytoplasmic flows induced by the contraction of the acto-myosin cortex. We explored the mechanism of symmetry breaking and AP polarity formation using self-recruitment model of posterior proteins. We found that the AP polarity pattern is established over wide range in the total mass of polarity proteins and the diffusion ratio in the cytosol to the membrane. We also showed that the advective transport in both membrane and cytosol during the establishment phase affects optimal time interval of establishment and positioning of the posterior domain, and plays a role to increase the robustness in the AP polarity formation by reducing the number of posterior domains for the sensitivity of initial conditions. We also demonstrated that a proper ratio of the total mass to cell size robustly regulate the length scale of the posterior domain.

  17. Assessment of capillary anion exchange ion chromatography tandem mass spectrometry for the quantitative profiling of the phosphometabolome and organic acids in biological extracts.

    PubMed

    Kvitvang, Hans F N; Kristiansen, Kåre A; Bruheim, Per

    2014-11-28

    Metabolic profiling has become an important tool in biological research, and the chromatographic separation of metabolites coupled with mass spectrometric detection is the most frequently used approach for such studies. The establishment of robust chromatographic methods for comprehensive coverage of the anionic metabolite pool is especially challenging. In this study, the development of a capillary ion exchange chromatography (capIC) - negative ESI tandem mass spectrometry (MS/MS) workflow for the quantitative profiling of the phosphometabolome (e.g., sugar phosphates and nucleotides) is presented. The chromatographic separation and MS/MS conditions were optimized, and the precision of repetitive injections and accuracy in terms of error percentage to true concentration were assessed. The precision is excellent for a capillary flow system with an average CV% of 8.5% for a 50-fmol standard injection and in the lower 2.4-4.4% range for higher concentrations (500-7,500 fmol). The limit of detection (LOD) ranges from 1 to 100 nM (5-500 fmol injected on column), and the limit of quantitation (LOQ) ranges from 1 to 500 nM (5-2,500 fmol injected on column). A fast gradient method with the injection of 50% methanol in water between analytical samples is needed to eliminate carry-over and ensure optimal re-equilibration of the column. Finally, the quantitative applicability of the system was tested on real biological matrices using the constant-volume standard addition method (SAM). Extracts of the human kidney Hek293 cell line were spiked with increasing concentrations of standards to determine the concentration of each metabolite in the sample. Forty-four metabolites were detected with an average uncertainty of 4.1%. Thus, the capIC-MS/MS method exhibits excellent selectivity, sensitivity and precision for the quantitative profiling of the phosphometabolome.

  18. Modeling velocity in gradient flows with coupled-map lattices with advection.

    PubMed

    Lind, Pedro G; Corte-Real, João; Gallas, Jason A C

    2002-07-01

    We introduce a simple model to investigate large scale behavior of gradient flows based on a lattice of coupled maps which, in addition to the usual diffusive term, incorporates advection, as an asymmetry in the coupling between nearest neighbors. This diffusive-advective model predicts traveling patterns to have velocities obeying the same scaling as wind velocities in the atmosphere, regarding the advective parameter as a sort of geostrophic wind. In addition, the velocity and wavelength of traveling wave solutions are studied. In general, due to the presence of advection, two regimes are identified: for strong diffusion the velocity varies linearly with advection, while for weak diffusion a power law is found with a characteristic exponent proportional to the diffusion.

  19. 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

  20. 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.

  1. Dynamics of disk galaxies under eccentric perturbations and the effect of radiative thermal exchange on the rotation of lower mass protostars

    NASA Astrophysics Data System (ADS)

    Zhang, Linchu

    2000-09-01

    In the first part of this dissertation, the dynamics of disk galaxies are treated using a representation in a number of circular rings*. The rings are assumed to be rigid and oscillate in a plane. Motion of matter within each ring is taken into account. Eccentric perturbations are studied. First the axisymmetric equilibrium configuration of the galaxy is discussed. After that eccentric perturbations are described. The ring representation is then applied and relevant equations of motion derived. Various formulas involving coefficients of terms in the equations of motion are derived. Angular momentum transport is then discussed with the results of numerical solutions of the equations of motion. Besides the disk, two other components: the galactic bulge, and the dark matter halo are also included, but only as passive sources of gravity. The central region of the disk is handled separately; it may contain a black hole. The second part of this dissertation treats protostars. It is shown that radiative thermal exchange can significantly reduce the angular momentum of a rapidly spinning protostar. The mechanism is especially important for high temperature and large surface area. Also, it is expected that the mechanism is most relevant to lower mass protostars, since they may be embedded inside H II regions which have high temperatures. *This first part of the dissertation is related to [15] (Lovelace, R. V. E., Zhang, L., Kornreich, D. A., & Haynes, M. P. 1999, THE ASTROPHYSICAL JOURNAL, 524, 634, published by the University of Chicago Press,© 1999.The American Astronomical Society. All rights reserved).

  2. 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

  3. Simultaneous detection of perchlorate and bromate using rapid high-performance ion exchange chromatography-tandem mass spectrometry and perchlorate removal in drinking water.

    PubMed

    West, Danielle M; Mu, Ruipu; Gamagedara, Sanjeewa; Ma, Yinfa; Adams, Craig; Eichholz, Todd; Burken, Joel G; Shi, Honglan

    2015-06-01

    Perchlorate and bromate occurrence in drinking water causes health concerns due to their effects on thyroid function and carcinogenicity, respectively. The purpose of this study was threefold: (1) to advance a sensitive method for simultaneous rapid detection of perchlorate and bromate in drinking water system, (2) to systematically study the occurrence of these two contaminants in Missouri drinking water treatment systems, and (3) to examine effective sorbents for minimizing perchlorate in drinking water. A rapid high-performance ion exchange chromatography-tandem mass spectrometry (HPIC-MS/MS) method was advanced for simultaneous detection of perchlorate and bromate in drinking water. The HPIC-MS/MS method was rapid, required no preconcentration of the water samples, and had detection limits for perchlorate and bromate of 0.04 and 0.01 μg/L, respectively. The method was applied to determine perchlorate and bromate concentrations in total of 23 selected Missouri drinking water treatment systems during differing seasons. The water systems selected include different source waters: groundwater, lake water, river water, and groundwater influenced by surface water. The concentrations of perchlorate and bromate were lower than or near to method detection limits in most of the drinking water samples monitored. The removal of perchlorate by various adsorbents was studied. A cationic organoclay (TC-99) exhibited effective removal of perchlorate from drinking water matrices.

  4. Structure-dependent degradation of polar compounds in weathered oils observed by atmospheric pressure photo-ionization hydrogen/deuterium exchange ultrahigh resolution mass spectrometry.

    PubMed

    Islam, Ananna; Kim, Donghwi; Yim, Un Hyuk; Shim, Won Joon; Kim, Sunghwan

    2015-10-15

    The resin fractions of fresh mixtures of three oils spilled during the M/V Hebei Spirit oil spill, as well as weathered oils collected at weathering stages II and IV from the oil spill site were analyzed and compared by atmospheric pressure photo-ionization hydrogen/deuterium exchange mass spectrometry (HDX MS). The significantly decreased abundance of N(+) and [N-H+D](+) ions suggested that secondary and tertiary amine-containing compounds were preferentially degraded during the early stage of weathering. [N+H](+) and [N+D](+) ions previously attributed to pyridine-type compounds degraded more slowly than secondary and tertiary amine-containing compounds. The preferential degradation of nitrogen-containing compounds was confirmed by photo-degradation experiments using 15 standard compounds. In addition, significant increases of [S1O1+H](+) and [S1O1+D](+) ions with higher DBE values were observed from fresh oil mixtures as compared to stages II and IV samples, and that could be linked with the decrease of higher DBE compounds of the S1 class. This study presented convincing arguments and evidence demonstrating that secondary and tertiary amines were more vulnerable to photo-degradation than compounds containing pyridine, and hence, preferential degradation depending on chemical structures must be considered in the production of hazardous or toxic components.

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

    PubMed

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

    2016-04-01

    The ability of proteins to bind and interact with protein partners plays fundamental roles in many cellular contexts. X-ray crystallography has been a powerful approach to understand protein-protein interactions; however, a challenge in the crystallization of proteins and their complexes is the presence of intrinsically disordered regions. In this article, we describe an application of hydrogen deuterium exchange mass spectrometry (HDX-MS) to identify dynamic regions within type III phosphatidylinositol 4 kinase beta (PI4KIIIβ) in complex with the GTPase Rab11. This information was then used to design deletions that allowed for the production of diffraction quality crystals. Importantly, we also used HDX-MS to verify that the new construct was properly folded, consistent with it being catalytically and functionally active. Structures of PI4KIIIβ in an Apo state and bound to the potent inhibitor BQR695 in complex with both GTPγS and GDP loaded Rab11 were determined. This hybrid HDX-MS/crystallographic strategy revealed novel aspects of the PI4KIIIβ-Rab11 complex, as well as the molecular mechanism of potency of a PI4K specific inhibitor (BQR695). This approach is widely applicable to protein-protein complexes, and is an excellent strategy to optimize constructs for high-resolution structural approaches. PMID:26756197

  6. 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

  7. 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

  8. Dissecting the Binding Mode of Low Affinity Phage Display Peptide Ligands to Protein Targets by Hydrogen/Deuterium Exchange Coupled to Mass Spectrometry

    PubMed Central

    2015-01-01

    Phage display (PD) is frequently used to discover peptides capable of binding to biological protein targets. The structural characterization of peptide–protein complexes is often challenging due to their low binding affinities and high structural flexibility. Here, we investigate the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize interactions of low affinity peptides with their cognate protein targets. The HDX-MS workflow was optimized to accurately detect low-affinity peptide–protein interactions by use of ion mobility, electron transfer dissociation, nonbinding control peptides, and statistical analysis of replicate data. We show that HDX-MS can identify regions in the two epigenetic regulator proteins KDM4C and KDM1A that are perturbed through weak interactions with PD-identified peptides. Two peptides cause reduced HDX on opposite sides of the active site of KDM4C, indicating distinct binding modes. In contrast, the perturbation site of another PD-selected peptide inhibiting the function of KDM1A maps to a GST-tag. Our results demonstrate that HDX-MS can validate and map weak peptide–protein interactions and pave the way for understanding and optimizing the binding of peptide scaffolds identified through PD and similar ligand discovery approaches. PMID:25325890

  9. 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.

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

    PubMed

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

    2016-04-01

    The ability of proteins to bind and interact with protein partners plays fundamental roles in many cellular contexts. X-ray crystallography has been a powerful approach to understand protein-protein interactions; however, a challenge in the crystallization of proteins and their complexes is the presence of intrinsically disordered regions. In this article, we describe an application of hydrogen deuterium exchange mass spectrometry (HDX-MS) to identify dynamic regions within type III phosphatidylinositol 4 kinase beta (PI4KIIIβ) in complex with the GTPase Rab11. This information was then used to design deletions that allowed for the production of diffraction quality crystals. Importantly, we also used HDX-MS to verify that the new construct was properly folded, consistent with it being catalytically and functionally active. Structures of PI4KIIIβ in an Apo state and bound to the potent inhibitor BQR695 in complex with both GTPγS and GDP loaded Rab11 were determined. This hybrid HDX-MS/crystallographic strategy revealed novel aspects of the PI4KIIIβ-Rab11 complex, as well as the molecular mechanism of potency of a PI4K specific inhibitor (BQR695). This approach is widely applicable to protein-protein complexes, and is an excellent strategy to optimize constructs for high-resolution structural approaches.

  11. 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

  12. 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

  13. Effective elimination of organic matter interference in boron isotopic analysis by thermal ionization mass spectrometry of coral/foraminifera: micro-sublimation technology combined with ion exchange.

    PubMed

    He, Maoyong; Xiao, Yingkai; Ma, Yunqi; Jin, Zhangdong; Xiao, Jun

    2011-03-30

    In order to better estimate the effectiveness of micro-sublimation technology on the elimination of organic matter interference during boron isotopic analysis, a series of improved experiments was carried out using simple apparatus. Recovery rates after micro-sublimation were measured for boric acid solutions with different B contents or different B/organic matter ratios. The improved micro-sublimation procedure combined with ion-exchange technology was then used to test natural samples (coral and foraminifera) for the separation of boron. Our results show that the time taken for 100% recovery of different amounts of B differed and that the proportions of B/organic matter within the natural organic matter have little effect on the relationship between the recovery rates of B and the micro-sublimation times. The experiments further confirm that the organic matter does indeed have an effect on boron isotope analyses by positive thermal ionization mass spectrometry and that the use of micro-sublimation can effectively remove interferences from the organic matter during boron isotopic analysis. PMID:21337635

  14. Time Acceleration Methods for Advection on the Cubed Sphere

    SciTech Connect

    Archibald, Richard K; Evans, Katherine J; White III, James B; Drake, John B

    2009-01-01

    Climate simulation will not grow to the ultrascale without new algorithms to overcome the scalability barriers blocking existing implementations. Until recently, climate simulations concentrated on the question of whether the climate is changing. The emphasis is now shifting to impact assessments, mitigation and adaptation strategies, and regional details. Such studies will require significant increases in spatial resolution and model complexity while maintaining adequate throughput. The barrier to progress is the resulting decrease in time step without increasing single-thread performance. In this paper we demonstrate how to overcome this time barrier for the first standard test defined for the shallow-water equations on a sphere. This paper explains how combining a multiwavelet discontinuous Galerkin method with exact linear part time-evolution schemes can overcome the time barrier for advection equations on a sphere. The discontinuous Galerkin method is a high-order method that is conservative, flexible, and scalable. The addition of multiwavelets to discontinuous Galerkin provides a hierarchical scale structure that can be exploited to improve computational efficiency in both the spatial and temporal dimensions. Exact linear part time-evolution schemes are explicit schemes that remain stable for implicit-size time steps.

  15. Population persistence under advection-diffusion in river networks.

    PubMed

    Ramirez, Jorge M

    2012-11-01

    An integro-differential equation on a tree graph is used to model the time evolution and spatial distribution of a population of organisms in a river network. Individual organisms become mobile at a constant rate, and disperse according to an advection-diffusion process with coefficients that are constant on the edges of the graph. Appropriate boundary conditions are imposed at the outlet and upstream nodes of the river network. The local rates of population growth/decay and that by which the organisms become mobile, are assumed constant in time and space. Imminent extinction of the population is understood as the situation whereby the zero solution to the integro-differential equation is stable. Lower and upper bounds for the eigenvalues of the dispersion operator, and related Sturm-Liouville problems are found. The analysis yields sufficient conditions for imminent extinction and/or persistence in terms of the values of water velocity, channel length, cross-sectional area and diffusivity throughout the river network.

  16. 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.

  17. Investigation of density-dependent gas advection of trichloroethylene: Experiment and a model validation exercise

    NASA Astrophysics Data System (ADS)

    Lenhard, R. J.; Oostrom, M.; Simmons, C. S.; White, M. D.

    1995-07-01

    An experiment was conducted to evaluate whether vapor-density effects are significant in transporting volatile organic compounds (VOC's) with high vapor pressure and molecular mass through the subsurface. Trichloroethylene (TCE) was chosen for the investigation because it is a common VOC contaminant with high vapor pressure and molecular mass. For the investigation, a 2-m-long by 1-m-high by 7.5-cm-thick flow cell was constructed with a network of sampling ports. The flow cell was packed with sand, and a water table was established near the lower boundary. Liquid TCE was placed near the upper boundary of the flow cell in a chamber from which vapors could enter and migrate through the sand. TCE concentrations in the gas phase were measured by extracting 25-μl gas samples with an air-tight syringe and analyzing them with a gas chromatograph. The evolution of the TCE gas plume in the sand was investigated by examining plots of TCE concentrations over the domain for specific times and for particular locations as a function of time. To help in this analysis, a numerical model was developed that can predict the simultaneous movements of a gas, a nonaqueous liquid and water in porous media. The model also considers interphase mass transfer by employing the phase equilibrium assumption. The model was tested with one- and two-dimensional analytical solutions of fluid flow before it was used to simulate the experiment. Comparisons between experimental data and simulation results when vapor-density effects are considered were very good. When vapor-density effects were ignored, agreement was poor. These analyses suggest that vapor-density effects should be considered and that density-driven vapor advection may be an important mechanism for moving VOC's with high vapor pressures and molecular mass through the subsurface.

