On-tissue Direct Monitoring of Global Hydrogen/Deuterium Exchange by MALDI Mass Spectrometry: Tissue Deuterium Exchange Mass Spectrometry (TDXMS)*

PubMed Central

Quanico, Jusal; Franck, Julien

2016-01-01

Hydrogen/deuterium exchange mass spectrometric (H/DXMS) methods for protein structural analysis are conventionally performed in solution. We present Tissue Deuterium Exchange Mass Spectrometry (TDXMS), a method to directly monitor deuterium uptake on tissue, as a means to better approximate the deuterium exchange behavior of proteins in their native microenvironment. Using this method, a difference in deuterium uptake behavior was observed when the same proteins were monitored in solution and on tissue. The higher maximum deuterium uptake at equilibrium for all proteins analyzed in solution suggests a more open conformation in the absence of interacting partners normally observed on tissue. We also demonstrate a difference in the deuterium uptake behavior of a few proteins across different morphological regions of the same tissue section. Modifications of the total number of hydrogens exchanged, as well as the kinetics of exchange, were both observed. These results provide information on the implication of protein interactions with partners as well as on the conformational changes related to these interactions, and illustrate the importance of examining protein deuterium exchange behavior in the presence of its specific microenvironment directly at the level of tissues. PMID:27512083

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.

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.

Hydrogen Exchange Mass Spectrometry

PubMed Central

Mayne, Leland

2018-01-01

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. PMID:26791986

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

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

Greiner, Miles; Childress, Amy; Hiibel, Sage

2014-12-16

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

Numerical simulation of life cycles of advection warm fog

NASA Technical Reports Server (NTRS)

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

1977-01-01

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

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

PubMed

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

2012-12-01

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

Minimizing Back Exchange in the Hydrogen Exchange-Mass Spectrometry Experiment

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

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

PubMed

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

2017-03-01

The role of hyaline hairs on the thallus of brown algae in the genus Fucus is long debated and several functions have been proposed. We used a novel motorized set-up for two-dimensional and three-dimensional mapping with O 2 microsensors to investigate the spatial heterogeneity of the diffusive boundary layer (DBL) and O 2 flux around single and multiple tufts of hyaline hairs on the thallus of Fucus vesiculosus. Flow was a major determinant of DBL thickness, where higher flow decreased DBL thickness and increased O 2 flux between the algal thallus and the surrounding seawater. However, the topography of the DBL varied and did not directly follow the contour of the underlying thallus. Areas around single tufts of hyaline hairs exhibited a more complex mass-transfer boundary layer, showing both increased and decreased thickness when compared with areas over smooth thallus surfaces. Over thallus areas with several hyaline hair tufts, the overall effect was an apparent increase in the boundary layer thickness. We also found indications for advective O 2 transport driven by pressure gradients or vortex shedding downstream from dense tufts of hyaline hairs that could alleviate local mass-transfer resistances. Mass-transfer dynamics around hyaline hair tufts are thus more complex than hitherto assumed and may have important implications for algal physiology and plant-microbe interactions. © 2017 The Author(s).

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

PubMed Central

Nørregaard, Rasmus Dyrmose

2017-01-01

The role of hyaline hairs on the thallus of brown algae in the genus Fucus is long debated and several functions have been proposed. We used a novel motorized set-up for two-dimensional and three-dimensional mapping with O2 microsensors to investigate the spatial heterogeneity of the diffusive boundary layer (DBL) and O2 flux around single and multiple tufts of hyaline hairs on the thallus of Fucus vesiculosus. Flow was a major determinant of DBL thickness, where higher flow decreased DBL thickness and increased O2 flux between the algal thallus and the surrounding seawater. However, the topography of the DBL varied and did not directly follow the contour of the underlying thallus. Areas around single tufts of hyaline hairs exhibited a more complex mass-transfer boundary layer, showing both increased and decreased thickness when compared with areas over smooth thallus surfaces. Over thallus areas with several hyaline hair tufts, the overall effect was an apparent increase in the boundary layer thickness. We also found indications for advective O2 transport driven by pressure gradients or vortex shedding downstream from dense tufts of hyaline hairs that could alleviate local mass-transfer resistances. Mass-transfer dynamics around hyaline hair tufts are thus more complex than hitherto assumed and may have important implications for algal physiology and plant–microbe interactions. PMID:28330986

Two-level schemes for the advection equation

NASA Astrophysics Data System (ADS)

Vabishchevich, Petr N.

2018-06-01

The advection equation is the basis for mathematical models of continuum mechanics. In the approximate solution of nonstationary problems it is necessary to inherit main properties of the conservatism and monotonicity of the solution. In this paper, the advection equation is written in the symmetric form, where the advection operator is the half-sum of advection operators in conservative (divergent) and non-conservative (characteristic) forms. The advection operator is skew-symmetric. Standard finite element approximations in space are used. The standard explicit two-level scheme for the advection equation is absolutely unstable. New conditionally stable regularized schemes are constructed, on the basis of the general theory of stability (well-posedness) of operator-difference schemes, the stability conditions of the explicit Lax-Wendroff scheme are established. Unconditionally stable and conservative schemes are implicit schemes of the second (Crank-Nicolson scheme) and fourth order. The conditionally stable implicit Lax-Wendroff scheme is constructed. The accuracy of the investigated explicit and implicit two-level schemes for an approximate solution of the advection equation is illustrated by the numerical results of a model two-dimensional problem.

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

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...

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.

Orbital Advection with Magnetohydrodynamics and Vector Potential

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

Lyra, Wladimir; McNally, Colin P.; Heinemann, Tobias

Orbital advection is a significant bottleneck in disk simulations, and a particularly tricky one when used in connection with magnetohydrodynamics. We have developed an orbital advection algorithm suitable for the induction equation with magnetic potential. The electromotive force is split into advection and shear terms, and we find that we do not need an advective gauge since solving the orbital advection implicitly precludes the shear term from canceling the advection term. We prove and demonstrate the third order in time accuracy of the scheme. The algorithm is also suited to non-magnetic problems. Benchmarked results of (hydrodynamical) planet–disk interaction and ofmore » the magnetorotational instability are reproduced. We include detailed descriptions of the construction and selection of stabilizing dissipations (or high-frequency filters) needed to generate practical results. The scheme is self-consistent, accurate, and elegant in its simplicity, making it particularly efficient for straightforward finite-difference methods. As a result of the work, the algorithm is incorporated in the public version of the Pencil Code, where it can be used by the community.« less

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.

Hydrogen Exchange and Mass Spectrometry: A Historical Perspective

PubMed Central

Englander, S. Walter

2012-01-01

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

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.

Modeling Sediment Detention Ponds Using Reactor Theory and Advection-Diffusion Concepts

NASA Astrophysics Data System (ADS)

Wilson, Bruce N.; Barfield, Billy J.

1985-04-01

An algorithm is presented to model the sedimentation process in detention ponds. This algorithm is based on a mass balance for an infinitesimal layer that couples reactor theory concepts with advection-diffusion processes. Reactor theory concepts are used to (1) determine residence time of sediment particles and to (2) mix influent sediment with previously stored flow. Advection-diffusion processes are used to model the (1) settling characteristics of sediment and the (2) vertical diffusion of sediment due to turbulence. Predicted results of the model are compared to those observed on two pilot scale ponds for a total of 12 runs. The average percent error between predicted and observed trap efficiency was 5.2%. Overall, the observed sedimentology values were predicted with reasonable accuracy.

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

NASA Technical Reports Server (NTRS)

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

1983-01-01

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

The role of horizontal thermal advection in regulating wintertime mean and extreme temperatures over the central United States during the past and future

NASA Astrophysics Data System (ADS)

Wang, F.; Vavrus, S. J.

2017-12-01

Horizontal temperature advection plays an especially prominent role in affecting winter climate over continental interiors, where both climatological conditions and extreme weather are strongly regulated by transport of remote air masses. Central North America is one such region, and it experienced a major cold-air outbreak (CAO) a few years ago that some have related to amplified Arctic warming. Despite the known importance of dynamics in shaping the winter climate of this sector and the potential for climate change to modify heat transport, limited attention has been paid to the regional impact of thermal advection. Here, we use a reanalysis product and output from the Community Earth System Model's Large Ensemble to quantify the roles of zonal and meridional temperature advection over the central U. S. during winter, both in the late 20th and 21st centuries. We frame our findings as a "tug of war" between opposing influences of the two advection components and between these dynamical forcings vs. thermodynamic changes under greenhouse warming. For example, Arctic amplification leads to much warmer polar air masses, causing a moderation of cold-air advection into the central U. S., yet the model also simulates a wavier mean circulation and stronger northerly flow during CAOs, favoring lower regional temperatures. We also compare the predominant warming effect of zonal advection and overall cooling effect of meridional temperature advection as an additional tug of war. During both historical and future periods, zonal temperature advection is stronger than meridional advection over the Central U. S. The model simulates a future weakening of both zonal and meridional temperature advection, such that westerly flow provides less warming and northerly flow less cooling. On the most extreme warm days in the past and future, both zonal and meridional temperature advection have positive (warming) contributions. On the most extreme cold days, meridional cold air advection

Advection-dominated Inflow/Outflows from Evaporating Accretion Disks.

PubMed

Turolla; Dullemond

2000-03-01

In this Letter we investigate the properties of advection-dominated accretion flows (ADAFs) fed by the evaporation of a Shakura-Sunyaev accretion disk (SSD). In our picture, the ADAF fills the central cavity evacuated by the SSD and extends beyond the transition radius into a coronal region. We find that, because of global angular momentum conservation, a significant fraction of the hot gas flows away from the black hole, forming a transsonic wind, unless the injection rate depends only weakly on radius (if r2sigma&d2;~r-xi, xi<1&solm0;2). The Bernoulli number of the inflowing gas is negative if the transition radius is less, similar100 Schwarzschild radii, so matter falling into the hole is gravitationally bound. The ratio of inflowing to outflowing mass is approximately 1/2, so in these solutions the accretion rate is of the same order as in standard ADAFs and much larger than in advection-dominated inflow/outflow models. The possible relevance of evaporation-fed solutions to accretion flows in black hole X-ray binaries is briefly discussed.

SAIDE: A Semi-Automated Interface for Hydrogen/Deuterium Exchange Mass Spectrometry.

PubMed

Villar, Maria T; Miller, Danny E; Fenton, Aron W; Artigues, Antonio

2010-01-01

Deuterium/hydrogen exchange in combination with mass spectrometry (DH MS) is a sensitive technique for detection of changes in protein conformation and dynamics. Since temperature, pH and timing control are the key elements for reliable and efficient measurement of hydrogen/deuterium content in proteins and peptides, we have developed a small, semiautomatic interface for deuterium exchange that interfaces the HPLC pumps with a mass spectrometer. This interface is relatively inexpensive to build, and provides efficient temperature and timing control in all stages of enzyme digestion, HPLC separation and mass analysis of the resulting peptides. We have tested this system with a series of standard tryptic peptides reconstituted in a solvent containing increasing concentration of deuterium. Our results demonstrate the use of this interface results in minimal loss of deuterium due to back exchange during HPLC desalting and separation. For peptides reconstituted in a buffer containing 100% deuterium, and assuming that all amide linkages have exchanged hydrogen with deuterium, the maximum loss of deuterium content is only 17% of the label, indicating the loss of only one deuterium molecule per peptide.

SAIDE: A Semi-Automated Interface for Hydrogen/Deuterium Exchange Mass Spectrometry

PubMed Central

Villar, Maria T.; Miller, Danny E.; Fenton, Aron W.; Artigues, Antonio

2011-01-01

Deuterium/hydrogen exchange in combination with mass spectrometry (DH MS) is a sensitive technique for detection of changes in protein conformation and dynamics. Since temperature, pH and timing control are the key elements for reliable and efficient measurement of hydrogen/deuterium content in proteins and peptides, we have developed a small, semiautomatic interface for deuterium exchange that interfaces the HPLC pumps with a mass spectrometer. This interface is relatively inexpensive to build, and provides efficient temperature and timing control in all stages of enzyme digestion, HPLC separation and mass analysis of the resulting peptides. We have tested this system with a series of standard tryptic peptides reconstituted in a solvent containing increasing concentration of deuterium. Our results demonstrate the use of this interface results in minimal loss of deuterium due to back exchange during HPLC desalting and separation. For peptides reconstituted in a buffer containing 100% deuterium, and assuming that all amide linkages have exchanged hydrogen with deuterium, the maximum loss of deuterium content is only 17% of the label, indicating the loss of only one deuterium molecule per peptide. PMID:25309638

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.

Magnetically advected winds

NASA Astrophysics Data System (ADS)

Contopoulos, I.; Kazanas, D.; Fukumura, K.

2017-11-01

Observations of X-ray absorption lines in magnetically driven disc winds around black hole binaries and active galactic nuclei yield a universal radial density profile ρ ∝ r-1.2 in the wind. This is in disagreement with the standard Blandford and Payne profile ρBP ∝ r-1.5 expected when the magnetic field is neither advected nor diffusing through the accretion disc. In order to account for this discrepancy, we establish a new paradigm for magnetically driven astrophysical winds according to which the large-scale ordered magnetic field that threads the disc is continuously generated by the Cosmic Battery around the inner edge of the disc and continuously diffuses outward. We obtain self-similar solutions of such magnetically advected winds (MAW) and discuss their observational ramifications.

Advective transport of CO2 in permeable media induced by atmospheric pressure fluctuations: 1. An analytical model

Treesearch

W. J. Massman

2006-01-01

Advective flows within soils and snowpacks caused by pressure fluctuations at the upper surface of either medium can significantly influence the exchange rate of many trace gases from the underlying substrate to the atmosphere. Given the importance of many of these trace gases in understanding biogeochemical cycling and global change, it is crucial to quantify (as much...

A serpentine laminating micromixer combining splitting/recombination and advection.

PubMed

Kim, Dong Sung; Lee, Se Hwan; Kwon, Tai Hun; Ahn, Chong H

2005-07-01

Mixing enhancement has drawn great attention from designers of micromixers, since the flow in a microchannel is usually characterized by a low Reynolds number (Re) which makes the mixing quite a difficult task to accomplish. In this paper, a novel integrated efficient micromixer named serpentine laminating micromixer (SLM) has been designed, simulated, fabricated and fully characterized. In the SLM, a high level of efficient mixing can be achieved by combining two general chaotic mixing mechanisms: splitting/recombination and chaotic advection. The splitting and recombination (in other terms, lamination) mechanism is obtained by the successive arrangement of "F"-shape mixing units in two layers. The advection is induced by the overall three-dimensional serpentine path of the microchannel. The SLM was realized by SU-8 photolithography, nickel electroplating, injection molding and thermal bonding. Mixing performance of the SLM was fully characterized numerically and experimentally. The numerical mixing simulations show that the advection acts favorably to realize the ideal vertical lamination of fluid flow. The mixing experiments based on an average mixing color intensity change of phenolphthalein show a high level of mixing performance was obtained with the SLM. Numerical and experimental results confirm that efficient mixing is successfully achieved from the SLM over the wide range of Re. Due to the simple and mass producible geometry of the efficient micromixer, SLM proposed in this study, the SLM can be easily applied to integrated microfluidic systems, such as micro-total-analysis-systems or lab-on-a-chip systems.

Evolution and advection of solar mesogranulation

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

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

A new mass-conservative method for solution of the one-dimensional advection-dispersion equation is derived and discussed. Test results demonstrate that the finite-volume Eulerian-Lagrangian localized adjoint method (FVELLAM) outperforms standard finite-difference methods, in terms of accuracy and efficiency, for solute transport problems that are dominated by advection. For dispersion-dominated problems, the performance of the method is similar to that of standard methods. Like previous ELLAM formulations, FVELLAM systematically conserves mass globally with all types of boundary conditions. FVELLAM differs from other ELLAM approaches in that 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, as used by most characteristic methods, of characteristic lines intersecting inflow boundaries. FVELLAM extends previous ELLAM results by obtaining mass conservation locally on Lagrangian space-time elements. Details of the integration, tracking, and boundary algorithms are presented. Test results are given for problems in Cartesian and radial coordinates.

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.

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

PubMed Central

Mazur, Sharlyn J.; Weber, Daniel P.

2018-01-01

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) provides information about protein conformational mobility under native conditions. The area between exchange curves, Abec, a functional data analysis concept, was adapted to the interpretation of HDX-MS data and provides a useful measure of exchange curve dissimilarity for tests of significance. Importantly, for most globular proteins under native conditions, Abec values provide an estimate of the log ratio of exchange-competent fractions in the two states, and thus are related to differences in the free energy of microdomain unfolding. PMID:28236290

Empirical Correction for Differences in Chemical Exchange Rates in Hydrogen Exchange-Mass Spectrometry Measurements.

PubMed

Toth, Ronald T; Mills, Brittney J; Joshi, Sangeeta B; Esfandiary, Reza; Bishop, Steven M; Middaugh, C Russell; Volkin, David B; Weis, David D

2017-09-05

A barrier to the use of hydrogen exchange-mass spectrometry (HX-MS) in many contexts, especially analytical characterization of various protein therapeutic candidates, is that differences in temperature, pH, ionic strength, buffering agent, or other additives can alter chemical exchange rates, making HX data gathered under differing solution conditions difficult to compare. Here, we present data demonstrating that HX chemical exchange rates can be substantially altered not only by the well-established variables of temperature and pH but also by additives including arginine, guanidine, methionine, and thiocyanate. To compensate for these additive effects, we have developed an empirical method to correct the hydrogen-exchange data for these differences. First, differences in chemical exchange rates are measured by use of an unstructured reporter peptide, YPI. An empirical chemical exchange correction factor, determined by use of the HX data from the reporter peptide, is then applied to the HX measurements obtained from a protein of interest under different solution conditions. We demonstrate that the correction is experimentally sound through simulation and in a proof-of-concept experiment using unstructured peptides under slow-exchange conditions (pD 4.5 at ambient temperature). To illustrate its utility, we applied the correction to HX-MS excipient screening data collected for a pharmaceutically relevant IgG4 mAb being characterized to determine the effects of different formulations on backbone dynamics.

Online hydrogen/deuterium exchange performed in the ion mobility cell of a hybrid mass spectrometer.

PubMed

Nagy, Kornél; Redeuil, Karine; Rezzi, Serge

2009-11-15

The present paper describes the performance of online, gas-phase hydrogen/deuterium exchange implemented in the ion mobility cell of a quadrupole time-of-flight mass spectrometer. Deuterium oxide and deuterated methanol were utilized to create deuterated vapor that is introduced into the ion mobility region of the mass spectrometer. Hydrogen/deuterium exchange occurs spontaneously in the milliseconds time frame without the need of switching the instrument into ion mobility mode. The exchange was studied in case of low molecular weight molecules and proteins. The observed number of exchanged hydrogens was equal to the number of theoretically exchangeable hydrogens for all low molecular weight compounds. This method needs only minimal instrumental modifications, is simple, cheap, environment friendly, compatible with ultraperformance liquid chromatography, and can be implemented on commercially available instruments. It does not compromise choice of liquid chromatographic solvents and accurate mass or parallel-fragmentation (MS(E)) methods. The performance of this method was compared to that of conventional alternatives where the deuterated solvent is introduced into the cone gas of the instrument. Although the degree of exchange was similar between the two methods, the "cone gas method" requires 10 times higher deuterated solvent volumes (50 muL/min) and offers reduced sensitivity in the tandem mass spectrometry (MS/MS) mode. The presented method is suggested as a standard future element of mass spectrometers to aid online structural characterization of unknowns and to study conformational changes of proteins with hydrogen/deuterium exchange.

Momentum Advection on a Staggered Mesh

NASA Astrophysics Data System (ADS)

Benson, David J.

1992-05-01

Eulerian and ALE (arbitrary Lagrangian-Eulerian) hydrodynamics programs usually split a timestep into two parts. The first part is a Lagrangian step, which calculates the incremental motion of the material. The second part is referred to as the Eulerian step, the advection step, or the remap step, and it accounts for the transport of material between cells. In most finite difference and finite element formulations, all the solution variables except the velocities are cell-centered while the velocities are edge- or vertex-centered. As a result, the advection algorithm for the momentum is, by necessity, different than the algorithm used for the other variables. This paper reviews three momentum advection methods and proposes a new one. One method, pioneered in YAQUI, creates a new staggered mesh, while the other two, used in SALE and SHALE, are cell-centered. The new method is cell-centered and its relationship to the other methods is discussed. Both pure advection and strong shock calculations are presented to substantiate the mathematical analysis. From the standpoint of numerical accuracy, both the staggered mesh and the cell-centered algorithms can give good results, while the computational costs are highly dependent on the overall architecture of a code.

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

PubMed

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

2008-03-01

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

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

DOEpatents

Liu, Wei; Canfield, Nathan L.

2016-11-15

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

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.

Linking Chaotic Advection with Subsurface Biogeochemical Processes

NASA Astrophysics Data System (ADS)

Mays, D. C.; Freedman, V. L.; White, S. K.; Fang, Y.; Neupauer, R.

2017-12-01

This work investigates the extent to which groundwater flow kinematics drive subsurface biogeochemical processes. In terms of groundwater flow kinematics, we consider chaotic advection, whose essential ingredient is stretching and folding of plumes. Chaotic advection is appealing within the context of groundwater remediation because it has been shown to optimize plume spreading in the laminar flows characteristic of aquifers. In terms of subsurface biogeochemical processes, we consider an existing model for microbially-mediated reduction of relatively mobile uranium(VI) to relatively immobile uranium(IV) following injection of acetate into a floodplain aquifer beneath a former uranium mill in Rifle, Colorado. This model has been implemented in the reactive transport code eSTOMP, the massively parallel version of STOMP (Subsurface Transport Over Multiple Phases). This presentation will report preliminary numerical simulations in which the hydraulic boundary conditions in the eSTOMP model are manipulated to simulate chaotic advection resulting from engineered injection and extraction of water through a manifold of wells surrounding the plume of injected acetate. This approach provides an avenue to simulate the impact of chaotic advection within the existing framework of the eSTOMP code.

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.

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.

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).

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.

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.

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.

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.

Evapotranspiration under advective conditions.

PubMed

Figuerola, Patricia I; Berliner, Pedro R

2005-07-01

Arid and semi-arid regions are heterogeneous landscapes in which irrigated fields are surrounded by arid areas. The advection of sensible heat flux from dry surfaces is a significant source of energy that has to be taken into consideration when evaluating the evaporation from crops growing in these areas. The basic requirement of most of the common methods for estimating evapotranspiration [Bowen ratio, aerodynamic and Penman-Monteith (PM) equation] is that the horizontal fluxes of sensible and latent heat are negligible when compared to the corresponding vertical fluxes. We carried out measurements above an irrigated tomato field in a desert area. Latent and sensible heat fluxes were measured using a four-level Bowen machine with aspirated psychrometers. Our results indicate that under advective conditions only measurements carried out in the lowest layer are satisfactory for the estimation of latent heat fluxes and that the use of the PM equation with an appropriately parameterized canopy resistance may be preferable.

Diffusion-advection within dynamic biological gaps driven by structural motion

NASA Astrophysics Data System (ADS)

Asaro, Robert J.; Zhu, Qiang; Lin, Kuanpo

2018-04-01

To study the significance of advection in the transport of solutes, or particles, within thin biological gaps (channels), we examine theoretically the process driven by stochastic fluid flow caused by random thermal structural motion, and we compare it with transport via diffusion. The model geometry chosen resembles the synaptic cleft; this choice is motivated by the cleft's readily modeled structure, which allows for well-defined mechanical and physical features that control the advection process. Our analysis defines a Péclet-like number, AD, that quantifies the ratio of time scales of advection versus diffusion. Another parameter, AM, is also defined by the analysis that quantifies the full potential extent of advection in the absence of diffusion. These parameters provide a clear and compact description of the interplay among the well-defined structural, geometric, and physical properties vis-a ̀-vis the advection versus diffusion process. For example, it is found that AD˜1 /R2 , where R is the cleft diameter and hence diffusion distance. This curious, and perhaps unexpected, result follows from the dependence of structural motion that drives fluid flow on R . AM, on the other hand, is directly related (essentially proportional to) the energetic input into structural motion, and thereby to fluid flow, as well as to the mechanical stiffness of the cleftlike structure. Our model analysis thus provides unambiguous insight into the prospect of competition of advection versus diffusion within biological gaplike structures. The importance of the random, versus a regular, nature of structural motion and of the resulting transient nature of advection under random motion is made clear in our analysis. Further, by quantifying the effects of geometric and physical properties on the competition between advection and diffusion, our results clearly demonstrate the important role that metabolic energy (ATP) plays in this competitive process.

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.

SQuAd - Approach for the Spatial Quantification of the Advection influence on the balance closure of greenhouse gases

NASA Astrophysics Data System (ADS)

Schuetze, C.; Barth, M.; Hehn, M.; Ziemann, A.

2016-12-01

The eddy-covariance (EC) method can provide information about turbulent fluxes of energy and greenhouse gases (GHG) accurately if all necessary corrections and conversions are applied to the measured raw data and all boundary conditions for the method are satisfied. Nevertheless and even in flat terrain, advection can occur leading to a closing gap of energy and matter balances. Without accounting for advection, annual estimates of CO2 sink strength are overestimated, because advection usually results in underestimation of nocturnal CO2 flux. Advection is produced by low-frequent exchange processes, which can occur due to the surface heterogeneity. To measure advective fluxes there is still and strongly a need for ground-based remote sensing techniques which provide the relevant GHG concentration together with wind components spatially resolved within the same voxel structure. The SQuAd-approach applies an integrated method combination of acoustic tomography and open-path optical remote sensing based on infrared spectroscopy with the aim to obtain spatially and temporally resolved information about wind components and GHG concentration. The monitoring approach focuses on the validation of the joint application of the two independent, non-intrusive methods concerning the ability to close the existent gap in GHG balance. The innovative combination of acoustic travel-time tomography (A-TOM) and open-path Fourier transform infrared spectroscopy (OP-FTIR) together with atmospheric modelling will enable an upscaling and enhancement of EC measurements. OP-FTIR instrumentation has the significant advantage of real-time simultaneous measurements of line-averaged concentrations for CO2 and other GHG with high precision. A-TOM is a scalable method to remotely resolve 3D wind and temperature fields. The presentation will give an overview about the proposed method combination and results of experimental validation tests at an ICOS site (flat grassland) in Eastern Germany.

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.

Generalized Fourier analyses of the advection-diffusion equation - Part I: one-dimensional domains

NASA Astrophysics Data System (ADS)

Christon, Mark A.; Martinez, Mario J.; Voth, Thomas E.

2004-07-01

This paper 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 speed, discrete diffusivity, artificial diffusivity, and grid-induced anisotropy. It is demonstrated that Fourier analysis provides an automatic process for separating the discrete advective operator into its symmetric and skew-symmetric components and characterizing the spectral behaviour of each operator. 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. It is demonstrated that streamline upwind Petrov-Galerkin and its control-volume finite element analogue, the streamline upwind control-volume method, produce both an artificial diffusivity and a concomitant phase speed adjustment in addition to the usual semi-discrete artifacts observed in the phase speed, group speed and diffusivity. The Galerkin finite element method and its streamline upwind derivatives are shown to exhibit super-convergent behaviour 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 behaviour. In Part II of this paper, we consider two-dimensional semi-discretizations of the advection-diffusion equation and also assess the affects of grid-induced anisotropy observed in the non-dimensional phase speed, and the discrete and artificial diffusivities. Although 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 analysis framework. Published in 2004 by John Wiley & Sons, Ltd.

Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry.

PubMed

Claesen, Jürgen; Burzykowski, Tomasz

2017-09-01

Hydrogen/Deuterium exchange (HDX) has been applied, since the 1930s, as an analytical tool to study the structure and dynamics of (small) biomolecules. The popularity of using HDX to study proteins increased drastically in the last two decades due to the successful combination with mass spectrometry (MS). Together with this growth in popularity, several technological advances have been made, such as improved quenching and fragmentation. As a consequence of these experimental improvements and the increased use of protein-HDXMS, large amounts of complex data are generated, which require appropriate analysis. Computational analysis of HDXMS requires several steps. A typical workflow for proteins consists of identification of (non-)deuterated peptides or fragments of the protein under study (local analysis), or identification of the deuterated protein as a whole (global analysis); determination of the deuteration level; estimation of the protection extent or exchange rates of the labile backbone amide hydrogen atoms; and a statistically sound interpretation of the estimated protection extent or exchange rates. Several algorithms, specifically designed for HDX analysis, have been proposed. They range from procedures that focus on one specific step in the analysis of HDX data to complete HDX workflow analysis tools. In this review, we provide an overview of the computational methods and discuss outstanding challenges. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:649-667, 2017. © 2016 Wiley Periodicals, Inc.

Emergent structures in reaction-advection-diffusion systems on a sphere.

PubMed

Krause, Andrew L; Burton, Abigail M; Fadai, Nabil T; Van Gorder, Robert A

2018-04-01

We demonstrate unusual effects due to the addition of advection into a two-species reaction-diffusion system on the sphere. We find that advection introduces emergent behavior due to an interplay of the traditional Turing patterning mechanisms with the compact geometry of the sphere. Unidirectional advection within the Turing space of the reaction-diffusion system causes patterns to be generated at one point of the sphere, and transported to the antipodal point where they are destroyed. We illustrate these effects numerically and deduce conditions for Turing instabilities on local projections to understand the mechanisms behind these behaviors. We compare this behavior to planar advection which is shown to only transport patterns across the domain. Analogous transport results seem to hold for the sphere under azimuthal transport or away from the antipodal points in unidirectional flow regimes.

Emergent structures in reaction-advection-diffusion systems on a sphere

NASA Astrophysics Data System (ADS)

Krause, Andrew L.; Burton, Abigail M.; Fadai, Nabil T.; Van Gorder, Robert A.

2018-04-01

We demonstrate unusual effects due to the addition of advection into a two-species reaction-diffusion system on the sphere. We find that advection introduces emergent behavior due to an interplay of the traditional Turing patterning mechanisms with the compact geometry of the sphere. Unidirectional advection within the Turing space of the reaction-diffusion system causes patterns to be generated at one point of the sphere, and transported to the antipodal point where they are destroyed. We illustrate these effects numerically and deduce conditions for Turing instabilities on local projections to understand the mechanisms behind these behaviors. We compare this behavior to planar advection which is shown to only transport patterns across the domain. Analogous transport results seem to hold for the sphere under azimuthal transport or away from the antipodal points in unidirectional flow regimes.

An Advection-Diffusion Concept for Solute Transport in Heterogeneous Unconsolidated Geological Deposits

NASA Astrophysics Data System (ADS)

Gillham, R. W.; Sudicky, E. A.; Cherry, J. A.; Frind, E. O.

1984-03-01

In layered permeable deposits with flow predominately parallel to the bedding, advection causes rapid solute transport in the more permeable layers. As the solute advances more rapidly in these layers, solute mass is continually transferred to the less permeable layers as a result of molecular diffusion due to the concentration gradient between the layers. The interlayer solute transfer causes the concentration to decline along the permeable layers at the expense of increasing the concentration in the less permeable layers, which produces strongly dispersed concentration profiles in the direction of flow. The key parameters affecting the dispersive capability of the layered system are the diffusion coefficients for the less permeable layers, the thicknesses of the layers, and the hydraulic conductivity contrasts between the layers. Because interlayer solute transfer by transverse molecular diffusion is a time-dependent process, the advection-diffusion concept predicts a rate of longitudinal spreading during the development of the dispersion process that is inconsistent with the classical Fickian dispersion model. A second consequence of the solute-storage effect offered by transverse diffusion into low-permeability layers is a rate of migration of the frontal portion of a contaminant in the permeable layers that is less than the groundwater velocity. Although various lines of evidence are presented in support of the advection-diffusion concept, more work is required to determine the range of geological materials for which it is applicable and to develop mathematical expressions that will make it useful as a predictive tool for application to field cases of contaminant migration.

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

NASA Astrophysics Data System (ADS)

Nagai, Tetsuro

2017-01-01

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

VAC: Versatile Advection Code

NASA Astrophysics Data System (ADS)

Tóth, Gábor; Keppens, Rony

2012-07-01

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

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.

Dynamic mass exchange in doubly degenerate binaries. I - 0.9 and 1.2 solar mass stars

NASA Technical Reports Server (NTRS)

Benz, W.; Cameron, A. G. W.; Press, W. H.; Bowers, R. L.

1990-01-01

The dynamic mass exchange process in doubly degenerate binaries was investigated using a three-dimensional numerical simulation of the evolution of a doubly degenerate binary system in which the primary is a 1.2-solar-mass white dwarf and the Roche lobe filling secondary is a 0.9-solar-mass dwarf. The results show that, in a little more than two orbital periods, the secondary is completely destroyed and transformed into a thick disk orbiting about the primary. Since only a very small fraction of the mass (0.0063 solar mass) escapes the system, the evolution of the binary results in the formation of a massive object. This object is composed of three parts, the initial white dwarf primary, a very hot pressure-supported spherical envelope, and a rotationally supported outer disk. The evolution of the system can be understood in terms of a simple analytical model where it is shown that the angular momentum carried by the mass during the transfer and stored in the disk determines the evolution of the system.

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

PubMed

Rajabi, Khadijeh

2015-01-01

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

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

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

An enriched finite element method to fractional advection-diffusion equation

NASA Astrophysics Data System (ADS)

Luan, Shengzhi; Lian, Yanping; Ying, Yuping; Tang, Shaoqiang; Wagner, Gregory J.; Liu, Wing Kam

2017-08-01

In this paper, an enriched finite element method with fractional basis [ 1,x^{α }] for spatial fractional partial differential equations is proposed to obtain more stable and accurate numerical solutions. For pure fractional diffusion equation without advection, the enriched Galerkin finite element method formulation is demonstrated to simulate the exact solution successfully without any numerical oscillation, which is advantageous compared to the traditional Galerkin finite element method with integer basis [ 1,x] . For fractional advection-diffusion equation, the oscillatory behavior becomes complex due to the introduction of the advection term which can be characterized by a fractional element Peclet number. For the purpose of addressing the more complex numerical oscillation, an enriched Petrov-Galerkin finite element method is developed by using a dimensionless fractional stabilization parameter, which is formulated through a minimization of the residual of the nodal solution. The effectiveness and accuracy of the enriched finite element method are demonstrated by a series of numerical examples of fractional diffusion equation and fractional advection-diffusion equation, including both one-dimensional and two-dimensional, steady-state and time-dependent cases.

Verification of Advective Bar Elements Implemented in the Aria Thermal Response Code.

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

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 tomore » 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.« less

Analytical solution for the advection-dispersion transport equation in layered media

USDA-ARS?s Scientific Manuscript database

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...

Advection and dispersion of bed load tracers

NASA Astrophysics Data System (ADS)

Lajeunesse, Eric; Devauchelle, Olivier; James, François

2018-05-01

We use the erosion-deposition model introduced by Charru et al. (2004) to numerically simulate the evolution of a plume of bed load tracers entrained by a steady flow. In this model, the propagation of the plume results from the stochastic exchange of particles between the bed and the bed load layer. We find a transition between two asymptotic regimes. The tracers, initially at rest, are gradually set into motion by the flow. During this entrainment regime, the plume is strongly skewed in the direction of propagation and continuously accelerates while spreading nonlinearly. With time, the skewness of the plume eventually reaches a maximum value before decreasing. This marks the transition to an advection-diffusion regime in which the plume becomes increasingly symmetrical, spreads linearly, and advances at constant velocity. We analytically derive the expressions of the position, the variance, and the skewness of the plume and investigate their asymptotic regimes. Our model assumes steady state. In the field, however, bed load transport is intermittent. We show that the asymptotic regimes become insensitive to this intermittency when expressed in terms of the distance traveled by the plume. If this finding applies to the field, it might provide an estimate for the average bed load transport rate.

Impact of Canopy Decoupling and Subcanopy Advection on the Annual Carbon Balance of a Boreal Scots Pine Forest as Derived From Eddy Covariance

NASA Astrophysics Data System (ADS)

Jocher, Georg; Marshall, John; Nilsson, Mats B.; Linder, Sune; De Simon, Giuseppe; Hörnlund, Thomas; Lundmark, Tomas; Näsholm, Torgny; Ottosson Löfvenius, Mikaell; Tarvainen, Lasse; Wallin, Göran; Peichl, Matthias

2018-02-01

Apparent net uptake of carbon dioxide (CO2) during wintertime by an ˜ 90 year old Scots pine stand in northern Sweden led us to conduct canopy decoupling and subcanopy advection investigations over an entire year. Eddy covariance (EC) measurements ran simultaneously above and within the forest canopy for that purpose. We used the correlation of above- and below-canopy standard deviation of vertical wind speed (σw) as decoupling indicator. We identified 0.33 m s-1 and 0.06 m s-1 as site-specific σw thresholds for above- and below-canopy coupling during nighttime (global radiation <20 W m-2) and 0.23 m s-1 and 0.06 m s-1 as daytime (global radiation >20 W m-2) σw thresholds. Decoupling occurred in 53% of the annual nighttime and 14% of the annual daytime. The annual net ecosystem exchange (NEE), gross ecosystem exchange (GEE), and ecosystem respiration (Reco) derived via two-level filtered EC data were -357 g C m-2, -1,138 g C m-2, and 781 g C m-2, respectively. In comparison, both single-level friction velocity (u*) and quality filtering resulted in 22% higher NEE, mainly caused by 16% lower Reco. GEE remained similar among filtering regimes. Accounting for changes of CO2 storage across the canopy in the single-level filtered data could only marginally decrease these discrepancies. Consequently, advection appears to be responsible for the major part of this divergence. We conclude that the two-level filter is necessary to adequately address decoupling and subcanopy advection at our site, and we recommend this filter for all forested EC sites.

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

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

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.

Mean and turbulent mass flux measurements in an idealised street network.

PubMed

Carpentieri, Matteo; Robins, Alan G; Hayden, Paul; Santi, Edoardo

2018-03-01

Pollutant mass fluxes are rarely measured in the laboratory, especially their turbulent component. They play a major role in the dispersion of gases in urban areas and modern mathematical models often attempt some sort of parametrisation. An experimental technique to measure mean and turbulent fluxes in an idealised urban array was developed and applied to improve our understanding of how the fluxes are distributed in a dense street canyon network. As expected, horizontal advective scalar fluxes were found to be dominant compared with the turbulent components. This is an important result because it reduces the complexity in developing parametrisations for street network models. On the other hand, vertical mean and turbulent fluxes appear to be approximately of the same order of magnitude. Building height variability does not appear to affect the exchange process significantly, while the presence of isolated taller buildings upwind of the area of interest does. One of the most interesting results, again, is the fact that even very simple and regular geometries lead to complex advective patterns at intersections: parametrisations derived from measurements in simpler geometries are unlikely to capture the full complexity of a real urban area. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spurious sea ice formation caused by oscillatory ocean tracer advection schemes

NASA Astrophysics Data System (ADS)

Naughten, Kaitlin A.; Galton-Fenzi, Benjamin K.; Meissner, Katrin J.; England, Matthew H.; Brassington, Gary B.; Colberg, Frank; Hattermann, Tore; Debernard, Jens B.

2017-08-01

Tracer advection schemes used by ocean models are susceptible to artificial oscillations: a form of numerical error whereby the advected field alternates between overshooting and undershooting the exact solution, producing false extrema. Here we show that these oscillations have undesirable interactions with a coupled sea ice model. When oscillations cause the near-surface ocean temperature to fall below the freezing point, sea ice forms for no reason other than numerical error. This spurious sea ice formation has significant and wide-ranging impacts on Southern Ocean simulations, including the disappearance of coastal polynyas, stratification of the water column, erosion of Winter Water, and upwelling of warm Circumpolar Deep Water. This significantly limits the model's suitability for coupled ocean-ice and climate studies. Using the terrain-following-coordinate ocean model ROMS (Regional Ocean Modelling System) coupled to the sea ice model CICE (Community Ice CodE) on a circumpolar Antarctic domain, we compare the performance of three different tracer advection schemes, as well as two levels of parameterised diffusion and the addition of flux limiters to prevent numerical oscillations. The upwind third-order advection scheme performs better than the centered fourth-order and Akima fourth-order advection schemes, with far fewer incidents of spurious sea ice formation. The latter two schemes are less problematic with higher parameterised diffusion, although some supercooling artifacts persist. Spurious supercooling was eliminated by adding flux limiters to the upwind third-order scheme. We present this comparison as evidence of the problematic nature of oscillatory advection schemes in sea ice formation regions, and urge other ocean/sea-ice modellers to exercise caution when using such schemes.

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. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Advection of Potential Temperature in the Atmosphere of Irradiated Exoplanets: A Robust Mechanism to Explain Radius Inflation

NASA Technical Reports Server (NTRS)

Tremblin, P.; Chabrier, G.; Mayne, N. J.; Amundsen, D. S.; Baraffe, I.; Debras, F.; Drummond, B.; Manners, J.; Fromang, S.

2017-01-01

The anomalously large radii of strongly irradiated exoplanets have remained a major puzzle in astronomy. Based on a two-dimensional steady-state atmospheric circulation model, the validity of which is assessed by comparison to three-dimensional calculations, we reveal a new mechanism, namely the advection of the potential temperature due to mass and longitudinal momentum conservation, a process occurring in the Earth's atmosphere or oceans. In the deep atmosphere, the vanishing heating flux forces the atmospheric structure to converge to a hotter adiabat than the one obtained with 1D calculations, implying a larger radius for the planet. Not only do the calculations reproduce the observed radius of HD 209458b, but also reproduce the observed correlation between radius inflation and irradiation for transiting planets. Vertical advection of potential temperature induced by non-uniform atmospheric heating thus provides a robust mechanism to explain the inflated radii of irradiated hot Jupiters.

Evolution of Advection Upstream Splitting Method Schemes

NASA Technical Reports Server (NTRS)

Liou, Meng-Sing

2010-01-01

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

Estimates of advection and diffusion in the Potomac estuary

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

Elliott, A.J.

1976-01-01

A two-layered dispersion model, suitable for application to partially-mixed estuaries, has been developed to provide hydrological interpretation of the results of biological sampling. The model includes horizontal and vertical advection plus both horizontal and vertical diffusion. A pseudo-geostrophic method, which includes a damping factor to account for internal eddy friction, is used to estimate the horizontal advective fluxes and the results are compared with field observations. A salt balance model is then used to estimate the effective diffusivities in the Potomac estuary during the Spring of 1974.

A semi-Lagrangian advection scheme for radioactive tracers in a regional spectral model

NASA Astrophysics Data System (ADS)

Chang, E.-C.; Yoshimura, K.

2015-06-01

In this study, the non-iteration dimensional-split semi-Lagrangian (NDSL) advection scheme is applied to the National Centers for Environmental Prediction (NCEP) regional spectral model (RSM) to alleviate the Gibbs phenomenon. The Gibbs phenomenon is a problem wherein negative values of positive-definite quantities (e.g., moisture and tracers) are generated by the spectral space transformation in a spectral model system. To solve this problem, the spectral prognostic specific humidity and radioactive tracer advection scheme is replaced by the NDSL advection scheme, which considers advection of tracers in a grid system without spectral space transformations. A regional version of the NDSL is developed in this study and is applied to the RSM. Idealized experiments show that the regional version of the NDSL is successful. The model runs for an actual case study suggest that the NDSL can successfully advect radioactive tracers (iodine-131 and cesium-137) without noise from the Gibbs phenomenon. The NDSL can also remove negative specific humidity values produced in spectral calculations without losing detailed features.

Observing mass exchange with the Lofoten Basin using surface drifters

NASA Astrophysics Data System (ADS)

Dugstad, Johannes S.; LaCasce, Joe; Koszalka, Inga M.; Fer, Ilker

2017-04-01

The Lofoten Basin in the Nordic Seas plays a central role in the global overturning circulation, acting as a reservoir for northward-flowing Atlantic water. Substantial heat loss occurs here, permitting the waters to become denser and eventually sink nearer the Arctic. Idealized modeling studies and theoretical arguments suggest the warm water enters the Lofoten Basin via eddy transport from the boundary current over the adjacent continental slope. But there is no observational evidence that this is the major contribution to mass exchange between the warm Atlantic Current and the Basin. How the basin waters exit also remains a mystery. Surface drifters offer an unique possibility to study the pathways of the boundary-basin exchange of mass and heat. We thereby examine trajectories of surface drifters released in the Nordic Seas in the POLEWARD and PROVOLO experiments, and supplemented by historical data from the Global Drifter Array. Contrary to the idea that the boundary current eddies are the main source, the results suggest that fluid is entering the Lofoten Basin from all sides. However, the drifters exit preferentially in the northeast corner of the basin. This asymmetry likely contributes to the extended residence times of the warm Atlantic waters in the Lofoten Basin. We consider various measures to quantify the effect, and test whether this is captured in a high resolution numerical model.

Using dual-domain advective-transport simulation to reconcile multiple-tracer ages and estimate dual-porosity transport parameters

NASA Astrophysics Data System (ADS)

Sanford, Ward E.; Niel Plummer, L.; Casile, Gerolamo; Busenberg, Ed; Nelms, David L.; Schlosser, Peter

2017-06-01

Dual-domain transport is an alternative conceptual and mathematical paradigm to advection-dispersion for describing the movement of dissolved constituents in groundwater. Here we test the use of a dual-domain algorithm combined with advective pathline tracking to help reconcile environmental tracer concentrations measured in springs within the Shenandoah Valley, USA. The approach also allows for the estimation of the three dual-domain parameters: mobile porosity, immobile porosity, and a domain exchange rate constant. Concentrations of CFC-113, SF6, 3H, and 3He were measured at 28 springs emanating from carbonate rocks. The different tracers give three different mean composite piston-flow ages for all the springs that vary from 5 to 18 years. Here we compare four algorithms that interpret the tracer concentrations in terms of groundwater age: piston flow, old-fraction mixing, advective-flow path modeling, and dual-domain modeling. Whereas the second two algorithms made slight improvements over piston flow at reconciling the disparate piston-flow age estimates, the dual-domain algorithm gave a very marked improvement. Optimal values for the three transport parameters were also obtained, although the immobile porosity value was not well constrained. Parameter correlation and sensitivities were calculated to help quantify the uncertainty. Although some correlation exists between the three parameters being estimated, a watershed simulation of a pollutant breakthrough to a local stream illustrates that the estimated transport parameters can still substantially help to constrain and predict the nature and timing of solute transport. The combined use of multiple environmental tracers with this dual-domain approach could be applicable in a wide variety of fractured-rock settings.

Advection of Potential Temperature in the Atmosphere of Irradiated Exoplanets: A Robust Mechanism to Explain Radius Inflation

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

Tremblin, P.; Chabrier, G.; Mayne, N. J.

The anomalously large radii of strongly irradiated exoplanets have remained a major puzzle in astronomy. Based on a two-dimensional steady-state atmospheric circulation model, the validity of which is assessed by comparison to three-dimensional calculations, we reveal a new mechanism, namely the advection of the potential temperature due to mass and longitudinal momentum conservation, a process occurring in the Earth’s atmosphere or oceans. In the deep atmosphere, the vanishing heating flux forces the atmospheric structure to converge to a hotter adiabat than the one obtained with 1D calculations, implying a larger radius for the planet. Not only do the calculations reproducemore » the observed radius of HD 209458b, but also reproduce the observed correlation between radius inflation and irradiation for transiting planets. Vertical advection of potential temperature induced by non-uniform atmospheric heating thus provides a robust mechanism to explain the inflated radii of irradiated hot Jupiters.« less

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

USGS Publications Warehouse

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

Evolution of passive movement in advective environments: General boundary condition

NASA Astrophysics Data System (ADS)

Zhou, Peng; Zhao, Xiao-Qiang

2018-03-01

In a previous work [16], Lou et al. studied a Lotka-Volterra competition-diffusion-advection system, where two species are supposed to differ only in their advection rates and the environment is assumed to be spatially homogeneous and closed (no-flux boundary condition), and showed that weaker advective movements are more beneficial for species to win the competition. In this paper, we aim to extend this result to a more general situation, where the environmental heterogeneity is taken into account and the boundary condition at the downstream end becomes very flexible including the standard Dirichlet, Neumann and Robin type conditions as special cases. Our main approaches are to exclude the existence of co-existence (positive) steady state and to provide a clear picture on the stability of semi-trivial steady states, where we introduced new ideas and techniques to overcome the emerging difficulties. Based on these two aspects and the theory of abstract competitive systems, we achieve a complete understanding on the global dynamics.

Using Rising Limb Analysis to Estimate Uptake of Reactive Solutes in Advective and Transient Storage Sub-compartments of Stream Ecosystems

NASA Astrophysics Data System (ADS)

Thomas, S. A.; Valett, H.; Webster, J. R.; Mulholland, P. J.; Dahm, C. N.

2001-12-01

Identifying the locations and controls governing solute uptake is a recent area of focus in studies of stream biogeochemistry. We introduce a technique, rising limb analysis (RLA), to estimate areal nitrate uptake in the advective and transient storage (TS) zones of streams. RLA is an inverse approach that combines nutrient spiraling and transient storage modeling to calculate total uptake of reactive solutes and the fraction of uptake occurring within the advective sub-compartment of streams. The contribution of the transient storage zones to solute loss is determined by difference. Twelve-hour coinjections of conservative (Cl-) and reactive (15NO3) tracers were conducted seasonally in several headwater streams among which AS/A ranged from 0.01 - 2.0. TS characteristics were determined using an advection-dispersion model modified to include hydrologic exchange with a transient storage compartment. Whole-system uptake was determined by fitting the longitudinal pattern of NO3 to first-order, exponential decay model. Uptake in the advective sub-compartment was determined by collecting a temporal sequence of samples from a single location beginning with the arrival of the solute front and concluding with the onset of plateau conditions (i.e. the rising limb). Across the rising limb, 15NO3:Cl was regressed against the percentage of water that had resided in the transient storage zone (calculated from the TS modeling). The y-intercept thus provides an estimate of the plateau 15NO3:Cl ratio in the absence of NO3 uptake within the transient storage zone. Algebraic expressions were used to calculate the percentage of NO3 uptake occurring in the advective and transient storage sub-compartments. Application of RLA successfully estimated uptake coefficients for NO3 in the subsurface when the physical dimensions of that habitat were substantial (AS/A > 0.2) and when plateau conditions at the sampling location consisted of waters in which at least 25% had resided in the

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.

Hydrogen exchange mass spectrometry of functional membrane-bound chemotaxis receptor complexes.

PubMed

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

2013-12-10

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 toward 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-deuterium exchange mass spectrometry (HDX-MS) measurements of global exchange of the CF demonstrate that the CF exhibits significantly slower exchange in functional complexes than in solution. Because the exchange rates in functional complexes are comparable to those of other proteins with similar structures, 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.

