WorldWideScience

Sample records for coupling transport microbial

  1. Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

    Energy Technology Data Exchange (ETDEWEB)

    WANG,YIFENG; PAPENGUTH,HANS W.

    2000-05-04

    Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation.

  2. Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

    International Nuclear Information System (INIS)

    Wang, Yifeng; Papenguth, Hans W.

    2000-01-01

    Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation

  3. Coupled Transport/Reaction Modelling of Copper Canister Corrosion Aided by Microbial Processes

    Energy Technology Data Exchange (ETDEWEB)

    Jinsong Liu [Royal Institute of Technology, Stockholm (Sweden). Dept. of Chemical Engineering and Technology

    2006-04-15

    Copper canister corrosion is an important issue in the concept of a nuclear fuel repository. Previous studies indicate that the oxygen-free copper canister could hold its integrity for more than 100,000 years in the repository environment. Microbial processes may reduce sulphate to sulphide and considerably increase the amount of sulphides available for corrosion. In this paper, a coupled transport/reaction model is developed to account for the transport of chemical species produced by microbial processes. The corroding agents like sulphide would come not only from the groundwater flowing in a fracture that intersects the canister, but also from the reduction of sulphate near the canister. The reaction of sulphate-reducing bacteria and the transport of sulphide in the bentonite buffer are included in the model. The depth of copper canister corrosion is calculated by the model. With representative 'central values' of the concentrations of sulphate and methane at repository depth at different sites in Fennoscandian Shield the corrosion depth predicted by the model is a few millimetres during 10{sup 5} years. As the concentrations of sulphate and methane are extremely site-specific and future climate changes may significantly influence the groundwater compositions at potential repository sites, sensitivity analyses have been conducted. With a broad perspective of the measured concentrations at different sites in Sweden and in Finland, and some possible mechanisms (like the glacial meltwater intrusion and interglacial seawater intrusion) that may introduce more sulphate into the groundwater at intermediate depths during future climate changes, higher concentrations of either/both sulphate and methane than what is used as the representative 'central' values would be possible. In worst cases. locally, half of the canister thickness could possibly be corroded within 10{sup 5} years.

  4. Coupled Transport/Reaction Modelling of Copper Canister Corrosion Aided by Microbial Processes

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jinsong [Royal Institute of Technology, Stockholm (Sweden). Dept. of Chemical Engineering and Technology

    2006-04-15

    Copper canister corrosion is an important issue in the concept of a nuclear fuel repository. Previous studies indicate that the oxygen-free copper canister could hold its integrity for more than 100,000 years in the repository environment. Microbial processes may reduce sulphate to sulphide and considerably increase the amount of sulphides available for corrosion. In this paper, a coupled transport/reaction model is developed to account for the transport of chemical species produced by microbial processes. The corroding agents like sulphide would come not only from the groundwater flowing in a fracture that intersects the canister, but also from the reduction of sulphate near the canister. The reaction of sulphate-reducing bacteria and the transport of sulphide in the bentonite buffer are included in the model. The depth of copper canister corrosion is calculated by the model. With representative 'central values' of the concentrations of sulphate and methane at repository depth at different sites in Fennoscandian Shield the corrosion depth predicted by the model is a few millimetres during 10{sup 5} years. As the concentrations of sulphate and methane are extremely site-specific and future climate changes may significantly influence the groundwater compositions at potential repository sites, sensitivity analyses have been conducted. With a broad perspective of the measured concentrations at different sites in Sweden and in Finland, and some possible mechanisms (like the glacial meltwater intrusion and interglacial seawater intrusion) that may introduce more sulphate into the groundwater at intermediate depths during future climate changes, higher concentrations of either/both sulphate and methane than what is used as the representative 'central' values would be possible. In worst cases. locally, half of the canister thickness could possibly be corroded within 10{sup 5} years.

  5. Coupled Transport/Reaction Modelling of Copper Canister Corrosion Aided by Microbial Processes

    International Nuclear Information System (INIS)

    Jinsong Liu

    2006-04-01

    Copper canister corrosion is an important issue in the concept of a nuclear fuel repository. Previous studies indicate that the oxygen-free copper canister could hold its integrity for more than 100,000 years in the repository environment. Microbial processes may reduce sulphate to sulphide and considerably increase the amount of sulphides available for corrosion. In this paper, a coupled transport/reaction model is developed to account for the transport of chemical species produced by microbial processes. The corroding agents like sulphide would come not only from the groundwater flowing in a fracture that intersects the canister, but also from the reduction of sulphate near the canister. The reaction of sulphate-reducing bacteria and the transport of sulphide in the bentonite buffer are included in the model. The depth of copper canister corrosion is calculated by the model. With representative 'central values' of the concentrations of sulphate and methane at repository depth at different sites in Fennoscandian Shield the corrosion depth predicted by the model is a few millimetres during 10 5 years. As the concentrations of sulphate and methane are extremely site-specific and future climate changes may significantly influence the groundwater compositions at potential repository sites, sensitivity analyses have been conducted. With a broad perspective of the measured concentrations at different sites in Sweden and in Finland, and some possible mechanisms (like the glacial meltwater intrusion and interglacial seawater intrusion) that may introduce more sulphate into the groundwater at intermediate depths during future climate changes, higher concentrations of either/both sulphate and methane than what is used as the representative 'central' values would be possible. In worst cases. locally, half of the canister thickness could possibly be corroded within 10 5 years

  6. Final Report Coupling in silico microbial models with reactive transport models to predict the fate of contaminants in the subsurface.

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, Derek R.

    2012-10-31

    This project successfully accomplished its goal of coupling genome-scale metabolic models with hydrological and geochemical models to predict the activity of subsurface microorganisms during uranium bioremediation. Furthermore, it was demonstrated how this modeling approach can be used to develop new strategies to optimize bioremediation. The approach of coupling genome-scale metabolic models with reactive transport modeling is now well enough established that it has been adopted by other DOE investigators studying uranium bioremediation. Furthermore, the basic principles developed during our studies will be applicable to much broader investigations of microbial activities, not only for other types of bioremediation, but microbial metabolism in diversity of environments. This approach has the potential to make an important contribution to predicting the impact of environmental perturbations on the cycling of carbon and other biogeochemical cycles.

  7. Dynamics of Coupled Contaminant and Microbial Transport in Heterogeneous Porous Media: Purdue Component

    Energy Technology Data Exchange (ETDEWEB)

    Cushman, J.H.; Madilyn Fletcher

    2000-06-01

    Dynamic microbial attachment/detachment occurs in subsurface systems in response to changing environmental conditions caused by contaminant movement and degradation. Understanding the environmental conditions and mechanisms by which anaerobic bacteria partition between aqueous and solid phases is a critical requirement for designing and evaluating in situ bioremediation efforts. This interdisciplinary research project, of which we report only the Purdue contribution, provides fundamental information on the attachment/detachment dynamics of bacteria in heterogeneous porous media. Fundamental results from the Purdue collaboration are: (a) development of a matched-index method for obtaining 3-D Lagrangian trajectories of microbial sized particles transporting within porous media or microflow cells, (b) application of advanced numerical methods to optimally design a microflow cell for studying anaerobic bacterial attachment/detachment phenomena, (c) development of two types of models for simulating bacterial movement and attachment/detachment in microflow cells and natural porous media, (d) application of stochastic analysis to upscale pore scale microbial attachment/detachment models to natural heterogeneous porous media, and (e) evaluation of the role nonlocality plays in microbial dynamics in heterogeneous porous media

  8. Dynamics of Coupled Contaminant and Microbial Transport in Heterogeneous Porous Media: Purdue Component. Final report

    International Nuclear Information System (INIS)

    Cushman, J.H.

    2000-01-01

    Dynamic microbial attachment/detachment occurs in subsurface systems in response to changing environmental conditions caused by contaminant movement and degradation. Understanding the environmental conditions and mechanisms by which anaerobic bacteria partition between aqueous and solid phases is a critical requirement for designing and evaluating in situ bioremediation efforts. This interdisciplinary research project, of which we report only the Purdue contribution, provides fundamental information on the attachment/detachment dynamics of bacteria in heterogeneous porous media. Fundamental results from the Purdue collaboration are: (a) development of a matched-index method for obtaining 3-D Lagrangian trajectories of microbial sized particles transporting within porous media or microflow cells, (b) application of advanced numerical methods to optimally design a microflow cell for studying anaerobic bacterial attachment/detachment phenomena, (c) development of two types of models for simulating bacterial movement and attachment/detachment in microflow cells and natural porous media, (d) application of stochastic analysis to upscale pore scale microbial attachment/detachment models to natural heterogeneous porous media, and (e) evaluation of the role nonlocality plays in microbial dynamics in heterogeneous porous media

  9. Dynamics of Coupled Contaminant and Microbial Transport in Heterogeneous Porous Media: Purdue Component

    Energy Technology Data Exchange (ETDEWEB)

    Cushman, J.H.

    2000-06-01

    Dynamic microbial attachment/detachment occurs in subsurface systems in response to changing environmental conditions caused by contaminant movement and degradation. Understanding the environmental conditions and mechanisms by which anaerobic bacteria partition between aqueous and solid phases is a critical requirement for designing and evaluating in situ bioremediation efforts. This interdisciplinary research project, of which we report only the Purdue contribution, provides fundamental information on the attachment/detachment dynamics of bacteria in heterogeneous porous media. Fundamental results from the Purdue collaboration are: (a) development of a matched-index method for obtaining 3-D Lagrangian trajectories of microbial sized particles transporting within porous media or microflow cells, (b) application of advanced numerical methods to optimally design a microflow cell for studying anaerobic bacterial attachment/detachment phenomena, (c) development of two types of models for simulating bacterial movement and attachment/detachment in microflow cells and natural porous media, (d) application of stochastic analysis to upscale pore scale microbial attachment/detachment models to natural heterogeneous porous media, and (e) evaluation of the role nonlocality plays in microbial dynamics in heterogeneous porous media.

  10. Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model

    International Nuclear Information System (INIS)

    Fang, Yilin; Scheibe, Timothy D.; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E.; Lovley, Derek R.

    2011-01-01

    The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species, multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

  11. Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

    Science.gov (United States)

    Fang, Yilin; Scheibe, Timothy D; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E; Lovley, Derek R

    2011-03-25

    The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

  12. Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model

    Science.gov (United States)

    Fang, Yilin; Scheibe, Timothy D.; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E.; Lovley, Derek R.

    2011-03-01

    The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

  13. Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

    Energy Technology Data Exchange (ETDEWEB)

    Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang [Univ. Da Coruna (Spain)

    2003-12-01

    The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behaviour and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by Banwart et al. Later, Banwart presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by Molinero who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulphate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of Molinero and extends the preliminary microbial model of Zhang by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfaphe concentration, thus adding additional evidence for the possibility

  14. Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

    International Nuclear Information System (INIS)

    Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang

    2003-12-01

    The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behaviour and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by Banwart et al. Later, Banwart presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by Molinero who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulphate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of Molinero and extends the preliminary microbial model of Zhang by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfaphe concentration, thus adding additional evidence for the possibility

  15. Coupled modeling of groundwater flow solute transport, chemical reactions and microbial processes in the 'SP' island

    Energy Technology Data Exchange (ETDEWEB)

    Samper, Javier; Molinero, Jorg; Changbing, Yang; Zhang, Guoxiang

    2003-12-01

    The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behavior and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by /Banwart et al, 1995/. Later, /Banwart et al, 1999/ presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by /Molinero, 2000/ who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulfate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of /Molinero, 2000/ and extends the preliminary microbial model of /Zhang, 2001/ by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfate concentration, thus

  16. Reply to 'Comment on kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' by J. Griffioen

    Science.gov (United States)

    Hunter, K. S.; Van Cappellen, P.

    2000-01-01

    Our paper, 'Kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' (Hunter et al., 1998), presents a theoretical exploration of biogeochemical reaction networks and their importance to the biogeochemistry of groundwater systems. As with any other model, the kinetic reaction-transport model developed in our paper includes only a subset of all physically, biologically and chemically relevant processes in subsurface environments. It considers aquifer systems where the primary energy source driving microbial activity is the degradation of organic matter. In addition to the primary biodegradation pathways of organic matter (i.e. respiration and fermentation), the redox chemistry of groundwaters is also affected by reactions not directly involving organic matter oxidation. We refer to the latter as secondary reactions. By including secondary redox reactions which consume reduced reaction products (e.g., Mn2+, FeS, H2S), and in the process compete with microbial heterotrophic populations for available oxidants (i.e. O2, NO3-, Mn(IV), Fe(III), SO42-), we predict spatio-temporal distributions of microbial activity which differ significantly from those of models which consider only the biodegradation reactions. That is, the secondary reactions have a significant impact on the distributions of the rates of heterotrophic and chemolithotrophic metabolic pathways. We further show that secondary redox reactions, as well as non-redox reactions, significantly influence the acid-base chemistry of groundwaters. The distributions of dissolved inorganic redox species along flowpaths, however, are similar in simulations with and without secondary reactions (see Figs. 3(b) and 7(b) in Hunter et al., 1998), indicating that very different biogeochemical reaction dynamics may lead to essentially the same chemical redox zonation of a groundwater system.

  17. Cation-Coupled Bicarbonate Transporters

    OpenAIRE

    Aalkjaer, Christian; Boedtkjer, Ebbe; Choi, Inyeong; Lee, Soojung

    2014-01-01

    Cation-coupled HCO3− transport was initially identified in the mid-1970s when pioneering studies showed that acid extrusion from cells is stimulated by CO2/HCO3− and associated with Na+ and Cl− movement. The first Na+-coupled bicarbonate transporter (NCBT) was expression-cloned in the late 1990s. There are currently five mammalian NCBTs in the SLC4-family: the electrogenic Na,HCO3-cotransporters NBCe1 and NBCe2 (SLC4A4 and SLC4A5 gene products); the electroneutral Na,HCO3-cotransporter NBCn1 ...

  18. Coupling a continuous watershed-scale microbial fate and transport model with a stochastic dose-response model to estimate risk of illness in an urban watershed.

    Science.gov (United States)

    Liao, Hehuan; Krometis, Leigh-Anne H; Kline, Karen

    2016-05-01

    Within the United States, elevated levels of fecal indicator bacteria (FIB) remain the leading cause of surface water-quality impairments requiring formal remediation plans under the federal Clean Water Act's Total Maximum Daily Load (TMDL) program. The sufficiency of compliance with numerical FIB criteria as the targeted endpoint of TMDL remediation plans may be questionable given poor correlations between FIB and pathogenic microorganisms and varying degrees of risk associated with exposure to different fecal pollution sources (e.g. human vs animal). The present study linked a watershed-scale FIB fate and transport model with a dose-response model to continuously predict human health risks via quantitative microbial risk assessment (QMRA), for comparison to regulatory benchmarks. This process permitted comparison of risks associated with different fecal pollution sources in an impaired urban watershed in order to identify remediation priorities. Results indicate that total human illness risks were consistently higher than the regulatory benchmark of 36 illnesses/1000 people for the study watershed, even when the predicted FIB levels were in compliance with the Escherichia coli geometric mean standard of 126CFU/100mL. Sanitary sewer overflows were associated with the greatest risk of illness. This is of particular concern, given increasing indications that sewer leakage is ubiquitous in urban areas, yet not typically fully accounted for during TMDL development. Uncertainty analysis suggested the accuracy of risk estimates would be improved by more detailed knowledge of site-specific pathogen presence and densities. While previous applications of the QMRA process to impaired waterways have mostly focused on single storm events or hypothetical situations, the continuous modeling framework presented in this study could be integrated into long-term water quality management planning, especially the United States' TMDL program, providing greater clarity to watershed

  19. Coupling a continuous watershed-scale microbial fate and transport model with a stochastic dose-response model to estimate risk of illness in an urban watershed

    Energy Technology Data Exchange (ETDEWEB)

    Liao, Hehuan, E-mail: hehuan86@vt.edu [Department of Biological Systems Engineering, Virginia Tech, 155 Ag Quad Lane, Blacksburg, VA 24061 (United States); Krometis, Leigh-Anne H. [Department of Biological Systems Engineering, Virginia Tech, 155 Ag Quad Lane, Blacksburg, VA 24061 (United States); Kline, Karen [Department of Biological Systems Engineering, Virginia Tech, 155 Ag Quad Lane, Blacksburg, VA 24061 (United States); Center for Watershed Studies, Virginia Tech, 155 Ag Quad Lane, Blacksburg, VA 24061 (United States)

    2016-05-01

    Within the United States, elevated levels of fecal indicator bacteria (FIB) remain the leading cause of surface water-quality impairments requiring formal remediation plans under the federal Clean Water Act's Total Maximum Daily Load (TMDL) program. The sufficiency of compliance with numerical FIB criteria as the targeted endpoint of TMDL remediation plans may be questionable given poor correlations between FIB and pathogenic microorganisms and varying degrees of risk associated with exposure to different fecal pollution sources (e.g. human vs animal). The present study linked a watershed-scale FIB fate and transport model with a dose-response model to continuously predict human health risks via quantitative microbial risk assessment (QMRA), for comparison to regulatory benchmarks. This process permitted comparison of risks associated with different fecal pollution sources in an impaired urban watershed in order to identify remediation priorities. Results indicate that total human illness risks were consistently higher than the regulatory benchmark of 36 illnesses/1000 people for the study watershed, even when the predicted FIB levels were in compliance with the Escherichia coli geometric mean standard of 126 CFU/100 mL. Sanitary sewer overflows were associated with the greatest risk of illness. This is of particular concern, given increasing indications that sewer leakage is ubiquitous in urban areas, yet not typically fully accounted for during TMDL development. Uncertainty analysis suggested the accuracy of risk estimates would be improved by more detailed knowledge of site-specific pathogen presence and densities. While previous applications of the QMRA process to impaired waterways have mostly focused on single storm events or hypothetical situations, the continuous modeling framework presented in this study could be integrated into long-term water quality management planning, especially the United States' TMDL program, providing greater clarity to

  20. Coupling a continuous watershed-scale microbial fate and transport model with a stochastic dose-response model to estimate risk of illness in an urban watershed

    International Nuclear Information System (INIS)

    Liao, Hehuan; Krometis, Leigh-Anne H.; Kline, Karen

    2016-01-01

    Within the United States, elevated levels of fecal indicator bacteria (FIB) remain the leading cause of surface water-quality impairments requiring formal remediation plans under the federal Clean Water Act's Total Maximum Daily Load (TMDL) program. The sufficiency of compliance with numerical FIB criteria as the targeted endpoint of TMDL remediation plans may be questionable given poor correlations between FIB and pathogenic microorganisms and varying degrees of risk associated with exposure to different fecal pollution sources (e.g. human vs animal). The present study linked a watershed-scale FIB fate and transport model with a dose-response model to continuously predict human health risks via quantitative microbial risk assessment (QMRA), for comparison to regulatory benchmarks. This process permitted comparison of risks associated with different fecal pollution sources in an impaired urban watershed in order to identify remediation priorities. Results indicate that total human illness risks were consistently higher than the regulatory benchmark of 36 illnesses/1000 people for the study watershed, even when the predicted FIB levels were in compliance with the Escherichia coli geometric mean standard of 126 CFU/100 mL. Sanitary sewer overflows were associated with the greatest risk of illness. This is of particular concern, given increasing indications that sewer leakage is ubiquitous in urban areas, yet not typically fully accounted for during TMDL development. Uncertainty analysis suggested the accuracy of risk estimates would be improved by more detailed knowledge of site-specific pathogen presence and densities. While previous applications of the QMRA process to impaired waterways have mostly focused on single storm events or hypothetical situations, the continuous modeling framework presented in this study could be integrated into long-term water quality management planning, especially the United States' TMDL program, providing greater clarity to watershed

  1. Reductive immobilization of U(VI) in Fe(III) oxide-reducing subsurface sediments: Analysis of coupled microbial-geochemical processes in experimental reactive transport systems. Final Scientific/Technical Report-EMSP 73914

    International Nuclear Information System (INIS)

    Eric E. Roden Matilde M. Urrutia Mark O. Barnett Clifford R. Lange

    2005-01-01

    The purpose of this research was to provide information to DOE on microbiological and geochemical processes underlying the potential use of dissimilatory metal-reducing bacteria (DMRB) to create subsurface redox barriers for immobilization of uranium and other redox-sensitive metal/radionuclide contaminants that were released to the environment in large quantities during Cold War nuclear weapons manufacturing operations. Several fundamental scientific questions were addressed in order to understand and predict how such treatment procedures would function under in situ conditions in the subsurface. These questions revolved the coupled microbial-geochemical phenomena which are likely to occur within a redox barrier treatment zone, and on the dynamic interactions between hydrologic flux and biogeochemical process rates. First, we assembled a robust conceptual understanding and numerical framework for modeling the kinetics of microbial Fe(III) oxide reduction and associated DMRB growth in sediments. Development of this framework is a critical prerequisite for predicting the potential effectiveness of DMRB-promoted subsurface bioremediation, since Fe(III) oxides are expected to be the primary source of electron-accepting capacity for growth and maintenance of DMRB in subsurface environments. We also defined in detail the kinetics of microbial (enzymatic) versus abiotic, ferrous iron-promoted reduction of U(VI) in the presence and absence of synthetic and natural Fe(III) oxide materials. The results of these studies suggest that (i) the efficiency of dissolved U(VI) scavenging may be influenced by the kinetics of enzymatic U(VI) reduction in systems with relative short fluid residence times; (2) association of U(VI) with diverse surface sites in natural soils and sediments has the potential to limit the rate and extent of microbial U(VI) reduction, and in turn modulate the effectiveness of in situ U(VI) bioremediation; and (3) abiotic, ferrous iron (Fe(II)) drive n U

  2. Modelling coupled microbial processes in the subsurface: Model development, verification, evaluation and application

    Science.gov (United States)

    Masum, Shakil A.; Thomas, Hywel R.

    2018-06-01

    To study subsurface microbial processes, a coupled model which has been developed within a Thermal-Hydraulic-Chemical-Mechanical (THCM) framework is presented. The work presented here, focuses on microbial transport, growth and decay mechanisms under the influence of multiphase flow and bio-geochemical reactions. In this paper, theoretical formulations and numerical implementations of the microbial model are presented. The model has been verified and also evaluated against relevant experimental results. Simulated results show that the microbial processes have been accurately implemented and their impacts on porous media properties can be predicted either qualitatively or quantitatively or both. The model has been applied to investigate biofilm growth in a sandstone core that is subjected to a two-phase flow and variable pH conditions. The results indicate that biofilm growth (if not limited by substrates) in a multiphase system largely depends on the hydraulic properties of the medium. When the change in porewater pH which occurred due to dissolution of carbon dioxide gas is considered, growth processes are affected. For the given parameter regime, it has been shown that the net biofilm growth is favoured by higher pH; whilst the processes are considerably retarded at lower pH values. The capabilities of the model to predict microbial respiration in a fully coupled multiphase flow condition and microbial fermentation leading to production of a gas phase are also demonstrated.

  3. Impact of Microbial Growth on Subsurface Perfluoroalkyl Acid Transport

    Science.gov (United States)

    Weathers, T. S.; Higgins, C. P.; Sharp, J.

    2014-12-01

    The fate and transport of poly and perfluoroalkyl substances (PFASs) in the presence of active microbial communities has not been widely investigated. These emerging contaminants are commonly utilized in aqueous film-forming foams (AFFF) and have often been detected in groundwater. This study explores the transport of a suite of perfluorocarboxylic acids and perfluoroalkylsulfonates, including perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS), in microbially active settings. Single point organic carbon normalized sorption coefficients derived by exposing inactive cellular material to PFASs result in more than an order of magnitude increase in sorption compared to soil organic carbon sorption coefficients found in literature. For example, the sorption coefficients for PFOS are 4.05±0.07 L/kg and 2.80±0.08 L/kg for cellular organic carbon and soil organic carbon respectively. This increase in sorption, coupled with enhanced extracellular polymeric substance production observed during growth of a common hydrocarbon degrading soil microbe exposed to source-level concentrations of PFASs (10 mg/L of 11 analytes, 110 mg/L total) may result in PFAS retardation in situ. To address the upscaling of this phenomenon, flow-through columns packed with low-organic carbon sediment and biostimulated with 10 mg/L glucose were exposed to PFAS concentrations from 15 μg/L to 10 mg/L of each 11 analytes. Breakthrough and tailing of each analyte was measured and modeled with Hydrus-1D to explore sorption coefficients over time for microbially active columns.

  4. Anomalous transport at weak coupling

    International Nuclear Information System (INIS)

    Chowdhury, Subham Dutta; David, Justin R.

    2015-01-01

    We evaluate the contribution of chiral fermions in d=2,4,6, chiral bosons, a chiral gravitino like theory in d=2 and chiral gravitinos in d=6 to all the leading parity odd transport coefficients at one loop. This is done by using finite temperature field theory to evaluate the relevant Kubo formulae. For chiral fermions and chiral bosons the relation between the parity odd transport coefficient and the microscopic anomalies including gravitational anomalies agree with that found by using the general methods of hydrodynamics and the argument involving the consistency of the Euclidean vacuum. For the gravitino like theory in d=2 and chiral gravitinos in d=6, we show that relation between the pure gravitational anomaly and parity odd transport breaks down. From the perturbative calculation we clearly identify the terms that contribute to the anomaly polynomial, but not to the transport coefficient for gravitinos. We also develop a simple method for evaluating the angular integrals in the one loop diagrams involved in the Kubo formulae. Finally we show that charge diffusion mode of an ideal 2 dimensional Weyl gas in the presence of a finite chemical potential acquires a speed, which is equal to half the speed of light.

  5. Coupled electron-photon radiation transport

    International Nuclear Information System (INIS)

    Lorence, L.; Kensek, R.P.; Valdez, G.D.; Drumm, C.R.; Fan, W.C.; Powell, J.L.

    2000-01-01

    Massively-parallel computers allow detailed 3D radiation transport simulations to be performed to analyze the response of complex systems to radiation. This has been recently been demonstrated with the coupled electron-photon Monte Carlo code, ITS. To enable such calculations, the combinatorial geometry capability of ITS was improved. For greater geometrical flexibility, a version of ITS is under development that can track particles in CAD geometries. Deterministic radiation transport codes that utilize an unstructured spatial mesh are also being devised. For electron transport, the authors are investigating second-order forms of the transport equations which, when discretized, yield symmetric positive definite matrices. A novel parallelization strategy, simultaneously solving for spatial and angular unknowns, has been applied to the even- and odd-parity forms of the transport equation on a 2D unstructured spatial mesh. Another second-order form, the self-adjoint angular flux transport equation, also shows promise for electron transport

  6. Coupling of transport and geochemical models

    International Nuclear Information System (INIS)

    Noy, D.J.

    1986-01-01

    This report considers mass transport in the far-field of a radioactive waste repository, and detailed geochemical modelling of the ground-water in the near-field. A parallel approach to this problem of coupling transport and geochemical codes is the subject of another CEC report (ref. EUR 10226). Both studies were carried out in the framework of the CEC project MIRAGE. (Migration of radionuclides in the geosphere)

  7. Coupled geochemical and solute transport code development

    International Nuclear Information System (INIS)

    Morrey, J.R.; Hostetler, C.J.

    1985-01-01

    A number of coupled geochemical hydrologic codes have been reported in the literature. Some of these codes have directly coupled the source-sink term to the solute transport equation. The current consensus seems to be that directly coupling hydrologic transport and chemical models through a series of interdependent differential equations is not feasible for multicomponent problems with complex geochemical processes (e.g., precipitation/dissolution reactions). A two-step process appears to be the required method of coupling codes for problems where a large suite of chemical reactions must be monitored. Two-step structure requires that the source-sink term in the transport equation is supplied by a geochemical code rather than by an analytical expression. We have developed a one-dimensional two-step coupled model designed to calculate relatively complex geochemical equilibria (CTM1D). Our geochemical module implements a Newton-Raphson algorithm to solve heterogeneous geochemical equilibria, involving up to 40 chemical components and 400 aqueous species. The geochemical module was designed to be efficient and compact. A revised version of the MINTEQ Code is used as a parent geochemical code

  8. Coupled transport in field-reversed configurations

    Science.gov (United States)

    Steinhauer, L. C.; Berk, H. L.; TAE Team

    2018-02-01

    Coupled transport is the close interconnection between the cross-field and parallel fluxes in different regions due to topological changes in the magnetic field. This occurs because perpendicular transport is necessary for particles or energy to leave closed field-line regions, while parallel transport strongly affects evolution of open field-line regions. In most toroidal confinement systems, the periphery, namely, the portion with open magnetic surfaces, is small in thickness and volume compared to the core plasma, the portion with closed surfaces. In field-reversed configurations (FRCs), the periphery plays an outsized role in overall confinement. This effect is addressed by an FRC-relevant model of coupled particle transport that is well suited for immediate interpretation of experiments. The focus here is particle confinement rather than energy confinement since the two track together in FRCs. The interpretive tool yields both the particle transport rate χn and the end-loss time τǁ. The results indicate that particle confinement depends on both χn across magnetic surfaces throughout the plasma and τǁ along open surfaces and that they provide roughly equal transport barriers, inhibiting particle loss. The interpretation of traditional FRCs shows Bohm-like χn and inertial (free-streaming) τǁ. However, in recent advanced beam-driven FRC experiments, χn approaches the classical rate and τǁ is comparable to classic empty-loss-cone mirrors.

  9. Development of a transport model for the microbial degradation of ...

    African Journals Online (AJOL)

    A mathematical model for first order reaction rate under isothermal condition was developed for predicting the diffusivity and transport rate of anthracene and pyrene during biodegradation using two microbial strains (corynebacteria spp and pseudomonas putida) in a heterogeneous porous medium. The formulation ...

  10. Coupling of transport and geochemical models

    International Nuclear Information System (INIS)

    Noy, D.J.

    1985-01-01

    This contract stipulated separate pieces of work to consider mass transport in the far-field of a repository, and more detailed geochemical modelling of the groundwater in the near-field. It was envisaged that the far-field problem would be tackled by numerical solutions to the classical advection-diffusion equation obtained by the finite element method. For the near-field problem the feasibility of coupling existing geochemical equilibrium codes to the three dimensional groundwater flow codes was to be investigated. This report is divided into two sections with one part devoted to each aspect of this contract. (author)

  11. Microbial transport : Adaptations to natural environments

    NARCIS (Netherlands)

    Konings, W.N

    2006-01-01

    The cytoplasmic membrane of bacteria is the matrix for metabolic energy transducing processes such as proton motive force generation and solute transport. Passive permeation of protons across the cytoplasmic membrane is a crucial determinant in the proton motive generating capacity of the organisms.

  12. Microbial transport : Adaptations to natural environments

    NARCIS (Netherlands)

    Konings, W.N

    The cytoplasmic membrane of bacteria is the matrix for metabolic energy transducing processes such as proton motive force generation and solute transport. Passive permeation of protons across the cytoplasmic membrane is a crucial determinant in the proton motive generating capacity of the organisms.

  13. Thermodynamically coupled mass transport processes in a saturated clay

    International Nuclear Information System (INIS)

    Carnahan, C.L.

    1984-01-01

    Gradients of temperature, pressure, and fluid composition in saturated clays give rise to coupled transport processes (thermal and chemical osmosis, thermal diffusion, ultrafiltration) in addition to the direct processes (advection and diffusion). One-dimension transport of water and a solute in a saturated clay subjected to mild gradients of temperature and pressure was simulated numerically. When full coupling was accounted for, volume flux (specific discharge) was controlled by thermal osmosis and chemical osmosis. The two coupled fluxes were oppositely directed, producing a point of stagnation within the clay column. Solute flows were dominated by diffusion, chemical osmosis, and thermal osmosis. Chemical osmosis produced a significant flux of solute directed against the gradient of solute concentration; this effect reduced solute concentrations relative to the case without coupling. Predictions of mass transport in clays at nuclear waste repositories could be significantly in error if coupled transport processes are not accounted for. 14 refs., 8 figs

  14. Thermodynamically coupled mass transport processes in a saturated clay

    International Nuclear Information System (INIS)

    Carnahan, C.L.

    1984-11-01

    Gradients of temperature, pressure, and fluid composition in saturated clays give rise to coupled transport processes (thermal and chemical osmosis, thermal diffusion, ultrafiltration) in addition to the direct processes (advection and diffusion). One-dimensional transport of water and a solute in a saturated clay subjected to mild gradients of temperature and pressure was simulated numerically. When full coupling was accounted for, volume flux (specific discharge) was controlled by thermal osmosis and chemical osmosis. The two coupled fluxes were oppositely directed, producing a point of stagnation within the clay column. Solute flows were dominated by diffusion, chemical osmosis, and thermal osmosis. Chemical osmosis produced a significant flux of solute directed against the gradient of solute concentration; this effect reduced solute concentrations relative to the case without coupling. Predictions of mass transport in clays at nuclear waste repositories could be significantly in error if coupled transport processes are not accounted for. 14 references, 8 figures, 1 table

  15. Modular coupling of transport and chemistry: theory and model applications

    International Nuclear Information System (INIS)

    Pfingsten, W.

    1994-06-01

    For the description of complex processes in the near-field of a radioactive waste repository, the coupling of transport and chemistry is necessary. A reason for the relatively minor use of coupled codes in this area is the high amount of computer time and storage capacity necessary for calculations by conventional codes, and lack of available data. The simple application of the sequentially coupled code MCOTAC, which couples one-dimensional advective, dispersive and diffusive transport with chemical equilibrium complexation and precipitation/dissolution reactions in a porous medium, shows some promising features with respect to applicability to relevant problems. Transport, described by random walk of multi-species particles, and chemical equilibrium calculations are solved separately, coupled only by an exchange term to ensure mass conservation. (For full text of the abstract see 25:072321)

  16. Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Graham, Emily B.; Crump, Alex R.; Resch, Charles T.; Fansler, Sarah; Arntzen, Evan; Kennedy, David W.; Fredrickson, Jim K.; Stegen, James C.

    2016-12-16

    Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptual model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.

  17. Modeling of coupled geochemical and transport processes: An overview

    International Nuclear Information System (INIS)

    Carnahan, C.L.

    1989-10-01

    Early coupled models associated with fluid flow and solute transport have been limited by assumed conditions of constant temperature, fully saturated fluid flow, and constant pore fluid velocity. Developments including coupling of chemical reactions to variable fields of temperature and fluid flow have generated new requirements for experimental data. As the capabilities of coupled models expand, needs are created for experimental data to be used for both input and validation. 25 refs

  18. Coupled electric and transport phenomena in porous media

    NARCIS (Netherlands)

    Li, Shuai

    2014-01-01

    The coupled electrical and transport properties of clay-containing porous media are the topics of interest in this study. Both experimental and numerical (pore network modeling) techniques are employed to gain insight into the macro-scale interaction between electrical and solute transport phenomena

  19. Mineral solubility and free energy controls on microbial reaction kinetics: Application to contaminant transport in the subsurface

    Energy Technology Data Exchange (ETDEWEB)

    Taillefert, Martial [Georgia Inst. of Technology, Atlanta, GA (United States); Van Cappellen, Philippe [Univ. of Waterloo, ON (Canada)

    2016-11-14

    Recent developments in the theoretical treatment of geomicrobial reaction processes have resulted in the formulation of kinetic models that directly link the rates of microbial respiration and growth to the corresponding thermodynamic driving forces. The overall objective of this project was to verify and calibrate these kinetic models for the microbial reduction of uranium(VI) in geochemical conditions that mimic as much as possible field conditions. The approach combined modeling of bacterial processes using new bioenergetic rate laws, laboratory experiments to determine the bioavailability of uranium during uranium bioreduction, evaluation of microbial growth yield under energy-limited conditions using bioreactor experiments, competition experiments between metabolic processes in environmentally relevant conditions, and model applications at the field scale. The new kinetic descriptions of microbial U(VI) and Fe(III) reduction should replace those currently used in reactive transport models that couple catabolic energy generation and growth of microbial populations to the rates of biogeochemical redox processes. The above work was carried out in collaboration between the groups of Taillefert (batch reactor experiments and reaction modeling) at Georgia Tech and Van Cappellen (retentostat experiments and reactive transport modeling) at University of Waterloo (Canada).

  20. Influences of Coupled Hydrologic and Microbial Processes on River Corridor Biogeochemistry and Ecology

    Science.gov (United States)

    Scheibe, T. D.; Song, H. S.; Stegen, J.; Graham, E.; Bao, J.; Goldman, A.; Zhou, T.; Crump, A.; Hou, Z.; Hammond, G. E.; Chen, X.; Huang, M.; Zhang, X.; Nelson, W. C.; Garayburu-Caruso, V. A.

    2017-12-01

    The exchange of water between rivers and surrounding subsurface environments (hydrologic exchange flows or HEFs) is a vital aspect of river ecology and watershed function. HEFs play a key role in water quality, nutrient cycling, and ecosystem health, and they modulate water temperatures and enhance exchange of terrestrial and aquatic nutrients, which lead to elevated biogeochemical activity. However, these coupled hydrologic and microbiological processes are not well understood, particularly in the context of large managed river systems with highly variable discharge, and are poorly represented in system-scale quantitative models. Using the 75 km Hanford Reach of the Columbia River as the research domain, we apply high-resolution flow simulations supported by field observations to understand how variable river discharge interacts with hydromorphic and hydrogeologic structures to generate HEFs and distributions of subsurface residence times. We combine this understanding of hydrologic processes with microbiological activity measurements and reactive transport models to elucidate the holistic impacts of variable discharge on river corridor (surface and subsurface) ecosystems. In particular, our project seeks to develop and test new conceptual and numerical models that explicitly incorporate i) the character (chemical speciation and thermodynamics) of natural organic matter as it varies along flow paths and through mixing of groundwater and surface water, and ii) the history-dependent response of microbial communities to varying time scales of inundation associated with fluctuations in river discharge. The results of these high-resolution mechanistic models are guiding formulation and parameterization of reduced-order models applicable at reach to watershed scales. New understanding of coupled hydrology and microbiology in the river corridor will play a key role in reduction of uncertainties associated with major Earth system biogeochemical fluxes, improving

  1. Numerical analysis of coupled water transport in wood with a focus on the coupling parameter sorption

    DEFF Research Database (Denmark)

    Hozjan, T.; Turk, G.; Rodman, U.

    2011-01-01

    This paper presents a study of sorption rate function in a so-called multi-Fickian or multi-phase model. This model describes the complex moisture transport system in wood, which consists of separate water-vapour and bound-water diffusion interacting through sorption. In the numerical example inf...... influence of the sorption rate function on water transport is presented. It can be seen that the sorption rate function has a noticeable influence on coupled water transport in wood....

  2. Elimination of pyraclostrobin by simultaneous microbial degradation coupled with the Fenton process in microbial fuel cells and the microbial community.

    Science.gov (United States)

    Zhao, Huanhuan; Kong, Chui-Hua

    2018-06-01

    The elimination of pyraclostrobin by simultaneous microbial degradation and Fenton oxidation was achieved in a microbial fuel cell (MFC) system. After 12 h of incubation, the removal rate of pyraclostrobin was 1.4 mg/L/h at the anode and 1.7 mg/L/h at the cathode. The pyraclostrobin concentration was less than the detection limit (0.1 mg/L) after 72 h at the anode and 24 h at the cathode. The air flow rate, temperature, and pH of the catholyte had significant effects on the generation of H 2 O 2 . The maximum production of H 2 O 2 was 1.2 mg/L after reaction for 20 h during the Fenton process. Microbial community analysis indicated that functional bacteria in the genera Chryseobacterium, Stenotrophomonas, Arcobacter, and Comamonas were predominant in the anodic biofilm. In conclusion, the MFC-Fenton system provides an effective approach for treating environmental contaminants. Copyright © 2018 Elsevier Ltd. All rights reserved.

  3. HYDROBIOGEOCHEM: A coupled model of HYDROlogic transport and mixed BIOGEOCHEMical kinetic/equilibrium reactions in saturated-unsaturated media

    Energy Technology Data Exchange (ETDEWEB)

    Yeh, G.T.; Salvage, K.M. [Pennsylvania State Univ., University Park, PA (United States). Dept. of Civil and Environmental Engineering; Gwo, J.P. [Oak Ridge National Lab., TN (United States); Zachara, J.M.; Szecsody, J.E. [Pacific Northwest National Lab., Richland, WA (United States)

    1998-07-01

    The computer program HYDROBIOGEOCHEM is a coupled model of HYDROlogic transport and BIOGEOCHEMical kinetic and/or equilibrium reactions in saturated/unsaturated media. HYDROBIOGEOCHEM iteratively solves the two-dimensional transport equations and the ordinary differential and algebraic equations of mixed biogeochemical reactions. The transport equations are solved for all aqueous chemical components and kinetically controlled aqueous species. HYDROBIOGEOCHEM is designed for generic application to reactive transport problems affected by both microbiological and geochemical reactions in subsurface media. Input to the program includes the geometry of the system, the spatial distribution of finite elements and nodes, the properties of the media, the potential chemical and microbial reactions, and the initial and boundary conditions. Output includes the spatial distribution of chemical and microbial concentrations as a function of time and space, and the chemical speciation at user-specified nodes.

  4. Tropical forest soil microbial communities couple iron and carbon biogeochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Dubinsky, E.A.; Silver, W.L.; Firestone, M.K.

    2009-10-15

    We report that iron-reducing bacteria are primary mediators of anaerobic carbon oxidation in upland tropical soils spanning a rainfall gradient (3500 - 5000 mm yr-1) in northeast Puerto Rico. The abundant rainfall and high net primary productivity of these tropical forests provide optimal soil habitat for iron-reducing and iron-oxidizing bacteria. Spatially and temporally dynamic redox conditions make iron-transforming microbial communities central to the belowground carbon cycle in these wet tropical forests. The exceedingly high abundance of iron-reducing bacteria (up to 1.2 x 10{sup 9} cells per gram soil) indicated that they possess extensive metabolic capacity to catalyze the reduction of iron minerals. In soils from the higher rainfall sites, measured rates of ferric iron reduction could account for up to 44 % of organic carbon oxidation. Iron reducers appeared to compete with methanogens when labile carbon availability was limited. We found large numbers of bacteria that oxidize reduced iron at sites with high rates of iron reduction and large numbers of iron-reducers. the coexistence of large populations of ironreducing and iron-oxidizing bacteria is evidence for rapid iron cycling between its reduced and oxidized states, and suggests that mutualistic interactions among these bacteria ultimately fuel organic carbon oxidation and inhibit CH4 production in these upland tropical forests.

  5. Coupling effect on the electronic transport through dimolecular junctions

    International Nuclear Information System (INIS)

    Long, Meng-Qiu; Wang, Lingling; Chen, Ke-Qiu; Li, Xiao-Fei; Zou, B.S.; Shuai, Z.

    2007-01-01

    Using nonequilibrium Green's function and first-principle calculations, we investigate the transport behaviors of a dimolecule device with two 1,4-Dithiolbenzenes (DTB) sandwiched between two gold electrodes. The results show that the intermolecular coupling effect plays an important role in the conducting behavior of the system. By changing the dihedral angles between the two DTB molecules, namely changing the magnitude of the intermolecular interaction, a different transport behavior can be observed in the system

  6. Modular coupling of transport and chemistry: theory and model applications

    International Nuclear Information System (INIS)

    Pfingsten, W.

    1994-06-01

    For the description of complex processes in the near-field of a radioactive waste repository, the coupling of transport and chemistry is necessary. A reason for the relatively minor use of coupled codes in this area is the high amount of computer time and storage capacity necessary for calculations by conventional codes, and lack of available data. The simple application of the sequentially coupled code MCOTAC, which couples one-dimensional advective, dispersive and diffusive transport with chemical equilibrium complexation and precipitation/dissolution reactions in a porous medium, shows some promising features with respect to applicability to relevant problems. Transport, described by a random walk of multi-species particles, and chemical equilibrium calculations are solved separately, coupled only by an exchange term to ensure mass conservation. The modular-structured code was applied to three problems: a) incongruent dissolution of hydrated silicate gels, b) dissolution of portlandite and c) calcite dissolution and hypothetical dolomite precipitation. This allows for a comparison with other codes and their applications. The incongruent dissolution of cement phases, important for degradation of cementitious materials in a repository, can be included in the model without the problems which occur with a directly coupled code. The handling of a sharp multi-mineral front system showed a much faster calculation time compared to a directly coupled code application. Altogether, the results are in good agreement with other code calculations. Hence, the chosen modular concept of MCOTAC is more open to an easy extension of the code to include additional processes like sorption, kinetically controlled processes, transport in two or three spatial dimensions, and adaptation to new developments in computing (hardware and software), an important factor for applicability. (author) figs., tabs., refs

  7. Incorporating Geochemical And Microbial Kinetics In Reactive Transport Models For Generation Of Acid Rock Drainage

    Science.gov (United States)

    Andre, B. J.; Rajaram, H.; Silverstein, J.

    2010-12-01

    Acid mine drainage, AMD, results from the oxidation of metal sulfide minerals (e.g. pyrite), producing ferrous iron and sulfuric acid. Acidophilic autotrophic bacteria such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans obtain energy by oxidizing ferrous iron back to ferric iron, using oxygen as the electron acceptor. Most existing models of AMD do not account for microbial kinetics or iron geochemistry rigorously. Instead they assume that oxygen limitation controls pyrite oxidation and thus focus on oxygen transport. These models have been successfully used for simulating conditions where oxygen availability is a limiting factor (e.g. source prevention by capping), but have not been shown to effectively model acid generation and effluent chemistry under a wider range of conditions. The key reactions, oxidation of pyrite and oxidation of ferrous iron, are both slow kinetic processes. Despite being extensively studied for the last thirty years, there is still not a consensus in the literature about the basic mechanisms, limiting factors or rate expressions for microbially enhanced oxidation of metal sulfides. An indirect leaching mechanism (chemical oxidation of pyrite by ferric iron to produce ferrous iron, with regeneration of ferric iron by microbial oxidation of ferrous iron) is used as the foundation of a conceptual model for microbially enhanced oxidation of pyrite. Using literature data, a rate expression for microbial consumption of ferrous iron is developed that accounts for oxygen, ferrous iron and pH limitation. Reaction rate expressions for oxidation of pyrite and chemical oxidation of ferrous iron are selected from the literature. A completely mixed stirred tank reactor (CSTR) model is implemented coupling the kinetic rate expressions, speciation calculations and flow. The model simulates generation of AMD and effluent chemistry that qualitatively agrees with column reactor and single rock experiments. A one dimensional reaction

  8. Coupled models in porous media: reactive transport and fractures

    International Nuclear Information System (INIS)

    Amir, L.

    2008-12-01

    This thesis deals with numerical simulation of coupled models for flow and transport in porous media. We present a new method for coupling chemical reactions and transport by using a Newton-Krylov method, and we also present a model of flow in fractured media, based on a domain decomposition method that takes into account the case of intersecting fractures. This study is composed of three parts: the first part contains an analysis, and implementation, of various numerical methods for discretizing advection-diffusion problems, in particular by using operator splitting methods. The second part is concerned with a fully coupled method for modeling transport and chemistry problems. The coupled transport-chemistry model is described, after discretization in time, by a system of nonlinear equations. The size of the system, namely the number of grid points times the number a chemical species, precludes a direct solution of the linear system. To alleviate this difficulty, we solve the system by a Newton-Krylov method, so as to avoid forming and factoring the Jacobian matrix. In the last part, we present a model of flow in 3D for intersecting fractures, by using a domain decomposition method. The fractures are treated as interfaces between sub-domains. We show existence and uniqueness of the solution, and we validate the model by numerical tests. (author)

  9. Inter-dot coupling effects on transport through correlated parallel

    Indian Academy of Sciences (India)

    Transport through symmetric parallel coupled quantum dot system has been studied, using non-equilibrium Green function formalism. The inter-dot tunnelling with on-dot and inter-dot Coulomb repulsion is included. The transmission coefficient and Landaur–Buttiker like current formula are shown in terms of internal states ...

  10. Methodology for coupling computational fluid dynamics and integral transport neutronics

    International Nuclear Information System (INIS)

    Thomas, J. W.; Zhong, Z.; Sofu, T.; Downar, T. J.

    2004-01-01

    The CFD code STAR-CD was coupled to the integral transport code DeCART in order to provide high-fidelity, full physics reactor simulations. An interface program was developed to perform the tasks of mapping the STAR-CD mesh to the DeCART mesh, managing all communication between STAR-CD and DeCART, and monitoring the convergence of the coupled calculations. The interface software was validated by comparing coupled calculation results with those obtained using an independently developed interface program. An investigation into the convergence characteristics of coupled calculations was performed using several test models on a multiprocessor LINUX cluster. The results indicate that the optimal convergence of the coupled field calculation depends on several factors, to include the tolerance of the STAR-CD solution and the number of DeCART transport sweeps performed before exchanging data between codes. Results for a 3D, multi-assembly PWR problem on 12 PEs of the LINUX cluster indicate the best performance is achieved when the STAR-CD tolerance and number of DeCART transport sweeps are chosen such that the two fields converge at approximately the same rate. (authors)

  11. Quantum transport in coupled resonators enclosed synthetic magnetic flux

    International Nuclear Information System (INIS)

    Jin, L.

    2016-01-01

    Quantum transport properties are instrumental to understanding quantum coherent transport processes. Potential applications of quantum transport are widespread, in areas ranging from quantum information science to quantum engineering, and not restricted to quantum state transfer, control and manipulation. Here, we study light transport in a ring array of coupled resonators enclosed synthetic magnetic flux. The ring configuration, with an arbitrary number of resonators embedded, forms a two-arm Aharonov–Bohm interferometer. The influence of magnetic flux on light transport is investigated. Tuning the magnetic flux can lead to resonant transmission, while half-integer magnetic flux quantum leads to completely destructive interference and transmission zeros in an interferometer with two equal arms. -- Highlights: •The light transport is investigated through ring array of coupled resonators enclosed synthetic magnetic field. •Aharonov–Bohm ring interferometer of arbitrary configuration is investigated. •The half-integer magnetic flux quantum leads to destructive interference and transmission zeros for two-arm at equal length. •Complete transmission is available via tuning synthetic magnetic flux.

  12. Coupled Transport Phenomena in the Opalinus Clay: Implications for Radionuclide Transport

    International Nuclear Information System (INIS)

    Soler, J.M.

    1999-09-01

    Coupled phenomena (thermal and chemical osmosis, hyperfiltration, coupled diffusion, thermal diffusion, thermal filtration, Dufour effect) may play an important role in fluid, solute and heat transport in clay-rich formations, such as the Opalinus Clay (OPA), which are being considered as potential hosts for radioactive waste repositories. In this study, the potential effects of coupled phenomena on radionuclide transport in the vicinity of a repository for vitrified high-level radioactive waste (HLW) and spent nuclear fuel (SF) hosted by the Opalinus Clay, at times equal to or greater than the expected lifetime of the waste canisters (about 1000 years), have been addressed. Firstly, estimates of the solute fluxes associated with chemical osmosis, hyperfiltration, thermal diffusion and thermal osmosis have been calculated. Available experimental data concerning coupled transport phenomena in compacted clays, and the hydrogeological and geochemical conditions to which the Opalinus Clay is subject, have been used for these estimates. These estimates suggest that thermal osmosis is the only coupled transport mechanism that could have a strong impact on solute and fluid transport in the vicinity of the repository. Secondly, estimates of the heat fluxes associated with thermal filtration and the Dufour effect in the vicinity of the repository have been calculated. The calculated heat fluxes are absolutely negligible compared to the heat flux caused by thermal conduction. As a further step to obtain additional insight into the effects of coupled phenomena on solute transport, the solute fluxes associated with advection, chemical diffusion, thermal and chemical osmosis, hyperfiltration and thermal diffusion have been incorporated into a simple one-dimensional transport equation. The analytical solution of this equation, with appropriate parameters, shows again that thermal osmosis is the only coupled transport mechanism that could have a strong effect on repository

  13. Coupled Transport Phenomena in the Opalinus Clay: Implications for Radionuclide Transport

    Energy Technology Data Exchange (ETDEWEB)

    Soler, J.M.

    1999-09-01

    Coupled phenomena (thermal and chemical osmosis, hyperfiltration, coupled diffusion, thermal diffusion, thermal filtration, Dufour effect) may play an important role in fluid, solute and heat transport in clay-rich formations, such as the Opalinus Clay (OPA), which are being considered as potential hosts for radioactive waste repositories. In this study, the potential effects of coupled phenomena on radionuclide transport in the vicinity of a repository for vitrified high-level radioactive waste (HLW) and spent nuclear fuel (SF) hosted by the Opalinus Clay, at times equal to or greater than the expected lifetime of the waste canisters (about 1000 years), have been addressed. Firstly, estimates of the solute fluxes associated with chemical osmosis, hyperfiltration, thermal diffusion and thermal osmosis have been calculated. Available experimental data concerning coupled transport phenomena in compacted clays, and the hydrogeological and geochemical conditions to which the Opalinus Clay is subject, have been used for these estimates. These estimates suggest that thermal osmosis is the only coupled transport mechanism that could have a strong impact on solute and fluid transport in the vicinity of the repository. Secondly, estimates of the heat fluxes associated with thermal filtration and the Dufour effect in the vicinity of the repository have been calculated. The calculated heat fluxes are absolutely negligible compared to the heat flux caused by thermal conduction. As a further step to obtain additional insight into the effects of coupled phenomena on solute transport, the solute fluxes associated with advection, chemical diffusion, thermal and chemical osmosis, hyperfiltration and thermal diffusion have been incorporated into a simple one-dimensional transport equation. The analytical solution of this equation, with appropriate parameters, shows again that thermal osmosis is the only coupled transport mechanism that could have a strong effect on repository

  14. Ion sampling and transport in Inductively Coupled Plasma Mass Spectrometry

    Science.gov (United States)

    Farnsworth, Paul B.; Spencer, Ross L.