  18. 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.

  19. Liquid chromatography/quadrupole time-of-flight mass spectrometry in combination with online hydrogen/deuterium exchange technique for structural elucidation of phase I metabolites of iso-phenylcyclopentylamine in rat bile.

    PubMed

    Liu, Xiaoxue; Wang, Suilou; Ding, Li; Chen, Xiaoping; Shen, Wenbin; Dong, Xin; Yun, Changhong; Lin, Hongda

    2014-10-01

    MS/MS experiment and accurate mass measurement are powerful tools in metabolite identification. However, sometimes these data do not provide enough information to assign an unambiguous structure to a metabolite. In combination with MS techniques, hydrogen/deuterium (H/D) exchange can provide additional information for structural elucidation by determination of the number of exchangeable hydrogen atoms in a structure. In this study, the principal phase I metabolites of iso-phenylcyclopentylamine in rat bile were identified by high-performance liquid chromatography with electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-Q-TOF-MS). Since N-oxidation may occur because of the existence of the primary amino group in the structure, it was difficult to differentiate the hydroxylated metabolites from N-oxides by ESI-Q-TOF-MS alone. Therefore, online H/D exchange technique was applied to solve this problem. Finally, 25 phase I metabolites were detected and structurally described, in which 11 were confirmed to be N-oxides. This study demonstrated the effectiveness of high-resolution mass spectrometry in combination with an online H/D exchange technique in rapid identification of drug metabolites, especially in discriminating hydroxylated metabolites from N-oxides.

  20. Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Gō model simulation.

    PubMed

    Gu, Zhenyu; Rao, Maithreyi K; Forsyth, William R; Finke, John M; Matthews, C Robert

    2007-11-23

    The structures of partially folded states appearing during the folding of a (betaalpha)(8) TIM barrel protein, the indole-3-glycerol phosphate synthase from Sulfolobus solfataricus (sIGPS), was assessed by hydrogen exchange mass spectrometry (HX-MS) and Gō model simulations. HX-MS analysis of the peptic peptides derived from the pulse-labeled product of the sub-millisecond folding reaction from the urea-denatured state revealed strong protection in the (betaalpha)(4) region, modest protection in the neighboring (betaalpha)(1-3) and (betaalpha)(5)beta(6) segments and no significant protection in the remaining N and C-terminal segments. These results demonstrate that this species is not a collapsed form of the unfolded state under native-favoring conditions nor is it the native state formed via fast-track folding. However, the striking contrast of these results with the strong protection observed in the (betaalpha)(2-5)beta(6) region after 5 s of folding demonstrates that these species represent kinetically distinct folding intermediates that are not identical as previously thought. A re-examination of the kinetic folding mechanism by chevron analysis of fluorescence data confirmed distinct roles for these two species: the burst-phase intermediate is predicted to be a misfolded, off-pathway intermediate, while the subsequent 5 s intermediate corresponds to an on-pathway equilibrium intermediate. Comparison with the predictions using a C(alpha) Gō model simulation of the kinetic folding reaction for sIGPS shows good agreement with the core of the structure offering protection against exchange in the on-pathway intermediate(s). Because the native-centric Gō model simulations do not explicitly include sequence-specific information, the simulation results support the hypothesis that the topology of TIM barrel proteins is a primary determinant of the folding free energy surface for the productive folding reaction. The early misfolding reaction must involve aspects of

  1. Gas to particle conversion-gas exchange technique for direct analysis of metal carbonyl gas by inductively coupled plasma mass spectrometry.

    PubMed

    Nishiguchi, Kohei; Utani, Keisuke; Gunther, Detlef; Ohata, Masaki

    2014-10-21

    A novel gas to particle conversion-gas exchange technique for the direct analysis of metal carbonyl gas by inductively coupled plasma mass spectrometry (ICPMS) was proposed and demonstrated in the present study. The technique is based on a transfer of gas into particle, which can be directly analyzed by ICPMS. Particles from metal carbonyl gases such as Cr(CO)6, Mo(CO)6, and W(CO)6 are formed by reaction with ozone (O3) and ammonium (NH3) gases within a newly developed gas to particle conversion device (GPD). The reaction mechanism of the gas to particle conversion is based on either oxidation of metal carbonyl gas by O3 or agglomeration of metal oxide with ammonium nitrate (NH4NO3) which is generated by the reaction of O3 and NH3. To separate the reaction gases (remaining O3 and NH3) from the formed particles, a previously reported gas exchange device (GED) was used and the in argon stabilized analyte particles were directly introduced and measured by ICPMS. This new technique provided limits of detection (LOD) of 0.15 pL L(-1) (0.32 ng m(-3)), 0.02 pL L(-1) (0.07 ng m(-3)), and 0.01 pL L(-1) (0.07 ng m(-3)) for Cr(CO)6, Mo(CO)6, and W(CO)6, respectively, which were 4-5 orders of magnitude lower than those conventional applied for detecting these gases, e.g., gas chromatography with electron captured detector (GC-ECD) as well as Fourier transform-infrared spectroscopy (FT-IR). The achieved LODs were also similar or slightly better than those for ICPMS coupled to GC. Since the gas to particle conversion technique can achieve the direct measurement of metal carbonyl gases as well as the removal of reaction and ambient gases from metal carbonyl gases, the technique is considered to be well suited to monitor gas quality in semiconductor industry, engine exhaust gases, and or waste incineration products.

  2. Gas to particle conversion-gas exchange technique for direct analysis of metal carbonyl gas by inductively coupled plasma mass spectrometry.

    PubMed

    Nishiguchi, Kohei; Utani, Keisuke; Gunther, Detlef; Ohata, Masaki

    2014-10-21

    A novel gas to particle conversion-gas exchange technique for the direct analysis of metal carbonyl gas by inductively coupled plasma mass spectrometry (ICPMS) was proposed and demonstrated in the present study. The technique is based on a transfer of gas into particle, which can be directly analyzed by ICPMS. Particles from metal carbonyl gases such as Cr(CO)6, Mo(CO)6, and W(CO)6 are formed by reaction with ozone (O3) and ammonium (NH3) gases within a newly developed gas to particle conversion device (GPD). The reaction mechanism of the gas to particle conversion is based on either oxidation of metal carbonyl gas by O3 or agglomeration of metal oxide with ammonium nitrate (NH4NO3) which is generated by the reaction of O3 and NH3. To separate the reaction gases (remaining O3 and NH3) from the formed particles, a previously reported gas exchange device (GED) was used and the in argon stabilized analyte particles were directly introduced and measured by ICPMS. This new technique provided limits of detection (LOD) of 0.15 pL L(-1) (0.32 ng m(-3)), 0.02 pL L(-1) (0.07 ng m(-3)), and 0.01 pL L(-1) (0.07 ng m(-3)) for Cr(CO)6, Mo(CO)6, and W(CO)6, respectively, which were 4-5 orders of magnitude lower than those conventional applied for detecting these gases, e.g., gas chromatography with electron captured detector (GC-ECD) as well as Fourier transform-infrared spectroscopy (FT-IR). The achieved LODs were also similar or slightly better than those for ICPMS coupled to GC. Since the gas to particle conversion technique can achieve the direct measurement of metal carbonyl gases as well as the removal of reaction and ambient gases from metal carbonyl gases, the technique is considered to be well suited to monitor gas quality in semiconductor industry, engine exhaust gases, and or waste incineration products. PMID:25247610

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. An operator splitting algorithm for the three-dimensional advection-diffusion equation

    NASA Astrophysics Data System (ADS)

    Khan, Liaqat Ali; Liu, Philip L.-F.

    1998-09-01

    Operator splitting algorithms are frequently used for solving the advection-diffusion equation, especially to deal with advection dominated transport problems. In this paper an operator splitting algorithm for the three-dimensional advection-diffusion equation is presented. The algorithm represents a second-order-accurate adaptation of the Holly and Preissmann scheme for three-dimensional problems. The governing equation is split into an advection equation and a diffusion equation, and they are solved by a backward method of characteristics and a finite element method, respectively. The Hermite interpolation function is used for interpolation of concentration in the advection step. The spatial gradients of concentration in the Hermite interpolation are obtained by solving equations for concentration gradients in the advection step. To make the composite algorithm efficient, only three equations for first-order concentration derivatives are solved in the diffusion step of computation. The higher-order spatial concentration gradients, necessary to advance the solution in a computational cycle, are obtained by numerical differentiations based on the available information. The simulation characteristics and accuracy of the proposed algorithm are demonstrated by several advection dominated transport problems.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. Partially Unfolded Forms of the Prion Protein Populated under Misfolding-promoting Conditions: CHARACTERIZATION BY HYDROGEN EXCHANGE MASS SPECTROMETRY AND NMR.

    PubMed

    Moulick, Roumita; Das, Ranabir; Udgaonkar, Jayant B

    2015-10-16

    The susceptibility of the cellular prion protein (PrP(C)) to convert to an alternative misfolded conformation (PrP(Sc)), which is the key event in the pathogenesis of prion diseases, is indicative of a conformationally flexible native (N) state. In the present study, hydrogen-deuterium exchange (HDX) in conjunction with mass spectrometry and nuclear magnetic resonance spectroscopy were used for the structural and energetic characterization of the N state of the full-length mouse prion protein, moPrP(23-231), under conditions that favor misfolding. The kinetics of HDX of 34 backbone amide hydrogens in the N state were determined at pH 4. In contrast to the results of previous HDX studies on the human and Syrian hamster prion proteins at a higher pH, various segments of moPrP were found to undergo different extents of subglobal unfolding events at pH 4, a pH at which the protein is known to be primed to misfold to a β-rich conformation. No residual structure around the disulfide bond was observed for the unfolded state at pH 4. The N state of the prion protein was observed to be at equilibrium with at least two partially unfolded forms (PUFs). These PUFs, which are accessed by stochastic fluctuations of the N state, have altered surface area exposure relative to the N state. One of these PUFs resembles a conformation previously implicated to be an initial intermediate in the conversion of monomeric protein into misfolded oligomer at pH 4. PMID:26306043

  20. Understanding the conformational impact of chemical modifications on monoclonal antibodies with diverse sequence variation using hydrogen/deuterium exchange mass spectrometry and structural modeling.

    PubMed

    Zhang, Aming; Hu, Ping; MacGregor, Paul; Xue, Yu; Fan, Haihong; Suchecki, Peter; Olszewski, Leonard; Liu, Aston

    2014-04-01

    Chemical modifications can potentially induce conformational changes near the modification site and thereby impact the safety and efficacy of protein therapeutics. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has emerged as a powerful analytical technique with high spatial resolution and sensitivity in detecting such local conformational changes. In this study, we utilized HDX-MS combined with structural modeling to examine the conformational impact on monoclonal antibodies (mAbs) caused by common chemical modifications including methionine (Met) oxidation, aspartic acid (Asp) isomerization, and asparagine (Asn) deamidation. Four mAbs with diverse sequences and glycosylation states were selected. The data suggested that the impact of Met oxidation was highly dependent on its location and glycosylation state. For mAbs with normal glycosylation in the Fc region, oxidation of the two conserved Met252 and Met428 (Kabat numbering) disrupted the interface interactions between the CH2 and CH3 domains, thus leading to a significant decrease in CH2 domain thermal stability as well as a slight increase in aggregation propensity. In contrast, Met oxidation in the variable region and CH3 domain had no detectable impact on mAb conformation. For aglycosylated mAb, Met oxidation could cause a more global conformational change to the whole CH2 domain, coincident with the larger decrease in thermal stability and significant increase in aggregation rate. Unlike Met oxidation, Asn deamidation and Asp isomerization mostly had very limited effects on mAb conformation, with the exception of succiminide intermediate formation which induced a measurable local conformational change to be more solvent protected. Structural modeling suggested that the succinimide intermediate was stabilized by adjacent aromatic amino acids through ring-ring stacking interactions. PMID:24597564

  1. Tomography-based monitoring of isothermal snow metamorphism under advective conditions

    NASA Astrophysics Data System (ADS)

    Ebner, P. P.; Schneebeli, M.; Steinfeld, A.

    2015-02-01

    Time-lapse X-ray micro-tomography was used to investigate the structural dynamics of isothermal snow metamorphism exposed to an advective airflow. Diffusion and advection across the snow pores were analysed in controlled laboratory experiments. The 3-D digital geometry obtained by tomographic scans was used in direct pore-level numerical simulations to determine the effective transport properties. The results showed that isothermal advection with saturated air have no influence on the coarsening rate that is typical for isothermal snow metamorphism. Diffusion originating in the Kelvin effect between snow structures dominates and is the main transport process in isothermal snow packs.

  2. 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.

  3. Removing volatile contaminants from the unsaturated zone by inducing advective air-phase transport

    USGS Publications Warehouse

    Baehr, A.L.; Hoag, G.E.; Marley, M.C.

    1989-01-01

    Organic liquids inadvertently spilled and then distributed in the unsaturated zone can pose a long-term threat to ground water. Many of these substances have significant volatility, and thereby establish a premise for contaminant removal from the unsaturated zone by inducing advective air-phase transport with wells screened in the unsaturated zone. In order to focus attention on the rates of mass transfer from liquid to vapour phases, sand columns were partially saturated with gasoline and vented under steady air-flow conditions. The ability of an equilibrium-based transport model to predict the hydrocarbon vapor flux from the columns implies an efficient rate of local phase transfer for reasonably high air-phase velocities. Thus the success of venting remediations will depend primarily on the ability to induce an air-flow field in a heterogeneous unsaturated zone that will intersect the distributed contaminant. To analyze this aspect of the technique, a mathematical model was developed to predict radially symmetric air flow induced by venting from a single well. This model allows for in-situ determinations of air-phase permeability, which is the fundamental design parameter, and for the analysis of the limitations of a single well design. A successful application of the technique at a site once contaminated by gasoline supports the optimism derived from the experimental and modeliing phases of this study, and illustrates the well construction and field methods used to document the volatile contaminant recovery. ?? 1989.

  4. 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.

  5. 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...

  6. Analysis of moisture advection during explosive cyclogenesis over North Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Ordóñez, Paulina; Liberato, Margarida L. R.; Pinto, Joaquim G.; Trigo, Ricardo M.