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

Conservative and bounded volume-of-fluid advection on unstructured grids

NASA Astrophysics Data System (ADS)

Ivey, Christopher B.; Moin, Parviz

2017-12-01

This paper presents a novel Eulerian-Lagrangian piecewise-linear interface calculation (PLIC) volume-of-fluid (VOF) advection method, which is three-dimensional, unsplit, and discretely conservative and bounded. The approach is developed with reference to a collocated node-based finite-volume two-phase flow solver that utilizes the median-dual mesh constructed from non-convex polyhedra. The proposed advection algorithm satisfies conservation and boundedness of the liquid volume fraction irrespective of the underlying flux polyhedron geometry, which differs from contemporary unsplit VOF schemes that prescribe topologically complicated flux polyhedron geometries in efforts to satisfy conservation. Instead of prescribing complicated flux-polyhedron geometries, which are prone to topological failures, our VOF advection scheme, the non-intersecting flux polyhedron advection (NIFPA) method, builds the flux polyhedron iteratively such that its intersection with neighboring flux polyhedra, and any other unavailable volume, is empty and its total volume matches the calculated flux volume. During each iteration, a candidate nominal flux polyhedron is extruded using an iteration dependent scalar. The candidate is subsequently intersected with the volume guaranteed available to it at the time of the flux calculation to generate the candidate flux polyhedron. The difference in the volume of the candidate flux polyhedron and the actual flux volume is used to calculate extrusion during the next iteration. The choice in nominal flux polyhedron impacts the cost and accuracy of the scheme; however, it does not impact the methods underlying conservation and boundedness. As such, various robust nominal flux polyhedron are proposed and tested using canonical periodic kinematic test cases: Zalesak's disk and two- and three-dimensional deformation. The tests are conducted on the median duals of a quadrilateral and triangular primal mesh, in two-dimensions, and on the median duals of a

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.

A novel finite volume discretization method for advection-diffusion systems on stretched meshes

NASA Astrophysics Data System (ADS)

Merrick, D. G.; Malan, A. G.; van Rooyen, J. A.

2018-06-01

This work is concerned with spatial advection and diffusion discretization technology within the field of Computational Fluid Dynamics (CFD). In this context, a novel method is proposed, which is dubbed the Enhanced Taylor Advection-Diffusion (ETAD) scheme. The model equation employed for design of the scheme is the scalar advection-diffusion equation, the industrial application being incompressible laminar and turbulent flow. Developed to be implementable into finite volume codes, ETAD places specific emphasis on improving accuracy on stretched structured and unstructured meshes while considering both advection and diffusion aspects in a holistic manner. A vertex-centered structured and unstructured finite volume scheme is used, and only data available on either side of the volume face is employed. This includes the addition of a so-called mesh stretching metric. Additionally, non-linear blending with the existing NVSF scheme was performed in the interest of robustness and stability, particularly on equispaced meshes. The developed scheme is assessed in terms of accuracy - this is done analytically and numerically, via comparison to upwind methods which include the popular QUICK and CUI techniques. Numerical tests involved the 1D scalar advection-diffusion equation, a 2D lid driven cavity and turbulent flow case. Significant improvements in accuracy were achieved, with L2 error reductions of up to 75%.

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.

First-Order Hyperbolic System Method for Time-Dependent Advection-Diffusion Problems

DTIC Science & Technology

2014-03-01

accuracy, with rapid convergence over each physical time step, typically less than five Newton iter - ations. 1 Contents 1 Introduction 3 2 Hyperbolic...however, we employ the Gauss - Seidel (GS) relaxation, which is also an O(N) method for the discretization arising from hyperbolic advection-diffusion system...advection-diffusion scheme. The linear dependency of the iterations on Table 1: Boundary layer problem ( Convergence criteria: Residuals < 10−8.) log10Re

Advection and Taylor-Aris dispersion in rivulet flow

NASA Astrophysics Data System (ADS)

Al Mukahal, F. H. H.; Duffy, B. R.; Wilson, S. K.

2017-11-01

Motivated by the need for a better understanding of the transport of solutes in microfluidic flows with free surfaces, the advection and dispersion of a passive solute in steady unidirectional flow of a thin uniform rivulet on an inclined planar substrate driven by gravity and/or a uniform longitudinal surface shear stress are analysed. Firstly, we describe the short-time advection of both an initially semi-infinite and an initially finite slug of solute of uniform concentration. Secondly, we describe the long-time Taylor-Aris dispersion of an initially finite slug of solute. In particular, we obtain the general expression for the effective diffusivity for Taylor-Aris dispersion in such a rivulet, and discuss in detail its different interpretations in the special case of a rivulet on a vertical substrate.

Numerical simulation of large-scale bed load particle tracer advection-dispersion in rivers with free bars

USGS Publications Warehouse

Iwasaki, Toshiki; Nelson, Jonathan M.; Shimizu, Yasuyuki; Parker, Gary

2017-01-01

Asymptotic characteristics of the transport of bed load tracer particles in rivers have been described by advection-dispersion equations. Here we perform numerical simulations designed to study the role of free bars, and more specifically single-row alternate bars, on streamwise tracer particle dispersion. In treating the conservation of tracer particle mass, we use two alternative formulations for the Exner equation of sediment mass conservation: the flux-based formulation, in which bed elevation varies with the divergence of the bed load transport rate, and the entrainment-based formulation, in which bed elevation changes with the net deposition rate. Under the condition of no net bed aggradation/degradation, a 1-D flux-based deterministic model that does not describe free bars yields no streamwise dispersion. The entrainment-based 1-D formulation, on the other hand, models stochasticity via the probability density function (PDF) of particle step length, and as a result does show tracer dispersion. When the formulation is generalized to 2-D to include free alternate bars, however, both models yield almost identical asymptotic advection-dispersion characteristics, in which streamwise dispersion is dominated by randomness inherent in free bar morphodynamics. This randomness can result in a heavy-tailed PDF of waiting time. In addition, migrating bars may constrain the travel distance through temporary burial, causing a thin-tailed PDF of travel distance. The superdiffusive character of streamwise particle dispersion predicted by the model is attributable to the interaction of these two effects.

Numerical simulation of large-scale bed load particle tracer advection-dispersion in rivers with free bars

NASA Astrophysics Data System (ADS)

Iwasaki, Toshiki; Nelson, Jonathan; Shimizu, Yasuyuki; Parker, Gary

2017-04-01

Asymptotic characteristics of the transport of bed load tracer particles in rivers have been described by advection-dispersion equations. Here we perform numerical simulations designed to study the role of free bars, and more specifically single-row alternate bars, on streamwise tracer particle dispersion. In treating the conservation of tracer particle mass, we use two alternative formulations for the Exner equation of sediment mass conservation: the flux-based formulation, in which bed elevation varies with the divergence of the bed load transport rate, and the entrainment-based formulation, in which bed elevation changes with the net deposition rate. Under the condition of no net bed aggradation/degradation, a 1-D flux-based deterministic model that does not describe free bars yields no streamwise dispersion. The entrainment-based 1-D formulation, on the other hand, models stochasticity via the probability density function (PDF) of particle step length, and as a result does show tracer dispersion. When the formulation is generalized to 2-D to include free alternate bars, however, both models yield almost identical asymptotic advection-dispersion characteristics, in which streamwise dispersion is dominated by randomness inherent in free bar morphodynamics. This randomness can result in a heavy-tailed PDF of waiting time. In addition, migrating bars may constrain the travel distance through temporary burial, causing a thin-tailed PDF of travel distance. The superdiffusive character of streamwise particle dispersion predicted by the model is attributable to the interaction of these two effects.

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

Distinguishing advective and powered motion in self-propelled colloids

NASA Astrophysics Data System (ADS)

Byun, Young-Moo; Lammert, Paul E.; Hong, Yiying; Sen, Ayusman; Crespi, Vincent H.

2017-11-01

Self-powered motion in catalytic colloidal particles provides a compelling example of active matter, i.e. systems that engage in single-particle and collective behavior far from equilibrium. The long-time, long-distance behavior of such systems is of particular interest, since it connects their individual micro-scale behavior to macro-scale phenomena. In such analyses, it is important to distinguish motion due to subtle advective effects—which also has long time scales and length scales—from long-timescale phenomena that derive from intrinsically powered motion. Here, we develop a methodology to analyze the statistical properties of the translational and rotational motions of powered colloids to distinguish, for example, active chemotaxis from passive advection by bulk flow.

Convective instability and boundary driven oscillations in a reaction-diffusion-advection model

NASA Astrophysics Data System (ADS)

Vidal-Henriquez, Estefania; Zykov, Vladimir; Bodenschatz, Eberhard; Gholami, Azam

2017-10-01

In a reaction-diffusion-advection system, with a convectively unstable regime, a perturbation creates a wave train that is advected downstream and eventually leaves the system. We show that the convective instability coexists with a local absolute instability when a fixed boundary condition upstream is imposed. This boundary induced instability acts as a continuous wave source, creating a local periodic excitation near the boundary, which initiates waves travelling both up and downstream. To confirm this, we performed analytical analysis and numerical simulations of a modified Martiel-Goldbeter reaction-diffusion model with the addition of an advection term. We provide a quantitative description of the wave packet appearing in the convectively unstable regime, which we found to be in excellent agreement with the numerical simulations. We characterize this new instability and show that in the limit of high advection speed, it is suppressed. This type of instability can be expected for reaction-diffusion systems that present both a convective instability and an excitable regime. In particular, it can be relevant to understand the signaling mechanism of the social amoeba Dictyostelium discoideum that may experience fluid flows in its natural habitat.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

An instrumented mooring line with sediment traps, current meters and recorders of temperature and conductivity was deployed just south of the Antarctic Polar Front (63° 26‧ S, 178° 03‧E; water depth 4400 m) from January 9th 1999 to January 10th 2000. Sediment traps at 900 and 3700 m had a single large cup to collect particulate material throughout the 1-year study whereas time-series sediment traps were used to characterize the temporal variability at 1300 and 2400 m. Samples were characterized via several parameters including total mass flux, elemental composition (organic carbon, total nitrogen, biogenic silica, and calcium carbonate), concentration of metals (aluminum, iron, barium, and manganese), 210Pb activity, and foraminifera identification. High vertical fluxes of biogenic particles were observed in both summer 1999 and 2000 as a result of seasonal algal blooms associated with sea ice retreat and water column stratification. During autumn and winter, several high energy events occurred and resulted in advecting resuspended biogenic particles from flat-topped summits of the Pacific Antarctic Ridge. Whereas the distance between seabed and uppermost sediment traps was sufficient to avoid lateral advection processes, resuspension was significant in the lowermost sediment traps accounting for ~ 60 and ~ 90% of the material caught at 2400 and 3700 m, respectively. Although resuspended material showed an elemental composition relatively similar to vertical summer fluxes, samples collected during high energy events contained benthic foraminifera and exhibited significantly higher 210Pb activity indicating a longer residence time in the water column. In addition, during quiescent periods characterized by low mass fluxes, the content of lithogenic particles increased at the expense of phytodetritus indicating the influence of material advected through the benthic nepheloid layer. Organic matter content was particularly high during these periods and showed

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.

Fractional vector calculus for fractional advection dispersion

NASA Astrophysics Data System (ADS)

Meerschaert, Mark M.; Mortensen, Jeff; Wheatcraft, Stephen W.

2006-07-01

We develop the basic tools of fractional vector calculus including a fractional derivative version of the gradient, divergence, and curl, and a fractional divergence theorem and Stokes theorem. These basic tools are then applied to provide a physical explanation for the fractional advection-dispersion equation for flow in heterogeneous porous media.

Actin Isoform-specific Conformational Differences Observed with Hydrogen/Deuterium Exchange and Mass Spectrometry*

PubMed Central

Stokasimov, Ema; Rubenstein, Peter A.

2009-01-01

Actin can exist in multiple conformations necessary for normal function. Actin isoforms, although highly conserved in sequence, exhibit different biochemical properties and cellular roles. We used amide proton hydrogen/deuterium (HD) exchange detected by mass spectrometry to analyze conformational differences between Saccharomyces cerevisiae and muscle actins in the G and F forms to gain insight into these differences. We also utilized HD exchange to study interdomain and allosteric communication in yeast-muscle hybrid actins to better understand the conformational dynamics of actin. Areas showing differences in HD exchange between G- and F-actins are areas of intermonomer contacts, consistent with the current filament models. Our results showed greater exchange for yeast G-actin compared with muscle actin in the barbed end pivot region and areas in subdomains 1 and 2 and for F-actin in monomer-monomer contact areas. These results suggest greater flexibility of the yeast actin monomer and filament compared with muscle actin. For hybrid G-actins, the muscle-like and yeastlike parts of the molecule generally showed exchange characteristics resembling their parent actins. A few exceptions were a peptide on top of subdomain 2 and the pivot region between subdomains 1 and 3 with muscle actin-like exchange characteristics although the areas were yeastlike. These results demonstrate that there is cross-talk between subdomains 1 and 2 and the large and small domains. Hybrid F-actin data showing greater exchange compared with both yeast and muscle actins are consistent with mismatched yeast-muscle interfaces resulting in decreased stability of the hybrid filament contacts. PMID:19605362

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.

Improved protein hydrogen/deuterium exchange mass spectrometry platform with fully automated data processing.

PubMed

Zhang, Zhongqi; Zhang, Aming; Xiao, Gang

2012-06-05

Protein hydrogen/deuterium exchange (HDX) followed by protease digestion and mass spectrometric (MS) analysis is accepted as a standard method for studying protein conformation and conformational dynamics. In this article, an improved HDX MS platform with fully automated data processing is described. The platform significantly reduces systematic and random errors in the measurement by introducing two types of corrections in HDX data analysis. First, a mixture of short peptides with fast HDX rates is introduced as internal standards to adjust the variations in the extent of back exchange from run to run. Second, a designed unique peptide (PPPI) with slow intrinsic HDX rate is employed as another internal standard to reflect the possible differences in protein intrinsic HDX rates when protein conformations at different solution conditions are compared. HDX data processing is achieved with a comprehensive HDX model to simulate the deuterium labeling and back exchange process. The HDX model is implemented into the in-house developed software MassAnalyzer and enables fully unattended analysis of the entire protein HDX MS data set starting from ion detection and peptide identification to final processed HDX output, typically within 1 day. The final output of the automated data processing is a set (or the average) of the most possible protection factors for each backbone amide hydrogen. The utility of the HDX MS platform is demonstrated by exploring the conformational transition of a monoclonal antibody by increasing concentrations of guanidine.

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).

A semi-Lagrangian advection scheme for radioactive tracers in the NCEP Regional Spectral Model (RSM)

NASA Astrophysics Data System (ADS)

Chang, E.-C.; Yoshimura, K.

2015-10-01

In this study, the non-iteration dimensional-split semi-Lagrangian (NDSL) advection scheme is applied to the National Centers for Environmental Prediction (NCEP) Regional Spectral Model (RSM) to alleviate the Gibbs phenomenon. The Gibbs phenomenon is a problem wherein negative values of positive-definite quantities (e.g., moisture and tracers) are generated by the spectral space transformation in a spectral model system. To solve this problem, the spectral prognostic specific humidity and radioactive tracer advection scheme is replaced by the NDSL advection scheme, which considers advection of tracers in a grid system without spectral space transformations. A regional version of the NDSL is developed in this study and is applied to the RSM. Idealized experiments show that the regional version of the NDSL is successful. The model runs for an actual case study suggest that the NDSL can successfully advect radioactive tracers (iodine-131 and cesium-137) without noise from the Gibbs phenomenon. The NDSL can also remove negative specific humidity values produced in spectral calculations without losing detailed features.

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.

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

PubMed

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

2003-01-01

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

Generalized fourier analyses of the advection-diffusion equation - Part II: two-dimensional domains

NASA Astrophysics Data System (ADS)

Voth, Thomas E.; Martinez, Mario J.; Christon, Mark A.

2004-07-01

Part I of this work presents a detailed multi-methods comparison of the spatial errors associated with the one-dimensional finite difference, finite element and finite volume semi-discretizations of the scalar advection-diffusion equation. In Part II we extend the analysis to two-dimensional domains and also consider the effects of wave propagation direction and grid aspect ratio on the phase speed, and the discrete and artificial diffusivities. The observed dependence of dispersive and diffusive behaviour on propagation direction makes comparison of methods more difficult relative to the one-dimensional results. For this reason, integrated (over propagation direction and wave number) error and anisotropy metrics are introduced to facilitate comparison among the various methods. With respect to these metrics, the consistent mass Galerkin and consistent mass control-volume finite element methods, and their streamline upwind derivatives, exhibit comparable accuracy, and generally out-perform their lumped mass counterparts and finite-difference based schemes. 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. Published in 2004 by John Wiley & Sons, Ltd.

A Study of the Physical Processes of an Advection Fog Boundary Layer

NASA Astrophysics Data System (ADS)

Liu, Duan Yang; Yan, Wen Lian; Yang, Jun; Pu, Mei Juan; Niu, Sheng Jie; Li, Zi Hua

2016-01-01

A large quantity of advection fog appeared in the Yangtze River delta region between 1 and 2 December 2009. Here, we detail the fog formation and dissipation processes and the background weather conditions. The fog boundary layer and its formation and dissipation mechanisms have also been analyzed using field data recorded in a northern suburb of Nanjing. The results showed the following: (1) This advection fog was generated by interaction between advection of a north-east cold ground layer and a south-east warm upper layer. The double-inversion structure generated by this interaction between the cold and warm advections and steady south-east vapour transport was the main cause of this long-lasting fog. The double-inversion structure provided good thermal conditions for the thick fog, and the south-east vapour transport was not only conducive to maintaining the thickness of the fog but also sustained its long duration. (2) The fog-top altitude was over 600 m for most of the time, and the fog reduced visibility to less than 100 m for approximately 12 h. (3) The low-level jet near the lower inversion layer also played a role in maintaining the thick fog system by promoting heat, momentum and south-east vapour transport.

Simulation of Helical Flow Hydrodynamics in Meanders and Advection-Turbulent Diffusion Using Smoothed Particle Hydrodynamics

NASA Astrophysics Data System (ADS)

Gusti, T. P.; Hertanti, D. R.; Bahsan, E.; Soeryantono, H.

2013-12-01

Particle-based numerical methods, such as Smoothed Particle Hydrodynamics (SPH), may be able to simulate some hydrodynamic and morphodynamic behaviors better than grid-based numerical methods. This study simulates hydrodynamics in meanders and advection and turbulent diffusion in straight river channels using Microsoft Excel and Visual Basic. The simulators generate three-dimensional data for hydrodynamics and one-dimensional data for advection-turbulent diffusion. Fluid at rest, sloshing, and helical flow are simulated in the river meanders. Spill loading and step loading are done to simulate concentration patterns associated with advection-turbulent diffusion. Results indicate that helical flow is formed due to disturbance in morphology and particle velocity in the stream and the number of particles does not have a significant effect on the pattern of advection-turbulent diffusion concentration.

Hydrogen-Exchange Mass Spectrometry for the Study of Intrinsic Disorder in Proteins

PubMed Central

Balasubramaniam, Deepa; Komives, Elizabeth A.

2012-01-01

Amide hydrogen/deuterium exchange detected by mass spectrometry (HXMS) is seeing wider use for the identification of intrinsically disordered parts of proteins. In this review, we discuss examples of how discovery of intrinsically disordered regions and their removal can aid in structure determination, biopharmaceutical quality control, the characterization of how posttranslational modifications affect weak structuring of disordered regions, the study of coupled folding and binding, and the characterization of amyloid formation. PMID:23099262

Anomalous scaling of a scalar field advected by turbulence

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

Kraichnan, R.H.

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.

Site-Specific Hydrogen Isotope Composition of Propane: Mass spectrometric methods, equilibrium temperature dependence, and kinetics of exchange

NASA Astrophysics Data System (ADS)

Xie, H.; Ponton, C.; Kitchen, N.; Lloyd, M. K.; Lawson, M.; Formolo, M. J.; Eiler, J. M.

2016-12-01

Intramolecular isotope ordering can constrain temperatures of synthesis, mechanisms of formation, and/or source substrates of organic compounds. Here we explore site-specific hydrogen isotope variations of propane. Statistical thermodynamic models predict that at equilibrium methylene hydrogen (-CH2-) in propane will be 10's of per mil higher in D/H ratio than methyl hydrogen (-CH3) at geologically relevant temperatures, and that this difference is highly temperature dependent ( 0.5-1 ‰/°C). Chemical-kinetic controls on site-specific D/H in propane could constrain the mechanisms, conditions and extents of propane synthesis or destruction. We have developed a method for measuring the difference in D/H ratio between methylene and methyl hydrogen in propane by gas source mass spectrometry. The data were measured using the Thermo Fisher Double Focusing Sector high resolution mass spectrometer (DFS), and involve comparison of the D/H ratios of molecular ion (C3H8+) and the ethyl fragmental ion (C2H5+). We demonstrate the accuracy and precision of this method through analysis of D-labeled and independently analyzed propanes. In the exchange experiments, propane was heated (100-200 oC) either alone or in the presence of D-enriched water (δD=1,1419 ‰ SMOW), with or without one of several potentially catalytic substrates for hours to weeks. Propane was found to exchange hydrogen with water vigorously at 200 °C in the presence of metal catalysts. In the presence of Ni catalyst, methylene hydrogen exchanges 2.5 times faster than methyl hydrogen. Hydrogen exchange in the presence of Pd catalyst is more effective and can equilibrate hydrogen isotope distribution on propane on the order of 7 days. Isotopic exchange in the presence of natural materials have also been tested, but is only measurable in the methylene group at 200 °C. High catalytic activity of Pd permits attainment of a bracketed, time-invariant equilibrium state that we use to calibrate the site

Assessing lateral flows and solute transport during floods in a conduit-flow-dominated karst system using the inverse problem for the advection-diffusion equation

NASA Astrophysics Data System (ADS)

Cholet, Cybèle; Charlier, Jean-Baptiste; Moussa, Roger; Steinmann, Marc; Denimal, Sophie

2017-07-01

The aim of this study is to present a framework that provides new ways to characterize the spatio-temporal variability of lateral exchanges for water flow and solute transport in a karst conduit network during flood events, treating both the diffusive wave equation and the advection-diffusion equation with the same mathematical approach, assuming uniform lateral flow and solute transport. A solution to the inverse problem for the advection-diffusion equations is then applied to data from two successive gauging stations to simulate flows and solute exchange dynamics after recharge. The study site is the karst conduit network of the Fourbanne aquifer in the French Jura Mountains, which includes two reaches characterizing the network from sinkhole to cave stream to the spring. The model is applied, after separation of the base from the flood components, on discharge and total dissolved solids (TDSs) in order to assess lateral flows and solute concentrations and compare them to help identify water origin. The results showed various lateral contributions in space - between the two reaches located in the unsaturated zone (R1), and in the zone that is both unsaturated and saturated (R2) - as well as in time, according to hydrological conditions. Globally, the two reaches show a distinct response to flood routing, with important lateral inflows on R1 and large outflows on R2. By combining these results with solute exchanges and the analysis of flood routing parameters distribution, we showed that lateral inflows on R1 are the addition of diffuse infiltration (observed whatever the hydrological conditions) and localized infiltration in the secondary conduit network (tributaries) in the unsaturated zone, except in extreme dry periods. On R2, despite inflows on the base component, lateral outflows are observed during floods. This pattern was attributed to the concept of reversal flows of conduit-matrix exchanges, inducing a complex water mixing effect in the saturated zone

Thermobaricity, cabbeling, and water-mass conversion

NASA Astrophysics Data System (ADS)

McDougall, Trevor J.

1987-05-01

The efficient mixing of heat and salt along neutral surfaces (by mesoscale eddies) is shown to lead to vertical advection through these neutral surfaces. This is due to the nonlinearities of the equation of state of seawater through terms like ∂2ρ/∂θ∂p (thermobaric effect) and ∂2ρ/∂ θ2 (cabbeling). Cabbeling always causes a sinking or downwelling of fluid through neutral surfaces, whereas thermobaricity can lead to a vertical velocity (relative to neutral surfaces) of either sign. In this paper it is shown that for reasonable values of the lateral scalar diffusivity (especially below a depth of 1000 m), these two processes cause vertical velocities of the order of 10-7 m s-1 through neutral surfaces (usually downward!) and cause water-mass conversion of a magnitude equal to that caused by a vertical diffusivity of 10-4 m2 s-1 (often equivalent to a negative diffusivity). Both thermobaricity and cabbeling can occur in the presence of any nonzero amount of small-scale turbulence and so will not be detected by microstructure measurements. The conservation equations for tracers are considered in a nonorthogonal coordinate frame that moves with neutral surfaces in the ocean. Since only mixing processes cause advection across neutral surfaces, it is useful to regard this vertical advection as a symptom of various mixing processes rather than as a separate physical process. It is possible to derive conservative equations for scalars that do not contain the vertical advective term explicity. In these conservation equations, the terms that represent mixing processes are substantially altered. It is argued that this form of the conservation equations is the most appropriate when considering water-mass transformation, and some examples are given of its application in the North Atlantic. It is shown that the variation of the vertical diffusivity with height does not cause water-mass transformation. Also, salt fingering is often 3-4 times more effective at

Advection by ocean currents modifies phytoplankton size structure.

PubMed

Font-Muñoz, Joan S; Jordi, Antoni; Tuval, Idan; Arrieta, Jorge; Anglès, Sílvia; Basterretxea, Gotzon

2017-05-01

Advection by ocean currents modifies phytoplankton size structure at small scales (1-10 cm) by aggregating cells in different regions of the flow depending on their size. This effect is caused by the inertia of the cells relative to the displaced fluid. It is considered that, at larger scales (greater than or equal to 1 km), biological processes regulate the heterogeneity in size structure. Here, we provide observational evidence of heterogeneity in phytoplankton size structure driven by ocean currents at relatively large scales (1-10 km). Our results reveal changes in the phytoplankton size distribution associated with the coastal circulation patterns. A numerical model that incorporates the inertial properties of phytoplankton confirms the role of advection on the distribution of phytoplankton according to their size except in areas with enhanced nutrient inputs where phytoplankton dynamics is ruled by other processes. The observed preferential concentration mechanism has important ecological consequences that range from the phytoplankton level to the whole ecosystem. © 2017 The Author(s).

Diffusion related isotopic fractionation effects with one-dimensional advective-dispersive transport.

PubMed

Xu, Bruce S; Lollar, Barbara Sherwood; Passeport, Elodie; Sleep, Brent E

2016-04-15

Aqueous phase diffusion-related isotope fractionation (DRIF) for carbon isotopes was investigated for common groundwater contaminants in systems in which transport could be considered to be one-dimensional. This paper focuses not only on theoretically observable DRIF effects in these systems but introduces the important concept of constraining "observable" DRIF based on constraints imposed by the scale of measurements in the field, and on standard limits of detection and analytical uncertainty. Specifically, constraints for the detection of DRIF were determined in terms of the diffusive fractionation factor, the initial concentration of contaminants (C0), the method detection limit (MDL) for isotopic analysis, the transport time, and the ratio of the longitudinal mechanical dispersion coefficient to effective molecular diffusion coefficient (Dmech/Deff). The results allow a determination of field conditions under which DRIF may be an important factor in the use of stable carbon isotope measurements for evaluation of contaminant transport and transformation for one-dimensional advective-dispersive transport. This study demonstrates that for diffusion-dominated transport of BTEX, MTBE, and chlorinated ethenes, DRIF effects are only detectable for the smaller molar mass compounds such as vinyl chloride for C0/MDL ratios of 50 or higher. Much larger C0/MDL ratios, corresponding to higher source concentrations or lower detection limits, are necessary for DRIF to be detectable for the higher molar mass compounds. The distance over which DRIF is observable for VC is small (less than 1m) for a relatively young diffusive plume (<100years), and DRIF will not easily be detected by using the conventional sampling approach with "typical" well spacing (at least several meters). With contaminant transport by advection, mechanical dispersion, and molecular diffusion this study suggests that in field sites where Dmech/Deff is larger than 10, DRIF effects will likely not be

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Theory of advection-driven long range biotic transport

USDA-ARS?s Scientific Manuscript database

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...

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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Variational optimization analysis of temperature and moisture advection in a severe storm environment

NASA Technical Reports Server (NTRS)

Mcfarland, M. J.

1975-01-01

Horizontal wind components, potential temperature, and mixing ratio fields associated with a severe storm environment in the south central U.S. were analyzed from synoptic upper air observations with a nonhomogeneous, anisotropic weighting function. Each data field was filtered with variational optimization analysis techniques. Variational optimization analysis was also performed on the vertical motion field and was used to produce advective forecasts of the potential temperature and mixing ratio fields. Results show that the dry intrusion is characterized by warm air, the advection of which produces a well-defined upward motion pattern. A corresponding downward motion pattern comprising a deep vertical circulation in the warm air sector of the low pressure system was detected. The axes alignment of maximum dry and warm advection with the axis of the tornado-producing squall line also resulted.

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.

Chemical mass transport between fluid fine tailings and the overlying water cover of an oil sands end pit lake

NASA Astrophysics Data System (ADS)

Dompierre, Kathryn A.; Barbour, S. Lee; North, Rebecca L.; Carey, Sean K.; Lindsay, Matthew B. J.

2017-06-01

Fluid fine tailings (FFT) are a principal by-product of the bitumen extraction process at oil sands mines. Base Mine Lake (BML)—the first full-scale demonstration oil sands end pit lake (EPL)—contains approximately 1.9 × 108 m3 of FFT stored under a water cover within a decommissioned mine pit. Chemical mass transfer from the FFT to the water cover can occur via two key processes: (1) advection-dispersion driven by tailings settlement; and (2) FFT disturbance due to fluid movement in the water cover. Dissolved chloride (Cl) was used to evaluate the water cover mass balance and to track mass transport within the underlying FFT based on field sampling and numerical modeling. Results indicated that FFT was the dominant Cl source to the water cover and that the FFT is exhibiting a transient advection-dispersion mass transport regime with intermittent disturbance near the FFT-water interface. The advective pore water flux was estimated by the mass balance to be 0.002 m3 m-2 d-1, which represents 0.73 m of FFT settlement per year. However, the FFT pore water Cl concentrations and corresponding mass transport simulations indicated that advection rates and disturbance depths vary between sample locations. The disturbance depth was estimated to vary with location between 0.75 and 0.95 m. This investigation provides valuable insight for assessing the geochemical evolution of the water cover and performance of EPLs as an oil sands reclamation strategy.

SEBAL-A: A remote sensing ET algorithm that accounts for advection with limited data. Part II: Test for transferability

USDA-ARS?s Scientific Manuscript database

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...

Analysis of phosphoinositide 3-kinase inhibitors by bottom-up electron-transfer dissociation hydrogen/deuterium exchange mass spectrometry

PubMed Central

Masson, Glenn R.; Maslen, Sarah L.

2017-01-01

Until recently, one of the major limitations of hydrogen/deuterium exchange mass spectrometry (HDX-MS) was the peptide-level resolution afforded by proteolytic digestion. This limitation can be selectively overcome through the use of electron-transfer dissociation to fragment peptides in a manner that allows the retention of the deuterium signal to produce hydrogen/deuterium exchange tandem mass spectrometry (HDX-MS/MS). Here, we describe the application of HDX-MS/MS to structurally screen inhibitors of the oncogene phosphoinositide 3-kinase catalytic p110α subunit. HDX-MS/MS analysis is able to discern a conserved mechanism of inhibition common to a range of inhibitors. Owing to the relatively minor amounts of protein required, this technique may be utilised in pharmaceutical development for screening potential therapeutics. PMID:28381646

Analytical solutions of the space-time fractional Telegraph and advection-diffusion equations

NASA Astrophysics Data System (ADS)

Tawfik, Ashraf M.; Fichtner, Horst; Schlickeiser, Reinhard; Elhanbaly, A.

2018-02-01

The aim of this paper is to develop a fractional derivative model of energetic particle transport for both uniform and non-uniform large-scale magnetic field by studying the fractional Telegraph equation and the fractional advection-diffusion equation. Analytical solutions of the space-time fractional Telegraph equation and space-time fractional advection-diffusion equation are obtained by use of the Caputo fractional derivative and the Laplace-Fourier technique. The solutions are given in terms of Fox's H function. As an illustration they are applied to the case of solar energetic particles.

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

PubMed Central

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

2013-01-01

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

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.

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

USDA-ARS?s Scientific Manuscript database

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

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.

A computational method for sharp interface advection

PubMed Central

Bredmose, Henrik; Jasak, Hrvoje

2016-01-01

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

A computational method for sharp interface advection.

PubMed

Roenby, Johan; Bredmose, Henrik; Jasak, Hrvoje

2016-11-01

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

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

USDA-ARS?s Scientific Manuscript database

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

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

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

Kordilla, Jannes, E-mail: jkordil@gwdg.de; Pan, Wenxiao, E-mail: Wenxiao.Pan@pnnl.gov; Tartakovsky, Alexandre, E-mail: alexandre.tartakovsky@pnnl.gov

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 formationmore » 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.« less

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.

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

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

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 ofmore » 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.« less

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.

Wind Tunnel Measurement of Turbulent and Advective Scalar Fluxes: A Case Study on Intersection Ventilation

PubMed Central

Kukačka, Libor; Nosek, Štĕpán; Kellnerová, Radka; Jurčáková, Klára; Jaňour, Zbyněk

2012-01-01

The objective of this study is to determine processes of pollution ventilation in the X-shaped street intersection in an idealized symmetric urban area for the changing approach flow direction. A unique experimental setup for simultaneous wind tunnel measurement of the flow velocity and the tracer gas concentration in a high temporal resolution is assembled. Advective horizontal and vertical scalar fluxes are computed from averaged measured velocity and concentration data within the street intersection. Vertical advective and turbulent scalar fluxes are computed from synchronized velocity and concentration signals measured in the plane above the intersection. All the results are obtained for five approach flow directions. The influence of the approach flow on the advective and turbulent fluxes is determined. The contribution of the advective and turbulent flux to the ventilation is discussed. Wind direction with the best dispersive conditions in the area is found. The quadrant analysis is applied to the synchronized signals of velocity and concentration fluctuation to determine events with the dominant contribution to the momentum flux and turbulent scalar flux. PMID:22649290

Wind tunnel measurement of turbulent and advective scalar fluxes: a case study on intersection ventilation.

PubMed

Kukačka, Libor; Nosek, Štĕpán; Kellnerová, Radka; Jurčáková, Klára; Jaňour, Zbyněk

2012-01-01

The objective of this study is to determine processes of pollution ventilation in the X-shaped street intersection in an idealized symmetric urban area for the changing approach flow direction. A unique experimental setup for simultaneous wind tunnel measurement of the flow velocity and the tracer gas concentration in a high temporal resolution is assembled. Advective horizontal and vertical scalar fluxes are computed from averaged measured velocity and concentration data within the street intersection. Vertical advective and turbulent scalar fluxes are computed from synchronized velocity and concentration signals measured in the plane above the intersection. All the results are obtained for five approach flow directions. The influence of the approach flow on the advective and turbulent fluxes is determined. The contribution of the advective and turbulent flux to the ventilation is discussed. Wind direction with the best dispersive conditions in the area is found. The quadrant analysis is applied to the synchronized signals of velocity and concentration fluctuation to determine events with the dominant contribution to the momentum flux and turbulent scalar flux.

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.

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.

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

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

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 liesmore » within the range of 60 to 90 mW/m{sup 2} in the Lhasa-Yanbajing area.« less

Hydrogen-deuterium exchange mass spectrometry reveals folding and allostery in protein-protein interactions.

PubMed

Ramirez-Sarmiento, Cesar A; Komives, Elizabeth A

2018-04-06

Hydrogen-deuterium exchange mass spectrometry (HDXMS) has emerged as a powerful approach for revealing folding and allostery in protein-protein interactions. The advent of higher resolution mass spectrometers combined with ion mobility separation and ultra performance liquid chromatographic separations have allowed the complete coverage of large protein sequences and multi-protein complexes. Liquid-handling robots have improved the reproducibility and accurate temperature control of the sample preparation. Many researchers are also appreciating the power of combining biophysical approaches such as stopped-flow fluorescence, single molecule FRET, and molecular dynamics simulations with HDXMS. In this review, we focus on studies that have used a combination of approaches to reveal (re)folding of proteins as well as on long-distance allosteric changes upon interaction. Copyright © 2018 Elsevier Inc. All rights reserved.

Analytical solutions of the one-dimensional advection-dispersion solute transport equation subject to time-dependent boundary conditions

USDA-ARS?s Scientific Manuscript database

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...

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.

Simulating contaminant attenuation, double-porosity exchange, and water age in aquifers using MOC3D

USGS Publications Warehouse

Goode, Daniel J.

1999-01-01

MOC3D is a general-purpose computer model developed by the U.S. Geological Survey (USGS) for simulation of three-dimensional solute transport in ground water (Konikow and others, 1996). The model is an update to the widely used USGS two-dimensional solute-transport model (MOC) and is implemented as an optional “package” for the ground-water flow model MODFLOW (Harbaugh and McDonald, 1996). Directly coupling the time-tested MOC transport algorithms with the widely used MODFLOW program makes MOC3D a powerful tool for simulation of solute transport in ground water in many hydrogeologic settings. The model simulates transport processes that include:Advection - Transport of dissolved solutes at the same rate as the average ground-water flow velocity.Diffusion - Spreading of solute from areas of high concentration to areas of low concentration, caused by “random” molecular motionDispersion - Diffusion-like spreading of solute that is caused primarily by spatial variability in aquifer properties, which results in spatial variability in transport velocity.Retardation - Reduction in the apparent solute velocity, compared to the ground-water velocity, caused by linear equilibrium sorption on aquifer materials.Decay - Disappearance of solute caused by reactions such as radioactive decay or biodegradation that are proportional to concentration.Growth - Creation (or disappearance) of solute mass caused by reactions that proceed independent of the solute concentration, such as some cases of biodegradationDouble-porosity exchange - rate-limited exchange of solute mass between mobile and immobile zones; for example, between fractures and the rock matrix.

Application of Atmospheric Pressure Photoionization H/D-exchange Mass Spectrometry for Speciation of Sulfur-containing Compounds.

PubMed

Acter, Thamina; Kim, Donghwi; Ahmed, Arif; Ha, Ji-Hyoung; Kim, Sunghwan

2017-08-01

Herein we report the observation of atmospheric pressure in-source hydrogen-deuterium exchange (HDX) of thiol group for the first time. The HDX for thiol group was optimized for positive atmospheric pressure photoionization (APPI) mass spectrometry (MS). The optimized HDX-MS was applied for 31 model compounds (thiols, thiophenes, and sulfides) to demonstrate that exchanged peaks were observed only for thiols. The optimized method has been successfully applied to the isolated fractions of sulfur-rich oil samples. The exchange of one and two thiol hydrogens with deuterium was observed in the thiol fraction; no HDX was observed in the other fractions. Thus, the results presented in this study demonstrate that the HDX-MS method using APPI ionization source can be effective for speciation of sulfur compounds. This method has the potential to be used to access corrosion problems caused by thiol-containing compounds. Graphical Abstract ᅟ.

Partitioned coupling of advection-diffusion-reaction systems and Brinkman flows

NASA Astrophysics Data System (ADS)

Lenarda, Pietro; Paggi, Marco; Ruiz Baier, Ricardo

2017-09-01

We present a partitioned algorithm aimed at extending the capabilities of existing solvers for the simulation of coupled advection-diffusion-reaction systems and incompressible, viscous flow. The space discretisation of the governing equations is based on mixed finite element methods defined on unstructured meshes, whereas the time integration hinges on an operator splitting strategy that exploits the differences in scales between the reaction, advection, and diffusion processes, considering the global system as a number of sequentially linked sets of partial differential, and algebraic equations. The flow solver presents the advantage that all unknowns in the system (here vorticity, velocity, and pressure) can be fully decoupled and thus turn the overall scheme very attractive from the computational perspective. The robustness of the proposed method is illustrated with a series of numerical tests in 2D and 3D, relevant in the modelling of bacterial bioconvection and Boussinesq systems.

Advantages of isotopic depletion of proteins for hydrogen/deuterium exchange experiments monitored by mass spectrometry.

PubMed

Bou-Assaf, George M; Chamoun, Jean E; Emmett, Mark R; Fajer, Piotr G; Marshall, Alan G

2010-04-15

Solution-phase hydrogen/deuterium exchange (HDX) monitored by mass spectrometry is an excellent tool to study protein-protein interactions and conformational changes in biological systems, especially when traditional methods such as X-ray crystallography or nuclear magnetic resonance are not feasible. Peak overlap among the dozens of proteolytic fragments (including those from autolysis of the protease) can be severe, due to high protein molecular weight(s) and the broad isotopic distributions due to multiple deuterations of many peptides. In addition, different subunits of a protein complex can yield isomeric proteolytic fragments. Here, we show that depletion of (13)C and/or (15)N for one or more protein subunits of a complex can greatly simplify the mass spectra, increase the signal-to-noise ratio of the depleted fragment ions, and remove ambiguity in assignment of the m/z values to the correct isomeric peptides. Specifically, it becomes possible to monitor the exchange progress for two isobaric fragments originating from two or more different subunits within the complex, without having to resort to tandem mass spectrometry techniques that can lead to deuterium scrambling in the gas phase. Finally, because the isotopic distribution for a small to medium-size peptide is essentially just the monoisotopic species ((12)C(c)(1)H(h)(14)N(n)(16)O(o)(32)S(s)), it is not necessary to deconvolve the natural abundance distribution for each partially deuterated peptide during HDX data reduction.

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

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...

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...

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.

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

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

PubMed

Sánchez-Garduño, Faustino; Pérez-Velázquez, Judith

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.

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

Local dynamics measured by hydrogen/deuterium exchange and mass spectrometry of creatine kinase digested by two proteases.

PubMed

Mazon, Hortense; Marcillat, Olivier; Forest, Eric; Vial, Christian

2005-12-01

Hydrogen/deuterium exchange coupled to mass spectrometry has been used to investigate the structure and dynamics of native dimeric cytosolic muscle creatine kinase. The protein was incubated in D2O for various time. After H/D exchange and rapid quenching of the reaction, the partially deuterated protein was cleaved in parallel by two different proteases (pepsin or type XIII protease from Aspergillus saitoi) to increase the sequence coverage and spatial resolution of deuterium incorporation. The resulting peptides were analyzed by liquid chromatography coupled to mass spectrometry. In comparison with the 3D structure of MM-CK, the analysis of the two independent proteolysis deuteration patterns allowed us to get new insights into CK local dynamics as compared to a previous study using pepsin [Mazon et al. Protein Science 13 (2004) 476-486]. In particular, we obtained more information on the kinetics and extent of deuterium exchange in the N- and C-terminal extremities represented by the 1-22 and 362-380 pepsin peptides. Indeed, we observed a very different behaviour of the 1-12 and 13-22 type XIII protease peptides, and similarly for the 362-373 and 374-380 peptides. Moreover, comparison of the deuteration patterns of type XIII protease segments of the large 90-126 pepsin peptide led us to identify a small relatively dynamic region (108-114).

Online Simultaneous Hydrogen/Deuterium Exchange of Multitarget Gas-Phase Molecules by Electrospray Ionization Mass Spectrometry Coupled with Gas Chromatography.

PubMed

Jeong, Eun Sook; Cha, Eunju; Cha, Sangwon; Kim, Sunghwan; Oh, Han Bin; Kwon, Oh-Seung; Lee, Jaeick

2017-11-21

In this study, a hydrogen/deuterium (H/D) exchange method using gas chromatography-electrospray ionization/mass spectrometry (GC-ESI/MS) was first investigated as a novel tool for online H/D exchange of multitarget analytes. The GC and ESI source were combined with a homemade heated column transfer line. GC-ESI/MS-based H/D exchange occurs in an atmospheric pressure ion source as a result of reacting the gas-phase analyte eluted from GC with charged droplets of deuterium oxide infused as the ESI spray solvent. The consumption of the deuterated solvent at a flow rate of 2 μL min -1 was more economical than that in online H/D exchange methods reported to date. In-ESI-source H/D exchange by GC-ESI/MS was applied to 11 stimulants with secondary amino or hydroxyl groups. After H/D exchange, the spectra of the stimulants showed unexchanged, partially exchanged, and fully exchanged ions showing various degrees of exchange. The relative abundances corrected for naturally occurring isotopes of the fully exchanged ions of stimulants, except for etamivan, were in the range 24.3-85.5%. Methylephedrine and cyclazodone showed low H/D exchange efficiency under acidic, neutral, and basic spray solvent conditions and nonexchange for etamivan with an acidic phenolic OH group. The in-ESI-source H/D exchange efficiency by GC-ESI/MS was sufficient to determine the number of hydrogen by elucidation of fragmentation from the spectrum. Therefore, this online H/D exchange technique using GC-ESI/MS has potential as an alternative method for simultaneous H/D exchange of multitarget analytes.

Multi-layer membrane model for mass transport in a direct ethanol fuel cell using an alkaline anion exchange membrane

NASA Astrophysics Data System (ADS)

Bahrami, Hafez; Faghri, Amir

2012-11-01

A one-dimensional, isothermal, single-phase model is presented to investigate the mass transport in a direct ethanol fuel cell incorporating an alkaline anion exchange membrane. The electrochemistry is analytically solved and the closed-form solution is provided for two limiting cases assuming Tafel expressions for both oxygen reduction and ethanol oxidation. A multi-layer membrane model is proposed to properly account for the diffusive and electroosmotic transport of ethanol through the membrane. The fundamental differences in fuel crossover for positive and negative electroosmotic drag coefficients are discussed. It is found that ethanol crossover is significantly reduced upon using an alkaline anion exchange membrane instead of a proton exchange membrane, especially at current densities higher than 500 A m

Diurnal cross-shore thermal exchange on a tropical forereef

NASA Astrophysics Data System (ADS)

Molina, L.; Pawlak, G.; Wells, J. R.; Monismith, S. G.; Merrifield, M. A.

2014-09-01

Observations of the velocity structure at the Kilo Nalu Observatory on the south shore of Oahu, Hawaii show that thermally driven baroclinic exchange is a dominant mechanism for cross-shore transport for this tropical forereef environment. Estimates of the exchange and net volume fluxes are comparable and show that the average residence time for the zone shoreward of the 12 m isobath is generally much less than 1 day. Although cross-shore wind stress influences the diurnal cross-shore exchange, surface heat flux is identified as the primary forcing mechanism from the phase relationships and from analysis of momentum and buoyancy balances for the record-averaged diurnal structure. Dynamic flow regimes are characterized based on a two-dimensional theoretical framework and the observations of the thermal structure at Kilo Nalu are shown to be in the unsteady temperature regime. Diurnal phasing and the cross-shore momentum balance suggest that turbulent stress divergence is an important driver of the baroclinic exchange. While the thermally driven exchange has a robust diurnal profile in the long term, there is high temporal variability on shorter time scales. Ensemble-averaged diurnal profiles indicate that the exchange is strongly modulated by surface heat flux, wind speed/direction, and alongshore velocity direction. The latter highlights the role of alongshore variability in the thermally driven exchange. Analysis of the thermal balance in the nearshore region indicates that the cross-shore exchange accounts for roughly 38% of the advective heat transport on a daily basis. This article was corrected on 10 OCT 2014. See the end of the full text for details.

Fluid Transport in Porous Media probed by Relaxation-Exchange NMR

NASA Astrophysics Data System (ADS)

Olaru, A. M.; Kowalski, J.; Sethi, V.; Blümich, B.

2011-12-01

The characterization of fluid transport in porous media represents a matter of high interest in fields like the construction industry, oil exploitation, and soil science. Moisture migration or flow at low rates, such as those occurring in soil during rain are difficult to characterize by classical high-field NMR velocimetry due to the dedicated hardware and elaborate techniques required for adequate signal encoding. The necessity of field studies raises additional technical problems, which can be solved only by the use of portable low-field NMR instruments. In this work we extend the use of low-field relaxation exchange experiments from the study of diffusive transport to that of advection. Relaxation exchange experiments were performed using a home-built Halbach magnet on model porous systems with controlled pore-size distributions and on natural porous systems (quartz sand with a broad pore-size distribution) exposed to unidirectional flow. Different flow rates leave distinctive marks on the exchange maps obtained by inverse Laplace transformation of the time domain results, due to the superposition of exchange, diffusion and inflow/outflow in multiple relaxation sites of the liquids in the porous media. In the case of slow velocities there is no loss of signal due to outflow, and the relaxation-exchange effects prevail, leading to a tilt of the diagonal distribution around a pivot point with increasing mixing time. The tilt suggests an asymmetry in the exchange between relaxation sites of large and small decay rates. Another observed phenomenon is the presence of a bigger number of exchange cross-peaks compared to the exchange maps obtained for the same systems in zero-flow conditions. We assume that this is due to enhanced exchange caused by the superposition of flow. For high velocities the outflow effects dominate and the relaxation-time distribution collapses towards lower values of the average relaxation times. In both cases the pore-size distribution has a

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.

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

The prediction of sea-surface temperature variations by means of an advective mixed-layer ocean model

NASA Technical Reports Server (NTRS)

Atlas, R. M.

1976-01-01

An advective mixed layer ocean model was developed by eliminating the assumption of horizontal homogeneity in an already existing mixed layer model, and then superimposing a mean and anomalous wind driven current field. This model is based on the principle of conservation of heat and mechanical energy and utilizes a box grid for the advective part of the calculation. Three phases of experiments were conducted: evaluation of the model's ability to account for climatological sea surface temperature (SST) variations in the cooling and heating seasons, sensitivity tests in which the effect of hypothetical anomalous winds was evaluated, and a thirty-day synoptic calculation using the model. For the case studied, the accuracy of the predictions was improved by the inclusion of advection, although nonadvective effects appear to have dominated.

Hybrid Multiscale Finite Volume Method for Advection-Diffusion Equations Subject to Heterogeneous Reactive Boundary Conditions

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

Barajas-Solano, David A.; Tartakovsky, A. M.

2016-10-13

We present a hybrid scheme for the coupling of macro and microscale continuum models for reactive contaminant transport in fractured and porous media. The transport model considered is the advection-dispersion equation, subject to linear heterogeneous reactive boundary conditions. The Multiscale Finite Volume method (MsFV) is employed to define an approximation to the microscale concentration field defined in terms of macroscopic or \\emph{global} degrees of freedom, together with local interpolator and corrector functions capturing microscopic spatial variability. The macroscopic mass balance relations for the MsFV global degrees of freedom are coupled with the macroscopic model, resulting in a global problem for the simultaneous time-stepping of all macroscopic degrees of freedom throughout the domain. In order to perform the hybrid coupling, the micro and macroscale models are applied over overlapping subdomains of the simulation domain, with the overlap denoted as the handshake subdomainmore » $$\\Omega^{hs}$$, over which continuity of concentration and transport fluxes between models is enforced. Continuity of concentration is enforced by posing a restriction relation between models over $$\\Omega^{hs}$$. Continuity of fluxes is enforced by prolongating the macroscopic model fluxes across the boundary of $$\\Omega^{hs}$$ to microscopic resolution. The microscopic interpolator and corrector functions are solutions to local microscopic advection-diffusion problems decoupled from the global degrees of freedom and from each other by virtue of the MsFV decoupling ansatz. The error introduced by the decoupling ansatz is reduced iteratively by the preconditioned GMRES algorithm, with the hybrid MsFV operator serving as the preconditioner.« less

Multi-decadal synthesis of benthic pelagic coupling in the western arctic: Role of cross-shelf advective processes

NASA Astrophysics Data System (ADS)

Dunton, Kenneth H.; Goodall, Jonathan L.; Schonberg, Susan V.; Grebmeier, Jacqueline M.; Maidment, David R.