    2017-08-01

    Quantitative accuracy and high sensitivity in inductively coupled plasma mass spectrometry (ICP-MS) depend on consistent and efficient extraction and transport of analyte ions from an inductively coupled plasma to a mass analyzer, where they are sorted and detected. In this review we examine the fundamental physical processes that control ion sampling and transport in ICP-MS and compare the results of theory and computerized models with experimental efforts to characterize the flow of ions through plasma mass spectrometers' vacuum interfaces. We trace the flow of ions from their generation in the plasma, into the sampling cone, through the supersonic expansion in the first vacuum stage, through the skimmer, and into the ion optics that deliver the ions to the mass analyzer. At each stage we consider idealized behavior and departures from ideal behavior that affect the performance of ICP-MS as an analytical tool.

  15. Wentzel-Bardeen singularity in coupled Luttinger liquids: Transport properties

    International Nuclear Information System (INIS)

    Martin, T.

    1994-01-01

    The recent progress on 1 D interacting electrons systems and their applications to study the transport properties of quasi one dimensional wires is reviewed. We focus on strongly correlated elections coupled to low energy acoustic phonons in one dimension. The exponents of various response functions are calculated, and their striking sensitivity to the Wentzel-Bardeen singularity is discussed. For the Hubbard model coupled to phonons the equivalent of a phase diagram is established. By increasing the filling factor towards half filling the WB singularity is approached. This in turn suppresses antiferromagnetic fluctuations and drives the system towards the superconducting regime, via a new intermediate (metallic) phase. The implications of this phenomenon on the transport properties of an ideal wire as well as the properties of a wire with weak or strong scattering are analyzed in a perturbative renormalization group calculation. This allows to recover the three regimes predicted from the divergence criteria of the response functions

  16. Influence of coupling phenomena on the transport through compacted clays

    Energy Technology Data Exchange (ETDEWEB)

    Rosanne, M.; Koudina, N.; Adler, P.M. [IPGP, Paris (France); Tevissen, E. [ANDRA, Dept. Etude-Experimentation et Calcul, Chatenay Malabry (France)

    2001-07-01

    Our principal motivation was to study the influence of the coupling phenomena on transport through compacted clays. Coupled transports may occur when a pressure gradient {nabla}P, and electrical field E and a concentration gradient {nabla}C interact. These three gradients induce three fluxes. A flow is generated characterized by the seepage velocity U; a solute flux J{sub L} and a current density I are generated. Close to equilibrium, when the gradients are not to large, the problem is linear and the fluxes are linear functions of the gradients. A first series of experiments was performed with argillite to determine the diagonal properties, i.e., permeability, conductivity, and diffusion coefficient. In a second series of experiments, the voltage resulting from an imposed concentration gradient between two reservoirs separated by a clay sample was systematically measured; this corresponds to the coefficient L{sub 13}. (orig.)

  17. Vibrationally coupled electron transport through single-molecule junctions

    Energy Technology Data Exchange (ETDEWEB)

    Haertle, Rainer

    2012-04-26

    vibrational effects have a profound influence on the transport characteristics of a single-molecule contact and play therefore a fundamental role in this transport problem. Our findings demonstrate that vibrationally coupled electron transport through a molecular junction involves two types of processes: (i) transport processes, where an electron tunnels through the molecular bridge from one lead to the other, and (ii) electron-hole pair creation processes, where an electron tunnels from one of the leads onto the molecular bridge and back to the same lead again. Transport processes directly contribute to the electrical current flowing through a molecular contact and involve both excitation and deexcitation processes of the vibrational modes of the junction. Electron-hole pair creation processes do not directly contribute to the electrical current and typically involve only deexcitation processes. Nevertheless, they constitute a cooling mechanism for the vibrational modes of a single-molecule junction that is as important as cooling by transport processes. As the level of vibrational excitation determines the efficiency of electron transport processes, they have an indirect influence on the electrical current flowing through the junction. As we show, however, this influence can be substantial, in particular, if the molecule is coupled asymmetrically to the leads. Accounting for all these processes and their complex interrelationship, we analyze a number of intriguing transport phenomena, including rectification, negative differential resistance, anomalous peak broadening, mode-selective vibrational excitation and vibrationally induced decoherence. Moreover, we show that higher levels of vibrational excitation are obtained for weaker electronic-vibrational coupling. Thus, based on physical grounds, we establish a relation between the weak electronic-vibrational coupling limit and the limit of large bias voltages, where the level of vibrational excitation in a molecular junction

  18. Fluid transport with time on peritoneal dialysis: the contribution of free water transport and solute coupled water transport

    NARCIS (Netherlands)

    Coester, Annemieke M.; Smit, Watske; Struijk, Dirk G.; Krediet, Raymond T.

    2009-01-01

    Ultrafiltration in peritoneal dialysis occurs through endothelial water channels (free water transport) and together with solutes across small pores: solute coupled water transport. A review is given of cross-sectional studies and on the results of longitudinal follow-up

  19. Transport zonation limits coupled nitrification-denitrification in permeable sediments

    DEFF Research Database (Denmark)

    Kessler, Adam John; Glud, R.N.; Cardenas, M.B.

    2013-01-01

    - and N-15-N-2 gas. The measured two-dimensional profiles correlate with computational model simulations, showing a deep pool of N-2 gas forming, and being advected to the surface below ripple peaks. Further isotope pairing calculations on these data indicate that coupled nitrification......-denitrification is severely limited in permeable sediments because the flow and transport field limits interaction between oxic and anoxic pore water. The approach allowed for new detailed insight into subsurface denitrification zones in complex permeable sediments....

  20. Coupling between solute transport and chemical reactions models

    International Nuclear Information System (INIS)

    Samper, J.; Ajora, C.

    1993-01-01

    During subsurface transport, reactive solutes are subject to a variety of hydrodynamic and chemical processes. The major hydrodynamic processes include advection and convection, dispersion and diffusion. The key chemical processes are complexation including hydrolysis and acid-base reactions, dissolution-precipitation, reduction-oxidation, adsorption and ion exchange. The combined effects of all these processes on solute transport must satisfy the principle of conservation of mass. The statement of conservation of mass for N mobile species leads to N partial differential equations. Traditional solute transport models often incorporate the effects of hydrodynamic processes rigorously but oversimplify chemical interactions among aqueous species. Sophisticated chemical equilibrium models, on the other hand, incorporate a variety of chemical processes but generally assume no-flow systems. In the past decade, coupled models accounting for complex hydrological and chemical processes, with varying degrees of sophistication, have been developed. The existing models of reactive transport employ two basic sets of equations. The transport of solutes is described by a set of partial differential equations, and the chemical processes, under the assumption of equilibrium, are described by a set of nonlinear algebraic equations. An important consideration in any approach is the choice of primary dependent variables. Most existing models cannot account for the complete set of chemical processes, cannot be easily extended to include mixed chemical equilibria and kinetics, and cannot handle practical two and three dimensional problems. The difficulties arise mainly from improper selection of the primary variables in the transport equations. (Author) 38 refs

  1. Microbial and Organic Fine Particle Transport Dynamics in Streams - a Combined Experimental and Stochastic Modeling Approach

    Science.gov (United States)

    Drummond, Jen; Davies-Colley, Rob; Stott, Rebecca; Sukias, James; Nagels, John; Sharp, Alice; Packman, Aaron

    2014-05-01

    Transport dynamics of microbial cells and organic fine particles are important to stream ecology and biogeochemistry. Cells and particles continuously deposit and resuspend during downstream transport owing to a variety of processes including gravitational settling, interactions with in-stream structures or biofilms at the sediment-water interface, and hyporheic exchange and filtration within underlying sediments. Deposited cells and particles are also resuspended following increases in streamflow. Fine particle retention influences biogeochemical processing of substrates and nutrients (C, N, P), while remobilization of pathogenic microbes during flood events presents a hazard to downstream uses such as water supplies and recreation. We are conducting studies to gain insights into the dynamics of fine particles and microbes in streams, with a campaign of experiments and modeling. The results improve understanding of fine sediment transport, carbon cycling, nutrient spiraling, and microbial hazards in streams. We developed a stochastic model to describe the transport and retention of fine particles and microbes in rivers that accounts for hyporheic exchange and transport through porewaters, reversible filtration within the streambed, and microbial inactivation in the water column and subsurface. This model framework is an advance over previous work in that it incorporates detailed transport and retention processes that are amenable to measurement. Solute, particle, and microbial transport were observed both locally within sediment and at the whole-stream scale. A multi-tracer whole-stream injection experiment compared the transport and retention of a conservative solute, fluorescent fine particles, and the fecal indicator bacterium Escherichia coli. Retention occurred within both the underlying sediment bed and stands of submerged macrophytes. The results demonstrate that the combination of local measurements, whole-stream tracer experiments, and advanced modeling

  2. Vibronic coupling effect on the electron transport through molecules

    Science.gov (United States)

    Tsukada, Masaru; Mitsutake, Kunihiro

    2007-03-01

    Electron transport through molecular bridges or molecular layers connected to nano-electrodes is determined by the combination of coherent and dissipative processes, controlled by the electron-vibron coupling, transfer integrals between the molecular orbitals, applied electric field and temperature. We propose a novel theoretical approach, which combines ab initio molecular orbital method with analytical many-boson model. As a case study, the long chain model of the thiophene oligomer is solved by a variation approach. Mixed states of moderately extended molecular orbital states mediated and localised by dress of vibron cloud are found as eigen-states. All the excited states accompanied by multiple quanta of vibration can be solved, and the overall carrier transport properties including the conductance, mobility, dissipation spectra are analyzed by solving the master equation with the transition rates estimated by the golden rule. We clarify obtained in a uniform systematic way, how the transport mode changes from a dominantly coherent transport to the dissipative hopping transport.

  3. Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth.

    Science.gov (United States)

    Du, Wei; Jongbloets, Joeri A; van Boxtel, Coco; Pineda Hernández, Hugo; Lips, David; Oliver, Brett G; Hellingwerf, Klaas J; Branco Dos Santos, Filipe

    2018-01-01

    Microbial bioengineering has the potential to become a key contributor to the future development of human society by providing sustainable, novel, and cost-effective production pipelines. However, the sustained productivity of genetically engineered strains is often a challenge, as spontaneous non-producing mutants tend to grow faster and take over the population. Novel strategies to prevent this issue of strain instability are urgently needed. In this study, we propose a novel strategy applicable to all microbial production systems for which a genome-scale metabolic model is available that aligns the production of native metabolites to the formation of biomass. Based on well-established constraint-based analysis techniques such as OptKnock and FVA, we developed an in silico pipeline-FRUITS-that specifically 'Finds Reactions Usable in Tapping Side-products'. It analyses a metabolic network to identify compounds produced in anabolism that are suitable to be coupled to growth by deletion of their re-utilization pathway(s), and computes their respective biomass and product formation rates. When applied to Synechocystis sp. PCC6803, a model cyanobacterium explored for sustainable bioproduction, a total of nine target metabolites were identified. We tested our approach for one of these compounds, acetate, which is used in a wide range of industrial applications. The model-guided engineered strain shows an obligatory coupling between acetate production and photoautotrophic growth as predicted. Furthermore, the stability of acetate productivity in this strain was confirmed by performing prolonged turbidostat cultivations. This work demonstrates a novel approach to stabilize the production of target compounds in cyanobacteria that culminated in the first report of a photoautotrophic growth-coupled cell factory. The method developed is generic and can easily be extended to any other modeled microbial production system.

  4. Transport regimes spanning magnetization-coupling phase space

    Science.gov (United States)

    Baalrud, Scott D.; Daligault, Jérôme

    2017-10-01

    The manner in which transport properties vary over the entire parameter-space of coupling and magnetization strength is explored. Four regimes are identified based on the relative size of the gyroradius compared to other fundamental length scales: the collision mean free path, Debye length, distance of closest approach, and interparticle spacing. Molecular dynamics simulations of self-diffusion and temperature anisotropy relaxation spanning the parameter space are found to agree well with the predicted boundaries. Comparison with existing theories reveals regimes where they succeed, where they fail, and where no theory has yet been developed.

  5. Cellular automaton model of coupled mass transport and chemical reactions

    International Nuclear Information System (INIS)

    Karapiperis, T.

    1994-01-01

    Mass transport, coupled with chemical reactions, is modelled as a cellular automaton in which solute molecules perform a random walk on a lattice and react according to a local probabilistic rule. Assuming molecular chaos and a smooth density function, we obtain the standard reaction-transport equations in the continuum limit. The model is applied to the reactions a + b ↔c and a + b →c, where we observe interesting macroscopic effects resulting from microscopic fluctuations and spatial correlations between molecules. We also simulate autocatalytic reaction schemes displaying spontaneous formation of spatial concentration patterns. Finally, we propose and discuss the limitations of a simple model for mineral-solute interaction. (author) 5 figs., 20 refs

  6. Coupled electron/photon transport in static external magnetic fields

    International Nuclear Information System (INIS)

    Halbleib, J.A. Sr.; Vandevender, W.H.

    A model is presented which describes coupled electron/photon transport in the presence of static magnetic fields of arbitrary spatial dependence. The method combines state-of-the-art condensed-history electron collisional Monte Carlo and single-scattering photon Monte Carlo, including electron energy-loss straggling and the production and transport of all generations of secondaries, with numerical field integration via the best available variable-step-size Runge-Kutta-Fehlberg or variable-order/variable-step-size Adams PECE differential equation solvers. A three-dimensional cartesian system is employed in the description of particle trajectories. Although the present model is limited to multilayer material configurations, extension to more complex material geometries should not be difficult. Among the more important options are (1) a feature which permits the neglect of field effects in regions where transport is collision dominated and (2) a method for describing the transport in variable-density media where electron energies and material densities are sufficiently low that the density effect on electronic stopping powers may be neglected. (U.S.)

  7. Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

    Energy Technology Data Exchange (ETDEWEB)

    Kieft, T.L.; Murphy, E.M.; Haldeman, D.L.; Amy, P.S.; Bjornstad, B.N.; McDonald, E.V.; Ringelberg, D.B.; White, D.C.; Stair, J.; Griffiths, R.P.; Gsell, T.C.; Holben, W.E.; Boone, D.R.

    1995-01-05

    Two chronosequence of unsaturated buried loess sediments ranging in age from <10,000 years to >1 million years were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession were inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Samples were collected by coring at two sites 40 km apart in the Palouse region of eastern Washington State near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the elevation of the Winona site is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was {approx}250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age: {approx}1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Sediments of equivalent age had equal quantities of microorganisms, but differing community types. Differences in community make-up between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the ages of the microbial communities can be constrained by porewater and sediment ages. In the shallower sediments (<9 m at Washtucna, <12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the populations may be

  8. Live Cell Discovery of Microbial Vitamin Transport and Enzyme-Cofactor Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Lindsey N.; Koech, Phillip K.; Plymale, Andrew E.; Landorf, Elizabeth V.; Konopka, Allan; Collart, Frank; Lipton, Mary S.; Romine, Margaret F.; Wright, Aaron T.

    2016-02-02

    The rapid completion of microbial genomes is inducing a conundrum in functional gene discovery. Novel methods are critically needed to shorten the gap between characterizing a microbial genome and experimentally validating bioinformatically-predicted functions. Of particular importance are transport mechanisms, used to shuttle nutrients and metabolites across cell mem-branes, such as B vitamins, which are indispensable to metabolic reactions crucial to the survival of diverse microbes ranging from members of environmental microbial communities to human pathogens. Methods to accurately assign function and specificity for a wide range of experimentally unidentified and/or predicted membrane-embedded transport proteins, and characterization of intra-cellular enzyme-cofactor/nutrient associations are needed to enable a significantly improved understanding of microbial biochemis-try and physiology, how microbes associate with others, and how they sense and respond to environmental perturbations. Chemical probes derived from B vitamins B1, B2, and B7 have allowed us to experimentally address the aforementioned needs by identifying B vitamin transporters and intracellular protein-cofactor associations through live cell labeling of the filamentous anoxygenic pho-toheterotroph, Chloroflexus aurantiacus J-10-fl, known for both B vitamin biosynthesis and environmental salvage. Our probes provide a unique opportunity to directly link cellular activity and protein function back to ecosystem and/or host dynamics by iden-tifying B vitamin transport and disposition mechanisms required for survival.

  9. A bioenergetics-kinetics coupled modeling study on subsurface microbial metabolism in a field biostimulation experiment

    Science.gov (United States)

    Jin, Q.; Zheng, Z.; Zhu, C.

    2006-12-01

    Microorganisms in nature conserve energy by catalyzing various geochemical reactions. To build a quantitative relationship between geochemical conditions and metabolic rates, we propose a bioenergetics-kinetics coupled modeling approach. This approach describes microbial community as a metabolic network, i.e., fermenting microbes degrade organic substrates while aerobic respirer, nitrate reducer, metal reducer, sulfate reducer, and methanogen consume the fermentation products. It quantifies the control of substrate availability and biological energy conservation on the metabolic rates using thermodynamically consistent rate laws. We applied this simulation approach to study the progress of microbial metabolism during a field biostimulation experiment conducted in Oak Ridge, Tennessee. In the experiment, ethanol was injected into a monitoring well and groundwater was sampled to monitor changes in the chemistry. With time, concentrations of ethanol and SO42- decreased while those of NH4+, Fe2+, and Mn2+ increased. The simulation results fitted well to the observation, indicating simultaneous ethanol degradation and terminal electron accepting processes. The rates of aerobic respiration and denitrification were mainly controlled by substrate concentrations while those of ethanol degradation, sulfate reduction, and methanogenesis were controlled dominantly by the energy availability. The simulation results suggested two different microbial growth statuses in the subsurface. For the functional groups with significant growth, variations with time in substrate concentrations demonstrated a typical S curve. For the groups without significant growth, initial decreases in substrate concentrations were linear with time. Injecting substrates followed by monitoring environmental chemistry therefore provides a convenient approach to characterize microbial growth in the subsurface where methods for direct observation are currently unavailable. This research was funded by the

  10. Transport spectroscopy of coupled donors in silicon nano-transistors

    Science.gov (United States)

    Moraru, Daniel; Samanta, Arup; Anh, Le The; Mizuno, Takeshi; Mizuta, Hiroshi; Tabe, Michiharu

    2014-01-01

    The impact of dopant atoms in transistor functionality has significantly changed over the past few decades. In downscaled transistors, discrete dopants with uncontrolled positions and number induce fluctuations in device operation. On the other hand, by gaining access to tunneling through individual dopants, a new type of devices is developed: dopant-atom-based transistors. So far, most studies report transport through dopants randomly located in the channel. However, for practical applications, it is critical to control the location of the donors with simple techniques. Here, we fabricate silicon transistors with selectively nanoscale-doped channels using nano-lithography and thermal-diffusion doping processes. Coupled phosphorus donors form a quantum dot with the ground state split into a number of levels practically equal to the number of coupled donors, when the number of donors is small. Tunneling-transport spectroscopy reveals fine features which can be correlated with the different numbers of donors inside the quantum dot, as also suggested by first-principles simulation results. PMID:25164032

  11. Coupled Eulerian-Lagrangian transport of large debris by tsunamis

    Science.gov (United States)

    Conde, Daniel A. S.; Ferreira, Rui M. L.; Sousa Oliveira, Carlos

    2016-04-01

    Tsunamis are notorious for the large disruption they can cause on coastal environments, not only due to the imparted momentum of the incoming wave but also due to its capacity to transport large quantities of solid debris, either from natural or human-made sources, over great distances. A 2DH numerical model under development at CERIS-IST (Ferreira et al., 2009; Conde, 2013) - STAV2D - capable of simulating solid transport in both Eulerian and Lagrangian paradigms will be used to assess the relevance of Lagrangian-Eulerian coupling when modelling the transport of solid debris by tsunamis. The model has been previously validated and applied to tsunami scenarios (Conde, 2013), being well-suited for overland tsunami propagation and capable of handling morphodynamic changes in estuaries and seashores. The discretization scheme is an explicit Finite Volume technique employing flux-vector splitting and a reviewed Roe-Riemann solver. Source term formulations are employed in a semi-implicit way, including the two-way coupling of the Lagrangian and Eulerian solvers by means of conservative mass and momentum transfers between fluid and solid phases. The model was applied to Sines Port, a major commercial port in Portugal, where two tsunamigenic scenarios are considered: an 8.5 Mw scenario, consistent with the Great Lisbon Earthquake and Tsunami of the 1st November 1755 (Baptista, 2009), and an hypothetical 9.5 Mw worst-case scenario based on the same historical event. Open-ocean propagation of these scenarios were simulated with GeoClaw model from ClawPack (Leveque, 2011). Following previous efforts on the modelling of debris transport by tsunamis in seaports (Conde, 2015), this work discusses the sensitivity of the obtained results with respect to the phenomenological detail of the employed Eulerian-Lagrangian formulation and the resolution of the mesh used in the Eulerian solver. The results have shown that the fluid to debris mass ratio is the key parameter regarding the

  12. Microbial electron transport and energy conservation – the foundation for optimizing bioelectrochemical systems

    Science.gov (United States)

    Kracke, Frauke; Vassilev, Igor; Krömer, Jens O.

    2015-01-01

    Microbial electrochemical techniques describe a variety of emerging technologies that use electrode–bacteria interactions for biotechnology applications including the production of electricity, waste and wastewater treatment, bioremediation and the production of valuable products. Central in each application is the ability of the microbial catalyst to interact with external electron acceptors and/or donors and its metabolic properties that enable the combination of electron transport and carbon metabolism. And here also lies the key challenge. A wide range of microbes has been discovered to be able to exchange electrons with solid surfaces or mediators but only a few have been studied in depth. Especially electron transfer mechanisms from cathodes towards the microbial organism are poorly understood but are essential for many applications such as microbial electrosynthesis. We analyze the different electron transport chains that nature offers for organisms such as metal respiring bacteria and acetogens, but also standard biotechnological organisms currently used in bio-production. Special focus lies on the essential connection of redox and energy metabolism, which is often ignored when studying bioelectrochemical systems. The possibility of extracellular electron exchange at different points in each organism is discussed regarding required redox potentials and effect on cellular redox and energy levels. Key compounds such as electron carriers (e.g., cytochromes, ferredoxin, quinones, flavins) are identified and analyzed regarding their possible role in electrode–microbe interactions. This work summarizes our current knowledge on electron transport processes and uses a theoretical approach to predict the impact of different modes of transfer on the energy metabolism. As such it adds an important piece of fundamental understanding of microbial electron transport possibilities to the research community and will help to optimize and advance bioelectrochemical

  13. Implications of Lagrangian transport for coupled chemistry-climate simulations

    Science.gov (United States)

    Stenke, A.; Dameris, M.; Grewe, V.; Garny, H.

    2008-10-01

    For the first time a purely Lagrangian transport algorithm is applied in a fully coupled chemistry-climate model (CCM). We use the Lagrangian scheme ATTILA for the transport of water vapour, cloud water and chemical trace species in the ECHAM4.L39(DLR)/CHEM (E39C) CCM. The advantage of the Lagrangian approach is that it is numerically non-diffusive and therefore maintains steeper and more realistic gradients than the operational semi-Lagrangian transport scheme. In case of radiatively active species changes in the simulated distributions feed back to model dynamics which in turn affect the modelled transport. The implications of the Lagrangian transport scheme for stratospheric model dynamics and tracer distributions in the upgraded model version E39C-ATTILA (E39C-A) are evaluated by comparison with observations and results of the E39C model with the operational semi-Lagrangian advection scheme. We find that several deficiencies in stratospheric dynamics in E39C seem to originate from a pronounced modelled wet bias and an associated cold bias in the extra-tropical lowermost stratosphere. The reduction of the simulated moisture and temperature bias in E39C-A leads to a significant advancement of stratospheric dynamics in terms of the mean state as well as annual and interannual variability. As a consequence of the favourable numerical characteristics of the Lagrangian transport scheme and the improved model dynamics, E39C-A generally shows more realistic stratospheric tracer distributions: Compared to E39C high stratospheric chlorine (Cly) concentrations extend further downward and agree now well with analyses derived from observations. Therefore E39C-A realistically covers the altitude of maximum ozone depletion in the stratosphere. The location of the ozonopause, i.e. the transition from low tropospheric to high stratospheric ozone values, is also clearly improved in E39C-A. Furthermore, the simulated temporal evolution of stratospheric Cly in the past is

  14. Coupled Modeling of Rhizosphere and Reactive Transport Processes

    Science.gov (United States)

    Roque-Malo, S.; Kumar, P.

    2017-12-01

    The rhizosphere, as a bio-diverse plant root-soil interface, hosts many hydrologic and biochemical processes, including nutrient cycling, hydraulic redistribution, and soil carbon dynamics among others. The biogeochemical function of root networks, including the facilitation of nutrient cycling through absorption and rhizodeposition, interaction with micro-organisms and fungi, contribution to biomass, etc., plays an important role in myriad Critical Zone processes. Despite this knowledge, the role of the rhizosphere on watershed-scale ecohydrologic functions in the Critical Zone has not been fully characterized, and specifically, the extensive capabilities of reactive transport models (RTMs) have not been applied to these hydrobiogeochemical dynamics. This study uniquely links rhizospheric processes with reactive transport modeling to couple soil biogeochemistry, biological processes, hydrologic flow, hydraulic redistribution, and vegetation dynamics. Key factors in the novel modeling approach are: (i) bi-directional effects of root-soil interaction, such as simultaneous root exudation and nutrient absorption; (ii) multi-state biomass fractions in soil (i.e. living, dormant, and dead biological and root materials); (iii) expression of three-dimensional fluxes to represent both vertical and lateral interconnected flows and processes; and (iv) the potential to include the influence of non-stationary external forcing and climatic factors. We anticipate that the resulting model will demonstrate the extensive effects of plant root dynamics on ecohydrologic functions at the watershed scale and will ultimately contribute to a better characterization of efflux from both agricultural and natural systems.

  15. Dual states estimation of a subsurface flow-transport coupled model using ensemble Kalman filtering

    KAUST Repository

    El Gharamti, Mohamad; Hoteit, Ibrahim; Valstar, Johan R.

    2013-01-01

    Modeling the spread of subsurface contaminants requires coupling a groundwater flow model with a contaminant transport model. Such coupling may provide accurate estimates of future subsurface hydrologic states if essential flow and contaminant data

  16. Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

    International Nuclear Information System (INIS)

    Kieft, T.L.; Murphy, E.M.; Haldeman, D.L.; Amy, P.S.; Bjornstad, B.N.; McDonald, E.V.; Ringelberg, D.B.; White, D.C.; Stair, J.; Griffiths, R.P.; Gsell, T.C.; Holben, W.E.; Boone, D.R.

    1995-01-01

    Two chronosequence of unsaturated buried loess sediments ranging in age from and lt;10,000 years to and gt;1 million years were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession were inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Samples were collected by coring at two sites 40 km apart in the Palouse region of eastern Washington State near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the elevation of the Winona site is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was(approx)250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age:(approx)1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Sediments of equivalent age had equal quantities of microorganisms, but differing community types. Differences in community make-up between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the ages of the microbial communities can be constrained by porewater and sediment ages. In the shallower sediments ( and lt;9 m at Washtucna, and lt;12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the

  17. Microbial behaviour and cross contamination between cargoes in containerized transportation of food

    DEFF Research Database (Denmark)

    Abban, Stephen

    Transportation is central to the global food and feed supply chain. Thus issues of safety, especially cross contamination with pathogens during food transit should be important in food handling operations. A large proportion of the worlds’ food cargo is moved using intermodal cargo containers...... chain, its role in food safety cannot be ignored. Unfortunately not much effort has been put, scientifically, into understanding the role of the various features of the transportation links in food cross contamination (compared to studies for homes, processing factories and farm yards). The PhD project...... has attempted to shed light on containerized food transport and some of its important attributes as regards hygiene and cross contamination. The overall aim of the study was to ‘identify possible microbial hazards and ways of cross contamination during containerized transportation of foods...

  18. Microbially Induced Calcite Precipitation (MICP) - A Technology for Managing Flow and Transport in Porous and Fractured Media

    Science.gov (United States)

    Phillips, A. J.; Hiebert, R.; Kirksey, J.; Lauchnor, E. G.; Rothman, A.; Spangler, L.; Esposito, R.; Gerlach, R.; Cunningham, A. B.

    2014-12-01

    Certain microorganisms e.g., Sporosarcina pasteurii contribute enzymes that catalyze reactions which in the presence of calcium, can create saturation conditions favorable for calcium carbonate precipitation (microbially-induced calcium carbonate precipitation (MICP)). MICP can be used for a number of engineering applications including securing geologic storage of CO2 or other fluids by sealing fractures, improving wellbore integrity, and stabilizing fractured and unstable porous media. MICP treatment has the advantage of the use of small microorganisms, ~2μm, suggesting applicability to treatment of small aperture fractures not accessible to traditional treatments, for example the use of fine cement. The promotion of MICP in the subsurface is a complex reactive transport problem coupling microbial, abiotic (geochemical), geomechanical and hydrodynamic processes. In the laboratory, MICP has been demonstrated to cement together heavily fractured shale and reduce the permeability of fractures in shale and sandstone cores up to five orders of magnitude under both ambient and subsurface relevant pressure conditions (Figure 1). Most recently, a MICP fracture treatment field study was performed at a well at the Southern Company Gorgas Steam Generation Plant (Alabama) (Figure 1). The Fayetteville Sandstone at approximately 1120' below ground surface was hydraulically fractured prior to MICP treatment. After 4 days of injection of 24 calcium pulses and 6 microbial inoculations, injectivity of brine into the formation was significantly reduced. The experiment also resulted in a reduction in pressure decay which is a measure of improved wellbore integrity. These promising results suggest the potential for MICP treatment to seal fractured pathways at the field scale to improve the long-term security of geologically-stored carbon dioxide or prevent leakage of shale gas or hydraulic fracturing fluids into functional overlying aquifers, reducing environmental impacts.

  19. Lagooning microbial fuel cells: A first approach by coupling electricity-producing microorganisms and algae

    International Nuclear Information System (INIS)

    Lobato, Justo; González del Campo, Araceli; Fernández, Francisco J.; Cañizares, Pablo; Rodrigo, Manuel A.

    2013-01-01

    Highlights: • An algae cathode of a MFC has been used without artificial mediators or catalysts. • To perform a lagooning wastewater treatment coupled with energy-producing MFC. • The producing electricity operates under day/night irradiation cycles, is shown. - Abstract: The paper focused on the start-up and performance characterisation of a new type of microbial fuel cell (MFC), in which an algae culture was seeded in the cathodic chamber to produce the oxygen required to complete the electrochemical reactions of the MFC, thus circumventing the need for a mechanical aerator. The system did not use mediators or high cost catalysts and it can be started-up easily using a straightforward three-stage procedure. The start-up consists of the separate production of the electricity-producing microorganisms and the algae cultures (stage I), replacement of the mechanical aeration system by the algae culture (stage II) and a change in the light dosage from a continuous input to a dynamic day/night profile. The MFC was operated under a regime of 12 h light and 12 h dark and was also operated in batch and continuous substrate-feeding modes. The same cell voltage was achieved when the cathode compartment was operated with air supplied by aerators, which means that this configuration can perform as well as the traditional one. The results also show the influence of both the organic load and light irradiation on electricity production and demonstrate that this type MFC is a robust and promising technology that can be considered as a first approach to perform a lagooning wastewater treatment with microbial fuel cells

  20. Coupling electrokinetics with microbial biodegradation enhances the removal of cycloparaffinic hydrocarbons in soils.

    Science.gov (United States)

    Yuan, Ye; Guo, Shuhai; Li, Fengmei; Wu, Bo; Yang, Xuelian; Li, Xuan

    2016-12-15

    An innovative approach that couples electrokinetics with microbial degradation to breakdown cycloparaffinic hydrocarbons in soils is described. Soils were spiked with cyclododecane, used as a model pollutant, at approximately 1000mgkg -1 . A mixture of petroleum-utilizing bacteria was added to achieve about 10 6 -10 7 CFUg -1 . Then, three treatments were applied for 25 days: (1) no electric field, control; (2) a constant voltage gradient of 1.3Vcm -1 in one direction; and (3) the same electric field, but with periodical switching of polarity. The degradation pathway of cyclododecane was not changed by the electric field, but the dynamic processes were remarkably enhanced, especially when the electric field was periodically switched. After 25 days, 79.9% and 87.0% of the cyclododecane was degraded in tests 2 and 3, respectively; both much higher than the 61.5% degraded in test 1. Analysis of the intermediate products strongly indicated that the competitive advantage of the electric field was the increase in ring-breaking of cyclododecane, resulting in greater concentrations of linear substances that were more susceptible to microbial attack, that is, β-oxidation. The conditions near the cathode were more favorable for the growth and metabolism of microorganisms, which also enhanced β-oxidation of the linear alkanoic acids. Therefore, when the electric field polarity was periodically switched, the functions of both the anode and cathode electrodes were applied across the whole soil cell, further increasing the degradation efficiency. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. A network model shows the importance of coupled processes in the microbial N cycle in the Cape Fear River Estuary

    Science.gov (United States)

    Hines, David E.; Lisa, Jessica A.; Song, Bongkeun; Tobias, Craig R.; Borrett, Stuart R.

    2012-06-01

    Estuaries serve important ecological and economic functions including habitat provision and the removal of nutrients. Eutrophication can overwhelm the nutrient removal capacity of estuaries and poses a widely recognized threat to the health and function of these ecosystems. Denitrification and anaerobic ammonium oxidation (anammox) are microbial processes responsible for the removal of fixed nitrogen and diminish the effects of eutrophication. Both of these microbial removal processes can be influenced by direct inputs of dissolved inorganic nitrogen substrates or supported by microbial interactions with other nitrogen transforming pathways such as nitrification and dissimilatory nitrate reduction to ammonium (DNRA). The coupling of nitrogen removal pathways to other transformation pathways facilitates the removal of some forms of inorganic nitrogen; however, differentiating between direct and coupled nitrogen removal is difficult. Network modeling provides a tool to examine interactions among microbial nitrogen cycling processes and to determine the within-system history of nitrogen involved in denitrification and anammox. To examine the coupling of nitrogen cycling processes, we built a nitrogen budget mass balance network model in two adjacent 1 cm3 sections of bottom water and sediment in the oligohaline portion of the Cape Fear River Estuary, NC, USA. Pathway, flow, and environ ecological network analyses were conducted to characterize the organization of nitrogen flow in the estuary and to estimate the coupling of nitrification to denitrification and of nitrification and DNRA to anammox. Centrality analysis indicated NH4+ is the most important form of nitrogen involved in removal processes. The model analysis further suggested that direct denitrification and coupled nitrification-denitrification had similar contributions to nitrogen removal while direct anammox was dominant to coupled forms of anammox. Finally, results also indicated that partial

  2. A Stochastic Multi-Media Model of Microbial Transport in Watersheds

    Science.gov (United States)

    Yeghiazarian, L.; Safwat, A.; Whiteaker, T.; Teklitz, A.; Nietch, C.; Maidment, D. R.; Best, E. P.

    2012-12-01

    Fecal contamination is the leading cause of surface-water impairment in the US, and fecal pathogens are capable of triggering massive outbreaks of gastrointestinal disease. The difficulty in prediction of water contamination has its roots in the stochastic variability of fecal pathogens in the environment, and in the complexity of microbial dynamics and interactions on the soil surface and in water. To address these challenges, we have developed a stochastic model whereby the transport of microorganisms in watersheds is considered in two broad categories: microorganisms that are attached to mineral or organic substrates in suspended sediment; and unattached microorganisms suspended in overland flow. The interactions of microorganisms with soil particles on the soil surface and in the overland flow lead to transitions of microorganisms between solid and aqueous media. The strength of attachment of microorganisms to soil particles is determined by the chemical characteristics of soils which are highly correlated with the particle size. The particle size class distribution in the suspended sediment is predicted by the Water Erosion Prediction Project (WEPP). The model is integrated with ArcGIS, resulting in a general transport-modeling framework applicable to a variety of biological and chemical surface water contaminants. Simulations are carried out for a case study of contaminant transport in the East Fork Little Miami River Watershed in Ohio. Model results include the spatial probability distribution of microbes in the watershed and can be used for assessment of (1) mechanisms dominating microbial transport, and (2) time and location of highest likelihood of microbial occurrence, thus yielding information on best water sampling strategies.

  3. Coupled Spatio-Temporal Patterns of Solute Transport, Metabolism and Nutrient Uptake in Streams

    Science.gov (United States)

    Kurz, M. J.; Schmidt, C.

    2017-12-01

    Slower flow velocities and longer residence times within stream transient storage (TS) zones facilitate interaction between solutes and microbial communities, potentially increasing local rates of metabolic activity. Multiple factors, including channel morphology and substrate, variable hydrology, and seasonal changes in biological and physical parameters, result in changes in the solute transport dynamics and reactivity of TS zones over time and space. These changes would be expected to, in turn, influence rates of whole-stream ecosystem functions such as metabolism and nutrient uptake. However, the linkages between solute transport and ecosystem functioning within TS zones, and the contribution of TS zones to whole-stream functioning, are not always so straight forward. This may be due, in part, to methodological challenges. In this study we investigated the influence of stream channel hydro-morphology and substrate type on reach (103 m) and sub-reach (102 m) scale TS and ecosystem functioning. Patterns in solute transport, metabolism and nitrate uptake were tracked from April through October in two contrasting upland streams using several methods. The two streams, located in the Harz Mountains, Germany, are characterized by differing size (0.02 vs. 0.3 m3/s), dominant stream channel substrate (bedrock vs. alluvium) and sub-reach morphology (predominance of pools, riffles and glides). Solute transport parameters and respiration rates at the reach and sub-reach scale were estimated monthly from coupled pulse injections of the reactive tracer resazurin (Raz) and conservative tracers uranine and salt. Raz, a weakly fluorescent dye, irreversibly transforms to resorufin (Rru) under mildly reducing conditions, providing a proxy for aerobic respiration. Daily rates of primary productivity, respiration and nitrate retention at the reach scale were estimated using the diel cycles in dissolved oxygen and nitrate concentrations measured by in-situ sensors. Preliminary

  4. Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand.

    Science.gov (United States)

    Hug, Katrin; Maher, William A; Stott, Matthew B; Krikowa, Frank; Foster, Simon; Moreau, John W

    2014-01-01

    Acid-sulfide hot springs are analogs of early Earth geothermal systems where microbial metal(loid) resistance likely first evolved. Arsenic is a metalloid enriched in the acid-sulfide hot spring Champagne Pool (Waiotapu, New Zealand). Arsenic speciation in Champagne Pool follows reaction paths not yet fully understood with respect to biotic contributions and coupling to biogeochemical sulfur cycling. Here we present quantitative arsenic speciation from Champagne Pool, finding arsenite dominant in the pool, rim and outflow channel (55-75% total arsenic), and dithio- and trithioarsenates ubiquitously present as 18-25% total arsenic. In the outflow channel, dimethylmonothioarsenate comprised ≤9% total arsenic, while on the outflow terrace thioarsenates were present at 55% total arsenic. We also quantified sulfide, thiosulfate, sulfate and elemental sulfur, finding sulfide and sulfate as major species in the pool and outflow terrace, respectively. Elemental sulfur concentration reached a maximum at the terrace. Phylogenetic analysis of 16S rRNA genes from metagenomic sequencing revealed the dominance of Sulfurihydrogenibium at all sites and an increased archaeal population at the rim and outflow channel. Several phylotypes were found closely related to known sulfur- and sulfide-oxidizers, as well as sulfur- and sulfate-reducers. Bioinformatic analysis revealed genes underpinning sulfur redox transformations, consistent with sulfur speciation data, and illustrating a microbial role in sulfur-dependent transformation of arsenite to thioarsenate. Metagenomic analysis also revealed genes encoding for arsenate reductase at all sites, reflecting the ubiquity of thioarsenate and a need for microbial arsenate resistance despite anoxic conditions. Absence of the arsenite oxidase gene, aio, at all sites suggests prioritization of arsenite detoxification over coupling to energy conservation. Finally, detection of methyl arsenic in the outflow channel, in conjunction with

  5. Energy Coupling Factor-Type ABC Transporters for Vitamin Uptake in Prokaryotes

    NARCIS (Netherlands)

    Erkens, Guus B.; Dosz-Majsnerowska, Maria; ter Beek, Josy; Slotboom, Dirk Jan

    2012-01-01

    Energy coupling factor (ECF) transporters are a subgroup of ATP-binding cassette (ABC) transporters involved in the uptake of vitamins and micronutrients in prokaryotes. In contrast to classical ABC importers, ECF transporters do not make use of water-soluble substrate binding proteins or domains

  6. Lattice Boltzmann based multicomponent reactive transport model coupled with geochemical solver for scale simulations

    NARCIS (Netherlands)

    Patel, R.A.; Perko, J.; Jaques, D.; De Schutter, G.; Ye, G.; Van Breugel, K.

    2013-01-01

    A Lattice Boltzmann (LB) based reactive transport model intended to capture reactions and solid phase changes occurring at the pore scale is presented. The proposed approach uses LB method to compute multi component mass transport. The LB multi-component transport model is then coupled with the

  7. Retention and transport of an anaerobic trichloroethene dechlorinating microbial culture in anaerobic porous media.

    Science.gov (United States)

    Zhang, Huixin; Ulrich, Ania C; Liu, Yang

    2015-06-01

    The influence of solution chemistry on microbial transport was examined using the strictly anaerobic trichloroethene (TCE) bioaugmentation culture KB-1(®). A column was employed to determine transport behaviors and deposition kinetics of three distinct functional species in KB-1(®), Dehalococcoides, Geobacter, and Methanomethylovorans, over a range of ionic strengths under a well-controlled anaerobic condition. A quantitative polymerase chain reaction (qPCR) was utilized to enumerate cell concentration and complementary techniques were implemented to evaluate cell surface electrokinetic potentials. Solution chemistry was found to positively affect the deposition rates, which was consistent with calculated Derjaguin-Landau-Verwey-Overbeek (DLVO) interaction energies. Retained microbial profiles showed spatially constant colloid deposition rate coefficients, in agreement with classical colloid filtration theory (CFT). It was interesting to note that the three KB-1(®) species displayed similar transport and retention behaviors under the defined experimental conditions despite their different cell electrokinetic properties. A deeper analysis of cell characteristics showed that factors, such as cell size and shape, concentration, and motility were involved in determining adhesion behavior. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. How LeuT shapes our understanding of the mechanisms of sodium-coupled neurotransmitter transporters.

    Science.gov (United States)

    Penmatsa, Aravind; Gouaux, Eric

    2014-03-01

    Neurotransmitter transporters are ion-coupled symporters that drive the uptake of neurotransmitters from neural synapses. In the past decade, the structure of a bacterial amino acid transporter, leucine transporter (LeuT), has given valuable insights into the understanding of architecture and mechanism of mammalian neurotransmitter transporters. Different conformations of LeuT, including a substrate-free state, inward-open state, and competitive and non-competitive inhibitor-bound states, have revealed a mechanistic framework for the transport and transport inhibition of neurotransmitters. The current review integrates our understanding of the mechanistic and pharmacological properties of eukaryotic neurotransmitter transporters obtained through structural snapshots of LeuT.

  9. Analysis of the coupling coordination between transportation infrastructure investment and economic development in Hubei province

    Directory of Open Access Journals (Sweden)

    Wenxia Zhai

    2017-06-01

    Full Text Available The relationship between transportation infrastructure investment and regional economic growth has been the focus of domestic and foreign academic research. Using the models of coupling degree and coupling coordination degree, this paper calculated the coupling degree and coupling coordination degree between the comprehensive level of transportation infrastructure investment and economic development in Hubei province and its 17 cities, and analyzed its temporal and spatial characteristics. The result showed that, from 2001 to 2013, the coupling and coupling coordination between transportation infrastructure investment and economic development in Hubei province were on a steady rise in the time sequence characteristics. It experienced the upgrade from the uncoordinated – nearly uncoordinated – barely coordinated – intermediately coordinated stages. In the year of 2013, the coupling and coupling coordination of transportation infrastructure investment and economic development in the 17 prefecture-level cities of Hubei Province showed a very uneven spatial difference. Good coordination, primary coordination, barely coordinate, and barely in-coordination are distributed in the province. The average coordination degree of the 17 prefecture-level cities in Hubei is relatively low, and there is a negative tend to expand the difference. This study has confirmed the relationship between transportation infrastructure investment and the economic development to be in an interactive coupling and coordination, but in different regions and different stages, the degree of coordination has obvious spatial and temporal differences.

  10. A Loose Relationship: Incomplete H+/Sugar Coupling in the MFS Sugar Transporter GlcP.

    Science.gov (United States)

    Bazzone, Andre; Zabadne, Annas J; Salisowski, Anastasia; Madej, M Gregor; Fendler, Klaus

    2017-12-19

    The glucose transporter from Staphylococcus epidermidis, GlcP Se , is a homolog of the human GLUT sugar transporters of the major facilitator superfamily. Together with the xylose transporter from Escherichia coli, XylE Ec , the other prominent prokaryotic GLUT homolog, GlcP Se , is equipped with a conserved proton-binding site arguing for an electrogenic transport mode. However, the electrophysiological analysis of GlcP Se presented here reveals important differences between the two GLUT homologs. GlcP Se , unlike XylE Ec , does not perform steady-state electrogenic transport at symmetrical pH conditions. Furthermore, when a pH gradient is applied, partially uncoupled transport modes can be generated. In contrast to other bacterial sugar transporters analyzed so far, in GlcP Se sugar binding, translocation and release are also accomplished by the deprotonated transporter. Based on these experimental results, we conclude that coupling of sugar and H + transport is incomplete in GlcP Se . To verify the viability of the observed partially coupled GlcP Se transport modes, we propose a universal eight-state kinetic model in which any degree of coupling is realized and H + /sugar symport represents only a specific instance. Furthermore, using sequence comparison with strictly coupled XylE Ec and similar sugar transporters, we identify an additional charged residue that may be essential for effective H + /sugar symport. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  11. Numerical modelling of biophysicochemical effects on multispecies reactive transport in porous media involving Pseudomonas putida for potential microbial enhanced oil recovery application.

    Science.gov (United States)

    Sivasankar, P; Rajesh Kanna, A; Suresh Kumar, G; Gummadi, Sathyanarayana N

    2016-07-01

    pH and resident time of injected slug plays a critical role in characterizing the reservoir for potential microbial enhanced oil recovery (MEOR) application. To investigate MEOR processes, a multispecies (microbes-nutrients) reactive transport model in porous media was developed by coupling kinetic and transport model. The present work differs from earlier works by explicitly determining parametric values required for kinetic model by experimental investigations using Pseudomonas putida at different pH conditions and subsequently performing sensitivity analysis of pH, resident time and water saturation on concentrations of microbes, nutrients and biosurfactant within reservoir. The results suggest that nutrient utilization and biosurfactant production are found to be maximum at pH 8 and 7.5 respectively. It is also found that the sucrose and biosurfactant concentrations are highly sensitive to pH rather than reservoir microbial concentration, while at larger resident time and water saturation, the microbial and nutrient concentrations were lesser due to enhanced dispersion. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. An innovative bioelectrochemical-anaerobic digestion-coupled system for in-situ ammonia recovery and biogas enhancement: process performance and microbial ecology

    DEFF Research Database (Denmark)

    Zhang, Yifeng; Angelidaki, Irini

    (SMRC) and a continuous stirred tank reactor (CSTR), to prevent ammonia toxicity during anaerobic digestion by in-situ ammonia recovery and electricity production. In batch experiment, the ammonia concentration in the CSTR decreased from 6 to 0.7 g-N/L with an average recovery rate of 0.18 g-N/L(CSTR...... performance was enhanced. In addition, the coexistence of other cations in CSTR or cathode had no negative effect on the ammonia transportation. In continuous reactor operation, 112% extra biogas production was achieved due to ammonia recovery. High-throughput molecular sequencing analysis showed an impact...... of ammonia recovery on the microbial community composition in the integrated system. Results clearly indicate the great potential of the SMRC-CSTR-coupled system for efficient and cost-effective ammonia recovery, energy production and treatment of ammonia-rich residues....

  13. Air-cathode structure optimization in separator-coupled microbial fuel cells

    KAUST Repository

    Zhang, Xiaoyuan

    2011-12-01

    Microbial fuel cells (MFC) with 30% wet-proofed air cathodes have previously been optimized to have 4 diffusion layers (DLs) in order to limit oxygen transfer into the anode chamber and optimize performance. Newer MFC designs that allow close electrode spacing have a separator that can also reduce oxygen transfer into the anode chamber, and there are many types of carbon wet-proofed materials available. Additional analysis of conditions that optimize performance is therefore needed for separator-coupled MFCs in terms of the number of DLs and the percent of wet proofing used for the cathode. The number of DLs on a 50% wet-proofed carbon cloth cathode significantly affected MFC performance, with the maximum power density decreasing from 1427 to 855mW/m 2 for 1-4 DLs. A commonly used cathode (30% wet-proofed, 4 DLs) produced a maximum power density (988mW/m 2) that was 31% less than that produced by the 50% wet-proofed cathode (1 DL). It was shown that the cathode performance with different materials and numbers of DLs was directly related to conditions that increased oxygen transfer. The coulombic efficiency (CE) was more affected by the current density than the oxygen transfer coefficient for the cathode. MFCs with the 50% wet-proofed cathode (2 DLs) had a CE of >84% (6.8A/m 2), which was substantially larger than that previously obtained using carbon cloth air-cathodes lacking separators. These results demonstrate that MFCs constructed with separators should have the minimum number of DLs that prevent water leakage and maximize oxygen transfer to the cathode. © 2011 Elsevier B.V.

  14. CARRIER TRANSPORT IN MESOSCOPIC SILICON-COUPLED SUPERCONDUCTING JUNCTIONS

    NARCIS (Netherlands)

    VANHUFFELEN, WM; KLAPWIJK, TM; HESLINGA, DR; DEBOER, MJ; VANDERPOST, N

    1993-01-01

    An overview is presented of experimental results on supercurrent flow and transport at finite voltages in a well-characterized, sandwich-type superconductor-semiconductor-superconductor junction. Carrier transport through the structure is found to be dominated by the interfaces. At low temperatures,

  15. A Coupled Chemical and Mass Transport Model for Concrete Durability

    DEFF Research Database (Denmark)

    Jensen, Mads Mønster; Johannesson, Björn; Geiker, Mette Rica

    2012-01-01

    In this paper a general continuum theory is used to evaluate the service life of cement based materials, in terms of mass transport processes and chemical degradation of the solid matrix. The model established is a reactive mass transport model, based on an extended version of the Poisson-Nernst-...

  16. Modelling the transport and decay processes of microbial tracers in a macro-tidal estuary.

    Science.gov (United States)

    Abu-Bakar, Amyrhul; Ahmadian, Reza; Falconer, Roger A

    2017-10-15

    The Loughor Estuary is a macro-tidal coastal basin, located along the Bristol Channel, in the South West of the U.K. The maximum spring tidal range in the estuary is up to 7.5 m, near Burry Port Harbour. This estuarine region can experience severe coastal flooding during high spring tides, including extreme flooding of the intertidal saltmarshes at Llanrhidian, as well as the lower industrial and residential areas at Llanelli and Gowerton. The water quality of this estuarine basin needs to comply with the designated standards for safe recreational bathing and shellfish harvesting industries. The waterbody however, potentially receives overloading of bacterial inputs that enter the estuarine system from both point and diffuse sources. Therefore, a microbial tracer study was carried out to get a better understanding of the faecal bacteria sources and to enable a hydro-environmental model to be refined and calibrated for both advection and dispersion transport. A two-dimensional hydro-environmental model has been refined and extended to predict the highest water level covering the intertidal floodplains of the Loughor Estuary. The validated hydrodynamic model for both water levels and currents, was included with the injected mass of microbial tracer, i.e. MS2 coliphage from upstream of the estuary, and modelled as a non-conservative tracer over several tidal cycles through the system. The calibration and validation of the transport and decay of microbial tracer was undertaken, by comparing the model results and the measured data at two different sampling locations. The refined model developed as a part of this study, was used to acquire a better understanding of the water quality processes and the potential sources of bacterial pollution in the estuary. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Effect of spin rotation coupling on spin transport

    International Nuclear Information System (INIS)

    Chowdhury, Debashree; Basu, B.