    2013-04-01

    The development of a mid-latitude cyclone may strongly be amplified by the presence of a very warm and moist air mass within its warm sector through enhanced latent heat release. In this work, a lagrangian approach is applied to examine the contribution of moisture advection to the deepening of cyclones over the North Atlantic Ocean. The warm sector is represented by a 5°x5° longitude/latitude moving box comprising the centre of the cyclone and its south-eastern area is defined for the tracks of different cyclones computed at 6-hourly intervals. Using the lagrangian particle model FLEXPART we evaluated the fresh water flux (E - P) along 2-days back-trajectories of the particles residing on the total column over the defined boxes for case studies occurring during winter months from 1980 to 2000. FLEXPART simulations were performed using one degree resolution and 60 model vertical levels available in ERA40 Reanalyses at 00, 06, 12, 18 UTC for each case. Sensitivity studies on the dimensions of the target area - chosen boxes representing the warm sector -, and on its relative position to the center, were performed. We have applied this methodology to several case studies of independent North Atlantic cyclones with notorious characteristics (e.g. deepening rate, wind speed, surface damages). Results indicate that the moisture transport is particularly relevant in what concerns the fast/explosive development stage of these extratropical cyclones. In particular, the advection of moist air from the subtropics towards the cyclone core is clearly associated with the warm conveyor belt of the cyclone. This methodology can be generalized to a much larger number of mid-latitude cyclones, providing a unique opportunity to analyze the moisture behavior associated with the explosive development. Acknowledgments: This work was partially supported by FEDER (Fundo Europeu de Desenvolvimento Regional) funds through the COMPETE (Programa Operacional Factores de Competitividade

  7. A Method for Measuring Subcanopy CO2 Advection

    NASA Astrophysics Data System (ADS)

    Staebler, R. M.; Fitzjarrald, D. R.

    2004-12-01

    Underestimation of nocturnal CO2 respiration under calm conditions remains an unsolved problem at many forest flux stations, and several groups are currently investigating the direct measurement of horizontal advection of CO2. This presentation will describe a systematic, relatively low-cost methodology developed to determine whether horizontal mean transport of CO2 accounts for the missing CO2 at the Harvard Forest (Petersham, MA). This methodology includes the characterization of subcanopy motions, determining the appropriate size of the subcanopy network required to make the measurements, developing a method of integrating the measurements in the vertical, and determining the required averaging time. Measurements were conducted over 4 years and produced data for 310 nights covering all seasons. Subcanopy flows were decoupled from the flows aloft 75% of the time. Conditions conducive to the generation of negative buoyancy near the forest floor, necessary for drainage flows to develop, were given in 92% of all nights. The occurrence of nocturnal drainage flows correlated well with "missing flux" problems ("deficit nights"), prompting us to propose an improvement on the commonly used friction velocity criterion (which requires u* to be larger than some empirical cut-off for the eddy fluxes to be considered credible). The "negative buoyancy forcing fraction", i.e. negative buoyancy as a fraction of the sum of the dynamic driving forces, can be shown to predict deficit nights significantly better than the u* cut-off. The appropriate horizontal size of the network of wind and CO2 sensors at the Harvard Forest was shown to be on the order of 100 m, ensuring that sensors were generally observing coherent processes on this scale or larger and thus displaying some correlation. Horizontal transport of CO2 was found to be restricted to the bottom ~10 m of the forest, facilitating the development of a method of integrating the horizontal CO2 gradients in the vertical

  8. 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.

  9. Study of the size-based environmental availability of metals associated to natural organic matter by stable isotope exchange and quadrupole inductively coupled plasma mass spectrometry coupled to asymmetrical flow field flow fractionation.

    PubMed

    Laborda, F; Ruiz-Beguería, S; Bolea, E; Castillo, J R

    2011-07-01

    The determination of the isotopically exchangeable fraction of metals in environmental solid samples (soils, composts, sediments, sludges, etc.) is used to know the amount of metal potentially available (E-value). Stable isotopes can be used for determination of E-values through the analysis of the aqueous phases from spiked suspensions. However, the presence of isotopically non-exchangeable metal forms in the aqueous phase led to overestimation of the E-values. In this paper, a method for monitoring the degree of isotopic exchange in function of the molecular mass and/or size of the metal form has been developed based on the direct coupling of asymmetrical flow field flow fractionation (AsFlFFF) with inductively coupled plasma mass spectrometry (ICP-MS) for on-line isotope ratio measurements. ICP-MS data acquisition parameters were stressed to avoid degradation of isotope ratio precision. Two sets of fractionation conditions were selected: a colloids separation, which allowed the separation of substances up to 1 μm, and a macromolecules separation, designed to resolve small size substances up to 50 kDa. The methodology was applied to study the environmental availability of copper and lead in compost samples, where metals are mainly associated to different forms of organic matter. No significant differences on isotopic exchange were observed over the size range studied, validating the E-values determined by direct analysis of the aqueous phases.

  10. 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...

  11. 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...

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Modifying SEBAL ET Algorithm to account for advection by using daily averages of weather data

    NASA Astrophysics Data System (ADS)

    Mkhwanazi, M. M.; Chavez, J. L.

    2013-12-01

    The use of Remote Sensing (RS) in crop evapotranspiration (ET) estimation is aimed at improving agricultural water management. The Surface Energy Balance Algorithm for Land (SEBAL) is one of several methods that have been developed for this purpose. This has been a preferred model as it requires minimal climate data. However, it has a noted downside of underestimating ET under advective conditions. This is primarily due to the use of evaporative fraction (EF) to extrapolate instantaneous ET to daily values, with the assumption that EF is constant throughout the day. A modified SEBAL model was used in this study, which requires daily averages of weather data to estimate advection which is then introduced into the 24-hour ET sub-model of SEBAL. The study was carried out in southeastern Colorado, a semi-arid area where afternoon advection is a common feature. ET estimated using the original and modified SEBAL was compared to the lysimeter-measured ET. Results showed that the modified SEBAL algorithm performed better in estimating daily ET in overall, but especially on days when there was advection. On non-advective days, the original SEBAL was more accurate. It is therefore recommended that the modified SEBAL be used only on advective days, and guidelines to help identify such days were proposed.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. The use of strong anion-exchange (SAX) magnetic particles for the extraction of therapeutic siRNA and their analysis by liquid chromatography/mass spectrometry.

    PubMed

    Ye, Guofeng; Beverly, Michael

    2011-11-15

    Traditional methods for extracting oligonucleotides from serum and other biological fluids are often time-consuming and require multiple steps. Magnetic particle based separation of oligonucleotides has gained importance recently due to the advantages of simplicity and high efficiency. Here we report the development and optimization of commercially available strong anion-exchange (SAX) magnetic beads for the extraction of siRNA from human serum. The beads allowed for rapid extraction of siRNA from human serum in 100-200 μL of liquid chromatography/mass spectrometry (LC/MS)-compatible buffer in less than 1 h for a 96-well plate with no further drying steps. Due to the strong cation-binding properties of oligonucleotides, volatile ammonium salts such as triethylammonium bicarbonate (TEAB), ammonium bicarbonate, and NH(4) Cl were used to elute the siRNA from the beads. For more hydrophobic siRNA sequences, the addition of 5-10% organic solvent was required for elution. The recovery of chemically modified siRNA from human serum was around 80% for two types of beads examined; however, the recovery for highly modified sequences differed greatly between the two types of beads. In addition to extracting highly modified oligonucleotides, the SAX beads were also able to extract liposomal formulated siRNAs from serum with no interference from the lipid formulation. The extraction of siRNA from human serum was linear over the tested range of 50 ng/mL to 10 µg/mL. Using this extraction methodology, we have created a workflow to monitor siRNA serum stability by LC/MS. Initial observations confirm that RNase A type degradation with strand cleavage on the 3' side of uridine or cytosine is the dominant cleavage pattern in serum. This finding has implications for the selection and modification of therapeutic siRNAs and demonstrates the utility of magnetic beads as a simple and rapid extraction technique for siRNA.

  2. 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.

  3. 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.

  4. 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.

  5. Dynamic properties of the thermosphere inferred from Pioneer Venus mass spectrometer measurements

    NASA Technical Reports Server (NTRS)

    Mayr, H. G.; Harris, I.; Niemann, H. B.; Brinton, H. C.; Spencer, N. W.; Taylor, H. A., Jr.; Hartle, R. E.; Hoegy, W. R.; Hunten, D. M.

    1980-01-01

    The data obtained by the Pioneer Venus spectrometer experiments indicate that the day-night temperature contrast on Venus is associated with wind velocities of about 200 m/s which transport oxygen, helium, and hydrogen toward the night side. A mass exchange with the mesosphere commensurate with an eddy diffusion coefficient of 3 x 10 to the 7th is required to buffer the horizontal advection so as to reproduce the observed day time bulge in oxygen and the small diurnal variations in helium. The observed time response and magnitude of the day-night density variations require transport processes to be effective over time periods between five and ten days, implying a superrotation rate or prevailing winds in excess of 50 m/s at the equator. Nonlinear mass transport results in wave steepening and contributes to the amplification of the density extrema in hydrogen and helium.

  6. Dynamic properties of the thermosphere inferred from Pioneer Venus mass spectrometer measurements

    NASA Astrophysics Data System (ADS)

    Mayr, H. G.; Harris, I.; Niemann, H. B.; Brinton, H. C.; Spencer, N. W.; Taylor, H. A.; Hartle, R. E.; Hoegy, W. R.; Hunten, D. M.

    1980-12-01

    The data obtained by the Pioneer Venus spectrometer experiments indicate that the day-night temperature contrast on Venus is associated with wind velocities of about 200 m/s which transport oxygen, helium, and hydrogen toward the night side. A mass exchange with the mesosphere commensurate with an eddy diffusion coefficient of 3 x 10 to the 7th is required to buffer the horizontal advection so as to reproduce the observed day time bulge in oxygen and the small diurnal variations in helium. The observed time response and magnitude of the day-night density variations require transport processes to be effective over time periods between five and ten days, implying a superrotation rate or prevailing winds in excess of 50 m/s at the equator. Nonlinear mass transport results in wave steepening and contributes to the amplification of the density extrema in hydrogen and helium.

  7. Capture zone delineation methodology based on the maximum concentration: Preventative groundwater well protection areas for heat exchange fluid mixtures

    NASA Astrophysics Data System (ADS)

    Okkonen, Jarkko; Neupauer, Roseanna M.

    2016-05-01

    Capture zones of water supply wells are most often delineated based on travel times of water or solute to the well, with the assumption that if the travel time is sufficiently large, the concentration of chemical at the well will not exceed the drinking water standards. In many situations, the likely source concentrations or release masses of contamination from the potential sources are unknown; therefore, the exact concentration at the well cannot be determined. In situations in which the source mass can be estimated with some accuracy, the delineation of the capture zone should be based on the maximum chemical concentration that can be expected at the well, rather than on an arbitrary travel time. We present a new capture zone delineation methodology that is based on this maximum chemical concentration. The method delineates capture zones by solving the adjoint of the advection-dispersion-reaction equation and relating the adjoint state and the known release mass to the expected chemical concentration at the well. We demonstrate the use of this method through a case study in which soil heat exchange systems are potential sources of contamination. The heat exchange fluid mixtures contain known fluid volumes and chemical concentrations; thus, in the event of a release, the release mass of the chemical is known. We also demonstrate the use of a concentration basis in quantifying other measures of well vulnerability including exposure time and time to exceed a predefined threshold concentration at the well.

  8. Enumeration of non-labile oxygen atoms in dissolved organic matter by use of ¹⁶O/ ¹⁸O exchange and Fourier transform ion-cyclotron resonance mass spectrometry.

    PubMed

    Kostyukevich, Yury; Kononikhin, Alexey; Zherebker, Alexander; Popov, Igor; Perminova, Irina; Nikolaev, Eugene

    2014-10-01

    We report a simple approach for enumeration of non-labile oxygen atoms in individual molecules of dissolved organic matter (DOM), using acid-catalyzed (16)O/(18)O exchange and ultrahigh-resolution Fourier-transform ion-cyclotron-resonance mass spectrometry (FTICR-MS). We found that by dissolving DOM in H2 (18)O at 95 °C for 20 days it is possible to replace all oxygen atoms of DOM molecules (excluding oxygen from ether groups) with (18)O. The number of exchanges in each molecule can be determined using high-resolution FTICR. Using the proposed method we identified the number of non-labile oxygen atoms in 231 molecules composing DOM. Also, using a previously developed hydrogen-deuterium (H/D)-exchange approach we identified the number of labile hydrogen atoms in 450 individual molecular formulas. In addition, we observed that several backbone hydrogen atoms can be exchanged for deuterium under acidic conditions. The method can be used for structural and chemical characterization of individual DOM molecules, comparing different DOM samples, and investigation of biological pathways of DOM in the environment.

  9. 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.

  10. Determination of microamounts of hafnium in zirconium using inductively coupled plasma atomic emission spectrometry and inductively coupled plasma mass spectrometry during their separation by ion exchange on Diphonix chelating resin.

    PubMed

    Smolik, Marek; Jakóbik-Kolon, Agata

    2009-04-01

    Inductively coupled plasma atomic emission spectrometry (ICP-AES) and inductively coupled plasma mass spectrometry (ICPMS) methods were applied to check the possibility of determination of hafnium in zirconium at a level lower than 100 ppm. A zirconium matrix of hafnium content lower than 10 ppm was obtained using a worked-out separation method exploiting ion exchange on Diphonix resin. Both methods give results in good agreement with each other as well as with those for certified reference material BCR-098 (Zircaloy-4). They were utilized in determination of Hf in the samples collected during separation of microamounts of hafnium from zirconium by the mentioned ion exchange. These results proved the earlier described method of separation on Diphonix resin to be effective even when the initial concentration of hafnium in zirconium decreases from 2.4% to 0.0082%.

  11. 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

  12. Mapping the structure of folding cores in TIM barrel proteins by hydrogen exchange mass spectrometry: the roles of motif and sequence for the indole-3-glycerol phosphate synthase from Sulfolobus solfataricus.

    PubMed

    Gu, Zhenyu; Zitzewitz, Jill A; Matthews, C Robert

    2007-04-27

    To test the roles of motif and amino acid sequence in the folding mechanisms of TIM barrel proteins, hydrogen-deuterium exchange was used to explore the structure of the stable folding intermediates for the of indole-3-glycerol phosphate synthase from Sulfolobus solfataricus (sIGPS). Previous studies of the urea denaturation of sIGPS revealed the presence of an intermediate that is highly populated at approximately 4.5 M urea and contains approximately 50% of the secondary structure of the native (N) state. Kinetic studies showed that this apparent equilibrium intermediate is actually comprised of two thermodynamically distinct species, I(a) and I(b). To probe the location of the secondary structure in this pair of stable on-pathway intermediates, the equilibrium unfolding process of sIGPS was monitored by hydrogen-deuterium exchange mass spectrometry. The intact protein and pepsin-digested fragments were studied at various concentrations of urea by electrospray and matrix-assisted laser desorption ionization time-of-flight mass spectrometry, respectively. Intact sIGPS strongly protects at least 54 amide protons from hydrogen-deuterium exchange in the intermediate states, demonstrating the presence of stable folded cores. When the protection patterns and the exchange mechanisms for the peptides are considered with the proposed folding mechanism, the results can be interpreted to define the structural boundaries of I(a) and I(b). Comparison of these results with previous hydrogen-deuterium exchange studies on another TIM barrel protein of low sequence identify, alpha-tryptophan synthase (alphaTS), indicates that the thermodynamic states corresponding to the folding intermediates are better conserved than their structures. Although the TIM barrel motif appears to define the basic features of the folding free energy surface, the structures of the partially folded states that appear during the folding reaction depend on the amino acid sequence. Markedly, the good

  13. Modelling of terrain-induced advective flow in Tibet: Implications for assessment of crustal heat flow

    SciTech Connect

    Hochstein, M.P.; Yang Zhongke

    1992-01-01

    In steep terrain the effect of advective flow can be significant, as it can distort the temperature field in the upper brittle crust. The effect was studied by modeling advective flow across a large valley system in Tibet which is associated with several geothermal hot spring systems, the Yanbajing Valley. It was found that, in this setting, all near-surface temperature gradients are significantly disturbed, attaining values differing by up to half an order of magnitude from those resulting from conductive heat transfer. Allowing for advective effects, it was found that the crustal heat flux within the Himalayan Geothermal Belt lies within the range of 60 to 90 mW/m{sup 2} in the Lhasa-Yanbajing area.