2005-12-01

Using geographic information systems (GIS) software and geostatistical techniques, we utilized three decades of water-column chlorophyll a data to examine the relative importance of autochthonous versus allochthonous sources of reduced carbon to benthic communities that occur from the northern Bering to the eastern Beaufort Sea shelf. Spatial trend analyses revealed areas of high benthic biomass (>300 g m -2) and chlorophyll (>150 mg m -2) on both the southern and northern Chukchi shelf; both areas are known as depositional centers for reduced organic matter that originates on the Bering Sea shelf and is advected northward in Anadyr and Bering shelf water masses. We found a significant correlation between biomass and chlorophyll a in the Chukchi Sea, reflective of the strong benthic-pelagic coupling in a system that is utilized heavily by benthic-feeding marine mammals. In contrast, there was no significant correlation between biomass and chlorophyll in the Beaufort Sea, which by comparison, is considerably less productive (biomass and chlorophyll, <75 g m -2 and <50 mg m -2, respectively). One notable exception is an area of relatively high biomass (50-100 g m -2) and chlorophyll (80 mg m -2) near Barter Island in the eastern Beaufort Sea. Compared to other adjacent areas in the Beaufort Sea, the chlorophyll values in the vicinity of Barter Island were considerably higher and likely reflect a long-hypothesized upwelling in that area and close coupling between the benthos and autochthonous production. In the Bering Sea, a drop in benthic biomass in 1994 compared with previous measurements (1974-1993) may support earlier observations that document a decline in biomass that began between the 1980s and 1990s in the Chirikov Basin and south of St. Lawrence Island. The results of this study indicate that the benthos is an excellent long-term indicator of both local and physical advective processes. In addition, this work provides further evidence that secondary

Advection-dominated Accretion Flow around a Kerr Black Hole

NASA Astrophysics Data System (ADS)

Manmoto, T.

2000-05-01

The effects of the spin of central black holes on the structure and the spectrum of optically thin, advection-dominated accretion flows (ADAFs) around rotating supermassive black holes are investigated. The global two-temperature structure of ADAFs in the Kerr metric is obtained numerically by solving the full relativistic hydrodynamical equations including the energy equations for the ions and for the electrons. The advected fraction of the dissipated energy is not treated as a parameter and the detailed radiation processes are calculated self-consistently. We find that the two-temperature structure of ADAFs is accurately calculated by setting the advected fraction of the dissipated energy to be unity. We find that the particles are hotter when a is positive than when a=0, while the particles are cooler when a is negative than when a=0. The changes in a have less effect on the electron temperature than on the ion temperature. The spectra of the emitted photons are also calculated by solving the equations of the general relativistic optics. The entire part of the spectra is enhanced when a is positive, while the entire part of the spectra is reduced when a is negative, in comparison with the case of a=0. The spectrum of the synchrotron photons and the Comptonized synchrotron photons are modified more largely by the black hole spin and the inclination angle than the spectrum of the bremsstrahlung photons. The effect of the inclination angle on the spectra increases as the value of a increases. In the case of a=-0.95, the inclination has little effect on the shape of the spectrum. The spectrum of Sgr A* from the radio band to the X-ray band is nicely reproduced with the model of an ADAF around a high-spin black hole. The existence of a high-spin black hole at the Galactic center is not ruled out by the ADAF model.

Vertical Structure of Radiation-pressure-dominated Thin Disks: Link between Vertical Advection and Convective Stability

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

Gong, Hong-Yu; Gu, Wei-Min, E-mail: guwm@xmu.edu.cn

2017-04-20

In the classic picture of standard thin accretion disks, viscous heating is balanced by radiative cooling through the diffusion process, and the radiation-pressure-dominated inner disk suffers convective instability. However, recent simulations have shown that, owing to the magnetic buoyancy, the vertical advection process can significantly contribute to energy transport. In addition, in comparing the simulation results with the local convective stability criterion, no convective instability has been found. In this work, following on from simulations, we revisit the vertical structure of radiation-pressure-dominated thin disks and include the vertical advection process. Our study indicates a link between the additional energy transportmore » and the convectively stable property. Thus, the vertical advection not only significantly contributes to the energy transport, but it also plays an important role in making the disk convectively stable. Our analyses may help to explain the discrepancy between classic theory and simulations on standard thin disks.« less

Anomalous transport regimes and asymptotic concentration distributions in the presence of advection and diffusion on a comb structure

NASA Astrophysics Data System (ADS)

Dvoretskaya, Olga A.; Kondratenko, Peter S.

2009-04-01

We study the transport of impurity particles on a comb structure in the presence of advection. The main body concentration and asymptotic concentration distributions are obtained. Seven different transport regimes occur on the comb structure with finite teeth: classical diffusion, advection, quasidiffusion, subdiffusion, slow classical diffusion, and two kinds of slow advection. Quasidiffusion deserves special attention. It is characterized by a linear growth of the mean-square displacement. However, quasidiffusion is an anomalous transport regime. We established that a change in transport regimes in time leads to a change in regimes in space. Concentration tails have a cascade structure, namely, consisting of several parts.

Numerical and analytical approaches to an advection-diffusion problem at small Reynolds number and large Péclet number

NASA Astrophysics Data System (ADS)

Fuller, Nathaniel J.; Licata, Nicholas A.

2018-05-01

Obtaining a detailed understanding of the physical interactions between a cell and its environment often requires information about the flow of fluid surrounding the cell. Cells must be able to effectively absorb and discard material in order to survive. Strategies for nutrient acquisition and toxin disposal, which have been evolutionarily selected for their efficacy, should reflect knowledge of the physics underlying this mass transport problem. Motivated by these considerations, in this paper we discuss the results from an undergraduate research project on the advection-diffusion equation at small Reynolds number and large Péclet number. In particular, we consider the problem of mass transport for a Stokesian spherical swimmer. We approach the problem numerically and analytically through a rescaling of the concentration boundary layer. A biophysically motivated first-passage problem for the absorption of material by the swimming cell demonstrates quantitative agreement between the numerical and analytical approaches. We conclude by discussing the connections between our results and the design of smart toxin disposal systems.

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.

Flagella-Driven Flows Circumvent Diffusive Bottlenecks that Inhibit Metabolite Exchange

NASA Astrophysics Data System (ADS)

Short, Martin; Solari, Cristian; Ganguly, Sujoy; Kessler, John; Goldstein, Raymond; Powers, Thomas

2006-03-01

The evolution of single cells to large and multicellular organisms requires matching the organisms' needs to the rate of exchange of metabolites with the environment. This logistic problem can be a severe constraint on development. For organisms with a body plan that approximates a spherical shell, such as colonies of the volvocine green algae, the required current of metabolites grows quadratically with colony radius whereas the rate at which diffusion can exchange metabolites grows only linearly with radius. Hence, there is a bottleneck radius beyond which the diffusive current cannot keep up with metabolic demands. Using Volvox carteri as a model organism, we examine experimentally and theoretically the role that advection of fluid by surface-mounted flagella plays in enhancing nutrient uptake. We show that fluid flow driven by the coordinated beating of flagella produces a convective boundary layer in the concentration of a diffusing solute which in turn renders the metabolite exchange rate quadratic in the colony radius. This enhanced transport circumvents the diffusive bottleneck, allowing increase in size and thus evolutionary transitions to multicellularity in the Volvocales.

Phase mixing versus nonlinear advection in drift-kinetic plasma turbulence

NASA Astrophysics Data System (ADS)

Schekochihin, A. A.; Parker, J. T.; Highcock, E. G.; Dellar, P. J.; Dorland, W.; Hammett, G. W.

2016-04-01

> A scaling theory of long-wavelength electrostatic turbulence in a magnetised, weakly collisional plasma (e.g. drift-wave turbulence driven by ion temperature gradients) is proposed, with account taken both of the nonlinear advection of the perturbed particle distribution by fluctuating flows and of its phase mixing, which is caused by the streaming of the particles along the mean magnetic field and, in a linear problem, would lead to Landau damping. It is found that it is possible to construct a consistent theory in which very little free energy leaks into high velocity moments of the distribution function, rendering the turbulent cascade in the energetically relevant part of the wavenumber space essentially fluid-like. The velocity-space spectra of free energy expressed in terms of Hermite-moment orders are steep power laws and so the free-energy content of the phase space does not diverge at infinitesimal collisionality (while it does for a linear problem); collisional heating due to long-wavelength perturbations vanishes in this limit (also in contrast with the linear problem, in which it occurs at the finite rate equal to the Landau damping rate). The ability of the free energy to stay in the low velocity moments of the distribution function is facilitated by the `anti-phase-mixing' effect, whose presence in the nonlinear system is due to the stochastic version of the plasma echo (the advecting velocity couples the phase-mixing and anti-phase-mixing perturbations). The partitioning of the wavenumber 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 time scales (which for high Hermite moments splits into two thresholds, one demarcating the wavenumber region where phase mixing predominates, the other where plasma echo does).

Molecular Dynamics Simulations Provide Atomistic Insight into Hydrogen Exchange Mass Spectrometry Experiments.

PubMed

Petruk, Ariel A; Defelipe, Lucas A; Rodríguez Limardo, Ramiro G; Bucci, Hernán; Marti, Marcelo A; Turjanski, Adrian G

2013-01-08

It is now clear that proteins are flexible entities that in solution switch between conformations to achieve their function. Hydrogen/Deuterium Exchange Mass Spectrometry (HX/MS) is an invaluable tool to understand dynamic changes in proteins modulated by cofactor binding, post-transductional modifications, or protein-protein interactions. ERK2MAPK, a protein involved in highly conserved signal transduction pathways of paramount importance for normal cellular function, has been extensively studied by HX/MS. Experiments of the ERK2MAPK in the inactive and active states (in the presence or absence of bound ATP) have provided valuable information on the plasticity of the MAPK domain. However, interpretation of the HX/MS data is difficult, and changes are mostly explained in relation to available X-ray structures, precluding a complete atomic picture of protein dynamics. In the present work, we have used all atom Molecular Dynamics simulations (MD) to provide a theoretical framework for the interpretation of HX/MS data. Our results show that detailed analysis of protein-solvent interaction along the MD simulations allows (i) prediction of the number of protons exchanged for each peptide in the HX/MS experiments, (ii) rationalization of the experimentally observed changes in exchange rates in different protein conditions at the residue level, and (iii) that at least for ERK2MAPK, most of the functionally observed differences in protein dynamics are related to what can be considered the native state conformational ensemble. In summary, the combination of HX/MS experiments with all atom MD simulations emerges as a powerful approach to study protein native state dynamics with atomic resolution.

Dealing with the Quaternion Antipodal Problem for Advecting Fields

DTIC Science & Technology

2017-12-01

public release; distribution is unlimited. NOTICES Disclaimers The findings in this report are not to be construed as an official Department of the Army...primary author’s email: <richard.c.becker.civ@mail.mil>. Quaternion representations of rotations are proposed for advecting rotations in large strain...products of quaternions to ameliorate these issues. The results of both are unique and continuous, but the former does not capture the correct

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. Copyright © 2015 Elsevier B.V. All rights reserved.

A family of compact high order coupled time-space unconditionally stable vertical advection schemes

NASA Astrophysics Data System (ADS)

Lemarié, Florian; Debreu, Laurent

2016-04-01

Recent papers by Shchepetkin (2015) and Lemarié et al. (2015) have emphasized that the time-step of an oceanic model with an Eulerian vertical coordinate and an explicit time-stepping scheme is very often restricted by vertical advection in a few hot spots (i.e. most of the grid points are integrated with small Courant numbers, compared to the Courant-Friedrichs-Lewy (CFL) condition, except just few spots where numerical instability of the explicit scheme occurs first). The consequence is that the numerics for vertical advection must have good stability properties while being robust to changes in Courant number in terms of accuracy. An other constraint for oceanic models is the strict control of numerical mixing imposed by the highly adiabatic nature of the oceanic interior (i.e. mixing must be very small in the vertical direction below the boundary layer). We examine in this talk the possibility of mitigating vertical Courant-Friedrichs-Lewy (CFL) restriction, while avoiding numerical inaccuracies associated with standard implicit advection schemes (i.e. large sensitivity of the solution on Courant number, large phase delay, and possibly excess of numerical damping with unphysical orientation). Most regional oceanic models have been successfully using fourth order compact schemes for vertical advection. In this talk we present a new general framework to derive generic expressions for (one-step) coupled time and space high order compact schemes (see Daru & Tenaud (2004) for a thorough description of coupled time and space schemes). Among other properties, we show that those schemes are unconditionally stable and have very good accuracy properties even for large Courant numbers while having a very reasonable computational cost.

Emergent scar lines in chaotic advection of passive directors

NASA Astrophysics Data System (ADS)

Hejazi, Bardia; Mehlig, Bernhard; Voth, Greg A.

2017-12-01

We examine the spatial field of orientations of slender fibers that are advected by a two-dimensional fluid flow. The orientation field of these passive directors are important in a wide range of industrial and geophysical flows. We introduce emergent scar lines as the dominant coherent structures in the orientation field of passive directors in chaotic flows. Previous work has identified the existence of scar lines where the orientation rotates by π over short distances, but the lines that were identified disappeared as time progressed. As a result, earlier work focused on topological singularities in the orientation field, which we find to play a negligible role at long times. We use the standard map as a simple time-periodic two-dimensional flow that produces Lagrangian chaos. This class of flows produces persistent patterns in passive scalar advection and we find that a different kind of persistent pattern develops in the passive director orientation field. We identify the mechanism by which emergent scar lines grow to dominate these patterns at long times in complex flows. Emergent scar lines form where the recent stretching of the fluid element is perpendicular to earlier stretching. Thus these scar lines can be labeled by their age, defined as the time since their stretching reached a maximum.

Development to term of sheep embryos reconstructed after inner cell mass/trophoblast exchange.

PubMed

Loi, Pasqualino; Galli, Cesare; Lazzari, Giovanna; Matsukawa, Kazutsugu; Fulka, Josef; Goeritz, Frank; Hildebrandt, Thomas B

2018-04-13

Here we report in vitro and term development of sheep embryos after the inner cell mass (ICM) from one set of sheep blastocysts were injected into the trophoblast vesicles of another set. We also observed successful in vitro development of chimeric blastocysts made from sheep trophoblast vesicles injected with bovine ICM. First, we dissected ICMs from 35 sheep blastocysts using a stainless steel microblade and injected them into 29 re-expanded sheep trophoblastic vesicles. Of the 25 successfully micromanipulated trophoblastic vesicles, 15 (51.7%) re-expanded normally and showed proper ICM integration. The seven most well reconstructed embryos were transferred for development to term. Three ewes receiving manipulated blastocysts were pregnant at day 45 (42.8%), and all delivered normal offspring (singletons, two females and one male, average weight: 3.54 ± 0.358 kg). Next, we monitored in vitro development of sheep trophoblasts injected with bovine ICMs. Of 17 injected trophoblastic vesicles, 10 (58.8%) re-expanded after 4 h in culture, and four (40%) exhibited integrated bovine ICM. Our results indicate that ICM/trophoblast exchange is feasible, allowing full term development with satisfactory lambing rate. Therefore, ICM exchange is a promising approach for endangered species conservation.

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

Multi-Scale Observation and Modelling of Energy and Matter Exchange in the Atmospheric Boundary-Layer (ScaleX Campaigns)

NASA Astrophysics Data System (ADS)

Zeeman, M. J.; Wolz, K.; Adler, B.; Brenner, C.; De Roo, F.; Emeis, S.; Kalthoff, N.; Mauder, M.; Schäfer, K.; Wohlfahrt, G.; Zhao, P.

2016-12-01

We investigated biosphere-atmosphere exchange processes in relation to the atmospheric boundary-layer (ABL) flow in a shallow valley. Land-use heterogeneity and topography can force local atmospheric flow patterns, including local circulations. Such flow patterns can impair current techniques for the quantification and source attribution of surface-exchange fluxes due to flux-divergence, advection and decoupling. Wind field, temperature and humidity structures in the ABL were observed in high resolution with spatially distributed observations in a 1 km3 experimental domain. Remote-sensing observations of wind, temperature and particles in the ABL (Raman-lidar; RASS; ceilometer; microwave radiometer; 3D Doppler-lidar) were combined with a high-resolution network of in-situ observations that included vertical and horizontal profiles of wind, temperature, carbon dioxide, methane and water vapor concentrations. The experiments were co-located with the long-term eddy covariance (EC) observatory Fendt (DE-Fen; ICOS, TERENO) and were part of international cooperative efforts in 2015 and 2016 (the ScaleX campaigns). The gathered experimental data offers a scale-transcending insight in local flow patterns in mountainous terrain and their influence on surface-exchange fluxes of energy and matter as observed by EC and flux-gradient methodology. In addition, the data is used for validation of Large-Eddy Simulations in complex terrain using PALM-LES. Within this modelling framework, virtual measurements are conducted to further assess the importance of three-dimensional advective and horizontal turbulent transport terms.

Modelling uncertainties in the diffusion-advection equation for radon transport in soil using interval arithmetic.

PubMed

Chakraverty, S; Sahoo, B K; Rao, T D; Karunakar, P; Sapra, B K

2018-02-01

Modelling radon transport in the earth crust is a useful tool to investigate the changes in the geo-physical processes prior to earthquake event. Radon transport is modeled generally through the deterministic advection-diffusion equation. However, in order to determine the magnitudes of parameters governing these processes from experimental measurements, it is necessary to investigate the role of uncertainties in these parameters. Present paper investigates this aspect by combining the concept of interval uncertainties in transport parameters such as soil diffusivity, advection velocity etc, occurring in the radon transport equation as applied to soil matrix. The predictions made with interval arithmetic have been compared and discussed with the results of classical deterministic model. The practical applicability of the model is demonstrated through a case study involving radon flux measurements at the soil surface with an accumulator deployed in steady-state mode. It is possible to detect the presence of very low levels of advection processes by applying uncertainty bounds on the variations in the observed concentration data in the accumulator. The results are further discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Influence of advections of particulate matter from biomass combustion on specific-cause mortality in Madrid in the period 2004-2009.

PubMed

Linares, C; Carmona, R; Tobías, A; Mirón, I J; Díaz, J

2015-05-01

Approximately, 20 % of particulate and aerosol emissions into the urban atmosphere are of natural origin (including wildfires and Saharan dust). During these natural episodes, PM10 and PM2.5 levels usually exceed World Health Organisation (WHO) health protection thresholds. This study sought to evaluate the possible effect of advections of particulate matter from biomass fuel combustion on daily specific-cause mortality among the general population and the segment aged ≥ 75 years in Madrid. Ecological time-series study in the city of Madrid from January 01, 2004 to December 31, 2009. The dependent variable analysed was daily mortality due to natural (ICD-10:A00-R99), circulatory (ICD-10:I00-I99), and respiratory (ICD-10:J00-J99) causes in the population, both general and aged ≥ 75 years. The following independent and control variables were considered: a) daily mean PM2.5 and PM10 concentrations; b) maximum daily temperature; c) daily mean O3 and NO2 concentrations; d) advection of particulate matter from biomass combustion ( http://www.calima.ws/ ), using a dichotomous variable and e) linear trend and seasonalities. We conducted a descriptive analysis, performed a test of means and, to ascertain relative risk, fitted a model using autoregressive Poisson regression and stratifying by days with and without biomass advection, in both populations. Of the 2192 days analysed, biomass advection occurred on 56, with mean PM2.5 and PM10 values registering a significant increase during these days. PM10 had a greater impact on organic mortality with advection (RRall ages = 1.035 [1.011-1.060]; RR  ≥  75 years = 1.066 [1.031-1.103]) than did PM2.5 without advection (RRall ages = 1.017 [1.009-1.025]; RR  ≥  75 years = 1.012 [1.003-1.022]). Among specific causes, respiratory-though not circulatory-causes were associated with PM10 on days with advection in ≥ 75 year age group. PM10, rather than PM2.5, were associated with an increase in natural

Advection within side-by-side liquid micro-cylinders in a cross-flow

NASA Astrophysics Data System (ADS)

Dong, Qingming; Sau, Amalendu

2017-11-01

The gaseous SO2 entrainment from outer air stream and dispersion in binary and ternary liquid micro-cylinders appearing side-by-side are examined hereby. The separation/attachment regulated non-uniform interfacial momentum exchange creates main stream driven "primary" and shear reversed "secondary" vortices in the liquid cylinders. At separation points, the sense of rotation of the generated "primary-secondary" vortex pair remains inward directed. We define such a vortex pair as the "inflow" type. However, at stagnation or attachment points, the sense of rotation of a "primary-primary" or "secondary-secondary" vortex pair remains outward directed, and such a vortex pair is defined as the "outflow" type. For the coupled water cylinders facing an oncoming stream contaminated by gaseous SO2, its absorption and internal transport are effectively controlled by dominant "inflow" and "outflow" natured dynamics of the said vortex pairs, besides by diffusion. The evolving "inflow" natured "primary-secondary" vortex pairs at separation points actively entrain the outer SO2, whereas the "outflow" natured vortex-pairs oppose SO2 entry through the stagnation regions. Moreover, the blockage induced steady-symmetric, steady-deflected, and flip-flopping air-jets through gaps, for varied gap-ratio (1 ≤ G/R ≤ 4) and Reynolds number (30 ≤ Re ≤ 160), create distinctive impact both on quantitative SO2 absorption (mso2 ') and convective nature of the SO2 transport in upper, lower, and middle cylinders, by virtue of modified strength and size of the inflow and outflow paired vortices. The present study shows that the tiny "secondary vortices" play important roles in SO2 entrainment and in effectively controlling the local absorption rate Rs o2. The sudden acceleration and upward/downward deflection of gap-flows enhanced near-neck advective SO2 entrainment by suitably strengthening the "inflow" natured local vortex dynamics. Conversely, for the reduced size of secondary vortices

STANDING SHOCK INSTABILITY IN ADVECTION-DOMINATED ACCRETION FLOWS

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

Le, Truong; Wood, Kent S.; Wolff, Michael T.

2016-03-10

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

Laser Processed Heat Exchangers

NASA Technical Reports Server (NTRS)

Hansen, Scott

2017-01-01

The Laser Processed Heat Exchanger project will investigate the use of laser processed surfaces to reduce mass and volume in liquid/liquid heat exchangers as well as the replacement of the harmful and problematic coatings of the Condensing Heat Exchangers (CHX). For this project, two scale unit test articles will be designed, manufactured, and tested. These two units are a high efficiency liquid/liquid HX and a high reliability CHX.

Cation exchange in a glacial till drumlin at a road salt storage facility

NASA Astrophysics Data System (ADS)

Ostendorf, David W.; Xing, Baoshan; Kallergis, Niki

2009-05-01

We use laboratory and field data to calibrate existing geochemical and transport models of cation exchange induced by contamination of an unconfined aquifer at a road salt storage facility built upon a glacial till drumlin in eastern Massachusetts. A Gaines and Thomas selectivity coefficient K models the equilibrium sodium and divalent cation distribution in the groundwater and solid matrix, while an existing method of characteristics model describes the advective transport of total dissolved cations and sorbed sodium. Laboratory isotherms of split spoon soil samples from the drumlin calibrate K with an average value of 0.0048 (L/g) 1/2 for a measured cation exchange capacity of 0.057 meq/g dry soil. Ten years of monitoring well data document groundwater flow and the advection of conservative chloride due to outdoor storage and handling of road salt at the site. The monitoring well cation data and retarded transport model offer an independent K calibration of 0.0040 to 0.0047 (L/g) 1/2: the consistency of the field and laboratory selectivity coefficient calibrations endorse this application of the Gaines and Thomas and method of characteristics models. The advancing deicing agent plume releases divalent cations from the till into the groundwater, so that monitoring well samples do not reflect the chemical composition of the road salt. In this regard, dissolved divalent cation milliequivalent concentrations are as high as 80% of the total dissolved cationic concentrations in the salt contaminated monitoring well samples, far greater than their 2.5% level in the road salt stored at the site. Cation exchange can thus obscure attempts to hindcast stored road salt sodium water table concentration from monitoring well sample stoichiometry, or to predict sodium impacts on groundwater or receiving stream quality downgradient of the well.

Cation exchange in a glacial till drumlin at a road salt storage facility.

PubMed

Ostendorf, David W; Xing, Baoshan; Kallergis, Niki

2009-05-12

We use laboratory and field data to calibrate existing geochemical and transport models of cation exchange induced by contamination of an unconfined aquifer at a road salt storage facility built upon a glacial till drumlin in eastern Massachusetts. A Gaines and Thomas selectivity coefficient K models the equilibrium sodium and divalent cation distribution in the groundwater and solid matrix, while an existing method of characteristics model describes the advective transport of total dissolved cations and sorbed sodium. Laboratory isotherms of split spoon soil samples from the drumlin calibrate K with an average value of 0.0048 (L/g)(1/2) for a measured cation exchange capacity of 0.057 meq/g dry soil. Ten years of monitoring well data document groundwater flow and the advection of conservative chloride due to outdoor storage and handling of road salt at the site. The monitoring well cation data and retarded transport model offer an independent K calibration of 0.0040 to 0.0047 (L/g)(1/2): the consistency of the field and laboratory selectivity coefficient calibrations endorse this application of the Gaines and Thomas and method of characteristics models. The advancing deicing agent plume releases divalent cations from the till into the groundwater, so that monitoring well samples do not reflect the chemical composition of the road salt. In this regard, dissolved divalent cation milliequivalent concentrations are as high as 80% of the total dissolved cationic concentrations in the salt contaminated monitoring well samples, far greater than their 2.5% level in the road salt stored at the site. Cation exchange can thus obscure attempts to hindcast stored road salt sodium water table concentration from monitoring well sample stoichiometry, or to predict sodium impacts on groundwater or receiving stream quality downgradient of the well.

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

NASA Astrophysics Data System (ADS)

Bischoff, James L.; Wooden, Joe; Murphy, Fred; Williams, Ross W.

2005-04-01

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 μm 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.

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.

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.

An adaptive semi-Lagrangian advection model for transport of volcanic emissions in the atmosphere

NASA Astrophysics Data System (ADS)

Gerwing, Elena; Hort, Matthias; Behrens, Jörn; Langmann, Bärbel

2018-06-01

The dispersion of volcanic emissions in the Earth atmosphere is of interest for climate research, air traffic control and human wellbeing. Current volcanic emission dispersion models rely on fixed-grid structures that often are not able to resolve the fine filamented structure of volcanic emissions being transported in the atmosphere. Here we extend an existing adaptive semi-Lagrangian advection model for volcanic emissions including the sedimentation of volcanic ash. The advection of volcanic emissions is driven by a precalculated wind field. For evaluation of the model, the explosive eruption of Mount Pinatubo in June 1991 is chosen, which was one of the largest eruptions in the 20th century. We compare our simulations of the climactic eruption on 15 June 1991 to satellite data of the Pinatubo ash cloud and evaluate different sets of input parameters. We could reproduce the general advection of the Pinatubo ash cloud and, owing to the adaptive mesh, simulations could be performed at a high local resolution while minimizing computational cost. Differences to the observed ash cloud are attributed to uncertainties in the input parameters and the course of Typhoon Yunya, which is probably not completely resolved in the wind data used to drive the model. The best results were achieved for simulations with multiple ash particle sizes.

Two-Relaxation-Time Lattice Boltzmann Method for Advective-Diffusive-Reactive Transport

NASA Astrophysics Data System (ADS)

Yan, Z.; Hilpert, M.

2016-12-01

The lattice Boltzmann method (LBM) has been applied to study a wide range of reactive transport in porous and fractured media. The single-relaxation-time (SRT) LBM, employing single relaxation time, is the most popular LBM due to its simplicity of understanding and implementation. Nevertheless, the SRT LBM may suffer from numerical instability for small value of the relaxation time. By contrast, the multiple-relaxation-time (MRT) LBM, employing multiple relaxation times, can improve the numerical stability through tuning the multiple relaxation times, but the complexity of implementing this method restricts its applications. The two-relaxation-time (TRT) LBM, which employs two relaxation times, combines the advantages of SRT and MRT LBMs. The TRT LBM can produce simulations with better accuracy and stability than the SRT one, and is easier to implement than the MRT one. This work evaluated the numerical accuracy and stability of the TRT method by comparing the simulation results with analytical solutions of Gaussian hill transport and Taylor dispersion under different advective velocities. The accuracy generally increased with the tunable relaxation time τ, and the stability first increased and then decreased as τ increased, showing an optimal TRT method emerging the best numerical stability. The free selection of τ enabled the TRT LBM to simulate the Gaussian hill transport and Taylor dispersion under relatively high advective velocity, under which the SRT LBM suffered from numerical instability. Finally, the TRT method was applied to study the contaminant degradation by chemotactic microorganisms in porous media, which acted as a reprehensive of reactive transport in this study, and well predicted the evolution of microorganisms and degradation of contaminants for different transport scenarios. To sum up, the TRT LBM produced simulation results with good accuracy and stability for various advective-diffusive-reactive transport through tuning the relaxation

Project Fog Drops 5. Task 1: A numerical model of advection fog. Task 2: Recommendations for simplified individual zero-gravity cloud physics experiments

NASA Technical Reports Server (NTRS)

Rogers, C. W.; Eadie, W. J.; Katz, U.; Kocmond, W. C.

1975-01-01

A two-dimensional numerical model was used to investigate the formation of marine advection fog. The model predicts the evolution of potential temperature, horizontal wind, water vapor content, and liquid water content in a vertical cross section of the atmosphere as determined by vertical turbulent transfer and horizontal advection, as well as radiative cooling and drop sedimentation. The model is designed to simulate the formation, development, or dissipation of advection fog in response to transfer of heat and moisture between the atmosphere and the surface as driven by advection over horizontal discontinuities in the surface temperature. Results from numerical simulations of advection fog formation are discussed with reference to observations of marine fog. A survey of candidate fog or cloud microphysics experiments which might be performed in the low gravity environment of a shuttle-type spacecraft in presented. Recommendations are given for relatively simple experiments which are relevent to fog modification problems.

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

NASA Astrophysics Data System (ADS)

Yao, Fengchao

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

Front-Eddy Influence on Water Column Properties, Phytoplankton Community Structure, and Cross-Shelf Exchange of Diatom Taxa in the Shelf-Slope Area off Concepción (˜36-37°S)

NASA Astrophysics Data System (ADS)

Morales, Carmen E.; Anabalón, Valeria; Bento, Joaquim P.; Hormazabal, Samuel; Cornejo, Marcela; Correa-Ramírez, Marco A.; Silva, Nelson

2017-11-01

In eastern boundary current systems (EBCSs), submesoscale to mesocale variability contributes to cross-shore exchanges of water properties, nutrients, and plankton. Data from a short-term summer survey and satellite time series (January-February 2014) were used to characterize submesoscale variability in oceanographic conditions and phytoplankton distribution across the coastal upwelling and coastal transition zones north of Punta Lavapié, and to explore cross-shelf exchanges of diatom taxa. A thermohaline front (FRN-1) flanked by a mesoscale anticyclonic intrathermocline eddy (ITE-1), or mode-water eddy, persisted during the time series and the survey was undertaken during a wind relaxation event. At the survey time, ITE-1 contributed to an onshore intrusion of warm oceanic waters (southern section) and an offshore advection of cold coastal waters (northern section), with the latter forming a cold, high chlorophyll-a filament. In situ phytoplankton and diatom biomasses were highest at the surface in FRN-1 and at the subsurface in ITE-1, whereas values in the coastal zone were lower and dominated by smaller cells. Diatom species typical of the coastal zone and species dominant in oceanic waters were both found in the FRN-1 and ITE-1 interaction area, suggesting that this mixture was the result of both offshore and onshore advection. Overall, front-eddy interactions in EBCSs could enhance cross-shelf exchanges of coastal and oceanic plankton, as well as sustain phytoplankton growth in the slope area through localized upward injections of nutrients in the frontal zone, combined with ITE-induced advection and vertical nutrient inputs to the surface layer.

Proton deflectometry characterization of Biermann-Battery field advection

NASA Astrophysics Data System (ADS)

Pollock, Bradley; Moore, Alastair; Meezan, Nathan; Eder, Dave; Kane, Jave; Strozzi, David; Wilks, Scott; Rinderknecht, Hans; Zylstra, Alex; Fujioka, Shinsuke; Kemp, Gregory; Moody, John

2017-10-01

Laser-foil interactions are well known to produce azimuthal magnetic fields around the laser spot due to the orthogonal density and temperature gradients that develop near the foil surface (the Biermann-Battery effect). Simulations show that these fields produced inside hohlraums used for indirect drive experiments at the National Ignition Facility (NIF); however, modeling these fields and their advection is very computationally expensive on the temporal and spatial scales relevant for typical NIF hohlraum experiments ( 10 ns, few mm). The hohlraum geometry also makes directly probing the fields somewhat challenging, limiting the available experimental data on these fields under NIF conditions. In particular, the relative contributions of frozen-in and Nernst advection of the field away from the hohlraum wall is not currently well understood. We have developed a new target platform for direct measurements of the field topology in a NIF-relevant configuration. Using a single cone of NIF, a 2.5 mm long, 5.4 mm diameter Au ring is illuminated with a similar beam geometry to that of one ring of beams in a full-scale hohlraum experiment. The ring target has no end caps, providing a clear line of sight for probing through the ring. A D3He filled exploding pusher placed 5 cm below the ring is illuminated by an additional 60 beams of NIF to produce protons, some of which propagate through the ring. Work was performed under the auspices of the U.S. Department of Energy by LLNL under Contract DE-AC52-07NA27344 and under LDRD support from LLNL.

Evaporation of Accretion Disks around Black Holes: The Disk-Corona Transition and the Connection to the Advection-dominated Accretion Flow.

PubMed

Liu; Yuan; Meyer; Meyer-Hofmeister; Xie

1999-12-10

We apply the disk-corona evaporation model (Meyer & Meyer-Hofmeister) originally derived for dwarf novae to black hole systems. This model describes the transition of a thin cool outer disk to a hot coronal flow. The mass accretion rate determines the location of this transition. For a number of well-studied black hole binaries, we take the mass flow rates derived from a fit of the advection-dominated accretion flow (ADAF) model to the observed spectra (for a review, see Narayan, Mahadevan, & Quataert) and determine where the transition of accretion via a cool disk to a coronal flow/ADAF would be located for these rates. We compare this with the observed location of the inner disk edge, as estimated from the maximum velocity of the Halpha emission line. We find that the transition caused by evaporation agrees with this determination in stellar disks. We also show that the ADAF and the "thin outer disk + corona" are compatible in terms of the physics in the transition region.

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

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

Haroldsen, P.E.; Gaskell, S.J.; Weintraub, S.T.

1991-04-01

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

Development to term of sheep embryos reconstructed after inner cell mass/trophoblast exchange

PubMed Central

LOI, Pasqualino; GALLI, Cesare; LAZZARI, Giovanna; MATSUKAWA, Kazutsugu; FULKA, Josef; GOERITZ, Frank; HILDEBRANDT, Thomas B.

2018-01-01

Here we report in vitro and term development of sheep embryos after the inner cell mass (ICM) from one set of sheep blastocysts were injected into the trophoblast vesicles of another set. We also observed successful in vitro development of chimeric blastocysts made from sheep trophoblast vesicles injected with bovine ICM. First, we dissected ICMs from 35 sheep blastocysts using a stainless steel microblade and injected them into 29 re-expanded sheep trophoblastic vesicles. Of the 25 successfully micromanipulated trophoblastic vesicles, 15 (51.7%) re-expanded normally and showed proper ICM integration. The seven most well reconstructed embryos were transferred for development to term. Three ewes receiving manipulated blastocysts were pregnant at day 45 (42.8%), and all delivered normal offspring (singletons, two females and one male, average weight: 3.54 ± 0.358 kg). Next, we monitored in vitro development of sheep trophoblasts injected with bovine ICMs. Of 17 injected trophoblastic vesicles, 10 (58.8%) re-expanded after 4 h in culture, and four (40%) exhibited integrated bovine ICM. Our results indicate that ICM/trophoblast exchange is feasible, allowing full term development with satisfactory lambing rate. Therefore, ICM exchange is a promising approach for endangered species conservation. PMID:29445070

Chemical-Specific Representation of Air-Soil Exchange and Soil Penetration in Regional Multimedia Models

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

McKone, T.E.; Bennett, D.H.

2002-08-01

In multimedia mass-balance models, the soil compartment is an important sink as well as a conduit for transfers to vegetation and shallow groundwater. Here a novel approach for constructing soil transport algorithms for multimedia fate models is developed and evaluated. The resulting algorithms account for diffusion in gas and liquid components; advection in gas, liquid, or solid phases; and multiple transformation processes. They also provide an explicit quantification of the characteristic soil penetration depth. We construct a compartment model using three and four soil layers to replicate with high reliability the flux and mass distribution obtained from the exact analyticalmore » solution describing the transient dispersion, advection, and transformation of chemicals in soil with fixed properties and boundary conditions. Unlike the analytical solution, which requires fixed boundary conditions, the soil compartment algorithms can be dynamically linked to other compartments (air, vegetation, ground water, surface water) in multimedia fate models. We demonstrate and evaluate the performance of the algorithms in a model with applications to benzene, benzo(a)pyrene, MTBE, TCDD, and tritium.« less

Probability and Cumulative Density Function Methods for the Stochastic Advection-Reaction Equation

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

Barajas-Solano, David A.; Tartakovsky, Alexandre M.

We present a cumulative density function (CDF) method for the probabilistic analysis of $d$-dimensional advection-dominated reactive transport in heterogeneous media. We employ a probabilistic approach in which epistemic uncertainty on the spatial heterogeneity of Darcy-scale transport coefficients is modeled in terms of random fields with given correlation structures. Our proposed CDF method employs a modified Large-Eddy-Diffusivity (LED) approach to close and localize the nonlocal equations governing the one-point PDF and CDF of the concentration field, resulting in a $(d + 1)$ dimensional PDE. Compared to the classsical LED localization, the proposed modified LED localization explicitly accounts for the mean-field advectivemore » dynamics over the phase space of the PDF and CDF. To illustrate the accuracy of the proposed closure, we apply our CDF method to one-dimensional single-species reactive transport with uncertain, heterogeneous advection velocities and reaction rates modeled as random fields.« less

The effect of coherent stirring on the advection-condensation of water vapour

NASA Astrophysics Data System (ADS)

Tsang, Yue-Kin; Vanneste, Jacques

2017-06-01

Atmospheric water vapour is an essential ingredient of weather and climate. The key features of its distribution can be represented by kinematic models which treat it as a passive scalar advected by a prescribed flow and reacting through condensation. Condensation acts as a sink that maintains specific humidity below a prescribed, space-dependent saturation value. To investigate how the interplay between large-scale advection, small-scale turbulence and condensation controls moisture distribution, we develop simple kinematic models which combine a single circulating flow with a Brownian-motion representation of turbulence. We first study the drying mechanism of a water-vapour anomaly released inside a vortex at an initial time. Next, we consider a cellular flow with a moisture source at a boundary. The statistically steady state attained shows features reminiscent of the Hadley cell such as boundary layers, a region of intense precipitation and a relative humidity minimum. Explicit results provide a detailed characterization of these features in the limit of strong flow.

The effect of coherent stirring on the advection-condensation of water vapour.

PubMed

Tsang, Yue-Kin; Vanneste, Jacques

2017-06-01

Atmospheric water vapour is an essential ingredient of weather and climate. The key features of its distribution can be represented by kinematic models which treat it as a passive scalar advected by a prescribed flow and reacting through condensation. Condensation acts as a sink that maintains specific humidity below a prescribed, space-dependent saturation value. To investigate how the interplay between large-scale advection, small-scale turbulence and condensation controls moisture distribution, we develop simple kinematic models which combine a single circulating flow with a Brownian-motion representation of turbulence. We first study the drying mechanism of a water-vapour anomaly released inside a vortex at an initial time. Next, we consider a cellular flow with a moisture source at a boundary. The statistically steady state attained shows features reminiscent of the Hadley cell such as boundary layers, a region of intense precipitation and a relative humidity minimum. Explicit results provide a detailed characterization of these features in the limit of strong flow.

Sea ice-induced cold air advection as a mechanism controlling tundra primary productivity

NASA Astrophysics Data System (ADS)

Macias-Fauria, M.; Karlsen, S. R.

2015-12-01

The recent sharp decline in Arctic sea ice extent, concentration, and volume leaves urgent questions regarding its effects on ecological processes. Changes in tundra productivity have been associated with sea ice dynamics on the basis that most tundra ecosystems lay close to the sea. Although some studies have addressed the potential effect of sea ice decline on the primary productivity of terrestrial arctic ecosystems (Bhatt et al., 2010), a clear picture of the mechanisms and patterns linking both processes remains elusive. We hypothesised that sea ice might influence tundra productivity through 1) cold air advection during the growing season (direct/weather effect) or 2) changes in regional climate induced by changes in sea ice (indirect/climate effect). We present a test on the direct/weather effect hypothesis: that is, tundra productivity is coupled with sea ice when sea ice remains close enough from land vegetation during the growing season for cold air advection to limit temperatures locally. We employed weekly MODIS-derived Normalised Difference Vegetation Index (as a proxy for primary productivity) and sea ice data at a spatial resolution of 232m for the period 2000-2014 (included), covering the Svalbard Archipelago. Our results suggest that sea ice-induced cold air advection is a likely mechanism to explain patterns of NDVI trends and heterogeneous spatial dynamics in the Svalbard archipelago. The mechanism offers the potential to explain sea ice/tundra productivity dynamics in other Arctic areas.

A stochastic-advective transport model for NAPL dissolution and degradation in non-uniform flows in porous media

NASA Astrophysics Data System (ADS)

Chan, T. P.; Govindaraju, Rao S.

2006-10-01

Remediation schemes for contaminated sites are often evaluated to assess their potential for source zone reduction of mass, or treatment of the contaminant between the source and a control plane (CP) to achieve regulatory limits. In this study, we utilize a stochastic stream tube model to explain the behavior of breakthrough curves (BTCs) across a CP. At the local scale, mass dissolution at the source is combined with an advection model with first-order decay for the dissolved plume. Field-scale averaging is then employed to account for spatial variation in mass within the source zone, and variation in the velocity field. Under the assumption of instantaneous mass transfer from the source to the moving liquid, semi-analytical expressions for the BTC and temporal moments are developed, followed by derivation of expressions for effective velocity, dispersion, and degradation coefficients using the method of moments. It is found that degradation strongly influences the behavior of moments and the effective parameters. While increased heterogeneity in the velocity field results in increased dispersion, degradation causes the center of mass of the plume to shift to earlier times, and reduces the dispersion of the BTC by lowering the concentrations in the tail. Modified definitions of effective parameters are presented for degrading solutes to account for the normalization constant (zeroth moment) that keeps changing with time or distance to the CP. It is shown that anomalous dispersion can result for high degradation rates combined with wide variation in velocity fluctuations. Implications of model results on estimating cleanup times and fulfillment of regulatory limits are discussed. Relating mass removal at the source to flux reductions past a control plane is confounded by many factors. Increased heterogeneity in velocity fields causes mass fluxes past a control plane to persist, however, aggressive remediation between the source and CP can reduce these fluxes.

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.

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.

Regulation of Phenylalanine Hydroxylase: Conformational Changes Upon Phenylalanine Binding Detected by H/D Exchange and Mass Spectrometry†

PubMed Central

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

2010-01-01

Phenylalanine acts as an allosteric activator of the tetrahydropterin-dependent enzyme phenylalanine hydroxylase. Hydrogen/deuterium exchange monitored by mass spectrometry has been used to gain insight into local conformational changes accompanying activation of rat phenylalanine hydroxylase by phenylalanine. Peptides in the regulatory and catalytic domains that lie in the interface between these two domains show large increases in the extent of deuterium incorporation from solvent in the presence of phenylalanine. In contrast, the effects of phenylalanine on the exchange kinetics of a mutant enzyme lacking the regulatory domain are limited to peptides surrounding the binding site for the amino acid substrate. These results support a model in which the N-terminus of the protein acts as an inhibitory peptide, with phenylalanine binding causing a conformational change in the regulatory domain that alters the interaction between the catalytic and regulatory domains. PMID:20307070

Development, Fabrication, and Testing of a Liquid/Liquid Microchannel Heat Exchanger for Constellation Spacecrafts

NASA Technical Reports Server (NTRS)

Hawkins-Reynolds, Ebony; Le,Hung; Stephans, Ryan A.

2009-01-01

Minimizing mass and volume is critically important for space hardware. Microchannel technology can be used to decrease both of these parameters for heat exchangers. Working in concert with NASA, Pacific Northwest National Laboratories (PNNL) has developed a microchannel liquid/liquid heat exchanger that has resulted in significant mass and volume savings. The microchannel heat exchanger delivers these improvements without sacrificing thermal and pressure drop performance. A conventional heat exchanger has been tested and the performance of it recorded to compare it to the microchannel heat exchanger that PNNL has fabricated. The microchannel heat exchanger was designed to meet all of the requirements of the baseline heat exchanger, while reducing the heat exchanger mass and volume. The baseline heat exchanger was designed to have an transfer approximately 3.1 kW for a specific set of inlet conditions. The baseline heat exchanger mass was 2.7 kg while the microchannel mass was only 2.0 kg. More impressive, however, was the volumetric savings associated with the microchannel heat exchanger. The microchannel heat exchanger was an order of magnitude smaller than the baseline heat exchanger (2180cm3 vs. 311 cm3). This paper will describe the test apparatus designed to complete performance tests for both heat exchangers. Also described in this paper will be the performance specifications for the microchannel heat exchanger and how they compare to the baseline heat exchanger.

Modelling debris transport within glaciers by advection in a full-Stokes ice flow model

NASA Astrophysics Data System (ADS)

Wirbel, Anna; Jarosch, Alexander H.; Nicholson, Lindsey

2017-04-01

As mountain glaciers recede worldwide, an increasing proportion of the remaining glacierized area is expected to become debris covered. The spatio-temporal development of a surface debris cover has profound effects on the glacier behaviour and meltwater generation, yet little is known about how glacier dynamics influence the spatial distribution of an emerging debris cover. Motivated by this lack of understanding, we present a coupled model to simulate advection and resulting deformation of debris features within glaciers. The finite element model developed in python consists of an advection scheme coupled to a full-Stokes ice flow model, using FEniCS as the numerical framework. We show results from numerical tests that demonstrate its suitability to model advection-dominated transport of concentration in a divergence-free velocity field. The capabilities of the coupled model are demonstrated by simulating transport of debris features of different initial size, shape and location through modelled velocity fields of representative mountain glaciers. The results indicate that deformation of initial debris inputs, as a consequence of being transported through the glacier, plays an important role in determining the location and rate of debris emergence at the glacier surface. The presented work lays the foundation for comprehensive simulations of realistic patterns of debris cover, their spatial and temporal variability and the timescales over which debris covers can form.

A New Family of Compact High Order Coupled Time-Space Unconditionally Stable Vertical Advection Schemes

NASA Astrophysics Data System (ADS)

Lemarié, F.; Debreu, L.

2016-02-01

Recent papers by Shchepetkin (2015) and Lemarié et al. (2015) have emphasized that the time-step of an oceanic model with an Eulerian vertical coordinate and an explicit time-stepping scheme is very often restricted by vertical advection in a few hot spots (i.e. most of the grid points are integrated with small Courant numbers, compared to the Courant-Friedrichs-Lewy (CFL) condition, except just few spots where numerical instability of the explicit scheme occurs first). The consequence is that the numerics for vertical advection must have good stability properties while being robust to changes in Courant number in terms of accuracy. An other constraint for oceanic models is the strict control of numerical mixing imposed by the highly adiabatic nature of the oceanic interior (i.e. mixing must be very small in the vertical direction below the boundary layer). We examine in this talk the possibility of mitigating vertical Courant-Friedrichs-Lewy (CFL) restriction, while avoiding numerical inaccuracies associated with standard implicit advection schemes (i.e. large sensitivity of the solution on Courant number, large phase delay, and possibly excess of numerical damping with unphysical orientation). Most regional oceanic models have been successfully using fourth order compact schemes for vertical advection. In this talk we present a new general framework to derive generic expressions for (one-step) coupled time and space high order compact schemes (see Daru & Tenaud (2004) for a thorough description of coupled time and space schemes). Among other properties, we show that those schemes are unconditionally stable and have very good accuracy properties even for large Courant numbers while having a very reasonable computational cost. To our knowledge no unconditionally stable scheme with such high order accuracy in time and space have been presented so far in the literature. Furthermore, we show how those schemes can be made monotonic without compromising their stability

OBSERVATION OF MAGNETIC RECONNECTION DRIVEN BY GRANULAR SCALE ADVECTION

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

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 lowermore » 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.« less

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...

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

Chaotic advection in a 2-D mixed convection flow

NASA Astrophysics Data System (ADS)

Tangborn, Andrew V.; Silevitch, Daniel M.; Howes, Tony

1995-06-01

Two-dimensional numerical simulations of particle advection in a channel flow with spatially periodic heating have been carried out. The velocity field is found to be periodic above a critical Rayleigh number of around 18 000 and a Reynolds number of 10. Particle motion becomes chaotic in the lower half plane almost immediately after this critical value is surpassed, as characterized by the power spectral density and Poincaré section of the flow. As the Rayleigh number is increased further, particle motion in the entire domain becomes chaotic.

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.

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

Chaotic Advection in the Alboran Sea: Lagrangian Analysis of Transport Processes in and out of the Western Alboran Gyre

NASA Astrophysics Data System (ADS)

Brett, G.; Rypina, I.; Pratt, L. J.

2016-12-01

The westernmost part of Mediterranean, the Alboran Sea, sits between the Iberian peninsula and Africa, just east of the Strait of Gibraltar. Atlantic water enters the Alboran through the strait in the form of the Atlantic Jet. After passing through the strait, this jet starts interacting with the Alboran recirculations, most notably with the Western Alboran Gyre - a persistent anticyclonic mesoscale eddy in the western Alboran. Past studies of Finite-Size Lyapunov Exponents in the Alboran (e.g. Sayol et. al 2013) have highlighted the periphery of the Western Alboran Gyre, implying that it has chaotic flow— motion characterized by exponential stretching and folding of fluid parcels. This work examines the near-surface exchange between the Atlantic Jet and the Western Alboran Gyre in a high-resolution regional run of the MIT general circulation model. We use Lagrangian methods from dynamical systems theory, specifically lobe analysis, to define the moving gyre boundary and quantify advective transport in and out of the gyre, avoiding spurious fluxes caused by the gyre moving across its time-mean boundaries. We also identify the stirring region, where exchanges with the Atlantic Jet occur, and the core of the gyre, where they do not. We demonstrate an intermittent path from the north-western upwelling region into the gyre, which may be important for the distribution of both temperature and plankton. Quantifying and qualifying the transport across the boundaries of this modeled mesoscale eddy may contribute to the future design of observational campaigns.

Magnetic flux and heat losses by diffusive, advective, and Nernst effects in MagLIF-like plasma

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

Velikovich, A. L., E-mail: sasha.velikovich@nrl.navy.mil; Giuliani, J. L., E-mail: sasha.velikovich@nrl.navy.mil; Zalesak, S. T.

2014-12-15

The MagLIF approach to inertial confinement fusion involves subsonic/isobaric compression and heating of a DT plasma with frozen-in magnetic flux by a heavy cylindrical liner. The losses of heat and magnetic flux from the plasma to the liner are thereby determined by plasma advection and gradient-driven transport processes, such as thermal conductivity, magnetic field diffusion and thermomagnetic effects. Theoretical analysis based on obtaining exact self-similar solutions of the classical collisional Braginskii's plasma transport equations in one dimension demonstrates that the heat loss from the hot plasma to the cold liner is dominated by the transverse heat conduction and advection, andmore » the corresponding loss of magnetic flux is dominated by advection and the Nernst effect. For a large electron Hall parameter ω{sub e}τ{sub e} effective diffusion coefficients determining the losses of heat and magnetic flux are both shown to decrease with ω{sub e}τ{sub e} as does the Bohm diffusion coefficient, which is commonly associated with low collisionality and two-dimensional transport. This family of exact solutions can be used for verification of codes that model the MagLIF plasma dynamics.« less

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...