    2013-01-01

    We have studied the spin rotation coupling (SRC) as an ingredient to explain different spin-related issues. This special kind of coupling can play the role of a Dresselhaus like coupling in certain conditions. Consequently, one can control the spin splitting, induced by the Dresselhaus like term, which is unusual in a semiconductor heterostructure. Within this framework, we also study the renormalization of the spin-dependent electric field and spin current due to the k → ⋅p → perturbation, by taking into account the interband mixing in the rotating system. In this paper we predict the enhancement of the spin-dependent electric field resulting from the renormalized spin rotation coupling. The renormalization factor of the spin electric field is different from that of the SRC or Zeeman coupling. The effect of renormalized SRC on spin current and Berry curvature is also studied. Interestingly, in the presence of this SRC-induced SOC it is possible to describe spin splitting as well as spin galvanic effect in semiconductors. -- Highlights: •Studied effect of spin rotation coupling on the spin electric field, spin current and Berry curvature. •In the k → ⋅p → framework we study the renormalization of spin electric field and spin current. •For an inertial system we have discussed the spin splitting. •Expression for the Berry phase in the inertial system is discussed. •The inertial spin galvanic effect is studied

  18. Effect of spin rotation coupling on spin transport

    Energy Technology Data Exchange (ETDEWEB)

    Chowdhury, Debashree, E-mail: debashreephys@gmail.com; Basu, B., E-mail: sribbasu@gmail.com

    2013-12-15

    We have studied the spin rotation coupling (SRC) as an ingredient to explain different spin-related issues. This special kind of coupling can play the role of a Dresselhaus like coupling in certain conditions. Consequently, one can control the spin splitting, induced by the Dresselhaus like term, which is unusual in a semiconductor heterostructure. Within this framework, we also study the renormalization of the spin-dependent electric field and spin current due to the k{sup →}⋅p{sup →} perturbation, by taking into account the interband mixing in the rotating system. In this paper we predict the enhancement of the spin-dependent electric field resulting from the renormalized spin rotation coupling. The renormalization factor of the spin electric field is different from that of the SRC or Zeeman coupling. The effect of renormalized SRC on spin current and Berry curvature is also studied. Interestingly, in the presence of this SRC-induced SOC it is possible to describe spin splitting as well as spin galvanic effect in semiconductors. -- Highlights: •Studied effect of spin rotation coupling on the spin electric field, spin current and Berry curvature. •In the k{sup →}⋅p{sup →} framework we study the renormalization of spin electric field and spin current. •For an inertial system we have discussed the spin splitting. •Expression for the Berry phase in the inertial system is discussed. •The inertial spin galvanic effect is studied.

  19. Regulation of Microbial Herbicide Transformation by Coupled Moisture and Oxygen Dynamics in Soil

    Science.gov (United States)

    Marschmann, G.; Pagel, H.; Uksa, M.; Streck, T.; Milojevic, T.; Rezanezhad, F.; Van Cappellen, P.

    2017-12-01

    The key processes of herbicide fate in agricultural soils are well-characterized. However, most of these studies are from batch experiments that were conducted under optimal aerobic conditions. In order to delineate the processes controlling herbicide (i.e., phenoxy herbicide 2-methyl-4-chlorophenoxyacetic acid, MCPA) turnover in soil under variable moisture conditions, we conducted a state-of-the-art soil column experiment, with a highly instrumented automated soil column system, under constant and oscillating water table regimes. In this system, the position of the water table was imposed using a computer-controlled, multi-channel pump connected to a hydrostatic equilibrium reservoir and a water storage reservoir. The soil samples were collected from a fertilized, arable and carbon-limited agricultural field site in Germany. The efflux of CO2 was determined from headspace gas measurements as an integrated signal of microbial respiration activity. Moisture and oxygen profiles along the soil column were monitored continuously using high-resolution moisture content probes and luminescence-based Multi Fiber Optode (MuFO) microsensors, respectively. Pore water and solid-phase samples were collected periodically at 8 depths and analyzed for MCPA, dissolved inorganic and organic carbon concentrations as well as the abundance of specific MCPA-degrading bacteria. The results indicated a clear effect of the water table fluctuations on CO2 fluxes, with lower fluxes during imbibition periods and enhanced CO2 fluxes after drainage. In this presentation, we focus on the results of temporal changes in the vertical distribution of herbicide, specific herbicide degraders, organic carbon concentration, moisture content and oxygen. We expect that the high spatial and temporal resolution of measurements from this experiment will allow robust calibration of a reactive transport model for the soil columns, with subsequent identification and quantification of rate limiting processes of

  20. Proton movement and coupling in the POT family of peptide transporters.

    Science.gov (United States)

    Parker, Joanne L; Li, Chenghan; Brinth, Allete; Wang, Zhi; Vogeley, Lutz; Solcan, Nicolae; Ledderboge-Vucinic, Gregory; Swanson, Jessica M J; Caffrey, Martin; Voth, Gregory A; Newstead, Simon

    2017-12-12

    POT transporters represent an evolutionarily well-conserved family of proton-coupled transport systems in biology. An unusual feature of the family is their ability to couple the transport of chemically diverse ligands to an inwardly directed proton electrochemical gradient. For example, in mammals, fungi, and bacteria they are predominantly peptide transporters, whereas in plants the family has diverged to recognize nitrate, plant defense compounds, and hormones. Although recent structural and biochemical studies have identified conserved sites of proton binding, the mechanism through which transport is coupled to proton movement remains enigmatic. Here we show that different POT transporters operate through distinct proton-coupled mechanisms through changes in the extracellular gate. A high-resolution crystal structure reveals the presence of ordered water molecules within the peptide binding site. Multiscale molecular dynamics simulations confirm proton transport occurs through these waters via Grotthuss shuttling and reveal that proton binding to the extracellular side of the transporter facilitates a reorientation from an inward- to outward-facing state. Together these results demonstrate that within the POT family multiple mechanisms of proton coupling have likely evolved in conjunction with variation of the extracellular gate. Copyright © 2017 the Author(s). Published by PNAS.

  1. Charge and Spin Transport in Spin-orbit Coupled and Topological Systems

    KAUST Repository

    Ndiaye, Papa Birame

    2017-01-01

    for next-generation technology, three classes of systems that possibly enhance the spin and charge transport efficiency: (i)- topological insulators, (ii)- spin-orbit coupled magnonic systems, (iii)- topological magnetic textures (skyrmions and 3Q magnetic

  2. Optimization studies of bio-hydrogen production in a coupled microbial electrolysis-dye sensitized solar cell system.

    Science.gov (United States)

    Ajayi, Folusho Francis; Kim, Kyoung-Yeol; Chae, Kyu-Jung; Choi, Mi-Jin; Chang, In Seop; Kim, In S

    2010-03-01

    Bio-hydrogen production in light-assisted microbial electrolysis cell (MEC) with a dye sensitized solar cell (DSSC) was optimized by connecting multiple MECs to a single dye (N719) sensitized solar cell (V(OC) approx. 0.7 V). Hydrogen production occurred simultaneously in all the connected MECs when the solar cell was irradiated with light. The amount of hydrogen produced in each MEC depends on the activity of the microbial catalyst on their anode. Substrate (acetate) to hydrogen conversion efficiencies ranging from 42% to 65% were obtained from the reactors during the experiment. A moderate light intensity of 430 W m(-2) was sufficient for hydrogen production in the coupled MEC-DSSC. A higher light intensity of 915 W m(-2), as well as an increase in substrate concentration, did not show any improvement in the current density due to limitation caused by the rate of microbial oxidation on the anode. A significant reduction in the surface area of the connected DSSC only showed a slight effect on current density in the coupled MEC-DSSC system when irradiated with light.

  3. Long distance electron transport in marine sediments: Microbial and geochemical implications

    DEFF Research Database (Denmark)

    Risgaard-Petersen, Nils; Larsen, Steffen; Pfeffer, Christian

    and promotes the formation of Mg-calcite and iron oxides in the oxic zone. Oxygen seems to be the major electron acceptor, and more than 40% of the oxygen consumption in sediments can be driven by long distance electron transfer from distant electron donors. The major e-donor is sulfide, which is oxidized......Anaerobic oxidation of organic matter in marine sediment is traditionally considered to be coupled to oxygen reduction via a cascade of redox processes and transport of intermittent electron donors and acceptors. Electric currents have been found to shortcut this cascade and directly couple...... oxidation of sulphide centimeters down in marine sediment to the reduction of oxygen at the very surface1 . This electric coupling of spatially separated redox half-reactions seems to be mediated by centimeter long filamentous Desulfubulbus affiliated bacteria with morphological and ultra...

  4. Coupling of Groundwater Transport and Plant Uptake Models

    DEFF Research Database (Denmark)

    Rein, Arno; Bauer-Gottwein, Peter; Trapp, Stefan

    2010-01-01

    in environmental systems at different scale. Feedback mechanisms between plants and hydrological systems can play an important role, however having received little attention to date. Here, a new model concept for dynamic plant uptake models applying analytical matrix solutions is presented, which can be coupled...

  5. Geometry and transport in a model of two coupled quadratic nonlinear waveguides

    DEFF Research Database (Denmark)

    Stirling, James R.; Bang, Ole; Christiansen, Peter Leth

    2008-01-01

    This paper applies geometric methods developed to understand chaos and transport in Hamiltonian systems to the study of power distribution in nonlinear waveguide arrays. The specific case of two linearly coupled X(2) waveguides is modeled and analyzed in terms of transport and geometry in the pha...

  6. Cambrian rivers and floodplains: the significance of microbial cementation, groundwater and aeolian sediment transport

    Science.gov (United States)

    Reesink, A. J. H.; Best, J.; Freiburg, J. T.; Nathan, W.

    2016-12-01

    Rivers that existed before land plants colonized the Earth are commonly considered to be unaffected by microbial activity on their floodplains, because the limited cementation produced by microbial activity is insufficient to stabilize the river banks. Although this assumption is likely correct, such emphasis on channel dynamics ignores the potential role of floodplain dynamics as an integral component of the river system. Detailed analysis of cores from the Cambrian Mount Simon Sandstone, Illinois, suggests that a significant proportion of the terrestrial sequence is composed of flat-bedded `crinkly' structures that provide evidence of cementation by soil crusts and microbial biofilms, and that promoted the adhesion of sediment to sticky surfaces. Wind ripples and local desert pavements were abundant. These findings highlight that sediment deposition on Cambrian floodplains was often dominated by wind in locations where the ground water table reached the surface, and was thus likely independent of sediment transport within the river channel. Erosion by wind would thus have been hindered by surface cementation and the formation of desert pavements. Such ground water control on deposition, and resistance to erosion by floodplain surface hardening, appear to have been the primary controls on Cambrian floodplain topography. Because floodplain topography poses a key control on channel and floodplain flow, these processes may have affected patterns of erosion and deposition, as well as reach-scale dynamics such as channel avulsions. The autonomous operation of wind-and-groundwater controlled floodplains makes pre-vegetated river systems more sensitive to climatic conditions such as precipitation and evaporation, and strikingly different from those that occurred after the development of land plants.

  7. Temporal moment analysis of solute transport in a coupled fracture ...

    Indian Academy of Sciences (India)

    by considering an inlet boundary condition of constant continuous source in a single fracture. The effect of various fracture-skin parameters like porosity, thickness and ... Study on fluid flow and transport of solute through fractures has been an .... of solutes is happening normal to the direction of flow due to the free molecular.

  8. Axial SPN and radial MOC coupled whole core transport calculation

    International Nuclear Information System (INIS)

    Cho, Jin-Young; Kim, Kang-Seog; Lee, Chung-Chan; Zee, Sung-Quun; Joo, Han-Gyu

    2007-01-01

    The Simplified P N (SP N ) method is applied to the axial solution of the two-dimensional (2-D) method of characteristics (MOC) solution based whole core transport calculation. A sub-plane scheme and the nodal expansion method (NEM) are employed for the solution of the one-dimensional (1-D) SP N equations involving a radial transverse leakage. The SP N solver replaces the axial diffusion solver of the DeCART direct whole core transport code to provide more accurate, transport theory based axial solutions. In the sub-plane scheme, the radial equivalent homogenization parameters generated by the local MOC for a thick plane are assigned to the multiple finer planes in the subsequent global three-dimensional (3-D) coarse mesh finite difference (CMFD) calculation in which the NEM is employed for the axial solution. The sub-plane scheme induces a much less nodal error while having little impact on the axial leakage representation of the radial MOC calculation. The performance of the sub-plane scheme and SP N nodal transport solver is examined by solving a set of demonstrative problems and the C5G7MOX 3-D extension benchmark problems. It is shown in the demonstrative problems that the nodal error reaching upto 1,400 pcm in a rodded case is reduced to 10 pcm by introducing 10 sub-planes per MOC plane and the transport error is reduced from about 150 pcm to 10 pcm by using SP 3 . Also it is observed, in the C5G7MOX rodded configuration B problem, that the eigenvalues and pin power errors of 180 pcm and 2.2% of the 10 sub-planes diffusion case are reduced to 40 pcm and 1.4%, respectively, for SP 3 with only about a 15% increase in the computing time. It is shown that the SP 5 case gives very similar results to the SP 3 case. (author)

  9. Efficient modeling of reactive transport phenomena by a multispecies random walk coupled to chemical equilibrium

    International Nuclear Information System (INIS)

    Pfingsten, W.

    1996-01-01

    Safety assessments for radioactive waste repositories require a detailed knowledge of physical, chemical, hydrological, and geological processes for long time spans. In the past, individual models for hydraulics, transport, or geochemical processes were developed more or less separately to great sophistication for the individual processes. Such processes are especially important in the near field of a waste repository. Attempts have been made to couple at least two individual processes to get a more adequate description of geochemical systems. These models are called coupled codes; they couple predominantly a multicomponent transport model with a chemical reaction model. Here reactive transport is modeled by the sequentially coupled code MCOTAC that couples one-dimensional advective, dispersive, and diffusive transport with chemical equilibrium complexation and precipitation/dissolution reactions in a porous medium. Transport, described by a random walk of multispecies particles, and chemical equilibrium calculations are solved separately, coupled only by an exchange term. The modular-structured code was applied to incongruent dissolution of hydrated silicate gels, to movement of multiple solid front systems, and to an artificial, numerically difficult heterogeneous redox problem. These applications show promising features with respect to applicability to relevant problems and possibilities of extensions

  10. The importance of OH − transport through anion exchange membrane in microbial electrolysis cells

    KAUST Repository

    Ye, Yaoli

    2018-01-11

    In two-chamber microbial electrolysis cells (MECs) with anion exchange membranes (AEMs), a phosphate buffer solution (PBS) is typically used to avoid increases in catholyte pH as Nernst equation calculations indicate that high pHs adversely impact electrochemical performance. However, ion transport between the chambers will also impact performance, which is a factor not included in those calculations. To separate the impacts of pH and ion transport on MEC performance, a high molecular weight polymer buffer (PoB), which was retained in the catholyte due to its low AEM transport and cationic charge, was compared to PBS in MECs and abiotic electrochemical half cells (EHCs). In MECs, catholyte pH control was less important than ion transport. MEC tests using the PoB catholyte, which had a higher buffer capacity and thus maintained a lower catholye pH (<8), resulted in a 50% lower hydrogen production rate (HPR) than that obtained using PBS (HPR = 0.7 m3-H2 m−3 d−1) where the catholyte rapidly increased to pH = 12. The main reason for the decreased performance using PoB was a lack of hydroxide ion transfer into the anolyte to balance pH. The anolyte pH in MECs rapidly decreased to 5.8 due to a lack of hydroxide ion transport, which inhibited current generation by the anode, whereas the pH was maintained at 6.8 using PBS. In abiotic tests in ECHs, where the cathode potential was set at −1.2 V, the HPR was 133% higher using PoB than PBS due to catholyte pH control, as the anolyte pH was not a factor in the performance. These results show that maintaining charge transfer to control anolyte pH is more important than obtaining a more neutral pH catholyte.

  11. Coupling of microbial nitrogen transformations and climate in sclerophyll forest soils from the Mediterranean Region of central Chile.

    Science.gov (United States)

    Pérez, Cecilia A; Armesto, Juan J

    2018-06-01

    The Mediterranean region of central Chile is experiencing extensive "mega-droughts" with detrimental effects for the environment and economy of the region. In the northern hemisphere, nitrogen (N) limitation of Mediterranean ecosystems has been explained by the decoupling between N inputs and plant uptake during the dormant season. In central Chile, soils have often been considered N-rich in comparison to other Mediterranean ecosystems of the world, yet the impacts of expected intensification of seasonal drought remain unknown. In this work, we seek to disentangle patterns of microbial N transformations and their seasonal coupling with climate in the Chilean sclerophyll forest-type. We aim to assess how water limitation affects microbial N transformations, thus addressing the impact of ongoing regional climate trends on soil N status. We studied four stands of the sclerophyll forest-type in Chile. Field measurements in surface soils showed a 67% decline of free-living diazotrophic activity (DA) and 59% decrease of net N mineralization rates during the summer rainless and dormant season, accompanied by a stimulation of in-situ denitrification rates to values 70% higher than in wetter winter. Higher rates of both free-living DA and net N mineralization found during spring, provided evidence for strong coupling of these two processes during the growing season. Overall, the experimental addition of water in the field to litter samples almost doubled DA but had no effect on denitrification rates. We conclude that coupling of microbial mediated soil N transformations during the wetter growing season explains the N enrichment of sclerophyll forest soils. Expected increases in the length and intensity of the dry period, according to climate change models, reflected in the current mega-droughts may drastically reduce biological N fixation and net N mineralization, increasing at the same time denitrification rates, thereby potentially reducing long-term soil N capital

  12. Indirect Inverse Substructuring Method for Multibody Product Transport System with Rigid and Flexible Coupling

    Directory of Open Access Journals (Sweden)

    Jun Wang

    2015-01-01

    Full Text Available The aim of this paper is to develop a new frequency response function- (FRF- based indirect inverse substructuring method without measuring system-level FRFs in the coupling DOFs for the analysis of the dynamic characteristics of a three-substructure coupled product transport system with rigid and flexible coupling. By enforcing the dynamic equilibrium conditions at the coupling coordinates and the displacement compatibility conditions, a closed-form analytical solution to inverse substructuring analysis of multisubstructure coupled product transport system is derived based on the relationship of easy-to-monitor component-level FRFs and the system-level FRFs at the coupling coordinates. The proposed method is validated by a lumped mass-spring-damper model, and the predicted coupling dynamic stiffness is compared with the direct computation, showing exact agreement. The method developed offers an approach to predict the unknown coupling dynamic stiffness from measured FRFs purely. The suggested method may help to obtain the main controlling factors and contributions from the various structure-borne paths for product transport system.

  13. Coupled-resonator waveguide perfect transport single-photon by interatomic dipole-dipole interaction

    Science.gov (United States)

    Yan, Guo-an; Lu, Hua; Qiao, Hao-xue; Chen, Ai-xi; Wu, Wan-qing

    2018-06-01

    We theoretically investigate single-photon coherent transport in a one-dimensional coupled-resonator waveguide coupled to two quantum emitters with dipole-dipole interactions. The numerical simulations demonstrate that the transmission spectrum of the photon depends on the two atoms dipole-dipole interactions and the photon-atom couplings. The dipole-dipole interactions may change the dip positions in the spectra and the coupling strength may broaden the frequency band width in the transmission spectrum. We further demonstrate that the typical transmission spectra split into two dips due to the dipole-dipole interactions. This phenomenon may be used to manufacture new quantum waveguide devices.

  14. Transverse transport in coupled strongly correlated electronic chains

    International Nuclear Information System (INIS)

    Capponi, S.; Poilblanc, D.

    1997-01-01

    One-particle interchain hopping in a system of coupled Luttinger liquids is investigated by use of exact diagonalizations techniques. We give numerical evidence that inter-chain coherent hopping (defined by a non-vanishing splitting) can be totally suppressed for the Luttinger liquid exponent α ∝ 0.4 or even smaller α values. The transverse conductivity is shown to exhibit a strong incoherent part even when coherent inter-chain hopping is believed to occur. Implications for the optical experiments in quasi-1D organic or high-T c superconductors is outlined. (orig.)

  15. Coupling of neutron transport equations. First results; Couplage d`equations en transport neutronique. premiere approche 1D monocinetique

    Energy Technology Data Exchange (ETDEWEB)

    Bal, G.

    1995-07-01

    To achieve whole core calculations of the neutron transport equation, we have to follow this 2 step method: space and energy homogenization of the assemblies; resolution of the homogenized equation on the whole core. However, this is no more valid when accidents occur (for instance depressurization causing locally strong heterogeneous media). One solution consists then in coupling two kinds of resolutions: a fine computation on the damaged cell (fine mesh, high number of energy groups) coupled with a coarse one everywhere else. We only deal here with steady state solutions (which already live in 6D spaces). We present here two such methods: The coupling by transmission of homogenized sections and the coupling by transmission of boundary conditions. To understand what this coupling is, we first restrict ourselves to 1D with respect to space in one energy group. The first two chapters deal with a recall of basic properties of the neutron transport equation. We give at chapter 3 some indications of the behaviour of the flux with respect to the cross sections. We present at chapter 4 some couplings and give some properties. Chapter 5 is devoted to a presentation of some numerical applications. (author). 9 refs., 7 figs.

  16. Development of a Coupled Fluid and Colloidall Particle Transport Model

    OpenAIRE

    Ripplinger, Scott

    2013-01-01

    A colloidal system usually refers to when very small particles are suspended within a solution. The study of these systems encompasses a variety of cases including bacteria in ground water, blood cells and platelets in blood plasma, and river silt transport. Taking a look at these kinds of systems using computer simulation can provide a great deal of insight into how they work. Most approaches to date do not look at the details of the system, however, and are specific to given system. In this...

  17. Some results on the neutron transport and the coupling of equations

    International Nuclear Information System (INIS)

    Bal, G.

    1997-01-01

    Neutron transport in nuclear reactors is well modeled by the linear Boltzmann transport equation. Its resolution is relatively easy but very expensive. To achieve whole core calculations, one has to consider simpler models, such as diffusion or homogeneous transport equations. However, the solutions may become inaccurate in particular situations (as accidents for instance). That is the reason why we wish to solve the equations on small area accurately and more coarsely on the remaining part of the core. It is than necessary to introduce some links between different discretizations or modelizations. In this note, we give some results on the coupling of different discretizations of all degrees of freedom of the integral-differential neutron transport equation (two degrees for the angular variable, on for the energy component, and two or three degrees for spatial position respectively in 2D (cylindrical symmetry) and 3D). Two chapters are devoted to the coupling of discrete ordinates methods (for angular discretization). The first one is theoretical and shows the well posing of the coupled problem, whereas the second one deals with numerical applications of practical interest (the results have been obtained from the neutron transport code developed at the R and D, which has been modified for introducing the coupling). Next, we present the nodal scheme RTN0, used for the spatial discretization. We show well posing results for the non-coupled and the coupled problems. At the end, we deal with the coupling of energy discretizations for the multigroup equations obtained by homogenization. Some theoretical results of the discretization of the velocity variable (well-posing of problems), which do not deal directly with the purposes of coupling, are presented in the annexes. (author)

  18. Computing and the electrical transport properties of coupled quantum networks

    Science.gov (United States)

    Cain, Casey Andrew

    In this dissertation a number of investigations were conducted on ballistic quantum networks in the mesoscopic range. In this regime, the wave nature of electron transport under the influence of transverse magnetic fields leads to interesting applications for digital logic and computing circuits. The work specifically looks at characterizing a few main areas that would be of interest to experimentalists who are working in nanostructure devices, and is organized as a series of papers. The first paper analyzes scaling relations and normal mode charge distributions for such circuits in both isolated and open (terminals attached) form. The second paper compares the flux-qubit nature of quantum networks to the well-established spintronics theory. The results found exactly contradict the conventional school of thought for what is required for quantum computation. The third paper investigates the requirements and limitations of extending the Thevenin theorem in classic electric circuits to ballistic quantum transport. The fourth paper outlines the optimal functionally complete set of quantum circuits that can completely satisfy all sixteen Boolean logic operations for two variables.

  19. Tunable coupled nanomechanical resonators for single-electron transport

    International Nuclear Information System (INIS)

    Scheible, Dominik V; Erbe, Artur; Blick, Robert H

    2002-01-01

    Nano-electromechanical systems (NEMS) are ideal for sensor applications and ultra-sensitive force detection, since their mechanical degree of freedom at the nanometre scale can be combined with semiconductor nano-electronics. We present a system of coupled nanomechanical beam resonators in silicon which is mechanically fully Q-tunable ∼700-6000. This kind of resonator can also be employed as a mechanical charge shuttle via an insulated metallic island at the tip of an oscillating cantilever. Application of our NEMS as an electromechanical single-electron transistor (emSET) is introduced and experimental results are discussed. Three animation clips demonstrate the manufacturing process of the NEMS, the Q-tuning experiment and the concept of the emSET

  20. Structure and function of subsurface microbial communities affecting radionuclide transport and bioimmobilization

    Energy Technology Data Exchange (ETDEWEB)

    Kostka, Joel E. [Florida State Univ., Tallahassee, FL (United States); Prakash, Om [Florida State Univ., Tallahassee, FL (United States); Green, Stefan J. [Florida State Univ., Tallahassee, FL (United States); Akob, Denise [Florida State Univ., Tallahassee, FL (United States); Jasrotia, Puja [Florida State Univ., Tallahassee, FL (United States); Kerkhof, Lee [Rutgers Univ., New Brunswick, NJ (United States); Chin, Kuk-Jeong [Georgia State Univ., Atlanta, GA (United States); Sheth, Mili [Georgia State Univ., Atlanta, GA (United States); Keller, Martin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Venkateswaran, Amudhan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Elkins, James G. [Univ. of Illinois, Urbana-Champaign, IL (United States); Stucki, Joseph W. [Univ. of Illinois, Urbana-Champaign, IL (United States)

    2012-05-01

    Our objectives were to: 1) isolate and characterize novel anaerobic prokaryotes from subsurface environments exposed to high levels of mixed contaminants (U(VI), nitrate, sulfate), 2) elucidate the diversity and distribution of metabolically active metal- and nitrate-reducing prokaryotes in subsurface sediments, and 3) determine the biotic and abiotic mechanisms linking electron transport processes (nitrate, Fe(III), and sulfate reduction) to radionuclide reduction and immobilization. Mechanisms of electron transport and U(VI) transformation were examined under near in situ conditions in sediment microcosms and in field investigations. Field sampling was conducted at the Oak Ridge Field Research Center (ORFRC), in Oak Ridge, Tennessee. The ORFRC subsurface is exposed to mixed contamination predominated by uranium and nitrate. In short, we effectively addressed all 3 stated objectives of the project. In particular, we isolated and characterized a large number of novel anaerobes with a high bioremediation potential that can be used as model organisms, and we are now able to quantify the function of subsurface sedimentary microbial communities in situ using state-of-the-art gene expression methods (molecular proxies).

  1. A Coupled Chemical and Mass Transport Model for Concrete Durability

    DEFF Research Database (Denmark)

    Jensen, Mads Mønster; Johannesson, Björn; Geiker, Mette Rica

    2012-01-01

    -Raphson iteration scheme arising from the non-linearity. The overall model is a transient problem, solved using a single parameter formulation. The sorption hysteresis and chemical equilibrium is included as source or sink terms. The advantages with this formulation is that each node in the discrete system has...... their individual sorption hysteresis isotherm which is of great importance when describing non fully water saturated system e.g. caused by time depended boundary conditions. Chemical equilibrium is also established in each node of the discrete system, where the rate of chemical degradation is determined.......g. charge balance, from the mass transport calculation could cause the above mentioned numerical problems. Two different test cases are studied, the sorption hysteresis in different depth of the sample, caused by time depended boundary condition and the chemical degradation of the solid matrix in a ten year...

  2. Coupling of solute transport and cell expansion in pea stems

    Science.gov (United States)

    Schmalstig, J. G.; Cosgrove, D. J.

    1990-01-01

    As cells expand and are displaced through the elongation zone of the epicotyl of etiolated pea (Pisum sativum L. var Alaska) seedlings, there is little net dilution of the cell sap, implying a coordination between cell expansion and solute uptake from the phloem. Using [14C] sucrose as a phloem tracer (applied to the hypogeous cotyledons), the pattern of label accumulation along the stem closely matched the growth rate pattern: high accumulation in the growing zone, little accumulation in nongrowing regions. Several results suggest that a major portion of phloem contents enters elongating cells through the symplast. We propose that the coordination between phloem transport and cell expansion is accomplished via regulatory pathways affecting both plasmodesmata conductivity and cell expansion.

  3. Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand

    Directory of Open Access Journals (Sweden)

    Katrin eHug

    2014-11-01

    Full Text Available Acid-sulfide hot springs are analogs of early Earth geothermal systems where microbial metal(loid resistance likely first evolved. Arsenic is a metalloid enriched in the acid-sulfide hot spring Champagne Pool (Waiotapu, New Zealand. Arsenic speciation in Champagne Pool follows reaction paths not yet fully understood with respect to biotic contributions and coupling to biogeochemical sulfur cycling. Here we present quantitative arsenic speciation from Champagne Pool, finding arsenite dominant in the pool, rim and outflow channel (55-75% total arsenic, and dithio- and trithioarsenates ubiquitously present as 18-25% total arsenic. In the outflow channel, dimethylmonothioarsenate comprised ≤9% total arsenic, while on the outflow terrace thioarsenates were present at 55% total arsenic. We also quantified sulfide, thiosulfate, sulfate and elemental sulfur, finding sulfide and sulfate as major species in the pool and outflow terrace, respectively. Elemental sulfur reached a maximum at the terrace. Phylogenetic analysis of 16S rRNA genes from metagenomic sequencing revealed the dominance of Sulfurihydrogenibium at all sites and an increased archaeal population at the rim and outflow channel. Several phylotypes were found closely related to known sulfur- and sulfide-oxidizers, as well as sulfur- and sulfate-reducers. Bioinformatic analysis revealed genes underpinning sulfur redox transformations, consistent with sulfur speciation data, and illustrating a microbial role in sulfur-dependent transformation of arsenite to thioarsenate. Metagenomic analysis also revealed genes encoding for arsenate reductase at all sites, reflecting the ubiquity of thioarsenate and a need for microbial arsenate resistance despite anoxic conditions. Absence of the arsenite oxidase gene, aio, at all sites suggests prioritization of arsenite detoxification over coupling to energy conservation. Finally, detection of methyl arsenic in the outflow channel, in conjunction with

  4. The lateral intercellular space as osmotic coupling compartment in isotonic transport

    DEFF Research Database (Denmark)

    Larsen, E.H.; Willumsen, N.J.; Mobjerg, N.

    2009-01-01

    coupling of water absorption to ion flow is energized by lateral Na+/K+ pumps. We show that the theory accounts quantitatively for steady- and time dependent states of solute-coupled fluid uptake by toad skin epithelium. Our experimental results exclude definitively three alternative theories of epithelial......Solute-coupled water transport and isotonic transport are basic functions of low- and high-resistance epithelia. These functions are studied with the epithelium bathed on the two sides with physiological saline of similar composition. Hence, at transepithelial equilibrium water enters...... the epithelial cells from both sides, and with the reflection coefficient of tight junction being larger than that of the interspace basement membrane, all of the water leaves the epithelium through the interspace basement membrane. The common design of transporting epithelia leads to the theory that an osmotic...

  5. Development and application of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

    Science.gov (United States)

    Hong, E.; Park, Y.; Muirhead, R.; Jeong, J.; Pachepsky, Y. A.

    2017-12-01

    Pathogenic microorganisms in recreational and irrigation waters remain the subject of concern. Water quality models are used to estimate microbial quality of water sources, to evaluate microbial contamination-related risks, to guide the microbial water quality monitoring, and to evaluate the effect of agricultural management on the microbial water quality. The Agricultural Policy/Environmental eXtender (APEX) is the watershed-scale water quality model that includes highly detailed representation of agricultural management. The APEX currently does not have microbial fate and transport simulation capabilities. The objective of this work was to develop the first APEX microbial fate and transport module that could use the APEX conceptual model of manure removal together with recently introduced conceptualizations of the in-stream microbial fate and transport. The module utilizes manure erosion rates found in the APEX. Bacteria survival in soil-manure mixing layer was simulated with the two-stage survival model. Individual survival patterns were simulated for each manure application date. Simulated in-stream microbial fate and transport processes included the reach-scale passive release of bacteria with resuspended bottom sediment during high flow events, the transport of bacteria from bottom sediment due to the hyporheic exchange during low flow periods, the deposition with settling sediment, and the two-stage survival. Default parameter values were available from recently published databases. The APEX model with the newly developed microbial fate and transport module was applied to simulate seven years of monitoring data for the Toenepi watershed in New Zealand. Based on calibration and testing results, the APEX with the microbe module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water under various agricultural

  6. Coupled Modeling of Flow, Transport, and Deformation during Hydrodynamically Unstable Displacement in Fractured Rocks

    Science.gov (United States)

    Jha, B.; Juanes, R.

    2015-12-01

    Coupled processes of flow, transport, and deformation are important during production of hydrocarbons from oil and gas reservoirs. Effective design and implementation of enhanced recovery techniques such as miscible gas flooding and hydraulic fracturing requires modeling and simulation of these coupled proceses in geologic porous media. We develop a computational framework to model the coupled processes of flow, transport, and deformation in heterogeneous fractured rock. We show that the hydrocarbon recovery efficiency during unstable displacement of a more viscous oil with a less viscous fluid in a fractured medium depends on the mechanical state of the medium, which evolves due to permeability alteration within and around fractures. We show that fully accounting for the coupling between the physical processes results in estimates of the recovery efficiency in agreement with observations in field and lab experiments.

  7. Multiscale Simulations for Coupled Flow and Transport Using the Generalized Multiscale Finite Element Method

    KAUST Repository

    Chung, Eric

    2015-12-11

    In this paper, we develop a mass conservative multiscale method for coupled flow and transport in heterogeneous porous media. We consider a coupled system consisting of a convection-dominated transport equation and a flow equation. We construct a coarse grid solver based on the Generalized Multiscale Finite Element Method (GMsFEM) for a coupled system. In particular, multiscale basis functions are constructed based on some snapshot spaces for the pressure and the concentration equations and some local spectral decompositions in the snapshot spaces. The resulting approach uses a few multiscale basis functions in each coarse block (for both the pressure and the concentration) to solve the coupled system. We use the mixed framework, which allows mass conservation. Our main contributions are: (1) the development of a mass conservative GMsFEM for the coupled flow and transport; (2) the development of a robust multiscale method for convection-dominated transport problems by choosing appropriate test and trial spaces within Petrov-Galerkin mixed formulation. We present numerical results and consider several heterogeneous permeability fields. Our numerical results show that with only a few basis functions per coarse block, we can achieve a good approximation.

  8. Effects of coupled thermal, hydrological and chemical processes on nuclide transport

    International Nuclear Information System (INIS)

    Carnahan, C.L.

    1987-03-01

    Coupled thermal, hydrological and chemical processes can be classified in two categories. One category consists of the ''Onsager'' type of processes driven by gradients of thermodynamic state variables. These processes occur simultaneously with the direct transport processes. In particular, thermal osmosis, chemical osmosis and ultrafiltration may be prominent in semipermeable materials such as clays. The other category consists of processes affected indirectly by magnitudes of thermodynamic state variables. An important example of this category is the effect of temperature on rates of chemical reactions and chemical equilibria. Coupled processes in both categories may affect transport of radionuclides. Although computational models of limited extent have been constructed, there exists no model that accounts for the full set of THC-coupled processes. In the category of Onsager coupled processes, further model development and testing is severely constrained by a deficient data base of phenomenological coefficients. In the second category, the lack of a general description of effects of heterogeneous chemical reactions on permeability of porous media inhibits progress in quantitative modeling of hydrochemically coupled transport processes. Until fundamental data necessary for further model development have been acquired, validation efforts will be limited necessarily to testing of incomplete models of nuclide transport under closely controlled experimental conditions. 34 refs., 2 tabs

  9. Multiscale Simulations for Coupled Flow and Transport Using the Generalized Multiscale Finite Element Method

    KAUST Repository

    Chung, Eric; Efendiev, Yalchin R.; Leung, Wing; Ren, Jun

    2015-01-01

    In this paper, we develop a mass conservative multiscale method for coupled flow and transport in heterogeneous porous media. We consider a coupled system consisting of a convection-dominated transport equation and a flow equation. We construct a coarse grid solver based on the Generalized Multiscale Finite Element Method (GMsFEM) for a coupled system. In particular, multiscale basis functions are constructed based on some snapshot spaces for the pressure and the concentration equations and some local spectral decompositions in the snapshot spaces. The resulting approach uses a few multiscale basis functions in each coarse block (for both the pressure and the concentration) to solve the coupled system. We use the mixed framework, which allows mass conservation. Our main contributions are: (1) the development of a mass conservative GMsFEM for the coupled flow and transport; (2) the development of a robust multiscale method for convection-dominated transport problems by choosing appropriate test and trial spaces within Petrov-Galerkin mixed formulation. We present numerical results and consider several heterogeneous permeability fields. Our numerical results show that with only a few basis functions per coarse block, we can achieve a good approximation.

  10. Edge and coupled core/edge transport modelling in tokamaks

    International Nuclear Information System (INIS)

    Lodestro, L.L.; Casper, T.A.; Cohen, R.H.

    1999-01-01

    Recent advances in the theory and modelling of tokamak edge, scrape-off-layer (SOL) and divertor plasmas are described. The effects of the poloidal E x B drift on inner/outer divertor-plate asymmetries within a 1D analysis are shown to be in good agreement with experimental trends; above a critical v ExB , the model predicts transitions to supersonic flow at the inboard midplane. 2D simulations show the importance of E x B flow in the private-flux region and of ∇ B-drifts. A theory of rough plasma-facing surfaces is given, predicting modifications to the SOL plasma. The parametric dependence of detached-plasma states in slab geometry has been explored; with sufficient pumping, the location of the ionization front can be controlled; otherwise only fronts near the plate or the X-point are stable. Studies with a more accurate Monte-Carlo neutrals model and a detailed non-LTE radiation-transport code indicate various effects are important for quantitative modelling. Detailed simulations of the DIII-D core and edge are presented; impurity and plasma flow are discussed and shown to be well modelled with UEDGE. (author)

  11. Edge and coupled core-edge transport modelling in tokamaks

    International Nuclear Information System (INIS)

    Lodestro, L.L.; Casper, T.A.; Cohen, R.H.

    2001-01-01

    Recent advances in the theory and modelling of tokamak edge, scrape-off-layer (SOL) and divertor plasmas are described. The effects of the poloidal ExB drift on inner/outer divertor-plate asymmetries within a 1D analysis are shown to be in good agreement with experimental trends; above a critical v ExB, the model predicts transitions to supersonic SOL flow at the inboard midplane. 2D simulations show the importance of ExB flow in the private-flux region and of ∇ B-drifts. A theory of rough plasma-facing surfaces is given, predicting modifications to the SOL plasma. The parametric dependence of detached-plasma states in slab geometry has been explored; with sufficient pumping, the location of the ionization front can be controlled; otherwise only fronts near the plate or the X-point are stable. Studies with a more accurate Monte-Carlo neutrals model and a detailed non-LTE radiation-transport code indicate various effects are important for quantitative modelling. Detailed simulations of the DIII-D core and edge are presented; impurity and plasma flow are discussed and shown to be well modelled with UEDGE. (author)

  12. CO2-ECBM related coupled physical and mechanical transport processes

    Science.gov (United States)

    Gensterblum, Yves; Satorius, Michael; Busch, Andreas; Krooß, Bernhard

    2013-04-01

    The interrelation of cleat transport processes and mechanical properties was investigated by permeability tests at different stress levels (60% to 130% of in-situ stress) with sorbing (CH4, CO2) and inert gases (N2, Ar, He) on a sub bituminous A coal from the Surat Basin, Queensland Australia. From the flow tests under controlled triaxial stress conditions the Klinkenberg-corrected "true" permeability coefficients and the Klinkenberg slip factors were derived. The "true"-, absolute or Klinkenberg corrected permeability shows a gas type dependence. Following the approach of Seidle et al. (1992) the cleat volume compressibility (cf) was calculated from observed changes in apparent permeability upon variation of external stress (at equal mean gas pressures). The observed effects also show a clear dependence on gas type. Due to pore or cleat compressibility the cleat aperture decreases with increasing effective stress. Vice versa we observe with increasing mean pressure at lower confining pressure an increase in permeability which we attribute to a cleat aperture widening. The cleat volume compressibility (cf) also shows a dependence on the mean pore pressure. Non-sorbing gases like helium and argon show higher apparent permeabilities than sorbing gases like methane. Permeability coefficients measured with successively increasing mean gas pressures were consistently lower than those determined at decreasing mean gas pressures. This permeability hysteresis is in accordance with results reported by Harpalani and McPherson (1985). The kinetics of matrix transport processes were studied by sorption tests on different particle sizes at various moisture contents and temperatures (cf. Busch et al., 2006). Methane uptake rates were determined from the pressure decline curves recorded for each particle-size fraction, and "diffusion coefficients" were calculated using several unipore and bidisperse diffusion models. While the CH4 sorption capacity of moisture-equilibrated coals

  13. The role of Rashba spin-orbit coupling in valley-dependent transport of Dirac fermions

    Energy Technology Data Exchange (ETDEWEB)

    Hasanirok, Kobra; Mohammadpour, Hakimeh

    2017-01-01

    At this work, spin- and valley-dependent electron transport through graphene and silicene layers are studied in the presence of Rashba spin- orbit coupling. We find that the transport properties of the related ferromagnetic/normal/ferromagnetic structure depend on the relevant parameters. A fully valley- and spin- polarized current is obtained. As another result, Rashba spin-orbit interaction plays important role in controlling the transmission characteristics.

  14. Coupled Particle Transport and Pattern Formation in a Nonlinear Leaky-Box Model

    Science.gov (United States)

    Barghouty, A. F.; El-Nemr, K. W.; Baird, J. K.

    2009-01-01

    Effects of particle-particle coupling on particle characteristics in nonlinear leaky-box type descriptions of the acceleration and transport of energetic particles in space plasmas are examined in the framework of a simple two-particle model based on the Fokker-Planck equation in momentum space. In this model, the two particles are assumed coupled via a common nonlinear source term. In analogy with a prototypical mathematical system of diffusion-driven instability, this work demonstrates that steady-state patterns with strong dependence on the magnetic turbulence but a rather weak one on the coupled particles attributes can emerge in solutions of a nonlinearly coupled leaky-box model. The insight gained from this simple model may be of wider use and significance to nonlinearly coupled leaky-box type descriptions in general.

  15. Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats

    Directory of Open Access Journals (Sweden)

    Jackson Z Lee

    2014-02-01

    Full Text Available Past studies of hydrogen cycling in hypersaline microbial mats have shown an active nighttime cycle, with production largely from Cyanobacteria and consumption from sulfate-reducing bacteria (SRB. However, the mechanisms and magnitude of hydrogen cycling have not been extensively studied. Two mats types near Guerrero Negro, Mexico -- permanently submerged Microcoleus microbial mats (GN-S, and intertidal Lyngbya microbial mats (GN-I -- were used in microcosm diel manipulation experiments with 3-(3,4-dichlorophenyl-1,1-dimethylurea (DCMU, molybdate, ammonium addition, and physical disruption to understand the processes responsible for hydrogen cycling between mat microbes. Across microcosms, H2 production occurred under dark anoxic conditions with simultaneous production of a suite of organic acids. H2 production was not significantly affected by inhibition of nitrogen fixation, but rather appears to result from constitutive fermentation of photosynthetic storage products by oxygenic phototrophs. Comparison to accumulated glycogen and to CO2 flux indicated that, in the GN-I mat, fermentation released almost all of the carbon fixed via photosynthesis during the preceding day, primarily as organic acids. Across mats, although oxygenic and anoxygenic phototrophs were detected, cyanobacterial [NiFe]-hydrogenase transcripts predominated. Molybdate inhibition experiments indicated that SRBs from a wide distribution of dsrA phylotypes were responsible for H2 consumption. Incubation with 13C-acetate and nanoSIMS (secondary ion mass-spectrometry indicated higher uptake in both Chloroflexi and SRBs relative to other filamentous bacteria. These manipulations and diel incubations confirm that Cyanobacteria were the main fermenters in Guerrero Negro mats and that the net flux of nighttime fermentation byproducts (not only hydrogen was largely regulated by the interplay between Cyanobacteria, SRBs, and Chloroflexi.

  16. BALTORO a general purpose code for coupling discrete ordinates and Monte-Carlo radiation transport calculations

    International Nuclear Information System (INIS)

    Zazula, J.M.

    1983-01-01

    The general purpose code BALTORO was written for coupling the three-dimensional Monte-Carlo /MC/ with the one-dimensional Discrete Ordinates /DO/ radiation transport calculations. The quantity of a radiation-induced /neutrons or gamma-rays/ nuclear effect or the score from a radiation-yielding nuclear effect can be analysed in this way. (author)

  17. Electron-vibron coupling effects on electron transport via a single-molecule magnet

    NARCIS (Netherlands)

    McCaskey, A.; Yamamoto, Y.; Warnock, M.; Burzuri, E.; Van der Zant, H.S.J.; Park, K.

    2015-01-01

    We investigate how the electron-vibron coupling influences electron transport via an anisotropic magnetic molecule, such as a single-molecule magnet (SMM) Fe4, by using a model Hamiltonian with parameter values obtained from density-functional theory (DFT). The magnetic anisotropy parameters,

  18. Numerical modeling of coupled water flow and heat transport in soil and snow

    Science.gov (United States)

    Thijs J. Kelleners; Jeremy Koonce; Rose Shillito; Jelle Dijkema; Markus Berli; Michael H. Young; John M. Frank; William Massman

    2016-01-01

    A one-dimensional vertical numerical model for coupled water flow and heat transport in soil and snow was modified to include all three phases of water: vapor, liquid, and ice. The top boundary condition in the model is driven by incoming precipitation and the surface energy balance. The model was applied to three different terrestrial systems: A warm desert bare...

  19. Coupled heat transfer in high temperature transporting system with semitransparent/opaque material

    International Nuclear Information System (INIS)

    Du Shenghua; Xia Xinjin

    2010-01-01

    The heat transfer model of the aerodynamic heating coupled with radiative cooling was developed. The thermal protect system includes the higher heat flux region with high temperature semitransparent material, the heat transporting channel and the lower heat flux region with metal. The control volume method was combined with the Monte Carlo method to calculate the coupled heat transfer of the transporting system, and the thermal equilibrium equation for the transporting channel was solved simultaneously. The effect of the aeroheating flux radio, the area ratio of radiative surfaces, the convective heat transfer coefficient of the heat transporting channel on the radiative surface temperature and the fluid temperature in the heat transporting channel were analyzed. The effect of radiation and conduction in the semitransparent material was discussed. The result shows that to increase the convective heat transfer coefficient in heat flux channel can enhance the heat transporting ability of the system, but the main parameter to effect on the temperature of the heat transporting system is the area ratio of radiative surfaces. (authors)

  20. American lobsters (Homarus americanus not surviving during air transport: evaluation of microbial spoilage

    Directory of Open Access Journals (Sweden)

    Erica Tirloni

    2016-05-01

    Full Text Available Eighteen American lobsters (Homarus americanus, dead during air transport, were analysed in order to evaluate the microbial population of meat, gills and gut: no specific studies have ever been conducted so far on the microbiological quality of American lobsters’ meats in terms of spoilage microbiota. The meat samples showed very limited total viable counts, in almost all the cases below the level of 6 Log CFU/g, while higher loads were found, as expected, in gut and gills, the most probable source of contamination. These data could justify the possibility to commercialise these notsurviving subjects, without quality concerns for the consumers. Most of the isolates resulted to be clustered with type strains of Pseudoalteromonas spp. (43.1% and Photobacterium spp. (24.1%, and in particular to species related to the natural marine environment. The distribution of the genera showed a marked inhomogeneity among the samples. The majority of the isolates identified resulted to possess proteolytic (69.3% and lipolytic ability (75.5%, suggesting their potential spoilage ability. The maintanance of good hygienical practices, especially during the production of ready-to-eat lobsters-based products, and a proper storage could limit the possible replication of these microorganisms.

  1. American Lobsters (Homarus Americanus) not Surviving During Air Transport: Evaluation of Microbial Spoilage.

    Science.gov (United States)

    Tirloni, Erica; Stella, Simone; Gennari, Mario; Colombo, Fabio; Bernardi, Cristian

    2016-04-19

    Eighteen American lobsters ( Homarus americanus ), dead during air transport, were analysed in order to evaluate the microbial population of meat, gills and gut: no specific studies have ever been conducted so far on the microbiological quality of American lobsters' meats in terms of spoilage microbiota. The meat samples showed very limited total viable counts, in almost all the cases below the level of 6 Log CFU/g, while higher loads were found, as expected, in gut and gills, the most probable source of contamination. These data could justify the possibility to commercialise these not-surviving subjects, without quality concerns for the consumers. Most of the isolates resulted to be clustered with type strains of Pseudoalteromonas spp. (43.1%) and Photobacterium spp. (24.1%), and in particular to species related to the natural marine environment. The distribution of the genera showed a marked inhomogeneity among the samples. The majority of the isolates identified resulted to possess proteolytic (69.3%) and lipolytic ability (75.5%), suggesting their potential spoilage ability. The maintanance of good hygienical practices, especially during the production of ready-to-eat lobsters-based products, and a proper storage could limit the possible replication of these microorganisms.

  2. A Mathematical Model of Solute Coupled Water Transport in Toad Intestine Incorporating Recirculation of the Actively Transported Solute

    DEFF Research Database (Denmark)

    Larsen, Erik Hviid; Sørensen, Jakob Balslev; Sørensen, Jens Nørkær

    2000-01-01

    those of tight junction and interspace basement membrane by convection-diffusion. With solute permeability of paracellular pathway large relative to paracellular water flow, the paracellular flux ratio of the solute (influx/outflux) is small (2-4) in agreement with experiments. The virtual solute......A mathematical model of an absorbing leaky epithelium is developed for analysis of solute coupled water transport. The non-charged driving solute diffuses into cells and is pumped from cells into the lateral intercellular space (lis). All membranes contain water channels with the solute passing...... increases with hydraulic conductance of the pathway carrying water from mucosal solution into lis. Uphill water transport is accomplished, but with high hydraulic conductance of cell membranes strength of transport is obscured by water flow through cells. Anomalous solvent drag occurs when back flux...

  3. Analysis of the Sodium Recirculation Theory of Solute Coupled Water Transport in Small Intestine

    DEFF Research Database (Denmark)

    Larsen, E. H.; Sørensen, Jens Nørkær; Sørensen, J. B.

    2002-01-01

    Our previous mathematical model of solute-coupled water transport through the intestinal epithelium is extended for dealing with electrolytes rather than electroneutral solutes. A 3Na+-2K+ pump in the lateral membranes provides the energy-requiring step for driving transjunctional and translateral......, computations predict that the concentration differences between lis and bathing solutions are small for all three ions. Nevertheless, the diffusion fluxes of the ions out of lis significantly exceed their mass transports. It is concluded that isotonic transport requires recirculation of all three ions....... The computed sodium recirculation flux that is required for isotonic transport corresponds to that estimated in experiments on toad small intestine. This result is shown to be robust and independent of whether the apical entrance mechanism for the sodium ion is a channel, a SGLT1 transporter driving inward...

  4. Medium-Throughput Screen of Microbially Produced Serotonin via a G-Protein-Coupled Receptor-Based Sensor.

    Science.gov (United States)

    Ehrenworth, Amy M; Claiborne, Tauris; Peralta-Yahya, Pamela

    2017-10-17

    Chemical biosensors, for which chemical detection triggers a fluorescent signal, have the potential to accelerate the screening of noncolorimetric chemicals produced by microbes, enabling the high-throughput engineering of enzymes and metabolic pathways. Here, we engineer a G-protein-coupled receptor (GPCR)-based sensor to detect serotonin produced by a producer microbe in the producer microbe's supernatant. Detecting a chemical in the producer microbe's supernatant is nontrivial because of the number of other metabolites and proteins present that could interfere with sensor performance. We validate the two-cell screening system for medium-throughput applications, opening the door to the rapid engineering of microbes for the increased production of serotonin. We focus on serotonin detection as serotonin levels limit the microbial production of hydroxystrictosidine, a modified alkaloid that could accelerate the semisynthesis of camptothecin-derived anticancer pharmaceuticals. This work shows the ease of generating GPCR-based chemical sensors and their ability to detect specific chemicals in complex aqueous solutions, such as microbial spent medium. In addition, this work sets the stage for the rapid engineering of serotonin-producing microbes.

  5. Coupling between a geochemical model and a transport model of dissolved elements

    International Nuclear Information System (INIS)

    Jacquier, P.