  14. Tomography-based monitoring of isothermal snow metamorphism under advective conditions

    NASA Astrophysics Data System (ADS)

    Ebner, P. P.; Schneebeli, M.; Steinfeld, A.

    2015-07-01

    Time-lapse X-ray microtomography was used to investigate the structural dynamics of isothermal snow metamorphism exposed to an advective airflow. The effect of diffusion and advection across the snow pores on the snow microstructure were analysed in controlled laboratory experiments and possible effects on natural snowpacks discussed. The 3-D digital geometry obtained by tomographic scans was used in direct pore-level numerical simulations to determine the effective permeability. The results showed that isothermal advection with saturated air have no influence on the coarsening rate that is typical for isothermal snow metamorphism. Isothermal snow metamorphism is driven by sublimation deposition caused by the Kelvin effect and is the limiting factor independently of the transport regime in the pores.

  15. 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.

  16. Two-Dimensional Advective Transport in Ground-Water Flow Parameter Estimation

    USGS Publications Warehouse

    Anderman, E.R.; Hill, M.C.; Poeter, E.P.

    1996-01-01

    Nonlinear regression is useful in ground-water flow parameter estimation, but problems of parameter insensitivity and correlation often exist given commonly available hydraulic-head and head-dependent flow (for example, stream and lake gain or loss) observations. To address this problem, advective-transport observations are added to the ground-water flow, parameter-estimation model MODFLOWP using particle-tracking methods. The resulting model is used to investigate the importance of advective-transport observations relative to head-dependent flow observations when either or both are used in conjunction with hydraulic-head observations in a simulation of the sewage-discharge plume at Otis Air Force Base, Cape Cod, Massachusetts, USA. The analysis procedure for evaluating the probable effect of new observations on the regression results consists of two steps: (1) parameter sensitivities and correlations calculated at initial parameter values are used to assess the model parameterization and expected relative contributions of different types of observations to the regression; and (2) optimal parameter values are estimated by nonlinear regression and evaluated. In the Cape Cod parameter-estimation model, advective-transport observations did not significantly increase the overall parameter sensitivity; however: (1) inclusion of advective-transport observations decreased parameter correlation enough for more unique parameter values to be estimated by the regression; (2) realistic uncertainties in advective-transport observations had a small effect on parameter estimates relative to the precision with which the parameters were estimated; and (3) the regression results and sensitivity analysis provided insight into the dynamics of the ground-water flow system, especially the importance of accurate boundary conditions. In this work, advective-transport observations improved the calibration of the model and the estimation of ground-water flow parameters, and use of

  17. 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.

  18. 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

  19. 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.

  20. Semi-Lagrangian advection-propagation (SLAP) scheme for three-dimensional interface tracking

    NASA Astrophysics Data System (ADS)

    Aldredge, R. C.

    2010-06-01

    A fully three-dimensional semi-Lagrangian scheme is developed for computing the evolution of advected self-propagating surfaces (e.g., premixed flames) governed by a level-set advection-propagation equation. The scheme provides third-order spatial accuracy and shape preservation. Example numerical simulations of three-dimensional front propagation are presented to illustrate the capability of the scheme of capturing cusp formation and associated surface-area annihilation as well as the formation and consumption of detached closed-surface pockets behind fronts propagating in highly vortical flow.

  1. Horizontal turbulent carbon dioxide flux divergence and energy balance closure: loose ends from an advection experiment in a Douglas-fir forest on a gentle slope

    NASA Astrophysics Data System (ADS)

    Leitch, A. S.; Nesic, Z.; Christen, A.; Black, T. A.

    2010-12-01

    An observational study was conducted during an eight-week period in the summer of 2009 at a forested site in British Columbia (“DF49”) to measure advective carbon dioxide (CO2) fluxes. The site is situated in a 35-m tall Douglas-fir forest on a 5-10 degree slope. Wind vector and CO2 concentration measurements were made at heights of 1, 2.6, 8, 20 and 42 m on the main flux tower, while CO2 concentration measurements were made 73.5 m upslope from the tower at heights of 1, 2.6, 8 and 20 m, creating a two-dimensional transect. Wind vector measurement was made with sonic anemometers. Eight thermostated LI-COR Inc. infrared gas analyzers (IRGAs) were paired using a solenoid valve switching system, creating four differential analyzers. The switching system, combined with a twice-daily polynomial IRGA calibration, enabled measurement of CO2 concentration differences at the four subcanopy measurement heights to an accuracy of 0.5 µmol mol-1 (horizontal) and 1 µmol mol-1 (vertical). The system also recorded semi-continuous CO2 and H2O traces at all sample points. Horizontal advective fluxes, averaged over the main measurement period (August 2 - 25), reached 5 µmol m-2 s-1 at night and 10 µmol m-2 s-1 in the afternoon (a net source to the atmosphere) and -2 µmol m-2 s-1 during the morning (net sink). Vertical advective fluxes averaged around zero during the night, 5 µmol m-2 s-1 during the morning and -5 µmol m-2 s-1 during the afternoon. A cumulative sum of advective flux-corrected net ecosystem exchange (NEE) over the main measurement period (-57 g C m-2) was close to that of the friction velocity-corrected NEE (-60 g C m-2), both predicting less carbon uptake by the Douglas-fir forest than the storage flux-corrected NEE (-86 g C m-2). Additional CO2 difference measurements made after the main sampling period along the 73.5-m transect demonstrated that horizontal CO2 differences increased monotonically down slope (on average) at the 2.6-m height, despite an

  2. Scaling hyporheic exchange and its influence on biogeochemical reactions in aquatic ecosystems

    NASA Astrophysics Data System (ADS)

    O'Connor, Ben L.; Harvey, Judson W.

    2008-12-01

    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.

  3. 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.

  4. Assessment of the possibility of establishing material cycling in an experimental model of the bio-technical life support system with plant and human wastes included in mass exchange

    NASA Astrophysics Data System (ADS)

    Tikhomirov, A. A.; Ushakova, S. A.; Velichko, V. V.; Tikhomirova, N. A.; Kudenko, Yu. A.; Gribovskaya, I. V.; Gros, J.-B.; Lasseur, Ch.

    2011-05-01

    A pilot model of a bio-technical life support system (BTLSS) including human and plant wastes has been developed at the Institute of Biophysics SB RAS (Krasnoyarsk, Russia). This paper describes the structure of the photosynthesizing unit of the system, which includes wheat, chufa and vegetables. The study substantiates the simultaneous use of neutral and biological substrates for cultivating plants. A novel physicochemical method for the involvement of human wastes in the cycling has been employed, which enables the use of recycled products as nutrients for plants. Inedible plant biomass was subjected to biological combustion in the soil-like substrate (SLS) and was thus involved in the system mass exchange; NaCl contained in native urine was returned to the human through the consumption of Salicornia europaea, an edible salt-concentrating plant. Mass transfer processes in the studied BLSS have been examined for different chemical components.

  5. 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.

  6. 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.

  7. 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...

  8. Analytical Advection-Dispersion Model for Transport and Plant Uptake of Solutes in the Root Zone

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We develop an advective-dispersive solute transport equation that includes plant uptake of water and solute, and present an analytical solution. Assumptions underlying the transport model include linear solute sorption, first-order plant uptake, and a uniform soil water content. We examine the lat...

  9. 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...

  10. 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.

  11. Advection of magnetic flux by accretion disks around neutron stars

    NASA Astrophysics Data System (ADS)

    Flores-Tulian, S.; Reisenegger, A.

    The aim of our research is to address why millisecond pulsars have relatively weak surface magnetic fields, of about 10^8 G, with a narrow spread. We propose that the accretion of plasma from the companion star fully screens the original neutron star field, but the accretion disk carries additional magnetic flux from the companion star, or itself can generate field by means of dynamo processes. For a strongly magnetized star, the field prevents the disk from approaching the star. The accretion is along the field lines and deposits the matter on the polar cap. Then, the accreted plasma flows, dragging with itself the magnetic field lines, from the pole to the equator (Payne & Melatos 2004). In a following stage, when the star becomes non-magnetic, because the field has been buried, the disk touches the star. We suggest that some effective mechanism of magnetic flux transport such as that proposed by Spruit & Uzdensky 2005 (or Bisnovatyi-Kogan & Lovelace 2007), operates and necessarily leads to a "strongly magnetized disk''. It becomes laminar because the magneto-rotational instability saturates (it is considered to be responsible for turbulence in the disk), and the magnetic difussivity is negligible. Then, the loss of angular momentum allowing the accretion is only caused by the magneto-centrifugal disk-wind (Blandford & Payne 1982). Meanwhile, the wind-driven transport of the magnetic flux by the disk re-magnetizes the star. This process continues until the Lorentz force due to the star's magnetic field forbids any further accretion of matter and magnetic flux, in the Ideal Magneto-Hydro-Dynamics approach. Additional of material can fall onto the star (but at lower rate) if some instability process sets in, allowing the diffusion of mass through the magnetic field lines (e.g the Interchange Instability, Spruit & Taam 1990). All these processes might lead to an asymptotic magnetic field of 10^8 G,as is inferred from observations. We are developing a self

  12. 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.

  13. 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.

  14. Quantification of numerical diffusivity due to TVD schemes in the advection equation

    NASA Astrophysics Data System (ADS)

    Bidadi, Shreyas; Rani, Sarma L.

    2014-03-01

    In this study, the numerical diffusivity νnum inherent to the Roe-MUSCL scheme has been quantified for the scalar advection equation. The Roe-MUSCL scheme employed is a combination of: (1) the standard extension of the original Roe's formulation to the advection equation, and (2) van Leer's Monotone Upwind Scheme for Conservation Laws (MUSCL) technique that applies a linear variable reconstruction in a cell along with a scaled limiter function. An explicit expression is derived for the numerical diffusivity in terms of the limiter function, the distance between the cell centers on either side of a face, and the face-normal velocity. The numerical diffusivity formulation shows that a scaled limiter function is more appropriate for MUSCL in order to consistently recover the central-differenced flux at the maximum value of the limiter. The significance of the scaling factor is revealed when the Roe-MUSCL scheme, originally developed for 1-D scenarios, is applied to 2-D scalar advection problems. It is seen that without the scaling factor, the MUSCL scheme may not necessarily be monotonic in multi-dimensional scenarios. Numerical diffusivities of the minmod, superbee, van Leer and Barth-Jesperson TVD limiters were quantified for four problems: 1-D advection of a step function profile, and 2-D advection of step, sinusoidal, and double-step profiles. For all the cases, it is shown that the superbee scheme provides the lowest numerical diffusivity that is also most confined to the vicinity of the discontinuity. The minmod scheme is the most diffusive, as well as active in regions away from high gradients. As expected, the grid resolution study demonstrates that the magnitude and the spatial extent of the numerical diffusivity decrease with increasing resolution.

  15. Operator Splitting Implicit Integration Factor Methods for Stiff Reaction-Diffusion-Advection Systems

    PubMed Central

    Zhao, Su; Ovadia, Jeremy; Liu, Xinfeng; Zhang, Yong-Tao; Nie, Qing

    2011-01-01

    For reaction-diffusion-advection equations, the stiffness from the reaction and diffusion terms often requires very restricted time step size, while the nonlinear advection term may lead to a sharp gradient in localized spatial regions. It is challenging to design numerical methods that can efficiently handle both difficulties. For reaction-diffusion systems with both stiff reaction and diffusion terms, implicit integration factor (IIF) method and its higher dimensional analog compact IIF (cIIF) serve as an efficient class of time-stepping methods, and their second order version is linearly unconditionally stable. For nonlinear hyperbolic equations, weighted essentially non-oscillatory (WENO) methods are a class of schemes with a uniformly high-order of accuracy in smooth regions of the solution, which can also resolve the sharp gradient in an accurate and essentially non-oscillatory fashion. In this paper, we couple IIF/cIIF with WENO methods using the operator splitting approach to solve reaction-diffusion-advection equations. In particular, we apply the IIF/cIIF method to the stiff reaction and diffusion terms and the WENO method to the advection term in two different splitting sequences. Calculation of local truncation error and direct numerical simulations for both splitting approaches show the second order accuracy of the splitting method, and linear stability analysis and direct comparison with other approaches reveals excellent efficiency and stability properties. Applications of the splitting approach to two biological systems demonstrate that the overall method is accurate and efficient, and the splitting sequence consisting of two reaction-diffusion steps is more desirable than the one consisting of two advection steps, because CWC exhibits better accuracy and stability. PMID:21666863

  16. High-resolution stochastic downscaling of climate models: simulating wind advection, cloud cover and precipitation

    NASA Astrophysics Data System (ADS)

    Peleg, Nadav; Fatichi, Simone; Burlando, Paolo

    2015-04-01

    A new stochastic approach to generate wind advection, cloud cover and precipitation fields is presented with the aim of formulating a space-time weather generator characterized by fields with high spatial and temporal resolution (e.g., 1 km x 1 km and 5 min). Its use is suitable for stochastic downscaling of climate scenarios in the context of hydrological, ecological and geomorphological applications. The approach is based on concepts from the Advanced WEather GENerator (AWE-GEN) presented by Fatichi et al. (2011, Adv. Water Resour.), the Space-Time Realizations of Areal Precipitation model (STREAP) introduced by Paschalis et al. (2013, Water Resour. Res.), and the High-Resolution Synoptically conditioned Weather Generator (HiReS-WG) presented by Peleg and Morin (2014, Water Resour. Res.). Advection fields are generated on the basis of the 500 hPa u and v wind direction variables derived from global or regional climate models. The advection velocity and direction are parameterized using Kappa and von Mises distributions respectively. A random Gaussian fields is generated using a fast Fourier transform to preserve the spatial correlation of advection. The cloud cover area, total precipitation area and mean advection of the field are coupled using a multi-autoregressive model. The approach is relatively parsimonious in terms of computational demand and, in the context of climate change, allows generating many stochastic realizations of current and projected climate in a fast and efficient way. A preliminary test of the approach is presented with reference to a case study in a complex orography terrain in the Swiss Alps.

  17. 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...

  18. 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. ...

  19. 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...

  20. 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)

  1. 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

  2. Development of anion-exchange/reversed-phase high performance liquid chromatography-inductively coupled plasma-mass spectrometry methods for the speciation of bio-available iodine and bromine from edible seaweed.

    PubMed

    Romarís-Hortas, Vanessa; Bermejo-Barrera, Pilar; Moreda-Piñeiro, Antonio

    2012-05-01

    Anion exchange high performance liquid chromatography hyphenated with inductively coupled plasma-mass spectrometry has been novelly applied to assess inorganic (iodide and iodate) and organic (3-iodotyrosine - MIT, and 3,5-diiodotyrosine - DIT) iodine species in a single chromatographic run. The optimized operating conditions (Dionex IonPac AS7, gradient elution with 175 mM ammonium nitrate plus 15% (v/v) methanol, pH 3.8, as a mobile phase and flow rates within the 0.5-1.5 mL min(-1) range) have also been used to perform inorganic bromine speciation analysis (bromide and bromate). The developed method has been applied for determining the bio-available contents of iodine and bromine species in dialyzates from edible seaweed. Reverse phase high performance liquid chromatography (Zorbax Eclipse XDB-C8, gradient elution with 0.2% (m/m) acetic acid, and 0.2% (m/m) acetic acid in methanol, as mobile phases, and a constant flow rate of 0.75 mL min(-1)) also hyphenated with inductively coupled plasma-mass spectrometry was used to confirm the presence of organic iodine species (MIT and DIT) in the dialyzates. The verification of the presence of iodinated amino acids (MIT and DIT) in the extracts was also performed by reverse phase high performance liquid chromatography-electrospray ionization-mass spectrometry (LTQ Orbitrap). The developed methods have provided good repeatability (RSD values lower than 10% for both anion exchange and reverse phase separations) and analytical recoveries within the 90-105% range for all cases. The in vitro bio-availability method consisted of a simulated gastric and an intestinal digestion/dialysis (10 kDa molecular weight cut-off - MWCO) two-stage procedure. Iodide and MIT were the main bio-available species quantified, whereas bromide was the major bromine species found in the extracts.