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.

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.

In Situ Self Assembly of Nanocomposites: Competition of Chaotic Advection and Interfacial Effects as Observed by X-Ray Diffreaction

PubMed Central

Ratnaweera, Dilru R.; Mahesha, Chaitra; Zumbrunnen, David A.; Perahia, Dvora

2015-01-01

The effects of chaotic advection on the in situ assembly of a hierarchal nanocomposite of Poly Amide 6, (nylon 6 or PA6) and platelet shape nanoparticles (NPs) were studied. The assemblies were formed by chaotic advection, where melts of pristine PA6 and a mixture of PA6 with NPs were segregated into discrete layers and extruded into film in a continuous process. The process assembles the nanocomposite into alternating pristine-polymer and oriented NP/polymer layers. The structure of these hierarchal assemblies was probed by X-rays as a processing parameter, N, was varied. This parameter provides a measure of the extent of in situ structuring by chaotic advection. We found that all assemblies are semi-crystalline at room temperature. Increasing N impacts the ratio of α to γ crystalline forms. The effects of the chaotic advection vary with the concentration of the NPs. For nanocomposites with lower NP concentrations the amount of the γ crystalline form increased with N. However, at higher NP concentrations, interfacial effects of the NP play a significant role in determining the structure, where the NPs oriented along the melt flow direction and the polymer chains oriented perpendicular to the NP surfaces. PMID:28347015

Equilibrium and kinetic folding of rabbit muscle triosephosphate isomerase by hydrogen exchange mass spectrometry.

PubMed

Pan, Hai; Raza, Ashraf S; Smith, David L

2004-03-05

Unfolding and refolding of rabbit muscle triosephosphate isomerase (TIM), a model for (betaalpha)8-barrel proteins, has been studied by amide hydrogen exchange/mass spectrometry. Unfolding was studied by destabilizing the protein in guanidine hydrochloride (GdHCl) or urea, pulse-labeling with 2H2O and analyzing the intact protein by HPLC electrospray ionization mass spectrometry. Bimodal isotope patterns were found in the mass spectra of the labeled protein, indicating two-state unfolding behavior. Refolding experiments were performed by diluting solutions of TIM unfolded in GdHCl or urea and pulse-labeling with 2H2O at different times. Mass spectra of the intact protein labeled after one to two minutes had three envelopes of isotope peaks, indicating population of an intermediate. Kinetic modeling indicates that the stability of the folding intermediate in water is only 1.5 kcal/mol. Failure to detect the intermediate in the unfolding experiments was attributed to its low stability and the high concentrations of denaturant required for unfolding experiments. The folding status of each segment of the polypeptide backbone was determined from the deuterium levels found in peptic fragments of the labeled protein. Analysis of these spectra showed that the C-terminal half folds to form the intermediate, which then forms native TIM with folding of the N-terminal half. These results show that TIM folding fits the (4+4) model for folding of (betaalpha)8-barrel proteins. Results of a double-jump experiment indicate that proline isomerization does not contribute to the rate-limiting step in the folding of TIM.

The vapor-phase multi-stage CMD test for characterizing contaminant mass discharge associated with VOC sources in the vadose zone: Application to three sites in different lifecycle stages of SVE operations.

PubMed

Brusseau, M L; Mainhagu, J; Morrison, C; Carroll, K C

2015-08-01

Vapor-phase multi-stage contaminant mass discharge (CMD) tests were conducted at three field sites to measure mass discharge associated with contaminant sources located in the vadose zone. The three sites represent the three primary stages of the soil vapor extraction (SVE) operations lifecycle-pre/initial-SVE, mid-lifecycle, and near-closure. A CMD of 32g/d was obtained for a site at which soil vapor SVE has been in operation for approximately 6years, and for which mass removal is currently in the asymptotic stage. The contaminant removal behavior exhibited for the vapor extractions conducted at this site suggests that there is unlikely to be a significant mass of non-vapor-phase contaminant (e.g., DNAPL, sorbed phase) remaining in the advective domains, and that most remaining mass is likely located in poorly accessible domains. Given the conditions for this site, this remaining mass is hypothesized to be associated with the low-permeability (and higher water saturation) region in the vicinity of the saturated zone and capillary fringe. A CMD of 25g/d was obtained for a site wherein SVE has been in operation for several years but concentrations and mass-removal rates are still relatively high. A CMD of 270g/d was obtained for a site for which there were no prior SVE operations. The behavior exhibited for the vapor extractions conducted at this site suggest that non-vapor-phase contaminant mass (e.g., DNAPL) may be present in the advective domains. Hence, the asymptotic conditions observed for this site most likely derive from a combination of rate-limited mass transfer from DNAPL (and sorbed) phases present in the advective domain as well as mass residing in lower-permeability ("non-advective") regions. The CMD values obtained from the tests were used in conjunction with a recently developed vapor-discharge tool to evaluate the impact of the measured CMDs on groundwater quality. Copyright © 2015 Elsevier B.V. All rights reserved.

Atlantic Water Advection and Ice Sheet-Ocean Feedbacks in the Arctic Ocean During the Last 200 ky

NASA Astrophysics Data System (ADS)

Spielhagen, R. F.; Mackensen, A.; Stein, R. H.

2016-12-01

Earlier work on Arctic deep-sea cores from the eastern Lomonosov Ridge and the Morris Jesup Rise had revealed that large-scale Eurasian ice sheet growth was initiated at times with seasonally open waters in the Arctic Ocean, indicating a role for the ocean in nearby ice sheet development in the last 200 ky. Here we present microfossil and geochemical data from new sediment cores obtained from the western and easternmost Lomonosov Ridge during the PS87 expedition (2014) of RV Polarstern, amended by data from refined analyses of the older cores. They allow to investigate in more detail the feedbacks between Atlantic Water (AW) advection, sea ice, and ice sheets. In all cores, high microfossil abundances are found just below layers rich in iceberg-rafted detritus, supporting the hypothesis of Arctic Ocean moisture supply for the growth of Eurasian ice sheets. On the other hand, the new microfaunal results suggest that the decay of the ice sheets and the enhanced freshwater discharge to the Arctic may have influenced the routing of subsurface AW in the Arctic Ocean, at least during marine isotope (sub)stages (MIS) 5a and 5e. In the early part of these relatively mild climatic intervals, faunal and isotopic data suggest a noticable advection of Atlantic Water, yet of rather low temperature and likely at depths comparable to the modern distribution (i.e., below 150 m) or even deeper. This may be explained by a more southerly position of AW cooling and submergence than today, caused by a thick layer of low saline waters near the surface which stemmed from the slow melting of ice sheet remnants on the Eurasian continent and shelves. In the second half of both MIS 5a and 5e, AW advection was significantly stronger and may have occurred at shallower depths, as indicated by unusually large amounts of small subpolar planktic foraminifers in central Arctic sediments. AW was apparently diverted northward from the Fram Strait and spread eastward along the Lomonosov Ridge. A

Quasielastic neutrino charged-current scattering off 12C: Effects of the meson exchange currents and large nucleon axial mass

NASA Astrophysics Data System (ADS)

Butkevich, A. V.; Luchuk, S. V.

2018-04-01

The quasielastic scattering of muon neutrino and electrons on a carbon target are analyzed using the relativistic distorted-wave impulse approximation (RDWIA). We also evaluate the contribution of the two-particle and two-hole meson exchange current (2 p -2 h MEC) to electroweak response functions. The nuclear model dependence of the (anti)neutrino cross sections is studied within the RDWIA+MEC approach and RDWIA model with the large nucleon axial mass. It is shown that the results for the squared momentum transfer distribution d σ /d Q2 and for invariant mass of the final hadronic system distribution d σ /d W obtained within these models are substantially different.

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

PubMed

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

2013-02-01

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

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.

Stock-specific advection of larval walleye (Sander vitreus) in western Lake Erie: Implications for larval growth, mixing, and stock discrimination

USGS Publications Warehouse

Fraker, Michael E.; Anderson, Eric J.; May, Cassandra J.; Chen, Kuan-Yu; Davis, Jeremiah J.; DeVanna, Kristen M.; DuFour, Mark R.; Marschall, Elizabeth A.; Mayer, Christine M.; Miner, Jeffery G.; Pangle, Kevin L.; Pritt, Jeremy J.; Roseman, Edward F.; Tyson, Jeffrey T.; Zhao, Yingming; Ludsin, Stuart A

2015-01-01

Physical processes can generate spatiotemporal heterogeneity in habitat quality for fish and also influence the overlap of pre-recruit individuals (e.g., larvae) with high-quality habitat through hydrodynamic advection. In turn, individuals from different stocks that are produced in different spawning locations or at different times may experience dissimilar habitat conditions, which can underlie within- and among-stock variability in larval growth and survival. While such physically-mediated variation has been shown to be important in driving intra- and inter-annual patterns in recruitment in marine ecosystems, its role in governing larval advection, growth, survival, and recruitment has received less attention in large lake ecosystems such as the Laurentian Great Lakes. Herein, we used a hydrodynamic model linked to a larval walleye (Sander vitreus) individual-based model to explore how the timing and location of larval walleye emergence from several spawning sites in western Lake Erie (Maumee, Sandusky, and Detroit rivers; Ohio reef complex) can influence advection pathways and mixing among these local spawning populations (stocks), and how spatiotemporal variation in thermal habitat can influence stock-specific larval growth. While basin-wide advection patterns were fairly similar during 2011 and 2012, smaller scale advection patterns and the degree of stock mixing varied both within and between years. Additionally, differences in larval growth were evident among stocks and among cohorts within stocks which were attributed to spatiotemporal differences in water temperature. Using these findings, we discuss the value of linked physical–biological models for understanding the recruitment process and addressing fisheries management problems in the world's Great Lakes.

Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence

NASA Astrophysics Data System (ADS)

Klotz, L.; Lemoult, G.; Frontczak, I.; Tuckerman, L. S.; Wesfreid, J. E.

2017-04-01

We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction.

Drainage and Landscape Evolution in the Bighorn Basin Accompanying Advection of the Yellowstone Hotspot Swell Through North America

NASA Astrophysics Data System (ADS)

Guerrero, E. F.; Meigs, A.

2012-12-01

Mantle plumes have been recognized to express themselves on the surface as long wavelength and low amplitude topographic swells. These swells are measured as positive geoid anomalies and include shorter wavelength topographic features such as volcanic edifices and pre-exisitng topography. Advection of the topographic swell is expected as the lithosphere passes over the plume uplift source. The hot spot swell occurs in the landscape as transient signal that is expressed with waxing and waning topography. Waxing topography occurs at the leading edge of the swell and is expressed as an increase in rock uplift that is preserved by rivers and landscapes. Advection of topography predicts a shift in a basin from deposition to incision, an increase in convexity of a transverse river's long profile and a lateral river migration in the direction of advection. The Yellowstone region has a strong positive geoid anomaly and the volcanic signal, which have been interpreted as the longer and shorter wavelength topographic expressions of the hot spot. These expressions of the hot spot developed in a part of North America with a compounded deformation and topographic history. Previous studies of the Yellowstone topographic swell have concentrated on the waning or trailing signal preserved in the Snake River Plain. Our project revisits the classic geomorphology study area in the Bighorn Basin of Wyoming and Montana, which is in leading edge of the swell. Present models identify the swell as having a 400 km in diameter and that it is centered on the Yellowstone caldera. If we assume advection to occur in concert with the caldera eruptive track, the Yellowstone swell has migrated to the northeast at a rate of 3 cm yr-1 and began acting on the Bighorn Basin's landscape between 3 and 2 Ma. The Bighorn Basin has an established history of a basin-wide switch from deposition to incision during the late Pliocene, yet the age control on the erosional evolution of the region is relative. This

Suspension concentration distribution in turbulent flows: An analytical study using fractional advection-diffusion equation

NASA Astrophysics Data System (ADS)

Kundu, Snehasis

2018-09-01

In this study vertical distribution of sediment particles in steady uniform turbulent open channel flow over erodible bed is investigated using fractional advection-diffusion equation (fADE). Unlike previous investigations on fADE to investigate the suspension distribution, in this study the modified Atangana-Baleanu-Caputo fractional derivative with a non-singular and non-local kernel is employed. The proposed fADE is solved and an analytical model for finding vertical suspension distribution is obtained. The model is validated against experimental as well as field measurements of Missouri River, Mississippi River and Rio Grande conveyance channel and is compared with the Rouse equation and other fractional model found in literature. A quantitative error analysis shows that the proposed model is able to predict the vertical distribution of particles more appropriately than previous models. The validation results shows that the fractional model can be equally applied to all size of particles with an appropriate choice of the order of the fractional derivative α. It is also found that besides particle diameter, parameter α depends on the mass density of particle and shear velocity of the flow. To predict this parameter, a multivariate regression is carried out and a relation is proposed for easy application of the model. From the results for sand and plastic particles, it is found that the parameter α is more sensitive to mass density than the particle diameter. The rationality of the dependence of α on particle and flow characteristics has been justified physically.

Advection of nematic liquid crystals by chaotic flow

NASA Astrophysics Data System (ADS)

O'Náraigh, Lennon

2017-04-01

Consideration is given to the effects of inhomogeneous shear flow (both regular and chaotic) on nematic liquid crystals in a planar geometry. The Landau-de Gennes equation coupled to an externally prescribed flow field is the basis for the study: this is solved numerically in a periodic spatial domain. The focus is on a limiting case where the advection is passive, such that variations in the liquid-crystal properties do not feed back into the equation for the fluid velocity. The main tool for analyzing the results (both with and without flow) is the identification of the fixed points of the dynamical equations without flow, which are relevant (to varying degrees) when flow is introduced. The fixed points are classified as stable/unstable and further as either uniaxial or biaxial. Various models of passive shear flow are investigated. When tumbling is present, the flow is shown to have a strong effect on the liquid-crystal morphology; however, the main focus herein is on the case without tumbling. Accordingly, the main result of the work is that only the biaxial fixed point survives as a solution of the Q-tensor dynamics under the imposition of a general flow field. This is because the Q-tensor experiences not only transport due to advection but also co-rotation relative to the local vorticity field. A second result is that all families of fixed points survive for certain specific velocity fields, which we classify. We single out for close study those velocity fields for which the influence of co-rotation effectively vanishes along the Lagrangian trajectories of the imposed velocity field. In this scenario, the system exhibits coarsening arrest, whereby the liquid-crystal domains are "frozen in" to the flow structures, and the growth in their size is thus limited.

Analytical Model of Advection and Erosion in a Rectangular Channel

NASA Astrophysics Data System (ADS)

Kaufman, Miron

2007-03-01

We consider the Boussinesq pressure driven creeping flow in a rectangular channel. We assume a particle to be made of primary fragments bound together. Particles are advected by the flow and they erode because of the shear stresses imparted by the fluid. The time evolution of the numbers of particles of different sizes is described by the Bateman equations of nuclear radioactivity. We find, by solving these differential equations, the numbers of particles of each possible size as functions of time.

Unification of some advection schemes in two dimensions

NASA Technical Reports Server (NTRS)

Sidilkover, D.; Roe, P. L.

1995-01-01

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

High-Order Residual-Distribution Hyperbolic Advection-Diffusion Schemes: 3rd-, 4th-, and 6th-Order

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza R.; Nishikawa, Hiroaki

2014-01-01

In this paper, spatially high-order Residual-Distribution (RD) schemes using the first-order hyperbolic system method are proposed for general time-dependent advection-diffusion problems. The corresponding second-order time-dependent hyperbolic advection- diffusion scheme was first introduced in [NASA/TM-2014-218175, 2014], where rapid convergences over each physical time step, with typically less than five Newton iterations, were shown. In that method, the time-dependent hyperbolic advection-diffusion system (linear and nonlinear) was discretized by the second-order upwind RD scheme in a unified manner, and the system of implicit-residual-equations was solved efficiently by Newton's method over every physical time step. In this paper, two techniques for the source term discretization are proposed; 1) reformulation of the source terms with their divergence forms, and 2) correction to the trapezoidal rule for the source term discretization. Third-, fourth, and sixth-order RD schemes are then proposed with the above techniques that, relative to the second-order RD scheme, only cost the evaluation of either the first derivative or both the first and the second derivatives of the source terms. A special fourth-order RD scheme is also proposed that is even less computationally expensive than the third-order RD schemes. The second-order Jacobian formulation was used for all the proposed high-order schemes. The numerical results are then presented for both steady and time-dependent linear and nonlinear advection-diffusion problems. It is shown that these newly developed high-order RD schemes are remarkably efficient and capable of producing the solutions and the gradients to the same order of accuracy of the proposed RD schemes with rapid convergence over each physical time step, typically less than ten Newton iterations.

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

PubMed

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

2008-02-01

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

Conformational Assessment of Adnectin and Adnectin-Drug Conjugate by Hydrogen/Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Huang, Richard Y.-C.; O'Neil, Steven R.; Lipovšek, Daša; Chen, Guodong

2018-05-01

Higher-order structure (HOS) characterization of therapeutic protein-drug conjugates for comprehensive assessment of conjugation-induced protein conformational changes is an important consideration in the biopharmaceutical industry to ensure proper behavior of protein therapeutics. In this study, conformational dynamics of a small therapeutic protein, adnectin 1, together with its drug conjugate were characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) with different spatial resolutions. Top-down HDX allows detailed assessment of the residue-level deuterium content in the payload conjugation region. HDX-MS dataset revealed the ability of peptide-based payload/linker to retain deuterium in HDX experiments. Combined results from intact, top-down, and bottom-up HDX indicated no significant conformational changes of adnectin 1 upon payload conjugation. [Figure not available: see fulltext.

Dynamical Mass Generation.

NASA Astrophysics Data System (ADS)

Mendel Horwitz, Roberto Ruben

1982-03-01

In the framework of the Glashow-Weinberg-Salem model without elementary scalar particles, we show that masses for fermions and intermediate vector bosons can be generated dynamically. The mechanism is the formation of fermion-antifermion pseudoscalar bound states of zero total four momentum, which form a condensate in the physical vacuum. The force responsible for the binding is the short distance part of the net Coulomb force due to photon and Z exchange. Fermions and bosons acquire masses through their interaction with this condensate. The neutrinos remain massless because their righthanded components have no interactions. Also the charge -1/3 quarks remain massless because the repulsive force from the Z exchange dominates over the Coulomb force. To correct this, we propose two possible modifications to the theory. One is to cut off the Z exchange at very small distances, so that all fermions except the neutrinos acquire masses, which are then, purely electromagnetic in origin. The other is to introduce an additional gauge boson that couples to all quarks with a pure vector coupling. To make this vector boson unobservable at usual energies, at least two new fermions must couple to it. The vector boson squared masses receive additive contributions from all the fermion squared masses. The photon remains massless and the masses of the Z and W('(+OR -)) bosons are shown to be related through the Weinberg angle in the conventional way. Assuming only three families of fermions, we obtain estimates for the top quark mass.

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

On the discrepancy between eddy covariance and lysimetry-based surface flux measurements under strongly advective conditions

NASA Astrophysics Data System (ADS)

Alfieri, Joseph G.; Kustas, William P.; Prueger, John H.; Hipps, Lawrence E.; Evett, Steven R.; Basara, Jeffrey B.; Neale, Christopher M. U.; French, Andrew N.; Colaizzi, Paul; Agam, Nurit; Cosh, Michael H.; Chavez, José L.; Howell, Terry A.

2012-12-01

Discrepancies can arise among surface flux measurements collected using disparate techniques due to differences in both the instrumentation and theoretical underpinnings of the different measurement methods. Using data collected primarily within a pair of irrigated cotton fields as a part of the 2008 Bushland Evapotranspiration and Remote Sensing Experiment (BEAREX08), flux measurements collected with two commonly-used methods, eddy covariance (EC) and lysimetry (LY), were compared and substantial differences were found. Daytime mean differences in the flux measurements from the two techniques could be in excess of 200 W m-2 under strongly advective conditions. Three causes for this disparity were found: (i) the failure of the eddy covariance systems to fully balance the surface energy budget, (ii) flux divergence due to the local advection of warm, dry air over the irrigated cotton fields, and (iii) the failure of lysimeters to accurately represent the surface properties of the cotton fields as a whole. Regardless of the underlying cause, the discrepancy among the flux measurements underscores the difficulty in collecting these measurements under strongly advective conditions. It also raises awareness of the uncertainty associated with in situ micrometeorological measurements and the need for caution when using such data for model validation or as observational evidence to definitively support or refute scientific hypotheses.

Dynamic characterization of external and internal mass transport in heterotrophic biofilms from microsensors measurements.

PubMed

Guimerà, Xavier; Dorado, Antonio David; Bonsfills, Anna; Gabriel, Gemma; Gabriel, David; Gamisans, Xavier

2016-10-01

Knowledge of mass transport mechanisms in biofilm-based technologies such as biofilters is essential to improve bioreactors performance by preventing mass transport limitation. External and internal mass transport in biofilms was characterized in heterotrophic biofilms grown on a flat plate bioreactor. Mass transport resistance through the liquid-biofilm interphase and diffusion within biofilms were quantified by in situ measurements using microsensors with a high spatial resolution (<50 μm). Experimental conditions were selected using a mathematical procedure based on the Fisher Information Matrix to increase the reliability of experimental data and minimize confidence intervals of estimated mass transport coefficients. The sensitivity of external and internal mass transport resistances to flow conditions within the range of typical fluid velocities over biofilms (Reynolds numbers between 0.5 and 7) was assessed. Estimated external mass transfer coefficients at different liquid phase flow velocities showed discrepancies with studies considering laminar conditions in the diffusive boundary layer near the liquid-biofilm interphase. The correlation of effective diffusivity with flow velocities showed that the heterogeneous structure of biofilms defines the transport mechanisms inside biofilms. Internal mass transport was driven by diffusion through cell clusters and aggregates at Re below 2.8. Conversely, mass transport was driven by advection within pores, voids and water channels at Re above 5.6. Between both flow velocities, mass transport occurred by a combination of advection and diffusion. Effective diffusivities estimated at different biofilm densities showed a linear increase of mass transport resistance due to a porosity decrease up to biofilm densities of 50 g VSS·L(-1). Mass transport was strongly limited at higher biofilm densities. Internal mass transport results were used to propose an empirical correlation to assess the effective diffusivity

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

PubMed Central

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

2015-01-01

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

Experimental design for estimating parameters of rate-limited mass transfer: Analysis of stream tracer studies

USGS Publications Warehouse

Wagner, Brian J.; Harvey, Judson W.

1997-01-01

Tracer experiments are valuable tools for analyzing the transport characteristics of streams and their interactions with shallow groundwater. The focus of this work is the design of tracer studies in high-gradient stream systems subject to advection, dispersion, groundwater inflow, and exchange between the active channel and zones in surface or subsurface water where flow is stagnant or slow moving. We present a methodology for (1) evaluating and comparing alternative stream tracer experiment designs and (2) identifying those combinations of stream transport properties that pose limitations to parameter estimation and therefore a challenge to tracer test design. The methodology uses the concept of global parameter uncertainty analysis, which couples solute transport simulation with parameter uncertainty analysis in a Monte Carlo framework. Two general conclusions resulted from this work. First, the solute injection and sampling strategy has an important effect on the reliability of transport parameter estimates. We found that constant injection with sampling through concentration rise, plateau, and fall provided considerably more reliable parameter estimates than a pulse injection across the spectrum of transport scenarios likely encountered in high-gradient streams. Second, for a given tracer test design, the uncertainties in mass transfer and storage-zone parameter estimates are strongly dependent on the experimental Damkohler number, DaI, which is a dimensionless combination of the rates of exchange between the stream and storage zones, the stream-water velocity, and the stream reach length of the experiment. Parameter uncertainties are lowest at DaI values on the order of 1.0. When DaI values are much less than 1.0 (owing to high velocity, long exchange timescale, and/or short reach length), parameter uncertainties are high because only a small amount of tracer interacts with storage zones in the reach. For the opposite conditions (DaI ≫ 1.0), solute

Visualizing Vector Fields Using Line Integral Convolution and Dye Advection

NASA Technical Reports Server (NTRS)

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

1996-01-01

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

New Solution of Diffusion-Advection Equation for Cosmic-Ray Transport Using Ultradistributions

NASA Astrophysics Data System (ADS)

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

2015-11-01

In this paper we exactly solve the diffusion-advection equation (DAE) for cosmic-ray transport. For such a purpose we use the Theory of Ultradistributions of J. Sebastiao e Silva, to give a general solution for the DAE. From the ensuing solution, we obtain several approximations as limiting cases of various situations of physical and astrophysical interest. One of them involves Solar cosmic-rays' diffusion.

Contour advection with surgery: A technique for investigating finescale structure in tracer transport

NASA Technical Reports Server (NTRS)

Waugh, Darryn W.; Plumb, R. Alan

1994-01-01

We present a trajectory technique, contour advection with surgery (CAS), for tracing the evolution of material contours in a specified (including observed) evolving flow. CAS uses the algorithms developed by Dritschel for contour dynamics/surgery to trace the evolution of specified contours. The contours are represented by a series of particles, which are advected by a specified, gridded, wind distribution. The resolution of the contours is preserved by continually adjusting the number of particles, and finescale features are produced that are not present in the input data (and cannot easily be generated using standard trajectory techniques). The reliability, and dependence on the spatial and temporal resolution of the wind field, of the CAS procedure is examined by comparisons with high-resolution numerical data (from contour dynamics calculations and from a general circulation model), and with routine stratospheric analyses. These comparisons show that the large-scale motions dominate the deformation field and that CAS can accurately reproduce small scales from low-resolution wind fields. The CAS technique therefore enables examination of atmospheric tracer transport at previously unattainable resolution.

Influence of bioturbation on sediment respiration in advection- and diffusion-dominated systems

NASA Astrophysics Data System (ADS)

Baranov, Viktor; Krause, Stefan; Lewandowski, Jörg

2017-04-01

Ecosystem engineers are organisms, whose impact on ecosystem functioning is large compared to their abundance and biomass. Classic examples of ecosystem engineers are burrowing organisms whose activity is affecting the sediment matrix and pore solutes in aquatic sediments; this is called bioturbation. Constant reworking of the sediment matrix and transport of solutes caused by activities of sediment-dwelling organisms are modifying habitats and resource availability. Despite that progress of studies on the interactions between the animal bioturbation and the sediment respiration was rather slow, mostly due to the existing methodological limitations. Conceptual framework, formulated by Mermelloid-Blondin and Rosenberg (2006) is suggesting that impact of bioturbation on the sediment biogeochemistry will be much larger in sediments with low hydraulic conductivities (diffusion-dominated) than in sediments with high hydraulic conductivities (advection-dominated). In order to test this hypothesis in application to the sediment respiration, we have used the resazurin-resorufin bioreactive tracer system, which allowed us to decouple respiration of the sediment of microbiota. Our work has shown that in diffusion-dominated sediments (organic rich lake sediments) bioturbator's (bloodworms, larvae of Diptera, Chironomidae) activity could increase sediment aerobic respiration by 300%. In addition to that, impact of the bioturbators on the diffusion-dominated sediments respiration is growing with increasing temperature. Total oxygen consumption (TOU) in such sediments is also increasing by about 50% in bioturbated sediments in comparison with uninhabited sediments. On the other hand, in advection-dominated sediments (sandy sediments from marine tidal flats, bioturbated by brittlestars) we have observed no increase in TOU, and only slight (25%) increase in aerobic respiration in the presence of bioturbators. It became evident that due to the high hydraulic conductivity of

Advection-diffusion model for the simulation of air pollution distribution from a point source emission

NASA Astrophysics Data System (ADS)

Ulfah, S.; Awalludin, S. A.; Wahidin

2018-01-01

Advection-diffusion model is one of the mathematical models, which can be used to understand the distribution of air pollutant in the atmosphere. It uses the 2D advection-diffusion model with time-dependent to simulate air pollution distribution in order to find out whether the pollutants are more concentrated at ground level or near the source of emission under particular atmospheric conditions such as stable, unstable, and neutral conditions. Wind profile, eddy diffusivity, and temperature are considered in the model as parameters. The model is solved by using explicit finite difference method, which is then visualized by a computer program developed using Lazarus programming software. The results show that the atmospheric conditions alone influencing the level of concentration of pollutants is not conclusive as the parameters in the model have their own effect on each atmospheric condition.

Images and Spectra of Time Dependent Two Component Advective Flow in Presence of Outflows

NASA Astrophysics Data System (ADS)

Chatterjee, Arka; Chakrabarti, Sandip K.; Ghosh, Himadri; Garain, Sudip K.

2018-05-01

Two Component Advective Flow (TCAF) successfully explains the spectral and temporal properties of outbursting or persistent sources. Images of static TCAF with Compton cloud or CENtrifugal pressure supported Boundary Layer (CENBOL) due to gravitational bending of photons have been studied before. In this paper, we study time dependent images of advective flows around a Schwarzschild black hole which include cooling effects due to Comptonization of soft photons from a Keplerian disks well as the self-consistently produced jets and outflows. We show the overall image of the disk-jet system after convolving with a typical beamwidth. A long exposure image with time dependent system need not show the black hole horizon conspicuously, unless one is looking at a soft state with no jet or the system along the jet axis. Assuming these disk-jet configurations are relevant to radio emitting systems also, our results would be useful to look for event horizons in high accretion rate Supermassive Black Holes in Seyfert galaxies, RL Quasars.

Numerical study of heat transfer characteristics in BOG heat exchanger

NASA Astrophysics Data System (ADS)

Yan, Yan; Pfotenhauer, John M.; Miller, Franklin; Ni, Zhonghua; Zhi, Xiaoqin

2016-12-01

In this study, a numerical study of turbulent flow and the heat transfer process in a boil-off liquefied natural gas (BOG) heat exchanger was performed. Finite volume computational fluid dynamics and the k - ω based shear stress transport model were applied to simulate thermal flow of BOG and ethylene glycol in a full-sized 3D tubular heat exchanger. The simulation model has been validated and compared with the engineering specification data from its supplier. In order to investigate thermal characteristics of the heat exchanger, velocity, temperature, heat flux and thermal response were studied under different mass flowrates in the shell-side. The shell-side flow pattern is mostly determined by viscous forces, which lead to a small velocity and low temperature buffer area in the bottom-right corner of the heat exchanger. Changing the shell-side mass flowrate could result in different distributions of the shell-side flow. However, the distribution in the BOG will remain in a relatively stable pattern. Heat flux increases along with the shell-side mass flowrate, but the increase is not linear. The ratio of increased heat flux to the mass flow interval is superior at lower mass flow conditions, and the threshold mass flow for stable working conditions is defined as greater than 0.41 kg/s.

Microtube strip heat exchanger

NASA Astrophysics Data System (ADS)

Doty, F. D.

1991-10-01

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.

Roles of cation valance and exchange on the retention and colloid-facilitated transport of functionalized multi-walled carbon nanotubes in a natural soil.

PubMed

Zhang, Miaoyue; Bradford, Scott A; Šimůnek, Jirka; Vereecken, Harry; Klumpp, Erwin

2017-02-01

Saturated soil column experiments were conducted to investigate the transport, retention, and release behavior of a low concentration (1 mg L -1 ) of functionalized 14 C-labeled multi-walled carbon nanotubes (MWCNTs) in a natural soil under various solution chemistries. Breakthrough curves (BTCs) for MWCNTS exhibited greater amounts of retardation and retention with increasing solution ionic strength (IS) or in the presence of Ca 2+ in comparison to K + , and retention profiles (RPs) for MWCNTs were hyper-exponential in shape. These BTCs and RPs were well described using the advection-dispersion equation with a term for time- and depth-dependent retention. Fitted values of the retention rate coefficient and the maximum retained concentration of MWCNTs were higher with increasing IS and in the presence of Ca 2+ in comparison to K + . Significant amounts of MWCNT and soil colloid release was observed with a reduction of IS due to expansion of the electrical double layer, especially following cation exchange (when K + displaced Ca 2+ ) that reduced the zeta potential of MWCNTs and the soil. Analysis of MWCNT concentrations in different soil size fractions revealed that >23.6% of the retained MWCNT mass was associated with water-dispersible colloids (WDCs), even though this fraction was only a minor portion of the total soil mass (2.38%). More MWCNTs were retained on the WDC fraction in the presence of Ca 2+ than K + . These findings indicated that some of the released MWCNTs by IS reduction and cation exchange were associated with the released clay fraction, and suggests the potential for facilitated transport of MWCNT by WDCs. Published by Elsevier Ltd.

The complementary relationship in estimation of regional evapotranspiration: An enhanced Advection-Aridity model

Treesearch

Michael T. Hobbins; Jorge A. Ramirez; Thomas C. Brown

2001-01-01

Long-term monthly evapotranspiration estimates from Brutsaert and Stricker’s Advection-Aridity model were compared with independent estimates of evapotranspiration derived from long-term water balances for 139 undisturbed basins across the conterminous United States. On an average annual basis for the period 1962-1988 the original model, which uses a Penman wind...

A reinterpretation of the data from the NASA Stratosphere-Troposphere Exchange Project

NASA Astrophysics Data System (ADS)

Newman, Paul A.; Schoeberl, Mark R.

Data obtained during the NASA Stratosphere Troposphere Exchange Project (STEP) Mid-Latitude Field Experiment displayed laminae of ozone, water, and condensation nuclei in the stratosphere in association with a mid-latitude stratosphere-troposphere folding event. Danielsen et al. (1991) constructed cross sections of these observations, and interpreted these quasi-horizontal laminae as evidence of ultra-low frequency gravity waves. We use a new technique to show that these laminae could have resulted from differential advection, rather than transport by ultra-low frequency gravity waves. This new technique uses reverse domain filling back trajectories on multiple isentropic surfaces in conjunction with modified potential vorticity to reveal the qualitative details of the constituent laminae.

Macro-microscopic mass formulae and nuclear mass predictions

NASA Astrophysics Data System (ADS)

Royer, G.; Guilbaud, M.; Onillon, A.

2010-12-01

Different mass formulae derived from the liquid drop model and the pairing and shell energies of the Thomas-Fermi model have been studied and compared. They include or not the diffuseness correction to the Coulomb energy, the charge exchange correction term, the curvature energy, different forms of the Wigner term and powers of the relative neutron excess I=(N-Z)/A. Their coefficients have been determined by a least square fitting procedure to 2027 experimental atomic masses (G. Audi et al. (2003) [1]). The Coulomb diffuseness correction Z/A term or the charge exchange correction Z/A term plays the main role to improve the accuracy of the mass formula. The Wigner term and the curvature energy can also be used separately but their coefficients are very unstable. The different fits lead to a surface energy coefficient of around 17-18 MeV. A large equivalent rms radius ( r=1.22-1.24 fm) or a shorter central radius may be used. An rms deviation of 0.54 MeV can be reached between the experimental and theoretical masses. The remaining differences come probably mainly from the determination of the shell and pairing energies. Mass predictions of selected expressions have been compared to 161 new experimental masses and the correct agreement allows to provide extrapolations to masses of 656 selected exotic nuclei.

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

NASA Astrophysics Data System (ADS)

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

2010-05-01

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

Air-sea Exchange of Polycyclic Aromatic Hydrocarbons (PAHs), Polychlorinated Biphenyls (PCBs), Organochlorine Pesticides (OCPs) and Polybrominated Diphenyl Ethers (PBDEs) in the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Lammel, G. P.; Heil, A.; Kukucka, P.; Meixner, F. X.; Mulder, M. D.; Prybilova, P.; Prokes, R.; Rusina, T. S.; Song, G. Z.; Vrana, B.

2015-12-01

The marine atmospheric environment is a receptor for persistent organic pollutants (POPs) which are advected from sources on land, primary, such as biomass burning by-products (PAHs, dioxins), and secondary, such as volatilization from contaminated soils (PCBs, pesticides). Primary sources do not exist in the marine environment, except for PAHs (ship engines) but following previous atmospheric deposition, the sea surface may turn to a secondary source by reversal of diffusive air-sea mass exchange. No monitoring is in place. We studied the vertical fluxes of a wide range of primary and secondary emitted POPs based on measurements in air and surface seawater at a remote coastal site in the eastern Mediterranean (2012). To this end, silicon rubbers were used as passive water samplers, vertical concentration gradients were determined in air and fluxes were quantified based on Eddy covariance. Diffusive air-sea exchange fluxes of hexachlorocyclohexanes (HCHs) and semivolatile PAHs were found close to phase equilibrium, except one PAH, retene, a wood burning tracer, was found seasonally net-volatilisational. Some PCBs, p,p'-DDE, penta- and hexachlorobenzene (PeCB, HCB) were mostly net-depositional, while PBDEs were net-volatilizational. Fluxes determined at a a remote coastal site ranged -33 - +2.4 µg m-2 d-1 for PAHs and -4.0 - +0.3 µg m-2 d-1for halogenated compounds (< 0 means net-deposition, > 0 means net-volatilization). It is concluded that nowadays in open seas more pollutants are undergoing reversal of the direction of air-sea exchange. Recgional fire activity records in combination with box model simulations suggest that deposition of retene during summer is followed by a reversal of air-sea exchange. The seawater surface as secondary source of pollution should be assessed based on flux measurements across seasons and over longer time periods.

Mixing by Unstirring: Hyperuniform Dispersion of Interacting Particles upon Chaotic Advection

NASA Astrophysics Data System (ADS)

Weijs, Joost H.; Bartolo, Denis

2017-07-01

We show how to achieve both fast and hyperuniform dispersions of particles in viscous fluids. To do so, we first extend the concept of critical random organization to chaotic drives. We show how palindromic sequences of chaotic advection cause microscopic particles to effectively interact at long range, thereby inhibiting critical self-organization. Based on this understanding we go around this limitation and design sequences of stirring and unstirring which simultaneously optimize the speed of particle spreading and the homogeneity of the resulting dispersions.

Monte Carlo investigation of anomalous transport in presence of a discontinuity and of an advection field

NASA Astrophysics Data System (ADS)

Marseguerra, M.; Zoia, A.

2007-04-01

Anomalous diffusion has recently turned out to be almost ubiquitous in transport problems. When the physical properties of the medium where the transport process takes place are stationary and constant at each spatial location, anomalous transport has been successfully analysed within the Continuous Time Random Walk (CTRW) model. In this paper, within a Monte Carlo approach to CTRW, we focus on the particle transport through two regions characterized by different physical properties, in presence of an external driving action constituted by an additional advective field, modelled within both the Galilei invariant and Galilei variant schemes. Particular attention is paid to the interplay between the distributions of space and time across the discontinuity. The resident concentration and the flux of the particles are finally evaluated and it is shown that at the interface between the two regions the flux is continuous as required by mass conservation, while the concentration may reveal a neat discontinuity. This result could open the route to the Monte Carlo investigation of the effectiveness of a physical discontinuity acting as a filter on particle concentration.

Probing Conformational Dynamics of Tau Protein by Hydrogen/Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Huang, Richard Y.-C.; Iacob, Roxana E.; Sankaranarayanan, Sethu; Yang, Ling; Ahlijanian, Michael; Tao, Li; Tymiak, Adrienne A.; Chen, Guodong

2018-01-01

Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer's disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau's fibrillization. HDX-MS studies including anti-tau antibody epitope mapping experiments provided molecular level details of the full-length tau's conformational dynamics and its regional solvent accessibility upon soluble aggregates formation. The results demonstrate that R3 region in the full-length tau's microtubule binding repeat region (MTBR) is stabilized in the aggregation process, leaving both N and C terminal regions to be solvent exposed in the soluble aggregates and fibrils. The findings also illustrate the practical utility of orthogonal analytical methodologies for the characterization of protein higher order structure. [Figure not available: see fulltext.

Advective pathways near the tip of the Antarctic Peninsula: Trends, variability and ecosystem implications

NASA Astrophysics Data System (ADS)

Renner, Angelika H. H.; Thorpe, Sally E.; Heywood, Karen J.; Murphy, Eugene J.; Watkins, Jon L.; Meredith, Michael P.

2012-05-01

Pathways and rates of ocean flow near the Antarctic Peninsula are strongly affected by frontal features, forcings from the atmosphere and the cryosphere. In the surface mixed layer, the currents advect material from the northwestern Weddell Sea on the eastern side of the Peninsula around the tip of the Peninsula to its western side and into the Scotia Sea, connecting populations of Antarctic krill (Euphausia superba) and supporting the ecosystem of the region. Modelling of subsurface drifters using a particle tracking algorithm forced by the velocity fields of a coupled sea ice-ocean model (ORCA025-LIM2) allows analysis of the seasonal and interannual variability of drifter pathways over 43 years. The results show robust and persistent connections from the Weddell Sea both to the west into the Bellingshausen Sea and across the Scotia Sea towards South Georgia, reproducing well the observations. The fate of the drifters is sensitive to their deployment location, in addition to other factors. From the shelf of the eastern Antarctic Peninsula, the majority enter the Bransfield Strait and subsequently the Bellingshausen Sea. When originating further offshore over the deeper Weddell Sea, drifters are more likely to cross the South Scotia Ridge and reach South Georgia. However, the wind field east and southeast of Elephant Island, close to the tip of the Peninsula, is crucial for the drifter trajectories and is highly influenced by the Southern Annular Mode (SAM). Increased advection and short travel times to South Georgia, and reduced advection to the western Antarctic Peninsula can be linked to strong westerlies, a signature of the positive phase of the SAM. The converse is true for the negative phase. Strong westerlies and shifts of ocean fronts near the tip of the Peninsula that are potentially associated with both the SAM and the El Niño-Southern Oscillation restrict the connection from the Weddell Sea to the west, and drifters then predominantly follow the open

Large time-step stability of explicit one-dimensional advection schemes

NASA Technical Reports Server (NTRS)

Leonard, B. P.

1993-01-01

There is a wide-spread belief that most explicit one-dimensional advection schemes need to satisfy the so-called 'CFL condition' - that the Courant number, c = udelta(t)/delta(x), must be less than or equal to one, for stability in the von Neumann sense. This puts severe limitations on the time-step in high-speed, fine-grid calculations and is an impetus for the development of implicit schemes, which often require less restrictive time-step conditions for stability, but are more expensive per time-step. However, it turns out that, at least in one dimension, if explicit schemes are formulated in a consistent flux-based conservative finite-volume form, von Neumann stability analysis does not place any restriction on the allowable Courant number. Any explicit scheme that is stable for c is less than 1, with a complex amplitude ratio, G(c), can be easily extended to arbitrarily large c. The complex amplitude ratio is then given by exp(- (Iota)(Nu)(Theta)) G(delta(c)), where N is the integer part of c, and delta(c) = c - N (less than 1); this is clearly stable. The CFL condition is, in fact, not a stability condition at all, but, rather, a 'range restriction' on the 'pieces' in a piece-wise polynomial interpolation. When a global view is taken of the interpolation, the need for a CFL condition evaporates. A number of well-known explicit advection schemes are considered and thus extended to large delta(t). The analysis also includes a simple interpretation of (large delta(t)) total-variation-diminishing (TVD) constraints.

Murt user`s guide: A hybrid Lagrangian-Eulerian finite element model of multiple-pore-region solute transport through subsurface media

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

Gwo, J.P.; Jardine, P.M.; Yeh, G.T.

Matrix diffusion, a diffusive mass transfer process,in the structured soils and geologic units at ORNL, is believe to be an important subsurface mass transfer mechanism; it may affect off-site movement of radioactive wastes and remediation of waste disposal sites by locally exchanging wastes between soil/rock matrix and macropores/fractures. Advective mass transfer also contributes to waste movement but is largely neglected by researchers. This report presents the first documented 2-D multiregion solute transport code (MURT) that incorporates not only diffusive but also advective mass transfer and can be applied to heterogeneous porous media under transient flow conditions. In this report, theoreticalmore » background is reviewed and the derivation of multiregion solute transport equations is presented. Similar to MURF (Gwo et al. 1994), a multiregion subsurface flow code, multiplepore domains as suggested by previous investigators (eg, Wilson and Luxmoore 1988) can be implemented in MURT. Transient or steady-state flow fields of the pore domains can be either calculated by MURF or by modelers. The mass transfer process is briefly discussed through a three-pore-region multiregion solute transport mechanism. Mass transfer equations that describe mass flux across pore region interfaces are also presented and parameters needed to calculate mass transfer coefficients detailed. Three applications of MURT (tracer injection problem, sensitivity analysis of advective and diffusive mass transfer, hillslope ponding infiltration and secondary source problem) were simulated and results discussed. Program structure of MURT and functions of MURT subroutiness are discussed so that users can adapt the code; guides for input data preparation are provided in appendices.« less

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.

Characteristics of stratosphere-troposphere exchange in a general circulation model

NASA Technical Reports Server (NTRS)

Mote, Philip W.; Holton, James R.; Boville, Byron A.

1994-01-01

In this study we examine mass exchange, water vapor exchange, and the behavior of idealized tracers and parcels to diagnose Stratosphere-Troposphere Exchange (STE) in the National Center for Atmospheric Research (NCAR) General Circulation Model (GCM), the Community Climate Model (CCM2). The CCM2 correctly represents the seasonality of mass exchange across 100 hPa, but values are uniformly too strong. Water vapor, however, indicates that tropical STE is not well represented in the CCM2; even though mean tropopause temperatures are colder than observed, the lower stratosphere is too moist. Most net mass flux occurs at water vapor mixing ratios of about 4-5 parts per million by volume (ppmv), about 1 ppmv too moist. Vertical resolution has little impact on the nature of tropical STE. In midlatitudes, CCM2 more successfully represents STE, which occurs in developing baroclinic waves and stationary anticyclones. Exchange from troposphere to stratosphere does occur but only influences the lowest few kilometers of the extratropical stratosphere, even for tracers with large vertical gradients.

Endocytic pathway rapidly delivers internalized molecules to lysosomes: an analysis of vesicle trafficking, clustering and mass transfer.

PubMed

Pangarkar, Chinmay; Dinh, Anh-Tuan; Mitragotri, Samir

2012-08-20

Lysosomes play a critical role in intracellular drug delivery. For enzyme-based therapies, they represent a potential target site whereas for nucleic acid or many protein drugs, they represent the potential degradation site. Either way, understanding the mechanisms and processes involved in routing of materials to lysosomes after cellular entry is of high interest to the field of drug delivery. Most therapeutic cargoes other than small hydrophobic molecules enter the cells through endocytosis. Endocytosed cargoes are routed to lysosomes via microtubule-based transport and are ultimately shared by various lysosomes via tethering and clustering of endocytic vesicles followed by exchange of their contents. Using a combined experimental and numerical approach, here we studied the rates of mass transfer into and among the endocytic vesicles in a model cell line, 3T3 fibroblasts. In order to understand the relationship of mass transfer with microtubular transport and vesicle clustering, we varied both properties through various pharmacological agents. At the same time, microtubular transport and vesicle clustering were modeled through diffusion-advection equations and the Smoluchowski equations, respectively. Our analysis revealed that the rate of mass transfer is optimally related to microtubular transport and clustering properties of vesicles. Further, the rate of mass transfer is highest in the innate state of the cell. Any perturbation to either microtubular transport or vesicle aggregation led to reduced mass transfer to lysosome. These results suggest that in the absence of an external intervention the endocytic pathway appears to maximize molecular delivery to lysosomes. Strategies are discussed to reduce mass transfer to lysosomes so as to extend the residence time of molecules in endosomes or late endosomes, thus potentially increasing the likelihood of their escape before disposition in the lysosomes. Copyright © 2012 Elsevier B.V. All rights reserved.

Metabolite identification of triptolide by data-dependent accurate mass spectrometric analysis in combination with online hydrogen/deuterium exchange and multiple data-mining techniques.

PubMed

Du, Fuying; Liu, Ting; Liu, Tian; Wang, Yongwei; Wan, Yakun; Xing, Jie

2011-10-30

Triptolide (TP), the primary active component of the herbal medicine Tripterygium wilfordii Hook F, has shown promising antileukemic and anti-inflammatory activity. The pharmacokinetic profile of TP indicates an extensive metabolic elimination in vivo; however, its metabolic data is rarely available partly because of the difficulty in identifying it due to the absence of appropriate ultraviolet chromophores in the structure and the presence of endogenous interferences in biological samples. In the present study, the biotransformation of TP was investigated by improved data-dependent accurate mass spectrometric analysis, using an LTQ/Orbitrap hybrid mass spectrometer in conjunction with the online hydrogen (H)/deuterium (D) exchange technique for rapid structural characterization. Accurate full-scan MS and MS/MS data were processed with multiple post-acquisition data-mining techniques, which were complementary and effective in detecting both common and uncommon metabolites from biological matrices. As a result, 38 phase I, 9 phase II and 8 N-acetylcysteine (NAC) metabolites of TP were found in rat urine. Accurate MS/MS data were used to support assignments of metabolite structures, and online H/D exchange experiments provided additional evidence for exchangeable hydrogen atoms in the structure. The results showed the main phase I metabolic pathways of TP are hydroxylation, hydrolysis and desaturation, and the resulting metabolites subsequently undergo phase II processes. The presence of NAC conjugates indicated the capability of TP to form reactive intermediate species. This study also demonstrated the effectiveness of LC/HR-MS(n) in combination with multiple post-acquisition data-mining methods and the online H/D exchange technique for the rapid identification of drug metabolites. Copyright © 2011 John Wiley & Sons, Ltd.

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.

Optimizing zonal advection of the Advanced Research WRF (ARW) dynamics for Intel MIC

NASA Astrophysics Data System (ADS)

Mielikainen, Jarno; Huang, Bormin; Huang, Allen H.

2014-10-01

The Weather Research and Forecast (WRF) model is the most widely used community weather forecast and research model in the world. There are two distinct varieties of WRF. The Advanced Research WRF (ARW) is an experimental, advanced research version featuring very high resolution. The WRF Nonhydrostatic Mesoscale Model (WRF-NMM) has been designed for forecasting operations. WRF consists of dynamics code and several physics modules. The WRF-ARW core is based on an Eulerian solver for the fully compressible nonhydrostatic equations. In the paper, we will use Intel Intel Many Integrated Core (MIC) architecture to substantially increase the performance of a zonal advection subroutine for optimization. It is of the most time consuming routines in the ARW dynamics core. Advection advances the explicit perturbation horizontal momentum equations by adding in the large-timestep tendency along with the small timestep pressure gradient tendency. We will describe the challenges we met during the development of a high-speed dynamics code subroutine for MIC architecture. Furthermore, lessons learned from the code optimization process will be discussed. The results show that the optimizations improved performance of the original code on Xeon Phi 5110P by a factor of 2.4x.

Low-Dissipation Advection Schemes Designed for Large Eddy Simulations of Hypersonic Propulsion Systems

NASA Technical Reports Server (NTRS)

White, Jeffrey A.; Baurle, Robert A.; Fisher, Travis C.; Quinlan, Jesse R.; Black, William S.