    1988-10-01

    In order to assess the safety analysis of an underground repository, the transport of radioelements in groundwater and their interactions with the geological medium are modelled. The objective of this work is the setting up and experimental validation of the coupling of a geochemical model with a transport model of dissolved elements. A laboratory experiment was developed at the CEA center of Cadarache. Flow-through experiments were carried out on columns filled with crushed limestone, where several inflow conditions were taken into account as the temperature, the presence of a pollutant (strontium chloride) at different concentrations. The results consist of the evolution of the chemical composition of the water at the outlet of the column. The final aim of the study is to explain these results with a coupled model where geochemical and transport phenomena are modelled in a two-step procedure. This code, called STELE, was built by introducing a geochemical code, CHIMERE, into an existing transport code, METIS. At this stage, the code CHIMERE can take into account: any chemical reaction in aqueous phase (complexation, acid-base reaction, redox equilibrium), dissolution-precipitation of minerals and solid phases, dissolution-degassing of gas. The paper intends to describe the whole process leading to the coupling which can be forecasted over the next years between geochemical and transport models

  6. Geophysical Monitoring of Coupled Microbial and Geochemical Processes During Stimulated Subsurface Bioremediation

    International Nuclear Information System (INIS)

    Williams, Kenneth H.; Kemna, Andreas; Wilkins, Michael J.; Druhan, Jennifer L.; Arntzen, Evan V.; N'Guessan, A. Lucie; Long, Philip E.; Hubbard, Susan S.; Banfield, Jillian F.

    2009-01-01

    Understanding how microorganisms alter their physical and chemical environment during bioremediation is hindered by our inability to resolve subsurface microbial activity with high spatial resolution. Here we demonstrate the use of a minimally invasive geophysical technique to monitor stimulated microbial activity during acetate amendment in an aquifer near Rifle, Colorado. During electrical induced polarization (IP) measurements, spatiotemporal variations in the phase response between imposed electric current and the resultant electric field correlated with changes in groundwater geochemistry accompanying stimulated iron and sulfate reduction and sulfide mineral precipitation. The magnitude of the phase response varied with measurement frequency (0.125 and 1 Hz) and was dependent upon the dominant metabolic process. The spectral effect was corroborated using a biostimulated column experiment containing Rifle sediments and groundwater. Fluids and sediments recovered from regions exhibiting an anomalous phase response were enriched in Fe(II), dissolved sulfide, and cell-associated FeS nanoparticles. The accumulation of mineral precipitates and electroactive ions altered the ability of pore fluids to conduct electrical charge, accounting for the anomalous IP response and revealing the usefulness of multifrequency IP measurements for monitoring mineralogical and geochemical changes accompanying stimulated subsurface bioremediation

  7. Coupled transport phenomena in a clay from a Callovo-Oxfordian formation; Phenomenes de transport couples dans les argiles du Callovo-Oxfordien

    Energy Technology Data Exchange (ETDEWEB)

    Paszkuta, M

    2005-06-15

    Low permeability materials containing clay play an important role in practical life and natural environment. Indeed, the ability of clay soils to act as semi permeable membranes, that inhibit the passage of electrolytes, is of great interest. The major objective of this thesis is to evaluate the transport properties of natural clays and in particular coupled transports when a pressure gradient, an electrical field, a concentration gradient and a temperature gradient interact. The material is a compact argillite extracted in East France from a Callovo-Oxfordian formation which was supplied to us by ANDRA. NaCl was used as the main solute. Two series of experiments were performed to measure permeability, diffusion, conductivity, the electro-osmotic coefficient and the Soret coefficient. (author)

  8. Bioelectricity Generation and Bioremediation of an Azo-Dye in a Microbial Fuel Cell Coupled Activated Sludge Process

    Science.gov (United States)

    Khan, Mohammad Danish; Abdulateif, Huda; Ismail, Iqbal M.; Sabir, Suhail; Khan, Mohammad Zain

    2015-01-01

    Simultaneous bioelectricity generation and dye degradation was achieved in the present study by using a combined anaerobic-aerobic process. The anaerobic system was a typical single chambered microbial fuel cell (SMFC) which utilizes acid navy blue r (ANB) dye along with glucose as growth substrate to generate electricity. Four different concentrations of ANB (50, 100, 200 and 400 ppm) were tested in the SMFC and the degradation products were further treated in an activated sludge post treatment process. The dye decolorization followed pseudo first order kinetics while the negative values of the thermodynamic parameter ∆G (change in Gibbs free energy) shows that the reaction proceeds with a net decrease in the free energy of the system. The coulombic efficiency (CE) and power density (PD) attained peak values at 10.36% and 2,236 mW/m2 respectively for 200 ppm of ANB. A further increase in ANB concentrations results in lowering of cell potential (and PD) values owing to microbial inhibition at higher concentrations of toxic substrates. Cyclic voltammetry studies revealed a perfect redox reaction was taking place in the SMFC. The pH, temperature and conductivity remain 7.5–8.0, 27(±2°C and 10.6–18.2 mS/cm throughout the operation. The biodegradation pathway was studied by the gas chromatography coupled with mass spectroscopy technique, suggested the preferential cleavage of the azo bond as the initial step resulting in to aromatic amines. Thus, a combined anaerobic-aerobic process using SMFC coupled with activated sludge process can be a viable option for effective degradation of complex dye substrates along with energy (bioelectricity) recovery. PMID:26496083

  9. Application of Mortar Coupling in Multiscale Modelling of Coupled Flow, Transport, and Biofilm Growth in Porous Media

    Science.gov (United States)

    Laleian, A.; Valocchi, A. J.; Werth, C. J.

    2017-12-01

    Multiscale models of reactive transport in porous media are capable of capturing complex pore-scale processes while leveraging the efficiency of continuum-scale models. In particular, porosity changes caused by biofilm development yield complex feedbacks between transport and reaction that are difficult to quantify at the continuum scale. Pore-scale models, needed to accurately resolve these dynamics, are often impractical for applications due to their computational cost. To address this challenge, we are developing a multiscale model of biofilm growth in which non-overlapping regions at pore and continuum spatial scales are coupled with a mortar method providing continuity at interfaces. We explore two decompositions of coupled pore-scale and continuum-scale regions to study biofilm growth in a transverse mixing zone. In the first decomposition, all reaction is confined to a pore-scale region extending the transverse mixing zone length. Only solute transport occurs in the surrounding continuum-scale regions. Relative to a fully pore-scale result, we find the multiscale model with this decomposition has a reduced run time and consistent result in terms of biofilm growth and solute utilization. In the second decomposition, reaction occurs in both an up-gradient pore-scale region and a down-gradient continuum-scale region. To quantify clogging, the continuum-scale model implements empirical relations between porosity and continuum-scale parameters, such as permeability and the transverse dispersion coefficient. Solutes are sufficiently mixed at the end of the pore-scale region, such that the initial reaction rate is accurately computed using averaged concentrations in the continuum-scale region. Relative to a fully pore-scale result, we find accuracy of biomass growth in the multiscale model with this decomposition improves as the interface between pore-scale and continuum-scale regions moves downgradient where transverse mixing is more fully developed. Also, this

  10. Porous media fluid flow, heat, and mass transport model with rock stress coupling

    International Nuclear Information System (INIS)

    Runchal, A.K.

    1980-01-01

    This paper describes the physical and mathematical basis of a general purpose porous media flow model, GWTHERM. The mathematical basis of the model is obtained from the coupled set of the classical governing equations for the mass, momentum and energy balance. These equations are embodied in a computational model which is then coupled externally to a linearly elastic rock-stress model. This coupling is rather exploratory and based upon empirical correlations. The coupled model is able to take account of time-dependent, inhomogeneous and anisotropic features of the hydrogeologic, thermal and transport phenomena. A number of applications of the model have been made. Illustrations from the application of the model to nuclear waste repositories are included

  11. Transport of microbial tracers in clean and organically contaminated silica sand in laboratory columns compared with their transport in the field

    International Nuclear Information System (INIS)

    Weaver, Louise; Sinton, Lester W.; Pang, Liping; Dann, Rod; Close, Murray

    2013-01-01

    Waste disposal on land and the consequent transport of bacterial and viral pathogens in soils and aquifers are of major concern worldwide. Pathogen transport can be enhanced in the presence of organic matter due to occupation of attachment sites in the aquifer materials thus preventing pathogen attachment leading to their faster transport for longer distances. Laboratory column studies were carried out to investigate the effect of organic matter, in the form of dissolved organic carbon (DOC), on the transport of Escherichia coli and MS2 phage in saturated clean silica sand. Transport rates of these microbial tracers were also studied in a contaminated field site. Laboratory column studies showed that low concentrations (0.17 mg L −1 ) of DOC had little effect on E. coli J6-2 removal and slightly reduced the attachment of MS2 phage. After progressive conditioning of the column with DOC (1.7 mg L −1 and 17 mg L −1 ), neither E. coli J6-2 nor MS2 phage showed any attachment and recovery rates increased dramatically (up to 100%). The results suggest that DOC can affect the transport rates of microbial contaminants. For E. coli J6-2 the predominant effect appeared to be an increase in the secondary energy minimum leading to an increase in E. coli attachment initially. However, after 17 mg L −1 DOC conditioning of the silica sand no attachment of E. coli was observed as the DOC took up attachment sites in the porous media. MS2 phage appeared to be affected predominantly by out-competition of binding sites in the clean silica sand and a steady reduction in attachment was observed as the DOC conditioning increased. Field study showed a high removal of both E. coli and MS2 phage, although E. coli was removed at a lower rate than MS2 phage. In the field it is likely that a combination of effects are seen as the aquifer material will be heterogeneous in its surface nanoscale properties, demonstrated by the differing removal of E. coli and MS2 phage compared to the

  12. The prototypical proton-coupled oligopeptide transporter YdgR from Escherichia coli facilitates chloramphenicol uptake into bacterial cells

    DEFF Research Database (Denmark)

    Prabhala, Bala K; Aduri, Nanda G; Sharma, Neha

    2018-01-01

    . However, to date no report exists on any specific transport protein that facilitates Cam uptake. The proton-coupled oligopeptide transporter (POT) YdgR from Escherichia coli is a prototypical member of the POT family, functioning in proton-coupled uptake of di- and tripeptides. By following bacterial...

  13. Abiotic/biotic coupling in the rhizosphere: a reactive transport modeling analysis

    Science.gov (United States)

    Lawrence, Corey R.; Steefel, Carl; Maher, Kate

    2014-01-01

    A new generation of models is needed to adequately simulate patterns of soil biogeochemical cycling in response changing global environmental drivers. For example, predicting the influence of climate change on soil organic matter storage and stability requires models capable of addressing complex biotic/abiotic interactions of rhizosphere and weathering processes. Reactive transport modeling provides a powerful framework simulating these interactions and the resulting influence on soil physical and chemical characteristics. Incorporation of organic reactions in an existing reactive transport model framework has yielded novel insights into soil weathering and development but much more work is required to adequately capture root and microbial dynamics in the rhizosphere. This endeavor provides many advantages over traditional soil biogeochemical models but also many challenges.

  14. Electronic transport through a quantum dot chain with strong dot-lead coupling

    International Nuclear Information System (INIS)

    Liu, Yu; Zheng, Yisong; Gong, Weijiang; Gao, Wenzhu; Lue, Tianquan

    2007-01-01

    By means of the non-equilibrium Green function technique, the electronic transport through an N-quantum-dot chain is theoretically studied. By calculating the linear conductance spectrum and the local density of states in quantum dots, we find the resonant peaks in the spectra coincides with the eigen-energies of the N-quantum-dot chain when the dot-lead coupling is relatively weak. With the increase of the dot-lead coupling, such a correspondence becomes inaccurate. When the dot-lead coupling exceeds twice the interdot coupling, such a mapping collapses completely. The linear conductance turn to reflect the eigen-energies of the (N-2)- or (N-1)-quantum dot chain instead. The two peripheral quantum dots do not manifest themselves in the linear conductance spectrum. More interestingly, with the further increase of the dot-lead coupling, the system behaves just like an (N-2)- or (N-1)-quantum dot chain in weak dot-lead coupling limit, since the resonant peaks becomes narrower with the increase of dot-lead coupling

  15. Influences of a Side-Coupled Triple Quantum Dot on Kondo Transport Through a Quantum Dot

    International Nuclear Information System (INIS)

    Jiang Zhaotan; Yang Yannan; Qin Zhijie

    2010-01-01

    Kondo transport properties through a Kondo-type quantum dot (QD) with a side-coupled triple-QD structure are systematically investigated by using the non-equilibrium Green's function method. We firstly derive the formulae of the current, the linear conductance, the transmission coefficient, and the local density of states. Then we carry out the analytical and numerical studies and some universal conductance properties are obtained. It is shown that the number of the conductance valleys is intrinsically determined by the side-coupled QDs and at most equal to the number of the QDs included in the side-coupled structure in the asymmetric limit. In the process of forming the conductance valleys, the side-coupled QD system plays the dominant role while the couplings between the Kondo-type QD and the side-coupled structure play the subsidiary and indispensable roles. To testify the validity of the universal conductance properties, another different kinds of side-coupled triple-QD structures are considered. It should be emphasized that these universal properties are applicable in understanding this kind of systems with arbitrary many-QD side structures.

  16. Coupled processes of fluid flow, solute transport, and geochemical reactions in reactive barriers

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jeongkon; Schwartz, Franklin W.; Xu, Tianfu; Choi, Heechul, and Kim, In S.

    2004-01-02

    A complex pattern of coupling between fluid flow and mass transport develops when heterogeneous reactions occur. For instance, dissolution and precipitation reactions can change a porous medium's physical properties, such as pore geometry and thus permeability. These changes influence fluid flow, which in turn impacts the composition of dissolved constituents and the solid phases, and the rate and direction of advective transport. Two-dimensional modeling studies using TOUGHREACT were conducted to investigate the coupling between flow and transport developed as a consequence of differences in density, dissolution precipitation, and medium heterogeneity. The model includes equilibrium reactions for aqueous species, kinetic reactions between the solid phases and aqueous constituents, and full coupling of porosity and permeability changes resulting from precipitation and dissolution reactions in porous media. In addition, a new permeability relationship is implemented in TOUGHREACT to examine the effects of geochemical reactions and density difference on plume migration in porous media. Generally, the evolutions in the concentrations of the aqueous phase are intimately related to the reaction-front dynamics. Plugging of the medium contributed to significant transients in patterns of flow and mass transport.

  17. An immersed body method for coupled neutron transport and thermal hydraulic simulations of PWR assemblies

    International Nuclear Information System (INIS)

    Jewer, S.; Buchan, A.G.; Pain, C.C.; Cacuci, D.G.

    2014-01-01

    Highlights: • A new method of coupled radiation transport, heat and momentum exchanges on fluids, and heat transfer simulations. • Simulation of the thermal hydraulics and radiative properties within whole PWR assemblies. • An immersed body method for modelling complex solid domains on practical computational meshes. - Abstract: A recently developed immersed body method is adapted and used to model a typical pressurised water reactor (PWR) fuel assembly. The approach is implemented with the numerical framework of the finite element, transient criticality code, FETCH which is composed of the neutron transport code, EVENT, and the CFD code, FLUIDITY. Within this framework the neutron transport equation, Navier–Stokes equations and a fluid energy conservation equation are solved in a coupled manner on a coincident structured or unstructured mesh. The immersed body method has been used to model the solid fuel pins. The key feature of this method is that the fluid/neutronic domain and the solid domain are represented by overlapping and non-conforming meshes. The main difficulty of this approach, for which a solution is proposed in this work, is the conservative mapping of the energy and momentum exchange between the fluid/neutronic mesh and the solid fuel pin mesh. Three numerical examples are presented which include a validation of the fuel pin submodel against an analytical solution; an uncoupled (no neutron transport solution) PWR fuel assembly model with a specified power distribution which was validated against the COBRA-EN subchannel analysis code; and finally a coupled model of a PWR fuel assembly with reflective neutron boundary conditions. Coupling between the fluid and neutron transport solutions is through the nuclear cross sections dependence on Doppler fuel temperature, coolant density and temperature, which was taken into account by using pre-calculated cross-section lookup tables generated using WIMS9a. The method was found to show good agreement

  18. Transport properties of a Kondo dot with a larger side-coupled noninteracting quantum dot

    International Nuclear Information System (INIS)

    Liu, Y S; Fan, X H; Xia, Y J; Yang, X F

    2008-01-01

    We investigate theoretically linear and nonlinear quantum transport through a smaller quantum dot in a Kondo regime connected to two leads in the presence of a larger side-coupled noninteracting quantum dot, without tunneling coupling to the leads. To do this we employ the slave boson mean field theory with the help of the Keldysh Green's function at zero temperature. The numerical results show that the Kondo conductance peak may develop multiple resonance peaks and multiple zero points in the conductance spectrum owing to constructive and destructive quantum interference effects when the energy levels of the large side-coupled noninteracting dot are located in the vicinity of the Fermi level in the leads. As the coupling strength between two quantum dots increases, the tunneling current through the quantum device as a function of gate voltage applied across the two leads is suppressed. The spin-dependent transport properties of two parallel coupled quantum dots connected to two ferromagnetic leads are also investigated. The numerical results show that, for the parallel configuration, the spin current or linear spin differential conductance are enhanced when the polarization strength in the two leads is increased

  19. Electron-vibron coupling effects on electron transport via a single-molecule magnet

    Science.gov (United States)

    McCaskey, Alexander; Yamamoto, Yoh; Warnock, Michael; Burzurí, Enrique; van der Zant, Herre S. J.; Park, Kyungwha

    2015-03-01

    We investigate how the electron-vibron coupling influences electron transport via an anisotropic magnetic molecule, such as a single-molecule magnet (SMM) Fe4, by using a model Hamiltonian with parameter values obtained from density-functional theory (DFT). The magnetic anisotropy parameters, vibrational energies, and electron-vibron coupling strengths of the Fe4 are computed using DFT. A giant spin model is applied to the Fe4 with only two charge states, specifically a neutral state with a total spin S =5 and a singly charged state with S =9 /2 , which is consistent with our DFT result and experiments on Fe4 single-molecule transistors. In sequential electron tunneling, we find that the magnetic anisotropy gives rise to new features in the conductance peaks arising from vibrational excitations. In particular, the peak height shows a strong, unusual dependence on the direction as well as magnitude of applied B field. The magnetic anisotropy also introduces vibrational satellite peaks whose position and height are modified with the direction and magnitude of applied B field. Furthermore, when multiple vibrational modes with considerable electron-vibron coupling have energies close to one another, a low-bias current is suppressed, independently of gate voltage and applied B field, although that is not the case for a single mode with a similar electron-vibron coupling. In the former case, the conductance peaks reveal a stronger B -field dependence than in the latter case. The new features appear because the magnetic anisotropy barrier is of the same order of magnitude as the energies of vibrational modes with significant electron-vibron coupling. Our findings clearly show the interesting interplay between magnetic anisotropy and electron-vibron coupling in electron transport via the Fe4. Similar behavior can be observed in transport via other anisotropic magnetic molecules.

  20. Structural basis for polyspecificity in the POT family of proton-coupled oligopeptide transporters

    DEFF Research Database (Denmark)

    Lyons, Joseph A.; Parker, Joanne L.; Solcan, Nicolae

    2014-01-01

    An enigma in the field of peptide transport is the structural basis for ligand promiscuity, as exemplified by PepT1, the mammalian plasma membrane peptide transporter. Here, we present crystal structures of di‐ and tripeptide‐bound complexes of a bacterial homologue of PepT1, which reveal at least...... two mechanisms for peptide recognition that operate within a single, centrally located binding site. The dipeptide was orientated laterally in the binding site, whereas the tripeptide revealed an alternative vertical binding mode. The co‐crystal structures combined with functional studies reveal...... that biochemically distinct peptide‐binding sites likely operate within the POT/PTR family of proton‐coupled symporters and suggest that transport promiscuity has arisen in part through the ability of the binding site to accommodate peptides in multiple orientations for transport...

  1. Experimental validation of GADRAS's coupled neutron-photon inverse radiation transport solver

    International Nuclear Information System (INIS)

    Mattingly, John K.; Mitchell, Dean James; Harding, Lee T.

    2010-01-01

    Sandia National Laboratories has developed an inverse radiation transport solver that applies nonlinear regression to coupled neutron-photon deterministic transport models. The inverse solver uses nonlinear regression to fit a radiation transport model to gamma spectrometry and neutron multiplicity counting measurements. The subject of this paper is the experimental validation of that solver. This paper describes a series of experiments conducted with a 4.5 kg sphere of α-phase, weapons-grade plutonium. The source was measured bare and reflected by high-density polyethylene (HDPE) spherical shells with total thicknesses between 1.27 and 15.24 cm. Neutron and photon emissions from the source were measured using three instruments: a gross neutron counter, a portable neutron multiplicity counter, and a high-resolution gamma spectrometer. These measurements were used as input to the inverse radiation transport solver to evaluate the solver's ability to correctly infer the configuration of the source from its measured radiation signatures.

  2. Numerical modelling of coupled fluid, heat, and solute transport in deformable fractured rock

    International Nuclear Information System (INIS)

    Chan, T.; Reid, J.A.K.

    1987-01-01

    This paper reports on a three-dimensional (3D) finite-element code, MOTIF (model of transport in fractured/porous media), developed to model the coupled processes of groundwater flow, heat transport, brine transport, and one-species radionuclide transport in geological media. Three types of elements are available: a 3D continuum element, a planar fracture element that can be oriented in any arbitrary direction in 3D space or pipe flow in 3D space, and a line element for simulating fracture flow in 2D space or pipe flow in 3D space. As a quality-assurance measure, the MOTIF code was verified by comparison of its results with analytical solutions and other published numerical solutions

  3. ITS - The integrated TIGER series of coupled electron/photon Monte Carlo transport codes

    International Nuclear Information System (INIS)

    Halbleib, J.A.; Mehlhorn, T.A.

    1985-01-01

    The TIGER series of time-independent coupled electron/photon Monte Carlo transport codes is a group of multimaterial, multidimensional codes designed to provide a state-of-the-art description of the production and transport of the electron/photon cascade. The codes follow both electrons and photons from 1.0 GeV down to 1.0 keV, and the user has the option of combining the collisional transport with transport in macroscopic electric and magnetic fields of arbitrary spatial dependence. Source particles can be either electrons or photons. The most important output data are (a) charge and energy deposition profiles, (b) integral and differential escape coefficients for both electrons and photons, (c) differential electron and photon flux, and (d) pulse-height distributions for selected regions of the problem geometry. The base codes of the series differ from one another primarily in their dimensionality and geometric modeling. They include (a) a one-dimensional multilayer code, (b) a code that describes the transport in two-dimensional axisymmetric cylindrical material geometries with a fully three-dimensional description of particle trajectories, and (c) a general three-dimensional transport code which employs a combinatorial geometry scheme. These base codes were designed primarily for describing radiation transport for those situations in which the detailed atomic structure of the transport medium is not important. For some applications, it is desirable to have a more detailed model of the low energy transport. The system includes three additional codes that contain a more elaborate ionization/relaxation model than the base codes. Finally, the system includes two codes that combine the collisional transport of the multidimensional base codes with transport in macroscopic electric and magnetic fields of arbitrary spatial dependence

  4. Coupled ion binding and structural transitions along the transport cycle of glutamate transporters

    OpenAIRE

    Verdon, Grégory; Oh, SeCheol; Serio, Ryan N; Boudker, Olga

    2014-01-01

    eLife digest Molecules of glutamate can carry messages between cells in the brain, and these signals are essential for thought and memory. Glutamate molecules can also act as signals to build new connections between brain cells and to prune away unnecessary ones. However, too much glutamate outside of the cells kills the brain tissue and can lead to devastating brain diseases. In a healthy brain, special pumps called glutamate transporters move these molecules back into the brain cells, where...

  5. Unconventional quantized edge transport in the presence of inter-edge coupling in intercalated graphene

    OpenAIRE

    Li, Yuanchang

    2016-01-01

    It is generally believed that the inter-edge coupling destroys the quantum spin Hall (QSH) effect along with the gap opening at the Dirac points. Using first-principles calculations, we find that the quantized edge transport persists in the presence of inter-edge coupling in Ta intercalated epitaxial graphene on SiC(0001), being a QSH insulator with the non-trivial gap of 81 meV. In this case, the band is characterized by two perfect Dirac cones with different Fermi velocities, yet only one m...

  6. A coupled hydrodynamic-hydrochemical modeling for predicting mineral transport in a natural acid drainage system.

    Science.gov (United States)

    Zegers Risopatron, G., Sr.; Navarro, L.; Montserrat, S., Sr.; McPhee, J. P.; Niño, Y.

    2017-12-01

    The geochemistry of water and sediments, coupled with hydrodynamic transport in mountainous channels, is of particular interest in central Chilean Andes due to natural occurrence of acid waters. In this paper, we present a coupled transport and geochemical model to estimate and understand transport processes and fate of minerals at the Yerba Loca Basin, located near Santiago, Chile. In the upper zone, water presentes low pH ( 3) and high concentrations of iron, aluminum, copper, manganese and zinc. Acidity and minerals are the consequence of water-rock interactions in hydrothermal alteration zones, rich in sulphides and sulphates, covered by seasonal snow and glaciers. Downstream, as a consequence of neutral to alkaline lateral water contributions (pH >7) along the river, pH increases and concentration of solutes decreases. The mineral transport model has three components: (i) a hydrodynamic model, where we use HEC-RAS to solve 1D Saint-Venant equations, (ii) a sediment transport model to estimate erosion and sedimentation rates, which quantify minerals transference between water and riverbed and (iii) a solute transport model, based on the 1D OTIS model which takes into account the temporal delay in solutes transport that typically is observed in natural channels (transient storage). Hydrochemistry is solved using PHREEQC, a software for speciation and batch reaction. Our results show that correlation between mineral precipitation and dissolution according to pH values changes along the river. Based on pH measurements (and according to literature) we inferred that main minerals in the water system are brochantite, ferrihydrite, hydrobasaluminite and schwertmannite. Results show that our model can predict the transport and fate of minerals and metals in the Yerba Loca Basin. Mineral dissolution and precipitation process occur for limited ranges of pH values. When pH values are increased, iron minerals (schwertmannite) are the first to precipitate ( 2.5

  7. Chemistry-transport coupling and retroactive effects on material properties within the context of a deep geological repository

    International Nuclear Information System (INIS)

    Bildstein, O.

    2010-06-01

    The author gives an overview of his research and teaching activities. His researches first dealt with the development of a simulation of the chemistry/transport coupling and of the retroactive effects on transport parameters, then with the chemistry/transport modelling and its coupling with mechanics, and finally with the multi-scale investigation of porous materials. Perspectives are discussed and publications are indicated

  8. Energy Conservation Tests of a Coupled Kinetic-kinetic Plasma-neutral Transport Code

    Energy Technology Data Exchange (ETDEWEB)

    Stotler, D. P.; Chang, C. S.; Ku, S. H.; Lang, J.; Park, G.

    2012-08-29

    A Monte Carlo neutral transport routine, based on DEGAS2, has been coupled to the guiding center ion-electron-neutral neoclassical PIC code XGC0 to provide a realistic treatment of neutral atoms and molecules in the tokamak edge plasma. The DEGAS2 routine allows detailed atomic physics and plasma-material interaction processes to be incorporated into these simulations. The spatial pro le of the neutral particle source used in the DEGAS2 routine is determined from the uxes of XGC0 ions to the material surfaces. The kinetic-kinetic plasma-neutral transport capability is demonstrated with example pedestal fueling simulations.

  9. A turbulent transport network model in MULTIFLUX coupled with TOUGH2

    International Nuclear Information System (INIS)

    Danko, G.; Bahrami, D.; Birkholzer, J.T.

    2011-01-01

    A new numerical method is described for the fully iterated, conjugate solution of two discrete submodels, involving (a) a transport network model for heat, moisture, and airflows in a high-permeability, air-filled cavity; and (b) a variably saturated fractured porous medium. The transport network submodel is an integrated-parameter, computational fluid dynamics solver, describing the thermal-hydrologic transport processes in the flow channel system of the cavity with laminar or turbulent flow and convective heat and mass transport, using MULTIFLUX. The porous medium submodel, using TOUGH2, is a solver for the heat and mass transport in the fractured rock mass. The new model solution extends the application fields of TOUGH2 by integrating it with turbulent flow and transport in a discrete flow network system. We present demonstrational results for a nuclear waste repository application at Yucca Mountain with the most realistic model assumptions and input parameters including the geometrical layout of the nuclear spent fuel and waste with variable heat load for the individual containers. The MULTIFLUX and TOUGH2 model elements are fully iterated, applying a programmed reprocessing of the Numerical Transport Code Functionalization model-element in an automated Outside Balance Iteration loop. The natural, convective airflow field and the heat and mass transport in a representative emplacement drift during postclosure are explicitly solved in the new model. The results demonstrate that the direction and magnitude of the air circulation patterns and all transport modes are strongly affected by the heat and moisture transport processes in the surrounding rock, justifying the need for a coupled, fully iterated model solution such as the one presented in the paper.

  10. ZZ ENDLIB, Coupled Electron and Photon Transport Library in ENDL Format

    International Nuclear Information System (INIS)

    2002-01-01

    Description of program or function: The LLNL Evaluated Nuclear Data Library has existed since 1958 in a succession of forms and formats. The present form is as a machine-independent character file format and contains data for the evaluated atomic relaxation data library (EADL), the evaluated photon interaction data library (EPDL), and the evaluated electron interaction data library (EEDL). The purpose of these libraries is to furnish data for coupled electron-photon transport calculations. In order to perform coupled photon-electron transport calculations, all three libraries are required. The UCRL-ID-117796 report included in the documentation for this package provides information on the contents and formats for all three libraries, which are included in this package. All of these libraries span atomic numbers, Z, from 1 to 100. Additionally the electron and photon interaction libraries cover the incident particle energy range from 10 eV to 100 GeV

  11. Long-range correlations in a simple stochastic model of coupled transport

    International Nuclear Information System (INIS)

    Larralde, Hernan; Sanders, David P

    2009-01-01

    We study coupled transport in the nonequilibrium stationary state of a model consisting of independent random walkers, moving along a one-dimensional channel, which carry a conserved energy-like quantity, with density and temperature gradients imposed by reservoirs at the ends of the channel. In our model, walkers interact with other walkers at the same site by sharing energy at each time step, but the amount of energy carried does not affect the motion of the walkers. We find that already in this simple model long-range correlations arise in the nonequilibrium stationary state which are similar to those observed in more realistic models of coupled transport. We derive an analytical expression for the source of these correlations, which we use to obtain semi-analytical results for the correlations themselves assuming a local-equilibrium hypothesis. These are in very good agreement with results from direct numerical simulations.

  12. Investigation of hurricane Ivan using the coupled ocean-atmosphere-wave-sediment transport (COAWST) model

    Science.gov (United States)

    Zambon, Joseph B.; He, Ruoying; Warner, John C.

    2014-01-01

    The coupled ocean–atmosphere–wave–sediment transport (COAWST) model is used to hindcast Hurricane Ivan (2004), an extremely intense tropical cyclone (TC) translating through the Gulf of Mexico. Sensitivity experiments with increasing complexity in ocean–atmosphere–wave coupled exchange processes are performed to assess the impacts of coupling on the predictions of the atmosphere, ocean, and wave environments during the occurrence of a TC. Modest improvement in track but significant improvement in intensity are found when using the fully atmosphere–ocean-wave coupled configuration versus uncoupled (e.g., standalone atmosphere, ocean, or wave) model simulations. Surface wave fields generated in the fully coupled configuration also demonstrates good agreement with in situ buoy measurements. Coupled and uncoupled model-simulated sea surface temperature (SST) fields are compared with both in situ and remote observations. Detailed heat budget analysis reveals that the mixed layer temperature cooling in the deep ocean (on the shelf) is caused primarily by advection (equally by advection and diffusion).

  13. Phosphoenolpyruvate-dependent fructose phosphotransferase system in Rhodopseudomonas sphaeroides : The coupling between transport and phosphorylation in inside-out vesicles

    NARCIS (Netherlands)

    Lolkema, Juke S.; Robillard, George T.

    The bacterial phosphotransferase systems are believed to catalyze the concomitant transport and phosphorylation of hexoses and hexitols. The transport is from the outside to the inside of the cell. An absolute coupling between transport and phosphorylation has however been questioned in the

  14. Fluid transportation mechanisms by a coupled system of elastic membranes and magnetic fluids

    International Nuclear Information System (INIS)

    Ido, Y.; Tanaka, K.; Sugiura, Y.

    2002-01-01

    The basic properties of the fluid transportation mechanism that is produced by the coupled waves propagating along a thin elastic membrane covering a magnetic fluid layer in a shallow and long rectangular vessel are investigated. It is shown that the progressive magnetic field induced by the rectangular pulses generates sinusoidal vibration of the displacement of elastic membrane and makes the system work more efficiently than the magnetic field induced by the pulse-width-modulation method

  15. Steady-state coupled transport of HNO3 through a hollow-fiber supported liquid membrane

    International Nuclear Information System (INIS)

    Noble, R.D.; Danesi, P.R.

    1987-01-01

    Nitric acid removal from an aqueous stream was accomplished by continuously passing the fluid through a hollow fiber supported liquid membrane (SLM). The nitric acid was extracted through the membrane wall by coupled transport. The system was modeled as a series of (SLM)-continuous stirred tank reactor (CSTR) pairs. An approximate technique was used to predict the steady state nitric acid concentration in the system. The comparison with experimental data was very good

  16. Denitrification coupled with methane anoxic oxidation and microbial community involved identification

    Directory of Open Access Journals (Sweden)

    Renata Medici Frayne Cuba

    2011-02-01

    Full Text Available In this work, the biological denitrification associated with anoxic oxidation of methane and the microbial diversity involved were studied. Kinetic tests for nitrate (NO3- and nitrite (NO2- removal and methane uptake were carried out in 100 mL batch reactors incubated in a shaker (40 rpm at 30 ºC. Denitrificant/methanotrophic biomass was taken from a laboratory scale reactor fed with synthetic nitrified substrates (40 mgN L-1 of NO3- and subsequently NO2- and methane as carbon source. Results obtained from nitrate removal followed a first order reaction, presenting a kinetic apparent constant (kNO3 of 0.0577±0.0057d-1. Two notable points of the denitrification rate (0.12gNO3--N g-1 AVS d-1 and 0.07gNO3--N g-1 AVS d-1 were observed in the beginning and on the seventh day of operation. When nitrite was added as an electron acceptor, denitrification rates were improved, presenting an apparent kinetic constant (kNO2 of 0.0722±0.0044d-1, a maximum denitrification rate of 0.6gNO2--N g-1AVS d-1, and minimum denitrification rate of 0.1gNO2--N g-1AVS d-1 at the beginning and end of the test, respectively. Endogenous material supporting denitrification and methane concentration dissolved in the substrate was discarded from the control experiments in the absence of methane and seed, respectively. Methylomonas sp. was identified in the reactors fed with nitrate and nitrite as well as uncultured bacterium.

  17. Coupled particle–fluid transport and magnetic separation in microfluidic systems with passive magnetic functionality

    International Nuclear Information System (INIS)

    Khashan, Saud A; Furlani, Edward P

    2013-01-01

    A study is presented of coupled particle–fluid transport and field-directed particle capture in microfluidic systems with passive magnetic functionality. These systems consist of a microfluidic flow cell on a substrate that contains embedded magnetic elements. Two systems are considered that utilize soft- and hard-magnetic elements, respectively. In the former, an external field is applied to magnetize the elements, and in the latter, they are permanently magnetized. The field produced by the magnetized elements permeates into the flow cell giving rise to an attractive force on magnetic particles that flow through it. The systems are studied using a novel numerical/closed-form modelling approach that combines numerical transport analysis with closed-form field analysis. Particle–fluid transport is computed using computational fluid dynamics (CFD), while the magnetic force that governs particle capture is obtained in closed form. The CFD analysis takes into account dominant particle forces and two-way momentum transfer between the particles and the fluid. The two-way particle–fluid coupling capability is an important feature of the model that distinguishes it from more commonly used and simplified one-way coupling analysis. The model is used to quantify the impact of two-way particle–fluid coupling on both the capture efficiency and the flow pattern in the systems considered. Many effects such as particle-induced flow-enhanced capture efficiency and flow circulation are studied that cannot be predicted using one-way coupling analysis. In addition, dilute particle dispersions are shown to exhibit significant localized particle–fluid coupling near the capture regions, which contradicts the commonly held view that two-way coupling can be ignored when analysing high-gradient magnetic separation involving such particle systems. Overall, the model demonstrates that two-way coupling needs to be taken into account for rigorous predictions of capture efficiency

  18. Mass transport in low permeability rocks under the influence of coupled thermomechanical and hydrochemical effects - an overview

    International Nuclear Information System (INIS)

    Tsang, C.F.

    1984-10-01

    The present paper gives a general overview of mass transport in low permeability rocks under the coupled thermomechanical and hydrochemical effects associated with a nuclear waste repository. A classification of coupled processes is given. Then an ess is presented. example of a coupled process is presented. Discussions of coupled processes based on a recent LBL Panel meeting are summarized. 5 references, 3 figures, 4 tables

  19. Coupled porohyperelastic mass transport (PHEXPT) finite element models for soft tissues using ABAQUS.

    Science.gov (United States)

    Vande Geest, Jonathan P; Simon, B R; Rigby, Paul H; Newberg, Tyler P

    2011-04-01

    Finite element models (FEMs) including characteristic large deformations in highly nonlinear materials (hyperelasticity and coupled diffusive/convective transport of neutral mobile species) will allow quantitative study of in vivo tissues. Such FEMs will provide basic understanding of normal and pathological tissue responses and lead to optimization of local drug delivery strategies. We present a coupled porohyperelastic mass transport (PHEXPT) finite element approach developed using a commercially available ABAQUS finite element software. The PHEXPT transient simulations are based on sequential solution of the porohyperelastic (PHE) and mass transport (XPT) problems where an Eulerian PHE FEM is coupled to a Lagrangian XPT FEM using a custom-written FORTRAN program. The PHEXPT theoretical background is derived in the context of porous media transport theory and extended to ABAQUS finite element formulations. The essential assumptions needed in order to use ABAQUS are clearly identified in the derivation. Representative benchmark finite element simulations are provided along with analytical solutions (when appropriate). These simulations demonstrate the differences in transient and steady state responses including finite deformations, total stress, fluid pressure, relative fluid, and mobile species flux. A detailed description of important model considerations (e.g., material property functions and jump discontinuities at material interfaces) is also presented in the context of finite deformations. The ABAQUS-based PHEXPT approach enables the use of the available ABAQUS capabilities (interactive FEM mesh generation, finite element libraries, nonlinear material laws, pre- and postprocessing, etc.). PHEXPT FEMs can be used to simulate the transport of a relatively large neutral species (negligible osmotic fluid flux) in highly deformable hydrated soft tissues and tissue-engineered materials.

  20. Coupled full core neutron transport/CFD simulations of pressurized water reactors

    International Nuclear Information System (INIS)

    Kochunas, B.; Stimpson, S.; Collins, B.; Downar, T.; Brewster, R.; Baglietto, E.; Yan, J.

    2012-01-01

    Recently as part of the CASL project, a capability to perform 3D whole-core coupled neutron transport and computational fluid dynamics (CFD) calculations was demonstrated. This work uses the 2D/1D transport code DeCART and the commercial CFD code STAR-CCM+. It builds on previous CASL work demonstrating coupling for smaller spatial domains. The coupling methodology is described along with the problem simulated and results are presented for fresh hot full power conditions. An additional comparison is made to an equivalent model that uses lower order T/H feedback to assess the importance and cost of high fidelity feedback to the neutronics problem. A simulation of a quarter core Combustion Engineering (CE) PWR core was performed with the coupled codes using a Fixed Point Gauss-Seidel iteration technique. The total approximate calculation requirements are nearly 10,000 CPU hours and 1 TB of memory. The problem took 6 coupled iterations to converge. The CFD coupled model and low order T/H feedback model compared well for global solution parameters, with a difference in the critical boron concentration and average outlet temperature of 14 ppm B and 0.94 deg. C, respectively. Differences in the power distribution were more significant with maximum relative differences in the core-wide pin peaking factor (Fq) of 5.37% and average relative differences in flat flux region power of 11.54%. Future work will focus on analyzing problems more relevant to CASL using models with less approximations. (authors)

  1. A time-dependent neutron transport model and its coupling to thermal-hydraulics

    International Nuclear Information System (INIS)

    Pautz, A.

    2001-01-01

    A new neutron transport code for time-dependent analyses of nuclear systems has been developed. The code system is based on the well-known Discrete Ordinates code DORT, which solves the steady-state neutron/photon transport equation in two dimensions for an arbitrary number of energy groups and the most common regular geometries. For the implementation of time-dependence a fully implicit first-order scheme was employed to minimize errors due to temporal discretization. This requires various modifications to the transport equation as well as the extensive use of elaborated acceleration mechanisms. The convergence criteria for fluxes, fission rates etc. had to be strongly tightened to ensure the reliability of results. To perform coupled analyses, an interface to the GRS system code ATHLET has been developed. The nodal power densities from the neutron transport code are passed to ATHLET to calculate thermal-hydraulic system parameters, e.g. fuel and coolant temperatures. These are in turn used to generate appropriate nuclear cross sections by interpolation of pre-calculated data sets for each time step. Finally, to demonstrate the transient capabilities of the coupled code system, the research reactor FRM-II has been analysed. Several design basis accidents were modelled, like the loss of off site power, loss of secondary heat sink and unintended control rod withdrawal. (author)

  2. STRUCTURE AND FUNCTION OF SUBSURFACE MICROBIAL COMMUNITIES AFFECTING RADIONUCLIDE TRANSPORT AND BIOIMMOBILIZATION

    Energy Technology Data Exchange (ETDEWEB)

    Joel E. Kostka; Lee Kerkhof; Kuk-Jeong Chin; Martin Keller; Joseph W. Stucki

    2011-06-15

    are new to science all show high sequence identity to sequences retrieved from ORFRC subsurface. (2) Based on physiological and phylogenetic characterization, two new species of subsurface bacteria were described: the metal-reducer Geobacter daltonii, and the denitrifier Rhodanobacter denitrificans. (3) Strains isolated from the ORFRC show that Rhodanobacter species are well adapted to the contaminated subsurface. Strains 2APBS1 and 116-2 grow at high salt (3% NaCl), low pH (3.5) and tolerate high concentrations of nitrate (400mM) and nitrite (100mM). Strain 2APBS1 was demonstrated to grow at in situ acidic pHs down to 2.5. (4) R. denitrificans strain 2APBS1 is the first described Rhodanobacter species shown to denitrify. Nitrate is almost entirely converted to N2O, which may account for the large accumulation of N2O in the ORFRC subsurface. (5) G. daltonii, isolated from uranium- and hydrocarbon-contaminated subsurface sediments of the ORFRC, is the first organism from the subsurface clade of the genus Geobacter that is capable of growth on aromatic hydrocarbons. (6) High quality draft genome sequences and a complete eco-physiological description are completed for R. denitrificans strain 2APBS1 and G. daltonii strain FRC-32. (7) Given their demonstrated relevance to DOE remediation efforts and the availability of detailed genotypic/phenotypic characterization, Rhodanobacter denitrificans strain 2APBS1 and Geobacter daltonii strain FRC-32 represent ideal model organisms to provide a predictive understanding of subsurface microbial activity through metabolic modeling. Tasks II and III-Diversity and distribution of active anaerobes and Mechanisms linking electron transport and the fate of radionuclides: (1) Our study showed that members of genus Rhodanobacter and Geobacter are abundant and active in the uranium and nitrate contaminated subsurface. In the contaminant source zone of the Oak Ridge site, Rhodanobacter spp. are the predominant, active organisms detected

  3. Separation of some metal ions using coupled transport supported liquid membranes

    International Nuclear Information System (INIS)

    Chaudhary, M.A.

    1993-01-01

    Liquid membrane extraction processes has become very popular due to their superiority in many ways over other separation techniques. In coupled transport membranes the metal ions can be transported across the membrane against their concentration gradient under the influence of chemical potential difference. Liquid membranes consisting of a carrier-cum-diluent, supported in microporous polymeric hydrophobic films have been studied for transport of metal ions like U(VI), Cr(VI), Be(II), V(V), Ti(IV), Zn(II), Cd(II), Hf(IV), W(VI), and Co(II). The present paper presents basic data with respect to flux and permeabilities of these metal ions across membranes based on experimental results and theoretical equations, using different carriers and diluents and provides a brief reference to possibility of such membranes for large scale applications. (author)

  4. Transport equations, Level Set and Eulerian mechanics. Application to fluid-structure coupling

    International Nuclear Information System (INIS)

    Maitre, E.

    2008-11-01

    My works were devoted to numerical analysis of non-linear elliptic-parabolic equations, to neutron transport equation and to the simulation of fabrics draping. More recently I developed an Eulerian method based on a level set formulation of the immersed boundary method to deal with fluid-structure coupling problems arising in bio-mechanics. Some of the more efficient algorithms to solve the neutron transport equation make use of the splitting of the transport operator taking into account its characteristics. In the present work we introduced a new algorithm based on this splitting and an adaptation of minimal residual methods to infinite dimensional case. We present the case where the velocity space is of dimension 1 (slab geometry) and 2 (plane geometry) because the splitting is simpler in the former

  5. An analytical model for predicting transport in a coupled vadose/phreatic system

    International Nuclear Information System (INIS)

    Tomasko, D.

    1997-05-01

    A simple analytical model is presented for predicting the transport of a contaminant in both the unsaturated (vadose) and saturated (phreatic) zones following a surficial spill. The model incorporates advection, dispersion, adsorption, and first-order decay in both zones and couples the transport processes at the water table. The governing equation is solved by using the method of Laplace transforms, with numerical inversion of the Laplace space equation for concentration. Because of the complexity of the functional form for the Laplace space solution, a numerical methodology using the real and imaginary parts of a Fourier series was implemented. To reduce conservatism in the model, dilution at the water table was also included. Verification of the model is demonstrated by its ability to reproduce the source history at the surface and to replicate appropriate one-dimensional transport through either the vadose or phreatic zone. Because of its simplicity and lack of detailed input data requirements, the model is recommended for scoping calculations

  6. Evaluation of the Universal Viral Transport system for long-term storage of virus specimens for microbial forensics.

    Science.gov (United States)

    Hosokawa-Muto, Junji; Fujinami, Yoshihito; Mizuno, Natsuko

    2015-08-01

    Forensic microbial specimens, including bacteria and viruses, are collected at biocrime and bioterrorism scenes. Although it is preferable that the pathogens in these samples are alive and kept in a steady state, the samples may be stored for prolonged periods before analysis. Therefore, it is important to understand the effects of storage conditions on the pathogens contained within such samples. To evaluate the capacity to preserve viable virus and the viral genome, influenza virus was added to the transport medium of the Universal Viral Transport system and stored for over 3 months at various temperatures, after which virus titrations and quantitative analysis of the influenza hemagglutinin gene were performed. Although viable viruses became undetectable 29 days after the medium was stored at room temperature, viruses in the medium stored at 4°C were viable even after 99 days. A quantitative PCR analysis indicated that the hemagglutinin gene was maintained for 99 days at both 4°C and room temperature. Therefore, long-term storage at 4°C has little effect on viable virus and viral genes, so the Universal Viral Transport system can be useful for microbial forensics. This study provides important information for the handling of forensic virus specimens. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  7. Development and evaluation of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

    Science.gov (United States)

    Hong, Eun-Mi; Park, Yongeun; Muirhead, Richard; Pachepsky, Yakov

    2017-04-01

    Pathogenic microorganisms in recreational and irrigation waters remain the subject of concern. Water quality models are used to estimate microbial quality of water sources, to evaluate microbial contamination-related risks, to guide the microbial water quality monitoring, and to evaluate the effect of agricultural management on the microbial water quality. The Agricultural Policy/Environmental eXtender (APEX) is the watershed-scale water quality model that includes highly detailed representation of agricultural management. The APEX currently does not have microbial fate and transport simulation capabilities. The objective of this work was to develop the first APEX microbial fate and transport module that could use the APEX conceptual model of manure removal together with recently introduced conceptualizations of the in-stream microbial fate and transport. The module utilizes manure erosion rates found in the APEX. The total number of removed bacteria was set to the concentrations of bacteria in soil-manure mixing layer and eroded manure amount. Bacteria survival in soil-manure mixing layer was simulated with the two-stage survival model. Individual survival patterns were simulated for each manure application date. Simulated in-stream microbial fate and transport processes included the reach-scale passive release of bacteria with resuspended bottom sediment during high flow events, the transport of bacteria from bottom sediment due to the hyporheic exchange during low flow periods, the deposition with settling sediment, and the two-stage survival. Default parameter values were available from recently published databases. The APEX model with the newly developed microbial fate and transport module was applied to simulate seven years of monitoring data for the Toenepi watershed in New Zealand. The stream network of the watershed ran through grazing lands with the daily bovine waste deposition. Based on calibration and testing results, the APEX with the microbe module

  8. Evaluating the influence of process parameters on soluble microbial products formation using response surface methodology coupled with grey relational analysis.

    Science.gov (United States)

    Xu, Juan; Sheng, Guo-Ping; Luo, Hong-Wei; Fang, Fang; Li, Wen-Wei; Zeng, Raymond J; Tong, Zhong-Hua; Yu, Han-Qing

    2011-01-01

    Soluble microbial products (SMPs) present a major part of residual chemical oxygen demand (COD) in the effluents from biological wastewater treatment systems, and the SMP formation is greatly influenced by a variety of process parameters. In this study, response surface methodology (RSM) coupled with grey relational analysis (GRA) method was used to evaluate the effects of substrate concentration, temperature, NH(4)(+)-N concentration and aeration rate on the SMP production in batch activated sludge reactors. Carbohydrates were found to be the major component of SMP, and the influential priorities of these factors were: temperature>substrate concentration > aeration rate > NH(4)(+)-N concentration. On the basis of the RSM results, the interactive effects of these factors on the SMP formation were evaluated, and the optimal operating conditions for a minimum SMP production in such a batch activated sludge system also were identified. These results provide useful information about how to control the SMP formation of activated sludge and ensure the bioreactor high-quality effluent. Copyright © 2010 Elsevier Ltd. All rights reserved.

  9. Co-culture microorganisms with different initial proportions reveal the mechanism of chalcopyrite bioleaching coupling with microbial community succession.

    Science.gov (United States)

    Ma, Liyuan; Wang, Xingjie; Feng, Xue; Liang, Yili; Xiao, Yunhua; Hao, Xiaodong; Yin, Huaqun; Liu, Hongwei; Liu, Xueduan

    2017-01-01

    The effect of co-culture microorganisms with different initial proportions on chalcopyrite bioleaching was investigated. Communities were rebuilt by six typical strains isolated from the same habitat. The results indicated, by community with more sulfur oxidizers at both 30 and 40°C, the final copper extraction rate was 19.8% and 6.5% higher, respectively, than that with more ferrous oxidizers. The variations of pH, redox potential, ferrous and copper ions in leachate also provided evidences that community with more sulfur oxidizers was more efficient. Community succession of free and attached cells revealed that initial proportions played decisive roles on community dynamics at 30°C, while communities shared similar structures, not relevant to initial proportions at 40°C. X-ray diffraction analysis confirmed different microbial functions on mineral surface. A mechanism model for chalcopyrite bioleaching was established coupling with community succession. This will provide theoretical basis for reconstructing an efficient community in industrial application. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. A Model to Couple Flow, Thermal and Reactive Chemical Transport, and Geo-mechanics in Variably Saturated Media

    Science.gov (United States)

    Yeh, G. T.; Tsai, C. H.

    2015-12-01

    This paper presents the development of a THMC (thermal-hydrology-mechanics-chemistry) process model in variably saturated media. The governing equations for variably saturated flow and reactive chemical transport are obtained based on the mass conservation principle of species transport supplemented with Darcy's law, constraint of species concentration, equation of states, and constitutive law of K-S-P (Conductivity-Degree of Saturation-Capillary Pressure). The thermal transport equation is obtained based on the conservation of energy. The geo-mechanic displacement is obtained based on the assumption of equilibrium. Conventionally, these equations have been implicitly coupled via the calculations of secondary variables based on primary variables. The mechanisms of coupling have not been obvious. In this paper, governing equations are explicitly coupled for all primary variables. The coupling is accomplished via the storage coefficients, transporting velocities, and conduction-dispersion-diffusion coefficient tensor; one set each for every primary variable. With this new system of equations, the coupling mechanisms become clear. Physical interpretations of every term in the coupled equations will be discussed. Examples will be employed to demonstrate the intuition and superiority of these explicit coupling approaches. Keywords: Variably Saturated Flow, Thermal Transport, Geo-mechanics, Reactive Transport.