  3. 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.

  4. Straining and advection contributions to the mixing process of the Patos Lagoon coastal plume, Brazil

    NASA Astrophysics Data System (ADS)

    Marques, Wilian C.; Fernandes, Elisa H. L.; Moller, Osmar O.

    2010-06-01

    The Southern Brazilian Shelf is a region influenced by freshwater, and the evolution of stratification can present important ecological consequences in this area. The aim of this paper was to investigate the importance of straining and advection processes that affect the stratification and destratification of the water column along the Southern Brazilian inner shelf, a region that is influenced by the Patos Lagoon coastal plume. The study was carried out through 3-D numerical modeling experiments and the results were analyzed using the potential energy anomaly equation and wavelet analysis. Results showed that the potential energy anomaly showed strong variability over a time scale of several days and followed the wind pattern over the study region, and was accompanied by the monthly modulation of river discharge and remote effects associated with variability in oceanic circulation. However, the most important events in synoptic time scales occurred in periods shorter than 20 days and were coincident with the passage of meteorological systems over the study region. Straining and advection were the most important mechanisms for the evolution of stratification in the adjacent coastal region. Nonlinearities and dispersion terms were as important as modulation effects, mainly during periods of high fluvial discharge. Close to the Patos Lagoon mouth, vertical advection explained most of the stratification evolution, due to the morphological characteristics in this region. In the frontal region and far field of the plume, the following two regions must be considered: the northeast part, which is characterized by the convergence of the coastal currents and ebb flows associated with the freshwater discharge that promote the domination of the cross-shore straining and advection, and the southwest part, which is controlled by the coastal currents that result in the domination by alongshore straining and advection and cross-shore advection terms. Close to the mouth of the

  5. [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).

  6. [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

  7. Two-dimensional atmospheric transport and chemistry model - Numerical experiments with a new advection algorithm

    NASA Technical Reports Server (NTRS)

    Shia, Run-Lie; Ha, Yuk Lung; Wen, Jun-Shan; Yung, Yuk L.

    1990-01-01

    Extensive testing of the advective scheme proposed by Prather (1986) has been carried out in support of the California Institute of Technology-Jet Propulsion Laboratory two-dimensional model of the middle atmosphere. The original scheme is generalized to include higher-order moments. In addition, it is shown how well the scheme works in the presence of chemistry as well as eddy diffusion. Six types of numerical experiments including simple clock motion and pure advection in two dimensions have been investigated in detail. By comparison with analytic solutions, it is shown that the new algorithm can faithfully preserve concentration profiles, has essentially no numerical diffusion, and is superior to a typical fourth-order finite difference scheme.

  8. Oxygen Advection and Diffusion in a Three Dimensional Vascular Anatomical Network

    PubMed Central

    Fang, Qianqian; Sakadžić, Sava; Ruvinskaya, Lana; Devor, Anna; Dale, Anders M.; Boas, David A.

    2008-01-01

    There is an increasing need for quantitative and computationally affordable models for analyzing tissue metabolism and hemodynamics in microvascular networks. In this work, we develop a hybrid model to solve for the time-varying oxygen advection-diffusion equation in the vessels and tissue. To obtain a three-dimensional temporal evolution of tissue oxygen concentration for realistic complex vessel networks, we used a graph-based advection model combined with a finite-element based diffusion model and an implicit time-advancing scheme. We validated this algorithm for both static and dynamic conditions. We also applied it to a complex vascular network obtained from a rodent somatosensory cortex. Qualitative agreement was found with in-vivo experiments. PMID:18958033

  9. 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.

  10. The impact of advective transport by the South Indian Ocean Countercurrent on the Madagascar plankton bloom

    NASA Astrophysics Data System (ADS)

    Huhn, F.; von Kameke, A.; Pérez-Muñuzuri, V.; Olascoaga, M. J.; Beron-Vera, F. J.

    2012-03-01

    Based on ten years (1998-2007) of satellite ocean color data we analyze the spatiotemporal patterns in the seasonal Madagascar plankton bloom with respect to the advection of the recently discovered Southern Indian Ocean Countercurrent (SICC). In maps of Finite-time Lyapunov Exponents (FTLE) and Finite-Time Zonal Drift (FTZD) computed from altimetry derived velocities we observe a narrow zonal jet that starts at ˜25°S at the southern tip of Madagascar, an important upwelling region, and extends to the east further than the largest plankton blooms (˜2500 km). In bloom years, the jet coincides with large parts of the northern boundary of the plankton bloom, acting as a barrier to meridional transport. Our findings suggest that advection is an important and so far underestimated mechanism for the eastward propagation and the extent of the plankton bloom. This supports the hypothesis of a single nutrient source south of Madagascar.

  11. Effects of upstream-biased third-order space correction terms on multidimensional Crowley advection schemes

    NASA Technical Reports Server (NTRS)

    Schlesinger, R. E.

    1985-01-01

    The impact of upstream-biased corrections for third-order spatial truncation error on the stability and phase error of the two-dimensional Crowley combined advective scheme with the cross-space term included is analyzed, putting primary emphasis on phase error reduction. The various versions of the Crowley scheme are formally defined, and their stability and phase error characteristics are intercompared using a linear Fourier component analysis patterned after Fromm (1968, 1969). The performances of the schemes under prototype simulation conditions are tested using time-dependent numerical experiments which advect an initially cone-shaped passive scalar distribution in each of three steady nondivergent flows. One such flow is solid rotation, while the other two are diagonal uniform flow and a strongly deformational vortex.

  12. 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.

  13. Advection and the Efficiency of Spectral Energy Transfer in Two-Dimensional Turbulence.

    PubMed

    Fang, Lei; Ouellette, Nicholas T

    2016-09-01

    We report measurements of the geometric alignment of the small-scale turbulent stress and the large-scale rate of strain that together lead to the net flux of energy from small scales to large scales in two-dimensional turbulence. We find that the instantaneous alignment between these two tensors is weak and, thus, that the spectral transport of energy is inefficient. We show, however, that the strain rate is much better aligned with the stress at times in the past, suggesting that the differential advection of the two is responsible for the inefficient spectral transfer. We provide evidence for this conjecture by measuring the alignment statistics conditioned on weakly changing stress history. Our results give new insight into the relationship between scale-to-scale energy transfer, geometric alignment, and advection in turbulent flows.

  14. 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.

  15. 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.

  16. 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.

  17. Comparison of Nonlinear and Linear Stabilization Schemes for Advection-Diffusion Equations

    NASA Astrophysics Data System (ADS)

    Grove, R. R.; Heister, T.

    2015-12-01

    Accurately solving advection-diffusion equations that appear in the finite element discretization of a mantle convection simulation is an important computational issue to the computational geoscience community. This is because it allows for users studying mantle convection to create reliable simulations for something as small and simple as a 2D simulation on their personal laptop to something as complex as a massively parallel 3D simulation on their university supercomputer. Standard finite element discretizations of advection-diffusion equations introduce unphysical oscillations around steep gradients. Therefore, stabilization must be added to the discrete formulation to obtain correct solutions. Using the open source scientific library ASPECT, the SUPG and Entropy Viscosity schemes are compared using stationary and non-stationary test equations. Differences in maximum overshoot and undershoot, smear, and convergence orders are compared to see if improvements can be made to the existing numerical method existing in ASPECT.

  18. Advection and the Efficiency of Spectral Energy Transfer in Two-Dimensional Turbulence

    NASA Astrophysics Data System (ADS)

    Fang, Lei; Ouellette, Nicholas T.

    2016-09-01

    We report measurements of the geometric alignment of the small-scale turbulent stress and the large-scale rate of strain that together lead to the net flux of energy from small scales to large scales in two-dimensional turbulence. We find that the instantaneous alignment between these two tensors is weak and, thus, that the spectral transport of energy is inefficient. We show, however, that the strain rate is much better aligned with the stress at times in the past, suggesting that the differential advection of the two is responsible for the inefficient spectral transfer. We provide evidence for this conjecture by measuring the alignment statistics conditioned on weakly changing stress history. Our results give new insight into the relationship between scale-to-scale energy transfer, geometric alignment, and advection in turbulent flows.

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

    NASA Astrophysics Data System (ADS)

    Rood, Richard B.

    1987-02-01

    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.

  20. 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.

  1. Advection and the Efficiency of Spectral Energy Transfer in Two-Dimensional Turbulence.

    PubMed

    Fang, Lei; Ouellette, Nicholas T

    2016-09-01

    We report measurements of the geometric alignment of the small-scale turbulent stress and the large-scale rate of strain that together lead to the net flux of energy from small scales to large scales in two-dimensional turbulence. We find that the instantaneous alignment between these two tensors is weak and, thus, that the spectral transport of energy is inefficient. We show, however, that the strain rate is much better aligned with the stress at times in the past, suggesting that the differential advection of the two is responsible for the inefficient spectral transfer. We provide evidence for this conjecture by measuring the alignment statistics conditioned on weakly changing stress history. Our results give new insight into the relationship between scale-to-scale energy transfer, geometric alignment, and advection in turbulent flows. PMID:27636478

  2. Scalar variance decay in chaotic advection and Batchelor-regime turbulence.

    PubMed

    Fereday, D R; Haynes, P H; Wonhas, A; Vassilicos, J C

    2002-03-01

    The decay of the variance of a diffusive scalar in chaotic advection flow (or equivalently Batchelor-regime turbulence) is analyzed using a model in which the advection is represented by an inhomogeneous baker's map on the unit square. The variance decays exponentially at large times, with a rate that has a finite limit as the diffusivity kappa tends to zero and is determined by the action of the inhomogeneous map on the gravest Fourier modes in the scalar field. The decay rate predicted by recent theoretical work that follows scalar evolution in linear flow and then averages over all stretching histories is shown to be incorrect. The exponentially decaying scalar field is shown to have a spatial power spectrum of the form P(k) approximately k(-sigma) at wave numbers small enough for diffusion to be neglected, with sigma<1.

  3. Two-dimensional atmospheric transport and chemistry model: numerical experiments with a new advection algorithm.

    PubMed

    Shia, R L; Ha, Y L; Wen, J S; Yung, Y L

    1990-05-20

    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. We generalize the original scheme to include higher-order moments. In addition, we show 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.

  4. Long-term Rates of Mafic Magma Emplacement and Implications for Heat Advection

    NASA Astrophysics Data System (ADS)

    White, S. M.; Spera, F. J.; Crisp, J. A.

    2003-12-01

    Rates of magmatism (magma emplacement rate) including both volcanic products and intrusive bodies were obtained for terrestrial petrotectonic systems where reliable volumes can be estimated and geochronological data exist. Approximately 50 estimates of magma emplacement rates have been extracted from the literature published between 1982 and 2003 for persistent basaltic systems with durations from 1 ka to ~5 Ma. Although the volcanic output is highly episodic, the data indicate that the mass output rate at individual hotspot volcanoes is on the order of 10-3 km3/yr when averaged over several thousand years. This differs from the estimated output rates of large igneous provinces, such as continental flood basalts and oceanic plateaus, which have maximal output rates on the order of 1 km3/yr per province. For globally averaged mid-ocean ridges, the total volcanic emplacement rate is only 10-6 km3/yr/100 km of ridge. Ratios of intrusive to extrusive emplacement are subject to much uncertainty, but generally lie in the range 6:1 to 10:1 for most crustal mafic magma systems. Recent seismic, geodetic, and gravity work suggests that there may be large regions of underplating and storage in subcrustal magma chambers in areas of basaltic volcanism previously not widely considered in intrusive volume estimates that may increase most of these ratios to 10:1. Rates of magmatism may be translated into excess heat flows for specific magmatic provinces to obtain estimates of advected heat transport via magmatism at regional scales over magmatic province timescales. For mafic eruption rate V and an intrusive/extrusive ratio of R, the volumetric rate of magma flow into the crust is RV. The excess heat power (J/yr) associated with magma transport from mantle to crust is RVρ δ T [Cp + δ h/(Tliquidus-Tsolidus)] where δ T is the temperature difference between the magma and host crust, δ h is the enthalpy of crystallization (250-400 kJ/kg dependent on magma composition), ρ is

  5. 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

  6. 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.

  7. Real-time HD Exchange Kinetics of Proteins from Buffered Aqueous Solution with Electrothermal Supercharging and Top-Down Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Going, Catherine C.; Xia, Zijie; Williams, Evan R.

    2016-06-01

    Electrothermal supercharging (ETS) with electrospray ionization produces highly charged protein ions from buffered aqueous solutions in which proteins have native folded structures. ETS increases the charge of ribonuclease A by 34%, whereas only a 6% increase in charge occurs for a reduced-alkylated form of this protein, which is unfolded and its structure is ~66% random coil in this solution. These results indicate that protein denaturation that occurs in the ESI droplets is the primary mechanism for ETS. ETS does not affect the extent of solution-phase hydrogen-deuterium exchange (HDX) that occurs for four proteins that have significantly different structures in solution, consistent with a droplet lifetime that is considerably shorter than observable rates of HDX. Rate constants for HDX of ubiquitin are obtained with a spatial resolution of ~1.3 residues with ETS and electron transfer dissociation of the 10+ charge-state using a single capillary containing a few μL of protein solution in which HDX continuously occurs. HDX protection at individual residues with ETS HDX is similar to that with reagent supercharging HDX and with solution-phase NMR, indicating that the high spray potentials required to induce ETS do not lead to HD scrambling.

  8. Trace enrichment and characterization of polyphenols in Bistort Rhizoma using weak anion-exchange solid phase extraction and high performance liquid chromatography-quadrupole time-of-flight mass spectrometry.

    PubMed

    Wang, Shao-Teng; Yang, Hua; Gao, Wen; Li, Hui-Jun; Li, Ping

    2016-02-01

    The analysis of trace constituents in herbal medicines has always been a challenge due to complex matrices and structural diversities. In this work, a pH-sensitive solid phase extraction (SPE) procedure capable of enriching trace polyphenols in Bistort Rhizoma (BR) was proposed and preliminary chemical characterization was accomplished by high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (HPLC-QTOF MS). A weak anion-exchange SPE column packed with divinylbenzene/vinylpyrrolidone bonding quaternary amine group was employed for anionic extraction, and the target fraction was obtained by eluting with acidic methanol (apparent pH 1.9). On the other hand, the MS/MS fragmentation rules of four reference polyphenols in negative ion mode were outlined. Using these rules, a total of 31 polyphenols including 20 benzoyl derivatives and 11 caffeoyl derivatives were screened out from BR extract, of which 26 trace members were found for the first time in this herb. Those findings demonstrated that the anion-exchange SPE could enhance the detection capability and selectivity for plant polyphenols in the LC-MS analysis and the strategy for deducing structures could be applied for analysis of polyphenols in BR and other herbal medicines.

  9. [Separation and identification of beta-casein from Chinese human milk by ion exchange chromatography-matrix-assisted laser desorption/ionization time of flight/time of flight mass spectrometry].