2012-01-01

The 2nd-order upwind inviscid flux scheme implemented in the multi-block, structured grid, cell centered, finite volume, high-speed reacting flow code VULCAN has been modified to reduce numerical dissipation. This modification was motivated by the desire to improve the codes ability to perform large eddy simulations. The reduction in dissipation was accomplished through a hybridization of non-dissipative and dissipative discontinuity-capturing advection schemes that reduces numerical dissipation while maintaining the ability to capture shocks. A methodology for constructing hybrid-advection schemes that blends nondissipative fluxes consisting of linear combinations of divergence and product rule forms discretized using 4th-order symmetric operators, with dissipative, 3rd or 4th-order reconstruction based upwind flux schemes was developed and implemented. A series of benchmark problems with increasing spatial and fluid dynamical complexity were utilized to examine the ability of the candidate schemes to resolve and propagate structures typical of turbulent flow, their discontinuity capturing capability and their robustness. A realistic geometry typical of a high-speed propulsion system flowpath was computed using the most promising of the examined schemes and was compared with available experimental data to demonstrate simulation fidelity.

Sensitivity of Age-of-Air Calculations to the Choice of Advection Scheme

NASA Technical Reports Server (NTRS)

Eluszkiewicz, Janusz; Hemler, Richard S.; Mahlman, Jerry D.; Bruhwiler, Lori; Takacs, Lawrence L.

2000-01-01

The age of air has recently emerged as a diagnostic of atmospheric transport unaffected by chemical parameterizations, and the features in the age distributions computed in models have been interpreted in terms of the models' large-scale circulation field. This study shows, however, that in addition to the simulated large-scale circulation, three-dimensional age calculations can also be affected by the choice of advection scheme employed in solving the tracer continuity equation, Specifically, using the 3.0deg latitude X 3.6deg longitude and 40 vertical level version of the Geophysical Fluid Dynamics Laboratory SKYHI GCM and six online transport schemes ranging from Eulerian through semi-Lagrangian to fully Lagrangian, it will be demonstrated that the oldest ages are obtained using the nondiffusive centered-difference schemes while the youngest ages are computed with a semi-Lagrangian transport (SLT) scheme. The centered- difference schemes are capable of producing ages older than 10 years in the mesosphere, thus eliminating the "young bias" found in previous age-of-air calculations. At this stage, only limited intuitive explanations can be advanced for this sensitivity of age-of-air calculations to the choice of advection scheme, In particular, age distributions computed online with the National Center for Atmospheric Research Community Climate Model (MACCM3) using different varieties of the SLT scheme are substantially older than the SKYHI SLT distribution. The different varieties, including a noninterpolating-in-the-vertical version (which is essentially centered-difference in the vertical), also produce a narrower range of age distributions than the suite of advection schemes employed in the SKYHI model. While additional MACCM3 experiments with a wider range of schemes would be necessary to provide more definitive insights, the older and less variable MACCM3 age distributions can plausibly be interpreted as being due to the semi-implicit semi

Direct simulation of groundwater age

USGS Publications Warehouse

Goode, Daniel J.

1996-01-01

A new method is proposed to simulate groundwater age directly, by use of an advection-dispersion transport equation with a distributed zero-order source of unit (1) strength, corresponding to the rate of aging. The dependent variable in the governing equation is the mean age, a mass-weighted average age. The governing equation is derived from residence-time-distribution concepts for the case of steady flow. For the more general case of transient flow, a transient governing equation for age is derived from mass-conservation principles applied to conceptual “age mass.” The age mass is the product of the water mass and its age, and age mass is assumed to be conserved during mixing. Boundary conditions include zero age mass flux across all noflow and inflow boundaries and no age mass dispersive flux across outflow boundaries. For transient-flow conditions, the initial distribution of age must be known. The solution of the governing transport equation yields the spatial distribution of the mean groundwater age and includes diffusion, dispersion, mixing, and exchange processes that typically are considered only through tracer-specific solute transport simulation. Traditional methods have relied on advective transport to predict point values of groundwater travel time and age. The proposed method retains the simplicity and tracer-independence of advection-only models, but incorporates the effects of dispersion and mixing on volume-averaged age. Example simulations of age in two idealized regional aquifer systems, one homogeneous and the other layered, demonstrate the agreement between the proposed method and traditional particle-tracking approaches and illustrate use of the proposed method to determine the effects of diffusion, dispersion, and mixing on groundwater age.

Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

PubMed Central

Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em

2015-01-01

We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers. PMID:26156459

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

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

2017-05-01

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.

Surface Layer Flux Processes During Cloud Intermittency and Advection above a Middle Rio Grande Riparian Forest, New Mexico

NASA Astrophysics Data System (ADS)

Cleverly, J. R.; Prueger, J.; Cooper, D. I.; Hipps, L.; Eichinger, W.

2002-12-01

An intensive field campaign was undertaken to bring together state-of-the-art methodologies for investigating surface layer physical characteristics over a desert riparian forest. Three-dimensional sonic eddy covariance (3SEC), LIDAR, SODAR, Radiosonde, one-dimensional propeller eddy covariance (1PEC), heat dissipation sap flux, and leaf gas exchange were simultaneously in use 13 -- 21 June 1999 at Bosque del Apache National Wildlife Refuge (NWR) in New Mexico. A one hour period of intense advection was identified by /line{v} >> 0 and /line{u} = 0, indicating that wind direction was transverse to the riparian corridor. The period of highest /line{v} was 1400 h on 20 June; this hour experienced intermittent cloud cover and enhanced mesoscale forcing of surface fluxes. High-frequency (20 Hz) time series of u, v, w, q, θ , and T were collected for spectral, cospectral, and wavelet analyses. These time series analyses illustrate scales at which processes co-occur. At high frequencies (> 0.015 Hz), /line{T' q'} > 0, and (KH)/ (KW) = 1. At low frequencies, however, /line{T' q'} < 0, and (KH)/(KW) !=q 1. Under these transient conditions, frequencies below 0.015 Hz are associated with advection. While power cospectra are useful in associating processes at certain frequencies, further analysis must be performed to determine whether such examples of aphasia are localized to transient events or constant through time. Continuous wavelet transformation (CWT) sacrifices localization in frequency space for localization in time. Mother wavelets were evaluated, and Daubechies order 10 wavelet was found to reduce red noise and leakage near the spectral gap. The spectral gap is a frequency domain between synoptic and turbulent scales. Low frequency turbulent structures near the spectral gap in the time series of /line{T' q'}, /line{w' T'}, and /line{w' q'} followed a perturbation--relaxation pattern to cloud cover. Further cloud cover in the same hour did not produce the low

Heat tracing to determine spatial patterns of hyporheic exchange across a river transect

NASA Astrophysics Data System (ADS)

Lu, Chengpeng; Chen, Shuai; Zhang, Ying; Su, Xiaoru; Chen, Guohao

2017-09-01

Significant spatial variability of water fluxes may exist at the water-sediment interface in river channels and has great influence on a variety of water issues. Understanding the complicated flow systems controlling the flux exchanges along an entire river is often limited due to averaging of parameters or the small number of discrete point measurements usually used. This study investigated the spatial pattern of the hyporheic flux exchange across a river transect in China, using the heat tracing approach. This was done with measurements of temperature at high spatial resolution during a 64-h monitoring period and using the data to identify the spatial pattern of the hyporheic exchange flux with the aid of a one-dimensional conduction-advection-dispersion model (VFLUX). The threshold of neutral exchange was considered as 126 L m-2 d-1 in this study and the heat tracing results showed that the change patterns of vertical hyporheic flux varied with buried depth along the river transect; however, the hyporheic flux was not simply controlled by the streambed hydraulic conductivity and water depth in the river transect. Also, lateral flow dominated the hyporheic process within the shallow high-permeability streambed, while the vertical flow was dominant in the deep low-permeability streambed. The spatial pattern of hyporheic exchange across the river transect was naturally controlled by the heterogeneity of the streambed and the bedform of the stream cross-section. Consequently, a two-dimensional conceptual illustration of the hyporheic process across the river transect is proposed, which could be applicable to river transects of similar conditions.

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

NASA Astrophysics Data System (ADS)

Hamuro, Yoshitomo

2017-03-01

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

Enriched reproducing kernel particle method for fractional advection-diffusion equation

NASA Astrophysics Data System (ADS)

Ying, Yuping; Lian, Yanping; Tang, Shaoqiang; Liu, Wing Kam

2018-06-01

The reproducing kernel particle method (RKPM) has been efficiently applied to problems with large deformations, high gradients and high modal density. In this paper, it is extended to solve a nonlocal problem modeled by a fractional advection-diffusion equation (FADE), which exhibits a boundary layer with low regularity. We formulate this method on a moving least-square approach. Via the enrichment of fractional-order power functions to the traditional integer-order basis for RKPM, leading terms of the solution to the FADE can be exactly reproduced, which guarantees a good approximation to the boundary layer. Numerical tests are performed to verify the proposed approach.

Mathematical theory of exchange-driven growth

NASA Astrophysics Data System (ADS)

Esenturk, Emre

2018-07-01

Exchange-driven growth is a process in which pairs of clusters interact by exchanging single unit of mass at a time. The rate of exchange is given by an interaction kernel which depends on the masses of the two interacting clusters. In this paper we establish the fundamental mathematical properties of the mean field rate equations of this process for the first time. We find two different classes of behavior depending on whether is symmetric or not. For the non-symmetric case, we prove global existence and uniqueness of solutions for kernels satisfying . This result is optimal in the sense that we show for a large class of initial conditions and kernels satisfying the solutions cannot exist. On the other hand, for symmetric kernels, we prove global existence of solutions for ( while existence is lost for ( In the intermediate regime we can only show local existence. We conjecture that the intermediate regime exhibits finite-time gelation in accordance with the heuristic results obtained for particular kernels.

Tuning a High Transmission Ion Guide to Prevent Gas-Phase Proton Exchange During H/D Exchange MS Analysis.

PubMed

Guttman, Miklos; Wales, Thomas E; Whittington, Dale; Engen, John R; Brown, Jeffery M; Lee, Kelly K

2016-04-01

Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for protein structural analysis has been adopted for many purposes, including biopharmaceutical development. One of the benefits of examining amide proton exchange by mass spectrometry is that it can readily resolve different exchange regimes, as evidenced by either binomial or bimodal isotope patterns. By careful analysis of the isotope pattern during exchange, more insight can be obtained on protein behavior in solution. However, one must be sure that any observed bimodal isotope patterns are not artifacts of analysis and are reflective of the true behavior in solution. Sample carryover and certain stationary phases are known as potential sources of bimodal artifacts. Here, we describe an additional undocumented source of deuterium loss resulting in artificial bimodal patterns for certain highly charged peptides. We demonstrate that this phenomenon is predominantly due to gas-phase proton exchange between peptides and bulk solvent within the initial stages of high-transmission conjoined ion guides. Minor adjustments of the ion guide settings, as reported here, eliminate the phenomenon without sacrificing signal intensity. Such gas-phase deuterium loss should be appreciated for all HDX-MS studies using such ion optics, even for routine studies not focused on interpreting bimodal spectra. Graphical Abstract ᅟ.

[Medical exchanges among China and Asiana countries].

PubMed

Chen, H

1996-01-01

Among the issues of medical exchanges, medicaments are more often encountered than medical issues, based on ancient Chinese literatures, early in the Han-Jin Dynasties, Thailand, Malaysia, Indonesia, and Brunei had exchanges with China, also in Sui-Tang Dynasties. In the Song-Yuan Dynasties, ancient Singapore and the Philippines also incorporated in exchanges of medicament and goods. In the Ming-Qing dynasties, these 6 Asian countries had even more close contact with China, especially in trades and medical exchanges among the masses, carried out in a large scale thus, promoting the advent and development of TCM in Asiana Regions.

Effect of Advection on Evaporative Fluxes and Vapor Isotopic Ratios: The Lake Size Effect

NASA Astrophysics Data System (ADS)

Feng, X.; Lauder, A. M.; Kopec, B. G.; Posmentier, E. S.

2015-12-01

It has been reported that advection of air from land can be identified hundreds of kilometers off shore. With advection, moisture builds up downwind, and the evaporative flux decreases and isotopic flux ratios increase with distance. If a lake is small relative to the equilibration distance, the fluxes of all water isotopologues averaged over the lake are different from those calculated using models without advection. The magnitude of the discrepancy depends on the lake size; we refer to this as the "lake size effect". In Kangerlussuaq, Greenland, we observed significant horizontal gradients in concentration, δD, and δ18O of vapor up to 5 km along the wind direction. Over a 0.5 km long lake, the observed average gradients were 1380 ppm/km for vapor content, 21‰/km for δD, 2.4‰/km for δ18O, and 5‰/km for d-excess. These gradients decreased with distance from the upwind shore. Over a stretch of another, much larger lake 4-5 km from the upwind shore, we observed gradients of 354 ppm/km, 1.5‰/km, 0.22‰/km and 0.3‰/km, for vapor concentration, δD, δ18O, and d-excess, respectively. These observations were modeled successfully using a two-dimensional (2-D, horizontal and vertical) steady state advection diffusion model. This model also computes evaporative fluxes. Using the model results, we assess the magnitude of the lake size effect and its impact on water balance calculations. Under the condition of our field observations and for lakes less than 500 m along the wind direction, the mean flux δ18O and δD were at least 2‰ lower than the corresponding values from a 1-D model (vertical only). If using biased isotopic flux values for water balance calculations, the lake size effect would lead to an underestimation of the lake I/E (input to evaporation) ratio. For example, if the lake effect is 1‰, the corresponding underestimation of the I/E ratio is about 10% if using δ18O, and less than 2% if using δD for the computation. This argues for

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.

Chaotic advection and heat transfer in two similar 2-D periodic flows and in their corresponding 3-D periodic flows

NASA Astrophysics Data System (ADS)

Vinsard, G.; Dufour, S.; Saatdjian, E.; Mota, J. P. B.

2016-03-01

Chaotic advection can effectively enhance the heat transfer rate between a boundary and fluids with high Prandtl number. These fluids are usually highly viscous and thus turbulent agitation is not a viable solution since the energy required to mix the fluid would be prohibitive. Here, we analyze previously obtained results on chaotic advection and heat transfer in two similar 2-D periodic flows and on their corresponding 3-D periodic flows when an axial velocity component is superposed. The two flows studied are the flow between eccentric rotating cylinders and the flow between confocal ellipses. For both of these flows the analysis is simplified because the Stokes equations can be solved analytically to obtain a closed form solution. For both 2-D periodic flows, we show that chaotic heat transfer is enhanced by the displacement of the saddle point location during one period. Furthermore, the enhancement by chaotic advection in the elliptical geometry is approximately double that obtained in the cylindrical geometry because there are two saddle points instead of one. We also explain why, for high eccentricity ratios, there is no heat transfer enhancement in the cylindrical geometry. When an axial velocity component is added to both of these flows so that they become 3-D, previous work has shown that there is an optimum modulation frequency for which chaotic advection and heat transfer enhancement is a maximum. Here we show that the optimum modulation frequency can be derived from results without an axial flow. We also explain by physical arguments other previously unanswered questions in the published data.

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

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.

Influence of sea ice cover and icebergs on circulation and water mass formation in a numerical circulation model of the Ross Sea, Antarctica

NASA Astrophysics Data System (ADS)

Dinniman, Michael S.; Klinck, John M.; Smith, Walker O.

2007-11-01

Satellite imagery shows that there was substantial variability in the sea ice extent in the Ross Sea during 2001-2003. Much of this variability is thought to be due to several large icebergs that moved through the area during that period. The effects of these changes in sea ice on circulation and water mass distributions are investigated with a numerical general circulation model. It would be difficult to simulate the highly variable sea ice from 2001 to 2003 with a dynamic sea ice model since much of the variability was due to the floating icebergs. Here, sea ice concentration is specified from satellite observations. To examine the effects of changes in sea ice due to iceberg C-19, simulations were performed using either climatological ice concentrations or the observed ice for that period. The heat balance around the Ross Sea Polynya (RSP) shows that the dominant term in the surface heat budget is the net exchange with the atmosphere, but advection of oceanic warm water is also important. The area average annual basal melt rate beneath the Ross Ice Shelf is reduced by 12% in the observed sea ice simulation. The observed sea ice simulation also creates more High-Salinity Shelf Water. Another simulation was performed with observed sea ice and a fixed iceberg representing B-15A. There is reduced advection of warm surface water during summer from the RSP into McMurdo Sound due to B-15A, but a much stronger reduction is due to the late opening of the RSP in early 2003 because of C-19.

On the origin of size-dependent and size-independent crystal growth: Influence of advection and diffusion

USGS Publications Warehouse

Kile, D.E.; Eberl, D.D.

2003-01-01

Crystal growth experiments were conducted using potassium alum and calcite crystals in aqueous solution under both non-stirred and stirred conditions to elucidate the mechanism for size-dependent (proportionate) and size-independent (constant) crystal growth. Growth by these two laws can be distinguished from each other because the relative size difference among crystals is maintained during proportionate growth, leading to a constant crystal size variance (??2) for a crystal size distribution (CSD) as the mean size increases. The absolute size difference among crystals is maintained during constant growth, resulting in a decrease in size variance. Results of these experiments show that for centimeter-sized alum crystals, proportionate growth occurs in stirred systems, whereas constant growth occurs in non-stirred systems. Accordingly, the mechanism for proportionate growth is hypothesized to be related to the supply of reactants to the crystal surface by advection, whereas constant growth is related to supply by diffusion. Paradoxically, micrometer-sized calcite crystals showed proportionate growth both in stirred and in non-stirred systems. Such growth presumably results from the effects of convection and Brownian motion, which promote an advective environment and hence proportionate growth for minute crystals in non-stirred systems, thereby indicating the importance of solution velocity relative to crystal size. Calcite crystals grown in gels, where fluid motion was minimized, showed evidence for constant, diffusion-controlled growth. Additional investigations of CSDs of naturally occurring crystals indicate that proportionate growth is by far the most common growth law, thereby suggesting that advection, rather than diffusion, is the dominant process for supplying reactants to crystal surfaces.

An Analytic Approach to Modeling Land-Atmosphere Interaction: 1. Construct and Equilibrium Behavior

NASA Astrophysics Data System (ADS)

Brubaker, Kaye L.; Entekhabi, Dara

1995-03-01

A four-variable land-atmosphere model is developed to investigate the coupled exchanges of water and energy between the land surface and atmosphere and the role of these exchanges in the statistical behavior of continental climates. The land-atmosphere system is substantially simplified and formulated as a set of ordinary differential equations that, with the addition of random noise, are suitable for analysis in the form of the multivariate Îto equation. The model treats the soil layer and the near-surface atmosphere as reservoirs with storage capacities for heat and water. The transfers between these reservoirs are regulated by four states: soil saturation, soil temperature, air specific humidity, and air potential temperature. The atmospheric reservoir is treated as a turbulently mixed boundary layer of fixed depth. Heat and moisture advection, precipitation, and layer-top air entrainment are parameterized. The system is forced externally by solar radiation and the lateral advection of air and water mass. The remaining energy and water mass exchanges are expressed in terms of the state variables. The model development and equilibrium solutions are presented. Although comparisons between observed data and steady state model results re inexact, the model appears to do a reasonable job of partitioning net radiation into sensible and latent heat flux in appropriate proportions for bare-soil midlatitude summer conditions. Subsequent work will introduce randomness into the forcing terms to investigate the effect of water-energy coupling and land-atmosphere interaction on variability and persistence in the climatic system.

Letter: Observation of the 16O/18O exchange during electrospray ionization.

PubMed

Kostyukevich, Yury; Kononikhin, Alexey; Popov, Igor; Nikolaev, Eugene

2015-01-01

Isotopic exchange approach coupled to high-resolution mass spectrometry has become the power analytical approach for a wide range of analytical and bioanalyticall applications. Considerable efforts have been dedicated to developing fast exchange techniques directly in the ionization source. But all such methods are limited to the hydrogen/deuterium exchange approaches. In this paper we demonstrate that certain types of oxygen atoms can also be exchanged for (18)O on the time scale of the ionization process. Using HIO(3) and NaIO(4) and by infusing the heavy water H(2)(18)O in the ESI source we have demonstrated that it is possible to obtain a high level of oxygen exchange. It was observed that the rate of this exchange depends to a large extent on the temperature of the desolvating capillary of the mass spectrometer. Several other species, such as peptides, oligonucleotides and low weight organic molecules, were subjected to in-ESI (16)O/(18)O exchange but the exchange was not observed.

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

NASA Astrophysics Data System (ADS)

Martinez, Michael J.

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

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

PubMed Central

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

2014-01-01

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

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. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Protein Folding—How and Why: By Hydrogen Exchange, Fragment Separation, and Mass Spectrometry

PubMed Central

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

2017-01-01

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

Boundary layers at a dynamic interface: air-sea exchange of heat and mass

NASA Astrophysics Data System (ADS)

Szeri, Andrew

2017-11-01

Exchange of mass or heat across a turbulent liquid-gas interface is a problem of critical interest, especially in air-sea transfer of natural and man-made gases involved in climate change. The goal in this research area is to determine the gas flux from air to sea or vice versa. For sparingly soluble non-reactive gases, this is controlled by liquid phase turbulent velocity fluctuations that act on the thin species concentration boundary layer on the liquid side of the interface. If the fluctuations in surface-normal velocity and gas concentration differences are known, then it is possible to determine the turbulent contribution to the gas flux. However, there is no suitable fundamental direct approach in the general case where neither of these quantities can be easily measured. A new approach is presented to deduce key aspects about the near-surface turbulent motions from remote measurements, which allows one to determine the gas transfer velocity, or gas flux per unit area if overall concentration differences are known. The approach is illustrated with conceptual examples.

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

PubMed

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

2008-05-01

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

On the advective Cahn-Hilliard Equation

NASA Astrophysics Data System (ADS)

O'Naraigh, Lennon; Thiffeault, Jean-Luc

2006-11-01

The advective Cahn-Hilliard equation describes the chef's problem of stirring olive oil and soy sauce. An efficient way of doing this is to choose a chaotic mixing protocol. Intuition suggests that bubbles of oil and soy will form on a certain scale, and previous studies of Cahn-Hilliard dynamics indicate the presence of one dominant length scale. See, for example, Berthier et al., 2001. The Cahn-Hilliard demixing mechanism however, contains a hyperdiffusion term and in this study we show how, by stirring the mixture at sufficiently large amplitude, we may excite the diffusion and overwhelm the demixing to create a homogeneous liquid. At intermediate amplitudes we see regions with oil and soy bubbles, and regions with hyperdiffusive filaments, implying that the problem in fact possesses two length scales. In this state, the system is in dynamical equilibrium and this is surprising, given that the homogenous state is unstable in the unstirred case. We compare our results with the case for a variable mobility, in which coarsening (growth of bubble size) is dominated by interfacial, rather than bulk, effects. The no-flow equivalent of this situation was considered by Zhu et al. (1999). We discuss the possibility that these results point in fact to the real-world limitations of the binary fluid model.

A third-order computational method for numerical fluxes to guarantee nonnegative difference coefficients for advection-diffusion equations in a semi-conservative form

NASA Astrophysics Data System (ADS)

Sakai, K.; Watabe, D.; Minamidani, T.; Zhang, G. S.

2012-10-01

According to Godunov theorem for numerical calculations of advection equations, there exist no higher-order schemes with constant positive difference coefficients in a family of polynomial schemes with an accuracy exceeding the first-order. We propose a third-order computational scheme for numerical fluxes to guarantee the non-negative difference coefficients of resulting finite difference equations for advection-diffusion equations in a semi-conservative form, in which there exist two kinds of numerical fluxes at a cell surface and these two fluxes are not always coincident in non-uniform velocity fields. The present scheme is optimized so as to minimize truncation errors for the numerical fluxes while fulfilling the positivity condition of the difference coefficients which are variable depending on the local Courant number and diffusion number. The feature of the present optimized scheme consists in keeping the third-order accuracy anywhere without any numerical flux limiter. We extend the present method into multi-dimensional equations. Numerical experiments for advection-diffusion equations showed nonoscillatory solutions.

Observational signatures of past mass-exchange episodes in massive binaries: the case of LSS 3074

NASA Astrophysics Data System (ADS)

Raucq, F.; Gosset, E.; Rauw, G.; Manfroid, J.; Mahy, L.; Mennekens, N.; Vanbeveren, D.

2017-05-01

Context. The role of mass and momentum exchanges in close massive binaries is very important in the subsequent evolution of the components. Such exchanges 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 close O-star binary LSS 3074 (O4 f + O6-7:(f):), which is a good candidate for a past Roche lobe overflow (RLOF) episode because of its very short orbital period, P = 2.185 days, and the luminosity classes of both components. Methods: We determined a new orbital solution for the system. We studied the photometric light curves to determine the inclination of the orbit and Roche lobe filling factors of both stars. Using phase-resolved spectroscopy, we performed the disentangling of the optical spectra of the two stars. We then analysed the reconstructed primary and secondary spectra 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. Results: We confirm the apparent low stellar masses and radii reported in previous studies. We also find a strong overabundance in nitrogen and a strong carbon and oxygen depletion in both primary and secondary atmospheres, together with a strong enrichment in helium of the primary star. Conclusions: We propose several possible evolutionary pathways through a RLOF process to explain the current parameters of the system. We confirm that the system is apparently in overcontact configuration and has lost a significant portion of its mass to its surroundings. We suggest that some of the discrepancies between the spectroscopic and photometric properties of LSS 3074 could stem from the impact of a strong radiation pressure of the primary. Based on observations collected at the European Southern Observatory (La Silla, Chile) and the Cerro Tololo Inter

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

PubMed

Hamuro, Yoshitomo

2017-03-01

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

Permeability generation and resetting of tracers during metamorphic fluid flow: implications for advection-dispersion models

NASA Astrophysics Data System (ADS)

Cartwright, Ian

Advection-dispersion fluid flow models implicitly assume that the infiltrating fluid flows through an already fluid-saturated medium. However, whether rocks contain a fluid depends on their reaction history, and whether any initial fluid escapes. The behaviour of different rocks may be illustrated using hypothetical marble compositions. Marbles with diverse chemistries (e.g. calcite + dolomite + quartz) are relatively reactive, and will generally produce a fluid during heating. By contrast, marbles with more restricted chemistries (e.g. calcite + quartz or calcite-only) may not. If the rock is not fluid bearing when fluid infiltration commences, mineralogical reactions may produce a reaction-enhanced permeability in calcite + dolomite + quartz or calcite + quartz, but not in calcite-only marbles. The permeability production controls the pattern of mineralogical, isotopic, and geochemical resetting during fluid flow. Tracers retarded behind the mineralogical fronts will probably be reset as predicted by the advection-dispersion models; however, tracers that are expected to be reset ahead of the mineralogical fronts cannot progress beyond the permeability generating reaction. In the case of very unreactive lithologies (e.g. pure calcite marbles, cherts, and quartzites), the first reaction to affect the rocks may be a metasomatic one ahead of which there is little pervasive resetting of any tracer. Centimetre-scale layering may lead to the formation of self-perpetuating fluid channels in rocks that are not fluid saturated due to the juxtaposition of reactants. Such layered rocks may show patterns of mineralogical resetting that are not predicted by advection-dispersion models. Patterns of mineralogical and isotopic resetting in marbles from a number of terrains, for example: Chillagoe, Marulan South, Reynolds Range (Australia); Adirondack Mountains, Old Woman Mountains, Notch Peak (USA); and Stephen Cross Quarry (Canada) vary as predicted by these models.

Identification of regions of rabbit muscle pyruvate kinase important for allosteric regulation by phenylalanine, detected by H/D exchange mass spectrometry†

PubMed Central

Prasannan, Charulata B.; Villar, Maria T.; Artigues, Antonio; Fenton, Aron W.

2013-01-01

Mass spectrometry has been used to determine the number of exchangeable backbone amide protons and the associated rate constants that are altered when rabbit muscle pyruvate kinase (rM1-PYK) binds either the allosteric inhibitor (phenylalanine) or a non-allosteric analogue of the inhibitor. Alanine is used as the non-allosteric analogue since it binds competitively with phenylalanine, but elicits a negligible allosteric inhibition, i.e. a negligible reduction of the affinity of rM1-PYK for the substrate, phosphoenolpyruvate (PEP). This experimental design is expected to distinguish changes in the protein caused by effector binding (i.e. those changes common upon the addition of alanine vs. phenylalanine) from changes associated with allosteric regulation (i.e. those elicited by the addition of phenylalanine binding, but not alanine binding). High quality peptic fragments covering 98% of the protein were identified. Changes in both the number of exchangeable protons per peptide and in the rate constant associated with exchange highlight regions of the protein with allosteric roles. The set of allosterically relevant peptides identified by this technique include residues previously identified by mutagenesis to have roles in the allosteric regulation by phenylalanine. PMID:23418858

MODFLOW-2000 : the U.S. Geological Survey modular ground-water model--documentation of the Advective-Transport Observation (ADV2) Package

USGS Publications Warehouse

Anderman, Evan R.; Hill, Mary Catherine

2001-01-01

Observations of the advective component of contaminant transport in steady-state flow fields can provide important information for the calibration of ground-water flow models. This report documents the Advective-Transport Observation (ADV2) Package, version 2, which allows advective-transport observations to be used in the three-dimensional ground-water flow parameter-estimation model MODFLOW-2000. The ADV2 Package is compatible with some of the features in the Layer-Property Flow and Hydrogeologic-Unit Flow Packages, but is not compatible with the Block-Centered Flow or Generalized Finite-Difference Packages. The particle-tracking routine used in the ADV2 Package duplicates the semi-analytical method of MODPATH, as shown in a sample problem. Particles can be tracked in a forward or backward direction, and effects such as retardation can be simulated through manipulation of the effective-porosity value used to calculate velocity. Particles can be discharged at cells that are considered to be weak sinks, in which the sink applied does not capture all the water flowing into the cell, using one of two criteria: (1) if there is any outflow to a boundary condition such as a well or surface-water feature, or (2) if the outflow exceeds a user specified fraction of the cell budget. Although effective porosity could be included as a parameter in the regression, this capability is not included in this package. The weighted sum-of-squares objective function, which is minimized in the Parameter-Estimation Process, was augmented to include the square of the weighted x-, y-, and z-components of the differences between the simulated and observed advective-front locations at defined times, thereby including the direction of travel as well as the overall travel distance in the calibration process. The sensitivities of the particle movement to the parameters needed to minimize the objective function are calculated for any particle location using the exact sensitivity

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...

A 2.5-dimensional viscous, resistive, advective magnetized accretion-outflow coupling in black hole systems: a higher order polynomial approximation

NASA Astrophysics Data System (ADS)

Ghosh, Shubhrangshu

2017-09-01

The correlated and coupled dynamics of accretion and outflow around black holes (BHs) are essentially governed by the fundamental laws of conservation as outflow extracts matter, momentum and energy from the accretion region. Here we analyze a robust form of 2.5-dimensional viscous, resistive, advective magnetized accretion-outflow coupling in BH systems. We solve the complete set of coupled MHD conservation equations self-consistently, through invoking a generalized polynomial expansion in two dimensions. We perform a critical analysis of the accretion-outflow region and provide a complete quasi-analytical family of solutions for advective flows. We obtain the physically plausible outflow solutions at high turbulent viscosity parameter α (≳ 0.3), and at a reduced scale-height, as magnetic stresses compress or squeeze the flow region. We found that the value of the large-scale poloidal magnetic field B P is enhanced with the increase of the geometrical thickness of the accretion flow. On the other hand, differential magnetic torque (-{r}2{\\bar{B}}\\varphi {\\bar{B}}z) increases with the increase in \\dot{M}. {\\bar{B}}{{P}}, -{r}2{\\bar{B}}\\varphi {\\bar{B}}z as well as the plasma beta β P get strongly augmented with the increase in the value of α, enhancing the transport of vertical flux outwards. Our solutions indicate that magnetocentrifugal acceleration plausibly plays a dominant role in effusing out plasma from the radial accretion flow in a moderately advective paradigm which is more centrifugally dominated. However in a strongly advective paradigm it is likely that the thermal pressure gradient would play a more contributory role in the vertical transport of plasma.

Exchange-driven growth.

PubMed

Ben-Naim, E; Krapivsky, P L

2003-09-01

We study a class of growth processes in which clusters evolve via exchange of particles. We show that depending on the rate of exchange there are three possibilities: (I) Growth-clusters grow indefinitely, (II) gelation-all mass is transformed into an infinite gel in a finite time, and (III) instant gelation. In regimes I and II, the cluster size distribution attains a self-similar form. The large size tail of the scaling distribution is Phi(x) approximately exp(-x(2-nu)), where nu is a homogeneity degree of the rate of exchange. At the borderline case nu=2, the distribution exhibits a generic algebraic tail, Phi(x) approximately x(-5). In regime III, the gel nucleates immediately and consumes the entire system. For finite systems, the gelation time vanishes logarithmically, T approximately [lnN](-(nu-2)), in the large system size limit N--> infinity. The theory is applied to coarsening in the infinite range Ising-Kawasaki model and in electrostatically driven granular layers.

Advection from the North Atlantic as the Forcing of Winter Greenhouse Effect Over Europe

NASA Technical Reports Server (NTRS)

Otterman, J.; Angell, J.; Atlas, R.; Bungato, D.; Shubert, S.; Starr, David OC.; Susskind, J.; Wu, M.-L. C.

2002-01-01

In winter, large interannual fluctuations in the surface temperature are observed over central Europe. Comparing warm February 1990 with cold February 1996, a satellite-retrieved surface (skin) temperature difference of 9.8 K is observed for the region 50-60 degrees N; 5-35 degrees E. Previous studies show that advection from the North Atlantic constitutes the forcing to such fluctuations. The advection is quantified by Index I(sub na), the average of the ocean-surface wind speed over the eastern North Atlantic when the direction is from the southwest (when the wind is from another direction, it counts as a zero speed to the average). Average I(sub na) for February 1990 was 10.6 m/s, but for February 1996 I(sub na) was only 2.4 m/s. A large value of I(sub na) means a strong southwesterly flow which brings warm and moist air into central Europe at low level, producing a steeper tropospheric lapse rate. Strong ascending motions at 700 mb are observed in association with the occurrence of enhanced warm, moist advection from the ocean in February 1990 producing clouds and precipitation. Total precipitable water and cloud-cover fraction have larger values in February 1990 than in 1996. The difference in the greenhouse effect between these two scenarios, this reduction in heat loss to space, can be translated into a virtual radiative heating of 2.6 W/square m above the February 1990 surface/atmosphere system, which contributes to a warming of the surface on the order of 2.6 K. Accepting this estimate as quantitatively meaningful, we evaluate the direct effect, the rise in the surface temperature in Europe as a result of maritime-air inflow, as 7.2 K (9.8 K-2.6 K). Thus, fractional reinforcement by the greenhouse effect is 2.6/7.2, or 36%, a substantial positive feedback.

Magnetic field advection in two interpenetrating plasma streams

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

Ryutov, D. D.; Kugland, N. L.; Levy, M. C.

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 coilsmore » 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.« less

Oligonucleotide gas-phase hydrogen/deuterium exchange with D2S in the collision cell of a quadrupole-Fourier transform ion cyclotron resonance mass spectrometer.

PubMed

Mo, Jingjie; Håkansson, Kristina

2007-10-15

We have implemented gas-phase hydrogen/deuterium exchange (HDX) experiments in the external collision cell of a hybrid quadrupole-Fourier transform ion cyclotron resonance mass spectrometer. In this configuration, multiply charged oligonucleotide anions undergo significant exchange with D(2)S at reaction intervals ranging from 0.11 to 60.1 s. For DNA homohexamers, relative exchange rates were dC(6) approximately dA(6) > dG(6) > dT(6), correlating with the gas-phase acidities of nucleobases (C > A > T > G), except for guanine. Our results are consistent with a relay mechanism in which D(2)S interacts with both a backbone phosphate group and a neutral nucleobase through hydrogen bonding. We propose that the faster exchange of polyguanosine compared to polythymidine is due to the larger size of guanine and the orientation of its labile hydrogens, which may result in gas-phase conformations more favorable for forming complexes with D(2)S. Similar trends were observed for RNA homohexamers, although their HDX rates were faster than for DNA, suggesting they can also exchange via another relay process involving the 2'-hydroxyl group. HDX of DNA duplexes further supports the involvement of nucleobase hydrogens because duplexes exchanged slower than their corresponding single strands, presumably due to the intermolecular hydrogen bonds between nucleobases. This work constitutes the first investigation of the mechanisms of oligonucleotide gas-phase HDX. Our results on duplexes show promise for application of this strategy to the characterization of structured nucleic acids.

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

PubMed

Cockenpot, S; Claude, C; Radakovitch, O

2015-05-01

The radon-222 mass balance is now commonly used to quantify water fluxes due to Submarine Groundwater Discharge (SGD) in coastal areas. One of the main loss terms of this mass balance, the radon evasion to the atmosphere, is based on empirical equations. This term is generally estimated using one among the many empirical equations describing the gas transfer velocity as a function of wind speed that have been proposed in the literature. These equations were, however, mainly obtained from areas of deep water and may be less appropriate for shallow areas. Here, we calculate the radon mass balance for a windy shallow coastal lagoon (mean depth of 6m and surface area of 1.55*10(8) m(2)) and use these data to estimate the radon loss to the atmosphere and the corresponding gas transfer velocity. We present new equations, adapted to our shallow water body, to express the gas transfer velocity as a function of wind speed at 10 m height (wind range from 2 to 12.5 m/s). When compared with those from the literature, these equations fit particularly well with the one of Kremer et al. (2003). Finally, we emphasize that some gas transfer exchange may always occur, even for conditions without wind. Copyright © 2015 Elsevier Ltd. All rights reserved.

Magnetized advective accretion flows: formation of magnetic barriers in magnetically arrested discs

NASA Astrophysics Data System (ADS)

Mondal, Tushar; Mukhopadhyay, Banibrata

2018-05-01

We discuss the importance of large-scale strong magnetic field in the removal of angular momentum outward, as well as the possible origin of different kinds of magnetic barrier in advective, geometrically thick, sub-Keplerian accretion flows around black holes. The origin of this large-scale strong magnetic field near the event horizon is due to the advection of the magnetic flux by the accreting gas from the environment, say, the interstellar medium or a companion star, because of flux freezing. In this simplest vertically averaged, 1.5-dimensional disc model, we choose the maximum upper limit of the magnetic field, which the disc around a black hole can sustain. In this so called magnetically arrested disc model, the accreting gas either decelerates or faces the magnetic barrier near the event horizon by the accumulated magnetic field depending on the geometry. The magnetic barrier may knock the matter to infinity. We suggest that these types of flow are the building block to produce jets and outflows in the accreting system. We also find that in some cases, when matter is trying to go back to infinity after knocking the barrier, matter is prevented being escaped by the cumulative action of strong gravity and the magnetic tension, hence by another barrier. In this way, magnetic field can lock the matter in between these two barriers and it might be a possible explanation for the formation of episodic jet.

Design and simulation of the micromixer with chaotic advection in twisted microchannels.

PubMed

Jen, Chun-Ping; Wu, Chung-Yi; Lin, Yu-Cheng; Wu, Ching-Yi

2003-05-01

Chaotic mixers with twisted microchannels were designed and simulated numerically in the present study. The phenomenon whereby a simple Eulerian velocity field may generate a chaotic response in the distribution of a Lagrangian marker is termed chaotic advection. Dynamic system theory indicates that chaotic particle motion can occur when a velocity field is either two-dimensional and time-dependent, or three-dimensional. In the present study, micromixers with three-dimensional structures of the twisted microchannel were designed in order to induce chaotic mixing. In addition to the basic T-mixer, three types of micromixers with inclined, oblique and wavelike microchannels were investigated. In the design of each twisted microchannel, the angle of the channels' bottoms alternates in each subsection. When the fluids enter the twisted microchannels, the flow sways around the varying structures within the microchannels. The designs of the twisted microchannels provide a third degree of freedom to the flow field in the microchannel. Therefore, chaotic regimes that lead to chaotic mixing may arise. The numerical results indicate that mixing occurs in the main channel and progressively larger mixing lengths are required as the Peclet number increased. The swaying of the flow in the twisted microchannel causes chaotic advection. Among the four micromixer designs, the micromixer with the inclined channel most improved mixing. Furthermore, using the inclined mixer with six subsections yielded optimum performance, decreasing the mixing length by up to 31% from that of the basic T-mixer.

Advection of sulfur dioxide over the western Atlantic Ocean during CITE 3

NASA Technical Reports Server (NTRS)

Thornton, D. C.; Bandy, A. R.; Beltz, N.; Driedger, A. R., III; Ferek, R.

1993-01-01

During the NASA Chemical Instrumentation Test and Evaluation 3 sulfur intercomparison over the western Atlantic Ocean, five techniques for the determination of sulfur dioxide were evaluated. The response times of the techniques varied from 3 to 30 min. Based on the ensemble of measurements reported, it was clear that advection of SO2 from the North American continent occurred in the boundary layer (altitude less than 1 km) with only one exception. The vertical distribution of SO2 above the boundary layer for the northern and southern Atlantic Ocean was remarkably similar duing this experiment.

A field study of air flow and turbulent features of advection fog

NASA Technical Reports Server (NTRS)

Connell, J. D.

1979-01-01

The setup and initial operation of a set of specialized meteorological data collection hardware are described. To study the life cycle of advection fogs at a lake test site, turbulence levels in the fog are identified, and correlated with the temperature gradients and mean wind profiles. A meteorological tower was instrumented to allow multiple-level measurements of wind and temperature on a continuous basis. Additional instrumentation was: (1)hydrothermograph, (2)microbarograph, (3)transmissometers, and (4)a boundary layer profiler. Two types of fogs were identified, and important differences in the turbulence scales were noted.

Spectral analysis of large-eddy advection in ET from eddy covariance towers and a large weighting lysimeter

USDA-ARS?s Scientific Manuscript database

Evapotranspiration was continuously measured by an array of eddy covariance systems and large weighting lysimeter in a cotton field in Bushland, Texas. The advective divergence from both horizontal and vertical directions were measured through profile measurements above canopy. All storage terms wer...

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.

Microtube strip heat exchanger

NASA Astrophysics Data System (ADS)

Doty, F. D.

1992-07-01

The purpose of this contract has been to explore the limits of miniaturization of heat exchangers with the goals of (1) improving the theoretical understanding of laminar heat exchangers, (2) evaluating various manufacturing difficulties, and (3) identifying major applications for the technology. A low-cost, ultra-compact heat exchanger could have an enormous impact on industry in the areas of cryocoolers and energy conversion. Compact cryocoolers based on the reverse Brayton cycle (RBC) would become practical with the availability of compact heat exchangers. Many experts believe that hardware advances in personal computer technology will rapidly slow down in four to six years unless lowcost, portable cryocoolers suitable for the desktop supercomputer can be developed. Compact refrigeration systems would permit dramatic advances in high-performance computer work stations with 'conventional' microprocessors operating at 150 K, and especially with low-cost cryocoolers below 77 K. NASA has also expressed strong interest in our MTS exchanger for space-based RBC cryocoolers for sensor cooling. We have demonstrated feasibility of higher specific conductance by a factor of five than any other work in high-temperature gas-to-gas exchangers. These laminar-flow, microtube exchangers exhibit extremely low pressure drop compared to alternative compact designs under similar conditions because of their much shorter flow length and larger total flow area for lower flow velocities. The design appears to be amenable to mass production techniques, but considerable process development remains. The reduction in materials usage and the improved heat exchanger performance promise to be of enormous significance in advanced engine designs and in cryogenics.

Parametric laws to model urban pollutant dispersion with a street network approach

NASA Astrophysics Data System (ADS)

Soulhac, L.; Salizzoni, P.; Mejean, P.; Perkins, R. J.

2013-03-01

This study discusses the reliability of the street network approach for pollutant dispersion modelling in urban areas. This is essentially based on a box model, with parametric relations that explicitly model the main phenomena that contribute to the street canyon ventilation: the mass exchanges between the street and the atmosphere, the pollutant advection along the street axes and the pollutant transfer at street intersections. In the first part of the paper the focus is on the development of a model for the bulk transfer street/atmosphere, which represents the main ventilation mechanisms for wind direction that are almost perpendicular to the axis of the street. We then discuss the role of the advective transfer along the street axis on its ventilation, depending on the length of the street and the direction of the external wind. Finally we evaluate the performances of a box model integrating parametric exchange laws for these transfer phenomena. To that purpose we compare the prediction of the model to wind tunnel experiments of pollutant dispersion within a street canyon placed in an idealised urban district.

Modelling debris transport within glaciers by advection in a full-Stokes ice flow model

NASA Astrophysics Data System (ADS)

Wirbel, Anna; Jarosch, Alexander H.; Nicholson, Lindsey

2018-01-01

Glaciers with extensive surface debris cover respond differently to climate forcing than those without supraglacial debris. In order to include debris-covered glaciers in projections of glaciogenic runoff and sea level rise and to understand the paleoclimate proxy recorded by such glaciers, it is necessary to understand the manner and timescales over which a supraglacial debris cover develops. Because debris is delivered to the glacier by processes that are heterogeneous in space and time, and these debris inclusions are altered during englacial transport through the glacier system, correctly determining where, when and how much debris is delivered to the glacier surface requires knowledge of englacial transport pathways and deformation. To achieve this, we present a model of englacial debris transport in which we couple an advection scheme to a full-Stokes ice flow model. The model performs well in numerical benchmark tests, and we present both 2-D and 3-D glacier test cases that, for a set of prescribed debris inputs, reproduce the englacial features, deformation thereof and patterns of surface emergence predicted by theory and observations of structural glaciology. In a future step, coupling this model to (i) a debris-aware surface mass balance scheme and (ii) a supraglacial debris transport scheme will enable the co-evolution of debris cover and glacier geometry to be modelled.

Fault-Tolerant Heat Exchanger

NASA Technical Reports Server (NTRS)

Izenson, Michael G.; Crowley, Christopher J.

2005-01-01

A compact, lightweight heat exchanger has been designed to be fault-tolerant in the sense that a single-point leak would not cause mixing of heat-transfer fluids. This particular heat exchanger is intended to be part of the temperature-regulation system for habitable modules of the International Space Station and to function with water and ammonia as the heat-transfer fluids. The basic fault-tolerant design is adaptable to other heat-transfer fluids and heat exchangers for applications in which mixing of heat-transfer fluids would pose toxic, explosive, or other hazards: Examples could include fuel/air heat exchangers for thermal management on aircraft, process heat exchangers in the cryogenic industry, and heat exchangers used in chemical processing. The reason this heat exchanger can tolerate a single-point leak is that the heat-transfer fluids are everywhere separated by a vented volume and at least two seals. The combination of fault tolerance, compactness, and light weight is implemented in a unique heat-exchanger core configuration: Each fluid passage is entirely surrounded by a vented region bridged by solid structures through which heat is conducted between the fluids. Precise, proprietary fabrication techniques make it possible to manufacture the vented regions and heat-conducting structures with very small dimensions to obtain a very large coefficient of heat transfer between the two fluids. A large heat-transfer coefficient favors compact design by making it possible to use a relatively small core for a given heat-transfer rate. Calculations and experiments have shown that in most respects, the fault-tolerant heat exchanger can be expected to equal or exceed the performance of the non-fault-tolerant heat exchanger that it is intended to supplant (see table). The only significant disadvantages are a slight weight penalty and a small decrease in the mass-specific heat transfer.

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.

A Babcock-Leighton solar dynamo model with multi-cellular meridional circulation in advection- and diffusion-dominated regimes

NASA Astrophysics Data System (ADS)

Belucz, B.; Dikpati, M.; Forgacs-Dajka, E.

2014-12-01

Babcock-Leighton type solar dynamo models with single cell meridional circulation are successful in reproducing many solarcycle features, and recently such a model was applied for solarcycle 24 amplitude prediction. It seems that cycle 24 amplitudeforecast may not be validated. One of the reasons is the assumption of a single cell meridional circulation. Recent observations andtheoretical models of meridional circulation do not indicate a single-celledflow pattern. So it is nessecary to examine the role of complexmulti-cellular circulation patterns in a Babcock-Leighton solar dynamo model in the advection and diffusion dominated regimes.By simulating a Babcock-Leighton solar dynamo model with multi-cellularflow, we show that the presence of a weak, second, high-latitudereverse cell speeds up the cycle and slighty enhances the poleward branch in the butterfly diagram, whereas the presence of a second cellin depth reverses the tilt of the butterfly wing and leads to ananti-solar type feature. If, instead, the butterfly diagram isconstructed from the middle of the convection zone in that case, a solar-like pattern can be retrieved. All the above cases behavequalitatively similar in advection and diffusion-dominated regimes.However, our dynamo with a meridional circulation containing fourcells in latitude behaves distinctly different in the two regimes, producing a solar-like butterfly diagram with fast cycles indiffusion-dominated regime, and a complex branches in the butterflydiagram in the advection-dominated regime. Another interestingfinding from our studies is that a four-celled flow pattern containing two in radius and two in latitude always producesquadrupolar parity as the relaxed solution.

Mode-locking in advection-reaction-diffusion systems: An invariant manifold perspective

NASA Astrophysics Data System (ADS)

Locke, Rory A.; Mahoney, John R.; Mitchell, Kevin A.

2018-01-01

Fronts propagating in two-dimensional advection-reaction-diffusion systems exhibit a rich topological structure. When the underlying fluid flow is periodic in space and time, the reaction front can lock to the driving frequency. We explain this mode-locking phenomenon using the so-called burning invariant manifolds (BIMs). In fact, the mode-locked profile is delineated by a BIM attached to a relative periodic orbit (RPO) of the front element dynamics. Changes in the type (and loss) of mode-locking can be understood in terms of local and global bifurcations of the RPOs and their BIMs. We illustrate these concepts numerically using a chain of alternating vortices in a channel geometry.

The Vapor-phase Multi-stage CMD Test for Characterizing Contaminant Mass Discharge Associated with VOC Sources in the Vadose Zone: Application to Three Sites in Different Lifecycle Stages of SVE Operations

PubMed Central

Brusseau, M.L.; Mainhagu, J.; Morrison, C.; Carroll, K.C.

2015-01-01

Vapor-phase multi-stage contaminant mass discharge (CMD) tests were conducted at three field sites to measure mass discharge associated with contaminant sources located in the vadose zone. The three sites represent the three primary stages along the soil vapor extraction (SVE) operations lifecycle- pre/initial-SVE, mid-lifecycle, and near-closure. A CMD of 32 g/d was obtained for a site at which soil vapor SVE has been in operation for approximately 6 years, and for which mass removal is currently in the asymptotic stage. The contaminant removal behavior exhibited for the vapor extractions conducted at this site suggests that there is unlikely to be a significant mass of non-vapor-phase contaminant (e.g., DNAPL, sorbed phase) remaining in the advective domains, and that most remaining mass is likely located in poorly accessible domains. Given the conditions for this site, this remaining mass is hypothesized to be associated with the low-permeability (and higher water saturation) region in the vicinity of the saturated zone and capillary fringe. A CMD of 25 g/d was obtained for a site wherein SVE has been in operation for several years but concentrations and mass-removal rates are still relatively high. A CMD of 270 g/d was obtained for a site for which there were no prior SVE operations. The behavior exhibited for the vapor extractions conducted at this site suggest that non-vapor-phase contaminant mass (e.g., DNAPL) may be present in the advective domains. Hence, the asymptotic conditions observed for this site most likely derive from a combination of rate-limited mass transfer from DNAPL (and sorbed) phases present in the advective domain as well as mass residing in lower-permeability (“non-advective”) regions. The CMD values obtained from the tests were used in conjunction with a recently developed vapor-discharge tool to evaluate the impact of the measured CMDs on groundwater quality. PMID:26047819

Magnetic flux and heat losses by diffusive, advective, and Nernst effects in magnetized liner inertial fusion-like plasma

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

Velikovich, A. L.; Giuliani, J. L.; Zalesak, S. T.