  11. Techniques to reduce memory requirements for coupled photon-electron transport

    International Nuclear Information System (INIS)

    Turcksin, Bruno; Ragusa, Jean; Morel, Jim

    2011-01-01

    In this work, we present two methods to decrease memory needs while solving the photon- electron transport equation. The coupled transport of electrons and photons is of importance in radiotherapy because it describes the interactions of X-rays with matter. One of the issues of discretized electron transport is that the electron scattering is highly forward peaked. A common approximation is to represent the peak in the scattering cross section by a Dirac distribution. This is convenient, but the integration over all angles of this distribution requires the use of Galerkin quadratures. By construction these quadratures impose that the number of flux moments be equal to the number of directions (number of angular fluxes), which is very demanding in terms of memory. In this study, we show that even if the number of moments is not as large as the number of directions, an accurate solution can be obtained when using Galerkin quadratures. Another method to decrease the memory needs involves choosing an appropriate reordering of the energy groups. We show in this paper that an appropriate alternation of photons/electrons groups allows to rewrite one transport problem of n groups as gcd successive transport problems of n/gcd groups where gcd is the greatest common divisor between the number of photon groups and the number of electron groups. (author)

  12. Spin-orbit coupling, electron transport and pairing instabilities in two-dimensional square structures

    Energy Technology Data Exchange (ETDEWEB)

    Kocharian, Armen N. [Department of Physics, California State University, Los Angeles, CA 90032 (United States); Fernando, Gayanath W.; Fang, Kun [Department of Physics, University of Connecticut, Storrs, Connecticut 06269 (United States); Palandage, Kalum [Department of Physics, Trinity College, Hartford, Connecticut 06106 (United States); Balatsky, Alexander V. [AlbaNova University Center Nordita, SE-106 91 Stockholm (Sweden)

    2016-05-15

    Rashba spin-orbit effects and electron correlations in the two-dimensional cylindrical lattices of square geometries are assessed using mesoscopic two-, three- and four-leg ladder structures. Here the electron transport properties are systematically calculated by including the spin-orbit coupling in tight binding and Hubbard models threaded by a magnetic flux. These results highlight important aspects of possible symmetry breaking mechanisms in square ladder geometries driven by the combined effect of a magnetic gauge field spin-orbit interaction and temperature. The observed persistent current, spin and charge polarizations in the presence of spin-orbit coupling are driven by separation of electron and hole charges and opposite spins in real-space. The modeled spin-flip processes on the pairing mechanism induced by the spin-orbit coupling in assembled nanostructures (as arrays of clusters) engineered in various two-dimensional multi-leg structures provide an ideal playground for understanding spatial charge and spin density inhomogeneities leading to electron pairing and spontaneous phase separation instabilities in unconventional superconductors. Such studies also fall under the scope of current challenging problems in superconductivity and magnetism, topological insulators and spin dependent transport associated with numerous interfaces and heterostructures.

  13. Spin-orbit coupling, electron transport and pairing instabilities in two-dimensional square structures

    Directory of Open Access Journals (Sweden)

    Armen N. Kocharian

    2016-05-01

    Full Text Available Rashba spin-orbit effects and electron correlations in the two-dimensional cylindrical lattices of square geometries are assessed using mesoscopic two-, three- and four-leg ladder structures. Here the electron transport properties are systematically calculated by including the spin-orbit coupling in tight binding and Hubbard models threaded by a magnetic flux. These results highlight important aspects of possible symmetry breaking mechanisms in square ladder geometries driven by the combined effect of a magnetic gauge field spin-orbit interaction and temperature. The observed persistent current, spin and charge polarizations in the presence of spin-orbit coupling are driven by separation of electron and hole charges and opposite spins in real-space. The modeled spin-flip processes on the pairing mechanism induced by the spin-orbit coupling in assembled nanostructures (as arrays of clusters engineered in various two-dimensional multi-leg structures provide an ideal playground for understanding spatial charge and spin density inhomogeneities leading to electron pairing and spontaneous phase separation instabilities in unconventional superconductors. Such studies also fall under the scope of current challenging problems in superconductivity and magnetism, topological insulators and spin dependent transport associated with numerous interfaces and heterostructures.

  14. Interpretation of heat and density pulse measurements in JET in terms of coupled transport

    International Nuclear Information System (INIS)

    Haas, J.C.M. de; O'Rourke, J.; Sips, A.C.C.; Lopes Cardozo, N.J.

    1990-01-01

    The perturbations of electron density and temperature profiles in a tokamak following a sawtooth collapse are considered. An analytic model for the interpretation of such perturbations is presented. It is shown that the perturbation can be decomposed into two contributions, which are eigenmodes of the linearised coupled diffusion equations for particle and energy. The approximations made in the analytical treatment are checked using computer simulations. Measurements of heat and density pulses in Joint European Torus are used to illustrate the power of the new approach. It is shown that using the coupled equations, an improved description of the heat and density pulses is obtained. The analysis yields the four diffusion coefficients in the linearised transport matrix. The non-zero off-diagonal elements explain certain salient features of the measurements, notably a marked decrease of the local density which occurs during the maximum of the temperature pulse. (author)

  15. Electrical and thermal transport in the quasiatomic limit of coupled Luttinger liquids

    Science.gov (United States)

    Szasz, Aaron; Ilan, Roni; Moore, Joel E.

    2017-02-01

    We introduce a new model for quasi-one-dimensional materials, motivated by intriguing but not yet well-understood experiments that have shown two-dimensional polymer films to be promising materials for thermoelectric devices. We consider a two-dimensional material consisting of many one-dimensional systems, each treated as a Luttinger liquid, with weak (incoherent) coupling between them. This approximation of strong interactions within each one-dimensional chain and weak coupling between them is the "quasiatomic limit." We find integral expressions for the (interchain) transport coefficients, including the electrical and thermal conductivities and the thermopower, and we extract their power law dependencies on temperature. Luttinger liquid physics is manifested in a violation of the Wiedemann-Franz law; the Lorenz number is larger than the Fermi liquid value by a factor between γ2 and γ4, where γ ≥1 is a measure of the electron-electron interaction strength in the system.

  16. Transport of microbial tracers in clean and organically contaminated silica sand in laboratory columns compared with their transport in the field

    Energy Technology Data Exchange (ETDEWEB)

    Weaver, Louise, E-mail: louise.weaver@esr.cri.nz; Sinton, Lester W.; Pang, Liping; Dann, Rod; Close, Murray

    2013-01-15

    Waste disposal on land and the consequent transport of bacterial and viral pathogens in soils and aquifers are of major concern worldwide. Pathogen transport can be enhanced in the presence of organic matter due to occupation of attachment sites in the aquifer materials thus preventing pathogen attachment leading to their faster transport for longer distances. Laboratory column studies were carried out to investigate the effect of organic matter, in the form of dissolved organic carbon (DOC), on the transport of Escherichia coli and MS2 phage in saturated clean silica sand. Transport rates of these microbial tracers were also studied in a contaminated field site. Laboratory column studies showed that low concentrations (0.17 mg L{sup −1}) of DOC had little effect on E. coli J6-2 removal and slightly reduced the attachment of MS2 phage. After progressive conditioning of the column with DOC (1.7 mg L{sup −1} and 17 mg L{sup −1}), neither E. coli J6-2 nor MS2 phage showed any attachment and recovery rates increased dramatically (up to 100%). The results suggest that DOC can affect the transport rates of microbial contaminants. For E. coli J6-2 the predominant effect appeared to be an increase in the secondary energy minimum leading to an increase in E. coli attachment initially. However, after 17 mg L{sup −1} DOC conditioning of the silica sand no attachment of E. coli was observed as the DOC took up attachment sites in the porous media. MS2 phage appeared to be affected predominantly by out-competition of binding sites in the clean silica sand and a steady reduction in attachment was observed as the DOC conditioning increased. Field study showed a high removal of both E. coli and MS2 phage, although E. coli was removed at a lower rate than MS2 phage. In the field it is likely that a combination of effects are seen as the aquifer material will be heterogeneous in its surface nanoscale properties, demonstrated by the differing removal of E. coli and MS2 phage

  17. The importance of OH − transport through anion exchange membrane in microbial electrolysis cells

    KAUST Repository

    Ye, Yaoli; Logan, Bruce

    2018-01-01

    In two-chamber microbial electrolysis cells (MECs) with anion exchange membranes (AEMs), a phosphate buffer solution (PBS) is typically used to avoid increases in catholyte pH as Nernst equation calculations indicate that high pHs adversely impact

  18. Description of the microbial ecology evaluation device, flight equipment, and ground transporter

    Science.gov (United States)

    Chassay, C. E.; Taylor, G. R.

    1973-01-01

    Exposure of test systems in space required the fabrication of specialized hardware termed a Microbial Ecology Evaluation Device that had individual test chambers and a complex optical filter system. The characteristics of this device and the manner in which it was deployed in space are described.

  19. A generic transport-reactive model for simulating microbially influenced mineral precipitation in porous medium

    NARCIS (Netherlands)

    Zhou, J.; Van Turnhout, A.G.; Heimovaara, T.J.; Afanasyev, M.

    2015-01-01

    The spatial and temporal distribution of precipitated minerals is one of the key factors governing various processes in the sub-surface environment, including microbially influenced corrosion (MIC) (Huang, 2002), bio-cementation (van Paassen et al., 2010) and sediment diagenesis (Paraska et al.,

  20. Using Multiscale Modeling to Study Coupled Flow, Transport, Reaction and Biofilm Growth Processes in Porous Media

    Science.gov (United States)

    Valocchi, A. J.; Laleian, A.; Werth, C. J.

    2017-12-01

    Perturbation of natural subsurface systems by fluid inputs may induce geochemical or microbiological reactions that change porosity and permeability, leading to complex coupled feedbacks between reaction and transport processes. Some examples are precipitation/dissolution processes associated with carbon capture and storage and biofilm growth associated with contaminant transport and remediation. We study biofilm growth due to mixing controlled reaction of multiple substrates. As biofilms grow, pore clogging occurs which alters pore-scale flow paths thus changing the mixing and reaction. These interactions are challenging to quantify using conventional continuum-scale porosity-permeability relations. Pore-scale models can accurately resolve coupled reaction, biofilm growth and transport processes, but modeling at this scale is not feasible for practical applications. There are two approaches to address this challenge. Results from pore-scale models in generic pore structures can be used to develop empirical relations between porosity and continuum-scale parameters, such as permeability and dispersion coefficients. The other approach is to develop a multiscale model of biofilm growth in which non-overlapping regions at pore and continuum spatial scales are coupled by a suitable method that ensures continuity of flux across the interface. Thus, regions of high reactivity where flow alteration occurs are resolved at the pore scale for accuracy while regions of low reactivity are resolved at the continuum scale for efficiency. This approach thus avoids the need for empirical upscaling relations in regions with strong feedbacks between reaction and porosity change. We explore and compare these approaches for several two-dimensional cases.

  1. Radiochemically-Supported Microbial Communities: A Potential Mechanism for Biocolloid Production of Importance to Actinide Transport

    Energy Technology Data Exchange (ETDEWEB)

    Moser, Duane P. [Desert Research Inst., Nevada University, Reno, NV (United States); Hamilton-Brehm, Scott D. [Desert Research Inst., Nevada University, Reno, NV (United States); Fisher, Jenny C. [Desert Research Inst., Nevada University, Reno, NV (United States); Bruckner, James C. [Desert Research Inst., Nevada University, Reno, NV (United States); Kruger, Brittany [Desert Research Inst., Nevada University, Reno, NV (United States); Sackett, Joshua [Desert Research Inst., Nevada University, Reno, NV (United States); Russell, Charles E. [Desert Research Inst., Nevada University, Reno, NV (United States); Onstott, Tullis C. [Princeton Univ., NJ (United States); Czerwinski, Ken [Univ. of Nevada, Las Vegas, NV (United States); Zavarin, Mavrik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Campbell, James H. [Northwest Missouri State Univ., Maryville, MO (United States)

    2014-06-01

    Due to the legacy of Cold War nuclear weapons testing, the Nevada National Security Site (NNSS, formerly known as the Nevada Test Site (NTS)) contains millions of Curies of radioactive contamination. Presented here is a summary of the results of the first comprehensive study of subsurface microbial communities of radioactive and nonradioactive aquifers at this site. To achieve the objectives of this project, cooperative actions between the Desert Research Institute (DRI), the Nevada Field Office of the National Nuclear Security Administration (NNSA), the Underground Test Area Activity (UGTA), and contractors such as Navarro-Interra (NI), were required. Ultimately, fluids from 17 boreholes and two water-filled tunnels were sampled (sometimes on multiple occasions and from multiple depths) from the NNSS, the adjacent Nevada Test and Training Range (NTTR), and a reference hole in the Amargosa Valley near Death Valley. The sites sampled ranged from highly-radioactive nuclear device test cavities to uncontaminated perched and regional aquifers. Specific areas sampled included recharge, intermediate, and discharge zones of a 100,000-km2 internally-draining province, known as the Death Valley Regional Flow System (DVRFS), which encompasses the entirety of the NNSS/NTTR and surrounding areas. Specific geological features sampled included: West Pahute and Ranier Mesas (recharge zone), Yucca and Frenchman Flats (transitional zone), and the Western edge of the Amargosa Valley near Death Valley (discharge zone). The original overarching question underlying the proposal supporting this work was stated as: Can radiochemically-produced substrates support indigenous microbial communities and subsequently stimulate biocolloid formation that can affect radionuclides in NNSS subsurface nuclear test/detonation sites? Radioactive and non-radioactive groundwater samples were thus characterized for physical parameters, aqueous geochemistry, and microbial communities using both DNA- and

  2. Continuous energy adjoint Monte Carlo for coupled neutron-photon transport

    Energy Technology Data Exchange (ETDEWEB)

    Hoogenboom, J.E. [Delft Univ. of Technology (Netherlands). Interfaculty Reactor Inst.

    2001-07-01

    Although the theory for adjoint Monte Carlo calculations with continuous energy treatment for neutrons as well as for photons is known, coupled neutron-photon transport problems present fundamental difficulties because of the discrete energies of the photons produced by neutron reactions. This problem was solved by forcing the energy of the adjoint photon to the required discrete value by an adjoint Compton scattering reaction or an adjoint pair production reaction. A mathematical derivation shows the exact procedures to follow for the generation of an adjoint neutron and its statistical weight. A numerical example demonstrates that correct detector responses are obtained compared to a standard forward Monte Carlo calculation. (orig.)

  3. Line photon transport in a non-homogeneous plasma using radiative coupling coefficients

    International Nuclear Information System (INIS)

    Florido, R.; Gil, J.M.; Rodriguez, R.; Rubiano, J.G.; Martel, P.; Florido, R.; Gil, J.M.; Rodriguez, R.; Rubiano, J.G.; Martel, P.; Minguez, E.

    2006-01-01

    We present a steady-state collisional-radiative model for the calculation of level populations in non-homogeneous plasmas with planar geometry. The line photon transport is taken into account following an angle- and frequency-averaged escape probability model. Several models where the same approach has been used can be found in the literature, but the main difference between our model and those ones is that the details of geometry are exactly treated in the definition of coupling coefficients and a local profile is taken into account in each plasma cell. (authors)

  4. Parallel processing implementation for the coupled transport of photons and electrons using OpenMP

    Science.gov (United States)

    Doerner, Edgardo

    2016-05-01

    In this work the use of OpenMP to implement the parallel processing of the Monte Carlo (MC) simulation of the coupled transport for photons and electrons is presented. This implementation was carried out using a modified EGSnrc platform which enables the use of the Microsoft Visual Studio 2013 (VS2013) environment, together with the developing tools available in the Intel Parallel Studio XE 2015 (XE2015). The performance study of this new implementation was carried out in a desktop PC with a multi-core CPU, taking as a reference the performance of the original platform. The results were satisfactory, both in terms of scalability as parallelization efficiency.

  5. Reactive transport modeling of coupled inorganic and organic processes in groundwater

    Energy Technology Data Exchange (ETDEWEB)

    Brun, Adam

    1997-12-31

    The main goals of this project are to develop and apply a reactive transport code for simulation of coupled organic and inorganic processes in the pollution plume in the ground water down-gradient from the Vejen landfill, Denmark. The detailed field investigations in this aquifer have previously revealed a complex pattern of strongly interdependent organic and inorganic processes. These processes occur simultaneously in a flow and transport system where the mixing of reactive species is influenced by the rather complex geology in the vicinity of the landfill. The removal of organic matter is influenced by the presence of various electron acceptors that also are involved in various inorganic geochemical reactions. It was concluded from the investigations that degradation of organic matter, complexation, mineral precipitation and dissolution, ion-exchange and inorganic redox reactions, as a minimum, should be included in the formulation of the model. The coupling of the organic and inorganic processes is developed based on a literature study. All inorganic processes are as an approximation described as equilibriumm processes. The organic processes are described by a maximum degradation rate that is decreased according to the availability of the participants in the processes, the actual pH, and the presence of inhibiting species. The reactive transport code consists of three separate codes, a flow and transport code, a geochemical code, and a biodegradation code. An iterative solution scheme couples the three codes. The coupled code was successfully verified for simple problems for which analytical solutions exist. For more complex problems the code was tested on synthetic cases and expected plume behavior was successfully simulated. Application of the code to the Vejen landfill aquifer was successful to the degree that the redox zonation down-gradient from the landfill was simulated correctly and that several of the simulated plumes showed a reasonable agreement with

  6. Application of the Arbitrarily High Order Method to Coupled Electron Photon Transport

    International Nuclear Information System (INIS)

    Duo, Jose Ignacio

    2004-01-01

    This work is about the application of the Arbitrary High Order Nodal Method to coupled electron photon transport.A Discrete Ordinates code was enhanced and validated which permited to evaluate the advantages of using variable spatial development order per particle.The results obtained using variable spatial development and adaptive mesh refinement following an a posteriori error estimator are encouraging.Photon spectra for clinical accelerator target and, dose and charge depositio profiles are simulated in one-dimensional problems using cross section generated with CEPXS code.Our results are in good agreement with ONELD and MCNP codes

  7. Discrete and continuum links to a nonlinear coupled transport problem of interacting populations

    Science.gov (United States)

    Duong, M. H.; Muntean, A.; Richardson, O. M.

    2017-07-01

    We are interested in exploring interacting particle systems that can be seen as microscopic models for a particular structure of coupled transport flux arising when different populations are jointly evolving. The scenarios we have in mind are inspired by the dynamics of pedestrian flows in open spaces and are intimately connected to cross-diffusion and thermo-diffusion problems holding a variational structure. The tools we use include a suitable structure of the relative entropy controlling TV-norms, the construction of Lyapunov functionals and particular closed-form solutions to nonlinear transport equations, a hydrodynamics limiting procedure due to Philipowski, as well as the construction of numerical approximates to both the continuum limit problem in 2D and to the original interacting particle systems.

  8. A numerical solution of the coupled proton-H atom transport equations for the proton aurora

    International Nuclear Information System (INIS)

    Basu, B.; Jasperse, J.R.; Grossbard, N.J.

    1990-01-01

    A numerical code has been developed to solve the coupled proton-H atom linear transport equations for the proton aurora. The transport equations have been simplified by using plane-parallel geometry and the forward-scattering approximations only. Otherwise, the equations and their numerical solutions are exact. Results are presented for the particle fluxes and the energy deposition rates, and they are compared with the previous analytical results that were obtained by using additional simplifying approximations. It is found that although the analytical solutions for the particle fluxes differ somewhat from the numerical solutions, the energy deposition rates calculated by the two methods agree to within a few percent. The accurate particle fluxes given by the numerical code are useful for accurate calculation of the characteristic quantities of the proton aurora, such as the ionization rates and the emission rates

  9. Coupled transport phenomena in a clay from a Callovo-Oxfordian formation

    International Nuclear Information System (INIS)

    Paszkuta, M.

    2005-06-01

    Low permeability materials containing clay play an important role in practical life and natural environment. Indeed, the ability of clay soils to act as semi permeable membranes, that inhibit the passage of electrolytes, is of great interest. The major objective of this thesis is to evaluate the transport properties of natural clays and in particular coupled transports when a pressure gradient, an electrical field, a concentration gradient and a temperature gradient interact. The material is a compact argillite extracted in East France from a Callovo-Oxfordian formation which was supplied to us by ANDRA. NaCl was used as the main solute. Two series of experiments were performed to measure permeability, diffusion, conductivity, the electro-osmotic coefficient and the Soret coefficient. (author)

  10. Transport, atom blockade, and output coupling in a Tonks-Girardeau gas

    International Nuclear Information System (INIS)

    Rutherford, L.; McCann, J. F.; Goold, J.; Busch, Th.

    2011-01-01

    Recent experiments have demonstrated how quantum-mechanical impurities can be created within strongly correlated quantum gases and used to probe the coherence properties of these systems [S. Palzer, C. Zipkes, C. Sias, and M. Koehl, Phys. Rev. Lett. 103, 150601 (2009).]. Here we present a phenomenological model to simulate such an output coupler for a Tonks-Girardeau gas that shows qualitative agreement with the experimental results for atom transport and output coupling. Our model allows us to explore nonequilibrium transport phenomena in ultracold quantum gases and leads us to predict a regime of atom blockade, where the impurity component becomes localized in the parent cloud despite the presence of gravity. We show that this provides a stable mixed-species quantum gas in the strongly correlated limit.

  11. Coupled effects of solution chemistry and hydrodynamics on the mobility and transport of quantum dot nanomaterials in the Vadose Zone

    Science.gov (United States)

    To investigate the coupled effects of solution chemistry and vadose zone processes on the mobility of quantum dot (QD) nanoparticles, laboratory scale transport experiments were performed. The complex coupled effects of ionic strength, size of QD aggregates, surface tension, contact angle, infiltrat...

  12. Modeling coupled nanoparticle aggregation and transport in porous media: a Lagrangian approach.

    Science.gov (United States)

    Taghavy, Amir; Pennell, Kurt D; Abriola, Linda M

    2015-01-01

    Changes in nanoparticle size and shape due to particle-particle interactions (i.e., aggregation or agglomeration) may significantly alter particle mobility and retention in porous media. To date, however, few modeling studies have considered the coupling of transport and particle aggregation processes. The majority of particle transport models employ an Eulerian modeling framework and are, consequently, limited in the types of collisions and aggregate sizes that can be considered. In this work, a more general Lagrangian modeling framework is developed and implemented to explore coupled nanoparticle aggregation and transport processes. The model was verified through comparison of model simulations to published results of an experimental and Eulerian modeling study (Raychoudhury et al., 2012) of carboxymethyl cellulose (CMC)-modified nano-sized zero-valent iron particle (nZVI) transport and retention in water-saturated sand columns. A model sensitivity analysis reveals the influence of influent particle concentration (ca. 70 to 700 mg/L), primary particle size (10-100 nm) and pore water velocity (ca. 1-6 m/day) on particle-particle, and, consequently, particle-collector interactions. Model simulations demonstrate that, when environmental conditions promote particle-particle interactions, neglecting aggregation effects can lead to under- or over-estimation of nanoparticle mobility. Results also suggest that the extent to which higher order particle-particle collisions influence aggregation kinetics will increase with the fraction of primary particles. This work demonstrates the potential importance of time-dependent aggregation processes on nanoparticle mobility and provides a numerical model capable of capturing/describing these interactions in water-saturated porous media. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. CFEST Coupled Flow, Energy & Solute Transport Version CFEST005 User’s Guide

    Energy Technology Data Exchange (ETDEWEB)

    Freedman, Vicky L.; Chen, Yousu; Gilca, Alex; Cole, Charles R.; Gupta, Sumant K.

    2006-07-20

    The CFEST (Coupled Flow, Energy, and Solute Transport) simulator described in this User’s Guide is a three-dimensional finite-element model used to evaluate groundwater flow and solute mass transport. Confined and unconfined aquifer systems, as well as constant and variable density fluid flows can be represented with CFEST. For unconfined aquifers, the model uses a moving boundary for the water table, deforming the numerical mesh so that the uppermost nodes are always at the water table. For solute transport, changes in concentra¬tion of a single dissolved chemical constituent are computed for advective and hydrodynamic transport, linear sorption represented by a retardation factor, and radioactive decay. Although several thermal parameters described in this User’s Guide are required inputs, thermal transport has not yet been fully implemented in the simulator. Once fully implemented, transport of thermal energy in the groundwater and solid matrix of the aquifer can also be used to model aquifer thermal regimes. The CFEST simulator is written in the FORTRAN 77 language, following American National Standards Institute (ANSI) standards. Execution of the CFEST simulator is controlled through three required text input files. These input file use a structured format of associated groups of input data. Example input data lines are presented for each file type, as well as a description of the structured FORTRAN data format. Detailed descriptions of all input requirements, output options, and program structure and execution are provided in this User’s Guide. Required inputs for auxillary CFEST utilities that aide in post-processing data are also described. Global variables are defined for those with access to the source code. Although CFEST is a proprietary code (CFEST, Inc., Irvine, CA), the Pacific Northwest National Laboratory retains permission to maintain its own source, and to distribute executables to Hanford subcontractors.

  14. Role of inter-tube coupling and quantum interference on electrical transport in carbon nanotube junctions

    Science.gov (United States)

    Tripathy, Srijeet; Bhattacharyya, Tarun Kanti

    2016-09-01

    Due to excellent transport properties, Carbon nanotubes (CNTs) show a lot of promise in sensor and interconnect technology. However, recent studies indicate that the conductance in CNT/CNT junctions are strongly affected by the morphology and orientation between the tubes. For proper utilization of such junctions in the development of CNT based technology, it is essential to study the electronic properties of such junctions. This work presents a theoretical study of the electrical transport properties of metallic Carbon nanotube homo-junctions. The study focuses on discerning the role of inter-tube interactions, quantum interference and scattering on the transport properties on junctions between identical tubes. The electronic structure and transport calculations are conducted with an Extended Hückel Theory-Non Equilibrium Green's Function based model. The calculations indicate conductance to be varying with a changing crossing angle, with maximum conductance corresponding to lattice registry, i.e. parallel configuration between the two tubes. Further calculations for such parallel configurations indicate onset of short and long range oscillations in conductance with respect to changing overlap length. These oscillations are attributed to inter-tube coupling effects owing to changing π orbital overlap, carrier scattering and quantum interference of the incident, transmitted and reflected waves at the inter-tube junction.

  15. A coupled reaction and transport model for assessing the injection, migration and fate of waste fluids

    International Nuclear Information System (INIS)

    Liu, X.; Ortoleva, P.

    1996-01-01

    The use of reaction-transport modeling for reservoir assessment and management in the context of deep well waste injection is evaluated. The study is based on CIRF.A (Chemical Interaction of Rock and Fluid), a fully coupled multiphase flow, contaminant transport, and fluid and mineral reaction model. Although SWIFT (Sandia Waste-Isolation Flow and Transport Model) is often the numerical model of choice, it can not account for chemical reactions involving rock, wastes, and formation fluids and their effects on contaminant transport, rock permeability and porosity, and the integrity of the reservoir and confining units. CIRF.A can simulate all these processes. Two field cases of waste injection were simulated by CIRF.A. Both observation data and simulation results show mineral precipitation in one case and rock dissolution in another case. Precipitation and dissolution change rock porosity and permeability, and hence the pattern of fluid migration. The model is shown to be invaluable in analyzing near borehole and reservoir-scale effects during waste injection and predicting the 10,000 year fate of the waste plume. The benefits of using underpressured compartments as waste repositories were also demonstrated by CIRF.A simulations

  16. Coupled hydrogeological and reactive transport modelling of the Simpevarp area (Sweden)

    International Nuclear Information System (INIS)

    Molinero, Jorge; Raposo, Juan R.; Galindez, Juan M.; Arcos, David; Guimera, Jordi

    2008-01-01

    The Simpevarp area is one of the alternative sites being considered for the deep geological disposal of high level radioactive waste in Sweden. In this paper, a coupled regional groundwater flow and reactive solute transport model of the Simpevarp area is presented that integrates current hydrogeological and hydrochemical data of the area. The model simulates the current hydrochemical pattern of the groundwater system in the area. To that aim, a conceptual hydrochemical model was developed in order to represent the dominant chemical processes. Groundwater flow conditions were reproduced by taking into account fluid-density-dependent groundwater flow and regional hydrogeologic boundary conditions. Reactive solute transport calculations were performed on the basis of the velocity field so obtained. The model was calibrated and sensitivity analyses were carried out in order to investigate the effects of heterogeneities of hydraulic conductivity in the subsurface medium. Results provided by the reactive transport model are in good agreement with much of the measured hydrochemical data. This paper emphasizes the appropriateness of the use of reactive solute transport models when water-rock interaction reactions are involved, and demonstrates what powerful tools they are for the interpretation of hydrogeological and hydrochemical data from site geological repository characterization programs, by providing a qualitative framework for data analysis and testing of conceptual assumptions in a process-oriented approach

  17. Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese.

    Science.gov (United States)

    Lovley, D R; Phillips, E J

    1988-06-01

    A dissimilatory Fe(III)- and Mn(IV)-reducing microorganism was isolated from freshwater sediments of the Potomac River, Maryland. The isolate, designated GS-15, grew in defined anaerobic medium with acetate as the sole electron donor and Fe(III), Mn(IV), or nitrate as the sole electron acceptor. GS-15 oxidized acetate to carbon dioxide with the concomitant reduction of amorphic Fe(III) oxide to magnetite (Fe(3)O(4)). When Fe(III) citrate replaced amorphic Fe(III) oxide as the electron acceptor, GS-15 grew faster and reduced all of the added Fe(III) to Fe(II). GS-15 reduced a natural amorphic Fe(III) oxide but did not significantly reduce highly crystalline Fe(III) forms. Fe(III) was reduced optimally at pH 6.7 to 7 and at 30 to 35 degrees C. Ethanol, butyrate, and propionate could also serve as electron donors for Fe(III) reduction. A variety of other organic compounds and hydrogen could not. MnO(2) was completely reduced to Mn(II), which precipitated as rhodochrosite (MnCO(3)). Nitrate was reduced to ammonia. Oxygen could not serve as an electron acceptor, and it inhibited growth with the other electron acceptors. This is the first demonstration that microorganisms can completely oxidize organic compounds with Fe(III) or Mn(IV) as the sole electron acceptor and that oxidation of organic matter coupled to dissimilatory Fe(III) or Mn(IV) reduction can yield energy for microbial growth. GS-15 provides a model for how enzymatically catalyzed reactions can be quantitatively significant mechanisms for the reduction of iron and manganese in anaerobic environments.

  18. Description of a neutron field perturbed by a probe using coupled Monte Carlo and discrete ordinates radiation transport calculations

    International Nuclear Information System (INIS)

    Zazula, J.M.

    1984-01-01

    This work concerns calculation of a neutron response, caused by a neutron field perturbed by materials surrounding the source or the detector. Solution of a problem is obtained using coupling of the Monte Carlo radiation transport computation for the perturbed region and the discrete ordinates transport computation for the unperturbed system. (author). 62 refs

  19. Quantum close coupling calculation of transport and relaxation properties for Hg-H_2 system

    International Nuclear Information System (INIS)

    Nemati-Kande, Ebrahim; Maghari, Ali

    2016-01-01

    Highlights: • Several relaxation cross sections are calculated for Hg-H_2 van der Waals complex. • These cross sections are calculated from exact close-coupling method. • Energy-dependent SBE cross sections are calculated for ortho- and para-H_2 + Hg systems. • Viscosity and diffusion coefficients are calculated using Mason-Monchick approximation. • The results obtained by Mason-Monchick approximation are compared to the exact close-coupling results. - Abstract: Quantum mechanical close coupling calculation of the state-to-state transport and relaxation cross sections have been done for Hg-H_2 molecular system using a high-level ab initio potential energy surface. Rotationally averaged cross sections were also calculated to obtain the energy dependent Senftleben-Beenakker cross sections at the energy range of 0.005–25,000 cm"−"1. Boltzmann averaging of the energy dependent Senftleben-Beenakker cross sections showed the temperature dependency over a wide temperature range of 50–2500 K. Interaction viscosity and diffusion coefficients were also calculated using close coupling cross sections and full classical Mason-Monchick approximation. The results were compared with each other and with the available experimental data. It was found that Mason-Monchick approximation for viscosity is more reliable than diffusion coefficient. Furthermore, from the comparison of the experimental diffusion coefficients with the result of the close coupling and Mason-Monchick approximation, it was found that the Hg-H_2 potential energy surface used in this work can reliably predict diffusion coefficient data.

  20. Quantum close coupling calculation of transport and relaxation properties for Hg-H{sub 2} system

    Energy Technology Data Exchange (ETDEWEB)

    Nemati-Kande, Ebrahim; Maghari, Ali, E-mail: maghari@ut.ac.ir

    2016-11-10

    Highlights: • Several relaxation cross sections are calculated for Hg-H{sub 2} van der Waals complex. • These cross sections are calculated from exact close-coupling method. • Energy-dependent SBE cross sections are calculated for ortho- and para-H{sub 2} + Hg systems. • Viscosity and diffusion coefficients are calculated using Mason-Monchick approximation. • The results obtained by Mason-Monchick approximation are compared to the exact close-coupling results. - Abstract: Quantum mechanical close coupling calculation of the state-to-state transport and relaxation cross sections have been done for Hg-H{sub 2} molecular system using a high-level ab initio potential energy surface. Rotationally averaged cross sections were also calculated to obtain the energy dependent Senftleben-Beenakker cross sections at the energy range of 0.005–25,000 cm{sup −1}. Boltzmann averaging of the energy dependent Senftleben-Beenakker cross sections showed the temperature dependency over a wide temperature range of 50–2500 K. Interaction viscosity and diffusion coefficients were also calculated using close coupling cross sections and full classical Mason-Monchick approximation. The results were compared with each other and with the available experimental data. It was found that Mason-Monchick approximation for viscosity is more reliable than diffusion coefficient. Furthermore, from the comparison of the experimental diffusion coefficients with the result of the close coupling and Mason-Monchick approximation, it was found that the Hg-H{sub 2} potential energy surface used in this work can reliably predict diffusion coefficient data.

  1. Modeling multicomponent ionic transport in groundwater with IPhreeqc coupling: Electrostatic interactions and geochemical reactions in homogeneous and heterogeneous domains

    DEFF Research Database (Denmark)

    Muniruzzaman, Muhammad; Rolle, Massimo

    2016-01-01

    is coupled with the geochemical code PHREEQC-3 by utilizing the IPhreeqc module, thus enabling to perform the geochemical calculations included in the PHREEQC's reaction package. The multicomponent reactive transport code is benchmarked with different 1-D and 2-D transport problems. Successively...... the electrostatic interactions during transport of charged ions in physically and chemically heterogeneous porous media. The modeling approach is based on the local charge balance and on the description of compound-specific and spatially variable diffusive/dispersive fluxes. The multicomponent ionic transport code......, conservative and reactive transport examples are presented to demonstrate the capability of the proposed model to simulate transport of charged species in heterogeneous porous media with spatially variable physical and chemical properties. The results reveal that the Coulombic cross-coupling between dispersive...

  2. Plasma Membrane Na+-Coupled Citrate Transporter (SLC13A5 and Neonatal Epileptic Encephalopathy

    Directory of Open Access Journals (Sweden)

    Yangzom D. Bhutia

    2017-02-01

    Full Text Available SLC13A5 is a Na+-coupled transporter for citrate that is expressed in the plasma membrane of specific cell types in the liver, testis, and brain. It is an electrogenic transporter with a Na+:citrate3− stoichiometry of 4:1. In humans, the Michaelis constant for SLC13A5 to transport citrate is ~600 μM, which is physiologically relevant given that the normal concentration of citrate in plasma is in the range of 150–200 μM. Li+ stimulates the transport function of human SLC13A5 at concentrations that are in the therapeutic range in patients on lithium therapy. Human SLC13A5 differs from rodent Slc13a5 in two important aspects: the affinity of the human transporter for citrate is ~30-fold less than that of the rodent transporter, thus making human SLC13A5 a low-affinity/high-capacity transporter and the rodent Slc13a5 a high-affinity/low-capacity transporter. In the liver, SLC13A5 is expressed exclusively in the sinusoidal membrane of the hepatocytes, where it plays a role in the uptake of circulating citrate from the sinusoidal blood for metabolic use. In the testis, the transporter is expressed only in spermatozoa, which is also only in the mid piece where mitochondria are located; the likely function of the transporter in spermatozoa is to mediate the uptake of citrate present at high levels in the seminal fluid for subsequent metabolism in the sperm mitochondria to generate biological energy, thereby supporting sperm motility. In the brain, the transporter is expressed mostly in neurons. As astrocytes secrete citrate into extracellular medium, the potential function of SLC13A5 in neurons is to mediate the uptake of circulating citrate and astrocyte-released citrate for subsequent metabolism. Slc13a5-knockout mice have been generated; these mice do not have any overt phenotype but are resistant to experimentally induced metabolic syndrome. Recently however, loss-of-function mutations in human SLC13A5 have been found to cause severe epilepsy

  3. Coupled Fluid, Energy, and Solute Transport (CFEST) model: Formulation and user's manual

    International Nuclear Information System (INIS)

    Gupta, S.K.; Cole, C.R.; Kincaid, C.T.; Monti, A.M.

    1987-10-01

    The CFEST (Coupled Fluid, Energy, and Solute Transport) code has been developed to analyze coupled hydrologic, thermal, and solute transport processes. It treats single-pahse Darcy ground-water flow in a horizontal or vertical plane, or in fully three-dimensional space under nonisothermal conditions. The code has the capability to model discontinuous and continuous layering, time-dependent and constant sources/sinks, and transient as well as steady-stae ground-water flow. The code offers a wide choice of boundary conditions such as precsribed heads, nodal injection or withdrawal, constant or spatially varying infiltration rates, and welemental source/sink. Initial conditions for the flow analysis can be prescribed pressure or hydraulic head. The heterogeneity in aquifer permeability and porosity can be described by geologic unit or explicity for given elements. Three-dimensional elelments are generated from user-defined well logs at each surface node. To facilitate interaction between disciplines, support programs are provided to plot the finite element grid, well logs, contour maps of input and output parameters, and vertical cross sections. Ground-water travel paths and times and volumetric rates from a specified point can be determined from support programs. This report includes governing partial differential equations, finite element formulation, a use's manual, verification test examples, sample problems, and source listings. 36 refs., 121 figs., 36 tabs

  4. Testing of a benchscale Reverse Osmosis/Coupled Transport system for treating contaminated groundwater

    International Nuclear Information System (INIS)

    Hodgson, K.M.; Lunsford, T.R.; Panjabi, G.

    1994-01-01

    The Reverse Osmosis/Coupled Transport process is a innovative means of removing radionuclides from contaminated groundwater at the Hanford Site. Specifically, groundwater in the 200 West Area of the Hanford Site has been contaminated with uranium, technetium, and nitrate. Investigations are proceeding to determine the most cost effective method to remove these contaminants. The process described in this paper combines three different membrane technologies (reverse osmosis, coupled transport, and nanofiltration to purify the groundwater while extracting and concentrating uranium, technetium, and nitrate into separate solutions. This separation allows for the future use of the radionuclides, if needed, and reduces the amount of waste that will need to be disposed of. This process has the potential to concentrate the contaminants into solutions with volumes in a ratio of 1/10,000 of the feed volume. This compares to traditional volume reductions of 10 to 100 for ion exchange and stand-alone reverse osmosis. The successful demonstration of this technology could result in significant savings in the overall cost of decontaminating the groundwater

  5. Mass-corrections for the conservative coupling of flow and transport on collocated meshes

    Energy Technology Data Exchange (ETDEWEB)

    Waluga, Christian, E-mail: waluga@ma.tum.de [Institute for Numerical Mathematics (M2), Technische Universität München, Boltzmannstraße 3, D-85748 Garching bei München (Germany); Wohlmuth, Barbara [Institute for Numerical Mathematics (M2), Technische Universität München, Boltzmannstraße 3, D-85748 Garching bei München (Germany); Rüde, Ulrich [Department of Computer Science 10, University Erlangen–Nuremberg, Cauerstr. 11, D-91058 Erlangen (Germany)

    2016-01-15

    Buoyancy-driven flow models demand a careful treatment of the mass-balance equation to avoid spurious source and sink terms in the non-linear coupling between flow and transport. In the context of finite-elements, it is therefore commonly proposed to employ sufficiently rich pressure spaces, containing piecewise constant shape functions to obtain local or even strong mass-conservation. In three-dimensional computations, this usually requires nonconforming approaches, special meshes or higher order velocities, which make these schemes prohibitively expensive for some applications and complicate the implementation into legacy code. In this paper, we therefore propose a lean and conservatively coupled scheme based on standard stabilized linear equal-order finite elements for the Stokes part and vertex-centered finite volumes for the energy equation. We show that in a weak mass-balance it is possible to recover exact conservation properties by a local flux-correction which can be computed efficiently on the control volume boundaries of the transport mesh. We discuss implementation aspects and demonstrate the effectiveness of the flux-correction by different two- and three-dimensional examples which are motivated by geophysical applications.

  6. Particle Communication and Domain Neighbor Coupling: Scalable Domain Decomposed Algorithms for Monte Carlo Particle Transport

    Energy Technology Data Exchange (ETDEWEB)

    O' Brien, M. J.; Brantley, P. S.

    2015-01-20

    In order to run Monte Carlo particle transport calculations on new supercomputers with hundreds of thousands or millions of processors, care must be taken to implement scalable algorithms. This means that the algorithms must continue to perform well as the processor count increases. In this paper, we examine the scalability of:(1) globally resolving the particle locations on the correct processor, (2) deciding that particle streaming communication has finished, and (3) efficiently coupling neighbor domains together with different replication levels. We have run domain decomposed Monte Carlo particle transport on up to 221 = 2,097,152 MPI processes on the IBM BG/Q Sequoia supercomputer and observed scalable results that agree with our theoretical predictions. These calculations were carefully constructed to have the same amount of work on every processor, i.e. the calculation is already load balanced. We also examine load imbalanced calculations where each domain’s replication level is proportional to its particle workload. In this case we show how to efficiently couple together adjacent domains to maintain within workgroup load balance and minimize memory usage.

  7. Some results on the neutron transport and the coupling of equations; Quelques resultats sur le transport neutronique et le couplage d`equations

    Energy Technology Data Exchange (ETDEWEB)

    Bal, G. [Electricite de France (EDF), Direction des Etudes et Recherches, 92 - Clamart (France)

    1997-12-31

    Neutron transport in nuclear reactors is well modeled by the linear Boltzmann transport equation. Its resolution is relatively easy but very expensive. To achieve whole core calculations, one has to consider simpler models, such as diffusion or homogeneous transport equations. However, the solutions may become inaccurate in particular situations (as accidents for instance). That is the reason why we wish to solve the equations on small area accurately and more coarsely on the remaining part of the core. It is than necessary to introduce some links between different discretizations or modelizations. In this note, we give some results on the coupling of different discretizations of all degrees of freedom of the integral-differential neutron transport equation (two degrees for the angular variable, on for the energy component, and two or three degrees for spatial position respectively in 2D (cylindrical symmetry) and 3D). Two chapters are devoted to the coupling of discrete ordinates methods (for angular discretization). The first one is theoretical and shows the well posing of the coupled problem, whereas the second one deals with numerical applications of practical interest (the results have been obtained from the neutron transport code developed at the R and D, which has been modified for introducing the coupling). Next, we present the nodal scheme RTN0, used for the spatial discretization. We show well posing results for the non-coupled and the coupled problems. At the end, we deal with the coupling of energy discretizations for the multigroup equations obtained by homogenization. Some theoretical results of the discretization of the velocity variable (well-posing of problems), which do not deal directly with the purposes of coupling, are presented in the annexes. (author). 34 refs.

  8. Coupling of WRF and Building-resolved CFD Simulations for Greenhouse Gas Transport and Dispersion

    Science.gov (United States)

    Prasad, K.; Hu, H.; McDermott, R.; Lopez-Coto, I.; Davis, K. J.; Whetstone, J. R.; Lauvaux, T.

    2014-12-01

    The Indianapolis Flux Experiment (INFLUX) aims to use a top-down inversion methodology to quantify sources of Greenhouse Gas (GHG) emissions over an urban domain with high spatial and temporal resolution. Atmospheric transport of tracer gases from an emission source to a tower mounted receptor are usually conducted using the Weather Research and Forecasting (WRF) model. WRF is used extensively in the atmospheric community to simulate mesoscale atmospheric transport. For such simulations, WRF employs a parameterized turbulence model and does not resolve the fine scale dynamics that are generated by the flow around buildings and communities that are part of a large city. Since the model domain includes the city of Indianapolis, much of the flow of interest is over an urban topography. The NIST Fire Dynamics Simulator (FDS) is a computational fluid dynamics model to perform large eddy simulations of flow around buildings, but it has not been nested within a larger-scale atmospheric transport model such as WRF. FDS has the potential to evaluate the impact of complex urban topography on near-field dispersion and mixing that cannot be simulated with a mesoscale atmospheric model, and which may be important to determining urban GHG emissions using atmospheric measurements. A methodology has been developed to run FDS as a sub-grid scale model within a WRF simulation. The coupling is based on nudging the FDS flow field towards the one computed by WRF, and is currently limited to one way coupling performed in an off-line mode. Using the coupled WRF / FDS model, NIST will investigate the effects of the urban canopy at horizontal resolutions of 2-10 m. The coupled WRF-FDS simulations will be used to calculate the dispersion of tracer gases in an urban domain and to evaluate the upwind areas that contribute to tower observations, referred to in the inversion community as influence functions. Predicted mixing ratios will be compared with tower measurements and WRF simulations

  9. Dual states estimation of a subsurface flow-transport coupled model using ensemble Kalman filtering

    KAUST Repository

    El Gharamti, Mohamad

    2013-10-01

    Modeling the spread of subsurface contaminants requires coupling a groundwater flow model with a contaminant transport model. Such coupling may provide accurate estimates of future subsurface hydrologic states if essential flow and contaminant data are assimilated in the model. Assuming perfect flow, an ensemble Kalman filter (EnKF) can be used for direct data assimilation into the transport model. This is, however, a crude assumption as flow models can be subject to many sources of uncertainty. If the flow is not accurately simulated, contaminant predictions will likely be inaccurate even after successive Kalman updates of the contaminant model with the data. The problem is better handled when both flow and contaminant states are concurrently estimated using the traditional joint state augmentation approach. In this paper, we introduce a dual estimation strategy for data assimilation into a one-way coupled system by treating the flow and the contaminant models separately while intertwining a pair of distinct EnKFs, one for each model. The presented strategy only deals with the estimation of state variables but it can also be used for state and parameter estimation problems. This EnKF-based dual state-state estimation procedure presents a number of novel features: (i) it allows for simultaneous estimation of both flow and contaminant states in parallel; (ii) it provides a time consistent sequential updating scheme between the two models (first flow, then transport); (iii) it simplifies the implementation of the filtering system; and (iv) it yields more stable and accurate solutions than does the standard joint approach. We conducted synthetic numerical experiments based on various time stepping and observation strategies to evaluate the dual EnKF approach and compare its performance with the joint state augmentation approach. Experimental results show that on average, the dual strategy could reduce the estimation error of the coupled states by 15% compared with the

  10. Charge and Spin Transport in Spin-orbit Coupled and Topological Systems

    KAUST Repository

    Ndiaye, Papa Birame

    2017-10-31

    In the search for low power operation of microelectronic devices, spin-based solutions have attracted undeniable increasing interest due to their intrinsic magnetic nonvolatility. The ability to electrically manipulate the magnetic order using spin-orbit interaction, associated with the recent emergence of topological spintronics with its promise of highly efficient charge-to-spin conversion in solid state, offer alluring opportunities in terms of system design. Although the related technology is still at its infancy, this thesis intends to contribute to this engaging field by investigating the nature of the charge and spin transport in spin-orbit coupled and topological systems using quantum transport methods. We identified three promising building blocks for next-generation technology, three classes of systems that possibly enhance the spin and charge transport efficiency: (i)- topological insulators, (ii)- spin-orbit coupled magnonic systems, (iii)- topological magnetic textures (skyrmions and 3Q magnetic state). Chapter 2 reviews the basics and essential concepts used throughout the thesis: the spin-orbit coupling, the mathematical notion of topology and its importance in condensed matter physics, then topological magnetism and a zest of magnonics. In Chapter 3, we study the spin-orbit torques at the magnetized interfaces of 3D topological insulators. We demonstrated that their peculiar form, compared to other spin-orbit torques, have important repercussions in terms of magnetization reversal, charge pumping and anisotropic damping. In Chapter 4, we showed that the interplay between magnon current jm and magnetization m in homogeneous ferromagnets with Dzyaloshinskii-Moriya (DM) interaction, produces a field-like torque as well as a damping-like torque. These DM torques mediated by spin wave can tilt the imeaveraged magnetization direction and are similar to Rashba torques for electronic systems. Moreover, the DM torque is more efficient when magnons are

  11. Geometry-coupled reactive fluid transport at the fracture scale -Application to CO 2 geologic storage

    KAUST Repository

    Kim, Seunghee

    2015-08-19

    Water acidification follows CO2 injection and leads to reactive fluid transport through pores and rock fractures, with potential implications to reservoirs and wells in CO2 geologic storage and enhanced oil recovery. Kinetic rate laws for dissolution reactions in calcite and anorthite are combined with Navier-Stokes law and advection-diffusion transport to perform geometry-coupled numerical simulations in order to study the evolution of chemical reactions, species concentration and fracture morphology. Results are summarized as a function of two dimensionless parameters: the Damköhler number Da which is the ratio between advection and reaction times, and the transverse Peclet number Pe defined as the ratio between the time for diffusion across the fracture and the time for advection along the fracture. Reactant species are readily consumed near the inlet in a carbonate reservoir when the flow velocity is low (low transverse Peclet number and Da>10-1). At high flow velocities, diffusion fails to homogenize the concentration field across the fracture (high transverse Peclet number Pe>10-1). When the reaction rate is low as in anorthite reservoirs (Da<10-1) reactant species are more readily transported towards the outlet. At a given Peclet number, a lower Damköhler number causes the flow channel to experience a more uniform aperture enlargement along the length of the fracture. When the length-to-aperture ratio is sufficiently large, say l/d>30, the system response resembles the solution for 1-D reactive fluid transport. A decreased length-to-aperture ratio slows the diffusive transport of reactant species to the mineral fracture surface, and analyses of fracture networks must take into consideration both the length and slenderness of individual fractures in addition to Pe and Da numbers.

  12. Geometry-coupled reactive fluid transport at the fracture scale -Application to CO 2 geologic storage

    KAUST Repository

    Kim, Seunghee; Santamarina, Carlos

    2015-01-01

    Water acidification follows CO2 injection and leads to reactive fluid transport through pores and rock fractures, with potential implications to reservoirs and wells in CO2 geologic storage and enhanced oil recovery. Kinetic rate laws for dissolution reactions in calcite and anorthite are combined with Navier-Stokes law and advection-diffusion transport to perform geometry-coupled numerical simulations in order to study the evolution of chemical reactions, species concentration and fracture morphology. Results are summarized as a function of two dimensionless parameters: the Damköhler number Da which is the ratio between advection and reaction times, and the transverse Peclet number Pe defined as the ratio between the time for diffusion across the fracture and the time for advection along the fracture. Reactant species are readily consumed near the inlet in a carbonate reservoir when the flow velocity is low (low transverse Peclet number and Da>10-1). At high flow velocities, diffusion fails to homogenize the concentration field across the fracture (high transverse Peclet number Pe>10-1). When the reaction rate is low as in anorthite reservoirs (Da<10-1) reactant species are more readily transported towards the outlet. At a given Peclet number, a lower Damköhler number causes the flow channel to experience a more uniform aperture enlargement along the length of the fracture. When the length-to-aperture ratio is sufficiently large, say l/d>30, the system response resembles the solution for 1-D reactive fluid transport. A decreased length-to-aperture ratio slows the diffusive transport of reactant species to the mineral fracture surface, and analyses of fracture networks must take into consideration both the length and slenderness of individual fractures in addition to Pe and Da numbers.

  13. Concatenating algorithms for parallel numerical simulations coupling radiation hydrodynamics with neutron transport

    International Nuclear Information System (INIS)

    Mo Zeyao

    2004-11-01

    Multiphysics parallel numerical simulations are usually essential to simplify researches on complex physical phenomena in which several physics are tightly coupled. It is very important on how to concatenate those coupled physics for fully scalable parallel simulation. Meanwhile, three objectives should be balanced, the first is efficient data transfer among simulations, the second and the third are efficient parallel executions and simultaneously developments of those simulation codes. Two concatenating algorithms for multiphysics parallel numerical simulations coupling radiation hydrodynamics with neutron transport on unstructured grid are presented. The first algorithm, Fully Loosely Concatenation (FLC), focuses on the independence of code development and the independence running with optimal performance of code. The second algorithm. Two Level Tightly Concatenation (TLTC), focuses on the optimal tradeoffs among above three objectives. Theoretical analyses for communicational complexity and parallel numerical experiments on hundreds of processors on two parallel machines have showed that these two algorithms are efficient and can be generalized to other multiphysics parallel numerical simulations. In especial, algorithm TLTC is linearly scalable and has achieved the optimal parallel performance. (authors)

  14. Development of a Coupled Ocean-Hydrologic Model to Simulate Pollutant Transport in Singapore Coastal Waters

    Science.gov (United States)

    Chua, V. P.