    PubMed

    Huang, Yu; Ren, Haowei; Liu, Biao; Liu, Ning; Li, Meng; Wang, Dongmao

    2013-05-01

    The selective precipitation of whole casein from skimmed milk was achieved by the addition of calcium salt under acidic pH. The effects of pH, centrifugal force and final concentration of CaCl2 on the separation of casein were studied by measuring the purity of final products using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The results showed that casein with the highest purity could be obtained with the pH of 4.3, the centrifugal force of 10 400 g and the final concentration of CaCl2 of 60 mmol/L. The casein was processed with DEAE anion exchange chromatography and three peaks were obtained. Then the third peak (peak III) was identified with Western-Blot method and matrix-assisted laser desorption/ionization time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS). The identification of Western-Blot showed that peak III can combine with the specificity of human milk beta-casein antibody, and it is proved to be human milk beta-casein. The fingerprints of peak III were nalyzed by Mascot searching, and the sequence coverage was 50%, further supporting it is human milk beta-casein. In conclusion, an effective method to obtain human milk beta-casein from milk samples through DEAE anion exchange chromatography was established, and it is suitable for the proteomics research requirements of the beta-casein from human milk.

  10. Role of advection in Arctic Ocean lower trophic dynamics: A modeling perspective

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    The Arctic Ocean (AO) is an oligotrophic system with a pronounced subsurface Chl-a maximum dominating productivity over the majority of the basin. Strong haline stratification of the AO and substantial ice cover suppress vertical mixing and restrict the vertical supply of nutrients to the photic zone. In such a vertically stratified oligotrophic system, the horizontal supply of nutrients by advection plays an important role in sustaining primary production. In this paper, we attempt to characterize the role of nutrient advection in the maintenance of the subsurface Chl-a maximum, using timescales to determine the connectivity between the photic zone of the deep AO, nutrient-rich Pacific and Atlantic inflow waters, and bottom waters of the wide continental shelves of the AO. Our study uses output from a general circulation model, Nucleus for European Modeling of the Ocean, coupled to a model of ocean biogeochemistry, Model of Ecosystem Dynamics, carbon Utilization, Sequestration, and Acidification. A Lagrangian particle tracking approach is used to back-track water from where it forms subsurface Chl-a maxima to the points of entry into the AO and to analyze nutrient transformation along the route. Our experiments show that advective timescales linking subsurface layers of the central AO with the nutrient-rich Pacific and Atlantic waters do not exceed 15-20 years and that the advective supply of shelf nutrients to the deep AO occurs on the timescale of about 5 years. We show substantial role of the continental shelf pump in sustaining up to 20% of total AO primary production.

  11. Trophodynamic and advective influences on Georges Bank larval cod and haddock

    NASA Astrophysics Data System (ADS)

    Werner, Francisco E.; Ian Perry, R.; Gregory Lough, R.; Naimie, Christopher E.

    Using a model-based approach, the relative effects of advective and trophodynamic (feeding and growth) processes are considered on populations of larval cod ( Gadus morhua) and haddock ( Melanogrammus aeglefinus) on Georges Bank. Building on previous studies that describe the role of advection, this study incorporates trophodynamic relationships to examine starvation mortality and growth rates at the level of individual larvae on the Bank. Estimates of prey concentrations and flow fields appropriate for late winter/early spring are used. Both trophodynamic processes and advection influence larval losses from the Bank where, in the absence of starvation, advective losses are on the order of one-fifth of the eggs and larvae spawned on the Bank. Starvation is most important in the first feeding larvae and is much reduced for older larvae. The contact rates between larval fish and zooplankton prey when turbulence is included are 2-5 times greater than the contact rates with no turbulence, and allow the model cod larvae to achieve growth rates similar to those observed on the Bank, although mean rates for larval haddock are still lower than observed. Turbulence-enhanced contact rates are thus determined to be a necessary component in our description of the growth of cod and haddock larvae on Georges Bank. Model cod larvae with growth rates comparable to those observed in the field are located below the surface layer (deeper than 25 m) and inside the 60 m isobath. The region of highest retention due to circulation processes (Werner et al., 1993; Fisheries Oceanography, 2, 43-64) coincides with the region of highest growth rates and highest larval survival. Therefore, there is a complementary interaction between trophodynamic and circulation processes, with those larvae most likely to remain on the Bank also being those in the most favorable feeding regions. Haddock larvae require higher prey densities than cod larvae to survive.

  12. Carbon dioxide seasonality in dynamically ventilated caves: the role of advective fluxes

    NASA Astrophysics Data System (ADS)

    Lang, Marek; Faimon, Jiří; Godissart, Jean; Ek, Camille

    2016-07-01

    The seasonality in cave CO2 levels was studied based on (1) a new data set from the dynamically ventilated Comblain-au-Pont Cave (Dinant Karst Basin, Belgium), (2) archive data from Moravian Karst caves, and (3) published data from caves worldwide. A simplified dynamic model was proposed for testing the effect of all conceivable CO2 fluxes on cave CO2 levels. Considering generally accepted fluxes, i.e., the direct diffusive flux from soils/epikarst, the indirect flux derived from dripwater degassing, and the input/output fluxes linked to cave ventilation, gives the cave CO2 level maxima of 1.9 × 10-2 mol m-3 (i.e., ˜ 440 ppmv), which only slightly exceed external values. This indicates that an additional input CO2 flux is necessary for reaching usual cave CO2 level maxima. The modeling indicates that the additional flux could be a convective advective CO2 flux from soil/epikarst driven by airflow (cave ventilation) and enhanced soil/epikarstic CO2 concentrations. Such flux reaching up to 170 mol s-1 is capable of providing the cave CO2 level maxima up to 3 × 10-2 mol m-3 (70,000 ppmv). This value corresponds to the maxima known from caves worldwide. Based on cave geometry, three types of dynamic caves were distinguished: (1) the caves with the advective CO2 flux from soil/epikarst at downward airflow ventilation mode, (2) the caves with the advective soil/epikarstic flux at upward airflow ventilation mode, and (3) the caves without any soil/epikarstic advective flux. In addition to CO2 seasonality, the model explains both the short-term and seasonal variations in δ13C in cave air CO2.

  13. Shadowing and the role of small diffusivity in the chaotic advection of scalars

    NASA Technical Reports Server (NTRS)

    Klapper, I.

    1992-01-01

    Using techniques from shadowing theory, the solution of the scalar advection-diffusion equation is studied. It is shown that, under certain circumstances, the effect of small scalar diffusivity is to smooth the zero-diffusivity solution by averaging local fine-scaled structure against a Gaussian. The method of study depends on shadowing and thus fails for nonuniformly stretching systems, its failure suggesting the ways in which the effects of asymptotically small molecular diffusion can become nonlocal in chaotic fluid flows.

  14. On the kinematics and efficiency of advective mixing during gastric digestion - A numerical analysis.

    PubMed

    Ferrua, Maria J; Xue, Zhengjun; Singh, R Paul

    2014-11-28

    The mixing performance of gastric contents during digestion is expected to have a major role on the rate and final bioavailability of nutrients within the body. The aim of this study was to characterize the ability of the human stomach to advect gastric contents with different rheological properties. The flow behavior of two Newtonian fluids (10(-3)Pas, 1Pas) and a pseudoplastic solution (K=0.223Pas(0.59)) during gastric digestion were numerically characterized within a simplified 3D model of the stomach geometry and motility during the process (ANSYS-FLUENT). The advective performances of each of these gastric flows were determined by analyzing the spatial distribution and temporal history of their stretching abilities (Lagrangian analysis). Results illustrate the limited influence that large retropulsive and vortex structures have on the overall dynamics of gastric flows. Even within the distal region, more than 50% of the flow experienced velocity and shear values lower than 10% of their respective maximums. While chaotic, gastric advection was always relatively poor (with Lyapunov exponents an order of magnitude lower than those of a laminar stirred tank). Contrary to expectations, gastric rheology had only a minor role on the advective properties of the flow (particularly within the distal region). As viscosity increased above 1St, the role of fluid viscosity became largely negligible. By characterizing the fluid dynamic and mixing conditions that develop during digestion, this work will inform the design of novel in vitro systems of enhanced biomechanical performance and facilitate a more accurate diagnosis of gastric digestion processes. PMID:25446267

  15. Approximate Solution of Time-Fractional Advection-Dispersion Equation via Fractional Variational Iteration Method

    PubMed Central

    İbiş, Birol

    2014-01-01

    This paper aims to obtain the approximate solution of time-fractional advection-dispersion equation (FADE) involving Jumarie's modification of Riemann-Liouville derivative by the fractional variational iteration method (FVIM). FVIM provides an analytical approximate solution in the form of a convergent series. Some examples are given and the results indicate that the FVIM is of high accuracy, more efficient, and more convenient for solving time FADEs. PMID:24578662

  16. The effect of passive mixing on pressure drop and oxygen mass fraction using opposing channel flow field design in a Proton Exchange Membrane Fuel Cell

    NASA Astrophysics Data System (ADS)

    Singh, Anant Bir

    This study investigates a flow field with opposing channel design. Previous studies on flow field designs have been focused on improving fuel utilization which often leads to increased pressure drop. This increased pressure drop is typical because standard designs employ either a single flow channel to clear blockages or dead end condition to force the flow through the gas diffusion layer. The disadvantage with these designs is the increased resistance to the flow which requires higher pressure, which becomes a parasitic loss that lowers the system efficiency. For this study the focus was to reduce the pressure drop by providing a less resistive path to the flow. To achieve a less resistive path, the inlet channel was split into two opposing channels. These channels are then recombined only to be split again for the next leg. Therefore, the split channel design should reduce the pressure drop which reduces the parasitic load and ultimately contributes to higher system efficiency. In addition the recombining of the streams at each leg should induce mixing. Having opposing channels should also increase cross flow under the lands to reduce mass transfer loses. The cathode side of the fuel cell is especially sensitive to the mass transport losses since air (oxygen mixed with nitrogen) is used for supplying oxygen unlike the anode side which uses pure hydrogen. To test the hypothesis of having benefits from an opposing channel design, both an experimental and analytical approach was taken. For the experiment, a serpentine flow field and opposing channel flow field plates were compared over several flow rates with compressed air. To test the hypothesis of increased mass transfer, the two flow fields were modeled using a CFD software package, COMSOL. It was found that the opposing channel configuration for high flow rate with multiple entry and exit conditions exhibited significant improvement over the single serpentine channel. Pressure drop was ⅓ less than the

  17. The Advective Flux and Temporal Evolution of Aerosols from the Western Pacific Rim as Observed during TRACE-P

    NASA Astrophysics Data System (ADS)

    Anderson, B. E.; Jordan, C. E.; Grant, W. B.; Browell, E. V.; Hudgins, C. H.; Winstead, E. L.; Thornhill, K. L.

    2002-12-01

    The 2001, NASA Transport and Chemical Evolution over the Pacific (TRACE-P) experiment was conducted during late winter and early spring, the time of year when eastward transport of dust and pollution from southern and central Asia reaches a maximum. From bases of operation in Hong Kong, Japan, and Hawaii, extensive measurements of trace species concentrations and characteristics were made from aboard a P-3B and DC-8 aircraft as they flew coordinated sampling missions within air masses at varying distances from the Asian coast and at altitudes ranging from near surface to over 12 km. Data recorded aboard the DC-8 included total condensation nuclei (CN) number densities and fractional volatility; aerosol size distributions, composition and optical properties; and multi-wavelength profiles of polarized, aerosol backscatter. Examining these data in light of simultaneous meteorological and chemical species measurements, we have calculated the advective flux and mean values of aerosol mass and physical properties at various locations within the Western Pacific Basin. At distances >100 km offshore, we find that the highest fluxes of sub-micron particles occurred below 2 km in the region downwind of Shanghai. These air masses exhibited CN concentrations approaching 50,000 cm-3 and visible scattering coefficients in excess of 200 Mm-1. For near-shore sampling between 26° and 36°N within this height range, these parameters averaged ~8,000 cm-3 and 130 Mm-, respectively, . As a result of dilution, surface deposition, and precipitation scavenging, these values rapidly diminished during eastward transport so that parcels sampled at low altitudes >1500 km from land typically contained ~1000 cm-3 CN and exhibited scattering coefficients <30 Mm-1. Because of the decreased strength of loss processes and greater atmospheric stability, parcels sampled in the 2- to 7-km height range were more apt to maintain their initial aerosol signatures during long-range transport.

  18. Phase mixing vs. nonlinear advection in drift-kinetic plasma turbulence

    NASA Astrophysics Data System (ADS)

    Schekochihin, A.; Parker, J.; Highcock, E.; Dellar, P.; Kanekar, A.; Dorland, W.; Hammett, G.; Loureiro, N.; Staines, C.; Stipani, L.

    2015-11-01

    A scaling theory of drift-kinetic turbulence in a weakly collisional plasma is proposed, with account both of the nonlinear advection of the perturbed particle distribution by the fluctuating ExB flow and of its parallel phase mixing, which in a linear problem causes Landau damping. It is found that little free energy leaks into high velocity moments of the distribution, rendering the turbulence in the energetically relevant part of the wave-number space essentially fluid-like. The velocity-space free-energy spectra expressed in terms of Hermite moments are steep power laws and so the energy content of the phase space does not diverge and collisional heating due to long-wavelength perturbations vanishes at inifinitesimal collisionality (both in contrast with the linear problem). The ability of the energy to stay in the low moments is facilitated by ``anti-phase-mixing,'' which in the nonlinear system is due to the stochastic version of plasma echo (the advecting flow couples the phase-mixing and anti-phase-mixing perturbations). The partitioning of the wave-number space between the (energetically dominant) region where this is the case and the region where linear phase mixing wins its competition with nonlinear advection is governed by the ``critical balance'' between linear and nonlinear timescales, which for high Hermite moments splits into two thresholds, one demarcating the wave-number region where phase mixing predominates, the other where plasma echo does.

  19. Reactive-Diffusive-Advective Traveling Waves in a Family of Degenerate Nonlinear Equations

    PubMed Central

    Sánchez-Garduño, Faustino

    2016-01-01

    This paper deals with the analysis of existence of traveling wave solutions (TWS) for a diffusion-degenerate (at D(0) = 0) and advection-degenerate (at h′(0) = 0) reaction-diffusion-advection (RDA) equation. Diffusion is a strictly increasing function and the reaction term generalizes the kinetic part of the Fisher-KPP equation. We consider different forms of the convection term h(u): (1)  h′(u) is constant k, (2)  h′(u) = ku with k > 0, and (3) it is a quite general form which guarantees the degeneracy in the advective term. In Case 1, we prove that the task can be reduced to that for the corresponding equation, where k = 0, and then previous results reported from the authors can be extended. For the other two cases, we use both analytical and numerical tools. The analysis we carried out is based on the restatement of searching TWS for the full RDA equation into a two-dimensional dynamical problem. This consists of searching for the conditions on the parameter values for which there exist heteroclinic trajectories of the ordinary differential equations (ODE) system in the traveling wave coordinates. Throughout the paper we obtain the dynamics by using tools coming from qualitative theory of ODE.

  20. Super-diffusion versus competitive advection processes on the solar surface

    NASA Astrophysics Data System (ADS)

    Del Moro, Dario; Berrilli, Francesco; Giovannelli, Luca; Scardigli, Stefano; Giannattasio, Fabio; Consolini, Giuseppe; Lepreti, Fabio

    2016-04-01

    From the analysis of the displacement spectrum of magnetic element, 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. 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. 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 confronted those results also to simulation of passive tracers advection. 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 also the simulation shows a super-diffusive displacement spectrum: its competitive advection process can reproduce the signature of super-diffusion. Therefore, it is not necessary to hypothesize a totally developed turbulence regime to explain the motion of the magnetic elements on the solar surface.