The magnetized liner inertial fusion (MagLIF) approach to inertial confinement fusion [Slutz et al., Phys. Plasmas 17, 056303 (2010); Cuneo et al., IEEE Trans. Plasma Sci. 40, 3222 (2012)] involves subsonic/isobaric compression and heating of a deuterium-tritium plasma with frozen-in magnetic flux by a heavy cylindrical liner. The losses of heat and magnetic flux from the plasma to the liner are thereby determined by plasma advection and gradient-driven transport processes, such as thermal conductivity, magnetic field diffusion, and thermomagnetic effects. Theoretical analysis based on obtaining exact self-similar solutions of the classical collisional Braginskii's plasma transport equations in one dimension demonstratesmore » that the heat loss from the hot compressed magnetized plasma to the cold liner is dominated by transverse heat conduction and advection, and the corresponding loss of magnetic flux is dominated by advection and the Nernst effect. For a large electron Hall parameter (ω{sub e}τ{sub e}≫1), the effective diffusion coefficients determining the losses of heat and magnetic flux to the liner wall are both shown to decrease with ω{sub e}τ{sub e} as does the Bohm diffusion coefficient cT/(16eB), which is commonly associated with low collisionality and two-dimensional transport. We demonstrate how this family of exact solutions can be used for verification of codes that model the MagLIF plasma dynamics.« less

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

Higher-Order Advection-Based Remap of Magnetic Fields in an Arbitrary Lagrangian-Eulerian Code

NASA Astrophysics Data System (ADS)

Cornille, Brian; White, Dan

2017-10-01

We will present methods formulated for the Eulerian advection stage of an arbitrary Lagrangian-Eulerian code for the new addition of magnetohydrodynamic (MHD) effects. The various physical fields are advanced in time using a Lagrangian formulation of the system. When this Lagrangian motion produces substantial distortion of the mesh, it can be difficult or impossible to progress the simulation forward. This is overcome by relaxation of the mesh while the physical fields are frozen. The code has already successfully been extended to include evolution of magnetic field diffusion during the Lagrangian motion stage. This magnetic field is discretized using an H(div) compatible finite element basis. The advantage of this basis is that the divergence-free constraint of magnetic fields is maintained exactly during the Lagrangian motion evolution. Our goal is to preserve this property during Eulerian advection as well. We will demonstrate this property and the importance of MHD effects in several numerical experiments. In pulsed-power experiments magnetic fields may be imposed or spontaneously generated. When these magnetic fields are present, the evolution of the experiment may differ from a comparable configuration without magnetic fields. Prepared by LLNL under Contract DE-AC52-07NA27344. Supported by DOE CSGF under Grant Number DE-FG02-97ER25308.

Development, Fabrication, and Testing of a Liquid/Liquid Microchannel Heat Exchanger for Constellation Spacecrafts

NASA Technical Reports Server (NTRS)

Hawkins-Reynolds, Ebony; Le, Hung; Stephan, Ryan

2010-01-01

Microchannel technology can be incorporated into heat exchanger designs to decrease the mass and volume of space hardware. The National Aeronautics and Space Administration at the Johnson Space Center (NASA JSC) partnered with Pacific Northwest National Laboratories (PNNL) to develop a liquid/liquid microchannel heat exchanger that has significant mass and volume savings without sacrificing thermal and pressure drop performance. PNNL designed the microchannel heat exchanger to the same performance design requirements of a conventional plate and fin liquid/liquid heat exchanger; 3 kW duty with inlet temperatures of 26 C and 4 C. Both heat exchangers were tested using the same test parameters on a test apparatus and performance data compared.

The 1923 Greco-Turkish Population Exchange: Successful Prevention of Genocide and Mass Atrocities

DTIC Science & Technology

2012-06-08

following World War I. Furthermore, it does not attempt to examine the logistics of the exchange but provides a broad understanding of the process. The...Greece and Turkey following World War I. Furthermore, it does not attempt to examine the logistics of the exchange but provides a broad understanding...

Mass balance modelling of contaminants in river basins: a flexible matrix approach.

PubMed

Warren, Christopher; Mackay, Don; Whelan, Mick; Fox, Kay

2005-12-01

A novel and flexible approach is described for simulating the behaviour of chemicals in river basins. A number (n) of river reaches are defined and their connectivity is described by entries in an n x n matrix. Changes in segmentation can be readily accommodated by altering the matrix entries, without the need for model revision. Two models are described. The simpler QMX-R model only considers advection and an overall loss due to the combined processes of volatilization, net transfer to sediment and degradation. The rate constant for the overall loss is derived from fugacity calculations for a single segment system. The more rigorous QMX-F model performs fugacity calculations for each segment and explicitly includes the processes of advection, evaporation, water-sediment exchange and degradation in both water and sediment. In this way chemical exposure in all compartments (including equilibrium concentrations in biota) can be estimated. Both models are designed to serve as intermediate-complexity exposure assessment tools for river basins with relatively low data requirements. By considering the spatially explicit nature of emission sources and the changes in concentration which occur with transport in the channel system, the approach offers significant advantages over simple one-segment simulations while being more readily applicable than more sophisticated, highly segmented, GIS-based models.

Kinetic theory of oxygen isotopic exchange between minerals and water

USGS Publications Warehouse

Criss, R.E.; Gregory, R.T.; Taylor, H.P.

1987-01-01

Kinetic and mass conservation equations are used to describe oxygen isotopic exchange between minerals and water in "closed" and open hydrothermal systems. In cases where n coexisting mineral phases having different reaction rates are present, the exchange process is described by a system of n + 1 simultaneous differential equations consisting of n pseudo first-order rate equations and a conservation of mass equation. The simultaneous solutions to these equations generate curved exchange trajectories on ??-?? plots. Families of such trajectories generated under conditions allowing for different fluid mole fractions, different fluid isotopic compositions, or different fluid flow rates are connected by positive-sloped isochronous lines. These isochrons reproduce the effects observed in hydrothermally exchanged mineral pairs including 1) steep positive slopes, 2) common reversals in the measured fractionation factors (??), and 3) measured fractionations that are highly variable over short distances where no thermal gradient can be geologically demonstrated. ?? 1987.

Derivation of a Multiparameter Gamma Model for Analyzing the Residence-Time Distribution Function for Nonideal Flow Systems as an Alternative to the Advection-Dispersion Equation

DOE PAGES

Embry, Irucka; Roland, Victor; Agbaje, Oluropo; ...

2013-01-01

A new residence-time distribution (RTD) function has been developed and applied to quantitative dye studies as an alternative to the traditional advection-dispersion equation (AdDE). The new method is based on a jointly combined four-parameter gamma probability density function (PDF). The gamma residence-time distribution (RTD) function and its first and second moments are derived from the individual two-parameter gamma distributions of randomly distributed variables, tracer travel distance, and linear velocity, which are based on their relationship with time. The gamma RTD function was used on a steady-state, nonideal system modeled as a plug-flow reactor (PFR) in the laboratory to validate themore » effectiveness of the model. The normalized forms of the gamma RTD and the advection-dispersion equation RTD were compared with the normalized tracer RTD. The normalized gamma RTD had a lower mean-absolute deviation (MAD) (0.16) than the normalized form of the advection-dispersion equation (0.26) when compared to the normalized tracer RTD. The gamma RTD function is tied back to the actual physical site due to its randomly distributed variables. The results validate using the gamma RTD as a suitable alternative to the advection-dispersion equation for quantitative tracer studies of non-ideal flow systems.« less

Accelerated Analyte Uptake on Single Beads in Microliter-scale Batch Separations using Acoustic Streaming: Plutonium Uptake by Anion Exchange for Analysis by Mass Spectrometry

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

Paxton, Walter F.; O'Hara, Matthew J.; Peper, Shane M.

2008-06-01

The use of acoustic streaming as a non-contact mixing platform to accelerate mass transport-limited diffusion processes in small volume heterogeneous reactions has been investigated. Single bead anion exchange of plutonium at nanomolar and sub-picomolar concentrations in 20 microliter liquid volumes was used to demonstrate the effect of acoustic mixing. Pu uptake rates on individual ~760 micrometer diameter AG 1x4 anion exchange resin beads were determined using acoustic mixing and compared with Pu uptake rates achieved by static diffusion alone. An 82 MHz surface acoustic wave (SAW) device was placed in contact with the underside of a 384-well microplate containing flat-bottomedmore » semiconical wells. Acoustic energy was coupled into the solution in the well, inducing acoustic streaming. Pu uptake rates were determined by the plutonium remaining in solution after specific elapsed time intervals, using liquid scintillation counting (LSC) for nanomolar concentrations and thermal ionization mass spectrometry (TIMS) analysis for the sub-picomolar concentration experiments. It was found that this small batch uptake reaction could be accelerated by a factor of about five-fold or more, depending on the acoustic power applied.« less

Using a Spectral Method to Evaluate Hyporheic Exchange and its Effect on Reach Scale Nitrate Removal.

NASA Astrophysics Data System (ADS)

Moren, I.; Worman, A. L. E.; Riml, J.

2017-12-01

Previous studies have shown that hyporheic exchange processes can be of great importance for the transport, retention and mass removal of nutrients in streams. Specifically, the flow of surface water through the hyporheic zone enhances redox-sensitive reactions such as coupled nitrification-denitrification. This self-cleaning capacity of streams can be utilized in stream restoration projects aiming to improve water quality by reconstructing the geomorphology of the streams. To optimize the effect of restoration actions we need quantitative understanding of the linkage between stream geomorphology, hyporheic exchange processes and the desired water quality targets. Here we propose an analytical, spectral methodology to evaluate how different stream geomorphologies induce hyporheic exchange on a wide range of spatial and temporal scales. Measurements of streambed topographies and surface water profiles from agricultural streams were used to calculate the average hyporheic exchange velocity and residence times and the result was compared with in-stream tracer test. Furthermore, the hyporheic exchange induced by steps in the surface water profile was derived as a comparison of the theoretical capacity of the system. Based on differences in hyporheic exchange, the mass removal of nitrate could be derived for the different geomorphologies. The maximum nitrate mass removal was found to be related to a specific Damkhöler number, which reflects that the mass removal can be either reaction or transport controlled. Therefore, although hyporheic exchange induced by steps in the surface water profile was generally larger than the hyporheic exchange in the observed natural reaches, this would not necessarily lead a larger nitrate mass removal provided that the hyporheic residence times are not long enough to facilitate denitrification processes. The study illustrates the importance to investigate a stream thoroughly before any remediation actions are implemented, specifically

Short-term temperature-dependent air-surface exchange and atmospheric concentrations of polychlorinated naphthalenes and organochlorine pesticides

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

Lee, R.G.M.; Burnett, V.; Harner, T.

2000-02-01

Atmospheric concentrations of five organochlorine (OC) pesticides, some of which have been banned for a number of years, and polychlorinated naphthalenes (PCNs) were measured at a U.K. site over periods of 6 h for 7 days resulting in 28 samples. Mean concentrations of the pesticides were {alpha}-HCH 90 pg m{sup {minus}3}, {gamma}-HCH 500, {rho},{rho}{prime}-DDE 8, dieldrin 63, endrin 22, and HCB 39. PCN mean homologue concentrations were {sub 3}CNs 67 pg m{sup {minus}3}, {sub 4}CNs 78, {sub 5}CNs 5, {sub 6}CNs 0.6, {sub 7}CNs 0.6, and {Sigma}PCNs 152. TEQ concentrations for those PCNs ascribed TEF values ranged between 0.36 andmore » 3.6 fg m{sup {minus}3} which corresponds to {approximately}3.0--30% of the TEQ concentrations of PCDD/Fs at the same site. All the compounds measured, except HCB, exhibited a strong temperature-dependent diurnal cycling. Results from Clausius-Clapeyron plots show that pesticide concentrations were controlled by temperature-driven air-surface recycling throughout the first 5 days when stable atmospheric conditions were dominant, while during the last 2 days advection became more influential as more unstable and cooler weather started to influence the site. PCN concentrations were controlled primarily by a mixture of recycling and advection throughout the first 5 days and then by advection in the final 2 days, suggesting that there are ongoing emissions from diffuse point sources of PCNs into the U.K. atmosphere. This study provides further evidence of the rapid air-surface exchange of semivolatile organic compounds (SOCs) and shows how different factors alone or in combination can produce rapid changes in the atmospheric concentrations of past and present SOCs.« less

Optimizing meridional advection of the Advanced Research WRF (ARW) dynamics for Intel Xeon Phi coprocessor

NASA Astrophysics Data System (ADS)

Mielikainen, Jarno; Huang, Bormin; Huang, Allen H.-L.

2015-05-01

The most widely used community weather forecast and research model in the world is the Weather Research and Forecast (WRF) model. Two distinct varieties of WRF exist. The one we are interested is the Advanced Research WRF (ARW) is an experimental, advanced research version featuring very high resolution. The WRF Nonhydrostatic Mesoscale Model (WRF-NMM) has been designed for forecasting operations. WRF consists of dynamics code and several physics modules. The WRF-ARW core is based on an Eulerian solver for the fully compressible nonhydrostatic equations. In the paper, we optimize a meridional (north-south direction) advection subroutine for Intel Xeon Phi coprocessor. Advection is of the most time consuming routines in the ARW dynamics core. It advances the explicit perturbation horizontal momentum equations by adding in the large-timestep tendency along with the small timestep pressure gradient tendency. We will describe the challenges we met during the development of a high-speed dynamics code subroutine for MIC architecture. Furthermore, lessons learned from the code optimization process will be discussed. The results show that the optimizations improved performance of the original code on Xeon Phi 7120P by a factor of 1.2x.

Nonlinear Advection of Tropospheric Humidity and Cloud and Evaporation Feedbacks in the Madden-Julian Oscillation

NASA Astrophysics Data System (ADS)

Sugiyama, M.; Emanuel, K.; Stone, P.

2006-05-01

Despite active research on the Madden-Julian Oscillation (MJO), general circulation models (GCMs) continue to suffer from poor simulations of this tropical intraseasonal variability, and the theory on the MJO remains elusive. To assist model development and deepen our understanding, we develop a simple new model of the MJO, using the Quasiequilibrium Tropical Circulation Model of Neelin and Zeng. The MJO-like disturbance develops as a single-column instability because of cloud-radiative and surface flux feedbacks, a mechanism identified by Sobel and Gildor in their study on a tropical hot spot. Two processes contribute to the eastward movement: Nonlinear advection of the tropospheric humidity to the west, and convergence-induced moistening to the east. The key to the model disturbance is the interplay between tropospheric humidity and precipitation, moisture-convection feedback. As the humidity field propagates eastward by advection and convergence-induced moistening, the precipitation field follows. This study points to possible research areas on GCM parameterizations: 1) the effect of tropospheric humidity on moist convection; 2) the impact of downdraft-enhanced gustiness on surface heat flux; and 3) relationship between precipitation and cloud-radiative forcing.

Advection of surface-derived organic carbon fuels microbial reduction in Bangladesh groundwater

PubMed Central

Mailloux, Brian J.; Trembath-Reichert, Elizabeth; Cheung, Jennifer; Watson, Marlena; Stute, Martin; Freyer, Greg A.; Ferguson, Andrew S.; Ahmed, Kazi Matin; Alam, Md. Jahangir; Buchholz, Bruce A.; Thomas, James; Layton, Alice C.; Zheng, Yan; Bostick, Benjamin C.; van Geen, Alexander

2013-01-01

Chronic exposure to arsenic (As) by drinking shallow groundwater causes widespread disease in Bangladesh and neighboring countries. The release of As naturally present in sediment to groundwater has been linked to the reductive dissolution of iron oxides coupled to the microbial respiration of organic carbon (OC). The source of OC driving this microbial reduction—carbon deposited with the sediments or exogenous carbon transported by groundwater—is still debated despite its importance in regulating aquifer redox status and groundwater As levels. Here, we used the radiocarbon (14C) signature of microbial DNA isolated from groundwater samples to determine the relative importance of surface and sediment-derived OC. Three DNA samples collected from the shallow, high-As aquifer and one sample from the underlying, low-As aquifer were consistently younger than the total sediment carbon, by as much as several thousand years. This difference and the dominance of heterotrophic microorganisms implies that younger, surface-derived OC is advected within the aquifer, albeit more slowly than groundwater, and represents a critical pool of OC for aquifer microbial communities. The vertical profile shows that downward transport of dissolved OC is occurring on anthropogenic timescales, but bomb 14C-labeled dissolved OC has not yet accumulated in DNA and is not fueling reduction. These results indicate that advected OC controls aquifer redox status and confirm that As release is a natural process that predates human perturbations to groundwater flow. Anthropogenic perturbations, however, could affect groundwater redox conditions and As levels in the future. PMID:23487743

Interaction of bacteria and ion-exchange particles and its potential in separation for matrix-assisted laser desorption/ionization mass spectrometric identification of bacteria in water.

PubMed

Guo, Zhongxian; Liu, Ying; Li, Shuping; Yang, Zhaoguang

2009-12-01

Identification of microbial contaminants in drinking water is a challenge to matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) due to low levels of microorganisms in fresh water. To avoid the time-consuming culture step of obtaining enough microbial cells for subsequent MALDI-MS analysis, a combination of membrane filtration and nanoparticles- or microparticles-based magnetic separation is a fast and efficient approach. In this work, the interaction of bacteria and fluidMAG-PAA, a cation-exchange superparamagnetic nanomaterial, was investigated by MALDI-MS analysis and transmission electron microscopy. FluidMAG-PAA selectively captured cells of Salmonella, Bacillus, Enterococcus and Staphylococcus aureus. This capture was attributed to the aggregation of negatively charged nanoparticles on bacterial cell regional surfaces that bear positive charges. Three types of non-porous silica-encapsulated anion-exchange magnetic microparticles (SiMAG-Q, SiMAG-PEI, SiMAG-DEAE) were capable of concentrating a variety of bacteria, and were compared with silica-free, smaller fluidMAG particles. Salmonella, Escherichia coli, Enterococcus and other bacteria spiked in aqueous solutions, tap water and reservoir water were separated and concentrated by membrane filtration and magnetic separation based on these ion-exchange magnetic materials, and then characterized by whole cell MALDI-MS. By comparing with the mass spectra of the isolates and pure cells, bacteria in fresh water can be rapidly detected at 1 x 10(3) colony-forming units (cfu)/mL. Copyright 2009 John Wiley & Sons, Ltd.

Online Hydrogen-Deuterium Exchange Traveling Wave Ion Mobility Mass Spectrometry (HDX-IM-MS): a Systematic Evaluation

NASA Astrophysics Data System (ADS)

Cryar, Adam; Groves, Kate; Quaglia, Milena

2017-06-01

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an important tool for measuring and monitoring protein structure. A bottom-up approach to HDX-MS provides peptide level deuterium uptake values and a more refined localization of deuterium incorporation compared with global HDX-MS measurements. The degree of localization provided by HDX-MS is proportional to the number of peptides that can be identified and monitored across an exchange experiment. Ion mobility spectrometry (IMS) has been shown to improve MS-based peptide analysis of biological samples through increased separation capacity. The integration of IMS within HDX-MS workflows has been commercialized but presently its adoption has not been widespread. The potential benefits of IMS, therefore, have not yet been fully explored. We herein describe a comprehensive evaluation of traveling wave ion mobility integrated within an online-HDX-MS system and present the first reported example of UDMSE acquisition for HDX analysis. Instrument settings required for optimal peptide identifications are described and the effects of detector saturation due to peak compression are discussed. A model system is utilized to confirm the comparability of HDX-IM-MS and HDX-MS uptake values prior to an evaluation of the benefits of IMS at increasing sample complexity. Interestingly, MS and IM-MS acquisitions were found to identify distinct populations of peptides that were unique to the respective methods, a property that can be utilized to increase the spatial resolution of HDX-MS experiments by >60%. [Figure not available: see fulltext.

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.

The role of advection and diffusion in waste disposal by sea urchin embryos

NASA Astrophysics Data System (ADS)

Clark, Aaron; Licata, Nicholas

2014-03-01

We determine the first passage probability for the absorption of waste molecules released from the microvilli of sea urchin embryos. We calculate a perturbative solution of the advection-diffusion equation for a linear shear profile similar to the fluid environment which the embryos inhabit. Rapid rotation of the embryo results in a concentration boundary layer of comparable thickness to the length of the microvilli. A comparison of the results to the regime of diffusion limited transport indicates that fluid flow is advantageous for efficient waste disposal.

North Atlantic Surface Winds Examined as the Source of Warm Advection into Europe in Winter

NASA Technical Reports Server (NTRS)

Otterman, J.; Angell, J. K.; Ardizzone, J.; Atlas, Robert; Schubert, S.; Starr, D.; Wu, M.-L.

2002-01-01

When from the southwest, North Atlantic ocean surface winds are known to bring warm and moist airmasses into central Europe in winter. By tracing backward trajectories from western Europe, we establish that these airmasses originate in the southwestern North Atlantic, in the very warm regions of the Gulf Stream. Over the eastern North Atlantic, Lt the gateway to Europe, the ocean-surface winds changed directions in the second half of the XXth century, those from the northwest and from the southeast becoming so infrequent, that the direction from the southwest became even more dominant. For the January-to-March period, the strength of south-westerlies in this region, as well as in the source region, shows in the years 1948-1995 a significant increase, above 0.2 m/sec/ decade. Based on the sensitivity of the surface temperature in Europe, slightly more than 1 C for a 1m/sec increase in the southwesterly wind, found in the previous studies, the trend in the warm advection accounts for a large part of the warming in Europe established for this period in several reports. However, for the most recent years, 1996-2001, the positive trend in the southwesterly advection appears to be is broken, which is consistent with unseasonally cold events reported in Europe in those winters. This study had, some bearing on evaluating the respective roles of the North Atlantic Oscillation and the Greenhouse Gas Global warming, GGG, in the strong winter warming observed for about half a century over the northern-latitude continents. Changes in the ocean-surface temperatures induced by GGG may have produced the dominant southwesterly direction of the North Atlantic winds. However, this implies a monotonically (apart from inherent interannual variability) increasing advection, and if the break in the trend which we observe after 1995 persists, this mechanism is counter-indicated. The 1948-1995 trend in the south-westerlies could then be considered to a large degree attributable to the

Physics-based agent to simulant correlations for vapor phase mass transport.

PubMed

Willis, Matthew P; Varady, Mark J; Pearl, Thomas P; Fouse, Janet C; Riley, Patrick C; Mantooth, Brent A; Lalain, Teri A

2013-12-15

Chemical warfare agent simulants are often used as an agent surrogate to perform environmental testing, mitigating exposure hazards. This work specifically addresses the assessment of downwind agent vapor concentration resulting from an evaporating simulant droplet. A previously developed methodology was used to estimate the mass diffusivities of the chemical warfare agent simulants methyl salicylate, 2-chloroethyl ethyl sulfide, di-ethyl malonate, and chloroethyl phenyl sulfide. Along with the diffusivity of the chemical warfare agent bis(2-chloroethyl) sulfide, the simulant diffusivities were used in an advection-diffusion model to predict the vapor concentrations downwind from an evaporating droplet of each chemical at various wind velocities and temperatures. The results demonstrate that the simulant-to-agent concentration ratio and the corresponding vapor pressure ratio are equivalent under certain conditions. Specifically, the relationship is valid within ranges of measurement locations relative to the evaporating droplet and observation times. The valid ranges depend on the relative transport properties of the agent and simulant, and whether vapor transport is diffusion or advection dominant. Published by Elsevier B.V.

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.

Back-exchange: a novel approach to quantifying oxygen diffusion and surface exchange in ambient atmospheres.

PubMed

Cooper, Samuel J; Niania, Mathew; Hoffmann, Franca; Kilner, John A

2017-05-17

A novel two-step Isotopic Exchange (IE) technique has been developed to investigate the influence of oxygen containing components of ambient air (such as H 2 O and CO 2 ) on the effective surface exchange coefficient (k*) of a common mixed ionic electronic conductor material. The two step 'back-exchange' technique was used to introduce a tracer diffusion profile, which was subsequently measured using Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS). The isotopic fraction of oxygen in a dense sample as a function of distance from the surface, before and after the second exchange step, could then be used to determine the surface exchange coefficient in each atmosphere. A new analytical solution was found to the diffusion equation in a semi-infinite domain with a variable surface exchange boundary, for the special case where D* and k* are constant for all exchange steps. This solution validated the results of a numerical, Crank-Nicolson type finite-difference simulation, which was used to extract the parameters from the experimental data. When modelling electrodes, D* and k* are important input parameters, which significantly impact performance. In this study La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3-δ (LSCF6428) was investigated and it was found that the rate of exchange was increased by around 250% in ambient air compared to high purity oxygen at the same pO 2 . The three experiments performed in this study were used to validate the back-exchange approach and show its utility.

Existence of solution for a general fractional advection-dispersion equation

NASA Astrophysics Data System (ADS)

Torres Ledesma, César E.

2018-05-01

In this work, we consider the existence of solution to the following fractional advection-dispersion equation -d/dt ( p {_{-∞}}It^{β }(u'(t)) + q {t}I_{∞}^{β }(u'(t))) + b(t)u = f(t, u(t)),t\\in R where β \\in (0,1) , _{-∞}It^{β } and tI_{∞}^{β } denote left and right Liouville-Weyl fractional integrals of order β respectively, 0

Solution of the advection-dispersion equation: Continuous load of finite duration

USGS Publications Warehouse

Runkel, R.L.

1996-01-01

Field studies of solute fate and transport in streams and rivers often involve an. experimental release of solutes at an upstream boundary for a finite period of time. A review of several standard references on surface-water-quality modeling indicates that the analytical solution to the constant-parameter advection-dispersion equation for this type of boundary condition has been generally overlooked. Here an exact analytical solution that considers a continuous load of unite duration is compared to an approximate analytical solution presented elsewhere. Results indicate that the exact analytical solution should be used for verification of numerical solutions and other solute-transport problems wherein a high level of accuracy is required. ?? ASCE.

An examination of dynamics crosstalk between SH2 and SH3 domains by hydrogen/deuterium exchange and mass spectrometry

PubMed Central

Hochrein, James M.; Lerner, Edwina C.; Schiavone, Anthony P.; Smithgall, Thomas E.; Engen, John R.

2006-01-01

The ability of proteins to regulate their own enzymatic activity can be facilitated by changes in structure or protein dynamics in response to external regulators. Because many proteins contain SH2 and SH3 domains, transmission of information between the domains is a potential method of allosteric regulation. To determine if ligand binding to one modular domain may alter structural dynamics in an adjacent domain, allowing potential transmission of information through the protein, we used hydrogen exchange and mass spectrometry to measure changes in protein dynamics in the SH3 and SH2 domains of hematopoietic cell kinase (Hck). Ligand binding to either domain had little or no effect on hydrogen exchange in the adjacent domain, suggesting that changes in protein structure or dynamics are not a means of SH2/SH3 crosstalk. Furthermore, ligands of varying affinity covalently attached to SH3/SH2 altered dynamics only in the domain to which they bind. Such results demonstrate that ligand binding may not structurally alter adjacent SH3/SH2 domains and implies that other aspects of protein architecture contribute to the multiple levels of regulation in proteins containing SH3 and SH2 domains. PMID:16322569

The Effect of Alongcoast Advection on Pacific Northwest Shelf and Slope Water Properties in Relation to Upwelling Variability

NASA Astrophysics Data System (ADS)

Stone, Hally B.; Banas, Neil S.; MacCready, Parker

2018-01-01

The Northern California Current System experiences highly variable seasonal upwelling in addition to larger basin-scale variability, both of which can significantly affect its water chemistry. Salinity and temperature fields from a 7 year ROMS hindcast model of this region (43°N-50°N), along with extensive particle tracking, were used to study interannual variability in water properties over both the upper slope and the midshelf bottom. Variation in slope water properties was an order of magnitude smaller than on the shelf. Furthermore, the primary relationship between temperature and salinity anomalies in midshelf bottom water consisted of variation in density (cold/salty versus warm/fresh), nearly orthogonal to the anomalies along density levels (cold/fresh versus warm/salty) observed on the upper slope. These midshelf anomalies were well-explained (R2 = 0.6) by the combination of interannual variability in local and remote alongshore wind stress, and depth of the California Undercurrent (CUC) core. Lagrangian analysis of upper slope and midshelf bottom water shows that both are affected simultaneously by large-scale alongcoast advection of water through the northern and southern boundaries. The amplitude of anomalies in bottom oxygen and dissolved inorganic carbon (DIC) on the shelf associated with upwelling variability are larger than those associated with typical variation in alongcoast advection, and are comparable to observed anomalies in this region. However, a large northern intrusion event in 2004 illustrates that particular, large-scale alongcoast advection anomalies can be just as effective as upwelling variability in changing shelf water properties on the interannual scale.

The Effect of Alongcoast Advection on Pacific Northwest Shelf and Slope Water Properties in Relation to Upwelling Variability

PubMed Central

Banas, Neil S.; MacCready, Parker

2018-01-01

Abstract The Northern California Current System experiences highly variable seasonal upwelling in addition to larger basin‐scale variability, both of which can significantly affect its water chemistry. Salinity and temperature fields from a 7 year ROMS hindcast model of this region (43°N–50°N), along with extensive particle tracking, were used to study interannual variability in water properties over both the upper slope and the midshelf bottom. Variation in slope water properties was an order of magnitude smaller than on the shelf. Furthermore, the primary relationship between temperature and salinity anomalies in midshelf bottom water consisted of variation in density (cold/salty versus warm/fresh), nearly orthogonal to the anomalies along density levels (cold/fresh versus warm/salty) observed on the upper slope. These midshelf anomalies were well‐explained (R 2 = 0.6) by the combination of interannual variability in local and remote alongshore wind stress, and depth of the California Undercurrent (CUC) core. Lagrangian analysis of upper slope and midshelf bottom water shows that both are affected simultaneously by large‐scale alongcoast advection of water through the northern and southern boundaries. The amplitude of anomalies in bottom oxygen and dissolved inorganic carbon (DIC) on the shelf associated with upwelling variability are larger than those associated with typical variation in alongcoast advection, and are comparable to observed anomalies in this region. However, a large northern intrusion event in 2004 illustrates that particular, large‐scale alongcoast advection anomalies can be just as effective as upwelling variability in changing shelf water properties on the interannual scale. PMID:29938149

Modification of a method-of-characteristics solute-transport model to incorporate decay and equilibrium-controlled sorption or ion exchange

USGS Publications Warehouse

Goode, D.J.; Konikow, Leonard F.

1989-01-01

The U.S. Geological Survey computer model of two-dimensional solute transport and dispersion in ground water (Konikow and Bredehoeft, 1978) has been modified to incorporate the following types of chemical reactions: (1) first-order irreversible rate-reaction, such as radioactive decay; (2) reversible equilibrium-controlled sorption with linear, Freundlich, or Langmuir isotherms; and (3) reversible equilibrium-controlled ion exchange for monovalent or divalent ions. Numerical procedures are developed to incorporate these processes in the general solution scheme that uses method-of- characteristics with particle tracking for advection and finite-difference methods for dispersion. The first type of reaction is accounted for by an exponential decay term applied directly to the particle concentration. The second and third types of reactions are incorporated through a retardation factor, which is a function of concentration for nonlinear cases. The model is evaluated and verified by comparison with analytical solutions for linear sorption and decay, and by comparison with other numerical solutions for nonlinear sorption and ion exchange.

Mesoscale variability of water masses in the Arabian Sea as revealed by ARGO floats

NASA Astrophysics Data System (ADS)

Carton, X.; L'Hegaret, P.

2011-06-01

By analysing ARGO float data over the last four years, some aspects of the mesoscale variability of water masses in the Arabian Sea are described. The Red Sea Water outflow is strong in the Southwestern Gulf of Aden, in particular when a cyclonic gyre predominates in this region. Salinities of 36.5 and temperatures of 16 °C are found there between 600 and 1000 m depths. The Red Sea Water is more dilute in the eastern part of the Gulf, and fragments of this water mass can be advected offshore across the gulf or towards its northern coast by the regional gyres. The Red Sea Water outflow is also detected along the northeastern coast of Socotra, and fragments of RSW are found between one and three degrees of latitude north of this island. In the whole Gulf of Aden, the correlation between the deep motions of the floats and the SSH measured by altimetry is strong, at regional scale. The finer scale details of the float trajectories are more often related to the anomalous water masses that they encounter. The Persian Gulf Water (PGW) is found in the float profiles near Ras ash Sharbatat (near 57° E, 18° N), again with 36.5 in salinity and about 18-19 °C in temperature. These observations were achieved in winter when the southwestward monsoon currents can advect PGW along the South Arabian coast. Fragments of PGW are found in the Arabian Sea between 18 and 20° N and 63 and 65° E, showing that this water mass can escape the Gulf of Oman southeastward, in particular during summer.

The effects of magnetic fields and protostellar feedback on low-mass cluster formation

NASA Astrophysics Data System (ADS)

Cunningham, Andrew J.; Krumholz, Mark R.; McKee, Christopher F.; Klein, Richard I.

2018-05-01

We present a large suite of simulations of the formation of low-mass star clusters. Our simulations include an extensive set of physical processes - magnetohydrodynamics, radiative transfer, and protostellar outflows - and span a wide range of virial parameters and magnetic field strengths. Comparing the outcomes of our simulations to observations, we find that simulations remaining close to virial balance throughout their history produce star formation efficiencies and initial mass function (IMF) peaks that are stable in time and in reasonable agreement with observations. Our results indicate that small-scale dissipation effects near the protostellar surface provide a feedback loop for stabilizing the star formation efficiency. This is true regardless of whether the balance is maintained by input of energy from large-scale forcing or by strong magnetic fields that inhibit collapse. In contrast, simulations that leave virial balance and undergo runaway collapse form stars too efficiently and produce an IMF that becomes increasingly top heavy with time. In all cases, we find that the competition between magnetic flux advection towards the protostar and outward advection due to magnetic interchange instabilities, and the competition between turbulent amplification and reconnection close to newly formed protostars renders the local magnetic field structure insensitive to the strength of the large-scale field, ensuring that radiation is always more important than magnetic support in setting the fragmentation scale and thus the IMF peak mass. The statistics of multiple stellar systems are similarly insensitive to variations in the initial conditions and generally agree with observations within the range of statistical uncertainty.

A Nonlinear Multigrid Solver for an Atmospheric General Circulation Model Based on Semi-Implicit Semi-Lagrangian Advection of Potential Vorticity

NASA Technical Reports Server (NTRS)

McCormick, S.; Ruge, John W.

1998-01-01

This work represents a part of a project to develop an atmospheric general circulation model based on the semi-Lagrangian advection of potential vorticity (PC) with divergence as the companion prognostic variable.

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. Copyright © 2010 John Wiley & Sons, Ltd.

A meshless method for solving two-dimensional variable-order time fractional advection-diffusion equation

NASA Astrophysics Data System (ADS)

Tayebi, A.; Shekari, Y.; Heydari, M. H.

2017-07-01

Several physical phenomena such as transformation of pollutants, energy, particles and many others can be described by the well-known convection-diffusion equation which is a combination of the diffusion and advection equations. In this paper, this equation is generalized with the concept of variable-order fractional derivatives. The generalized equation is called variable-order time fractional advection-diffusion equation (V-OTFA-DE). An accurate and robust meshless method based on the moving least squares (MLS) approximation and the finite difference scheme is proposed for its numerical solution on two-dimensional (2-D) arbitrary domains. In the time domain, the finite difference technique with a θ-weighted scheme and in the space domain, the MLS approximation are employed to obtain appropriate semi-discrete solutions. Since the newly developed method is a meshless approach, it does not require any background mesh structure to obtain semi-discrete solutions of the problem under consideration, and the numerical solutions are constructed entirely based on a set of scattered nodes. The proposed method is validated in solving three different examples including two benchmark problems and an applied problem of pollutant distribution in the atmosphere. In all such cases, the obtained results show that the proposed method is very accurate and robust. Moreover, a remarkable property so-called positive scheme for the proposed method is observed in solving concentration transport phenomena.

Ion-exchange equilibrium of N-acetyl-D-neuraminic acid on a strong anionic exchanger.

PubMed

Wu, Jinglan; Ke, Xu; Zhang, Xudong; Zhuang, Wei; Zhou, Jingwei; Ying, Hanjie

2015-09-15

N-acetyl-D-neuraminic acid (Neu5Ac) is a high value-added product widely applied in the food industry. A suitable equilibrium model is required for purification of Neu5Ac based on ion-exchange chromatography. Hence, the equilibrium uptake of Neu5Ac on a strong anion exchanger, AD-1 was investigated experimentally and theoretically. The uptake of Neu5Ac by the hydroxyl form of the resin occurred primarily by a stoichiometric exchange of Neu5Ac(-) and OH(-). The experimental data showed that the selectivity coefficient for the exchange of Neu5Ac(-) with OH(-) was a non-constant quantity. Subsequently, the Saunders' model, which took into account the dissociation reactions of Neu5Ac and the condition of electroneutrality, was used to correlate the Neu5Ac sorption isotherms at various solution pHs and Neu5Ac concentrations. The model provided an excellent fit to the binary exchange data for Cl(-)/OH(-) and Neu5Ac(-)/OH(-), and an approximate prediction of equilibrium in the ternary system Cl(-)/Neu5Ac(-)/OH(-). This basic information combined with the general mass transfer model could lay the foundation for the prediction of dynamic behavior of fixed bed separation process afterwards. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multiscale modelling of dual-porosity porous media; a computational pore-scale study for flow and solute transport

NASA Astrophysics Data System (ADS)

de Vries, Enno T.; Raoof, Amir; van Genuchten, Martinus Th.

2017-07-01

Many environmental and agricultural applications involve the transport of water and dissolved constituents through aggregated soil profiles, or porous media that are structured, fractured or macroporous in other ways. During the past several decades, various process-based macroscopic models have been used to simulate contaminant transport in such media. Many of these models consider advective-dispersive transport through relatively large inter-aggregate pore domains, while exchange with the smaller intra-aggregate pores is assumed to be controlled by diffusion. Exchange of solute between the two domains is often represented using a first-order mass transfer coefficient, which is commonly obtained by fitting to observed data. This study aims to understand and quantify the solute exchange term by applying a dual-porosity pore-scale network model to relatively large domains, and analysing the pore-scale results in terms of the classical dual-porosity (mobile-immobile) transport formulation. We examined the effects of key parameters (notably aggregate porosity and aggregate permeability) on the main dual-porosity model parameters, i.e., the mobile water fraction (ϕm) and the mass transfer coefficient (α). Results were obtained for a wide range of aggregate porosities (between 0.082 and 0.700). The effect of aggregate permeability was explored by varying pore throat sizes within the aggregates. Solute breakthrough curves (BTCs) obtained with the pore-scale network model at several locations along the domain were analysed using analytical solutions of the dual-porosity model to obtain estimates of ϕm and α. An increase in aggregate porosity was found to decrease ϕm and increase α, leading to considerable tailing in the BTCs. Changes in the aggregate pore throat size affected the relative flow velocity between the intra- and inter-aggregate domains. Higher flow velocities within the aggregates caused a change in the transport regime from diffusion dominated to more

Water Mass Variability at the Mid-Atlantic Ridge and in the Eastern North Atlantic

NASA Astrophysics Data System (ADS)

Köllner, Manuela; Klein, Birgit; Kieke, Dagmar; Klein, Holger; Roessler, Achim; Rhein, Monika

2017-04-01

The strong warming and salinification of the Eastern North Atlantic starting in the mid 1990s has been attributed to a westward contraction of the sub-polar gyre and stronger inflow of waters from the sub-tropical gyre. Temporal changes in the shape and strength of the two gyres have been related to the major mode of atmospheric variability in the Atlantic sector, the NAO. Hydrographic conditions along the Northwest European shelf are thus the result of different processes such as variations in transports, varying relative contributions of water masses from the two gyres and property trends in the source water masses. The North Atlantic Current (NAC) can be regarded as the southern border of the sub-polar gyre transporting water from the tropical regions northward. On its way towards the Mid Atlantic Ridge (MAR) the NAC has partly mixed with waters from the sub-polar gyre and crosses the MAR split into several branches. For the study we analyzed data of water mass variability and transport fluctuations from the RACE (Regional circulation and Global change) project (2012-2015) which provided time series of transports and hydrographic anomalies from moored instruments at the western flank of the MAR. The time depending positions of the NAC branches over the MAR were obtained from mooring time series and compared to sea surface velocities from altimeter data. The results show a high variability of NAC pathways over the MAR. Transition regimes with strong meandering and eddies could be observed as well as periods of strong NAC branches over the Fracture Zones affecting water mass exchange at all depth levels. A positive temperature trend at depths between 1000-2000 m was found at the Faraday Fracture Zone (FFZ). This warming trend was also detected by Argo floats crossing the MAR close to the FFZ region. During the second phase of RACE (RACE-II, 2016-2018) a mooring array across the eastern shelf break at Goban Spur was deployed to monitor the poleward Eastern Boundary

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

Analysis of factors affecting gas exchange in intravascular blood gas exchanger.

PubMed

Niranjan, S C; Clark, J W; San, K Y; Zwischenberger, J B; Bidani, A

1994-10-01

A mathematical model of an intravascular hollow-fiber gas-exchange device, called IVOX, has been developed using a Krogh cylinder-like approach with a repeating unit structure comprised of a single fiber with gas flowing through its lumen surrounded by a coaxial cylinder of blood flowing in the opposite direction. Species mass balances on O2 and CO2 result in a nonlinear coupled set of convective-diffusion parabolic partial differential equations that are solved numerically using an alternating-direction implicit finite-difference method. Computed results indicated the presence of a large resistance to gas transport on the external (blood) side of the hollow-fiber exchanger. Increasing gas flow through the device favored CO2 removal from but not O2 addition to blood. Increasing blood flow over the device favored both CO2 removal as well as O2 addition. The rate of CO2 removal increased linearly with the transmural PCO2 gradient imposed across the device. The effect of fiber crimping on blood phase mass transfer resistance was evaluated indirectly by varying species blood diffusivity. Computed results indicated that CO2 excretion by IVOX can be significantly enhanced with improved bulk mixing of vena caval blood around the IVOX fibers.

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

PubMed

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

2012-02-07

Described here is a mass spectrometry-based protocol to study the thermodynamic stability of proteins and protein-ligand complexes using the chemical denaturant dependence of the slow H/D exchange reaction of the imidazole C(2) proton in histidine side chains. The protocol is developed using several model protein systems including: ribonuclease (Rnase) A, myoglobin, bovine carbonic anhydrase (BCA) II, hemoglobin (Hb), and the hemoglobin-haptoglobin (Hb-Hp) protein complex. Folding free energies consistent with those previously determined by other more conventional techniques were obtained for the two-state folding proteins, Rnase A and myoglobin. The protocol successfully detected a previously observed partially unfolded intermediate stabilized in the BCA II folding/unfolding reaction, and it could be used to generate a K(d) value of 0.24 nM for the Hb-Hp complex. The compatibility of the protocol with conventional mass spectrometry-based proteomic sample preparation and analysis methods was also demonstrated in an experiment in which the protocol was used to detect the binding of zinc to superoxide dismutase in the yeast cell lysate sample. The yeast cell sample analyses also helped define the scope of the technique, which requires the presence of globally protected histidine residues in a protein's three-dimensional structure for successful application. © 2011 American Chemical Society

Implicit and semi-implicit schemes in the Versatile Advection Code: numerical tests

NASA Astrophysics Data System (ADS)

Toth, G.; Keppens, R.; Botchev, M. A.

1998-04-01

We describe and evaluate various implicit and semi-implicit time integration schemes applied to the numerical simulation of hydrodynamical and magnetohydrodynamical problems. The schemes were implemented recently in the software package Versatile Advection Code, which uses modern shock capturing methods to solve systems of conservation laws with optional source terms. The main advantage of implicit solution strategies over explicit time integration is that the restrictive constraint on the allowed time step can be (partially) eliminated, thus the computational cost is reduced. The test problems cover one and two dimensional, steady state and time accurate computations, and the solutions contain discontinuities. For each test, we confront explicit with implicit solution strategies.

Observations of the microclimate of a lake under cold air advective conditions

NASA Technical Reports Server (NTRS)

Bill, R. G., Jr.; Sutherland, R. A.; Bartholic, J. F.

1977-01-01

The moderating effects of Lake Apopka, Florida, on downwind surface temperatures were evaluated under cold air advective conditions. Point temperature measurements north and south of the lake and data obtained from the NOAA satellite and a thermal scanner flown at 1.6 km, indicate that, under conditions of moderate winds (approximately 4m/sec), surface temperatures directly downwind may be higher than surrounding surface temperatures by as much as 5 C. With surface wind speed less than 1m/sec, no substantial temperature effects were observed. Results of this study are being used in land use planning, lake level control and in agriculture for selecting planting sites.

Multigrid techniques for the solution of the passive scalar advection-diffusion equation

NASA Technical Reports Server (NTRS)

Phillips, R. E.; Schmidt, F. W.

1985-01-01

The solution of elliptic passive scalar advection-diffusion equations is required in the analysis of many turbulent flow and convective heat transfer problems. The accuracy of the solution may be affected by the presence of regions containing large gradients of the dependent variables. The multigrid concept of local grid refinement is a method for improving the accuracy of the calculations in these problems. In combination with the multilevel acceleration techniques, an accurate and efficient computational procedure is developed. In addition, a robust implementation of the QUICK finite-difference scheme is described. Calculations of a test problem are presented to quantitatively demonstrate the advantages of the multilevel-multigrid method.

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

PubMed

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

2015-12-04

Dextran, a family of natural polysaccharides, consists of an α (1→6) linked-glucose main (backbone) chain having a number of branches. The determination of the types and the quantities of branches in dextran is important in understanding its various biological roles. In this study, a hyphenated method using high-performance anion exchange chromatography (HPAEC) in parallel with pulsed amperometric detection (PAD) and mass spectrometry (MS) was applied to qualitative and quantitative analysis of dextran branches. A rotary cation-exchange cartridge array desalter was used for removal of salt from the HPAEC eluent making it MS compatible. MS and MS/MS were used to provide structural information on the enzymatically prepared dextran oligosaccharides. PAD provides quantitative data on the ratio of enzyme-resistant, branched dextran oligosaccharides. Both the types and degree of branching found in a variety of dextrans could be simultaneously determined online using this method. Copyright © 2015 Elsevier B.V. All rights reserved.

Resolving the intermediate and deep advective flows in the Indian Ocean by using temperature, salinity, oxygen and phosphate data: the interplay of biogeochemical and geophysical tracers

NASA Astrophysics Data System (ADS)

Metzl, N.; Moore, B.; Poisson, A.

1990-10-01

For computing large-scale advective flow in the Indian ocean (including the Indian-Antarctic sector), we use a box-model approach and perturbed inverse method. The top 400 meters is not considered in this study, in view of the dominant seasonal dynamics. We use 1244 hydrographic stations, to estimate mean values for temperature, salinity, oxygen and phosphate concentratons. Fifty perturbed inversions of steady-state tracers conservations and thermal-wind equations are done using box-averages standard deviations and a 25% perturbation on the thermal-wind coefficients. The mean solutions represent the large-scale advective flow and carbon-decomposition rates in which we are interested. Solutions with only advective processes are first considered. The broad features of the circulation in the Indian Ocean are resolved in the intermediate levels, but in deeper layers, an input from North Atlantic Deep Water (NADW) is not apparent. Inspection of oxygen and phosphate residuals reveals a biochemical signal. Therefore, we introduce in the oxygen and phosphate budgets a linear parameterization (Redfield ratios) for the organic-decomposition processes. The structure of the residuals for oxygen and phosphate is changed in that the biochemical signal vanishes. The advective solutions are nearly the same in intermediate waters; however, in deep layers the new solution shows an inflow of 11 (±8) Sv of NADW south of Africa. The calculated total organic decomposition of 0.93 (±0.25) 10 15g C year -1 is about one fifth of the estimated world ocean amount, but total residuals of oxygen and phosphate lead to an unexplained 0.5 10 15g C year -1 missing carbon sink. The new solution does contain unrealistic elements (e.g. large deep flow between Indonesia and Australia). Finally, to investigate this last result, we add one advective constraint at the Indonesia-Australia boundary. This addition changes the circulation in the northeastern part of the Indian Ocean. The circumpolar flow

Simulation of advective flow under steady-state and transient recharge conditions, Camp Edwards, Massachusetts Military Reservation, Cape Cod, Massachusetts

USGS Publications Warehouse

Walter, Donald A.; Masterson, John P.

2003-01-01

The U.S. Geological Survey has developed several ground-water models in support of an investigation of ground-water contamination being conducted by the Army National Guard Bureau at Camp Edwards, Massachusetts Military Reservation on western Cape Cod, Massachusetts. Regional and subregional steady-state models and regional transient models were used to (1) improve understanding of the hydrologic system, (2) simulate advective transport of contaminants, (3) delineate recharge areas to municipal wells, and (4) evaluate how model discretization and time-varying recharge affect simulation results. A water-table mound dominates ground-water-flow patterns. Near the top of the mound, which is within Camp Edwards, hydraulic gradients are nearly vertically downward and horizontal gradients are small. In downgradient areas that are further from the top of the water-table mound, the ratio of horizontal to vertical gradients is larger and horizontal flow predominates. The steady-state regional model adequately simulates advective transport in some areas of the aquifer; however, simulation of ground-water flow in areas with local hydrologic boundaries, such as ponds, requires more finely discretized subregional models. Subregional models also are needed to delineate recharge areas to municipal wells that are inadequately represented in the regional model or are near other pumped wells. Long-term changes in recharge rates affect hydraulic heads in the aquifer and shift the position of the top of the water-table mound. Hydraulic-gradient directions do not change over time in downgradient areas, whereas they do change substantially with temporal changes in recharge near the top of the water-table mound. The assumption of steady-state hydraulic conditions is valid in downgradient area, where advective transport paths change little over time. In areas closer to the top of the water-table mound, advective transport paths change as a function of time, transient and steady-state paths

Radiochemical methodology for the determination of the mass balance of suspended particulate materials exchanged at the inlets of the Venice Lagoon

NASA Astrophysics Data System (ADS)

Degetto, S.; Cantaluppi, C.

2004-11-01

The Venice Lagoon is connected to the Adriatic Sea by three inlets, with an average daily water inflow of 345∗10 6 m 3. Due to the diversion of the major rivers out of the lagoon (done in the past centuries), the sediment supply from the drainage basin is now very low when compared to the amount of sediment exchanged at the inlets (<1%). The limited sediment supply and the combined action of natural and anthropic pressures (e.g. waves, ships, fishing activities, dredging for navigation purposes) have caused in the last few decades a significant erosion of mudflats and salt-marshes. In order to investigate the history and the characteristics of the above phenomenon, with particular regard to the most recent years and the future trend, a wide radiochemical survey has been carried out in the whole lagoon, including the characterisation of the suspended particulate matter entering and leaving the lagoon in different tidal and meteorological conditions, with the aim of obtaining an indirect estimate of the sediment mass balance of the lagoon. The proposed radiochemical methodology, which is based on concentration measurements of airborne radionuclides in suspended particulate matter, appears to be an useful alternative to direct methods (e.g. bathymetric campaigns in the lagoon or mass fluxes measurements of the suspended particulate materials exchanged at the inlets). The results obtained, which show a complex sedimentary situation, highlight the erosion acting in some central and southern lagoon areas but recognise also the present accumulation phase coming into view in the northern lagoon.