    2015-12-01

    Intensive agricultural, economic and industrial activities in Singapore and Malaysia have made our coastal areas under high risk of water pollution. A coupled ocean-hydrologic model is employed to perform three-dimensional simulations of flow and pollutant transport in Singapore coastal waters. The hydrologic SWAT model is coupled with the coastal ocean SUNTANS model by outputting streamflow and pollutant concentrations from the SWAT model and using them as inputs for the SUNTANS model at common boundary points. The coupled model is calibrated with observed sea surface elevations and velocities, and high correlation coefficients that exceed 0.97 and 0.91 are found for sea surface elevations and velocities, respectively. The pollutants are modeled as Gaussian passive tracers, and are released at five upstream locations in Singapore coastal waters. During the Northeast monsoon, pollutants released in Source 1 (Johor River), Source 2 (Tiram River), Source 3 (Layang River) and Source 4 (Layau River) enter the Singapore Strait after 4 days of release and reach Sentosa Island within 9 days. Meanwhile, pollutants released in Source 5 (Kallang River) reach Sentosa Island after 4 days. During the Southwest monsoon, the dispersion time is roughly doubled, with pollutants from Sources 1 - 4 entering the Singapore Strait only after 12 days of release due to weak currents.

  15. A fully coupled Monte Carlo/discrete ordinates solution to the neutron transport equation. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Baker, Randal Scott [Univ. of Arizona, Tucson, AZ (United States)

    1990-01-01

    The neutron transport equation is solved by a hybrid method that iteratively couples regions where deterministic (SN) and stochastic (Monte Carlo) methods are applied. Unlike previous hybrid methods, the Monte Carlo and SN regions are fully coupled in the sense that no assumption is made about geometrical separation or decoupling. The hybrid method provides a new means of solving problems involving both optically thick and optically thin regions that neither Monte Carlo nor SN is well suited for by themselves. The fully coupled Monte Carlo/SN technique consists of defining spatial and/or energy regions of a problem in which either a Monte Carlo calculation or an SN calculation is to be performed. The Monte Carlo region may comprise the entire spatial region for selected energy groups, or may consist of a rectangular area that is either completely or partially embedded in an arbitrary SN region. The Monte Carlo and SN regions are then connected through the common angular boundary fluxes, which are determined iteratively using the response matrix technique, and volumetric sources. The hybrid method has been implemented in the SN code TWODANT by adding special-purpose Monte Carlo subroutines to calculate the response matrices and volumetric sources, and linkage subrountines to carry out the interface flux iterations. The common angular boundary fluxes are included in the SN code as interior boundary sources, leaving the logic for the solution of the transport flux unchanged, while, with minor modifications, the diffusion synthetic accelerator remains effective in accelerating SN calculations. The special-purpose Monte Carlo routines used are essentially analog, with few variance reduction techniques employed. However, the routines have been successfully vectorized, with approximately a factor of five increase in speed over the non-vectorized version.

  16. Coupled Ca2+/H+ transport by cytoplasmic buffers regulates local Ca2+ and H+ ion signaling.

    Science.gov (United States)

    Swietach, Pawel; Youm, Jae-Boum; Saegusa, Noriko; Leem, Chae-Hun; Spitzer, Kenneth W; Vaughan-Jones, Richard D

    2013-05-28

    Ca(2+) signaling regulates cell function. This is subject to modulation by H(+) ions that are universal end-products of metabolism. Due to slow diffusion and common buffers, changes in cytoplasmic [Ca(2+)] ([Ca(2+)]i) or [H(+)] ([H(+)]i) can become compartmentalized, leading potentially to complex spatial Ca(2+)/H(+) coupling. This was studied by fluorescence imaging of cardiac myocytes. An increase in [H(+)]i, produced by superfusion of acetate (salt of membrane-permeant weak acid), evoked a [Ca(2+)]i rise, independent of sarcolemmal Ca(2+) influx or release from mitochondria, sarcoplasmic reticulum, or acidic stores. Photolytic H(+) uncaging from 2-nitrobenzaldehyde also raised [Ca(2+)]i, and the yield was reduced following inhibition of glycolysis or mitochondrial respiration. H(+) uncaging into buffer mixtures in vitro demonstrated that Ca(2+) unloading from proteins, histidyl dipeptides (HDPs; e.g., carnosine), and ATP can underlie the H(+)-evoked [Ca(2+)]i rise. Raising [H(+)]i tonically at one end of a myocyte evoked a local [Ca(2+)]i rise in the acidic microdomain, which did not dissipate. The result is consistent with uphill Ca(2+) transport into the acidic zone via Ca(2+)/H(+) exchange on diffusible HDPs and ATP molecules, energized by the [H(+)]i gradient. Ca(2+) recruitment to a localized acid microdomain was greatly reduced during intracellular Mg(2+) overload or by ATP depletion, maneuvers that reduce the Ca(2+)-carrying capacity of HDPs. Cytoplasmic HDPs and ATP underlie spatial Ca(2+)/H(+) coupling in the cardiac myocyte by providing ion exchange and transport on common buffer sites. Given the abundance of cellular HDPs and ATP, spatial Ca(2+)/H(+) coupling is likely to be of general importance in cell signaling.

  17. Investigations of the role of nonlinear couplings in structure formation and transport regulation in plasma turbulence

    Science.gov (United States)

    Holland, Christopher George

    Studies of nonlinear couplings and dynamics in plasma turbulence are presented. Particular areas of focus are analytic studies of coherent structure formation in electron temperature gradient turbulence, measurement of nonlinear energy transfer in simulations of plasma turbulence, and bispectral analysis of experimental and computational data. The motivation for these works has been to develop and expand the existing theories of plasma transport, and verify the nonlinear predictions of those theories in simulation and experiment. In Chapter II, we study electromagnetic secondary instabilities of electron temperature gradient turbulence. The growth rate for zonal flow generation via modulational instability of electromagnetic ETG turbulence is calculated, as well as that for zonal (magnetic) field generation. In Chapter III, the stability and saturation of streamers in ETG turbulence is considered, and shown to depend sensitively upon geometry and the damping rates of the Kelvin-Helmholtz mode. Requirements for a credible theory of streamer transport are presented. In addition, a self-consistent model for interactions between ETG and ITG (ion temperature gradient) turbulence is presented. In Chapter IV, the nonlinear transfer of kinetic and internal energy is measured in simulations of plasma turbulence. The regulation of turbulence by radial decorrelation due to zonal flows and generation of zonal flows via the Reynolds stress are explicitly demonstrated, and shown to be symmetric facets of a single nonlinear process. Novel nonlinear saturation mechanisms for zonal flows are discussed. In Chapter V, measurements of fluctuation bicoherence in the edge of the DIII-D tokamak are presented. It is shown that the bicoherence increases transiently before a L-H transition, and decays to its initial value after the barrier has formed. The increase in bicoherence is localized to the region where the transport barrier forms, and shows strong coupling between well

  18. Na+-coupled bicarbonate transporters in duodenum, collecting ducts and choroid plexus.

    Science.gov (United States)

    Praetorius, Jeppe

    2010-01-01

    Epithelia cover the internal and external surfaces of the organism and form barriers between the various compartments. Some of these epithelia are specialized for effective transmembrane or even transepithelial movement of acid-base equivalents. Certain epithelia with a high rate of HCO3- transport express a few potent Na+-coupled acid-base transporters to gain a net HCO3- movement across the epithelium. Examples of such epithelia are renal proximal tubules and pancreatic ducts. In contrast, multiple Na+-coupled HCO3- transporters are expressed in other HCO3- secreting epithelia, such as the duodenal mucosa or the choroid plexus, which maintain suitable intracellular pH despite a variable demand for secreting HCO3-. In the duodenum, the epithelial cells must secrete HCO3- for neutralization of the gastric acid, and at the same time prevent cellular acidification. During the neutralization, large quantities of CO2 are formed in the duodenal lumen, which enter the epithelial cells. This would tend to lower intracellular pH and require effective counteracting mechanisms to avoid cell death and to maintain HCO3- secretion. The choroid plexus secretes the cerebrospinal fluid (CSF) and controls the pH of the otherwise poorly buffered CSF. The pCO2 of CSF fluctuates with plasma pCO2, and the choroid plexus must regulate the HCO3- secretion to minimize the effects of these fluctuations on CSF pH. This is done while maintaining pH neutrality in the epithelial cells. Thus, the Na+-HCO3- cotransporters appear to be involved in HCO3- import in more epithelia, where Na+/H+ exchangers were until recently thought to be sufficient for maintaining intracellular pH.

  19. Reactive Transport and Coupled THM Processes in Engineering Barrier Systems (EBS)

    International Nuclear Information System (INIS)

    Steefel, Carl; Rutqvist, Jonny; Tsang, Chin-Fu; Liu, Hui-Hai; Sonnenthal, Eric; Houseworth, Jim; Birkholzer, Jens

    2010-01-01

    Geological repositories for disposal of high-level nuclear wastes generally rely on a multi-barrier system to isolate radioactive wastes from the biosphere. The multi-barrier system typically consists of a natural barrier system, including repository host rock and its surrounding subsurface environment, and an engineering barrier system (EBS). EBS represents the man-made, engineered materials placed within a repository, including the waste form, waste canisters, buffer materials, backfill and seals (OECD, 2003). EBS plays a significant role in the containment and long-term retardation of radionuclide release. EBS is involved in complex thermal, hydrogeological, mechanical, chemical and biological processes, such as heat release due to radionuclide decay, multiphase flow (including gas release due to canister corrosion), swelling of buffer materials, radionuclide diffusive transport, waste dissolution and chemical reactions. All these processes are related to each other. An in-depth understanding of these coupled processes is critical for the performance assessment (PA) for EBS and the entire repository. Within the EBS group of Used Fuel Disposition (UFD) Campaign, LBNL is currently focused on (1) thermal-hydraulic-mechanical-chemical (THMC) processes in buffer materials (bentonite) and (2) diffusive transport in EBS associated with clay host rock, with a long-term goal to develop a full understanding of (and needed modeling capabilities to simulate) impacts of coupled processes on radionuclide transport in different components of EBS, as well as the interaction between near-field host rock (e.g., clay) and EBS and how they effect radionuclide release. This final report documents the progress that LBNL has made in its focus areas. Specifically, Section 2 summarizes progress on literature review for THMC processes and reactive-diffusive radionuclide transport in bentonite. The literature review provides a picture of the state-of-the-art of the relevant research areas

  20. Reactive Transport and Coupled THM Processes in Engineering Barrier Systems (EBS)

    Energy Technology Data Exchange (ETDEWEB)

    Steefel, Carl; Rutqvist, Jonny; Tsang, Chin-Fu; Liu, Hui-Hai; Sonnenthal, Eric; Houseworth, Jim; Birkholzer, Jens

    2010-08-31

    Geological repositories for disposal of high-level nuclear wastes generally rely on a multi-barrier system to isolate radioactive wastes from the biosphere. The multi-barrier system typically consists of a natural barrier system, including repository host rock and its surrounding subsurface environment, and an engineering barrier system (EBS). EBS represents the man-made, engineered materials placed within a repository, including the waste form, waste canisters, buffer materials, backfill and seals (OECD, 2003). EBS plays a significant role in the containment and long-term retardation of radionuclide release. EBS is involved in complex thermal, hydrogeological, mechanical, chemical and biological processes, such as heat release due to radionuclide decay, multiphase flow (including gas release due to canister corrosion), swelling of buffer materials, radionuclide diffusive transport, waste dissolution and chemical reactions. All these processes are related to each other. An in-depth understanding of these coupled processes is critical for the performance assessment (PA) for EBS and the entire repository. Within the EBS group of Used Fuel Disposition (UFD) Campaign, LBNL is currently focused on (1) thermal-hydraulic-mechanical-chemical (THMC) processes in buffer materials (bentonite) and (2) diffusive transport in EBS associated with clay host rock, with a long-term goal to develop a full understanding of (and needed modeling capabilities to simulate) impacts of coupled processes on radionuclide transport in different components of EBS, as well as the interaction between near-field host rock (e.g., clay) and EBS and how they effect radionuclide release. This final report documents the progress that LBNL has made in its focus areas. Specifically, Section 2 summarizes progress on literature review for THMC processes and reactive-diffusive radionuclide transport in bentonite. The literature review provides a picture of the state-of-the-art of the relevant research areas

  1. Antiresonance and decoupling in electronic transport through parallel-coupled quantum-dot structures with laterally-coupled Majorana zero modes

    Science.gov (United States)

    Zhang, Ya-Jing; Zhang, Lian-Lian; Jiang, Cui; Gong, Wei-Jiang

    2018-02-01

    We theoretically investigate the electronic transport through a parallel-coupled multi-quantum-dot system, in which the terminal dots of a one-dimensional quantum-dot chain are embodied in the two arms of an Aharonov-Bohm interferometer. It is found that in the structures of odd(even) dots, all their even(odd) molecular states have opportunities to decouple from the leads, and in this process antiresonance occurs which are accordant with the odd(even)-numbered eigenenergies of the sub-molecule without terminal dots. Next when Majorana zero modes are introduced to couple laterally to the terminal dots, the antiresonance and decoupling phenomena still co-exist in the quantum transport process. Such a result can be helpful in understanding the special influence of Majorana zero mode on the electronic transport through quantum-dot systems.

  2. Microbial community responses to 17 years of altered precipitation are seasonally dependent and coupled to co-varying effects of water content on vegetation and soil C

    Science.gov (United States)

    Sorensen, Patrick O.; Germino, Matthew J.; Feris, Kevin P.

    2013-01-01

    Precipitation amount and seasonal timing determine the duration and distribution of water available for plant and microbial activity in the cold desert sagebrush steppe. In this study, we sought to determine if a sustained shift in the amount and timing of precipitation would affect soil microbial diversity, community composition, and soil carbon (C) storage. Field plots were irrigated (+200 mm) during the dormant or growing-season for 17 years. Microbial community responses were assessed over the course of a year at two depths (15–20 cm, 95–100 cm) by terminal restriction fragment length polymorphism (T-RFLP), along with co-occurring changes in plant cover and edaphic properties. Bacterial richness, Shannon Weaver diversity, and composition in shallow soils (15–20 cm) as well as evenness in deep soils (95–100 cm) differed across irrigation treatments during July. Irrigation timing affected fungal community diversity and community composition during the dormant season and most strongly in deep soils (95–100 cm). Dormant-season irrigation increased the ratio of shrubs to forbs and reduced soil C in shallow soils by 16% relative to ambient conditions. It is unclear whether or not soil C will continue to decline with continued treatment application or if microbial adaptation could mitigate sustained soil C losses. Future changes in precipitation timing will affect soil microbes in a seasonally dependent manner and be coupled to co-varying effects of water content on vegetation and soil C.

  3. Membrane topology of rat sodium-coupled neutral amino acid transporter 2 (SNAT2).

    Science.gov (United States)

    Ge, Yudan; Gu, Yanting; Wang, Jiahong; Zhang, Zhou

    2018-07-01

    Sodium-coupled neutral amino acid transporter 2 (SNAT2) is a subtype of the amino acid transport system A that is widely expressed in mammalian tissues. It plays critical roles in glutamic acid-glutamine circulation, liver gluconeogenesis and other biological pathway. However, the topology of the SNAT2 amino acid transporter is unknown. Here we identified the topological structure of SNAT2 using bioinformatics analysis, Methoxy-polyethylene glycol maleimide (mPEG-Mal) chemical modification, protease cleavage assays, immunofluorescence and examination of glycosylation. Our results show that SNAT2 contains 11 transmembrane domains (TMDs) with an intracellular N terminus and an extracellular C terminus. Three N-glycosylation sites were verified at the largest extracellular loop. This model is consistent with the previous model of SNAT2 with the exception of a difference in number of glycosylation sites. This is the first time to confirm the SNAT2 membrane topology using experimental methods. Our study on SNAT2 topology provides valuable structural information of one of the solute carrier family 38 (SLC38) members. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. ITS, TIGER System of Coupled Electron Photon Transport by Monte-Carlo

    International Nuclear Information System (INIS)

    Halbleib, J.A.; Mehlhorn, T.A.; Young, M.F.

    1996-01-01

    1 - Description of program or function: ITS permits a state-of-the-art Monte Carlo solution of linear time-integrated coupled electron/ photon radiation transport problems with or without the presence of macroscopic electric and magnetic fields of arbitrary spatial dependence. 2 - Method of solution: Through a machine-portable utility that emulates the basic features of the CDC UPDATE processor, the user selects one of eight codes for running on a machine of one of four (at least) major vendors. With the ITS-3.0 release the PSR-0245/UPEML package is included to perform these functions. The ease with which this utility is applied combines with an input scheme based on order-independent descriptive keywords that makes maximum use of defaults and internal error checking to provide experimentalists and theorists alike with a method for the routine but rigorous solution of sophisticated radiation transport problems. Physical rigor is maximized by employing the best available cross sections and sampling distributions, and the most complete physical model for describing the production and transport of the electron/ photon cascade from 1.0 GeV down to 1.0 keV. Flexibility of construction permits the codes to be tailored to specific applications and the capabilities of the codes to be extended to more complex applications through update procedures. 3 - Restrictions on the complexity of the problem: - Restrictions and/or limitations for ITS depend upon the local operating system

  5. Transport and trapping of dust particles in a potential well created by inductively coupled diffused plasmas.

    Science.gov (United States)

    Choudhary, Mangilal; Mukherjee, S; Bandyopadhyay, P

    2016-05-01

    A versatile linear dusty (complex) plasma device is designed to study the transport and dynamical behavior of dust particles in a large volume. Diffused inductively coupled plasma is generated in the background of argon gas. A novel technique is used to introduce the dust particles in the main plasma by striking a secondary direct current glow discharge. These dust particles are found to get trapped in an electrostatic potential well, which is formed due to the combination of the ambipolar electric field caused by diffusive plasma and the field produced by the charged glass wall of the vacuum chamber. According to the requirements, the volume of the dust cloud can be controlled very precisely by tuning the plasma and discharge parameters. The present device can be used to address the underlying physics behind the transport of dust particles, self-excited dust acoustic waves, and instabilities. The detailed design of this device, plasma production and characterization, trapping and transport of the dust particle, and some of the preliminary experimental results are presented.

  6. Self-Adjoint Angular Flux Equation for Coupled Electron-Photon Transport

    International Nuclear Information System (INIS)

    Liscum-Powell, J.L.; Lorence, L.J. Jr.; Morel, J.E.; Prinja, A.K.

    1999-01-01

    Recently, Morel and McGhee described an alternate second-order form of the transport equation called the self adjoint angular flux (SAAF) equation that has the angular flux as its unknown. The SAAF formulation has all the advantages of the traditional even- and odd-parity self-adjoint equations, with the added advantages that it yields the full angular flux when it is numerically solved, it is significantly easier to implement reflective and reflective-like boundary conditions, and in the appropriate form it can be solved in void regions. The SAAF equation has the disadvantage that the angular domain is the full unit sphere and, like the even- and odd- parity form, S n source iteration cannot be implemented using the standard sweeping algorithm. Also, problems arise in pure scattering media. Morel and McGhee demonstrated the efficacy of the SAAF formulation for neutral particle transport. Here we apply the SAAF formulation to coupled electron-photon transport problems using multigroup cross-sections from the CEPXS code and S n discretization

  7. Self-adjoint angular flux equation for coupled electron-photon transport

    International Nuclear Information System (INIS)

    Liscum-Powell, J.L.; Prinja, A.K.; Morel, J.E.; Lorence, L.J. Jr.

    1999-01-01

    Recently, Morel and McGhee described an alternate second-order form of the transport equation called the self-adjoint angular flux (SAAF) equation that has the angular flux as its unknown. The SAAF formulation has all the advantages of the traditional even- and odd-parity self-adjoint equations, with the added advantages that it yields the full angular flux when it is numerically solved, it is significantly easier to implement reflective and reflective-like boundary conditions, and in the appropriate form it can be solved in void regions. The SAAF equation has the disadvantage that the angular domain is the full unit sphere, and, like the even- and odd-parity form, S n source iteration cannot be implemented using the standard sweeping algorithm. Also, problems arise in pure scattering media. Morel and McGhee demonstrated the efficacy of the SAAF formulation for neutral particle transport. Here, the authors apply the SAAF formulation to coupled electron-photon transport problems using multigroup cross sections from the CEPXS code and S n discretization

  8. Fast Flows in the Magnetotail and Energetic Particle Transport: Multiscale Coupling in the Magnetosphere

    Science.gov (United States)

    Lin, Y.; Wang, X.; Fok, M. C. H.; Buzulukova, N.; Perez, J. D.; Chen, L. J.

    2017-12-01

    The interaction between the Earth's inner and outer magnetospheric regions associated with the tail fast flows is calculated by coupling the Auburn 3-D global hybrid simulation code (ANGIE3D) to the Comprehensive Inner Magnetosphere/Ionosphere (CIMI) model. The global hybrid code solves fully kinetic equations governing the ions and a fluid model for electrons in the self-consistent electromagnetic field of the dayside and night side outer magnetosphere. In the integrated computation model, the hybrid simulation provides the CIMI model with field data in the CIMI 3-D domain and particle data at its boundary, and the transport in the inner magnetosphere is calculated by the CIMI model. By joining the two existing codes, effects of the solar wind on particle transport through the outer magnetosphere into the inner magnetosphere are investigated. Our simulation shows that fast flows and flux ropes are localized transients in the magnetotail plasma sheet and their overall structures have a dawn-dusk asymmetry. Strong perpendicular ion heating is found at the fast flow braking, which affects the earthward transport of entropy-depleted bubbles. We report on the impacts from the temperature anisotropy and non-Maxwellian ion distributions associated with the fast flows on the ring current and the convection electric field.

  9. Direct-coupled-ray method for design-oriented three-dimensional transport analysis

    International Nuclear Information System (INIS)

    Bucholz, J.A.; Poncelet, C.G.

    1977-01-01

    A fast three-dimensional design-oriented transport method has been developed for the solution of both neutron and gamma transport problems. It combines a nodal approach with analytic integral transport to achieve relative speed and accuracy. An analytic solution is obtained for the angular flux in each of the 14 directions defined by the six faces and eight corners of a cubic mesh block. The scheme used to accommodate high-order anisotropic scattering is based on the formulation of ray-to-ray scattering probabilities in an integral sense. A variable mesh approximation has also been introduced to provide greater flexibility. The details of a direct-coupled-ray (DCR) → P 1 conversion technique have been developed but not yet implemented. The DCR method, as implemented in the TRANS3 code, has been used in a number of liquid-metal fast breeder reactor shielding applications. These included a one-dimensional deep penetration configuration and one-, two-, and three dimensional representations of the lower axial shield of the Clinch River Breeder Reactor. Comparisons with ANISN and DOT-III solutions indicated good to excellent agreement in most situations

  10. ITS Version 6 : the integrated TIGER series of coupled electron/photon Monte Carlo transport codes.

    Energy Technology Data Exchange (ETDEWEB)

    Franke, Brian Claude; Kensek, Ronald Patrick; Laub, Thomas William

    2008-04-01

    ITS is a powerful and user-friendly software package permitting state-of-the-art Monte Carlo solution of lineartime-independent coupled electron/photon radiation transport problems, with or without the presence of macroscopic electric and magnetic fields of arbitrary spatial dependence. Our goal has been to simultaneously maximize operational simplicity and physical accuracy. Through a set of preprocessor directives, the user selects one of the many ITS codes. The ease with which the makefile system is applied combines with an input scheme based on order-independent descriptive keywords that makes maximum use of defaults and internal error checking to provide experimentalists and theorists alike with a method for the routine but rigorous solution of sophisticated radiation transport problems. Physical rigor is provided by employing accurate cross sections, sampling distributions, and physical models for describing the production and transport of the electron/photon cascade from 1.0 GeV down to 1.0 keV. The availability of source code permits the more sophisticated user to tailor the codes to specific applications and to extend the capabilities of the codes to more complex applications. Version 6, the latest version of ITS, contains (1) improvements to the ITS 5.0 codes, and (2) conversion to Fortran 90. The general user friendliness of the software has been enhanced through memory allocation to reduce the need for users to modify and recompile the code.

  11. Review on modeling development for multiscale chemical reactions coupled transport phenomena in solid oxide fuel cells

    International Nuclear Information System (INIS)

    Andersson, Martin; Yuan, Jinliang; Sunden, Bengt

    2010-01-01

    A literature study is performed to compile the state-of-the-art, as well as future potential, in SOFC modeling. Principles behind various transport processes such as mass, heat, momentum and charge as well as for electrochemical and internal reforming reactions are described. A deeper investigation is made to find out potentials and challenges using a multiscale approach to model solid oxide fuel cells (SOFCs) and combine the accuracy at microscale with the calculation speed at macroscale to design SOFCs, based on a clear understanding of transport phenomena, chemical reactions and functional requirements. Suitable methods are studied to model SOFCs covering various length scales. Coupling methods between different approaches and length scales by multiscale models are outlined. Multiscale modeling increases the understanding for detailed transport phenomena, and can be used to make a correct decision on the specific design and control of operating conditions. It is expected that the development and production costs will be decreased and the energy efficiency be increased (reducing running cost) as the understanding of complex physical phenomena increases. It is concluded that the connection between numerical modeling and experiments is too rare and also that material parameters in most cases are valid only for standard materials and not for the actual SOFC component microstructures.

  12. Microbial mediation of radionuclide transport -significance for the nuclear fuel waste management program

    International Nuclear Information System (INIS)

    Champ, D.R.

    1984-08-01

    The role that microbially catalyzed processes may play in determining, or altering, radionuclide migration is an unresolved question in the Nuclear Fuel Waste Management Program. This report documents the results of a review of the available information on the existence and biochemical capabilities of micro-organisms and the potential for their involvement in processes affecting the migration of radionuclides of interest. The potential was judged sufficient to warrant conducting experiments to assess their role. The outline of an experimental program to address the role of micro-organisms is presented

  13. Development of CO2 inversion system based on the adjoint of the global coupled transport model

    Science.gov (United States)

    Belikov, Dmitry; Maksyutov, Shamil; Chevallier, Frederic; Kaminski, Thomas; Ganshin, Alexander; Blessing, Simon

    2014-05-01

    We present the development of an inverse modeling system employing an adjoint of the global coupled transport model consisting of the National Institute for Environmental Studies (NIES) Eulerian transport model (TM) and the Lagrangian plume diffusion model (LPDM) FLEXPART. NIES TM is a three-dimensional atmospheric transport model, which solves the continuity equation for a number of atmospheric tracers on a grid spanning the entire globe. Spatial discretization is based on a reduced latitude-longitude grid and a hybrid sigma-isentropic coordinate in the vertical. NIES TM uses a horizontal resolution of 2.5°×2.5°. However, to resolve synoptic-scale tracer distributions and to have the ability to optimize fluxes at resolutions of 0.5° and higher we coupled NIES TM with the Lagrangian model FLEXPART. The Lagrangian component of the forward and adjoint models uses precalculated responses of the observed concentration to the surface fluxes and 3-D concentrations field simulated with the FLEXPART model. NIES TM and FLEXPART are driven by JRA-25/JCDAS reanalysis dataset. Construction of the adjoint of the Lagrangian part is less complicated, as LPDMs calculate the sensitivity of measurements to the surrounding emissions field by tracking a large number of "particles" backwards in time. Developing of the adjoint to Eulerian part was performed with automatic differentiation tool the Transformation of Algorithms in Fortran (TAF) software (http://www.FastOpt.com). This method leads to the discrete adjoint of NIES TM. The main advantage of the discrete adjoint is that the resulting gradients of the numerical cost function are exact, even for nonlinear algorithms. The overall advantages of our method are that: 1. No code modification of Lagrangian model is required, making it applicable to combination of global NIES TM and any Lagrangian model; 2. Once run, the Lagrangian output can be applied to any chemically neutral gas; 3. High-resolution results can be obtained over

  14. Simulating selenium and nitrogen fate and transport in coupled stream-aquifer systems of irrigated regions

    Science.gov (United States)

    Shultz, Christopher D.; Bailey, Ryan T.; Gates, Timothy K.; Heesemann, Brent E.; Morway, Eric D.

    2018-01-01

    Elevated levels of selenium (Se) in aqueous environments can harm aquatic life and endanger livestock and human health. Although Se occurs naturally in the rocks and soils of many alluvial aquifers, mining and agricultural activities can increase its rate of mobilization and transport to surface waters. Attention is given here to regions where nonpoint source return flows from irrigated lands carry pollutant loads to aquifers and streams, contributing to concentrations that violate regulatory and performance standards. Of particular concern is the heightened level and mobilization of Se influenced by nitrate (NO3), a harmful pollutant in its own right. We present a numerical model that simulates the reactive transport of Se and nitrogen (N) species in a coupled groundwater-surface water system. Building upon a conceptual model that incorporates the major processes affecting Se and NO3 transport in an irrigated watershed, the model links the finite-difference models MODFLOW, UZF-RT3D, and OTIS, to simulate flow and reactive transport of multiple chemical species in both the aquifer and a stream network, with mass exchange between the two. The capability of the new model is showcased by calibration, testing, and application to a 500 km2 region in Colorado’s Lower Arkansas River Valley using a rich data set gathered over a 10-yr period. Simulation of spatial and temporal distributions of Se concentration reveals conditions that exceed standards in groundwater for approximately 20% of the area. For the Arkansas River, standards are exceeded by 290%–450%. Simulation indicates that river concentrations of NO3 alone are near the current interim standard for the total of all dissolved N species. These results indicate the need for future use of the developed model to investigate the prospects for land and water best management practices to decrease pollutant levels.

  15. Simulating selenium and nitrogen fate and transport in coupled stream-aquifer systems of irrigated regions

    Science.gov (United States)

    Shultz, Christopher D.; Bailey, Ryan T.; Gates, Timothy K.; Heesemann, Brent E.; Morway, Eric D.

    2018-05-01

    Elevated levels of selenium (Se) in aqueous environments can harm aquatic life and endanger livestock and human health. Although Se occurs naturally in the rocks and soils of many alluvial aquifers, mining and agricultural activities can increase its rate of mobilization and transport to surface waters. Attention is given here to regions where nonpoint source return flows from irrigated lands carry pollutant loads to aquifers and streams, contributing to concentrations that violate regulatory and performance standards. Of particular concern is the heightened level and mobilization of Se influenced by nitrate (NO3), a harmful pollutant in its own right. We present a numerical model that simulates the reactive transport of Se and nitrogen (N) species in a coupled groundwater-surface water system. Building upon a conceptual model that incorporates the major processes affecting Se and NO3 transport in an irrigated watershed, the model links the finite-difference models MODFLOW, UZF-RT3D, and OTIS, to simulate flow and reactive transport of multiple chemical species in both the aquifer and a stream network, with mass exchange between the two. The capability of the new model is showcased by calibration, testing, and application to a 500 km2 region in Colorado's Lower Arkansas River Valley using a rich data set gathered over a 10-yr period. Simulation of spatial and temporal distributions of Se concentration reveals conditions that exceed standards in groundwater for approximately 20% of the area. For the Arkansas River, standards are exceeded by 290%-450%. Simulation indicates that river concentrations of NO3 alone are near the current interim standard for the total of all dissolved N species. These results indicate the need for future use of the developed model to investigate the prospects for land and water best management practices to decrease pollutant levels.

  16. Radiochemically-supported microbial communities. A potential mechanism for biocolloid production of importance to actinide transport

    Energy Technology Data Exchange (ETDEWEB)

    Moser, Duane P. [Desert Research Institute, Las Vegas, NV (United States); Hamilton-Brehm, Scott D. [Desert Research Institute, Las Vegas, NV (United States); Fisher, Jenny C. [Univ. of Wisconsin, Milwaukee, WI (United States); Bruckner, James C. [Desert Research Institute, Las Vegas, NV (United States); Kruger, Brittany [Desert Research Institute, Las Vegas, NV (United States); Sackett, Joshua [Desert Research Institute, Las Vegas, NV (United States); Russell, Charles E. [Desert Research Institute, Las Vegas, NV (United States); Onstott, Tullis C. [Princeton Univ., NJ (United States); Czerwinski, Ken [Univ. of Nevada, Las Vegas, NV (United States); Zavarin, Mavrik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Campbell, James H. [Northwest Missouri State Univ., Maryville, MO (United States)

    2015-03-20

    The work described here revealed the presence of diverse microbial communities located across 19 subsurface sites at the NNSS/NTTR and nearby locations. Overall, the diversity of microorganisms was high for subsurface habitats and variable between sites. As of this writing, preparations are being made to combine the Illumina sequences and 16S rRNA clone libraries with other non-NNSS/NTTR well sites of Southern Nevada Regional Flow System for a publication manuscript describing our very broad landscape scale survey of subsurface microbial diversity. Isolates DRI-13 and DRI-14 remain to be fully characterized and named in accordance with the conventions established by Bergey's Manual of Systematic Bacteriology. In preparation to be published, these microorganisms will be submitted to the American Type Culture Collection (ATCC) and the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ).It is anticipated that the data resulting from this study in combination with other data sets that will allow us to produce a number of publications that will be impactful to the subsurface microbiology community.

  17. Couplings

    Science.gov (United States)

    Stošić, Dušan; Auroux, Aline

    Basic principles of calorimetry coupled with other techniques are introduced. These methods are used in heterogeneous catalysis for characterization of acidic, basic and red-ox properties of solid catalysts. Estimation of these features is achieved by monitoring the interaction of various probe molecules with the surface of such materials. Overview of gas phase, as well as liquid phase techniques is given. Special attention is devoted to coupled calorimetry-volumetry method. Furthermore, the influence of different experimental parameters on the results of these techniques is discussed, since it is known that they can significantly influence the evaluation of catalytic properties of investigated materials.

  18. Evidence of G-protein-coupled receptor and substrate transporter heteromerization at a single molecule level.

    Science.gov (United States)

    Fischer, Jana; Kleinau, Gunnar; Rutz, Claudia; Zwanziger, Denise; Khajavi, Noushafarin; Müller, Anne; Rehders, Maren; Brix, Klaudia; Worth, Catherine L; Führer, Dagmar; Krude, Heiko; Wiesner, Burkhard; Schülein, Ralf; Biebermann, Heike

    2018-06-01

    G-protein-coupled receptors (GPCRs) can constitute complexes with non-GPCR integral membrane proteins, while such interaction has not been demonstrated at a single molecule level so far. We here investigated the potential interaction between the thyrotropin receptor (TSHR) and the monocarboxylate transporter 8 (MCT8), a member of the major facilitator superfamily (MFS), using fluorescence cross-correlation spectroscopy (FCCS). Both the proteins are expressed endogenously on the basolateral plasma membrane of the thyrocytes and are involved in stimulation of thyroid hormone production and release. Indeed, we demonstrate strong interaction between both the proteins which causes a suppressed activation of G q/11 by TSH-stimulated TSHR. Thus, we provide not only evidence for a novel interaction between the TSHR and MCT8, but could also prove this interaction on a single molecule level. Moreover, this interaction forces biased signaling at the TSHR. These results are of general interest for both the GPCR and the MFS research fields.

  19. A coupled model of transport-reaction-mechanics with trapping. Part I - Small strain analysis

    Science.gov (United States)

    Salvadori, A.; McMeeking, R.; Grazioli, D.; Magri, M.

    2018-05-01

    A fully coupled model for mass and heat transport, mechanics, and chemical reactions with trapping is proposed. It is rooted in non-equilibrium rational thermodynamics and assumes that displacements and strains are small. Balance laws for mass, linear and angular momentum, energy, and entropy are stated. Thermodynamic restrictions are identified, based on an additive strain decomposition and on the definition of the Helmholtz free energy. Constitutive theory and chemical kinetics are studied in order to finally write the governing equations for the multi-physics problem. The field equations are solved numerically with the finite element method, stemming from a three-fields variational formulation. Three case-studies on vacancies redistribution in metals, hydrogen embrittlement, and the charge-discharge of active particles in Li-ion batteries demonstrate the features and the potential of the proposed model.

  20. Transport Through a Precessing Spin Coupled to Noncollinearly Polarized Ferromagnetic Leads

    International Nuclear Information System (INIS)

    Wang Xianchao; Xin Zihua; Feng Liya

    2010-01-01

    The quantum electronic transport through a precessing magnetic spin coupled to noncollinearly polarized ferromagnetic leads (F-MS-F) has been studied in this paper. The nonequilibrium Green function approach is used to calculate local density of states (LDOS) and current in the presence of external bias. The characters of LDOS and the electronic current are obtained. The tunneling current is investigated for different precessing angle and different configurations of the magnetization of the leads. The investigation reveals that when the precessing angle takes θ < π/2 and negative bias is applied, the resonant tunneling current appears, otherwise, it appears when positive bias is applied. When the leads are totally polarized and the precessing angel takes 0, the tunneling current changes with the configuration of two leads; and it becomes zero when the two leads are antiparallel. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  1. Coupled force-balance and particle-occupation rate equations for high-field electron transport

    International Nuclear Information System (INIS)

    Lei, X. L.

    2008-01-01

    It is pointed out that in the framework of balance-equation approach, the coupled force-balance and particle-occupation rate equations can be used as a complete set of equations to determine the high-field transport of semiconductors in both strong and weak electron-electron interaction limits. We call to attention that the occupation rate equation conserves the total particle number and maintains the energy balance of the relative electron system, and there is no need to introduce any other term in it. The addition of an energy-drift term in the particle-occupation rate equation [Phys. Rev. B 71, 195205 (2005)] is physically inadequate for the violation of the total particle-number conservation and the energy balance. It may lead to a substantial unphysical increase of the total particle number by the application of a dc electric field

  2. Spin-orbit coupling effects, interactions and superconducting transport in nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Schulz, Andreas

    2010-05-15

    the RKKY Hamiltonian on both RSOC and interaction strength and an anisotropic range function. In the second part of this thesis we focus on the study of superconducting transport in a quantum dot Josephson junctions coupled to a two-level system, which serves as a simple model for a conformational degree of freedom of a molecular dot or a break junction. We first address the limit of weak coupling to the leads and calculate the critical current through the junction perturbatively to lowest nonvanishing order in the tunneling couplings, allowing for arbitrary charging energy U and TLS parameters. We show that the critical current can change by orders of magnitude due to the two-level system. In particular, the {pi}-junction behavior, generally present for strong interactions, can be completely suppressed. We also study the influence of the Josephson current on the state of the TLS in the regime of weak charging energy. Within a wide range of parameters, our calculations predict that the TLS is quite sensitive to a variation of the phase difference {phi} across the junction. Conformational changes, up to a a complete reversal, can be induced by varying {phi}. This allows for the dissipationless control (including switching) of the TLS. (orig.)

  3. Spin-orbit coupling effects, interactions and superconducting transport in nanostructures

    International Nuclear Information System (INIS)

    Schulz, Andreas

    2010-05-01

    the RKKY Hamiltonian on both RSOC and interaction strength and an anisotropic range function. In the second part of this thesis we focus on the study of superconducting transport in a quantum dot Josephson junctions coupled to a two-level system, which serves as a simple model for a conformational degree of freedom of a molecular dot or a break junction. We first address the limit of weak coupling to the leads and calculate the critical current through the junction perturbatively to lowest nonvanishing order in the tunneling couplings, allowing for arbitrary charging energy U and TLS parameters. We show that the critical current can change by orders of magnitude due to the two-level system. In particular, the π-junction behavior, generally present for strong interactions, can be completely suppressed. We also study the influence of the Josephson current on the state of the TLS in the regime of weak charging energy. Within a wide range of parameters, our calculations predict that the TLS is quite sensitive to a variation of the phase difference φ across the junction. Conformational changes, up to a a complete reversal, can be induced by varying φ. This allows for the dissipationless control (including switching) of the TLS. (orig.)

  4. Coupling fine particle and bedload transport in gravel-bedded streams

    Science.gov (United States)

    Park, Jungsu; Hunt, James R.

    2017-09-01

    Fine particles in the silt- and clay-size range are important determinants of surface water quality. Since fine particle loading rates are not unique functions of stream discharge this limits the utility of the available models for water quality assessment. Data from 38 minimally developed watersheds within the United States Geological Survey stream gauging network in California, USA reveal three lines of evidence that fine particle release is coupled with bedload transport. First, there is a transition in fine particle loading rate as a function of discharge for gravel-bedded sediments that does not appear when the sediment bed is composed of sand, cobbles, boulders, or bedrock. Second, the discharge at the transition in the loading rate is correlated with the initiation of gravel mobilization. Third, high frequency particle concentration and discharge data are dominated by clockwise hysteresis where rising limb discharges generally have higher concentrations than falling limb discharges. These three observations across multiple watersheds lead to a conceptual model that fine particles accumulate within the sediment bed at discharges less than the transition and then the gravel bed fluidizes with fine particle release at discharges above the transition discharge. While these observations were individually recognized in the literature, this analysis provides a consistent conceptual model based on the coupling of fine particle dynamics with filtration at low discharges and gravel bed fluidization at higher discharges.

  5. Coupling Solute and Fine Particle Transport with Sand Bed Morphodynamics within a Field Experiment

    Science.gov (United States)

    Phillips, C. B.; Ortiz, C. P.; Schumer, R.; Jerolmack, D. J.; Packman, A. I.

    2017-12-01

    Fine suspended particles are typically considered to pass through streams and rivers as wash load without interacting with the bed, however experiments have demonstrated that hyporheic flow causes advective exchange of fine particles with the stream bed, yielding accumulation of fine particle deposits within the bed. Ultimately, understanding river morphodynamics and ecosystem dynamics requires coupling both fine particle and solute transport with bed morphodynamics. To better understand the coupling between these processes we analyze a novel dataset from a controlled field experiment conducted on Clear Run, a 2nd order sand bed stream located within the North Carolina coastal plain. Data include concentrations of continuously injected conservative solutes and fine particulate tracers measured at various depths within the stream bed, overhead time lapse images of bed forms, stream discharge, and geomorphological surveys of the stream. We use image analysis of bed morphodynamics to assess exchange, retention, and remobilization of solutes and fine particles during constant discharge and a short duration experimental flood. From the images, we extract a time series of bedform elevations and scour depths for the duration of the experiment. The high-resolution timeseries of bed elevation enables us to assess coupling of bed morphodynamics with both the solute and fine particle flux during steady state mobile bedforms prior to the flood and to changing bedforms during the flood. These data allow the application of a stochastic modeling framework relating bed elevation fluctuations to fine particle residence times. This combined experimental and modeling approach ultimately informs our ability to predict not only the fate of fine particulate matter but also associated nutrient and carbon dynamics within streams and rivers.

  6. Microbial biosensors

    International Nuclear Information System (INIS)

    Le Yu; Chen, Wilfred; Mulchandani, Ashok

    2006-01-01

    A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

  7. Solute transport in coupled inland-coastal water systems. General conceptualisation and application to Forsmark

    International Nuclear Information System (INIS)

    Jarsjoe, Jerker; Destouni, Georgia; Persson, Klas; Prieto, Carmen

    2007-12-01

    diffuse and occurring through SGD, small transient streams and/or coastal wetlands. Regarding transport quantifications, hydrogeochemical characteristics and pollution source loads may generally differ between larger, monitored catchments and smaller unmonitored coastal catchments. Since national hydrological monitoring data systematically exclude smaller, coastal catchments, they may not be representative for conditions in Forsmark (or Laxemar-Simpevarp). This emphasises the importance of extending in time the recently started hydrological and hydrogeochemical data series in the Forsmark and Laxemar-Simpevarp coastal catchment areas, since they are in effect unmonitored from a hydrological viewpoint, due to the lack of extended discharge time series. In the performed initial demonstration analysis of solute transport pathways from deep groundwater to recipients at the surface, we considered the main scenarios: (I) transport in the Quaternary deposits-bedrock interface zone only, and (II) transport in the coupled groundwater-surface water system. Considering mean travel times from each model cell to the coast, and disregarding travel times in the deep bedrock domain itself (which may be added to the here presented values), results show that travel times in scenario (II) were less than 4 years in 90% of the considered model area. Travel times were longer in scenario (I) with values higher than 10 years in 40% of the catchment area. These results are based on the assumption that the pathways do not go through zones of near-stagnant groundwater. If they would do so (and the above assumption is violated), results show that travel times can be considerably longer, for instance exceeding 400 years in half of the model area in scenario (I). Considering possible solute attenuation (caused by e.g. biogeochemical reactions or decay) along the hydrological transport pathways to inland surface waters and to the coast, we estimate solute mass delivery factors, representing the

  8. Development of a Photosynthetic Microbial Electrochemical Cell (PMEC Reactor Coupled with Dark Fermentation of Organic Wastes: Medium Term Perspectives

    Directory of Open Access Journals (Sweden)

    Samir Bensaid

    2015-01-01

    Full Text Available In this article the concept, the materials and the exploitation potential of a photosynthetic microbial electrochemical cell for the production of hydrogen driven by solar power are investigated. In a photosynthetic microbial electrochemical cell, which is based on photosynthetic microorganisms confined to an anode and heterotrophic bacteria confined to a cathode, water is split by bacteria hosted in the anode bioactive film. The generated electrons are conveyed through external “bio-appendages” developed by the bacteria to transparent nano-pillars made of indium tin oxide (ITO, Fluorine-doped tin oxide (FTO or other conducting materials, and then transferred to the cathode. On the other hand, the generated protons diffuse to the cathode via a polymer electrolyte membrane, where they are reduced by the electrons by heterotrophic bacteria growing attached to a similar pillared structure as that envisaged for the anode and supplemented with a specific low cost substrate (e.g., organic waste, anaerobic digestion outlet. The generated oxygen is released to the atmosphere or stored, while the produced pure hydrogen leaves the electrode through the porous layers. In addition, the integration of the photosynthetic microbial electrochemical cell system with dark fermentation as acidogenic step of anaerobic digester, which is able to produce additional H2, and the use of microbial fuel cell, feed with the residues of dark fermentation (mainly volatile fatty acids, to produce the necessary extra-bias for the photosynthetic microbial electrochemical cell is here analyzed to reveal the potential benefits to this novel integrated technology.

  9. Coupled plasma-neutral transport model for the scrape-off region

    International Nuclear Information System (INIS)

    Galambos, J.D.; Peng, Y.K.M.; Heifetz, D.

    1985-03-01

    Analysis of the scrape-off region requires treatment of the plasma transport along and across the field lines and inclusion of the neutral transport effects. A method for modeling the scrape-off region that is presented here uses separate models for each of these aspects that are coupled together through an iteration procedure that requires only minimal numerical effort. The method is applied here to estimate the neutral pumping rates in the pump-limiter and divertor options for a proposed deuterium-tritium (D-T) ignition experiment. High neutral recycling in the vicinity of the neutralizer plate dramatically affects pumping rates for both the pump-limiter and divertor. In both cases, the plasma flow into the channel surrounding the neutralizer plate is greatly reduced by the neutral recycling. The fraction of this flow that is pumped can be large (> 50%), but in general it is dependent on the particular geometry and plasma conditions. It is estimated that pumping speeds approximately greater than 10 5 L/s are adequate for the exhaust requirements in the pump-limiter and the divertor cases. Also, high neutral recycling on the front surface of the limiter tends to increase the neutral pumping rate

  10. Majorana transport in superconducting nanowire with Rashba and Dresselhaus spin-orbit couplings.

    Science.gov (United States)

    You, Jia-Bin; Shao, Xiao-Qiang; Tong, Qing-Jun; Chan, A H; Oh, C H; Vedral, Vlatko

    2015-06-10

    The tunneling experiment is a key technique for detecting Majorana fermion (MF) in solid state systems. We use Keldysh non-equilibrium Green function method to study two-lead tunneling in superconducting nanowire with Rashba and Dresselhaus spin-orbit couplings. A zero-bias dc conductance peak appears in our setup which signifies the existence of MF and is in accordance with previous experimental results on InSb nanowire. Interestingly, due to the exotic property of MF, there exists a hole transmission channel which makes the currents asymmetric at the left and right leads. The ac current response mediated by MF is also studied here. To discuss the impacts of Coulomb interaction and disorder on the transport property of Majorana nanowire, we use the renormalization group method to study the phase diagram of the wire. It is found that there is a topological phase transition under the interplay of superconductivity and disorder. We find that the Majorana transport is preserved in the superconducting-dominated topological phase and destroyed in the disorder-dominated non-topological insulator phase.

  11. Majorana transport in superconducting nanowire with Rashba and Dresselhaus spin–orbit couplings

    International Nuclear Information System (INIS)

    You, Jia-Bin; Shao, Xiao-Qiang; Tong, Qing-Jun; Oh, C H; Vedral, Vlatko; Chan, A H

    2015-01-01

    The tunneling experiment is a key technique for detecting Majorana fermion (MF) in solid state systems. We use Keldysh non-equilibrium Green function method to study two-lead tunneling in superconducting nanowire with Rashba and Dresselhaus spin–orbit couplings. A zero-bias dc conductance peak appears in our setup which signifies the existence of MF and is in accordance with previous experimental results on InSb nanowire. Interestingly, due to the exotic property of MF, there exists a hole transmission channel which makes the currents asymmetric at the left and right leads. The ac current response mediated by MF is also studied here. To discuss the impacts of Coulomb interaction and disorder on the transport property of Majorana nanowire, we use the renormalization group method to study the phase diagram of the wire. It is found that there is a topological phase transition under the interplay of superconductivity and disorder. We find that the Majorana transport is preserved in the superconducting-dominated topological phase and destroyed in the disorder-dominated non-topological insulator phase. (paper)

  12. Cross-separatrix Coupling in Nonlinear Global Electrostatic Turbulent Transport in C-2U

    Science.gov (United States)

    Lau, Calvin; Fulton, Daniel; Bao, Jian; Lin, Zhihong; Binderbauer, Michl; Tajima, Toshiki; Schmitz, Lothar; TAE Team

    2017-10-01

    In recent years, the progress of the C-2/C-2U advanced beam-driven field-reversed configuration (FRC) experiments at Tri Alpha Energy, Inc. has pushed FRCs to transport limited regimes. Understanding particle and energy transport is a vital step towards an FRC reactor, and two particle-in-cell microturbulence codes, the Gyrokinetic Toroidal Code (GTC) and A New Code (ANC), are being developed and applied toward this goal. Previous local electrostatic GTC simulations find the core to be robustly stable with drift-wave instability only in the scrape-off layer (SOL) region. However, experimental measurements showed fluctuations in both regions; one possibility is that fluctuations in the core originate from the SOL, suggesting the need for non-local simulations with cross-separatrix coupling. Current global ANC simulations with gyrokinetic ions and adiabatic electrons find that non-local effects (1) modify linear growth-rates and frequencies of instabilities and (2) allow instability to move from the unstable SOL to the linearly stable core. Nonlinear spreading is also seen prior to mode saturation. We also report on the progress of the first turbulence simulations in the SOL. This work is supported by the Norman Rostoker Fellowship.

  13. Coupling between particle and heat transport during power modulation experiments in Tore Supra

    International Nuclear Information System (INIS)

    Zou, X.L.; Giruzzi, G.; Artaud, J.F.; Bouquey, F.; Bremond, S.; Clary, J.; Darbos, C.; Eury, S.P.; Lennholm, M.; Magne, R.; Segui, J.L.

    2004-01-01

    Power modulations are a powerful tool often used to investigate heat transport processes in tokamaks. In some situations, this could also be an interesting method for the investigation of the particle transport due to the anomalous pinch. Low frequency (∼ 1 Hz) power modulation experiments, using both electron cyclotron resonance heating (ECRH) and ion cyclotron resonance heating (ICRH), have been performed in the Tore Supra tokamak. Strong coupling has been observed between the temperature and density modulations during the low frequency ECRH and ICRH modulation experiments. It has been shown that mechanisms as outgassing, Ware pinch effect, curvature driven pinch are not likely to be responsible for this density modulation. Because of its dependence on temperature or temperature gradient, the thermodiffusion is a serious candidate to be the driving source for this density modulation. This analysis shows that low frequency power modulation experiments have a great potential for the investigation of the anomalous particle pinch in tokamaks. Future plans will include the use of more precise density profile measurements using X-mode reflectometry

  14. Novel macrocyclic carriers for proton-coupled liquid membrane transport. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Lamb, J.D.; Izatt, R.M.; Bradshaw, J.S.; Shirts, R.B.

    1996-08-24

    The objective of this research program is to elucidate the chemical principles which are responsible for the cation selectivity and permeability of liquid membranes containing macrocyclic carriers. Several new macrocyclic carriers were synthesized during the last three year period. In addition, new, more convenient synthetic routes were achieved for several nitrogen-containing bicyclic and tricyclic macrocycles. The cation binding properties of these macrocycles were investigated by potentiometric titration, calorimetric titration, solvent extraction and NMR techniques. In addition, hydrophobic macrocycles were incorporated into dual hollow fiber and other membrane systems to investigate their membrane performance, especially in the proton-coupled transport mode. A study of the effect of methoxyalkyl macrocycle substituents on metal ion transport was completed. A new calorimeter was constructed which made it possible to study the thermodynamics of macrocycle-cation binding to very high temperatures. Measurements of thermodynamic data for the interaction of crown ethers with alkali and alkaline earth cations were achieved to 473 K. Molecular modeling work was begun for the first time on this project and fundamental principles were identified and developed for the establishment of working models in the future.