  1. Solving turbulent diffusion flame in cylindrical frame applying an improved advective kinetics scheme

    NASA Astrophysics Data System (ADS)

    Darbandi, Masoud; Ghafourizadeh, Majid

    2015-12-01

    In this work, we derive a few new advective flux approximation expressions, apply them in a hybrid finite-volume-element (FVE) formulation, and solve the turbulent reacting flow governing equations in the cylindrical frame. To derive these advective-kinetic-based expressions, we benefit from the advantages of a physical influence scheme (PIS) basically, extend it to the cylindrical frame suitably, and approximate the required advective flux terms at the cell faces more accurately. The present numerical scheme not only respects the physics of flow correctly but also resolves the pressure-velocity coupling problem automatically. We also suggest a bi-implicit algorithm to solve the set of coupled turbulent reacting flow governing equations, in which the turbulence and chemistry governing equations are solved simultaneously. To evaluate the accuracy of new derived FVE-PIS expressions, we compare the current solutions with other available numerical solutions and experimental data. The comparisons show that the new derived expressions provide some more advantages over the past numerical approaches in solving turbulent diffusion flame in the cylindrical frame. Indeed, the current method and formulations can be used to solve and analyze the turbulent diffusion flames in the cylindrical coordinates very reliably.

  2. Universal limiter for transient interpolation modeling of the advective transport equations: The ULTIMATE conservative difference scheme

    NASA Technical Reports Server (NTRS)

    Leonard, B. P.

    1988-01-01

    A fresh approach is taken to the embarrassingly difficult problem of adequately modeling simple pure advection. An explicit conservative control-volume formation makes use of a universal limiter for transient interpolation modeling of the advective transport equations. This ULTIMATE conservative difference scheme is applied to unsteady, one-dimensional scalar pure advection at constant velocity, using three critical test profiles: an isolated sine-squared wave, a discontinuous step, and a semi-ellipse. The goal, of course, is to devise a single robust scheme which achieves sharp monotonic resolution of the step without corrupting the other profiles. The semi-ellipse is particularly challenging because of its combination of sudden and gradual changes in gradient. The ULTIMATE strategy can be applied to explicit conservation schemes of any order of accuracy. Second-order schemes are unsatisfactory, showing steepening and clipping typical of currently popular so-called high resolution shock-capturing of TVD schemes. The ULTIMATE third-order upwind scheme is highly satisfactory for most flows of practical importance. Higher order methods give predictably better step resolution, although even-order schemes generate a (monotonic) waviness in the difficult semi-ellipse simulation. Little is to be gained above ULTIMATE fifth-order upwinding which gives results close to the ultimate for which one might hope.

  3. A Comparative Study of Indoor Radon Contributed by Diffusive and Advective Transport through Intact Concrete

    NASA Astrophysics Data System (ADS)

    Chauhan, R. P.; Kumar, Amit

    The present work is aimed that out of diffusive and advective transport which is dominant process for indoor radon entry under normal room conditions. For this purpose the radon diffusion coefficient and permeability of concrete were measured by specially designed experimental set up. The radon diffusion coefficient of concrete was measured by continuous radon monitor. The measured value was (3.78 ± 0.39)×10-8 m2/s and found independent of the radon gas concentration in source chamber. The radon permeability of concrete varied between 1.85×10-17 to 1.36×10-15 m2 for the bulk pressure difference fewer than 20 Pa to 73.3 kPa. From the measured diffusion coefficient and absolute permeability, the radon flux from the concrete surface having concentrations gradient 12-40 kBq/m3 and typical floor thickness 0.1 m was calculated by the application of Fick and Darcy laws. Using the measured flux attributable to diffusive and advective transport, the indoor radon concentration for a typical Indian model room having dimension (5×6×7) m3 was calculated under average room ventilation (0.63 h-1). The results showed that the contribution of diffusive transport through intact concrete is dominant over the advective transport, as expected from the low values of concrete permeability.

  4. Reactive-Diffusive-Advective Traveling Waves in a Family of Degenerate Nonlinear Equations

    PubMed Central

    Sánchez-Garduño, Faustino

    2016-01-01

    This paper deals with the analysis of existence of traveling wave solutions (TWS) for a diffusion-degenerate (at D(0) = 0) and advection-degenerate (at h′(0) = 0) reaction-diffusion-advection (RDA) equation. Diffusion is a strictly increasing function and the reaction term generalizes the kinetic part of the Fisher-KPP equation. We consider different forms of the convection term h(u): (1)  h′(u) is constant k, (2)  h′(u) = ku with k > 0, and (3) it is a quite general form which guarantees the degeneracy in the advective term. In Case 1, we prove that the task can be reduced to that for the corresponding equation, where k = 0, and then previous results reported from the authors can be extended. For the other two cases, we use both analytical and numerical tools. The analysis we carried out is based on the restatement of searching TWS for the full RDA equation into a two-dimensional dynamical problem. This consists of searching for the conditions on the parameter values for which there exist heteroclinic trajectories of the ordinary differential equations (ODE) system in the traveling wave coordinates. Throughout the paper we obtain the dynamics by using tools coming from qualitative theory of ODE. PMID:27689131

  5. Straining and advection contributions to the mixing process in the Patos Lagoon estuary, Brazil

    NASA Astrophysics Data System (ADS)

    Marques, Wilian C.; Fernandes, Elisa H. L.; Rocha, Luiz A. O.

    2011-03-01

    The estuarine area of coastal lagoons and freshwater-influenced regions presents periodically stratified and destratified conditions. The Patos Lagoon, one of the most important hydrological resources in South America, is located in the southernmost part of Brazil and exhibits such variable conditions. Therefore the aim of this study was to investigate the contributions of straining and advection to the modulation of stratification conditions in the Patos Lagoon estuarine region using potential energy anomaly budgets. This study was based a three-dimensional hydrodynamic numerical model that provided information for the potential energy anomaly equation and wavelet analysis. Results from the potential energy anomaly time series revealed strong variability over a timescale of several days following local wind action and the river discharge pattern. Each part of the estuary exhibited contrasting regimes that were spatially distributed with a different balance of terms. The upper part was dominated by along-shore currents associated with east-west wind component and gravitational flux. Contribution from cross-shore advection became important in the middle part of the estuary, where there was an increase in superficial area observed. The lower region was controlled by the north-south wind component being influenced by advection, cross-shore straining, and transversal circulation, suggesting that current velocity maintained transversal pressure gradients and further circulation. Nonlinear interactions between deviations in the dispersion terms and vertical density and velocity were important everywhere but were associated with modulation effects.

  6. A Petroleum Vapor Intrusion Model Involving Upward Advective Soil Gas Flow Due to Methane Generation.

    PubMed

    Yao, Yijun; Wu, Yun; Wang, Yue; Verginelli, Iason; Zeng, Tian; Suuberg, Eric M; Jiang, Lin; Wen, Yuezhong; Ma, Jie

    2015-10-01

    At petroleum vapor intrusion (PVI) sites at which there is significant methane generation, upward advective soil gas transport may be observed. To evaluate the health and explosion risks that may exist under such scenarios, a one-dimensional analytical model describing these processes is introduced in this study. This new model accounts for both advective and diffusive transport in soil gas and couples this with a piecewise first-order aerobic biodegradation model, limited by oxygen availability. The predicted results from the new model are shown to be in good agreement with the simulation results obtained from a three-dimensional numerical model. These results suggest that this analytical model is suitable for describing cases involving open ground surface beyond the foundation edge, serving as the primary oxygen source. This new analytical model indicates that the major contribution of upward advection to indoor air concentration could be limited to the increase of soil gas entry rate, since the oxygen in soil might already be depleted owing to the associated high methane source vapor concentration.

  7. RADIATION PRESSURE-SUPPORTED ACCRETION DISKS: VERTICAL STRUCTURE, ENERGY ADVECTION, AND CONVECTIVE STABILITY

    SciTech Connect

    Gu Weimin

    2012-07-10

    By taking into account the local energy balance per unit volume between the viscous heating and the advective cooling plus the radiative cooling, we investigate the vertical structure of radiation pressure-supported accretion disks in spherical coordinates. Our solutions show that the photosphere of the disk is close to the polar axis and therefore the disk seems to be extremely thick. However, the density profile implies that most of the accreted matter exists in a moderate range around the equatorial plane. We show that the well-known polytropic relation between the pressure and the density is unsuitable for describing the vertical structure of radiation pressure-supported disks. More importantly, we find that the energy advection is significant even for slightly sub-Eddington accretion disks. We argue that the non-negligible advection may help us understand why the standard thin disk model is likely to be inaccurate above {approx}0.3 Eddington luminosity, which was found by some works on black hole spin measurement. Furthermore, the solutions satisfy the Solberg-Hoiland conditions, which indicate the disk to be convectively stable. In addition, we discuss the possible link between our disk model and ultraluminous X-ray sources.

  8. Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC/ESI-MS/MS) Study for the Identification and Characterization of In Vivo Metabolites of Cisplatin in Rat Kidney Cancer Tissues: Online Hydrogen/Deuterium (H/D) Exchange Study

    PubMed Central

    Bandu, Raju; Ahn, Hyun Soo; Lee, Joon Won; Kim, Yong Woo; Choi, Seon Hee; Kim, Hak Jin; Kim, Kwang Pyo

    2015-01-01

    In vivo rat kidney tissue metabolites of an anticancer drug, cisplatin (cis-diamminedichloroplatinum [II]) (CP) which is used for the treatment of testicular, ovarian, bladder, cervical, esophageal, small cell lung, head and neck cancers, have been identified and characterized by using liquid chromatography positive ion electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) in combination with on line hydrogen/deuterium exchange (HDX) experiments. To identify in vivo metabolites, kidney tissues were collected after intravenous administration of CP to adult male Sprague-Dawley rats (n = 3 per group). The tissue samples were homogenized and extracted using newly optimized metabolite extraction procedure which involves liquid extraction with phosphate buffer containing ethyl acetate and protein precipitation with mixed solvents of methanol-water-chloroform followed by solid-phase clean-up procedure on Oasis HLB 3cc cartridges and then subjected to LC/ESI-HRMS analysis. A total of thirty one unknown in vivo metabolites have been identified and the structures of metabolites were elucidated using LC-MS/MS experiments combined with accurate mass measurements. Online HDX experiments have been used to further support the structural characterization of metabolites. The results showed that CP undergoes a series of ligand exchange biotransformation reactions with water and other nucleophiles like thio groups of methionine, cysteine, acetylcysteine, glutathione and thioether. This is the first research approach focused on the structure elucidation of biotransformation products of CP in rats, and the identification of metabolites provides essential information for further pharmacological and clinical studies of CP, and may also be useful to develop various effective new anticancer agents. PMID:26244343

  9. "TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis

    PubMed Central

    Nikamanon, Pornpat; Pun, Elroy; Chou, Wayne; Koter, Marek D; Gershon, Paul D

    2008-01-01

    Background Protein-amide proton hydrogen-deuterium exchange (HDX) is used to investigate protein conformation, conformational changes and surface binding sites for other molecules. To our knowledge, software tools to automate data processing and analysis from sample fractionating (LC-MALDI) mass-spectrometry-based HDX workflows are not publicly available. Results An integrated data pipeline (Solvent Explorer/TOF2H) has been developed for the processing of LC-MALDI-derived HDX data. Based on an experiment-wide template, and taking an ab initio approach to chromatographic and spectral peak finding, initial data processing is based on accurate mass-matching to fully deisotoped peaklists accommodating, in MS/MS-confirmed peptide library searches, ambiguous mass-hits to non-target proteins. Isotope-shift re-interrogation of library search results allows quick assessment of the extent of deuteration from peaklist data alone. During raw spectrum editing, each spectral segment is validated in real time, consistent with the manageable spectral numbers resulting from LC-MALDI experiments. A semi-automated spectral-segment editor includes a semi-automated or automated assessment of the quality of all spectral segments as they are pooled across an XIC peak for summing, centroid mass determination, building of rates plots on-the-fly, and automated back exchange correction. The resulting deuterium uptake rates plots from various experiments can be averaged, subtracted, re-scaled, error-barred, and/or scatter-plotted from individual spectral segment centroids, compared to solvent exposure and hydrogen bonding predictions and receive a color suggestion for 3D visualization. This software lends itself to a "divorced" HDX approach in which MS/MS-confirmed peptide libraries are built via nano or standard ESI without source modification, and HDX is performed via LC-MALDI using a standard MALDI-TOF. The complete TOF2H package includes additional (eg LC analysis) modules. Conclusion

  10. Manitoba Exchange.

    ERIC Educational Resources Information Center

    Coss, Maurice

    Planning ideas and follow-up activities are described for a reciprocal exchange program between groups of 5th and 6th grade students in Manitoba who are "twinned" with another school in the province. Emphasis is on providing learning experiences which help students become familiar with the economic activity in the area, with the local government…

  11. Heat exchanger

    DOEpatents

    Wolowodiuk, Walter

    1976-01-06

    A heat exchanger of the straight tube type in which different rates of thermal expansion between the straight tubes and the supply pipes furnishing fluid to those tubes do not result in tube failures. The supply pipes each contain a section which is of helical configuration.

  12. Heat exchanger

    DOEpatents

    Daman, Ernest L.; McCallister, Robert A.

    1979-01-01

    A heat exchanger is provided having first and second fluid chambers for passing primary and secondary fluids. The chambers are spaced apart and have heat pipes extending from inside one chamber to inside the other chamber. A third chamber is provided for passing a purge fluid, and the heat pipe portion between the first and second chambers lies within the third chamber.

  13. Estimating ground-water exchange with lakes using water-budget and chemical mass-balance approaches for ten lakes in ridge areas of Polk and Highlands counties, Florida

    USGS Publications Warehouse

    Sacks, L.A.; Swancar, Amy; Lee, T.M.

    1998-01-01

    Water budget and chemical mass-balance approaches were used to estimate ground-water exchange with 10 lakes in ridge areas of Polk and Highlands Counties, Florida. At each lake, heads were monitored in the surficial aquifer system and deeper Upper Floridan aquifer, lake stage and rainfall were measured continuously, and lakes and wells were sampled three times between October 1995 and December 1996. The water-budget approach computes net ground-water flow (ground-water inflow minus outflow) as the residual of the monthly waterbudget equation. Net ground-water flow varied seasonally at each of the 10 lakes, and was notably different between lakes, illustrating short-term differences in ground-water fluxes. Monthly patterns in net ground-water flow were related to monthly patterns of other hydrologic variables such as rainfall, ground-water flow patterns, and head differences between the lake and the Upper Floridan aquifer. The chemical mass-balance approach combines the water budget and solute or isotope mass-balance equations, and assumes steady-state conditions. Naturally occurring tracers that were analyzed for include calcium, magnesium, sodium, potassium, chloride, and bromide, the isotopes deuterium and oxygen-18. Chloride and sodium were the most successful solute tracers; however, their concentrations in ground water typically varied spatially, and in places were similar to that in lake water, limiting their sensitivity as tracers. In contrast, the isotopes were more robust tracers because the isotopic composition of ground water was relatively uniform and was distinctly different from the lake water. Groundwater inflow computed using the chemical massbalance method varied significantly between lakes, and ranged from less than 10 to more than 150 inches per year. Both water-budget and chemical mass-balance approaches had limitations, but the multiple lines of evidence gained using both approaches improved the understanding of the role of ground water in the

  14. Integrated strong cation-exchange hybrid monolith coupled with capillary zone electrophoresis and simultaneous dynamic pH junction for large-volume proteomic analysis by mass spectrometry.