On the error propagation of semi-Lagrange and Fourier methods for advection problems☆

PubMed Central

Einkemmer, Lukas; Ostermann, Alexander

2015-01-01

In this paper we study the error propagation of numerical schemes for the advection equation in the case where high precision is desired. The numerical methods considered are based on the fast Fourier transform, polynomial interpolation (semi-Lagrangian methods using a Lagrange or spline interpolation), and a discontinuous Galerkin semi-Lagrangian approach (which is conservative and has to store more than a single value per cell). We demonstrate, by carrying out numerical experiments, that the worst case error estimates given in the literature provide a good explanation for the error propagation of the interpolation-based semi-Lagrangian methods. For the discontinuous Galerkin semi-Lagrangian method, however, we find that the characteristic property of semi-Lagrangian error estimates (namely the fact that the error increases proportionally to the number of time steps) is not observed. We provide an explanation for this behavior and conduct numerical simulations that corroborate the different qualitative features of the error in the two respective types of semi-Lagrangian methods. The method based on the fast Fourier transform is exact but, due to round-off errors, susceptible to a linear increase of the error in the number of time steps. We show how to modify the Cooley–Tukey algorithm in order to obtain an error growth that is proportional to the square root of the number of time steps. Finally, we show, for a simple model, that our conclusions hold true if the advection solver is used as part of a splitting scheme. PMID:25844018

Direct and Quantitative Characterization of Dynamic Ligand Exchange between Coordination-Driven Self-Assembled Supramolecular Polygons

PubMed Central

Zheng, Yao-Rong; Stang, Peter J.

2009-01-01

The direct observation of dynamic ligand exchange beween Pt-N coordination-driven self-assembled supramolecular polygons (triangles and rectangles) has been achieved using stable isotope labeling (1H/2D) of the pyridyl donors and electrospray ionization mass spectrometry (ESI-MS) together with NMR spectroscopy. Both the thermodynamic and kinetic aspects of such exchange processes have been established based on quantitative mass spectral results. Further investigation showed that the exchange is highly dependent on experimental conditions such as temperature, solvent, and the counter anions. PMID:19243144

Direct and quantitative characterization of dynamic ligand exchange between coordination-driven self-assembled supramolecular polygons.

PubMed

Zheng, Yao-Rong; Stang, Peter J

2009-03-18

The direct observation of dynamic ligand exchange between Pt-N coordination-driven self-assembled supramolecular polygons (triangles and rectangles) has been achieved using stable (1)H/(2)D isotope labeling of the pyridyl donors and electrospray ionization mass spectrometry combined with NMR spectroscopy. Both the thermodynamic and kinetic aspects of such exchange processes have been established on the basis of quantitative mass spectral results. Further investigation has shown that the exchange is highly dependent on experimental conditions such as temperature, solvent, and the counteranions.

Partial cooperative unfolding in proteins as observed by hydrogen exchange mass spectrometry

PubMed Central

Engen, John R.; Wales, Thomas E.; Chen, Shugui; Marzluff, Elaine M.; Hassell, Kerry M.; Weis, David D.; Smithgall, Thomas E.

2013-01-01

Many proteins do not exist in a single rigid conformation. Protein motions, or dynamics, exist and in many cases are important for protein function. The analysis of protein dynamics relies on biophysical techniques that can distinguish simultaneously existing populations of molecules and their rates of interconversion. Hydrogen exchange (HX) detected by mass spectrometry (MS) is contributing to our understanding of protein motions by revealing unfolding and dynamics on a wide timescale, ranging from seconds to hours to days. In this review we discuss HX MS-based analyses of protein dynamics, using our studies of multi-domain kinases as examples. Using HX MS, we have successfully probed protein dynamics and unfolding in the isolated SH3, SH2 and kinase domains of the c-Src and Abl kinase families, as well as the role of inter- and intra-molecular interactions in the global control of kinase function. Coupled with high-resolution structural information, HX MS has proved to be a powerful and versatile tool for the analysis of the conformational dynamics in these kinase systems, and has provided fresh insight regarding the regulatory control of these important signaling proteins. HX MS studies of dynamics are applicable not only to the proteins we illustrate here, but to a very wide range of proteins and protein systems, and should play a role in both classification of and greater understanding of the prevalence of protein motion. PMID:23682200

Ion Mobility Spectrometry-Mass Spectrometry Coupled with Gas-Phase Hydrogen/Deuterium Exchange for Metabolomics Analyses

NASA Astrophysics Data System (ADS)

Maleki, Hossein; Karanji, Ahmad K.; Majuta, Sandra; Maurer, Megan M.; Valentine, Stephen J.

2018-02-01

Ion mobility spectrometry-mass spectrometry (IMS-MS) in combination with gas-phase hydrogen/deuterium exchange (HDX) and collision-induced dissociation (CID) is evaluated as an analytical method for small-molecule standard and mixture characterization. Experiments show that compound ions exhibit unique HDX reactivities that can be used to distinguish different species. Additionally, it is shown that gas-phase HDX kinetics can be exploited to provide even further distinguishing capabilities by using different partial pressures of reagent gas. The relative HDX reactivity of a wide variety of molecules is discussed in light of the various molecular structures. Additionally, hydrogen accessibility scoring (HAS) and HDX kinetics modeling of candidate ( in silico) ion structures is utilized to estimate the relative ion conformer populations giving rise to specific HDX behavior. These data interpretation methods are discussed with a focus on developing predictive tools for HDX behavior. Finally, an example is provided in which ion mobility information is supplemented with HDX reactivity data to aid identification efforts of compounds in a metabolite extract.

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. Copyright © 2016 Elsevier B.V. All rights reserved.

Methanol exchange dynamics between a temperate cropland soil and the atmosphere

NASA Astrophysics Data System (ADS)

Bachy, A.; Aubinet, M.; Amelynck, C.; Schoon, N.; Bodson, B.; Moureaux, C.; Delaplace, P.; De Ligne, A.; Heinesch, B.

2018-03-01

Soil methanol (CH3OH) exchange is often considered as several orders of magnitude smaller than plant methanol exchange. However, for some ecosystems, it is significant in regard with plant exchange and worth thus better consideration. Our study sought to gain a better understanding of soil exchange. Methanol flux was measured at the ecosystem scale on a bare agricultural soil over two contrasted periods using the disjunct eddy covariance by mass scanning technique. A proton-transfer-reaction mass spectrometer was used for the methanol ambient mixing ratio measurements. Bi-directional exchange dynamics were observed. Methanol emission occurred under dry and warm conditions and correlated best with soil surface temperature, whereas methanol uptake occurred under wet and mild conditions and correlated well with the methanol ambient concentration. After having tested a physical adsorption-desorption model and by confronting our data with the literature, we propose that the exchange was ruled by both a physical adsorption/desorption mechanism and by a methanol source, which still needs to be identified. The soil emission decreased when the vegetation developed. The reasons for the decrease still need to be determined. Overall, the dynamics observed at our site were similar to those reported by other studies for both cropland and forest ecosystems. The mechanism proposed in our work can thus be possibly applied to other sites or ecosystems. In addition, the methanol exchange rate was in the upper range of the exchange rates reported by other soil studies, suggesting that cropland soils are more important methanol exchangers than those in other ecosystems and should therefore be further investigated.

Advection of Karenia brevis blooms from the Florida Panhandle towards Mississippi coastal waters.

PubMed

Soto, Inia M; Cambazoglu, Mustafa Kemal; Boyette, Adam D; Broussard, Kristina; Sheehan, Drew; Howden, Stephan D; Shiller, Alan M; Dzwonkowski, Brian; Hode, Laura; Fitzpatrick, Patrick J; Arnone, Robert A; Mickle, Paul F; Cressman, Kimberly

2018-02-01

Harmful Algal Blooms (HABs) of Karenia brevis have been documented along coastal waters of every state bordering the Gulf of Mexico (GoM). Some Gulf Coast locations, such as Florida and Texas, suffer from recurrent intense and spatially large blooms, while others such as Mississippi seem to rarely observe them. The main objective of this work is to understand the dynamics that led to the K. brevis bloom in Mississippi coastal waters in fall 2015. Blooms of K. brevis from the Florida Panhandle region are often advected westward towards the Mississippi-Alabama coast; however there is interannual variability in their presence and intensity in Mississippi coastal waters. The 2015 K. brevis bloom was compared to the 2007 Florida Panhandle K. brevis bloom, which showed a westward advection pattern, but did not intensify along the Mississippi coast. Cell counts and flow cytometry were obtained from the Mississippi Department of Marine Resources, Alabama Department of Public Health, Florida Fish and Wildlife Conservation Commission and The University of Southern Mississippi. Ocean color satellite imagery from the Moderate Resolution Imaging Spectroradiometer onboard the Aqua satellite was used to detect and delineate the blooms in 2007 and 2015. Two different regional applications of NCOM-Navy Coastal Ocean Model (1-km resolution NCOM-GoM/Gulf of Mexico and 6-km resolution NCOM-IASNFS/Intra Americas Sea Nowcast Forecast System) were used to understand the circulation and transport pathways. A Lagrangian particle tracking software was used to track the passive movement of particles released at different locations for both bloom events. Ancillary data (e.g., nutrients, wind, salinity, river discharge) from local buoys, monitoring stations and coincident oceanographic cruises were also included in the analysis. The blooms of K. brevis reached the Mississippi coast both years; however, the bloom in 2007 lasted only a few days and there is no evidence that it entered the

Charge exchange of solar wind ions in the Comet Halley coma

NASA Technical Reports Server (NTRS)

Shelley, E. G.; Ing-H. afgoldstein, B. E. AGGOLDSTEIN, R.; Ing-H. afgoldstein, B. E. AGGOLDSTEIN, R.

1986-01-01

The He(2+) and He(+) radial profiles measured by the Giotto mass spectrometer on the inbound trajectory to comet Halley are compared to a simple 1-dimensional charge exchange model. Results indicate that charge exchange alone cannot account for the observed radial profiles of He(2+) and He(+).

On the anisotropic advection-diffusion equation with time dependent coefficients

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

Hernandez-Coronado, Hector; Coronado, Manuel; Del-Castillo-Negrete, Diego B.

The advection-diffusion equation with time dependent velocity and anisotropic time dependent diffusion tensor is examined in regard to its non-classical transport features and to the use of a non-orthogonal coordinate system. Although this equation appears in diverse physical problems, particularly in particle transport in stochastic velocity fields and in underground porous media, a detailed analysis of its solutions is lacking. In order to study the effects of the time-dependent coefficients and the anisotropic diffusion on transport, we solve analytically the equation for an initial Dirac delta pulse. Here, we discuss the solutions to three cases: one based on power-law correlationmore » functions where the pulse diffuses faster than the classical rate ~t, a second case specically designed to display slower rate of diffusion than the classical one, and a third case to describe hydrodynamic dispersion in porous media« less

On the anisotropic advection-diffusion equation with time dependent coefficients

DOE PAGES

Hernandez-Coronado, Hector; Coronado, Manuel; Del-Castillo-Negrete, Diego B.

2017-02-01

The advection-diffusion equation with time dependent velocity and anisotropic time dependent diffusion tensor is examined in regard to its non-classical transport features and to the use of a non-orthogonal coordinate system. Although this equation appears in diverse physical problems, particularly in particle transport in stochastic velocity fields and in underground porous media, a detailed analysis of its solutions is lacking. In order to study the effects of the time-dependent coefficients and the anisotropic diffusion on transport, we solve analytically the equation for an initial Dirac delta pulse. Here, we discuss the solutions to three cases: one based on power-law correlationmore » functions where the pulse diffuses faster than the classical rate ~t, a second case specically designed to display slower rate of diffusion than the classical one, and a third case to describe hydrodynamic dispersion in porous media« less

Long-Term Multiwavelength Observations of GRS 1758-258 and the Advection-dominated Accretion Flow Model

NASA Astrophysics Data System (ADS)

Keck, John W.; Craig, William W.; Hailey, Charles J.; Harrison, Fiona; Hong, Jae Sub; Kahn, Steven M.; Lubin, Philip M.; McLean, Ryan; Pivovaroff, Michael J.; Seiffert, Michael; Wurtz, Ron; Ziock, Klaus P.

2001-12-01

We present a long-term multiwavelength light curve of Galactic black hole candidate GRS 1758-258 by combining previously published and archival data from Granat, ROSAT, the Compton Gamma Ray Observatory, the Rossi X-Ray Timing Explorer, BeppoSAX, ASCA, EXOSAT, and the Very Large Array. In addition, we include the first spectral results from the balloon-borne Gamma-Ray Arcminute Telescope Imaging System (GRATIS). In light of divergent analyses of the 1991-1993 ROSAT observations, we have reanalyzed these data; we find that the soft X-rays track the hard X-rays and that the fits require no blackbody component-indicating that GRS 1758-258 did not go to the high state in 1993. We offer an interpretation of these long-baseline data based on the advection-dominated accretion flow (ADAF) model for a system with m<~mcrit. We find that the 1990-1993 coeval hard and soft X-ray observations support the ADAF predictions. We discuss a new way to constrain black hole mass with spectral data and the ADAF theory and apply this technique to GRS 1758-258 to find M1>~8-9 Msolar at an assumed distance of 8.5 kpc. Further investigations of the ADAF model allow us to evaluate the model critically against the 1996 data and flux-flux diagram of Barret, McClintock, & Grindlay and to understand the limits of the latter's ``X-ray burster box.''

Experiments on fragmentation and thermo-chemical exchanges during planetary core formation

NASA Astrophysics Data System (ADS)

Wacheul, Jean-Baptiste; Le Bars, Michael

2018-03-01

The initial thermo-chemical state of telluric planets was largely controlled by mixing following the collision of differentiated proto-planets. Up to now, most models of planet formation simply assume that the iron core of the impactors immediately broke up to form an "iron rain" within a large-scale magma ocean, leading to the rapid equilibration of the whole metal with the whole mantle. Only recent studies have focused on resolving the fluid mechanics of the problem, with the aim to define more relevant diffusion-advection models of thermal and chemical exchanges within and between the two fluids. Furthermore, the influence of the viscosity ratio on this dynamical process is generally neglected, whilst it is known to play a role in the breakup of the initial iron diapirs and in the shape of the resulting droplets. Here we report the results of analog laboratory experiments matching the dynamical regime of the geophysical configuration. High speed video recording allows us to describe and characterize the fluid dynamics of the system, and temperature measurements allow us to quantify the diffusive exchanges integrated during the fall of the liquid metal. We find that the early representation of this flow as an iron rain is far from the experimental results. The equilibration coefficient at a given depth depends both on the initial size of the metal diapir and on the viscosity of the ambient fluid, whereas the falling speed is only controlled by the initial size. Various scalings for the diffusive exchanges coming from the literature are tested. We find good agreement with the turbulent thermal model developed by Deguen et al. (2014).

Numerical modeling and analytical modeling of cryogenic carbon capture in a de-sublimating heat exchanger

NASA Astrophysics Data System (ADS)

Yu, Zhitao; Miller, Franklin; Pfotenhauer, John M.

2017-12-01

Both a numerical and analytical model of the heat and mass transfer processes in a CO2, N2 mixture gas de-sublimating cross-flow finned duct heat exchanger system is developed to predict the heat transferred from a mixture gas to liquid nitrogen and the de-sublimating rate of CO2 in the mixture gas. The mixture gas outlet temperature, liquid nitrogen outlet temperature, CO2 mole fraction, temperature distribution and de-sublimating rate of CO2 through the whole heat exchanger was computed using both the numerical and analytic model. The numerical model is built using EES [1] (engineering equation solver). According to the simulation, a cross-flow finned duct heat exchanger can be designed and fabricated to validate the models. The performance of the heat exchanger is evaluated as functions of dimensionless variables, such as the ratio of the mass flow rate of liquid nitrogen to the mass flow rate of inlet flue gas.

Analysis of two-phase flow inter-subchannel mass and momentum exchanges by the two-fluid model approach

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

Ninokata, H.; Deguchi, A.; Kawahara, A.

1995-09-01

A new void drift model for the subchannel analysis method is presented for the thermohydraulics calculation of two-phase flows in rod bundles where the flow model uses a two-fluid formulation for the conservation of mass, momentum and energy. A void drift model is constructed based on the experimental data obtained in a geometrically simple inter-connected two circular channel test sections using air-water as working fluids. The void drift force is assumed to be an origin of void drift velocity components of the two-phase cross-flow in a gap area between two adjacent rods and to overcome the momentum exchanges at themore » phase interface and wall-fluid interface. This void drift force is implemented in the cross flow momentum equations. Computational results have been successfully compared to experimental data available including 3x3 rod bundle data.« less

Estimating the solute transport parameters of the spatial fractional advection-dispersion equation using Bees Algorithm

NASA Astrophysics Data System (ADS)

Mehdinejadiani, Behrouz

2017-08-01

This study represents the first attempt to estimate the solute transport parameters of the spatial fractional advection-dispersion equation using Bees Algorithm. The numerical studies as well as the experimental studies were performed to certify the integrity of Bees Algorithm. The experimental ones were conducted in a sandbox for homogeneous and heterogeneous soils. A detailed comparative study was carried out between the results obtained from Bees Algorithm and those from Genetic Algorithm and LSQNONLIN routines in FracFit toolbox. The results indicated that, in general, the Bees Algorithm much more accurately appraised the sFADE parameters in comparison with Genetic Algorithm and LSQNONLIN, especially in the heterogeneous soil and for α values near to 1 in the numerical study. Also, the results obtained from Bees Algorithm were more reliable than those from Genetic Algorithm. The Bees Algorithm showed the relative similar performances for all cases, while the Genetic Algorithm and the LSQNONLIN yielded different performances for various cases. The performance of LSQNONLIN strongly depends on the initial guess values so that, compared to the Genetic Algorithm, it can more accurately estimate the sFADE parameters by taking into consideration the suitable initial guess values. To sum up, the Bees Algorithm was found to be very simple, robust and accurate approach to estimate the transport parameters of the spatial fractional advection-dispersion equation.

Estimating the solute transport parameters of the spatial fractional advection-dispersion equation using Bees Algorithm.

PubMed

Mehdinejadiani, Behrouz

2017-08-01

This study represents the first attempt to estimate the solute transport parameters of the spatial fractional advection-dispersion equation using Bees Algorithm. The numerical studies as well as the experimental studies were performed to certify the integrity of Bees Algorithm. The experimental ones were conducted in a sandbox for homogeneous and heterogeneous soils. A detailed comparative study was carried out between the results obtained from Bees Algorithm and those from Genetic Algorithm and LSQNONLIN routines in FracFit toolbox. The results indicated that, in general, the Bees Algorithm much more accurately appraised the sFADE parameters in comparison with Genetic Algorithm and LSQNONLIN, especially in the heterogeneous soil and for α values near to 1 in the numerical study. Also, the results obtained from Bees Algorithm were more reliable than those from Genetic Algorithm. The Bees Algorithm showed the relative similar performances for all cases, while the Genetic Algorithm and the LSQNONLIN yielded different performances for various cases. The performance of LSQNONLIN strongly depends on the initial guess values so that, compared to the Genetic Algorithm, it can more accurately estimate the sFADE parameters by taking into consideration the suitable initial guess values. To sum up, the Bees Algorithm was found to be very simple, robust and accurate approach to estimate the transport parameters of the spatial fractional advection-dispersion equation. Copyright © 2017 Elsevier B.V. All rights reserved.

High Temperature Composite Heat Exchangers

NASA Technical Reports Server (NTRS)

Eckel, Andrew J.; Jaskowiak, Martha H.

2002-01-01

High temperature composite heat exchangers are an enabling technology for a number of aeropropulsion applications. They offer the potential for mass reductions of greater than fifty percent over traditional metallics designs and enable vehicle and engine designs. Since they offer the ability to operate at significantly higher operating temperatures, they facilitate operation at reduced coolant flows and make possible temporary uncooled operation in temperature regimes, such as experienced during vehicle reentry, where traditional heat exchangers require coolant flow. This reduction in coolant requirements can translate into enhanced range or system payload. A brief review of the approaches and challengers to exploiting this important technology are presented, along with a status of recent government-funded projects.

Forecasting Global Horizontal Irradiance Using the LETKF and a Combination of Advected Satellite Images and Sparse Ground Sensors

NASA Astrophysics Data System (ADS)

Harty, T. M.; Lorenzo, A.; Holmgren, W.; Morzfeld, M.

2017-12-01

The irradiance incident on a solar panel is the main factor in determining the power output of that panel. For this reason, accurate global horizontal irradiance (GHI) estimates and forecasts are critical when determining the optimal location for a solar power plant, forecasting utility scale solar power production, or forecasting distributed, behind the meter rooftop solar power production. Satellite images provide a basis for producing the GHI estimates needed to undertake these objectives. The focus of this work is to combine satellite derived GHI estimates with ground sensor measurements and an advection model. The idea is to use accurate but sparsely distributed ground sensors to improve satellite derived GHI estimates which can cover large areas (the size of a city or a region of the United States). We use a Bayesian framework to perform the data assimilation, which enables us to produce irradiance forecasts and associated uncertainties which incorporate both satellite and ground sensor data. Within this framework, we utilize satellite images taken from the GOES-15 geostationary satellite (available every 15-30 minutes) as well as ground data taken from irradiance sensors and rooftop solar arrays (available every 5 minutes). The advection model, driven by wind forecasts from a numerical weather model, simulates cloud motion between measurements. We use the Local Ensemble Transform Kalman Filter (LETKF) to perform the data assimilation. We present preliminary results towards making such a system useful in an operational context. We explain how localization and inflation in the LETKF, perturbations of wind-fields, and random perturbations of the advection model, affect the accuracy of our estimates and forecasts. We present experiments showing the accuracy of our forecasted GHI over forecast-horizons of 15 mins to 1 hr. The limitations of our approach and future improvements are also discussed.

Nanomodified polymer materials for regenerative heat exchangers

NASA Astrophysics Data System (ADS)

Shchegolkov, Alexander; Shchegolkov, Alexey; Dyachkova, Tatyana

2017-11-01

The paper presents thermophysical properties of nanomodified paraffin mixed with polymers as polyethylene or fluoroplastic, which may be effectively used for the development of heat exchange elements of personal protective equipment. It has been experimentally shown that the heat exchangers based on the nanomodified polymer composites have twofold mass compared to the standard regenerative heat exchanger with comparable dimensions. The best result has been obtained on the basis of composite containing polyethylene and paraffin modified with CNTs, which thermal conductivity is 1.6 times higher than forconventional paraffin. The application of carbon nanostructures as the modifiers of heat storage materials improves cooling efficiency by 14.9-17.9 °C by creating more comfortable conditions for breathing via personal protective equipment.

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

Thermo-aerodynamic efficiency of non-circular ducts with vortex enhancement of heat exchange in different types of compact heat exchangers

NASA Astrophysics Data System (ADS)

Vasilev, V. Ya; Nikiforova, S. A.

2018-03-01

Experimental studies of thermo-aerodynamic characteristics of non-circular ducts with discrete turbulators on walls and interrupted channels have confirmed the rational enhancement of convective heat transfer, in which the growth of heat transfer outstrips or equals the growth of aerodynamic losses. Determining the regularities of rational (energy-saving) enhancement of heat transfer and the proposed method for comparing the characteristics of smooth-channel (without enhancement) heat exchangers with effective analogs provide new results, confirming the high efficiency of vortex enhancement of convective heat transfer in non-circular ducts of plate-finned heat exchange surfaces. This allows creating heat exchangers with much smaller mass and volume for operation in energy-saving modes.

Anomalous scaling of a passive scalar advected by the Navier-Stokes velocity field: two-loop approximation.

PubMed

Adzhemyan, L Ts; Antonov, N V; Honkonen, J; Kim, T L

2005-01-01

The field theoretic renormalization group and operator-product expansion are applied to the model of a passive scalar quantity advected by a non-Gaussian velocity field with finite correlation time. The velocity is governed by the Navier-Stokes equation, subject to an external random stirring force with the correlation function proportional to delta(t- t')k(4-d-2epsilon). It is shown that the scalar field is intermittent already for small epsilon, its structure functions display anomalous scaling behavior, and the corresponding exponents can be systematically calculated as series in epsilon. The practical calculation is accomplished to order epsilon2 (two-loop approximation), including anisotropic sectors. As for the well-known Kraichnan rapid-change model, the anomalous scaling results from the existence in the model of composite fields (operators) with negative scaling dimensions, identified with the anomalous exponents. Thus the mechanism of the origin of anomalous scaling appears similar for the Gaussian model with zero correlation time and the non-Gaussian model with finite correlation time. It should be emphasized that, in contrast to Gaussian velocity ensembles with finite correlation time, the model and the perturbation theory discussed here are manifestly Galilean covariant. The relevance of these results for real passive advection and comparison with the Gaussian models and experiments are briefly discussed.

Modeling effects of moisture content and advection on odor causing VOCs volatilization from stored swine manure.

PubMed

Liao, C M; Liang, H M

2000-05-01

Two models for evaluating the contents and advection of manure moisture on odor causing volatile organic compounds (VOC-odor) volatilization from stored swine manure were studied for their ability to predict the volatilization rate (indoor air concentration) and cumulative exposure dose: a MJ-I model and a MJ-II model. Both models simulating depletion of source contaminant via volatilization and degradation based on an analytical model adapted from the behavior assessment model of Jury et al. In the MJ-I model, manure moisture movement was negligible, whereas in the MJ-II model, time-dependent indoor air concentrations was a function of constant manure moisture contents and steady-state moisture advection. Predicted indoor air concentrations and inhaled doses for the study VOC-odors of p-cresol, toluene, and p-xylene varied by up to two to three orders of magnitude depending on the manure moisture conditions. The sensitivity analysis of both models suggests that when manure moisture movement exists, simply MJ-I model is inherently not sufficient to represent a more generally volatilization process, which can even become stringent as moisture content increases. The conclusion illustrates how one needs to include a wide variety of manure moisture values in order to fully assess the complex volatilization mechanisms that are present in a real situation.

Traveling-wave device with mass flux suppression

DOEpatents

Swift, Gregory W.; Backhaus, Scott N.; Gardner, David L.

2000-01-01

A traveling-wave device is provided with the conventional moving pistons eliminated. Acoustic energy circulates in a direction through a fluid within a torus. A side branch may be connected to the torus for transferring acoustic energy into or out of the torus. A regenerator is located in the torus with a first heat exchanger located on a first side of the regenerator downstream of the regenerator relative to the direction of the circulating acoustic energy; and a second heat exchanger located on an upstream side of the regenerator. The improvement is a mass flux suppressor located in the torus to minimize time-averaged mass flux of the fluid. In one embodiment, the device further includes a thermal buffer column in the torus to thermally isolate the heat exchanger that is at the operating temperature of the device.

Using operational active remote sensing devices to detect Saharan dust advections and evaluate their contribution to the PM10 levels: The EU LIFE+ "DIAPASON" project

NASA Astrophysics Data System (ADS)

Gobbi, Gian Paolo; Wille, Holger; Sozzi, Roberto; Barnaba, Francesca; Costabile, Francesca; Angelini, Federico; Frey, Steffen; Bolignano, Andrea; Morelli, Matteo

2013-04-01

The contribution of Saharan-dust advections to both daily and annual PM average mass concentrations can be significant all over Southern Europe. The Directive 2008/50/EC allows subtraction of PM10 exceedances caused by natural contributions from the statistic used to determine air-quality levels in Europe. To this purpose, the Commission Staff Working Paper 6771/11 (EC, 2011) provides specific Guidelines on methods to quantify and subtract the contribution of these sources in the framework of the Air Quality Directive. For Saharan dust, the EC methodology is largely based on a thorough analysis performed over the Iberian Peninsula (Escudero et al, 2007), although revision of the current methodology is in progress. In line with the EC Guidelines, the DIAPASON project ("Desert-dust Impact on Air quality through model-Predictions and Advanced Sensors ObservatioNs"), funded under the EC LIFE+ program, has been formulated to provide a robust, user-oriented, and demonstrated method to assess the presence of desert dust and evaluate its contribution to PM10 levels at the monitoring sites. To this end, in addition to satellite-based data and model forecasts already included in the EC Guidelines, DIAPASON will take advantage, in both the Project implementation and demonstration phase, of innovative and affordable technologies (partly prototyped within the project itself), namely operational Polarization Lidar-Ceilometers (PLC) capable of detecting and profiling dust clouds from the ground up to 10 km altitude. The PLC prototypes have been already finalized during the initial phase of the Project. Three of them will be networked in relevant air quality monitoring stations located in the Rome metropolitan area (Italy) during the DIAPASON observational phase (one-year long field campaign) starting in March 2013. The Rome region was chosen as the DIAPASON pilot scale area since highly impacted by urban pollution and frequently affected by Saharan dust transport events. In fact

Advective transport of CO2 in permeable media induced by atmospheric pressure fluctuations: 2. Observational evidence under snowpacks

Treesearch

W. J. Massman; J. M. Frank

2006-01-01

Meadow and forest CO2 amounts sampled beneath an approximately meter deep (steady state) snowpack at a subalpine site in southern Rocky Mountains of Wyoming are observed to vary by nearly 200 ppm over periods ranging from 4 to 15 days. This work employs the model of periodic, pressure-induced, advective transport in permeable media developed in...

Automated measurement of respiratory gas exchange by an inert gas dilution technique

NASA Technical Reports Server (NTRS)

Sawin, C. F.; Rummel, J. A.; Michel, E. L.

1974-01-01

A respiratory gas analyzer (RGA) has been developed wherein a mass spectrometer is the sole transducer required for measurement of respiratory gas exchange. The mass spectrometer maintains all signals in absolute phase relationships, precluding the need to synchronize flow and gas composition as required in other systems. The RGA system was evaluated by comparison with the Douglas bag technique. The RGA system established the feasibility of the inert gas dilution method for measuring breath-by-breath respiratory gas exchange. This breath-by-breath analytical capability permits detailed study of transient respiratory responses to exercise.

Exact PDF equations and closure approximations for advective-reactive transport

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

Venturi, D.; Tartakovsky, Daniel M.; Tartakovsky, Alexandre M.

2013-06-01

Mathematical models of advection–reaction phenomena rely on advective flow velocity and (bio) chemical reaction rates that are notoriously random. By using functional integral methods, we derive exact evolution equations for the probability density function (PDF) of the state variables of the advection–reaction system in the presence of random transport velocity and random reaction rates with rather arbitrary distributions. These PDF equations are solved analytically for transport with deterministic flow velocity and a linear reaction rate represented mathematically by a heterog eneous and strongly-correlated random field. Our analytical solution is then used to investigate the accuracy and robustness of the recentlymore » proposed large-eddy diffusivity (LED) closure approximation [1]. We find that the solution to the LED-based PDF equation, which is exact for uncorrelated reaction rates, is accurate even in the presence of strong correlations and it provides an upper bound of predictive uncertainty.« less

Significance of Thermal Fluvial Incision and Bedrock Transfer due to Ice Advection on Greenland Ice Sheet Topography

NASA Astrophysics Data System (ADS)

Crozier, J. A.; Karlstrom, L.; Yang, K.

2017-12-01

Ice sheet surface topography reflects a complicated combination of processes that act directly upon the surface and that are products of ice advection. Using recently-available high resolution ice velocity, imagery, ice surface elevation, and bedrock elevation data sets, we seek to determine the domain of significance of two important processes - thermal fluvial incision and transfer of bedrock topography through the ice sheet - on controlling surface topography in the ablation zone. Evaluating such controls is important for understanding how melting of the GIS surface during the melt season may be directly imprinted in topography through supraglacial drainage networks, and indirectly imprinted through its contribution to basal sliding that affects bedrock transfer. We use methods developed by (Karlstrom and Yang, 2016) to identify supraglacial stream networks on the GIS, and use high resolution surface digital elevation models as well as gridded ice velocity and melt rate models to quantify surface processes. We implement a numerically efficient Fourier domain bedrock transfer function (Gudmundsson, 2003) to predict surface topography due to ice advection over bedrock topography obtained from radar. Despite a number of simplifying assumptions, the bedrock transfer function predicts the observed ice sheet surface in most regions of the GIS with ˜90% accuracy, regardless of the presence or absence of supraglacial drainage networks. This supports the hypothesis that bedrock is the most significant driver of ice surface topography on wavelengths similar to ice thickness. Ice surface topographic asymmetry on the GIS is common, with slopes in the direction of ice flow steeper than those faced opposite to ice flow, consistent with bedrock transfer theory. At smaller wavelengths, topography consistent with fluvial erosion by surface hydrologic features is evident. We quantify the effect of ice advection versus fluvial thermal erosion on supraglacial longitudinal stream

P39-T Analysis of Oligosaccharides by Capillary-Scale High-Performance Anion-Exchange Chromatography with Pulsed Amperometric Detection (CHPAEC-PAD) and On-Line Electrospray-Ionization Ion-Trap Mass Spectrometry (CHPAEC-ITMS)

PubMed Central

Bruggink, C.; Koeleman, C.; Barreto, V.; Lui, Y.; Pohl, C.; Ingendoh, A.; Wuhrer, M.; Hokke, C.; Deelder, A.

2007-01-01

High-pH anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD) is an established technique for selective separation and analysis of underivatized carbohydrates. The miniaturization of chromatographic techniques by means of capillary columns, and on-line coupling to mass spectrometry are critical to the further development of glycan analysis methods that are compatible with the current requirements in clinical settings. A system has been developed based on the Dionex BioLC equipped with a microbore gradient pump with PEEK flow splitter, a FAMOS micro autosampler, a modified electrochemical cell for on-line capillary PAD, and a capillary column (380 μm i.d.) packed with a new type of anion-exchange resin. This system operates with sensitivity in the low femtomol range. In addition, an on-line capillary desalter has been developed to allow direct coupling to the Bruker Esquire 3000 ion-trap mass spectrometer with electrospray ionization interface (ESI-IT-MS). Both systems have been evaluated using oligosaccharide standards as well as urine samples exhibiting various lysosomal oligosaccharide storage diseases. Initial data indicate that the robust and selective anion-exchange system, in combination with ESI-IT-MS for structure confirmation and analysis, provides a powerful platform that complements existing nano/capillary LC-MS methods for analytical determination of oligosaccharides in biological matrices.

Inter-annual variability of exchange processes at the outer Black Sea shelf

NASA Astrophysics Data System (ADS)

Shapiro, Georgy; Wobus, Fred; Yuan, Dongliang; Wang, Zheng

2014-05-01

The advection of cold water below the surface mixed layer has a significant role in shaping the properties of the Cold Intermediate Layer (CIL) in the Black Sea, and thus the horizontal redistribution of nutrients. The minimal temperature of the CIL in the southwest deep region of the sea in summer was shown to be lower than the winter surface temperature at the same location, indicating the horizontal advective nature of CIL formation in the area (Kolesnikov, 1953). In addition to advection in the deep area of the sea, the transport of cold waters from the northwest Black Sea shelf across the shelf break in winter was shown to contribute to the formation of the CIL (Filippov, 1968; Staneva and Stanev, 1997). However less is known of the exchanges between the CIL waters and the outer shelf areas in summer, when a surface mixed layer and the underlying seasonal thermocline are formed. Ivanov et al. (1997) suggested that the cross frontal exchange within the CIL is strongly inhibited, so that CIL waters formed in the deep sea (i.e. offshore of the Rim Current) do not replenish the CIL waters onshore of the Rim Current (also known as near-bottom shelf waters, or BSW), due to strong cross frontal gradients in potential vorticity (PV). To the contrary, Shapiro et al. (2011) analysed in-situ observations over the period of 1950-2001 and showed a high correlation between the CIL temperatures in the open sea and outer shelf. However, the statistical methods alone were not able to clearly establish the relation between the cause and the consequences. In this study we use a 3D numerical model of the Black Sea (NEMO-SHELF-BLS) to quantify the exchange of CIL waters between the open sea and the outer northwest Black Sea shelf and to assess its significance for the replenishment of BSW on the outer shelf. The model has a resolution of 1/16º latitude × 1/12º longitude and 33 levels in the vertical. In order to represent near-bottom processes better, the model uses a hybrid

Preliminary SP-100/Stirling Heat Exchanger Designs

NASA Astrophysics Data System (ADS)

Schmitz, Paul; Tower, Leonard; Dawson, Ronald; Blue, Brain; Dunn, Pat

1994-07-01

Analytic modeling of several heat exchanger concepts to couple the SP-100 nuclear reactor primary lithium loop and the Space Stirling Power Convertor(SSPC)was performed. Four 25 kWe SSPC's are used to produce the required 100 kW of electrical power. This design work focused on the interface between a single SSPC and the primary lithium loop. Manifolding to separate and collect the four channel flow was not modeled. This work modeled two separate types of heat exchanger interfaces (conductive coupling and radiative coupling) to explore their relative advantages and disadvantages. The minimum mass design of the conductively coupled concepts was 18 kg or 0.73 kg/kWe for a single 25 kWe convertor. The minimum mass radiatively coupled concept was 41 kg or 1.64 kg/kWe. The direct conduction heat exchanger provides a lighter weight system because of its ability to operate the Stirling convertor evaporator at higher heat fluxes than those attainable by the radiatively coupled systems. Additionally the conductively coupled concepts had relatively small volumes and provide potentially simpler assembly. Their disadvantages were the tight tolerances and material joining problems associated with this refractory to superalloy interface. The advantages of the radiatively coupled designs were the minimal material interface problems.

Preliminary SP-100/Stirling heat exchanger designs

NASA Astrophysics Data System (ADS)

Schmitz, Paul; Tower, Leonard; Dawson, Ronald; Blue, Brian; Dunn, Pat

1993-12-01

Analytic modeling of several heat exchanger concepts to couple the SP-100 nuclear reactor primary lithium loop and the Space Stirling Power Convertor (SSPC) was performed. Four 25 kWe SSPC's are used to produce the required 100 kW of electrical power. This design work focused on the interface between a single SSPC and the primary lithium loop. Manifolding to separate and collect the four channel flow was not modeled. This work modeled two separate types of heat exchanger interfaces (conductive coupling and radiative coupling) to explore their relative advantages and disadvantages. The minimum mass design of the conductively coupled concepts was 18 kg or 0.73 kg/kWe for a single 25 kWe convertor. The minimum mass radiatively coupled concept was 41 kg or 1.64 kg/kWe. The direct conduction heat exchanger provides a lighter weight system because of its ability to operate the Stirling convertor evaporator at higher heat fluxes than those attainable by the radiatively coupled systems. Additionally the conductively coupled concepts had relatively small volumes and provide potentially simpler assembly. Their disadvantages were the tight tolerances and material joining problems associated with this refractory to superalloy interface. The advantages of the radiatively coupled designs were the minimal material interface problems.

Preliminary SP-100/Stirling heat exchanger designs

NASA Technical Reports Server (NTRS)

Schmitz, Paul; Tower, Leonard; Dawson, Ronald; Blue, Brian; Dunn, Pat

1993-01-01

Analytic modeling of several heat exchanger concepts to couple the SP-100 nuclear reactor primary lithium loop and the Space Stirling Power Convertor (SSPC) was performed. Four 25 kWe SSPC's are used to produce the required 100 kW of electrical power. This design work focused on the interface between a single SSPC and the primary lithium loop. Manifolding to separate and collect the four channel flow was not modeled. This work modeled two separate types of heat exchanger interfaces (conductive coupling and radiative coupling) to explore their relative advantages and disadvantages. The minimum mass design of the conductively coupled concepts was 18 kg or 0.73 kg/kWe for a single 25 kWe convertor. The minimum mass radiatively coupled concept was 41 kg or 1.64 kg/kWe. The direct conduction heat exchanger provides a lighter weight system because of its ability to operate the Stirling convertor evaporator at higher heat fluxes than those attainable by the radiatively coupled systems. Additionally the conductively coupled concepts had relatively small volumes and provide potentially simpler assembly. Their disadvantages were the tight tolerances and material joining problems associated with this refractory to superalloy interface. The advantages of the radiatively coupled designs were the minimal material interface problems.

Lagrangian Modeling of Arctic Ocean Circulation Pathways: Impact of Advection on Spread of Pollutants

NASA Astrophysics Data System (ADS)

Kelly, S.; Popova, E.; Aksenov, Y.; Marsh, R.; Yool, A.

2018-04-01

Sea-ice-free summers are projected to become a prominent feature of the Arctic environment in the coming decades. From a shipping perspective, this means larger areas of open water in the summer, thinner and less compact ice all year round, and longer operating seasons. Therefore, the possibility for easier navigation along trans-Arctic shipping routes arises. The Northern Sea Route (NSR) is one trans-Arctic route, and it offers a potential 10 day shortcut between Western Europe and the Far East. More ships transiting the NSR means an increased risk of an accident, and associated oil spill, occurring. Previous research suggests that current infrastructure is insufficient for increased shipping. Therefore, should an oil spill occur, the window for a successful clean-up will be short. In the event of a failed recovery, the long-term fate of the unrecovered pollutants must be considered, at least until the next melt season when it could become accessible again. Here we investigate the role of oceanic advection in determining the long-term fate of Arctic pollutants using a high-resolution ocean model along with Lagrangian particle-tracking to simulate the spread of pollutants. The resulting "advective footprints" of pollutants are proposed as an informative metric for analyzing such experiments. We characterize the circulation along different parts of the NSR, defining three main regions in the Eurasian Arctic, and relate the distinctive circulation pathways of each to the long-term fate of spilled oil. We conclude that a detailed understanding of ocean circulation is critical for determining the long-term fate of Arctic pollutants.

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

Advection in polar and sub-polar environments: Impacts on high latitude marine ecosystems

NASA Astrophysics Data System (ADS)

Hunt, George L.; Drinkwater, Kenneth F.; Arrigo, Kevin; Berge, Jørgen; Daly, Kendra L.; Danielson, Seth; Daase, Malin; Hop, Haakon; Isla, Enrique; Karnovsky, Nina; Laidre, Kristin; Mueter, Franz J.; Murphy, Eugene J.; Renaud, Paul E.; Smith, Walker O.; Trathan, Philip; Turner, John; Wolf-Gladrow, Dieter

2016-12-01

We compare and contrast the ecological impacts of atmospheric and oceanic circulation patterns on polar and sub-polar marine ecosystems. Circulation patterns differ strikingly between the north and south. Meridional circulation in the north provides connections between the sub-Arctic and Arctic despite the presence of encircling continental landmasses, whereas annular circulation patterns in the south tend to isolate Antarctic surface waters from those in the north. These differences influence fundamental aspects of the polar ecosystems from the amount, thickness and duration of sea ice, to the types of organisms, and the ecology of zooplankton, fish, seabirds and marine mammals. Meridional flows in both the North Pacific and the North Atlantic oceans transport heat, nutrients, and plankton northward into the Chukchi Sea, the Barents Sea, and the seas off the west coast of Greenland. In the North Atlantic, the advected heat warms the waters of the southern Barents Sea and, with advected nutrients and plankton, supports immense biomasses of fish, seabirds and marine mammals. On the Pacific side of the Arctic, cold waters flowing northward across the northern Bering and Chukchi seas during winter and spring limit the ability of boreal fish species to take advantage of high seasonal production there. Southward flow of cold Arctic waters into sub-Arctic regions of the North Atlantic occurs mainly through Fram Strait with less through the Barents Sea and the Canadian Archipelago. In the Pacific, the transport of Arctic waters and plankton southward through Bering Strait is minimal. In the Southern Ocean, the Antarctic Circumpolar Current and its associated fronts are barriers to the southward dispersal of plankton and pelagic fishes from sub-Antarctic waters, with the consequent evolution of Antarctic zooplankton and fish species largely occurring in isolation from those to the north. The Antarctic Circumpolar Current also disperses biota throughout the Southern Ocean

Enhanced transpiration by riparian buffer trees in response to advection in a humid temperate agricultural landscape

USGS Publications Warehouse

Hernandez-Santana, V.; Asbjornsen, H.; Sauer, T.; Isenhart, T.; Schilling, K.; Schultz, Ronald

2011-01-01

Riparian buffers are designed as management practices to increase infiltration and reduce surface runoff and transport of sediment and nonpoint source pollutants from crop fields to adjacent streams. Achieving these ecosystem service goals depends, in part, on their ability to remove water from the soil via transpiration. In these systems, edges between crop fields and trees of the buffer systems can create advection processes, which could influence water use by trees. We conducted a field study in a riparian buffer system established in 1994 under a humid temperate climate, located in the Corn Belt region of the Midwestern U.S. (Iowa). The goals were to estimate stand level transpiration by the riparian buffer, quantify the controls on water use by the buffer system, and determine to what extent advective energy and tree position within the buffer system influence individual tree transpiration rates. We primarily focused on the water use response (determined with the Heat Ratio Method) of one of the dominant species (Acer saccharinum) and a subdominant (Juglans nigra). A few individuals of three additional species (Quercus bicolor, Betula nigra, Platanus occidentalis) were monitored over a shorter time period to assess the generality of responses. Meteorological stations were installed along a transect across the riparian buffer to determine the microclimate conditions. The differences found among individuals were attributed to differences in species sap velocities and sapwood depths, location relative to the forest edge and prevailing winds and canopy exposure and dominance. Sapflow rates for A. saccharinum trees growing at the SE edge (prevailing winds) were 39% greater than SE interior trees and 30% and 69% greater than NW interior and edge trees, respectively. No transpiration enhancement due to edge effect was detected in the subdominant J. nigra. The results were interpreted as indicative of advection effects from the surrounding crops. Further, significant

Development of mass measurement equipment using an electronic mass-comparator for gravimetric preparation of reference gas mixtures

NASA Astrophysics Data System (ADS)

Matsumoto, Nobuhiro; Watanabe, Takuro; Maruyama, Masaaki; Horimoto, Yoshiyuki; Maeda, Tsuneaki; Kato, Kenji

2004-06-01

The gravimetric method is the most popular method for preparing reference gas mixtures with high accuracy. We have designed and manufactured novel mass measurement equipment for gravimetric preparation of reference gas mixtures. This equipment consists of an electronic mass-comparator with a maximum capacity of 15 kg and readability of 1 mg and an automatic cylinder exchanger. The structure of this equipment is simpler and the cost is much lower than a conventional mechanical knife-edge type large balance used for gravimetric preparation of primary gas mixtures in Japan. This cylinder exchanger can mount two cylinders alternatively on the weighing pan of the comparator. In this study, the performance of the equipment has been evaluated. At first, the linearity and repeatability of the mass measurement were evaluated using standard mass pieces. Then, binary gas mixtures of propane and nitrogen were prepared and compared with those prepared with the conventional knife-edge type balance. The comparison resulted in good consistency at the compatibility criterion described in ISO6143:2001.

Advective and Conductive Heat Flow Budget Across the Wagner Basin, Northern Gulf of California

NASA Astrophysics Data System (ADS)

Neumann, F.; Negrete-Aranda, R.; Contreras, J.; Müller, C.; Hutnak, M.; Gonzalez-Fernandez, A.; Harris, R. N.; Sclater, J. G.

2015-12-01

In May 2015, we conducted a cruise across the northern Gulf of California, an area of continental rift basin formation and rapid deposition of sediments. The cruise was undertaken aboard the R/V Alpha Helix; our goal was to study variation in superficial conductive heat flow, lateral changes in the shallow thermal conductivity structure, and advective transport of heat across the Wagner basin. We used a Fielax heat flow probe with 22 thermistors that can penetrate up to 6 m into the sediment cover. The resulting data set includes 53 new heat flow measurements collected along three profiles. The longest profile (42 km) contains 30 measurements spaced 1-2 km apart. The western part of the Wagner basin (hanging wall block) exhibit low to normal conductive heat flow whereas the eastern part of the basin (foot wall block) heat flow is high to very high (up to 2500 mWm-2). Two other short profiles (12 km long each) focused on resolving an extremely high heat flow anomaly up to 15 Wm-2 located near the intersection between the Wagner bounding fault system and the Cerro Prieto fault. We hypothesize that the contrasting heat flow values observed across the Wagner basin are due to horizontal water circulation through sand layers and fault pathways of high permeability. Circulation appears to be from west (recharge zone) to east (discharge zone). Additionally, our results reveal strong vertical advection of heat due to dehydration reactions and compaction of fine grained sediments.

Temporal evolution of photon energy emitted from two-component advective flows: origin of time lag

NASA Astrophysics Data System (ADS)

Chatterjee, Arka; Chakrabarti, Sandip K.; Ghosh, Himadri

2017-12-01

X-ray time lag of black hole candidates contains important information regarding the emission geometry. Recently, study of time lags from observational data revealed very intriguing properties. To investigate the real cause of this lag behavior with energy and spectral states, we study photon paths inside a two-component advective flow (TCAF) which appears to be a satisfactory model to explain the spectral and timing properties. We employ the Monte Carlo simulation technique to carry out the Comptonization process. We use a relativistic thick disk in Schwarzschild geometry as the CENtrifugal pressure supported BOundary Layer (CENBOL) which is the Compton cloud. In TCAF, this is the post-shock region of the advective component. Keplerian disk on the equatorial plane which is truncated at the inner edge i.e. at the outer boundary of the CENBOL, acts as the soft photon source. Ray-tracing code is employed to track the photons to a distantly located observer. We compute the cumulative time taken by a photon during Comptonization, reflection and following the curved geometry on the way to the observer. Time lags between various hard and soft bands have been calculated. We study the variation of time lags with accretion rates, CENBOL size and inclination angle. Time lags for different energy channels are plotted for different inclination angles. The general trend of variation of time lag with QPO frequency and energy as observed in satellite data is reproduced.

Cloud Microphysics Budget in the Tropical Deep Convective Regime

NASA Technical Reports Server (NTRS)

Li, Xiao-Fan; Sui, C.-H.; Lau, K.-M.; Einaudi, Franco (Technical Monitor)

2001-01-01

Cloud microphysics budgets in the tropical deep convective regime are analyzed based on a 2-D cloud resolving simulation. The model is forced by the large-scale vertical velocity and zonal wind and large-scale horizontal advections derived from TOGA COARE for a 20-day period. The role of cloud microphysics is first examined by analyzing mass-weighted mean heat budget and column-integrated moisture budget. Hourly budgets show that local changes of mass-weighted mean temperature and column-integrated moisture are mainly determined by the residuals between vertical thermal advection and latent heat of condensation and between vertical moisture advection and condensation respectively. Thus, atmospheric thermodynamics depends on how cloud microphysical processes are parameterized. Cloud microphysics budgets are then analyzed for raining conditions. For cloud-vapor exchange between cloud system and its embedded environment, rainfall and evaporation of raindrop are compensated by the condensation and deposition of supersaturated vapor. Inside the cloud system, the condensation of supersaturated vapor balances conversion from cloud water to raindrop, snow, and graupel through collection and accretion processes. The deposition of supersaturated vapor balances conversion from cloud ice to snow through conversion and riming processes. The conversion and riming of cloud ice and the accretion of cloud water balance conversion from snow to graupel through accretion process. Finally, the collection of cloud water and the melting of graupel increase raindrop to compensate the loss of raindrop due to rainfall and the evaporation of raindrop.