  15. Coupled transport/reaction model of the properties of bentonite buffer in a repository

    International Nuclear Information System (INIS)

    Liu, Jinsong; Neretnieks, I.

    1996-11-01

    Two mechanisms that can affect the long-term properties of the bentonite buffer surrounding the canister in a final repository of spent nuclear fuel are studied. The two mechanisms are the oxidation of reducing minerals in the buffer by radiolytically generated oxidant, and the low-temperature alteration of Na-montmorillonite in the bentonite buffer to illite. A coupled mass transport with geochemical reaction model is used. Four cases have been considered, which differ in the assumptions of whether the radiolytically generated oxidant first oxidizes uraninite in the spent fuel, or it is directly transported to the bentonite to oxidize the pyrite. The cases also differ in the assumptions of varying initial concentrations of pyrite in the bentonite buffer. The modelling results show that, at low temperatures, the sodium montmorillonite in the bentonite buffer is chemically stable with respect to the chemical conditions of the near field. Alteration to illite and thus an increase in hydraulic conductivity and loss of swelling ability is not likely to occur. The radiolytically generated oxidant can possibly oxidize the reducing minerals in the bentonite buffer. A redox front can be generated. In all the cases considered in this study, the modelling results indicate that slightly less than 1% by weight of pyrite in the bentonite buffer will be able to ensure that the redox front does not penetrate through the bentonite buffer within 1 million years. 31 refs

  16. Simulating Salt Movement using a Coupled Salinity Transport Model in a Variably Saturated Agricultural Groundwater System

    Science.gov (United States)

    Tavakoli Kivi, S.; Bailey, R. T.; Gates, T. K.

    2017-12-01

    Salinization is one of the major concerns in irrigated agricultural fields. Increasing salinity concentrations are due principally to a high water table that results from excessive irrigation, canal seepage, and a lack of efficient drainage systems, and lead to decreasing crop yield. High groundwater salinity loading to nearby river systems also impacts downstream areas, with saline river water diverted for application on irrigated fields. To assess the different strategies for salt remediation, we present a reactive transport model (UZF-RT3D) coupled with a salinity equilibrium chemistry module for simulating the fate and transport of salt ions in a variably-saturated agricultural groundwater system. The developed model accounts not for advection, dispersion, nitrogen and sulfur cycling, oxidation-reduction, sorption, complexation, ion exchange, and precipitation/dissolution of salt minerals. The model is applied to a 500 km2 region within the Lower Arkansas River Valley (LARV) in southeastern Colorado, an area acutely affected by salinization in the past few decades. The model is tested against salt ion concentrations in the saturated zone, total dissolved solid concentrations in the unsaturated zone, and salt groundwater loading to the Arkansas River. The model now can be used to investigate salinity remediation strategies.

  17. Coupling between particle and heat transport during power modulation experiments in Tore Supra

    Energy Technology Data Exchange (ETDEWEB)

    Zou, X.L.; Giruzzi, G.; Artaud, J.F.; Bouquey, F.; Bremond, S.; Clary, J.; Darbos, C.; Eury, S.P.; Lennholm, M.; Magne, R.; Segui, J.L

    2004-07-01

    Power modulations are a powerful tool often used to investigate heat transport processes in tokamaks. In some situations, this could also be an interesting method for the investigation of the particle transport due to the anomalous pinch. Low frequency ({approx} 1 Hz) power modulation experiments, using both electron cyclotron resonance heating (ECRH) and ion cyclotron resonance heating (ICRH), have been performed in the Tore Supra tokamak. Strong coupling has been observed between the temperature and density modulations during the low frequency ECRH and ICRH modulation experiments. It has been shown that mechanisms as outgassing, Ware pinch effect, curvature driven pinch are not likely to be responsible for this density modulation. Because of its dependence on temperature or temperature gradient, the thermodiffusion is a serious candidate to be the driving source for this density modulation. This analysis shows that low frequency power modulation experiments have a great potential for the investigation of the anomalous particle pinch in tokamaks. Future plans will include the use of more precise density profile measurements using X-mode reflectometry.

  18. Three-Dimensional Network Model for Coupling of Fracture and Mass Transport in Quasi-Brittle Geomaterials

    Directory of Open Access Journals (Sweden)

    Peter Grassl

    2016-09-01

    Full Text Available Dual three-dimensional networks of structural and transport elements were combined to model the effect of fracture on mass transport in quasi-brittle geomaterials. Element connectivity of the structural network, representing elasticity and fracture, was defined by the Delaunay tessellation of a random set of points. The connectivity of transport elements within the transport network was defined by the Voronoi tessellation of the same set of points. A new discretisation strategy for domain boundaries was developed to apply boundary conditions for the coupled analyses. The properties of transport elements were chosen to evolve with the crack opening values of neighbouring structural elements. Through benchmark comparisons involving non-stationary transport and fracture, the proposed dual network approach was shown to be objective with respect to element size and orientation.

  19. Phase-coherent transport and spin-orbit-coupling in III/V-semiconductor nanowires

    International Nuclear Information System (INIS)

    Estevez Hernandez, Sergio

    2009-01-01

    Semiconductor nanowires fabricated by a bottom-up approach are not only interesting for the realization of future nanoscaled devices but also appear to be very attractive model systems to tackle fundamental questions concerning the transport in strongly confined systems. In order to avoid the problem connected with carrier depletion, narrowband gap semiconductors, i.e., InAs or InN, or core-shell Nanowires, i.e., GaAs/AlGaAs, are preferred. The underlying reason is that in InAs or InN the Fermi-level pinning in the conduction band results in a carrier accumulation at the surface. In fact, the tubular topology of the surface electron gas opens up the possibility to observe unconventional quantum transport phenomena. When the phase-coherence length in the nanowire is comparable to its dimensions the conductance fluctuates if a magnetic field is applied or if the electron concentration is changed by means of a gate electrode. These so-called universal conductance fluctuations being in the order of e 2 /h originate from the fact that in small disordered samples, electron interference effects are not averaged out. In this work are analyzed universal conductance fluctuations to study the quantum transport properties in InN, InAs and GaAs/AlGaAs nanowires. With the use of a magnetic field and a back-gate electrode the universal conductance fluctuations and localizations effects were analyzed. Since InN and InAs are narrow band gap semiconductors, one naturally expects spin-orbit coupling effects. Because this phenomena is of importance for spin electronic applications. However, owing to the cylindrical symmetry of the InN and InAs nanowires, the latter effect was observable and actually be used to determine the strength of spin-orbit coupling. In order to clearly separate the weak antilocalization effect from the conductance fluctuations, the averaging of the magnetoconductance at different gate voltages was essential. The low-temperature quantum transport properties of

  20. Solute transport in coupled inland-coastal water systems. General conceptualisation and application to Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Jarsjoe, Jerker; Destouni, Georgia; Persson, Klas; Prieto, Carmen (Dept. of Physical Geography, Quaternary Geology, Stockholm Univ., Stockholm (Sweden))

    2007-12-15

    diffuse and occurring through SGD, small transient streams and/or coastal wetlands. Regarding transport quantifications, hydrogeochemical characteristics and pollution source loads may generally differ between larger, monitored catchments and smaller unmonitored coastal catchments. Since national hydrological monitoring data systematically exclude smaller, coastal catchments, they may not be representative for conditions in Forsmark (or Laxemar-Simpevarp). This emphasises the importance of extending in time the recently started hydrological and hydrogeochemical data series in the Forsmark and Laxemar-Simpevarp coastal catchment areas, since they are in effect unmonitored from a hydrological viewpoint, due to the lack of extended discharge time series. In the performed initial demonstration analysis of solute transport pathways from deep groundwater to recipients at the surface, we considered the main scenarios: (I) transport in the Quaternary deposits-bedrock interface zone only, and (II) transport in the coupled groundwater-surface water system. Considering mean travel times from each model cell to the coast, and disregarding travel times in the deep bedrock domain itself (which may be added to the here presented values), results show that travel times in scenario (II) were less than 4 years in 90% of the considered model area. Travel times were longer in scenario (I) with values higher than 10 years in 40% of the catchment area. These results are based on the assumption that the pathways do not go through zones of near-stagnant groundwater. If they would do so (and the above assumption is violated), results show that travel times can be considerably longer, for instance exceeding 400 years in half of the model area in scenario (I). Considering possible solute attenuation (caused by e.g. biogeochemical reactions or decay) along the hydrological transport pathways to inland surface waters and to the coast, we estimate solute mass delivery factors, representing the

  1. Coupled UV-exposure and microbial decomposition improves measures of organic matter degradation and light models in humic lake

    DEFF Research Database (Denmark)

    Madsen-Østerbye, Mikkel; Kragh, Theis; Pedersen, Ole

    2018-01-01

    Increasing terrestrial input of colored dissolved organic matter (CDOM) to temperate softwater lakes has reduced transparency, distribution of pristine rosette plants and overall biodiversity in recent decades. We examined microbial and UV-induced reduction of absorption by CDOM and dissolved org...

  2. Illumina sequencing-based analysis of a microbial community enriched under anaerobic methane oxidation condition coupled to denitrification revealed coexistence of aerobic and anaerobic methanotrophs.

    Science.gov (United States)

    Siniscalchi, Luciene Alves Batista; Leite, Laura Rabelo; Oliveira, Guilherme; Chernicharo, Carlos Augusto Lemos; de Araújo, Juliana Calabria

    2017-07-01

    Methane is produced in anaerobic environments, such as reactors used to treat wastewaters, and can be consumed by methanotrophs. The composition and structure of a microbial community enriched from anaerobic sewage sludge under methane-oxidation condition coupled to denitrification were investigated. Denaturing gradient gel electrophoresis (DGGE) analysis retrieved sequences of Methylocaldum and Chloroflexi. Deep sequencing analysis revealed a complex community that changed over time and was affected by methane concentration. Methylocaldum (8.2%), Methylosinus (2.3%), Methylomonas (0.02%), Methylacidiphilales (0.45%), Nitrospirales (0.18%), and Methanosarcinales (0.3%) were detected. Despite denitrifying conditions provided, Nitrospirales and Methanosarcinales, known to perform anaerobic methane oxidation coupled to denitrification (DAMO) process, were in very low abundance. Results demonstrated that aerobic and anaerobic methanotrophs coexisted in the reactor together with heterotrophic microorganisms, suggesting that a diverse microbial community was important to sustain methanotrophic activity. The methanogenic sludge was a good inoculum to enrich methanotrophs, and cultivation conditions play a selective role in determining community composition.

  3. Hydrology and phosphorus transport simulation in a lowland polder by a coupled modeling system.

    Science.gov (United States)

    Yan, Renhua; Huang, Jiacong; Li, Lingling; Gao, Junfeng

    2017-08-01

    Modeling the rain-runoff processes and phosphorus transport processes in lowland polders is critical in finding reasonable measures to alleviate the eutrophication problem of downstream rivers and lakes. This study develops a lowland Polder Hydrology and Phosphorus modeling System (PHPS) by coupling the WALRUS-paddy model and an improved phosphorus module of a Phosphorus Dynamic model for lowland Polder systems (PDP). It considers some important hydrological characteristics, such as groundwater-unsaturated zone coupling, groundwater-surface water feedback, human-controlled irrigation and discharge, and detailed physical and biochemical cycles of phosphorus in surface water. The application of the model in the Jianwei polder shows that the simulated phosphorus matches well with the measured values. The high precision of this model combined with its low input data requirement and efficient computation make it practical and easy to the water resources management of Chinese polders. Parameter sensitivity analysis demonstrates that K uptake , c Q2 , c W1 , and c Q1 exert a significant effect on the modeled results, whereas K resuspensionMax , K settling , and K mineralization have little effect on the modeled total phosphorus. Among the three types of uncertainties (i.e., parameter, initial condition, and forcing uncertainties), forcing uncertainty produces the strongest effect on the simulated phosphorus. Based on the analysis result of annual phosphorus balance when considering the high import from irrigation and fertilization, lowland polder is capable of retaining phosphorus and reducing phosphorus export to surrounding aquatic ecosystems because of their special hydrological regulation regime. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Calcium-Mediated Regulation of Proton-Coupled Sodium Transport - Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Schumaker, Karen S [Professor

    2013-10-24

    The long-term goal of our experiments was to understand mechanisms that regulate energy coupling by ion currents in plants. Activities of living organisms require chemical, mechanical, osmotic or electrical work, the energy for which is supplied by metabolism. Adenosine triphosphate (ATP) has long been recognized as the universal energy currency, with metabolism supporting the synthesis of ATP and the hydrolysis of ATP being used for the subsequent work. However, ATP is not the only energy currency in living organisms. A second and very different energy currency links metabolism to work by the movement of ions passing from one side of a membrane to the other. These ion currents play a major role in energy capture and they support a range of physiological processes from the active transport of nutrients to the spatial control of growth and development. In Arabidopsis thaliana (Arabidopsis), the activity of a plasma membrane Na+/H+ exchanger, SALT OVERLY SENSITIVE1 (SOS1), is essential for regulation of sodium ion homeostasis during plant growth in saline conditions. Mutations in SOS1 result in severely reduced seedling growth in the presence of salt compared to the growth of wild type. SOS1 is a secondary active transporter coupling movement of sodium ions out of the cell using energy stored in the transplasma membrane proton gradient, thereby preventing the build-up of toxic levels of sodium in the cytosol. SOS1 is regulated by complexes containing the SOS2 and CALCINEURIN B-LIKE10 (CBL10) or SOS3 proteins. CBL10 and SOS3 (also identified as CBL4) encode EF-hand calcium sensors that interact physically with and activate SOS2, a serine/threonine protein kinase. The CBL10/SOS2 or SOS3/SOS2 complexes then activate SOS1 Na+/H+ exchange activity. We completed our studies to understand how SOS1 activity is regulated. Specifically, we asked: (1) how does CBL10 regulate SOS1 activity? (2) What role do two putative CBL10-interacting proteins play in SOS1 regulation? (3) Are

  5. Sodium-coupled neutral amino acid (System N/A) transporters of the SLC38 gene family.

    Science.gov (United States)

    Mackenzie, Bryan; Erickson, Jeffrey D

    2004-02-01

    The sodium-coupled neutral amino acid transporters (SNAT) of the SLC38 gene family resemble the classically-described System A and System N transport activities in terms of their functional properties and patterns of regulation. Transport of small, aliphatic amino acids by System A subtypes (SNAT1, SNAT2, and SNAT4) is rheogenic and pH sensitive. The System N subtypes SNAT3 and SNAT5 also countertransport H(+), which may be key to their operation in reverse, and have narrower substrate profiles than do the System A subtypes. Glutamine emerges as a favored substrate throughout the family, except for SNAT4. The SLC38 transporters undoubtedly play many physiological roles including the transfer of glutamine from astrocyte to neuron in the CNS, ammonia detoxification and gluconeogenesis in the liver, and the renal response to acidosis. Probing their regulation has revealed additional roles, and recent work has considered SLC38 transporters as therapeutic targets in neoplasia.

  6. Transport of amino acids and GABA analogues via the human proton-coupled amino acid transporter, hPAT1

    DEFF Research Database (Denmark)

    Larsen, Mie; Larsen, Birger Brodin; Frølund, Bente

    2008-01-01

    The objective of this study was to investigate transepithelial amino acid transport as a function of Caco-2 cell culture time. Furthermore, the objective was to investigate apical uptake characteristics of hPAT1-mediated transport under various experimental conditions. Apical amino acid uptake......, which has been shown to function as a carboxylic acid bioisostere for substrates of the GABA receptor and transport systems....

  7. Gate tunable spin transport in graphene with Rashba spin-orbit coupling

    Science.gov (United States)

    Tan, Xiao-Dong; Liao, Xiao-Ping; Sun, Litao

    2016-10-01

    Recently, it attracts much attention to study spin-resolved transport properties in graphene with Rashba spin-orbit coupling (RSOC). One remarkable finding is that Klein tunneling in single layer graphene (SLG) with RSOC (SLG + R for short below) behaves as in bi-layer graphene (BLG). Based on the effective Dirac theory, we reconsider this tunneling problem and derive the analytical solution for the transmission coefficients. Our result shows that Klein tunneling in SLG + R and BLG exhibits completely different behaviors. More importantly, we find two new transmission selection rules in SLG + R, i.e., the single band to single band (S → S) and the single band to multiple bands (S → M) transmission regimes, which strongly depend on the relative height among Fermi level, RSOC, and potential barrier. Interestingly, in the S → S transmission regime, only normally incident electrons have capacity to pass through the barrier, while in the S → M transmission regime the angle-dependent tunneling becomes very prominent. Using the transmission coefficients, we also derive spin-resolved conductance analytically, and conductance oscillation with the increasing barrier height and zero conductance gap are found in SLG + R. The present study offers new insights and opportunities for developing graphene-based spin devices.

  8. Interband coupling and transport interband scattering in s± superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Kogan, Vladimir [Ames Lab., Ames, IA (United States); Prozorov, Ruslan [Ames Lab., Ames, IA (United States); Iowa State Univ., Ames, IA (United States)

    2016-04-04

    A two-band model with repulsive interband coupling and interband transport (potential) scattering is considered to elucidate their effects on material properties. In agreement with previous work, we find that the bands order parameters Δ1,2 differ and the large is at the band with a smaller normal density of states (DOS), Nn2 < Nn1. However, the bands energy gaps, as determined by the energy dependence of the DOS, are equal due to scattering. For each temperature, the gaps turn zero at a certain critical interband scattering rate, i.e. for strong enough scattering the model material becomes gappless. In the gapless state, the DOS at the band 2 is close to the normal state value, whereas at the band 1 it has a V-shape with non-zero minimum. When the normal bands DOS' are mismatched, Nn1 6= Nn2, the critical temperature Tc is suppressed even in the absence of interband scattering, Tc(Nn1) has a dome-like shape. With increasing interband scattering, the London penetration depth at low temperatures evolves from being exponentially at to the powerlaw and even to near linear behavior in the gapless state, the latter being easily misinterpreted as caused by order parameter nodes.

  9. Transport in semiconductor nanowire superlattices described by coupled quantum mechanical and kinetic models.

    Science.gov (United States)

    Alvaro, M; Bonilla, L L; Carretero, M; Melnik, R V N; Prabhakar, S

    2013-08-21

    In this paper we develop a kinetic model for the analysis of semiconductor superlattices, accounting for quantum effects. The model consists of a Boltzmann-Poisson type system of equations with simplified Bhatnagar-Gross-Krook collisions, obtained from the general time-dependent Schrödinger-Poisson model using Wigner functions. This system for superlattice transport is supplemented by the quantum mechanical part of the model based on the Ben-Daniel-Duke form of the Schrödinger equation for a cylindrical superlattice of finite radius. The resulting energy spectrum is used to characterize the Fermi-Dirac distribution that appears in the Bhatnagar-Gross-Krook collision, thereby coupling the quantum mechanical and kinetic parts of the model. The kinetic model uses the dispersion relation obtained by the generalized Kronig-Penney method, and allows us to estimate radii of quantum wire superlattices that have the same miniband widths as in experiments. It also allows us to determine more accurately the time-dependent characteristics of superlattices, in particular their current density. Results, for several experimentally grown superlattices, are discussed in the context of self-sustained coherent oscillations of the current density which are important in an increasing range of current and potential applications.

  10. Sensitivity of Deep Soil Organic Carbon Age to Sorption, Transport and Microbial Interactions - Insights from a Calibrated Process Model

    Science.gov (United States)

    Ahrens, B.; Schrumpf, M.; Reichstein, M.

    2013-12-01

    Subsoil soil organic carbon (SOC) is characterized by conventional radiocarbon ages on the order of centuries to millennia. Most vertically explicit SOC turnover models represent this persistence of deep SOC by one pool that has millennial turnover times. This approach lumps different stabilizing mechanisms such as chemical recalcitrance, sorptive stabilization and energy limitation into a single rate constant. As an alternative, we present a continuous, vertically explicit SOC decomposition model that allows for stabilization via sorption and microbial interactions (COMISSION model). We compare the COMISSION model with the SOC profile of a Haplic Podzol under a Norway spruce forest. In the COMISSION model two pools receive aboveground litter input and vertically distributed root litter input. The readily leachable and soluble fraction of litter input enters a dissolved organic carbon pool (DOC), while the rest enters the residue pool which represents polymeric, non-soluble SOC. The residue pool is depolymerized with extracellular enzymes produced by a microbial pool to enter the DOC pool which represents SOC potentially available for assimilation by microbes. The adsorption/desorption of DOC from/to mineral surfaces controls the availability of carbon in the DOC pool for assimilatory uptake by microbes. The sorption of DOC is modeled with dynamic Langmuir equations. The desorbed part of the DOC pool not only constitutes the substrate for the microbial pool, but is also transported via advection. Interactions of microbes with the residue and DOC pool are modeled with Michaelis-Menten kinetics - this not only allows representing ';priming', but also the retardation of decomposition via energy limitation in the deep soil where substrate is scarce. Further, soil organic matter is recycled within the soil profile through microbial processing - dead microbes either enter the DOC or the residue pool, and thereby also contribute to longer residence times with soil depth

  11. Metal Transport, Heavy Metal Speciation and Microbial Fixation Through Fluvial Subenvironments, Lower Coeur D'Alene River Valley, Idaho

    Science.gov (United States)

    Hooper, R. L.; Mahoney, J. B.

    2001-12-01

    The lower Coeur d'Alene River Valley of northern Idaho is the site of extensive lead and zinc contamination resulting from both direct riverine tailings disposal and flood remobilization of contaminated sediments derived from the Coeur d'Alene mining district upstream. Variations in the hydrologic regime, redox conditions, porosity/permeability, organic content and microbial activity results in complicated metal transport pathways. Documentation of these pathways is a prerequisite to effective remediation, and requires accurate analysis of lateral and vertical variations. An analytical approach combining sequential extraction, electron microscopy, and microanalysis provides a comprehensive assessment of particulate speciation in this complex hydrologic system. Rigorously controlled sample preparation and a new sequential extraction protocol provide unprecedented insight into the role of metal sequestration in fluvial subenvironments. Four subenvironments were investigated: bedload, overbank (levee), marsh, and lacustrine. Periodic floods remobilize primary ore minerals and secondary minerals from upstream tailings (primarily oxyhydroxides, sulfides and carbonates). The bedload in the lower valley is a reducing environment and acts as a sink for detrital carbonates and sulfides moving downstream. In addition, authigenic/biogenic Fe, Pb and Zn sulfides and phosphates are common in bedload sediments near the sediment/water interface. Flood redistribution of oxide, sulfide and carbonate phases results in periodic contaminant recharge generating a complex system of metal dissolution, mobilization, migration and precipitation. In levee environments, authigenic sulfides from flood scouring are quickly oxidized resulting in development of oxide coated grain surfaces. Stability of detrital minerals on the levee is variable depending on sediment permeability, grain size and mineralogy resulting in a complex stratigraphy of oxide zones mottled with zones dominated by detrital

  12. Coupled Metagenomic and Chemical Analyses of Degrading Fungal Necromass and Implications for Microbial Contributions to Stable Soil OC

    Science.gov (United States)

    Schreiner, K. M.; Morgan, B. S. T.; Schultz, J.; Blair, N. E.; Egerton-Warburton, L. M.

    2014-12-01

    Fungi comprise a significant portion of total soil biomass, the turnover of which must represent a dominant flux within the soil carbon cycle. Fungal OC can turn over on time scales of days to months, but this process is poorly understood. Here, we examined temporal changes in the chemical and microbial community composition of fungal necromass during a 2 month decomposition experiment in which Fusarium avenaceum (a common saprophyte) was exposed to a natural soil microbial community. Over the course of the experiment, residual fungal necromass was harvested and analyzed using FTIR and thermochemolysis-GCMS to examine chemical changes in the tissue. Additionally, genomic DNA was extracted from tissues, amplified with barcoded ITS primers, and sequenced using the high-throughput Illumina platform to examine changes in microbial community composition. Up to 80% of the fungal necromass turned over in the first week. This rapid degradation phase corresponded to colonization of the necromass by known chitinolytic soil fungi including Mortierella species. Zygomycetes and Ascomycetes were among the dominant fungal species involved in degradation with very small contributions from Basidiomycetes. At the end of the 2 month degradation, only 15% of the original necromass remained. The residual material was rich in amide and C-O moieties which is consistent with previous work predicting that peptidoglycans are the main residual product from microbial tissue degradation. Straight-chain fatty acids exhibit varying degradation profiles, with some fatty acids (e.g. C16 and C18:1) degrading more rapidly than bulk tissue, others maintaining steady concentrations relative to bulk OC (e.g. C18), and some increasing in concentration throughout the degradation (e.g. C24). These results indicate that the turnover of fungal necromass has the potential to significantly influence a variety of soil OC properties, including C/N ratios, lipid biomarker distributions, and OC turnover times.

  13. Modeling coupled thermal, flow, transport and geochemical processes controlling near field long-term evolution

    International Nuclear Information System (INIS)

    Zhou, W.; Arthur, R.; Xu, T.; Pruess, K.

    2005-01-01

    Full text of publication follows: Bentonite is planned for use as a buffer material in the Swedish nuclear waste disposal concept (KBS-3). Upon emplacement, the buffer is expected to experience a complex set of coupled processes involving heating, re-saturation, reaction and transport of groundwater imbibed from the host rock. The effect of these processes may eventually lead to changes in desirable physical and rheological properties of the buffer, but these processes are not well understood. In this paper, a new quantitative model is evaluated to help improve our understanding of the long-term performance of buffer materials. This is an extension of a previous study [1] that involved simple thermal and chemical models applied to a fully saturated buffer. The thermal model in the present study uses heating histories for spent fuel in a single waste package [2]. The model uses repository dimensions, such as borehole and tunnel spacings [2], which affect the temperature distribution around the waste package. At the time of emplacement, bentonite is partially saturated with water having a different composition than the host-rock groundwater. The present model simulates water imbibition from the host rock into the bentonite under capillary and hydraulic pressure gradients. The associated chemical reactions and solute transport are simulated using Aespoe water composition [3]. The initial mineralogy of bentonite is assumed to be dominated by Na-smectite with much smaller amounts of anhydrite and calcite. Na-smectite dissolution is assumed to be kinetically-controlled while all other reactions are assumed to be at equilibrium controlled. All equilibrium and kinetic constants are temperature dependent. The modeling tool used is TOUGHREACT, developed by Lawrence Berkeley National Laboratory [4]. TOUGHREACT is a numerical model that is well suited for near-field simulations because it accounts for feedback between porosity and permeability changes from mineral

  14. Coupled transport and chemistry in clay stone studied by advective displacement: experiments and model

    International Nuclear Information System (INIS)

    Landesman, C.; Grambow, B.; Bailly, C.; Ribet, S.; Perrigaud, K.; Baty, V.; Giffaut, E.

    2010-01-01

    Document available in extended abstract form only. Full text of publication entered in this record. For assessing the mass transfer resistance of the Callovo-Oxfordian clay rock formation in case of implementing a nuclear waste repository, various strongly coupled processes need to be understood and quantified both in near and far field: multi-species diffusion/advection, mineral/pore water interaction, interaction with the waste matrix and engineered barrier material, radionuclide retention, colloid transport, pore water chemistry evolution etc. To study many of these processes in their interrelationship simultaneously, a series of high pressure stainless steel advection cell was designed and clay cores from different locations of different calcite and clay contents were machined to fit the inner diameter of the cells with a precision of 50 μm. After assembling, simulated oxygen free clay pore water with bromine tracer was pushed by a High Pressure pump through the reactor by a pressure of up 100 bars at temperatures between 20 and 90 deg. C and the out-flowing water was collected, protected from air and analyzed by ICP-MS, COT meter and ion chromatography in regular time intervals. The water flow rate was between 0.02 and 1.2 mL/ d, corresponding to a clay rock permeabilities between 10 -12 and 10 -14 m/s at 25 deg. C. Permeabilities increase with temperature as expected due to reduction of viscosity of water. The experiments last up to 2 years. The first drops of out flowing allow estimating the initial pore water composition. This is particular useful to assess mobile natural organic matter contents, Se concentrations and temperature effect on clay water composition. Results show that only very small organic molecules are mobile. Temperature had only little effect on water composition. After few months both tritiated (HTO) water and 36 Cl were added and from the evolution of the activities in the out flowing water dispersion coefficients and accessible

  15. The two Na+ sites in the human serotonin transporter play distinct roles in the ion coupling and electrogenicity of transport.

    Science.gov (United States)

    Felts, Bruce; Pramod, Akula Bala; Sandtner, Walter; Burbach, Nathan; Bulling, Simon; Sitte, Harald H; Henry, L Keith

    2014-01-17

    Neurotransmitter transporters of the SLC6 family of proteins, including the human serotonin transporter (hSERT), utilize Na(+), Cl(-), and K(+) gradients to induce conformational changes necessary for substrate translocation. Dysregulation of ion movement through monoamine transporters has been shown to impact neuronal firing potentials and could play a role in pathophysiologies, such as depression and anxiety. Despite multiple crystal structures of prokaryotic and eukaryotic SLC transporters indicating the location of both (or one) conserved Na(+)-binding sites (termed Na1 and Na2), much remains uncertain in regard to the movements and contributions of these cation-binding sites in the transport process. In this study, we utilize the unique properties of a mutation of hSERT at a single, highly conserved asparagine on TM1 (Asn-101) to provide several lines of evidence demonstrating mechanistically distinct roles for Na1 and Na2. Mutations at Asn-101 alter the cation dependence of the transporter, allowing Ca(2+) (but not other cations) to functionally replace Na(+) for driving transport and promoting 5-hydroxytryptamine (5-HT)-dependent conformational changes. Furthermore, in two-electrode voltage clamp studies in Xenopus oocytes, both Ca(2+) and Na(+) illicit 5-HT-induced currents in the Asn-101 mutants and reveal that, although Ca(2+) promotes substrate-induced current, it does not appear to be the charge carrier during 5-HT transport. These findings, in addition to functional evaluation of Na1 and Na2 site mutants, reveal separate roles for Na1 and Na2 and provide insight into initiation of the translocation process as well as a mechanism whereby the reported SERT stoichiometry can be obtained despite the presence of two putative Na(+)-binding sites.

  16. The Two Na+ Sites in the Human Serotonin Transporter Play Distinct Roles in the Ion Coupling and Electrogenicity of Transport*

    Science.gov (United States)

    Felts, Bruce; Pramod, Akula Bala; Sandtner, Walter; Burbach, Nathan; Bulling, Simon; Sitte, Harald H.; Henry, L. Keith

    2014-01-01

    Neurotransmitter transporters of the SLC6 family of proteins, including the human serotonin transporter (hSERT), utilize Na+, Cl−, and K+ gradients to induce conformational changes necessary for substrate translocation. Dysregulation of ion movement through monoamine transporters has been shown to impact neuronal firing potentials and could play a role in pathophysiologies, such as depression and anxiety. Despite multiple crystal structures of prokaryotic and eukaryotic SLC transporters indicating the location of both (or one) conserved Na+-binding sites (termed Na1 and Na2), much remains uncertain in regard to the movements and contributions of these cation-binding sites in the transport process. In this study, we utilize the unique properties of a mutation of hSERT at a single, highly conserved asparagine on TM1 (Asn-101) to provide several lines of evidence demonstrating mechanistically distinct roles for Na1 and Na2. Mutations at Asn-101 alter the cation dependence of the transporter, allowing Ca2+ (but not other cations) to functionally replace Na+ for driving transport and promoting 5-hydroxytryptamine (5-HT)-dependent conformational changes. Furthermore, in two-electrode voltage clamp studies in Xenopus oocytes, both Ca2+ and Na+ illicit 5-HT-induced currents in the Asn-101 mutants and reveal that, although Ca2+ promotes substrate-induced current, it does not appear to be the charge carrier during 5-HT transport. These findings, in addition to functional evaluation of Na1 and Na2 site mutants, reveal separate roles for Na1 and Na2 and provide insight into initiation of the translocation process as well as a mechanism whereby the reported SERT stoichiometry can be obtained despite the presence of two putative Na+-binding sites. PMID:24293367

  17. CRACKER - a program coupling chemistry and transport. Version 92-11

    Energy Technology Data Exchange (ETDEWEB)

    Emren, A [Chalmers Univ. of Technology, Gothenburg (Sweden). Dept. of Nuclear Technology

    1992-12-01

    CRACKER is a program coupling chemistry and transport. It simulates chemical reactions of groundwater flowing through a plane fracture. Properties like initial composition of the water, mineralogical composition of the rock and temperature gradients and flow velocity of the water serve as input for the modelling. The program is designed to handle heterogeneous rock properties, like redox fronts, regions with different mineralogy etc. It is even able to handle the common situation of a rock violating the phase rule. In the CRACKER model, a rock is formed by a more or less random distribution of minerals across the surfaces of a fracture. Water moves along the fracture (in present version at a constant velocity). No diffusion parallel to the flow direction is simulated. CRACKER is a package of several programs, most of them written in C. Chemical equilibrium calculations are mostly performed by the well-known geochemical program PHREEQE. The main program, CRACKER, manages information flow and determines which subprograms to use for specific tasks. Further it is responsible for the user interface. Essentially a simulation proceeds by alternate call to the HACKER and PHREEQE subprograms. HACKER is responsible for generating the rock, water propagation, mixing of waters and sampling the results. PHREEQE is used to solve the chemical equilibrium equations. The directory structure and the data structures used by CRACKER are described in separate sections. Further, the different subprograms are described with respect to purposes and methods used to handle the problems. The purpose of each first level function in the subprograms is described. (author).

  18. CRACKER - a program coupling chemistry and transport. Version 92-11

    International Nuclear Information System (INIS)

    Emren, A.

    1992-12-01

    CRACKER is a program coupling chemistry and transport. It simulates chemical reactions of groundwater flowing through a plane fracture. Properties like initial composition of the water, mineralogical composition of the rock and temperature gradients and flow velocity of the water serve as input for the modelling. The program is designed to handle heterogeneous rock properties, like redox fronts, regions with different mineralogy etc. It is even able to handle the common situation of a rock violating the phase rule. In the CRACKER model, a rock is formed by a more or less random distribution of minerals across the surfaces of a fracture. Water moves along the fracture (in present version at a constant velocity). No diffusion parallel to the flow direction is simulated. CRACKER is a package of several programs, most of them written in C. Chemical equilibrium calculations are mostly performed by the well-known geochemical program PHREEQE. The main program, CRACKER, manages information flow and determines which subprograms to use for specific tasks. Further it is responsible for the user interface. Essentially a simulation proceeds by alternate call to the HACKER and PHREEQE subprograms. HACKER is responsible for generating the rock, water propagation, mixing of waters and sampling the results. PHREEQE is used to solve the chemical equilibrium equations. The directory structure and the data structures used by CRACKER are described in separate sections. Further, the different subprograms are described with respect to purposes and methods used to handle the problems. The purpose of each first level function in the subprograms is described. (author)

  19. Coupling between solute transport and chemical reactions models. Acoplamiento de modelos de transporte de solutos y de modelos de reacciones quimicas

    Energy Technology Data Exchange (ETDEWEB)

    Samper, J.; Ajora, C. (Instituto de Ciencias de la Tierra, CSIC, Barcerlona (Spain))

    1993-01-01

    During subsurface transport, reactive solutes are subject to a variety of hydrodynamic and chemical processes. The major hydrodynamic processes include advection and convection, dispersion and diffusion. The key chemical processes are complexation including hydrolysis and acid-base reactions, dissolution-precipitation, reduction-oxidation, adsorption and ion exchange. The combined effects of all these processes on solute transport must satisfy the principle of conservation of mass. The statement of conservation of mass for N mobile species leads to N partial differential equations. Traditional solute transport models often incorporate the effects of hydrodynamic processes rigorously but oversimplify chemical interactions among aqueous species. Sophisticated chemical equilibrium models, on the other hand, incorporate a variety of chemical processes but generally assume no-flow systems. In the past decade, coupled models accounting for complex hydrological and chemical processes, with varying degrees of sophistication, have been developed. The existing models of reactive transport employ two basic sets of equations. The transport of solutes is described by a set of partial differential equations, and the chemical processes, under the assumption of equilibrium, are described by a set of nonlinear algebraic equations. An important consideration in any approach is the choice of primary dependent variables. Most existing models cannot account for the complete set of chemical processes, cannot be easily extended to include mixed chemical equilibria and kinetics, and cannot handle practical two and three dimensional problems. The difficulties arise mainly from improper selection of the primary variables in the transport equations. (Author) 38 refs.

  20. The natural diet of a hexactinellid sponge: Benthic pelagic coupling in a deep-sea microbial food web

    Science.gov (United States)

    Pile, Adele J.; Young, Craig M.

    2006-07-01

    Dense communities of shallow-water suspension feeders are known to sidestep the microbial loop by grazing on ultraplankton at its base. We quantified the diet, rates of water processing, and abundance of the deep-sea hexactinellid sponge Sericolophus hawaiicus, and found that, like their demosponge relatives in shallow water, hexactinellids are a significant sink for ultraplankton. S. hawaiicus forms a dense bed of sponges on the Big Island of Hawaii between 360 and 460 m depth, with a mean density of 4.7 sponges m -2. Grazing of S. hawaiicus on ultraplankton was quantified from in situ samples using flow cytometry, and was found to be unselective. Rates of water processing were determined with dye visualization and ranged from 1.62 to 3.57 cm s -1, resulting in a processing rate of 7.9±2.4 ml sponge -1 s -1. The large amount of water processed by these benthic suspension feeders results in the transfer of approximately 55 mg carbon and 7.3 mg N d -1 m -2 from the water column to the benthos. The magnitude of this flux places S. hawaiicus squarely within the functional group of organisms that link the pelagic microbial food web to the benthos.

  1. Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from Guaymas Basin

    Directory of Open Access Journals (Sweden)

    Ying eHe

    2013-06-01

    Full Text Available Deep-sea hydrothermal vent chimneys contain a high diversity of microorganisms, yet the metabolic activity and the ecological functions of the microbial communities remain largely unexplored. In this study, a metagenomic approach was applied to characterize the metabolic potential in a Guaymas hydrothermal vent chimney and to conduct comparative genomic analysis among a variety of environments with sequenced metagenomes. Complete clustering of functional gene categories with a comparative metagenomic approach showed that this Guaymas chimney metagenome was clustered most closely with a chimney metagenome from Juan de Fuca. All chimney samples were enriched with genes involved in recombination and repair, chemotaxis and flagellar assembly, highlighting their roles in coping with the fluctuating extreme deep-sea environments. A high proportion of transposases was observed in all the metagenomes from deep-sea chimneys, supporting the previous hypothesis that horizontal gene transfer may be common in the deep-sea vent chimney biosphere. In the Guaymas chimney metagenome, thermophilic sulfate reducing microorganisms including bacteria and archaea were found predominant, and genes coding for the degradation of refractory organic compounds such as cellulose, lipid, pullullan, as well as a few hydrocarbons including toluene, ethylbenzene and o-xylene were identified. Therefore, this oil-immersed chimney supported a thermophilic microbial community capable of oxidizing a range of hydrocarbons that served as electron donors for sulphate reduction under anaerobic conditions.

  2. ITS Version 3.0: The Integrated TIGER Series of coupled electron/photon Monte Carlo transport codes

    International Nuclear Information System (INIS)

    Halbleib, J.A.; Kensek, R.P.; Valdez, G.D.; Mehlhorn, T.A.; Seltzer, S.M.; Berger, M.J.

    1993-01-01

    ITS is a powerful and user-friendly software package permitting state-of-the-art Monte Carlo solution of linear time-independent coupled electron/photon radiation transport problems, with or without the presence of macroscopic electric and magnetic fields. It combines operational simplicity and physical accuracy in order to provide experimentalists and theorists alike with a method for the routine but rigorous solution of sophisticated radiation transport problems. Flexibility of construction permits tailoring of the codes to specific applications and extension of code capabilities to more complex applications through simple update procedures

  3. ITS Version 3.0: The Integrated TIGER Series of coupled electron/photon Monte Carlo transport codes

    Energy Technology Data Exchange (ETDEWEB)

    Halbleib, J.A.; Kensek, R.P.; Valdez, G.D.; Mehlhorn, T.A. [Sandia National Labs., Albuquerque, NM (United States); Seltzer, S.M.; Berger, M.J. [National Inst. of Standards and Technology, Gaithersburg, MD (United States). Ionizing Radiation Div.

    1993-06-01

    ITS is a powerful and user-friendly software package permitting state-of-the-art Monte Carlo solution of linear time-independent coupled electron/photon radiation transport problems, with or without the presence of macroscopic electric and magnetic fields. It combines operational simplicity and physical accuracy in order to provide experimentalists and theorists alike with a method for the routine but rigorous solution of sophisticated radiation transport problems. Flexibility of construction permits tailoring of the codes to specific applications and extension of code capabilities to more complex applications through simple update procedures.

  4. Woody debris transport modelling by a coupled DE-SW approach

    Science.gov (United States)

    Persi, Elisabetta; Petaccia, Gabriella; Sibilla, Stefano

    2016-04-01

    The presence of wood in rivers is gaining more and more attention: on one side, the inclusion of woody debris in streams is emphasized for its ecological benefits; on the other hand, particular attention must be paid to its management, not to affect hydraulic safety. Recent events have shown that wood can be mobilized during floodings (Comiti et al. 2008, Lange and Bezzola 2006), aggravating inundations, in particular near urban areas. For this reason, the inclusion of woody debris influence on the prediction of flooded areas is an important step toward the reduction of hydraulic risk. Numerical modelling plays an important role to this purpose. Ruiz-Villanueva et al. (2014) use a two-dimensional numerical model to calculate the kinetics of cylindrical woody debris transport, taking into account also the hydrodynamic effects of wood. The model here presented couples a Discrete Element approach (DE) for the calculation of motion of a cylindrical log with the solution of the Shallow Water Equations (SW), in order to simulate woody debris transport in a two-dimensional stream. In a first step, drag force, added mass force and side force are calculated from flow and log velocities, assuming a reference area and hydrodynamic coefficients taken from literature. Then, the equations of dynamics are solved to model the planar roto-translation of the wooden cylinder. Model results and its physical reliability are clearly affected by the values of the drag and side coefficients, which in turn depend upon log submergence and angle towards the flow direction. Experimental studies to evaluate drag and side coefficients can be found for a submerged cylinder, with various orientations (Gippel et al. 1996; Hoang et al. 2015). To extend such results to the case of a floating (non-totally submerged) cylinder, the authors performed a series of laboratory tests whose outcomes are implemented in the proposed DE-SW model, to assess the effects of these values on the dynamic of woody

  5. Characteristics of nonlocally-coupled transition of the heat transport in LHD

    International Nuclear Information System (INIS)

    Tamura, N.; Ida, K.; Tanaka, K.; Tokuzawa, T.; Itoh, K.; Shimozuma, T.; Kubo, S.; Tsuchiya, H.; Nagayama, Y.; Kawahata, K.; Sudo, S.; Yamada, H.; Inagaki, S.

    2010-01-01

    A comparison of characteristics between a nonlocal transport phenomenon and an electron internal transport barrier (ITB) in the Large Helical Device is performed with a transient transport analysis and from the viewpoint of a dynamic behavior of transport state. The electron ITB is characterized by a jump of electron temperature gradient. In contrast, the transient transport analysis indicates the nonlocal transport phenomenon is characterized by a jump of electron heat flux. And seen from the viewpoint of the dynamic behavior of transport state, the physical mechanism of the appearance of the nonlocal transport phenomenon is found to be qualitatively different from that of the formation of the electron ITB. (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  6. Peptide Selectivity of the Proton-Coupled Oligopeptide Transporter from Neisseria meningitidis

    DEFF Research Database (Denmark)

    Sharma, Neha; Aduri, Nanda G; Iqbal, Anna

    2016-01-01

    POT). It has been shown that the gene encoding this transporter is upregulated during infection. NmPOT conformed to the typical chain length preference as observed in prototypical transporters of this family. In contrast to prototypical transporters, it was unable to accommodate a positively charged peptide...

  7. Optimizing the design of large-scale ground-coupled heat pump systems using groundwater and heat transport modeling

    Energy Technology Data Exchange (ETDEWEB)

    Fujii, H.; Itoi, R.; Fujii, J. [Kyushu University, Fukuoka (Japan). Faculty of Engineering, Department of Earth Resources Engineering; Uchida, Y. [Geological Survey of Japan, Tsukuba (Japan)

    2005-06-01

    In order to predict the long-term performance of large-scale ground-coupled heat pump (GCHP) systems, it is necessary to take into consideration well-to-well interference, especially in the presence of groundwater flow. A mass and heat transport model was developed to simulate the behavior of this type of system in the Akita Plain, northern Japan. The model was used to investigate different operational schemes and to maximize the heat extraction rate from the GCHP system. (author)

  8. Coupling ANIMO and MT3DMS for 3D regional-scale modeling of nutrient transport in soil and groundwater

    Science.gov (United States)

    Janssen, G.; Del Val Alonso, L.; Groenendijk, P.; Griffioen, J.

    2012-12-01

    We developed an on-line coupling between the 1D/quasi-2D nutrient transport model ANIMO and the 3D groundwater transport model code MT3DMS. ANIMO is a detailed, process-oriented model code for the simulation of nitrate leaching to groundwater, N- and P-loads on surface waters and emissions of greenhouse gasses. It is the leading nutrient fate and transport code in the Netherlands where it is used primarily for the evaluation of fertilization related legislation. In addition, the code is applied frequently in international research projects. MT3DMS is probably the most commonly used groundwater solute transport package worldwide. The on-line model coupling ANIMO-MT3DMS combines the state-of-the-art descriptions of the biogeochemical cycles in ANIMO with the advantages of using a 3D approach for the transport through the saturated domain. These advantages include accounting for regional lateral transport, considering groundwater-surface water interactions more explicitly, and the possibility of using MODFLOW to obtain the flow fields. An additional merit of the on-line coupling concept is that it preserves feedbacks between the saturated and unsaturated zone. We tested ANIMO-MT3DMS by simulating nutrient transport for the period 1970-2007 in a Dutch agricultural polder catchment covering an area of 118 km2. The transient groundwater flow field had a temporal resolution of one day and was calculated with MODFLOW-MetaSWAP. The horizontal resolution of the model grid was 100x100m and consisted of 25 layers of varying thickness. To keep computation times manageable, we prepared MT3DMS for parallel computing, which in itself is a relevant development for a large community of groundwater transport modelers. For the parameterization of the soil, we applied a standard classification approach, representing the area by 60 units with unique combinations of soil type, land use and geohydrological setting. For the geochemical parameterization of the deeper subsurface, however, we

  9. An incident flux expansion transport theory method suitable for coupling to diffusion theory methods in hexagonal geometry

    International Nuclear Information System (INIS)

    Hayward, Robert M.; Rahnema, Farzad; Zhang, Dingkang

    2013-01-01

    Highlights: ► A new hybrid stochastic–deterministic transport theory method to couple with diffusion theory. ► The method is implemented in 2D hexagonal geometry. ► The new method produces excellent results when compared with Monte Carlo reference solutions. ► The method is fast, solving all test cases in less than 12 s. - Abstract: A new hybrid stochastic–deterministic transport theory method, which is designed to couple with diffusion theory, is presented. The new method is an extension of the incident flux response expansion method, and it combines the speed of diffusion theory with the accuracy of transport theory. With ease of use in mind, the new method is derived in such a way that it can be implemented with only minimal modifications to an existing diffusion theory method. A new angular expansion, which is necessary for the diffusion theory coupling, is developed in 2D and 3D. The method is implemented in 2D hexagonal geometry, and an HTTR benchmark problem is used to test its accuracy in a standalone configuration. It is found that the new method produces excellent results (with average relative error in partial current less than 0.033%) when compared with Monte Carlo reference solutions. Furthermore, the method is fast, solving all test cases in less than 12 s

  10. Modeling Coupled Water and Heat Transport in the Root Zone of Winter Wheat under Non-Isothermal Conditions

    Directory of Open Access Journals (Sweden)

    Rong Ren

    2017-04-01

    Full Text Available Temperature is an integral part of soil quality in terms of moisture content; coupling between water and heat can render a soil fertile, and plays a role in water conservation. Although it is widely recognized that both water and heat transport are fundamental factors in the quantification of soil mass and energy balance, their computation is still limited in most models or practical applications in the root zone under non-isothermal conditions. This research was conducted to: (a implement a fully coupled mathematical model that contains the full coupled process of soil water and heat transport with plants focused on the influence of temperature gradient on soil water redistribution and on the influence of change in soil water movement on soil heat flux transport; (b verify the mathematical model with detailed field monitoring data; and (c analyze the accuracy of the model. Results show the high accuracy of the model in predicting the actual changes in soil water content and temperature as a function of time and soil depth. Moreover, the model can accurately reflect changes in soil moisture and heat transfer in different periods. With only a few empirical parameters, the proposed model will serve as guide in the field of surface irrigation.

  11. Non-canonical distribution and non-equilibrium transport beyond weak system-bath coupling regime: A polaron transformation approach

    Science.gov (United States)

    Xu, Dazhi; Cao, Jianshu

    2016-08-01

    The concept of polaron, emerged from condense matter physics, describes the dynamical interaction of moving particle with its surrounding bosonic modes. This concept has been developed into a useful method to treat open quantum systems with a complete range of system-bath coupling strength. Especially, the polaron transformation approach shows its validity in the intermediate coupling regime, in which the Redfield equation or Fermi's golden rule will fail. In the polaron frame, the equilibrium distribution carried out by perturbative expansion presents a deviation from the canonical distribution, which is beyond the usual weak coupling assumption in thermodynamics. A polaron transformed Redfield equation (PTRE) not only reproduces the dissipative quantum dynamics but also provides an accurate and efficient way to calculate the non-equilibrium steady states. Applications of the PTRE approach to problems such as exciton diffusion, heat transport and light-harvesting energy transfer are presented.

  12. RF Coupling into the Fuel Tank of a Large Transport Aircraft from Intentionally Transmitting Peds in the Passenger Cabin

    Science.gov (United States)

    Nguyen, Truong X.; Dudley, Kenneth L.; Scearce, Stephen A.; Ely, Jay J.; Richardson, Robert E.; Hatfield, Michael O.

    2000-01-01

    An investigation was performed to study the potential for radio frequency (RF) power radiated from Portable Electronic Devices (PEDs) to create an arcing/sparking event within the fuel tank of a large transport aircraft. This paper describes the experimental methods used for measuring RF coupling to the fuel tank and Fuel Quantity Indication System (FQIS) wiring from PED sources located in the passenger cabin. To allow comparison of voltage/current data obtained in a laboratory chamber FQIS installation to an actual aircraft FQIS installation, aircraft fuel tank RF reverberation characteristics were also measured. Results from the measurements, along with a survey of threats from typical intentional transmitting PEDs are presented. The resulting worst-case power coupled onto fuel tank FQIS wiring is derived. The same approach can be applied to measure RF coupling into various other aircraft systems.

  13. Dimer and cluster approach for the evaluation of electronic couplings governing charge transport: Application to two pentacene polymorphs

    International Nuclear Information System (INIS)

    Canola, Sofia; Pecoraro, Claudia; Negri, Fabrizia

    2016-01-01

    Hole transport properties are modeled for two polymorphs of pentacene: the single crystal polymorph and the thin film polymorph relevant for organic thin-film transistor applications. Electronic couplings are evaluated in the standard dimer approach but also considering a cluster approach in which the central molecule is surrounded by a large number of molecules quantum-chemically described. The effective electronic couplings suitable for the parametrization of a tight-binding model are derived either from the orthogonalization scheme limited to HOMO orbitals and from the orthogonalization of the full basis of molecular orbitals. The angular dependent mobilities estimated for the two polymorphs using the predicted pattern of couplings display different anisotropy characteristics as suggested from experimental investigations.

  14. Dimer and cluster approach for the evaluation of electronic couplings governing charge transport: Application to two pentacene polymorphs

    Energy Technology Data Exchange (ETDEWEB)

    Canola, Sofia; Pecoraro, Claudia; Negri, Fabrizia

    2016-10-20

    Hole transport properties are modeled for two polymorphs of pentacene: the single crystal polymorph and the thin film polymorph relevant for organic thin-film transistor applications. Electronic couplings are evaluated in the standard dimer approach but also considering a cluster approach in which the central molecule is surrounded by a large number of molecules quantum-chemically described. The effective electronic couplings suitable for the parametrization of a tight-binding model are derived either from the orthogonalization scheme limited to HOMO orbitals and from the orthogonalization of the full basis of molecular orbitals. The angular dependent mobilities estimated for the two polymorphs using the predicted pattern of couplings display different anisotropy characteristics as suggested from experimental investigations.