    PubMed

    Zhang, Zhenbin; Sun, Liangliang; Zhu, Guijie; Yan, Xiaojing; Dovichi, Norman J

    2015-06-01

    A sulfonate-silica hybrid strong cation-exchange (SCX) monolith was synthesized at the proximal end of a capillary zone electrophoresis column and used for on-line solid-phase extraction (SPE) sample preconcentration. Sample was prepared in an acidic buffer and deposited onto the SCX-SPE monolith and eluted using a basic buffer. Electrophoresis was performed in an acidic buffer. This combination of buffers results in formation of a dynamic pH junction, which allows use of relatively large elution buffer volume while maintaining peak efficiency and resolution. All experiments were performed with a 50 µm ID capillary, a 1cm long SCX-SPE monolith, a 60cm long separation capillary, and a electrokinetically pumped nanospray interface. The volume of the capillary is 1.1 µL. By loading 21 µL of a 1×10(-7) M angiotensin II solution, an enrichment factor of 3000 compared to standard electrokinetic injection was achieved on this platform while retaining efficient electrophoretic performance (N=44,000 plates). The loading capacity of the sulfonate SCX hybrid monolith was determined to be ~15 pmol by frontal analysis with 10(-5) M angiotensin II. The system was also applied to the analysis of a 10(-4) mg/mL bovine serum albumin tryptic digest; the protein coverage was 12% and 11 peptides were identified. Finally, by loading 5.5 µL of a 10(-3) mg/mL E. coli digest, 109 proteins and 271 peptides were identified in a 20 min separation; the median separation efficiency generated by these peptides was 25,000 theoretical plates.

  15. Selective determination of pharmaceuticals and illicit drugs in wastewaters using a novel strong cation-exchange solid-phase extraction combined with liquid chromatography-tandem mass spectrometry.

    PubMed

    Gilart, Núria; Cormack, P A G; Marcé, Rosa Maria; Fontanals, Núria; Borrull, Francesc

    2014-01-17

    In this study, two materials are presented with strong cation-exchange (SCX) behaviour synthesised by two different approaches and then crushed for their application as sorbents for solid-phase extraction (SPE) to extract a group of pharmaceuticals and illicit drugs selectively from wastewater samples. The first SCX polymer was obtained by copolymerisation of three monomers: 2-acrylamido-2-methylpropane sulphonic acid (AMPSA), 2-hydroxyethyl methacrylate (HEMA) and pentaerythritol triacrylate (PETRA), while the second was obtained by post-modification with sulphuric acid (H2SO4) of a copolymer based on HEMA and divinylbenzene (DVB). After their syntheses, both polymers were evaluated as SPE sorbents, with all parameters affecting SPE being optimised, such as sample pH, washing and elution solvents and volumes. Thanks to the sulphonic groups present in the structure of the polymers, all of the compounds with basic functionalities were retained on the sorbents after the washing step, removing the acidic analytes and other interfering compounds, providing successful results in terms of ion suppression/enhancement (-12% and 21%) when wastewater samples were analysed. However, AMPSA/HEMA/PETRA (20/60/20) failed to retain the analytes after loading wastewater samples (25 or 50mL), decreasing analyte recovery values significantly, whereas the sulphonated HEMA/DVB (50/50) enabled good SPE performance with recovery values between 70% and 98%, except for ranitidine and EDDP (39% and 43%, respectively). Therefore, this polymer was selected for further method validation and quantification of wastewater samples, providing low method detection limits (MDLs) in this matrix (from 2 to 40ngL(-1)). Finally, most of the studied compounds were detected and quantified in wastewater samples, especially atenolol, ranitidine, cocaine and its metabolite benzoylecgonine. PMID:24369996

  16. Liquid droplet heat exchanger studies

    NASA Technical Reports Server (NTRS)

    Bruckner, A. P.; Hedges, D. E.; Yungster, S.

    1987-01-01

    Recent analytical and experimental investigations of the liquid droplet heat exchanger (LDHX) concept for space power applications are described. The performance of the LDHX is compared to that of a conventional heat exchanger for heat rejection applications in a Brayton cycle, using the mass-specific heat exchanger effectiveness as a figure of merit. It is shown that the LDHX has an order of magnitude advantage over the conventional heat exchanger. Furthermore, significant improvement in cycle efficiency and power to mass ratio is possible. Two-phase flow experiments in a laboratory scale LDHX, using air and water as the two media, show very good agreement with the quasi-one-dimensional model used in the parametric studies.

  17. A family of Eulerian-Lagrangian localized adjoint methods for multi-dimensional advection-reaction equations

    SciTech Connect

    Wang, H.; Man, S.; Ewing, R.E.; Qin, G.; Lyons, S.L.; Al-Lawatia, M.

    1999-06-10

    Many difficult problems arise in the numerical simulation of fluid flow processes within porous media in petroleum reservoir simulation and in subsurface contaminant transport and remediation. The authors develop a family of Eulerian-Lagrangian localized adjoint methods for the solution of the initial-boundary value problems for first-order advection-reaction equations on general multi-dimensional domains. Different tracking algorithms, including the Euler and Runge-Kutta algorithms, are used. The derived schemes, which are full mass conservative, naturally incorporate inflow boundary conditions into their formulations and do not need any artificial outflow boundary conditions. Moreover, they have regularly structured, well-conditioned, symmetric, and positive-definite coefficient matrices, which can be efficiently solved by the conjugate gradient method in an optimal order number of iterations without any preconditioning needed. Numerical results are presented to compare the performance of the ELLAM schemes with many well studied and widely used methods, including the upwind finite difference method, the Galerkin and the Petrov-Galerkin finite element methods with backward-Euler or Crank-Nicolson temporal discretization, the streamline diffusion finite element methods, the monotonic upstream-centered scheme for conservation laws (MUSCL), and the Minmod scheme.

  18. Stochastic interpretation of the advection-diffusion equation and its relevance to bed load transport

    NASA Astrophysics Data System (ADS)

    Ancey, C.; Bohorquez, P.; Heyman, J.

    2015-12-01

    The advection-diffusion equation is one of the most widespread equations in physics. It 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). Phenomenological laws are usually sufficient to derive this equation and interpret its terms. Stochastic models can also be used to derive it, with the significant advantage that they provide information on the statistical properties of particle activity. These models are quite useful when sediment transport exhibits large fluctuations (typically at low transport rates), making the measurement of mean values difficult. Among these stochastic models, the most common approach consists of random walk models. For instance, they have been used to model the random displacement of tracers in rivers. Here we explore an alternative approach, which involves monitoring the evolution of the number of particles moving within an array of cells of finite length. Birth-death Markov processes are well suited to this objective. While the topic has been explored in detail for diffusion-reaction systems, the treatment of advection has received no attention. We therefore look into the possibility of deriving the advection-diffusion equation (with a source term) within the framework of birth-death Markov processes. We show that in the continuum limit (when the cell size becomes vanishingly small), we can derive an advection-diffusion equation for particle activity. Yet while this derivation is formally valid in the continuum limit, it runs into difficulty in practical applications involving cells or meshes of finite length. Indeed, within our stochastic framework, 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

  19. Vertical advection from oxic or anoxic water from the main pycnocline as a cause of rapid extinction or rapid radiations

    NASA Astrophysics Data System (ADS)

    Wilde, Pat; Quinby-Hunt, Mary S.; Berry, William B. N.

    The vast majority of oceanic biomass lives in the surface wind-mixed layer (0-100 m) of the ocean, trophically dependent on light or primary production based on photosynthesis. Waters from the main pycnocline (100-1000 m) or deeper naturally contain decay products from sinking organic matter as a function of the oxidation state of the waters. Such products, in proper concentrations, can inhibit photosynthetic growth or are toxic or debilitating to respirors. Usually, physical oceanographic processes of vertical circulation are slow or volumetrically small enough to permit conditioning or mixing of toxicants of the deep waters with surface waters so that the deleterious effects of deep water are neutralized or localized. However, rapid global to regional scale vertical advection of deep waters into the surface mixed layer could create an ecologic crisis for various marine groups through a combination of: (1) direct toxicity; (2) reduction or modification of nutrient and food supplies through inhibition of photosynthesis; (3) chronic debilitation caused by contact with such toxic waters; or (4) increased predation by more adaptive or less effected taxa. Such events are not necessarily universally deleterious as they could offer new opportunities for taxa ecologically restricted under prior conditions. During cool climates with oxic deep waters, a crisis may be caused by upwelling of metals concentrated with depth and resulting in reduced primary productivity, as well as metal toxic and/or chronic reactions in higher groups. During warm climates with anoxic to dysaerobic waters in the pycnocline, a crisis may result from contact with anoxic waters with a maximum effect on respirors and a minimal to enhanced effect on phytoplankton. Upwelling may come from three redox zones: I- oxic; II- nitric; and III- sulfatic. Each zone would be the source of waters of differing chemistries that could be advected into the photic zone. The effect on specific taxa will be selective

  20. Investigation of the interaction between sources and sinks of atmospheric ammonia in an upland landscape using a simplified dispersion-exchange model

    NASA Astrophysics Data System (ADS)

    Loubet, Benjamin; Milford, Celia; Sutton, Mark A.; Cellier, Pierre

    2001-10-01

    Exchange of atmospheric ammonia (NH3) with vegetation is characterized by the juxtaposition of sources and sinks at a landscape level. Such situations lead to a large fraction of the landscape being exposed to local advection effects that if not accounted for, introduce errors in standard micrometeorological measurements of NH3 exchange with the surface. In this study, a simplified dispersion - exchange model for NH3 (Flux Interpretation by Dispersion and Exchange over Short Range, FIDES) is evaluated and used to assess the advection fluxes at 260 m downwind of an isolated pasture, grazed with sheep, using the measurements of a classical three-point NH3 gradient system located on adjacent moorland. The method consists of fitting the measured and modeled concentration profile by adjusting at the same time the emission strength of the local source and the exchange rate of NH3 to the moorland area downwind. A local dispersion and surface exchange model such as FIDES has proved to be a valuable tool to estimate advection corrections, given sound estimates of background NH3 concentrations, source location, and standard meteorological parameters. According to the model results the advection fluxes at the moorland measurement site, at 1.0 m height and 260 m downwind of the grazed pasture, were positive. For 80% of the situations they ranged between 30% and 60% of the vertical flaxes. In stable conditions the advection fluxes were large and more sensitive to the surface exchange parameters. These results demonstrate that if not accounted for, advection fluxes may lead to a severe underestimate of the NH3 deposition to seminatural ecosystems, such as moorland, in the vicinity of ground level agricultural sources.

  1. Rapid Measurements of Aerosol Ionic Composition and 3-10 nm Particle Size Distributions On The NASA P3 To Better Quantify Processes Affecting Aerosols Advected From East Asia

    NASA Technical Reports Server (NTRS)

    Weber, Rodney J.

    2004-01-01

    The Particle Into Liquid Sample (PILS) was deployed on the NASA P3 for airborne measurements of fine particle ionic chemical composition. The data have been quality assured and reside in the NASA data archive. We have analyzed our data to characterize the sources and atmospheric processing of fine aerosol particles advected from the region during the experiments. Fine particle water-soluble potassium was found to serve as a useful aerosol tracer for biomass smoke. Ratios of PILS potassium to sulfate are used as a means of estimating the percent contribution of biomass burning to fine particle mass in mixed plumes advecting from Asia. The high correlations between K+ and NO3(sup -) and NH4(sup +)' indicated that biomass burning was a significant source of these aerosol compounds in the region. It is noteworthy that the air mass containing the highest concentrations of fine particles recorded in all of ACE-Asia and TRACE-P appeared to be advecting from the Bejing/Tientsin urban region and also had the highest K(+), NO3(sup -) and NH4(sup +) concentrations of both studies. Based on K+/SO4(sup 2-) ratio's, we estimated that the plume was composed of approx. 60% biomass burning emissions, possibly from the use of bio-fuels in the urban regions.

  2. THE INTERPLAY BETWEEN GEOCHEMICAL REACTIONS AND ADVECTION-DISPERSION IN CONTAMINANT TRANSPORT AT A URANIUM MILL TAILINGS SITE

    EPA Science Inventory

    It is well known that the fate and transport of contaminants in the subsurface are controlled by complex processes including advection, dispersion-diffusion, and chemical reactions. However, the interplay between the physical transport processes and chemical reactions, and their...

  3. A two-sided fractional conservation of mass equation

    NASA Astrophysics Data System (ADS)

    Olsen, Jeffrey S.; Mortensen, Jeff; Telyakovskiy, Aleksey S.

    2016-05-01

    A two-sided fractional conservation of mass equation is derived by using left and right fractional Mean Value Theorems. This equation extends the one-sided fractional conservation of mass equation of Wheatcraft and Meerschaert. Also, a two-sided fractional advection-dispersion equation is derived. The derivations are based on Caputo fractional derivatives.

  4. Inter-annual variability of air mass and acidified pollutants transboundary exchange in the north-eastern part of the EANET region

    NASA Astrophysics Data System (ADS)

    Gromov, Sergey A.; Trifonova-Yakovleva, Alisa; Gromov, Sergey S.

    2016-04-01

    Anthropogenic emissions, be it exhaust gases or aerosols, stem from multitude of sources and may survive long-range transport within the air masses they were emitted into. So they follow regional and global transport pathways varying under different climatological regimes. Transboundary transfer of pollutants occurs this way and has a significant impact on the ecological situation of the territories neighbouring those of emission sources, as found in a few earlier studies examining the environmental monitoring data [1]. In this study, we employ a relatively facile though robust technique for estimating the transboundary air and concomitant pollutant fluxes using actual or climatological meteorological and air pollution monitoring data. Practically, we assume pollutant transfer being proportional to the horizontal transport of air enclosed in the lower troposphere and to the concentration of the pollutant of interest. The horizontal transport, in turn, is estimated using the mean layer wind direction and strength, or their descriptive statistics at the individual transects of the boundary of interest. The domain of our interest is the segment of Russian continental border in East Asia spanning from 88° E (southern Middle Siberia) to 135° E (Far East at Pacific shore). The data on atmospheric pollutants concentration are available from the Russian monitoring sites of the region-wide Acid Deposition Monitoring Network in East Asia (EANET, http://www.eanet.asia/) Mondy (Baikal area) and Primorskaya (near Vladivostok). The data comprises multi-year continuous measurement of gas-phase and particulate species abundances in air with at least biweekly sampling rate starting from 2000. In the first phase of our study, we used climatological dataset on winds derived from the aerological soundings at Russian stations along the continental border for the 10-year period (1961-1970) by the Research Institute of Hydrometeorological Information - World Data Centre (RIHMI-WDC) [3

  5. Nonlinear Advection Algorithms Applied to Inter-related Tracers: Errors and Implications for Modeling Aerosol-Cloud Interactions

    SciTech Connect

    Ovtchinnikov, Mikhail; Easter, Richard C.

    2009-02-01

    Monotonicity constraints and gradient preserving flux corrections employed by many advection algorithms used in atmospheric models make these algorithms non-linear. Consequently, any relations among model variables transported separately are not necessarily preserved in such models. These errors cannot be revealed by traditional algorithm testing based on advection of a single tracer. New type of tests are developed and conducted to evaluate the preservation of a sum of several number mixing ratios advected independently of each other, as is the case, for example, in models using bin or sectional representation of aerosol or cloud particle size distribution. The tests show that when three tracers are advected in 1D uniform constant velocity flow, local errors in the sum can be on the order of 10%. When cloud-like interactions are allowed among the tracers, errors in total sum of three mixing ratios can reach up to 30%. Several approaches to eliminate the error are suggested, all based on advecting the sum as a separate variable and then normalizing mixing ratios for individual tracers to match the total sum. A simple scalar normalization preserves the total number mixing ratio and positive definiteness of the variables but the monotonicity constraint for individual tracers is no longer maintained. More involved flux normalization procedures are developed for the flux based advection algorithms to maintain the monotonicity for individual scalars and their sum.

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