Analysing hyporheic exchange processes during unsteady flow in a small gravel bed river

NASA Astrophysics Data System (ADS)

Kurtenbach, Andreas; Schuetz, Tobias; Krein, Andreas; Bierl, Reinhard

2017-04-01

Quantifying hyporheic exchange in gravel dominated rivers still remains a challenging task in stream ecology and hydrology, in particular during unsteady flow. We adopted three strategies to decipher exchange processes with the hyporheic zone during unsteady boundary conditions. First, artificial floods were generated in the mid-mountain gravel bed river system of the Olewiger Bach, Germany (24 km2). The advantage of the artificial flood approach lies in the selective control of governing processes by experimental design. Consequently, hydraulic boundary conditions such as maximum discharge, runoff volume and flood duration are steerable during the field experiments and the composition of the discharged water (e.g. low conductivity values) is known. Second, hyporheic exchange was analysed via heat dynamics using air, water and sediment pore water temperatures. Temperature dynamics in the hyporheic zone were monitored at the head, mid and tail of a riffle using specific lances (length: 67 cm, Ø: 3cm) containing temperature sensors in depths of 2, 5, 10, 15, 25, 45 and 65 cm. Short-term temperature variability during the unsteady artificial flood waves were analysed in high resolution of 10-30 seconds. In order to capture long-term seasonal fluctuations and dynamics during natural floods temperature was continuously measured at 5-min resolution. However, heat transfer in the hyporheic zone is affected by both advective and conductive transport. In a third strategy we therefore measure electrical conductivity and selected solutes in pore water during three artificial floods in 2015. Pore water was sampled from different sediment depths (5, 15, 25 and 45 cm) via stainless steel multilevel probes (length: 58 cm, Ø: 4cm). The investigation of temperature and pore water dynamics reveals that precedent hydrological conditions and ground-water levels are significant determinants for hyporheic exchange during unsteady flow. Stable groundwater stratification in spring for

Winter to Spring Transition in Europe 48-45 degrees N: From Temperature Control by Advection to Control by Insolation

NASA Technical Reports Server (NTRS)

Otterman, J.; Ardizzone, J.; Atlas, R.; Hu, H.; Jusem, J. C.; Starr, D.

1999-01-01

As established in previous studies, and analyzed further herein for the years 1988-1998, warm advection from the North Atlantic is the predominant control of the surface-air temperature in northern-latitude Europe in late winter. This thesis is supported by the substantial correlation Cti between the speed of the southwesterly surface winds over the eastern North Atlantic, as quantified by a specific Index Ina, and the 2-meter level temperature Ts over central Europe (48-54 deg N; 5-25 deg E), for January, February and early March. In mid-March and subsequently, the correlation Cti drops drastically (quite often it is negative). The change in the relationship between Ts and Ina marks a transition in the control of the surface-air temperature. As (a) the sun rises higher in the sky, (b) the snows melt (the surface absorptivity can increase by a factor of 3.0), (c) the ocean-surface winds weaken, and (d) the temperature difference between land and ocean (which we analyze) becomes small, absorption of insolation replaces the warm advection as the dominant control of the continental temperature. We define the onset of spring by this transition, which evaluated for the period of our study occurs at pentad 16 (Julian Date 76, that is, March 16). The control by insolation means that the surface is cooler under cloudy conditions than under clear skies. This control produces a much smaller interannual variability of the surface temperature and of the lapse rate than prevailing in winter, when the control is by advection. Regional climatic data would be of greatest value for agriculture and forestry if compiled for well-defined seasons. For continental northern latitudes, analysis presented here of factors controlling the surface temperature appears an appropriate tool for this task.

Budget analysis of Escherichia coli at a southern Lake Michigan Beach

USGS Publications Warehouse

Thupaki, P.; Phanikumar, M.S.; Beletsky, D.; Schwab, D.J.; Nevers, M.B.; Whitman, R.L.

2010-01-01

Escherichia coli (EC) concentrations at two beaches impacted by river plume dynamics in southern Lake Michigan were analyzed using three-dimensional hydrodynamic and transport models. The relative importance of various physical and biological processes influencing the fate and transport of EC were examined via budget analysis and a first-order sensitivity analysis of model parameters. The along-shore advective fluxofEC(CFU/m2·s)was found to be higher compared to its crossshore counterpart; however, the sum of diffusive and advective components was of a comparable magnitude in both directions showing the importance of cross-shore exchange in EC transport. Examination of individual terms in the EC mass balance equation showed that vertical turbulent mixing in the water column dominated the overall EC transport for the summer conditions simulated. Dilution due to advection and diffusion accounted for a large portion of the total EC budget in the nearshore, and the net EC loss rate within the water column (CFU/m3·s) was an order of magnitude smaller compared to the horizontal and vertical transport rates. This result has important implications for modeling EC at recreational beaches; however, the assessment of the magnitude of EC loss rate is complicated due to the strong coupling between vertical exchange and depth-dependent EC loss processes such as sunlight inactivation and settling. Sensitivity analysis indicated that solar inactivation has the greatest impact on EC loss rates. Although these results are site-specific, they clearly bring out the relative importance of various processes involved.

Analytical solutions for benchmarking cold regions subsurface water flow and energy transport models: one-dimensional soil thaw with conduction and advection

USGS Publications Warehouse

Kurylyk, Barret L.; McKenzie, Jeffrey M; MacQuarrie, Kerry T. B.; Voss, Clifford I.

2014-01-01

Numerous cold regions water flow and energy transport models have emerged in recent years. Dissimilarities often exist in their mathematical formulations and/or numerical solution techniques, but few analytical solutions exist for benchmarking flow and energy transport models that include pore water phase change. This paper presents a detailed derivation of the Lunardini solution, an approximate analytical solution for predicting soil thawing subject to conduction, advection, and phase change. Fifteen thawing scenarios are examined by considering differences in porosity, surface temperature, Darcy velocity, and initial temperature. The accuracy of the Lunardini solution is shown to be proportional to the Stefan number. The analytical solution results obtained for soil thawing scenarios with water flow and advection are compared to those obtained from the finite element model SUTRA. Three problems, two involving the Lunardini solution and one involving the classic Neumann solution, are recommended as standard benchmarks for future model development and testing.

Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation

NASA Astrophysics Data System (ADS)

Hamuro, Yoshitomo

2017-05-01

Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation.

Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation.

PubMed

Hamuro, Yoshitomo

2017-05-01

Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation. Graphical Abstract ᅟ.

KRAS G12C Drug Development: Discrimination between Switch II Pocket Configurations Using Hydrogen/Deuterium-Exchange Mass Spectrometry

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

Lu, Jia; Harrison, Rane A.; Li, Lianbo

KRAS G12C, the most common RAS mutation found in non-small-cell lung cancer, has been the subject of multiple recent covalent small-molecule inhibitor campaigns including efforts directed at the guanine nucleotide pocket and separate work focused on an inducible pocket adjacent to the switch motifs. Multiple conformations of switch II have been observed, suggesting that switch II pocket (SIIP) binders may be capable of engaging a range of KRAS conformations. Here we report the use of hydrogen/deuterium-exchange mass spectrometry (HDX MS) to discriminate between conformations of switch II induced by two chemical classes of SIIP binders. We investigated the structural basismore » for differences in HDX MS using X-ray crystallography and discovered a new SIIP configuration in response to binding of a quinazoline chemotype. These results have implications for structure-guided drug design targeting the RAS SIIP.« less

System for exchanging tools and end effectors on a robot

DOEpatents

Burry, David B.; Williams, Paul M.

1991-02-19

A system and method for exchanging tools and end effectors on a robot permits exchange during a programmed task. The exchange mechanism is located off the robot, thus reducing the mass of the robot arm and permitting smaller robots to perform designated tasks. A simple spring/collet mechanism mounted on the robot is used which permits the engagement and disengagement of the tool or end effector without the need for a rotational orientation of the tool to the end effector/collet interface. As the tool changing system is not located on the robot arm no umbilical cords are located on robot.

System for exchanging tools and end effectors on a robot

DOEpatents

Burry, D.B.; Williams, P.M.

1991-02-19

A system and method for exchanging tools and end effectors on a robot permits exchange during a programmed task. The exchange mechanism is located off the robot, thus reducing the mass of the robot arm and permitting smaller robots to perform designated tasks. A simple spring/collet mechanism mounted on the robot is used which permits the engagement and disengagement of the tool or end effector without the need for a rotational orientation of the tool to the end effector/collet interface. As the tool changing system is not located on the robot arm no umbilical cords are located on robot. 12 figures.

Sea breezes and advective effects in southwest James Bay

NASA Technical Reports Server (NTRS)

Mckendry, Ian; Roulet, Nigel

1994-01-01

Observations from a transect extending 100 km inland during the Northern Wetlands Study (NOWES) in 1990 show that the sea breeze develops on approximately 25% of days during summer and may penetrate up to 100 km inland on occasions. The sea breeze exhibits a marked diurnal clockwise rotation as a result of the Coriolis effect along the unobstructed coastline. The marine advective effect is shown to depend on gradient wind direction. With northwesterly upper level flow the sea breeze tends to be northeasterly in direction and is associated with decreased temperatures and vapor pressure deficits (VPD). With southwesterly upper level flow the sea breeze tends to have a southeasterly direction and less effect on temperatures and VPD. This is attributed to shorter residence times of air parcels over water. For two cases, Colorado State University mesoscale model simulations show good agreement with surface wind observations and suggest that under northwesterly gradient flow, Bowen ratios are increased in the onshore flow along western James Bay, while during southwesterly gradient flow these effects are negligible. These results have implications for the interpretation of local climate, ecology, and hydrology as well as land-based and airborne turbulent flux measurements made during NOWES.

Use of deuterium labeling by high-temperature solid-state hydrogen-exchange reaction for mass spectrometric analysis of bradykinin biotransformation.

PubMed

Kopylov, Arthur T; Myasoedov, Nikolay F; Dadayan, Alexander K; Zgoda, Victor G; Medvedev, Alexei E; Zolotarev, Yurii A

2016-06-15

Studies of molecular biodegradation by mass spectrometry often require synthetic compounds labeled with stable isotopes as internal standards. However, labeling is very expensive especially when a large number of compounds are needed for analysis of biotransformation. Here we describe an approach for qualitative and quantitative analysis using bradykinin (BK) and its in vitro degradation metabolites as an example. Its novelty lies in the use of deuterated peptides which are obtained by a high-temperature solid-state exchange (HSCIE) reaction. Deuterated and native BK were analyzed by positive electrospray ionization high-resolution mass spectrometry (ESI-HRMS) using an Orbitrap Fusion mass spectrometer. High-energy collision-induced dissociation (HCD) experiments were performed on [M+H](+) and [M+2H](2+) ions in targeted-MS(2) mode with adjusted normalized HCD value. After the HSCIE reaction, each amino acid residue of the deuterated peptide contained deuterium atoms and the average degree of substitution was 5.5 atoms per the peptide molecule. The deuterated peptide demonstrated the same chromatographic mobility as the unlabeled counterpart, and lack of racemization during substitution with deuterium. Deuterium-labeled and unlabeled BKs were incubated with human plasma and their corresponding fragments BK(1-5) and BK(1-7), well known as the major metabolites, were detected. Quantitative assays demonstrated applicability of the heavy peptide for both sequencing and quantification of generated fragments. Applicability of the HSCIE deuterated peptide for analysis of routes of its degradation has been shown in in vitro experiments. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Experimental study of copper-alkali ion exchange in glass

NASA Astrophysics Data System (ADS)

Gonella, F.; Caccavale, F.; Bogomolova, L. D.; D'Acapito, F.; Quaranta, A.

1998-02-01

Copper-alkali ion exchange was performed by immersing different silicate glasses (soda-lime and BK7) in different molten eutectic salt baths (CuSO4:Na2SO4 and CuSO4:K2SO4). The obtained optical waveguides were characterized by m-lines spectroscopy for the determination of refractive index profiles, and by secondary ion mass spectrometry for the concentration profiles of the ion species involved in the exchange process. The different oxidation states of copper inside the glass structure were studied by electron paramagnetic resonance and x-ray absorption techniques. Interdiffusion copper coefficients were also determined. The Cu-alkali exchange was observed to give rise to local structural rearrangement of the atoms in the glass matrix. The Cu+ ion was found to mainly govern the exchange process, while competition between Cu-Na and K-Na exchanges occurred when a potassium sulfate bath was used. In this case, significant waveguide modal birefringence was observed.

Mapping the contact surfaces in the Lamin A:AIMP3 complex by hydrogen/deuterium exchange FT-ICR mass spectrometry.

PubMed

Tao, Yeqing; Fang, Pengfei; Kim, Sunghoon; Guo, Min; Young, Nicolas L; Marshall, Alan G

2017-01-01

Aminoacyl-tRNA synthetases-interacting multifunctional protein3 (AIMP3/p18) is involved in the macromolecular tRNA synthetase complex via its interaction with several aminoacyl-tRNA synthetases. Recent reports reveal a novel function of AIMP3 as a tumor suppressor by accelerating cellular senescence and causing defects in nuclear morphology. AIMP3 specifically mediates degradation of mature Lamin A (LmnA), a major component of the nuclear envelope matrix; however, the mechanism of how AIMP3 interacts with LmnA is unclear. Here we report solution-phase hydrogen/deuterium exchange (HDX) for AIMP3, LmnA, and AIMP3 in association with the LmnA C-terminus. Reversed-phase LC coupled with LTQ 14.5 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) results in high mass accuracy and resolving power for comparing the D-uptake profiles for AIMP3, LmnA, and their complex. The results show that the AIMP3-LmnA interaction involves one of the two putative binding sites and an adjacent novel interface on AIMP3. LmnA binds AIMP3 via its extreme C-terminus. Together these findings provide a structural insight for understanding the interaction between AIMP3 and LmnA in AIMP3 degradation.

Application of advection-diffusion routing model to flood wave propagation: A case study on Big Piney River, Missouri USA

Treesearch

Yang Yang; Theodore A. Endreny; David J. Nowak

2016-01-01

Flood wave propagation modeling is of critical importance to advancing water resources management and protecting human life and property. In this study, we investigated how the advection-diffusion routing model performed in flood wave propagation on a 16 km long downstream section of the Big Piney River, MO. Model performance was based on gaging station data at the...

SPEEDUP{trademark} ion exchange column model

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

Hang, T.

2000-03-06

A transient model to describe the process of loading a solute onto the granular fixed bed in an ion exchange (IX) column has been developed using the SpeedUp{trademark} software package. SpeedUp offers the advantage of smooth integration into other existing SpeedUp flowsheet models. The mathematical algorithm of a porous particle diffusion model was adopted to account for convection, axial dispersion, film mass transfer, and pore diffusion. The method of orthogonal collocation on finite elements was employed to solve the governing transport equations. The model allows the use of a non-linear Langmuir isotherm based on an effective binary ionic exchange process.more » The SpeedUp column model was tested by comparing to the analytical solutions of three transport problems from the ion exchange literature. In addition, a sample calculation of a train of three crystalline silicotitanate (CST) IX columns in series was made using both the SpeedUp model and Purdue University's VERSE-LC code. All test cases showed excellent agreement between the SpeedUp model results and the test data. The model can be readily used for SuperLig{trademark} ion exchange resins, once the experimental data are complete.« less

Global Warming, New Climate, New Atmospheric Circulation and New Water Cycle in North Africa

NASA Astrophysics Data System (ADS)

Karrouk, M. S.

2017-12-01

Atlantic ridge at Greenland, which imposes on the jet stream a positive ripple, very strongly marked poleward, bringing cosmic cold advection of polar air masses winter over from Europe to North Africa. Hence the enormous meridian heat exchanges north-south, and south-north.

Advection, dispersion, and filtration of fine particles within emergent vegetation of the Florida Everglades

USGS Publications Warehouse

Huang, Y.H.; Saiers, J.E.; Harvey, J.W.; Noe, G.B.; Mylon, S.

2008-01-01

The movement of particulate matter within wetland surface waters affects nutrient cycling, contaminant mobility, and the evolution of the wetland landscape. Despite the importance of particle transport in influencing wetland form and function, there are few data sets that illuminate, in a quantitative way, the transport behavior of particulate matter within surface waters containing emergent vegetation. We report observations from experiments on the transport of 1 ??m latex microspheres at a wetland field site located in Water Conservation Area 3A of the Florida Everglades. The experiments involved line source injections of particles inside two 4.8-m-long surface water flumes constructed within a transition zone between an Eleocharis slough and Cladium jamaicense ridge and within a Cladium jamaicense ridge. We compared the measurements of particle transport to calculations of two-dimensional advection-dispersion model that accounted for a linear increase in water velocities with elevation above the ground surface. The results of this analysis revealed that particle spreading by longitudinal and vertical dispersion was substantially greater in the ridge than within the transition zone and that particle capture by aquatic vegetation lowered surface water particle concentrations and, at least for the timescale of our experiments, could be represented as an irreversible, first-order kinetics process. We found generally good agreement between our field-based estimates of particle dispersion and water velocity and estimates determined from published theory, suggesting that the advective-dispersive transport of particulate matter within complex wetland environments can be approximated on the basis of measurable properties of the flow and aquatic vegetation. Copyright 2008 by the American Geophysical Union.

Toxic Alexandrium blooms in the western Gulf of Maine: The plume advection hypothesis revisited

USGS Publications Warehouse

Anderson, D.M.; Keafer, B.A.; Geyer, W.R.; Signell, R.P.; Loder, T.C.

2005-01-01

The plume advection hypothesis links blooms of the toxic dinoflagellate Alexandrium fundyense in the western Gulf of Maine (GOM) to a buoyant plume derived from river outflows. This hypothesis was examined with cruise and moored-instrument observations in 1993 when levels of paralytic shellfish poisoning (PSP) toxins were high, and in 1994 when toxicity was low. A coupled physical-biological model simulated hydrography and A. fundyense distributions. Initial A. fundyense populations were restricted to low-salinity nearshore waters near Casco Bay, but also occurred in higher salinity waters along the plume boundary. This suggests two sources of cells - those from shallow-water cyst populations and those transported to shore from offshore blooms in the eastern segment of the Maine coastal current (EMCC). Observations confirm the role of the plume in A. fundyense transport and growth. Downwelling-favorable winds in 1993 transported the plume and its cells rapidly alongshore, enhancing toxicity and propagating PSP to the south. In 1994, sustained upwelling moved the plume offshore, resulting in low toxicity in intertidal shellfish. A. fundyense blooms were likely nutrient limited, leading to low growth rates and moderate cell abundances. These observations and mechanisms were reproduced by coupled physical-biological model simulations. The plume advection hypothesis provides a viable explanation for outbreaks of PSP in the western GOM, but should be refined to include two sources for cells that populate the plume and two major pathways for transport: one within the low-salinity plume and another where A. fundyense cells originating in the EMCC are transported along the outer boundary of the plume front with the western segment of the Maine coastal current.

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.

Mass and tracer transport within oceanic Lagrangian coherent vortices as diagnosed in a global mesoscale eddying climate model

NASA Astrophysics Data System (ADS)

Tarshish, Nathaniel; Abernathey, Ryan; Dufour, Carolina; Frenger, Ivy; Griffies, Stephen

2017-04-01

Transient ocean mesoscale fluctuations play a central role in the global climate system, transporting climate relevant tracers such as heat and carbon. In satellite observations and numerical simulations, mesoscale vortices feature prominently as collectively rotating regions that remain visibly coherent. Prior studies on transport from ocean vortices typically rely on Eulerian identification methods, in which vortices are identified by selecting closed contours of Eulerian fields (e.g. sea surface height, or the Okubo-Weiss parameter) that satisfy geometric criteria and anomaly thresholds. In contrast, recent studies employ Lagrangian analysis of virtual particle trajectories initialized within the selected Eulerian contours, revealing significant discrepancies between the advection of the contour's material interior and the evolution of the Eulerian field contour. This work investigates the global mass and tracer transport associated with materially coherent surface ocean vortices. Further, it addresses differences between Eulerian and Lagrangian analyses for the detection of vortices. To do so, we use GFDL's CM2.6 coupled climate model with 5-10km horizontal grid spacing. We identify coherent vortices in CM2.6 by implementing the Rotationally Coherent Lagrangian Vortex (RCLV) framework, which recently emerged from dynamical systems theory. This approach involves the numerical advection of millions of Lagrangian particles and guarantees material coherence by construction. We compute the statistics, spatial distribution, and lifetimes of coherent vortices in addition to calculating the associated mass and tracer transports. We offer compelling evidence that Eulerian vortex methods are poorly suited to answer questions of mass and tracer transport.

Signature of Two-Component Advective Flow in several Black Hole candidates obtained through time-of-arrival analysis of RXTE/ASM Data

NASA Astrophysics Data System (ADS)

Ghosh, Arindam; Chakrabarti, Sandip K.

2018-05-01

We study several Galactic black hole candidates using long-time RXTE/ASM X-ray data to search for telltale signatures of differences in viscous timescales in the two components used in the Two-Component Advective Flow (TCAF) paradigm. In high-mass X-ray binaries (HMXBs) mainly winds are accreted. This nearly inviscid and dominant sub-Keplerian flow falls almost freely towards the black hole. A standard Keplerian disc can form out of this sub-Keplerian matter in presence of a significant viscosity and could be small in size. However, in low-mass X-ray binaries (LMXBs), highly viscous and larger Keplerian accretion disc is expected to form inside the sub-Keplerian disc due to the Roche-lobe overflow. Due to two viscous timescales in these two components, it is expected to have a larger lag between the times-of-arrival of these components in LMXBs than that in HMXBs. Direct cross-correlation between the photon fluxes will not reveal this lag since they lack linear dependence; however, they are coupled through the viscous processes which bring in both matter. To quantify the aforesaid time lag, we introduce an index (Θ), which is a proxy of the usual photon index (Γ). Thus, when Θ, being dynamically responsive to both fluxes, is considered as a reference, the arrival time lag between the two fluxes in LMXBs is found to be much larger than that in HMXBs. Our result establishes the presence of two dynamical components in accretion and shows that the Keplerian disc size indeed is smaller in HMXBs as compared to that in LMXBs.

A Stellar-mass Black Hole in the Ultra-luminous X-ray Source M82 X-1

NASA Technical Reports Server (NTRS)

Okajima, Takashi; Ebisawa, Ken; Kawaguchi, Toshihiro

2007-01-01

We have analyzed the archival XMM-Newton data of the archetypal Ultra-Luminous X-ray Source (ULX) M82 X-1 with an LO5 ksec exposure when the source was in the steady state. Thanks to the high photon statistics from the large effective area and long exposure, we were able to discriminate different X-ray continuum spectral models. Neither the standard accretion disk model (where the radial dependency of the disk effective temperature is T(r) proportional to r(sup -3/4)) nor a power-law model gives a satisfactory fit. In fact, observed curvature of the M82 X-1 spectrum was just between those of the two models. When the exponent of the radial dependence (p in T(r) proportional to r(sup -P)) of the disk temperature is allowed to be free, we obtained p = 0.61 (sup +0.03)(sub -0.02). Such a reduction of p from the standard value 3/4 under extremely high mass accretion rates is predicted from the accretion disk theory as a consequence of the radial energy advection. Thus, the accretion disk in M82 X-1 is considered to be in the Slim disk state, where an optically thick Advection Dominant Accretion Flow (ADAF) is taking place. We have applied a theoretical slim disk spectral model to M82 X-1, and estimated the black hole mass approximately equal to 19 - 32 solar mass. We conclude that M82 X-1 is a stellar black hole which has been produced through evolution of an extremely massive star, shining at a several times the super-Eddington luminosity.

Experimental study on heat transfer performance of fin-tube exchanger and PSHE for waste heat recovery

NASA Astrophysics Data System (ADS)

Chen, Ting; Bae, Kyung Jin; Kwon, Oh Kyung

2018-02-01

In this paper, heat transfer characteristics of fin-tube heat exchanger and primary surface heat exchanger (PSHE) used in waste heat recovery were investigated experimentally. The flow in the fin-tube heat exchanger is cross flow and in PSHE counter flow. The variations of friction factor and Colburn j factor with air mass flow rate, and Nu number with Re number are presented. Various comparison methods are used to evaluate heat transfer performance, and the results show that the heat transfer rate of the PSHE is on average 17.3% larger than that of fin-tube heat exchanger when air mass flow rate is ranging from 1.24 to 3.45 kg/min. However, the PSHE causes higher pressure drop, and the fin-tube heat exchanger has a wider application range which leads to a 31.7% higher value of maximum heat transfer rate compared to that of the PSHE. Besides, under the same fan power per unit frontal surface, a higher heat transfer rate value is given in the fin-tube heat exchanger.

Quasi-horizontal transport and mixing in the Antarctic stratosphre

NASA Technical Reports Server (NTRS)

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

1994-01-01

The quasi-horizontal transport and mixing properties of the Antarctic stratosphere are investigated with a simi-Lagrangian transport model and a 'contour advection' technique for the winter and spring of 1992 using analyzed winds from the United Kingdom Meteorological Office data assimiliation system. Transport calculations show that passive tracers are well mixed inside the polar vortex as well as in the midlatitude 'surf zone.' A the vortex edge, strong radial gradients in the tracer fields are well preserved, and their evolutions follow that of the potential vorticity until some time after the breakdown of the polar vortex. In the middle stratosphere there is little tracer exchange across the vortex edge in August and September. Some vortex air is eroded into the surf zone in filamentary form in October, and very strong exchange of air occurs between high and middle latitudes in November. In the lower stratosphere the vortex is not so isolated from the midlatitudes as in the middle stratosphere, and there is more mass exchange across the vortex edge. Calculations of the lengthening of material contours using the contour advection technique show that in the middle stratosphere, strong stirring (i.e., stretching and folding of material elements) occurs in the inner vortex, while the strongest stirring occurs in the midlatitude surf zone and the weakest occurs at the vortex edge. In the lower strtosphere, strong stirring occurs in the inner vortex. Stirring is moderate at the vortex edge and in the midlatitudes.

Surface water mass composition changes captured by cores of Arctic land-fast sea ice

NASA Astrophysics Data System (ADS)

Smith, I. J.; Eicken, H.; Mahoney, A. R.; Van Hale, R.; Gough, A. J.; Fukamachi, Y.; Jones, J.

2016-04-01

In the Arctic, land-fast sea ice growth can be influenced by fresher water from rivers and residual summer melt. This paper examines a method to reconstruct changes in water masses using oxygen isotope measurements of sea ice cores. To determine changes in sea water isotope composition over the course of the ice growth period, the output of a sea ice thermodynamic model (driven with reanalysis data, observations of snow depth, and freeze-up dates) is used along with sea ice oxygen isotope measurements and an isotopic fractionation model. Direct measurements of sea ice growth rates are used to validate the output of the sea ice growth model. It is shown that for sea ice formed during the 2011/2012 ice growth season at Barrow, Alaska, large changes in isotopic composition of the ocean waters were captured by the sea ice isotopic composition. Salinity anomalies in the ocean were also tracked by moored instruments. These data indicate episodic advection of meteoric water, having both lower salinity and lower oxygen isotopic composition, during the winter sea ice growth season. Such advection of meteoric water during winter is surprising, as no surface meltwater and no local river discharge should be occurring at this time of year in that area. How accurately changes in water masses as indicated by oxygen isotope composition can be reconstructed using oxygen isotope analysis of sea ice cores is addressed, along with methods/strategies that could be used to further optimize the results. The method described will be useful for winter detection of meteoric water presence in Arctic fast ice regions, which is important for climate studies in a rapidly changing Arctic. Land-fast sea ice effective fractionation coefficients were derived, with a range of +1.82‰ to +2.52‰. Those derived effective fractionation coefficients will be useful for future water mass component proportion calculations. In particular, the equations given can be used to inform choices made when

Pu Anion Exchange Process Intensification

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

Taylor-Pashow, Kathryn M. L.

This research is focused on improving the efficiency of the anion exchange process for purifying plutonium. While initially focused on plutonium, the technology could also be applied to other ion-exchange processes. Work in FY17 focused on the improvement and optimization of porous foam columns that were initially developed in FY16. These foam columns were surface functionalized with poly(4-vinylpyridine) (PVP) to provide the Pu specific anion-exchange sites. Two different polymerization methods were explored for maximizing the surface functionalization with the PVP. The open-celled polymeric foams have large open pores and large surface areas available for sorption. The fluid passes through themore » large open pores of this material, allowing convection to be the dominant mechanism by which mass transport takes place. These materials generally have very low densities, open-celled structures with high cell interconnectivity, small cell sizes, uniform cell size distributions, and high structural integrity. These porous foam columns provide advantages over the typical porous resin beads by eliminating the slow diffusion through resin beads, making the anion-exchange sites easily accessible on the foam surfaces. The best performing samples exceeded the Pu capacity of the commercially available resin, and also offered the advantage of sharper elution profiles, resulting in a more concentrated product, with less loss of material to the dilute heads and tails cuts. An alternate approach to improving the efficiency of this process was also explored through the development of a microchannel array system for performing the anion exchange.« less

Boundary layers at a dynamic interface: Air-sea exchange of heat and mass

NASA Astrophysics Data System (ADS)

Szeri, Andrew J.

2017-04-01

Exchange of mass or heat across a turbulent liquid-gas interface is a problem of critical interest, especially in air-sea transfer of natural and anthropogenic gases involved in the study of climate. The goal in this research area is to determine the gas flux from air to sea or vice versa. For sparingly soluble nonreactive gases, this is controlled by liquid phase turbulent velocity fluctuations that act on the thin species concentration boundary layer on the liquid side of the interface. If the fluctuations in surface-normal velocity w' and gas concentration c' are known, then it is possible to determine the turbulent contribution to the gas flux. However, there is no suitable fundamental direct approach in the general case where neither w' nor c' can be easily measured. A new approach is presented to deduce key aspects about the near-surface turbulent motions from measurements that can be taken by an infrared (IR) camera. An equation is derived with inputs being the surface temperature and heat flux, and a solution method developed for the surface-normal strain experienced over time by boundary layers at the interface. Because the thermal and concentration boundary layers experience the same near-surface fluid motions, the solution for the surface-normal strain determines the gas flux or gas transfer velocity. Examples illustrate the approach in the cases of complete surface renewal, partial surface renewal, and insolation. The prospects for use of the approach in flows characterized by sheared interfaces or rapid boundary layer straining are explored.

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 %.

[The relationship of the saturation density of multilayer cell cultures to their mass exchange with the medium].

PubMed

Akatov, V S; Lavrovskaia, V P

1991-01-01

Chinese hamster fibroblasts (CHF) and NIH 3T3 cells were cultured on a glass substrate at different distances from the porous membrane separating the cells from the perfusing medium. It is shown that with perfusion of medium above the membrane there is no movement of the medium near the cells. In both the types of culture, the cells grow in multilayers, however the multilayer character of growth in CHF is more pronounced than in NIH 3T3 cells. The saturation density of the cultures depends on the cell-membrane separation, and at separations of no more than 0.2 mm exceeds the saturation density in the monolayer by 8-10 fold. The dependences of the saturation density on separation are different for CHE and NIH 3T3 cells, indicating qualitative differences in the inhibition of cell growth in monolayers between these cultures. The results obtained indicate that the inhibition of cell growth in monolayer is due to mass exchange limitations, rather than to intercellular contact interactions.

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

PubMed

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

2014-06-02

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

Predicting Protein Aggregation during Storage in Lyophilized Solids Using Solid State Amide Hydrogen/Deuterium Exchange with Mass Spectrometric Analysis (ssHDX-MS)

PubMed Central

2015-01-01

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. PMID:24816133

Model unification and scale-adaptivity in the Eddy-Diffusivity Mass-Flux (EDMF) approach

NASA Astrophysics Data System (ADS)

Neggers, R.; Siebesma, P.

2011-12-01

It has long been understood that the turbulent-convective transport of heat, moisture and momentum plays an important role in the dynamics and climate of the earth's atmosphere. Accordingly, the representation of these processes in General Circulation Models (GCMs) has always been an active research field. Turbulence and convection act on temporal and spatial scales that are unresolved by most present-day GCMs, and have to be represented through parametric relations. Over the years a variety of schemes has been successfully developed. Although differing widely in their details, only two basic transport models stand at the basis of most of these schemes. The first is the diffusive transport model, which can only act down-gradient. An example is the turbulent mixing at small scales. The second is the advective transport model, which can act both down-gradient and counter-gradient. A good example is the transport of heat and moisture by convective updrafts that overshoot into stable layers of air. In practice, diffusive models often make use of a K-profile method or a prognostic TKE budget, while advective models make use of a rising (and entraining) plume budget. While most transport schemes classicaly apply either the diffusive model or advective model, the relatively recently introduced Eddy-Diffusivity Mass-Flux (EDMF) approach aims to combine both techniques. By applying advection and diffusion simultaneously, one can make use of the benefits of both approaches. Since its emergence about a decade ago, the EDMF approach has been successfully applied in both research and operational circulation models. This presentation is dedicated to the EDMF framework. Apart from a short introduction to the EDMF concept and a short overview of its current implementations, our main goal is to elaborate on the opportunities EDMF brings in addressing some long-standing problems in the parameterization of turbulent-convective transport. The first problem is the need for a unified

Coulombic interactions during advection-dominated transport of ions in porous media

NASA Astrophysics Data System (ADS)

Muniruzzaman, Muhammad; Stolze, Lucien; Rolle, Massimo

2017-04-01

Solute transport of charged species in porous media is significantly affected by the electrochemical migration term resulting from the charge-induced interactions among dissolved ions and with solid surfaces. Therefore, the characterization of such Coulombic interactions and their effect on multicomponent ionic transport is of critical importance for assessing the fate of charged solutes in porous media. In this work we present a detailed investigation of the electrochemical effects during conservative multicomponent ionic transport in homogeneous and heterogeneous domains by means of laboratory bench-scale experiments and numerical simulations. The investigation aims at quantifying the key role of small-scale electrostatic interactions in flow-through systems, especially when advection is the dominant mass-transfer process. Considering dilute solutions of strong electrolytes (e.g., MgCl2 and NaBr) we report results showing the important role of Coulombic interactions in the lateral displacement of the different ionic species for steady-state transport scenarios in which the solutions are continuously injected through different portions of the flow-through chamber [1, 2]. Successively, we focus our attention on transient transport and pulse injection of the electrolytes. In these experiments high-resolution spatial and temporal monitoring of the ions' concentrations (600 samples; 1800 concentration measurements), at closely spaced outlet ports (5 mm), allowed us resolving the effects of charge interactions on the temporal breakthrough and spatial profiles of the cations and anions [3]. The interpretation of the experimental results requires a multicomponent modeling approach with an accurate description of local hydrodynamic dispersion, as well as the explicit quantification of the dispersive fluxes' cross-coupling due to the Coulombic interactions between the charged species. A new 2-D simulator [4], coupling the solution of the multicomponent ionic transport

Complex Heat Exchangers for Improved Performance

NASA Astrophysics Data System (ADS)

Bran, Gabriela Alejandra

After a detailed literature review, it was determined that there was a need for a more comprehensive study on the transient behavior of heat exchangers. Computational power was not readily available when most of the work on transient heat exchangers was done (1956 - 1986), so most of these solutions have restrictions, or very specific assumptions. More recently, authors have obtained numerical solutions for more general problems (2003 - 2013), but they have investigated very specific conditions, and cases. For a more complex heat exchanger (i.e. with heat generation), the transient solutions from literature are no longer valid. There was a need to develop a numerical model that relaxes the restrictions of current solutions to explore conditions that have not been explored. A one dimensional transient heat exchanger model was developed. There are no restrictions on the fluids and wall conditions. The model is able to obtain a numerical solution for a wide range of fluid properties and mass flow rates. Another innovative characteristic of the numerical model is that the boundary and initial conditions are not limited to constant values. The boundary conditions can be a function of time (i.e. sinusoidal signal), and the initial conditions can be a function of position. Four different cases were explored in this work. In the first case, the start-up of a system was investigated where the whole system is assumed to be at the same temperature. In the second case, the new steady state in case one gets disrupted by a smaller inlet temperature step change. In the third case, the new steady state in case one gets disrupted by a step change in one of the mass flow rates. The response of these three cases show that there are different transient behaviors, and they depend on the conditions imposed on the system. The fourth case is a system that has a sinusoidal time varying inlet temperature for one of the flows. The results show that the sinusoidal behavior at the inlet

Passive advection of a vector field: Anisotropy, finite correlation time, exact solution, and logarithmic corrections to ordinary scaling

NASA Astrophysics Data System (ADS)

Antonov, N. V.; Gulitskiy, N. M.

2015-10-01

In this work we study the generalization of the problem considered in [Phys. Rev. E 91, 013002 (2015), 10.1103/PhysRevE.91.013002] to the case of finite correlation time of the environment (velocity) field. The model describes a vector (e.g., magnetic) field, passively advected by a strongly anisotropic turbulent flow. Inertial-range asymptotic behavior is studied by means of the field theoretic renormalization group and the operator product expansion. The advecting velocity field is Gaussian, with finite correlation time and preassigned pair correlation function. Due to the presence of distinguished direction n , all the multiloop diagrams in this model vanish, so that the results obtained are exact. The inertial-range behavior of the model is described by two regimes (the limits of vanishing or infinite correlation time) that correspond to the two nontrivial fixed points of the RG equations. Their stability depends on the relation between the exponents in the energy spectrum E ∝k⊥1 -ξ and the dispersion law ω ∝k⊥2 -η . In contrast to the well-known isotropic Kraichnan's model, where various correlation functions exhibit anomalous scaling behavior with infinite sets of anomalous exponents, here the corrections to ordinary scaling are polynomials of logarithms of the integral turbulence scale L .

Numerical Solution of a 3-D Advection-Dispersion Model for Dissolved Oxygen Distribution in Facultative Ponds

NASA Astrophysics Data System (ADS)

Sunarsih; Sasongko, Dwi P.; Sutrisno

2018-02-01

This paper describes a mathematical model for the dissolved oxygen distribution in the plane of a facultative pond with a certain depth. The purpose of this paper is to determine the variation of dissolved oxygen concentration in facultative ponds. The 3-dimensional advection-diffusion equation is solved using the finite difference method Forward Time Central Space (FTCS). Numerical results show that the aerator greatly affects the occurrence of oxygen concentration variations in the facultative pond in the certain depth. The concentration of dissolved oxygen decreases as the depth of the pond increases.

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

Synoptic Formation of Double Tropopauses

NASA Astrophysics Data System (ADS)

Liu, Chengji; Barnes, Elizabeth

2018-01-01

Double tropopauses are ubiquitous in the midlatitude winter hemisphere and represent the vertical stacking of two stable tropopause layers separated by a less stable layer. By analyzing COSMIC GPS data, reanalysis, and eddy life cycle simulations, we demonstrate that they often occur during Rossby wave breaking and act to increase the stratosphere-to-troposphere exchange of mass. We further investigate the adiabatic formation of double tropopauses and propose two mechanisms by which they can occur. The first mechanism operates at the tropopause break in the subtropics where the higher tropical tropopause sits on one side of the break and the lower extratropical tropopause sits on the other. The double tropopauses are then formed by differential meridional advection of the higher and lower tropopauses on the two sides of the tropopause break. We show that anticyclonic wave breaking can form double tropopauses mainly by providing stronger poleward advection of the higher tropopause in its poleward lobe. Cyclonic wave breaking mainly forms double tropopauses by providing stronger equatorward advection of the lower tropopause in its equatorward lobe. We demonstrate in the COSMIC GPS data and reanalysis that about half of the double tropopauses in the Northern Hemisphere winter can be directly attributed to such differential advection. For the second mechanism, adiabatic destabilization of the air above the tropopause contributes to the formation of a double tropopause. In this case, a tropopause inversion layer is necessary for this destabilization to result in a double tropopause.

Implementation of two-component advective flow solution in XSPEC

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

Passive advection-dispersion in networks of pipes: Effect of connectivity and relationship to permeability

NASA Astrophysics Data System (ADS)

Bernabé, Y.; Wang, Y.; Qi, T.; Li, M.

2016-02-01

The main purpose of this work is to investigate the relationship between passive advection-dispersion and permeability in porous materials presumed to be statistically homogeneous at scales larger than the pore scale but smaller than the reservoir scale. We simulated fluid flow through pipe network realizations with different pipe radius distributions and different levels of connectivity. The flow simulations used periodic boundary conditions, allowing monitoring of the advective motion of solute particles in a large periodic array of identical network realizations. In order to simulate dispersion, we assumed that the solute particles obeyed Taylor dispersion in individual pipes. When a particle entered a pipe, a residence time consistent with local Taylor dispersion was randomly assigned to it. When exiting the pipe, the particle randomly proceeded into one of the pipes connected to the original one according to probabilities proportional to the outgoing volumetric flow in each pipe. For each simulation we tracked the motion of at least 6000 solute particles. The mean fluid velocity was 10-3 ms-1, and the distance traveled was on the order of 10 m. Macroscopic dispersion was quantified using the method of moments. Despite differences arising from using different types of lattices (simple cubic, body-centered cubic, and face-centered cubic), a number of general observations were made. Longitudinal dispersion was at least 1 order of magnitude greater than transverse dispersion, and both strongly increased with decreasing pore connectivity and/or pore size variability. In conditions of variable hydraulic radius and fixed pore connectivity and pore size variability, the simulated dispersivities increased as power laws of the hydraulic radius and, consequently, of permeability, in agreement with previously published experimental results. Based on these observations, we were able to resolve some of the complexity of the relationship between dispersivity and permeability.

Advection from the North Atlantic as the Forcing of Winter Greenhouse Effect Over Europe

NASA Technical Reports Server (NTRS)

Otterman, Jay; Angell, J.; Atlas, Robert; Bungato, D.; Schubert, S.; Starr, D.; Susskind, J.; Wu, M.-L. C.

2001-01-01

In winter, large interannual fluctuations in the surface skin temperature are observed over central Europe: we observe a difference of 9.8 K comparing warm February 1990 with cold February 1996 for the region 50-60 degrees N; 5-35 degrees E. Previous studies show that advection from the North Atlantic constitutes the forcing to such fluctuations. The advection is quantified by Index I(sub na), the average of the ocean-surface wind speed over the eastern North Atlantic when the direction is from the southwest (when the wind is from another direction, it counts as a zero speed to the average). Average Ina for February 1990 was 10.6 in s(exp -1), but for February 1996 I(sub na) was only 2.4 m s(exp -1). A large value of I(sub na) means a strong southwesterly flow which brings warm and moist air into Europe at low level, producing a steeper tropospheric lapse rate. Strong ascending motions result, which we observe in February 1990 at 700 mb. The near-surface moisture rises to higher (and cooler) levels, producing clouds and precipitation. Total preciptable water and cloud-cover fraction have larger values in February 1990 than in 1996. The difference in the greenhouse effect between these two scenarios can be translated into a virtual irradiating source of 2.6 W m(exp -2) above the February 1990 atmosphere, which, as an order of magnitude estimate, contributes to the warming of the surface by 2.6 K. If we accept this estimate as numerically pertinent, the direct effect stands as 7.2 K (9.8 K - 2.6 K), and therefore its greenhouse-effect reinforcement is by 36%. This constitutes a substantial positive feedback to the direct effect, which is the inflow of warm air to the low troposphere over Europe.

Picophytoplankton variability: Influence of winter convective mixing and advection in the northeastern Arabian Sea

NASA Astrophysics Data System (ADS)

Bemal, Suchandan; Anil, Arga Chandrashekar; Shankar, D.; Remya, R.; Roy, Rajdeep

2018-04-01

The deepening of mixed layer and ensuing changes in optical and physicochemical properties of euphotic zone can influence phytoplankton community dynamics in the northeastern Arabian Sea during winter monsoon. The response of picophytoplankton community to such changes during winter convective mixing is not well understood. Herein, we have compared variations in the picophytoplankton community structure during early (November-December 2012), peak (end-January 2014) and late (mid-February 2015) winter monsoon from three separate cruises in the southern northeastern Arabian Sea. The higher Synechococcus abundance owing to entrainment of nutrients in mixed layer was observed during peak winter monsoon, while the concomitant changes in nitrate concentration, light and oxygen environment restricted Prochlorococcus growth resulting in lower abundance during the same period. This highlights the diverse responses of picophytoplankton groups to physicochemical changes of water column during winter convective mixing. The divinyl chlorophyll b/a ratio (marker for Prochlorococcus ecotypes) indicated prevalence of one low-light adapted ecotype (sensitive to light shock) in sub-surface water, one high-light adapted ecotype in surface water during early winter monsoon and both disappeared during intense mixing period in peak winter monsoon. Subsequently, a distinct low-light adapted ecotype, capable to tolerate light shock, was noticed during late winter monsoon and we argue that this ecotype is introduced to southern northeastern Arabian Sea through advection from north by sub-surface circulation. The total picophytoplankton biomass available to microbial loop is restored during late winter monsoon, when stratification begins, with a higher abundance of Synechococcus and the re-occurrence of Prochlorococcus population in the region. These inferences indicate that variability in picophytoplankton community structure and their contribution to the microbial loop are driven by

Ionic solubility and solutal advection governed augmented evaporation kinetics of salt solution pendant droplets

NASA Astrophysics Data System (ADS)

Jaiswal, Vivek; Harikrishnan, A. R.; Khurana, Gargi; Dhar, Purbarun

2018-01-01

The presence of dispersed inclusions is known to modify the interfacial characteristics in liquids by adsorption-desorption of the ions at interfaces. The present article reports the influencing role of dissolved ions in a polar fluid on its evaporation dynamics. The evaporation dynamics of pendant droplets of aqueous solutions of variant simple salts and concentrations have been experimentally studied. The presence of salts is observed to enhance the evaporation rate (obeying the classical D2 law), and the enhancement has been found to hold a direct proportionality to the concentration of the dissolved salt. Furthermore, it is observed that the degree of enhancement in the evaporation rate is also directly proportional to the solubility of the salt in question. The phenomenon is explained based on the chemical kinetics and thermodynamics of hydration of the ionic species in the polar fluid. The classical evaporation rate constant formulation is found to be inadequate in modeling the enhanced species transport. Additional probing via particle image velocimetry reveals augmented internal circulation within the evaporating salt based drops compared to pure water. Mapping the dynamic surface tension reveals that a salt concentration gradient is generated between the bulk and periphery of the droplet and it could be responsible for the internal advection cells visualized. A thermo-solutal Marangoni and Rayleigh convection based mathematical formulation has been put forward, and it is shown that the enhanced solute-thermal convection could play a major role in enhanced evaporation. The internal circulation mapped from experiments is found to be in good quantitative agreement with the model predictions. Scaling analysis further reveals that the stability of the solutal Marangoni convection surpasses the thermal counterpart with higher salt concentration and solubility. The present article sheds insight into the possible domineering role of conjugate thermohydraulic and

Structural characterisation by both positive- and negative-ion electrospray mass spectrometry of partially methyl-esterified oligogalacturonides purified by semi-preparative high-performance anion-exchange chromatography.

PubMed

Quéméner, Bernard; Désiré, Cédric; Lahaye, Marc; Debrauwer, Laurent; Negroni, Luc

2003-01-01

The off-line coupling of high-performance anion-exchange chromatography (HPAEC) to electrospray ionisation/ion trap mass spectrometry (ESI-ITMS) is described. The Dionex carbohydrate membrane desalter (CMD) has been assessed as an on-line chromatographic desalting system to remove the high sodium concentration necessary for the HPAEC separation of partially methyl-esterified oligogalacturonides. The developed HPAEC configuration proved to be suitable for indirect coupling with ESI-ITMS. This paper provides some interesting features of positive- and negative-ion multistage tandem mass spectrometry (MS(n)) analysis of these acidic oligosaccharides. The spectra acquired in both negative- and positive-ion modes show characteristic fragment ions resulting from glycosidic bond and cross-ring cleavages. Some new mass spectrometric fragmentation routes are also described. The positive-ion mode gave more complex spectra but was as informative as the negative-ion mode. ESI-ITMS was revealed to be, as previously reported from direct use on an unseparated enzymatic digest, a powerful sequencing technique for the determination of linkage type and the methyl ester distribution of partially methyl-esterified oligogalacturonides. Moreover, unlike matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF MS), it gives valuable information on the elution behaviour of these oligomers in relation to their structure, namely the HPAEC co-elution of isomeric structures.

Effective matrix diffusion in kilometer‐scale transport in fractured crystalline rock

USGS Publications Warehouse

Shapiro, Allen M.

2001-01-01

Concentrations of tritium (3H) and dichlorodifluoromethane (CFC‐12) in water samples taken from glacial drift and fractured crystalline rock over 4 km2 in central New Hampshire are interpreted to identify a conceptual model of matrix diffusion and the magnitude of the diffusion coefficient. Dispersion and mass transfer to and from fractures has affected the 3H concentration to the extent that the peak 3H concentration of the 1960s is no longer distinguishable. Because of heterogeneity in the bedrock the sparsely distributed chemical data do not warrant a three‐dimensional transport model. Instead, a one‐dimensional model of CFC‐12 and 3H migration along flow lines in the glacial drift and bedrock is used to place bounds on the processes affecting kilometer‐scale transport, arid model parameters are varied to reproduce the measured relation between 3H and CFC‐12, rather than their spatial distributions. A model of mass exchange to and from fractures that is dependent on the time‐varying concentration gradient at fracture surfaces qualitatively reproduces the measured relation between 3H and CFC‐12 with an upper bound for the fracture dispersivity approximately equal to 250 m and a lower bound for the effective matrix diffusion coefficient equal to 1 m2 yr−1. The diffusion coefficient at the kilometer scale is at least 3 orders of magnitude greater than laboratory estimates of diffusion in crystalline rock. The large diffusion coefficient indicates that diffusion into an immobile fluid phase (rock matrix) is masked at the kilometer scale by advective mass exchange between fractures with large contrasts in trarismissivity. The measured transmissivity of fractures in the study area varies over more than 6 orders of magnitude. Advective mass exchange from high‐permeability fractures to low‐permeability fractures results in short migration distances of a chemical constituent in low‐permeability fractures over an extended period of time

Modeling the MJO rain rates using parameterized large scale dynamics: vertical structure, radiation, and horizontal advection of dry air

NASA Astrophysics Data System (ADS)

Wang, S.; Sobel, A. H.; Nie, J.

2015-12-01

Two Madden Julian Oscillation (MJO) events were observed during October and November 2011 in the equatorial Indian Ocean during the DYNAMO field campaign. Precipitation rates and large-scale vertical motion profiles derived from the DYNAMO northern sounding array are simulated in a small-domain cloud-resolving model using parameterized large-scale dynamics. Three parameterizations of large-scale dynamics --- the conventional weak temperature gradient (WTG) approximation, vertical mode based spectral WTG (SWTG), and damped gravity wave coupling (DGW) --- are employed. The target temperature profiles and radiative heating rates are taken from a control simulation in which the large-scale vertical motion is imposed (rather than directly from observations), and the model itself is significantly modified from that used in previous work. These methodological changes lead to significant improvement in the results.Simulations using all three methods, with imposed time -dependent radiation and horizontal moisture advection, capture the time variations in precipitation associated with the two MJO events well. The three methods produce significant differences in the large-scale vertical motion profile, however. WTG produces the most top-heavy and noisy profiles, while DGW's is smoother with a peak in midlevels. SWTG produces a smooth profile, somewhere between WTG and DGW, and in better agreement with observations than either of the others. Numerical experiments without horizontal advection of moisture suggest that that process significantly reduces the precipitation and suppresses the top-heaviness of large-scale vertical motion during the MJO active phases, while experiments in which the effect of cloud on radiation are disabled indicate that cloud-radiative interaction significantly amplifies the MJO. Experiments in which interactive radiation is used produce poorer agreement with observation than those with imposed time-varying radiative heating. Our results highlight the