  15. Optimization of membrane stack configuration for efficient hydrogen production in microbial reverse-electrodialysis electrolysis cells coupled with thermolytic solutions

    KAUST Repository

    Luo, Xi

    2013-07-01

    Waste heat can be captured as electrical energy to drive hydrogen evolution in microbial reverse-electrodialysis electrolysis cells (MRECs) by using thermolytic solutions such as ammonium bicarbonate. To determine the optimal membrane stack configuration for efficient hydrogen production in MRECs using ammonium bicarbonate solutions, different numbers of cell pairs and stack arrangements were tested. The optimum number of cell pairs was determined to be five based on MREC performance and a desire to minimize capital costs. The stack arrangement was altered by placing an extra low concentration chamber adjacent to anode chamber to reduce ammonia crossover. This additional chamber decreased ammonia nitrogen losses into anolyte by 60%, increased the coulombic efficiency to 83%, and improved the hydrogen yield to a maximum of 3.5mol H2/mol acetate, with an overall energy efficiency of 27%. These results improve the MREC process, making it a more efficient method for renewable hydrogen gas production. © 2013 Elsevier Ltd.

  16. Numerical modeling of watershed-scale radiocesium transport coupled with biogeochemical cycling in forests

    Science.gov (United States)

    Mori, K.; Tada, K.; Tawara, Y.; Tosaka, H.; Ohno, K.; Asami, M.; Kosaka, K.

    2015-12-01

    Since the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident, intensive monitoring and modeling works on radionuclide transfer in environment have been carried out. Although Cesium (Cs) concentration has been attenuating due to both physical and environmental half-life (i.e., wash-off by water and sediment), the attenuation rate depends clearly on the type of land use and land cover. In the Fukushima case, studying the migration in forest land use is important for predicting the long-term behavior of Cs because most of the contaminated region is covered by forests. Atmospheric fallout is characterized by complicated behavior in biogeochemical cycle in forests which can be described by biotic/abiotic interactions between many components. In developing conceptual and mathematical model on Cs transfer in forest ecosystem, defining the dominant components and their interactions are crucial issues (BIOMASS, 1997-2001). However, the modeling of fate and transport in geosphere after Cs exports from the forest ecosystem is often ignored. An integrated watershed modeling for simulating spatiotemporal redistribution of Cs that includes the entire region from source to mouth and surface to subsurface, has been recently developed. Since the deposited Cs can migrate due to water and sediment movement, the different species (i.e., dissolved and suspended) and their interactions are key issues in the modeling. However, the initial inventory as source-term was simplified to be homogeneous and time-independent, and biogeochemical cycle in forests was not explicitly considered. Consequently, it was difficult to evaluate the regionally-inherent characteristics which differ according to land uses, even if the model was well calibrated. In this study, we combine the different advantages in modeling of forest ecosystem and watershed. This enable to include more realistic Cs deposition and time series of inventory can be forced over the land surface. These processes are integrated

  17. CryoEM structure of the human SLC4A4 sodium-coupled acid-base transporter NBCe1.

    Science.gov (United States)

    Huynh, Kevin W; Jiang, Jiansen; Abuladze, Natalia; Tsirulnikov, Kirill; Kao, Liyo; Shao, Xuesi; Newman, Debra; Azimov, Rustam; Pushkin, Alexander; Zhou, Z Hong; Kurtz, Ira

    2018-03-02

    Na + -coupled acid-base transporters play essential roles in human biology. Their dysfunction has been linked to cancer, heart, and brain disease. High-resolution structures of mammalian Na + -coupled acid-base transporters are not available. The sodium-bicarbonate cotransporter NBCe1 functions in multiple organs and its mutations cause blindness, abnormal growth and blood chemistry, migraines, and impaired cognitive function. Here, we have determined the structure of the membrane domain dimer of human NBCe1 at 3.9 Å resolution by cryo electron microscopy. Our atomic model and functional mutagenesis revealed the ion accessibility pathway and the ion coordination site, the latter containing residues involved in human disease-causing mutations. We identified a small number of residues within the ion coordination site whose modification transformed NBCe1 into an anion exchanger. Our data suggest that symporters and exchangers utilize comparable transport machinery and that subtle differences in their substrate-binding regions have very significant effects on their transport mode.

  18. Coupled incompressible Smoothed Particle Hydrodynamics model for continuum-based modelling sediment transport

    Science.gov (United States)

    Pahar, Gourabananda; Dhar, Anirban

    2017-04-01

    A coupled solenoidal Incompressible Smoothed Particle Hydrodynamics (ISPH) model is presented for simulation of sediment displacement in erodible bed. The coupled framework consists of two separate incompressible modules: (a) granular module, (b) fluid module. The granular module considers a friction based rheology model to calculate deviatoric stress components from pressure. The module is validated for Bagnold flow profile and two standardized test cases of sediment avalanching. The fluid module resolves fluid flow inside and outside porous domain. An interaction force pair containing fluid pressure, viscous term and drag force acts as a bridge between two different flow modules. The coupled model is validated against three dambreak flow cases with different initial conditions of movable bed. The simulated results are in good agreement with experimental data. A demonstrative case considering effect of granular column failure under full/partial submergence highlights the capability of the coupled model for application in generalized scenario.

  19. Modeling of radiation transport in coupled atmosphere-snow-ice-ocean systems

    International Nuclear Information System (INIS)

    Stamnes, K.; Hamre, B.; Stamnes, J. J.; Ryzhikov, G.; Biryulina, M.

    2009-01-01

    A radiative transfer model for coupled atmosphere-snow-ice-ocean systems is used to develop accurate and efficient tools for computing the BRDF of sea ice for a wide range of situations occurring in nature. (authors)

  20. Electrical and thermal transport in the quasi-atomic limit of coupled Luttinger liquids

    OpenAIRE

    Szasz, Aaron; Ilan, Roni; Moore, Joel E.

    2016-01-01

    We introduce a new model for quasi one-dimensional materials, motivated by intriguing but not yet well-understood experiments that have shown two-dimensional polymer films to be promising materials for thermoelectric devices. We consider a two-dimensional material consisting of many one-dimensional systems, each treated as a Luttinger liquid, with weak (incoherent) coupling between them. This approximation of strong interactions within each one-dimensional chain and weak coupling between them...

  1. Analysis of coupled proton and water transport in a PEM fuel cell using the binary friction membrane model

    International Nuclear Information System (INIS)

    Carnes, B.; Djilali, N.

    2006-01-01

    Transport of liquid water within a polymer electrolyte membrane (PEM) is critical to the operation of a PEM fuel cell, due to the strong dependence of the membrane transport coefficients on water content. In addition, enhanced predictive abilities are particularly significant in the context of passive air breathing fuel cell designs where lower water contents will prevail in the membrane. We investigate and analyze the numerical predictions of a recently proposed rational model for transport of protons and water in a PEM, when compared to a widely used empirical model. While the performance is similar for a saturated membrane, for PEMs with low water content, the difference in computed current density and membrane water crossover can be substantial. The effects of coupling partially saturated gas diffusion electrodes (GDLs) with the membrane are studied in both a 1D and 2D context. In addition, a simplified 1D analytical membrane water transport model is validated against the complete 1D model predictions. Our numerical results predict a higher current density and more uniform membrane hydration using a dry cathode instead of a dry anode, and illustrate that the strongest 2D effects are for water vapor transport

  2. Transportation over long distance and thermal energy storage, coupling with energetic valuation processes from waste. State of art. Extended abstract

    International Nuclear Information System (INIS)

    Megret, O.; Bequet, L.; Manificat, A.; Weber, C.

    2011-12-01

    This study aims, on one hand, to realize a state of art about over long distance transport and heat energy storage and, on the other hand, to examine their coupling with waste valuation systems. After reminding the adequate context of development with those solutions and too showing the importance of the stake linked to the current work, we first expose the introductive elements in terms of storage and heat energy transport. The second chapter deals with the description of some materials, equipment and systems concerning heat storage energy. Afterward, the over long distance heat transport systems are detailed in the third chapter. In the fourth chapter, it is about waste valuation techniques and heat energy potentials users. The fifth chapter sums up the different techniques of storage and heat transport that are applicable to waste field according to the appropriate sector. Finally, the sixth chapter goes about 3 case-works in 3 fields: housing/commercial, industrial laundry and high temperature industry (steel industry). The purpose is to determine the implementation feasibility of the different techniques of storage and waste heat transport. (authors)

  3. A 2D/1D coupling neutron transport method based on the matrix MOC and NEM methods

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, H.; Zheng, Y.; Wu, H.; Cao, L. [School of Nuclear Science and Technology, Xi' an Jiaotong University, No. 28, Xianning West Road, Xi' an, Shaanxi 710049 (China)

    2013-07-01

    A new 2D/1D coupling method based on the matrix MOC method (MMOC) and nodal expansion method (NEM) is proposed for solving the three-dimensional heterogeneous neutron transport problem. The MMOC method, used for radial two-dimensional calculation, constructs a response matrix between source and flux with only one sweep and then solves the linear system by using the restarted GMRES algorithm instead of the traditional trajectory sweeping process during within-group iteration for angular flux update. Long characteristics are generated by using the customization of commercial software AutoCAD. A one-dimensional diffusion calculation is carried out in the axial direction by employing the NEM method. The 2D and ID solutions are coupled through the transverse leakage items. The 3D CMFD method is used to ensure the global neutron balance and adjust the different convergence properties of the radial and axial solvers. A computational code is developed based on these theories. Two benchmarks are calculated to verify the coupling method and the code. It is observed that the corresponding numerical results agree well with references, which indicates that the new method is capable of solving the 3D heterogeneous neutron transport problem directly. (authors)

  4. A 2D/1D coupling neutron transport method based on the matrix MOC and NEM methods

    International Nuclear Information System (INIS)

    Zhang, H.; Zheng, Y.; Wu, H.; Cao, L.

    2013-01-01

    A new 2D/1D coupling method based on the matrix MOC method (MMOC) and nodal expansion method (NEM) is proposed for solving the three-dimensional heterogeneous neutron transport problem. The MMOC method, used for radial two-dimensional calculation, constructs a response matrix between source and flux with only one sweep and then solves the linear system by using the restarted GMRES algorithm instead of the traditional trajectory sweeping process during within-group iteration for angular flux update. Long characteristics are generated by using the customization of commercial software AutoCAD. A one-dimensional diffusion calculation is carried out in the axial direction by employing the NEM method. The 2D and ID solutions are coupled through the transverse leakage items. The 3D CMFD method is used to ensure the global neutron balance and adjust the different convergence properties of the radial and axial solvers. A computational code is developed based on these theories. Two benchmarks are calculated to verify the coupling method and the code. It is observed that the corresponding numerical results agree well with references, which indicates that the new method is capable of solving the 3D heterogeneous neutron transport problem directly. (authors)

  5. The coupling of the neutron transport application RATTLESNAKE to the nuclear fuels performance application BISON under the MOOSE framework

    Energy Technology Data Exchange (ETDEWEB)

    Gleicher, Frederick N.; Williamson, Richard L.; Ortensi, Javier; Wang, Yaqi; Spencer, Benjamin W.; Novascone, Stephen R.; Hales, Jason D.; Martineau, Richard C.

    2014-10-01

    The MOOSE neutron transport application RATTLESNAKE was coupled to the fuels performance application BISON to provide a higher fidelity tool for fuel performance simulation. This project is motivated by the desire to couple a high fidelity core analysis program (based on the self-adjoint angular flux equations) to a high fidelity fuel performance program, both of which can simulate on unstructured meshes. RATTLESNAKE solves self-adjoint angular flux transport equation and provides a sub-pin level resolution of the multigroup neutron flux with resonance treatment during burnup or a fast transient. BISON solves the coupled thermomechanical equations for the fuel on a sub-millimeter scale. Both applications are able to solve their respective systems on aligned and unaligned unstructured finite element meshes. The power density and local burnup was transferred from RATTLESNAKE to BISON with the MOOSE Multiapp transfer system. Multiple depletion cases were run with one-way data transfer from RATTLESNAKE to BISON. The eigenvalues are shown to agree well with values obtained from the lattice physics code DRAGON. The one-way data transfer of power density is shown to agree with the power density obtained from an internal Lassman-style model in BISON.

  6. Microbial air quality in mass transport buses and work-related illness among bus drivers of Bangkok Mass Transit Authority.

    Science.gov (United States)

    Luksamijarulkul, Pipat; Sundhiyodhin, Viboonsri; Luksamijarulkul, Soavalug; Kaewboonchoo, Orawan

    2004-06-01

    The air quality in mass transport buses, especially air-conditioned buses may affect bus drivers who work full time. Bus numbers 16, 63, 67 and 166 of the Seventh Bus Zone of Bangkok Mass Transit Authority were randomly selected to investigate for microbial air quality. Nine air-conditioned buses and 2-4 open-air buses for each number of the bus (36 air-conditioned buses and 12 open-air buses) were included. Five points of in-bus air samples in each studied bus were collected by using the Millipore A ir Tester Totally, 180 and 60 air samples collected from air-conditioned buses and open-air buses were cultured for bacterial and fungal counts. The bus drivers who drove the studied buses were interviewed towards histories of work-related illness while working. The results revealed that the mean +/- SD of bacterial counts in the studied open-air buses ranged from 358.50 +/- 146.66 CFU/m3 to 506 +/- 137.62 CFU/m3; bus number 16 had the highest level. As well as the mean +/- SD of fungal counts which ranged from 93.33 +/- 44.83 CFU/m3 to 302 +/- 294.65 CFU/m3; bus number 166 had the highest level. Whereas, the mean +/- SD of bacterial counts in the studied air-conditioned buses ranged from 115.24 +/- 136.01 CFU/m3 to 244.69 +/- 234.85 CFU/m3; bus numbers 16 and 67 had the highest level. As well as the mean +/- SD of fungal counts which rangedfrom 18.84 +/- 39.42 CFU/m3 to 96.13 +/- 234.76 CFU/m3; bus number 166 had the highest level. When 180 and 60 studied air samples were analyzed in detail, it was found that 33.33% of the air samples from open-air buses and 6.11% of air samples from air-conditioned buses had a high level of bacterial counts (> 500 CFU/m3) while 6.67% of air samples from open-air buses and 2.78% of air samples from air-conditioned buses had a high level of fungal counts (> 500 CFU/m3). Data from the history of work-related illnesses among the studied bus drivers showed that 91.67% of open-air bus drivers and 57.28% of air-conditioned bus drivers had

  7. Accumulation and transport of microbial-size particles in a pressure protected model burn unit: CFD simulations and experimental evidence

    Directory of Open Access Journals (Sweden)

    Mimoun Maurice

    2011-03-01

    Full Text Available Abstract Background Controlling airborne contamination is of major importance in burn units because of the high susceptibility of burned patients to infections and the unique environmental conditions that can accentuate the infection risk. In particular the required elevated temperatures in the patient room can create thermal convection flows which can transport airborne contaminates throughout the unit. In order to estimate this risk and optimize the design of an intensive care room intended to host severely burned patients, we have relied on a computational fluid dynamic methodology (CFD. Methods The study was carried out in 4 steps: i patient room design, ii CFD simulations of patient room design to model air flows throughout the patient room, adjacent anterooms and the corridor, iii construction of a prototype room and subsequent experimental studies to characterize its performance iv qualitative comparison of the tendencies between CFD prediction and experimental results. The Electricité De France (EDF open-source software Code_Saturne® (http://www.code-saturne.org was used and CFD simulations were conducted with an hexahedral mesh containing about 300 000 computational cells. The computational domain included the treatment room and two anterooms including equipment, staff and patient. Experiments with inert aerosol particles followed by time-resolved particle counting were conducted in the prototype room for comparison with the CFD observations. Results We found that thermal convection can create contaminated zones near the ceiling of the room, which can subsequently lead to contaminate transfer in adjacent rooms. Experimental confirmation of these phenomena agreed well with CFD predictions and showed that particles greater than one micron (i.e. bacterial or fungal spore sizes can be influenced by these thermally induced flows. When the temperature difference between rooms was 7°C, a significant contamination transfer was observed to

  8. Summer nitrogenous nutrient transport and its fate in the Taiwan Strait: A coupled physical-biological modeling approach

    Science.gov (United States)

    Wang, Jia; Hong, Huasheng; Jiang, Yuwu; Chai, Fei; Yan, Xiao-Hai

    2013-09-01

    In order to understand the fate of nutrients in the Taiwan Strait during summer, we built a coupled physical-biological numerical ocean model, which can capture the basic hydrographic and biological features within the strait. The nutrient that we chose to model is dissolved inorganic nitrogen (DIN). The model includes individual reservoirs for nitrate (NO3) and ammonium (NH4). Both the observational evidence and model results show that NO3 in the strait originates primarily from the upwelling subsurface water in the northern South China Sea (SCS) that enters the strait via the eastern and western routes separated by the Taiwan Bank. The coupled physical and biological effects on the NO3 transport at these two routes are highlighted in the study. For the western route, the shallow topography and the coastal upwelling intensify the biological uptake of NO3 in the whole water column. Consequently, the nitrogenous contribution by this route is mainly in form of the particulate organic nitrogen (PON). In contrast, NO3 is transported conservatively below the nitricline at the deep eastern route, contributing the whole NO3 supply in the TWS. The model estimates the fluxes of DIN and PON into the TWS, from the northern SCS, are 1.8 and 4 kmol s-1, respectively. Over half (˜1 kmol s-1) of the DIN is synthesized into PON by the phytoplankton in the strait. Overall, this study estimates the physical and biological effects on the nutrient transport in the TWS during summer.

  9. Inverse engineering for fast transport and spin control of spin-orbit-coupled Bose-Einstein condensates in moving harmonic traps

    Science.gov (United States)

    Chen, Xi; Jiang, Ruan-Lei; Li, Jing; Ban, Yue; Sherman, E. Ya.

    2018-01-01

    We investigate fast transport and spin manipulation of tunable spin-orbit-coupled Bose-Einstein condensates in a moving harmonic trap. Motivated by the concept of shortcuts to adiabaticity, we design inversely the time-dependent trap position and spin-orbit-coupling strength. By choosing appropriate boundary conditions we obtain fast transport and spin flip simultaneously. The nonadiabatic transport and relevant spin dynamics are illustrated with numerical examples and compared with the adiabatic transport with constant spin-orbit-coupling strength and velocity. Moreover, the influence of nonlinearity induced by interatomic interaction is discussed in terms of the Gross-Pitaevskii approach, showing the robustness of the proposed protocols. With the state-of-the-art experiments, such an inverse engineering technique paves the way for coherent control of spin-orbit-coupled Bose-Einstein condensates in harmonic traps.

  10. Mechanical coupling of microtubule-dependent motor teams during peroxisome transport in Drosophila S2 cells.

    Science.gov (United States)

    De Rossi, María Cecilia; Wetzler, Diana E; Benseñor, Lorena; De Rossi, María Emilia; Sued, Mariela; Rodríguez, Daniela; Gelfand, Vladimir; Bruno, Luciana; Levi, Valeria

    2017-12-01

    Intracellular transport requires molecular motors that step along cytoskeletal filaments actively dragging cargoes through the crowded cytoplasm. Here, we explore the interplay of the opposed polarity motors kinesin-1 and cytoplasmic dynein during peroxisome transport along microtubules in Drosophila S2 cells. We used single particle tracking with nanometer accuracy and millisecond time resolution to extract quantitative information on the bidirectional motion of organelles. The transport performance was studied in cells expressing a slow chimeric plus-end directed motor or the kinesin heavy chain. We also analyzed the influence of peroxisomes membrane fluidity in methyl-β-ciclodextrin treated cells. The experimental data was also confronted with numerical simulations of two well-established tug of war scenarios. The velocity distributions of retrograde and anterograde peroxisomes showed a multimodal pattern suggesting that multiple motor teams drive transport in either direction. The chimeric motors interfered with the performance of anterograde transport and also reduced the speed of the slowest retrograde team. In addition, increasing the fluidity of peroxisomes membrane decreased the speed of the slowest anterograde and retrograde teams. Our results support the existence of a crosstalk between opposed-polarity motor teams. Moreover, the slowest teams seem to mechanically communicate with each other through the membrane to trigger transport. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Development of a coupled dynamics code with transport theory capability and application to accelerator driven systems transients

    International Nuclear Information System (INIS)

    Cahalan, J.E.; Ama, T.; Palmiotti, G.; Taiwo, T.A.; Yang, W.S.

    2000-01-01

    The VARIANT-K and DIF3D-K nodal spatial kinetics computer codes have been coupled to the SAS4A and SASSYS-1 liquid metal reactor accident and systems analysis codes. SAS4A and SASSYS-1 have been extended with the addition of heavy liquid metal (Pb and Pb-Bi) thermophysical properties, heat transfer correlations, and fluid dynamics correlations. The coupling methodology and heavy liquid metal modeling additions are described. The new computer code suite has been applied to analysis of neutron source and thermal-hydraulics transients in a model of an accelerator-driven minor actinide burner design proposed in an OECD/NEA/NSC benchmark specification. Modeling assumptions and input data generation procedures are described. Results of transient analyses are reported, with emphasis on comparison of P1 and P3 variational nodal transport theory results with nodal diffusion theory results, and on significance of spatial kinetics effects

  12. Illustration of the Alliances platform chemistry/transport coupling capacities through the simulation of a cement/clay interaction

    International Nuclear Information System (INIS)

    Dimier, A.; Michau, N.; Montarnal, Ph.; Corrihons, F.

    2003-01-01

    Safety studies in a subsurface environment and in an underground waste disposal necessitate numerical tools for reactive transport modelling. In these systems, hydrogeological and chemical processes are closely related and their interdependence must be analysed to study migration of species. We will illustrate here the capacities of the Alliances tool to simulate such a phenomenology by studying the evolution of a clay/cement interface over time. The goal being defined, the two main employed software to build up a multidimensional tool have been chosen, namely PhreeqC and Chess for chemistry. A common model has been developed whose aim is to allow models comparison while switching between the chemistry tools. For transport, Castem and Mt3d-99 have been introduced with the same philosophy of structure. It is worth noting that other tools could be introduced, the only requirement being to satisfy the specific data-model and building up the appropriate methods. Qualification cases have been built up to define the platform application field. It has been defined with one and two dimensional cases enabling a comparison with analytic solutions or an intercomparison with other reactive transport codes. To illustrate this in the chemistry coupling field, we focus on a clay cement interface with an ion exchange linked to the Ca-montmorillonite. This case has been defined at ANDRA to be used as a reference test case for chemistry coupling validation. Results show a good agreement between platform results and whose of PhreeqC with its own internal coupling. The clay/cement interface is reproduced with the same accuracy

  13. Investigations of the role of nonlinear couplings in structure formation and transport regulation: Experiment, simulation, and theory

    International Nuclear Information System (INIS)

    Holland, C.; Kim, E.J.; Champeaux, S.; Gurcan, O.; Rosenbluth, M.N.; Diamond, P.H.; Tynan, G.R.; Nevins, W.; Candy, J.

    2003-01-01

    Understanding the physics of shear flow and structure formation in plasmas is a central problem for the advancement of magnetic fusion because of the roles such flows are believed to play in regulating turbulence and transport levels. In this paper, we report on integrated experimental, computational, and theoretical studies of sheared zonal flows and radially extended convective cells, with the aim of assessing the results of theory experiment and theory-simulation comparisons. In particular, simulations are used as test beds for verifying analytical predictions and demonstrating the suitability of techniques such as bispectral analysis for isolating nonlinear couplings in data. Based on intriguing initial results suggesting increased levels of nonlinear coupling occur during L-H transitions, we have undertaken a comprehensive study of bispectral quantities in fluid and gyrokinetic simulations, and compared these results with theoretical expectations. Topics of study include locality and directionality of energy transfer, amplitude scaling, and parameter dependences. Techniques for inferring nonlinear coupling coefficients from data are discussed, and initial results from experimental data are presented. Future experimental studies are motivated. We also present work investigating the role of structures in transport. Analysis of simulation data indicates that the turbulent heat flux can be represented as an ensemble of 'heat pulses' of varying sizes, with a power law distribution. The slope of the power law is shown to determine global transport scaling (i.e. Bohm or gyro-Bohm). Theoretical work studying the dynamics of the largest cells (termed 'streamers') is presented, as well as results from ongoing analysis studying connections between heat pulse distribution and bispectral quantities. (author)

  14. Spin-orbit-coupled transport and spin torque in a ferromagnetic heterostructure

    KAUST Repository

    Wang, Xuhui; Ortiz Pauyac, Christian; Manchon, Aurelien

    2014-01-01

    Ferromagnetic heterostructures provide an ideal platform to explore the nature of spin-orbit torques arising from the interplay mediated by itinerant electrons between a Rashba-type spin-orbit coupling and a ferromagnetic exchange interaction. For such a prototypic system, we develop a set of coupled diffusion equations to describe the diffusive spin dynamics and spin-orbit torques. We characterize the spin torque and its two prominent—out-of-plane and in-plane—components for a wide range of relative strength between the Rashba coupling and ferromagnetic exchange. The symmetry and angular dependence of the spin torque emerging from our simple Rashba model is in an agreement with experiments. The spin diffusion equation can be generalized to incorporate dynamic effects such as spin pumping and magnetic damping.

  15. Spin-orbit-coupled transport and spin torque in a ferromagnetic heterostructure

    KAUST Repository

    Wang, Xuhui

    2014-02-07

    Ferromagnetic heterostructures provide an ideal platform to explore the nature of spin-orbit torques arising from the interplay mediated by itinerant electrons between a Rashba-type spin-orbit coupling and a ferromagnetic exchange interaction. For such a prototypic system, we develop a set of coupled diffusion equations to describe the diffusive spin dynamics and spin-orbit torques. We characterize the spin torque and its two prominent—out-of-plane and in-plane—components for a wide range of relative strength between the Rashba coupling and ferromagnetic exchange. The symmetry and angular dependence of the spin torque emerging from our simple Rashba model is in an agreement with experiments. The spin diffusion equation can be generalized to incorporate dynamic effects such as spin pumping and magnetic damping.

  16. Charge transport in 2DEG/s-wave superconductor junction with Dresselhaus-type spin-orbit coupling

    International Nuclear Information System (INIS)

    Sawa, Y.; Yokoyama, T.; Tanaka, Y.

    2007-01-01

    We study spin-dependent charge transport in superconducting junctions. We consider ballistic two-dimensional electron gas (2DEG)/s-wave superconductor junctions with Dresselhaus-type spin-orbit coupling (DSOC). We calculate the conductance normalized by that in the normal state of superconductor in order to study the effect of DSOC in 2DEG on conductance, changing the height of insulating barrier. We find the DSOC suppresses the conductance for low insulating barrier, while it can slightly enhance the conductance for high insulating barrier. It has a reentrant dependence on DSOC for middle strength insulating barrier. The effect of DSOC is weaken as the insulating barrier becomes high

  17. Spin and tunneling dynamics in an asymmetrical double quantum dot with spin-orbit coupling: Selective spin transport device

    Science.gov (United States)

    Singh, Madhav K.; Jha, Pradeep K.; Bhattacherjee, Aranya B.

    2017-09-01

    In this article, we study the spin and tunneling dynamics as a function of magnetic field in a one-dimensional GaAs double quantum dot with both the Dresselhaus and Rashba spin-orbit coupling. In particular, we consider different spatial widths for the spin-up and spin-down electronic states. We find that the spin dynamics is a superposition of slow as well as fast Rabi oscillations. It is found that the Rashba interaction strength as well as the external magnetic field strongly modifies the slow Rabi oscillations which is particularly useful for implementing solid state selective spin transport device.

  18. Extremely Large Magnetoresistance at Low Magnetic Field by Coupling the Nonlinear Transport Effect and the Anomalous Hall Effect.

    Science.gov (United States)

    Luo, Zhaochu; Xiong, Chengyue; Zhang, Xu; Guo, Zhen-Gang; Cai, Jianwang; Zhang, Xiaozhong

    2016-04-13

    The anomalous Hall effect of a magnetic material is coupled to the nonlinear transport effect of a semiconductor material in a simple structure to achieve a large geometric magnetoresistance (MR) based on a diode-assisted mechanism. An extremely large MR (>10(4) %) at low magnetic fields (1 mT) is observed at room temperature. This MR device shows potential for use as a logic gate for the four basic Boolean logic operations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Methodology of Continuous-Energy Adjoint Monte Carlo for Neutron, Photon, and Coupled Neutron-Photon Transport

    International Nuclear Information System (INIS)

    Hoogenboom, J. Eduard

    2003-01-01

    Adjoint Monte Carlo may be a useful alternative to regular Monte Carlo calculations in cases where a small detector inhibits an efficient Monte Carlo calculation as only very few particle histories will cross the detector. However, in general purpose Monte Carlo codes, normally only the multigroup form of adjoint Monte Carlo is implemented. In this article the general methodology for continuous-energy adjoint Monte Carlo neutron transport is reviewed and extended for photon and coupled neutron-photon transport. In the latter cases the discrete photons generated by annihilation or by neutron capture or inelastic scattering prevent a direct application of the general methodology. Two successive reaction events must be combined in the selection process to accommodate the adjoint analog of a reaction resulting in a photon with a discrete energy. Numerical examples illustrate the application of the theory for some simplified problems

  20. An inexact Newton method for fully-coupled solution of the Navier-Stokes equations with heat and mass transport

    Energy Technology Data Exchange (ETDEWEB)

    Shadid, J.N.; Tuminaro, R.S. [Sandia National Labs., Albuquerque, NM (United States); Walker, H.F. [Utah State Univ., Logan, UT (United States). Dept. of Mathematics and Statistics

    1997-02-01

    The solution of the governing steady transport equations for momentum, heat and mass transfer in flowing fluids can be very difficult. These difficulties arise from the nonlinear, coupled, nonsymmetric nature of the system of algebraic equations that results from spatial discretization of the PDEs. In this manuscript the authors focus on evaluating a proposed nonlinear solution method based on an inexact Newton method with backtracking. In this context they use a particular spatial discretization based on a pressure stabilized Petrov-Galerkin finite element formulation of the low Mach number Navier-Stokes equations with heat and mass transport. The discussion considers computational efficiency, robustness and some implementation issues related to the proposed nonlinear solution scheme. Computational results are presented for several challenging CFD benchmark problems as well as two large scale 3D flow simulations.

  1. Improvement of the symbolic Monte-Carlo method for the transport equation: P1 extension and coupling with diffusion

    International Nuclear Information System (INIS)

    Clouet, J.F.; Samba, G.

    2005-01-01

    We use asymptotic analysis to study the diffusion limit of the Symbolic Implicit Monte-Carlo (SIMC) method for the transport equation. For standard SIMC with piecewise constant basis functions, we demonstrate mathematically that the solution converges to the solution of a wrong diffusion equation. Nevertheless a simple extension to piecewise linear basis functions enables to obtain the correct solution. This improvement allows the calculation in opaque medium on a mesh resolving the diffusion scale much larger than the transport scale. Anyway, the huge number of particles which is necessary to get a correct answer makes this computation time consuming. Thus, we have derived from this asymptotic study an hybrid method coupling deterministic calculation in the opaque medium and Monte-Carlo calculation in the transparent medium. This method gives exactly the same results as the previous one but at a much lower price. We present numerical examples which illustrate the analysis. (authors)

  2. Coupling of the spatial dynamic of picoplankton and nanoflagellate grazing pressure and carbon flow of the microbial food web in the subtropical pelagic continental shelf ecosystem

    Science.gov (United States)

    Chiang, K.-P.; Tsai, A.-Y.; Tsai, P.-J.; Gong, G.-C.; Tsai, S.-F.

    2013-01-01

    In order to investigate the mechanism of spatial dynamics of picoplankton community (bacteria and Synechococcus spp.) and estimate the carbon flux of the microbial food web in the oligotrophic Taiwan Warm Current Water of subtropical marine pelagic ecosystem, we conducted size-fractionation experiments in five cruises by the R/V Ocean Research II during the summers of 2010 and 2011 in the southern East China Sea. We carried out culture experiments using surface water which, according to a temperature-salinity (T-S) diagram, is characterized as oligotrophic Taiwan Current Warm Water. We found a negative correlation bettween bacteria growth rate and temperature, indicating that the active growth of heterotrophic bacteria might be induced by nutrients lifted from deep layer by cold upwelling water. This finding suggests that the area we studied was a bottom-up control pelagic ecosystem. We suggest that the microbial food web of an oligotrophic ecosystem may be changed from top-down control to resource supply (bottom-up control) when a physical force brings nutrient into the oligotrophic ecosystem. Upwelling brings nutrient-rich water to euphotic zone and promotes bacteria growth, increasing the picoplankton biomass which increased the consumption rate of nanoflagellate. The net growth rate (growth rate-grazing rate) becomes negative when the densities of bacteria and Synechococcus spp. are lower than the threshold values. The interaction between growth and grazing will limit the abundances of bacteria (105-106 cells mL-1 and Synechococcus spp. (104-105 cells mL-1) within a narrow range, forming a predator-prey eddy. Meanwhile, 62% of bacteria production and 55% of Synechococcus spp. production are transported to higher trophic level (nanoflagellate), though the cascade effect might cause an underestimation of both percentages of transported carbon. Based on the increasing number of sizes we found in the size-fractionation experiments, we estimated that the predation

  3. Dual continuum models of fully coupled non-isothermal multiphase flow and reactive transport in porous media

    International Nuclear Information System (INIS)

    Zheng, L.; Samper, J.

    2005-01-01

    Full text of publication follows: Double porosity, double permeability and dual continuum models (DCM) are widely used for modeling preferential water flow and mass transport in unsaturated and fractured media. Here we present a DCM of fully coupled non-isothermal multiphase flow and reactive transport model for the FEBEX compacted bentonite, a material which exhibits a double porosity behavior.. FEBEX (Full-scale Engineered Barrier EXperiment) is a demonstration and research project dealing with the bentonite engineered barrier designed for sealing and containment of a high level radioactive waste repository. Our DCM considers inter-aggregate macro-pores, and intra-aggregate and interlayer micro-pores. Two types of DCMs are tested: the dual continuum connected matrix (DCCM) and the dual continuum dis connected matrix (DCDM). Liquid flow in macro-pores is described with a mass conservation equation accounting for Darcian flow, chemical and thermal osmosis. In DCCM, water flux in micropores is calculated with a modified Darcy's law by adding a chemical osmosis term. A simple mass balance equation is used for DCDM which contains a storage and a water exchange term for water in micropores. A mixed type of water exchange term is adopted which includes a second order term accounting for water transfer due to the difference in liquid pressure and a first order term accounting for the gradient in chemical osmosis pressure. Equations of mass conservation for liquid, gas and heat in macro-pores and liquid mass conservation in micropores are solved by using a Newton-Raphson method. Two transport equations with a coupling interaction term are used to describe solute transport in macro- and micro-pores. The coupling term contains a first order diffusion term and a convection term (solute exchange due to water exchange). Transport equations as well as chemical reactions in the two domains are solved by means of a sequential iteration method. All these feature have been

  4. Subsurface Transport Over Reactive Multiphases (STORM): A Parallel, Coupled, Nonisothermal Multiphase Flow, Reactive Transport, and Porous Medium Alteration Simulator, Version 3.0

    International Nuclear Information System (INIS)

    Bacon, Diana H.; White, Mark D.; McGrail, B PETER

    2004-01-01

    The U.S. Department of Energy must approve a performance assessment (PA) to support the design, construction, approval, and closure of disposal facilities for immobilized low-activity waste (ILAW) currently stored in underground tanks at Hanford, Washington. A critical component of the PA is to provide quantitative estimates of radionuclide release rates from the engineered portion of the disposal facilities. Computer simulations are essential for this purpose because impacts on groundwater resources must be projected to periods of 10,000 years and longer. The computer code selected for simulating the radionuclide release rates is the Subsurface Transport Over Reactive Multiphases (STORM) simulator. The STORM simulator solves coupled conservation equations for component mass and energy that describe subsurface flow over aqueous and gas phases through variably saturated geologic media. The resulting flow fields are used to sequentially solve conservation equations for reactive aqueous phase transport through variably saturated geologic media. These conservation equations for component mass, energy, and solute mass are partial differential equations that mathematically describe flow and transport through porous media. The STORM simulator solves the governing-conservation equations and constitutive functions using numerical techniques for nonlinear systems. The partial differential equations governing thermal and fluid flow processes are solved by the integral volume finite difference method. These governing equations are solved simultaneously using Newton-Raphson iteration. The partial differential equations governing reactive solute transport are solved using either an operator split technique where geochemical reactions and solute transport are solved separately, or a fully coupled technique where these equations are solved simultaneously. The STORM simulator is written in the FORTRAN 77 language, following American National Standards Institute (ANSI) standards

  5. Electrochemical-mechanical coupled modeling and parameterization of swelling and ionic transport in lithium-ion batteries

    Science.gov (United States)

    Sauerteig, Daniel; Hanselmann, Nina; Arzberger, Arno; Reinshagen, Holger; Ivanov, Svetlozar; Bund, Andreas

    2018-02-01

    The intercalation and aging induced volume changes of lithium-ion battery electrodes lead to significant mechanical pressure or volume changes on cell and module level. As the correlation between electrochemical and mechanical performance of lithium ion batteries at nano and macro scale requires a comprehensive and multidisciplinary approach, physical modeling accounting for chemical and mechanical phenomena during operation is very useful for the battery design. Since the introduced fully-coupled physical model requires proper parameterization, this work also focuses on identifying appropriate mathematical representation of compressibility as well as the ionic transport in the porous electrodes and the separator. The ionic transport is characterized by electrochemical impedance spectroscopy (EIS) using symmetric pouch cells comprising LiNi1/3Mn1/3Co1/3O2 (NMC) cathode, graphite anode and polyethylene separator. The EIS measurements are carried out at various mechanical loads. The observed decrease of the ionic conductivity reveals a significant transport limitation at high pressures. The experimentally obtained data are applied as input to the electrochemical-mechanical model of a prismatic 10 Ah cell. Our computational approach accounts intercalation induced electrode expansion, stress generation caused by mechanical boundaries, compression of the electrodes and the separator, outer expansion of the cell and finally the influence of the ionic transport within the electrolyte.

  6. Cation Transport Coupled to ATP Hydrolysis by the (Na, K)-ATPase: An Integrated, Animated Model

    Science.gov (United States)

    Leone, Francisco A.; Furriel, Rosa P. M.; McNamara, John C.; Horisberger, Jean D.; Borin, Ivana A.

    2010-01-01

    An Adobe[R] animation is presented for use in undergraduate Biochemistry courses, illustrating the mechanism of Na[superscript +] and K[superscript +] translocation coupled to ATP hydrolysis by the (Na, K)-ATPase, a P[subscript 2c]-type ATPase, or ATP-powered ion pump that actively translocates cations across plasma membranes. The enzyme is also…

  7. Development of a fluorescence-activated cell sorting method coupled with whole genome amplification to analyze minority and trace Dehalococcoides genomes in microbial communities.

    Science.gov (United States)

    Lee, Patrick K H; Men, Yujie; Wang, Shanquan; He, Jianzhong; Alvarez-Cohen, Lisa

    2015-02-03

    Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10(6) cells or ∼1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing ∼10% and ∼1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.

  8. Microbial nitrate removal in biologically enhanced treated coal gasification wastewater of low COD to nitrate ratio by coupling biological denitrification with iron and carbon micro-electrolysis.

    Science.gov (United States)

    Zhang, Zhengwen; Han, Yuxing; Xu, Chunyan; Ma, Wencheng; Han, Hongjun; Zheng, Mengqi; Zhu, Hao; Ma, Weiwei

    2018-04-21

    Mixotrophic denitrification coupled biological denitrification with iron and carbon micro-electrolysis (IC-ME) is a promising emerging bioprocess for nitrate removal of biologically enhanced treated coal gasification wastewater (BECGW) with low COD to nitrate ratio. TN removal efficiency in R1 with IC-ME assisted was 16.64% higher than R2 with scrap zero valent iron addition, 23.05% higher than R3 with active carbon assisted, 30.51% higher than R4 with only active sludge addition, 80.85% higher than R5 utilizing single IC-ME as control. Fe 2+ generated from IC-ME decreased the production of N 2 O and enriched more Nitrate-reducing Fe(Ⅱ) oxidation bacteria (NRFOB) Acidovorax and Thiobacillus, which could convert nitrate to nitrogen gas. And the presence of Fe 3+ , as the Fe 2+ oxidation product, could stimulate the growth of Fe(III)-reducing strain (FRB) that indicated by redundancy analysis. Microbial network analysis demonstrated FRB Geothrix had a co-occurrence relationship with other bacteria, revealing its dominant involvement in nitrate removal of BECGW. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Coupled flow and salinity transport modelling in semi-arid environments

    DEFF Research Database (Denmark)

    Bauer-Gottwein, Peter; Held, R.J.; Zimmermann, S.

    2006-01-01

    Numerical groundwater modelling is used as the base for sound aquifer system analysis and water resources assessment. In many cases, particularly in semi-arid and arid regions, groundwater flow is intricately linked to salinity transport. A case in point is the Shashe River Valley in Botswana. A ...

  10. Coupled electron-phonon transport from molecular dynamics with quantum baths

    DEFF Research Database (Denmark)

    Lu, Jing Tao; Wang, J. S.

    2009-01-01

    Based on generalized quantum Langevin equations for the tight-binding wavefunction amplitudes and lattice displacements, electron and phonon quantum transport are obtained exactly using molecular dynamics (MD) in the ballistic regime. The electron-phonon interactions can be handled with a quasi...

  11. COUPLED FREE AND DISSOLVED PHASE TRANSPORT: NEW SIMULATION CAPABILITIES AND PARAMETER INVERSION

    Science.gov (United States)

    The vadose zone free-phase simulation capabilities of the US EPA Hydrocarbon Spill Screening Model (HSSM) (Weaver et al., 1994) have been linked with the 3-D multi-species dissolved-phase contaminant transport simulator MT3DMS (Zheng and Wang, 1999; Zheng, 2005). The linkage pro...

  12. Transport from diffuse sources of contamination and its application to a coupled unsaturated - saturated system

    NARCIS (Netherlands)

    Ommen, van H.C.

    1988-01-01

    A simple theory to predict groundwater quality upon contamination from diffuse sources was developed. It appeared that an analogy exists between the predominant transport phenomena and the reaction of a reservoir, in which perfect mixing takes place. Such an analogy enables a simple

  13. Simulation of wind-induced snow transport in alpine terrain using a fully coupled snowpack/atmosphere model

    Science.gov (United States)

    Vionnet, V.; Martin, E.; Masson, V.; Guyomarc'h, G.; Naaim-Bouvet, F.; Prokop, A.; Durand, Y.; Lac, C.

    2013-06-01

    In alpine regions, wind-induced snow transport strongly influences the spatio-temporal evolution of the snow cover throughout the winter season. To gain understanding on the complex processes that drive the redistribution of snow, a new numerical model is developed. It couples directly the detailed snowpack model Crocus with the atmospheric model Meso-NH. Meso-NH/Crocus simulates snow transport in saltation and in turbulent suspension and includes the sublimation of suspended snow particles. A detailed representation of the first meters of the atmosphere allows a fine reproduction of the erosion and deposition process. The coupled model is evaluated against data collected around the experimental site of Col du Lac Blanc (2720 m a.s.l., French Alps). For this purpose, a blowing snow event without concurrent snowfall has been selected and simulated. Results show that the model captures the main structures of atmospheric flow in alpine terrain, the vertical profile of wind speed and the snow particles fluxes near the surface. However, the horizontal resolution of 50 m is found to be insufficient to simulate the location of areas of snow erosion and deposition observed by terrestrial laser scanning. When activated, the sublimation of suspended snow particles causes a reduction in deposition of 5.3%. Total sublimation (surface + blowing snow) is three times higher than surface sublimation in a simulation neglecting blowing snow sublimation.

  14. Simulation of wind-induced snow transport and sublimation in alpine terrain using a fully coupled snowpack/atmosphere model

    Science.gov (United States)

    Vionnet, V.; Martin, E.; Masson, V.; Guyomarc'h, G.; Naaim-Bouvet, F.; Prokop, A.; Durand, Y.; Lac, C.

    2014-03-01

    In alpine regions, wind-induced snow transport strongly influences the spatio-temporal evolution of the snow cover throughout the winter season. To gain understanding on the complex processes that drive the redistribution of snow, a new numerical model is developed. It directly couples the detailed snowpack model Crocus with the atmospheric model Meso-NH. Meso-NH/Crocus simulates snow transport in saltation and in turbulent suspension and includes the sublimation of suspended snow particles. The coupled model is evaluated against data collected around the experimental site of Col du Lac Blanc (2720 m a.s.l., French Alps). First, 1-D simulations show that a detailed representation of the first metres of the atmosphere is required to reproduce strong gradients of blowing snow concentration and compute mass exchange between the snowpack and the atmosphere. Secondly, 3-D simulations of a blowing snow event without concurrent snowfall have been carried out. Results show that the model captures the main structures of atmospheric flow in alpine terrain. However, at 50 m grid spacing, the model reproduces only the patterns of snow erosion and deposition at the ridge scale and misses smaller scale patterns observed by terrestrial laser scanning. When activated, the sublimation of suspended snow particles causes a reduction of deposited snow mass of 5.3% over the calculation domain. Total sublimation (surface + blowing snow) is three times higher than surface sublimation in a simulation neglecting blowing snow sublimation.

  15. 3-D pore-scale resolved model for coupled species/charge/fluid transport in a vanadium redox flow battery

    International Nuclear Information System (INIS)

    Qiu Gang; Joshi, Abhijit S.; Dennison, C.R.; Knehr, K.W.; Kumbur, E.C.; Sun Ying

    2012-01-01

    The vanadium redox flow battery (VRFB) has emerged as a viable grid-scale energy storage technology that offers cost-effective energy storage solutions for renewable energy applications. In this paper, a novel methodology is introduced for modeling of the transport mechanisms of electrolyte flow, species and charge in the VRFB at the pore scale of the electrodes; that is, at the level where individual carbon fiber geometry and electrolyte flow are directly resolved. The detailed geometry of the electrode is obtained using X-ray computed tomography (XCT) and calibrated against experimentally determined pore-scale characteristics (e.g., pore and fiber diameter, porosity, and surface area). The processed XCT data is then used as geometry input for modeling of the electrochemical processes in the VRFB. The flow of electrolyte through the pore space is modeled using the lattice Boltzmann method (LBM) while the finite volume method (FVM) is used to solve the coupled species and charge transport and predict the performance of the VRFB under various conditions. An electrochemical model using the Butler–Volmer equations is used to provide species and charge coupling at the surfaces of the carbon fibers. Results are obtained for the cell potential distribution, as well as local concentration, overpotential and current density profiles under galvanostatic discharge conditions. The cell performance is investigated as a function of the electrolyte flow rate and external drawing current. The model developed here provides a useful tool for building the structure–property–performance relationship of VRFB electrodes.

  16. Stimulation of Na+/K+ ATPase activity and Na+ coupled glucose transport by β-catenin

    International Nuclear Information System (INIS)

    Sopjani, Mentor; Alesutan, Ioana; Wilmes, Jan; Dermaku-Sopjani, Miribane; Lam, Rebecca S.; Koutsouki, Evgenia; Jakupi, Muharrem; Foeller, Michael; Lang, Florian

    2010-01-01

    Research highlights: → The oncogenic transcription factor β-catenin stimulates the Na + /K + -ATPase. → β-Catenin stimulates SGLT1 dependent Na + , glucose cotransport. → The effects are independent of transcription. → β-Catenin sensitive transport may contribute to properties of proliferating cells. -- Abstract: β-Catenin is a multifunctional protein stimulating as oncogenic transcription factor several genes important for cell proliferation. β-Catenin-regulated genes include the serum- and glucocorticoid-inducible kinase SGK1, which is known to stimulate a variety of transport systems. The present study explored the possibility that β-catenin influences membrane transport. To this end, β-catenin was expressed in Xenopus oocytes with or without SGLT1 and electrogenic transport determined by dual electrode voltage clamp. As a result, expression of β-catenin significantly enhanced the ouabain-sensitive current of the endogeneous Na + /K + -ATPase. Inhibition of vesicle trafficking by brefeldin A revealed that the stimulatory effect of β-catenin on the endogenous Na + /K + -ATPase was not due to enhanced stability of the pump protein in the cell membrane. Expression of β-catenin further enhanced glucose-induced current (Ig) in SGLT1-expressing oocytes. In the absence of SGLT1 Ig was negligible irrespective of β-catenin expression. The stimulating effect of β-catenin on both Na + /K + ATPase and SGLT1 activity was observed even in the presence of actinomycin D, an inhibitor of transcription. The experiments disclose a completely novel function of β-catenin, i.e. the regulation of transport.

  17. Coupled Membrane Transport Parameters for Ionic Species in All-Vanadium Redox Flow Batteries

    International Nuclear Information System (INIS)

    Ashraf Gandomi, Yasser; Aaron, D.S.; Mench, M.M.

    2016-01-01

    Highlights: • Real-time crossover of vanadium species was investigated with a novel system. • Concentration and electrostatic potential gradient-induced crossover was separated. • Interaction coefficients were introduced to account for state of charge dependence. • Electric-field-induced crossover is asymmetric for charge and discharge processes. • Net vanadium crossover is from negative to positive half-cell at open-circuit. - Abstract: One of the major sources of capacity loss in all-vanadium redox flow batteries (VRFBs) is the undesired transport of active vanadium species across the ion-exchange membrane, generically termed crossover. In this work, a novel system has been designed and built to investigate the concentration- and electrostatic potential gradient-driven crossover for all vanadium species through the membrane in real-time. For this study, a perfluorosulphonic acid membrane separator (Nafion ® 117) was used. The test system utilizes ultraviolet/visible (UV/Vis) spectroscopy to differentiate vanadium ion species and separates contributions to crossover stemming from concentration and electrostatic potential gradients. It is shown that the rate of species transport through the ion-exchange membrane is state of charge dependent and, as a result, interaction coefficients have been deduced which can be used to better estimate expected crossover over a range of operating conditions. The electric field was shown to increase the negative-to-positive transport of V(II)/V(III) and suppress the positive-to-negative transport of V(IV)/V(V) during discharge, with an inverse trend during charging conditions. Electric-field-induced transport coefficients were deduced directly from experimental data.

  18. A coupled diffusion-transport computational method and its application for the determination of space dependent angular flux distributions at a cold neutron source

    International Nuclear Information System (INIS)

    Turgut, M.H.

    1985-01-01

    A fast calculation program ''BRIDGE'' was developed for the calculation of a Cold Neutron Source (CNS) at a radial beam tube of the FRG-I reactor, which couples a total assembly diffusion calculation to a transport calculation for a certain subregion. For the coupling flux and current boundary values at the common surfaces are taken from the diffusion calculation and are used as driving conditions in the transport calculation. 'Equivalence Theorie' is used for the transport feedback effect on the diffusion calculation to improve the consistency of the boundary values. The optimization of a CNS for maximizing the subthermal flux in the wavelength range 4 - 6 A is discussed. (orig.) [de

  19. Global weak solutions for coupled transport processes in concrete walls at high temperatures

    OpenAIRE

    Beneš, Michal; Štefan, Radek

    2012-01-01

    We consider an initial-boundary value problem for a fully nonlinear coupled parabolic system with nonlinear boundary conditions modelling hygro-thermal behavior of concrete at high temperatures. We prove a global existence of a weak solution to this system on an arbitrary time interval. The main result is proved by an approximation procedure. This consists in proving the existence of solutions to mollified problems using the Leray-Schauder theorem, for which a priori estimates are obtained. T...

  20. Dynamical theory of single-photon transport in a one-dimensional waveguide coupled to identical and nonidentical emitters

    Science.gov (United States)

    Liao, Zeyang; Nha, Hyunchul; Zubairy, M. Suhail

    2016-11-01

    We develop a general dynamical theory for studying a single-photon transport in a one-dimensional (1D) waveguide coupled to multiple emitters which can be either identical or nonidentical. In this theory, both the effects of the waveguide and non-waveguide vacuum modes are included. This theory enables us to investigate the propagation of an emitter excitation or an arbitrary single-photon pulse along an array of emitters coupled to a 1D waveguide. The dipole-dipole interaction induced by the non-waveguide modes, which is usually neglected in the literature, can significantly modify the dynamics of the emitter system as well as the characteristics of the output field if the emitter separation is much smaller than the resonance wavelength. Nonidentical emitters can also strongly couple to each other if their energy difference is less than or of the order of the dipole-dipole energy shift. Interestingly, if their energy difference is close but nonzero, a very narrow transparency window around the resonance frequency can appear which does not occur for identical emitters. This phenomenon may find important applications in quantum waveguide devices such as optical switches and ultranarrow single-photon frequency comb generator.

  1. Development of whole core thermal-hydraulic analysis program ACT. 3. Coupling core module with primary heat transport system module

    International Nuclear Information System (INIS)

    Ohtaka, Masahiko; Ohshima, Hiroyuki

    1998-10-01

    A whole core thermal-hydraulic analysis program ACT is being developed for the purpose of evaluating detailed in-core thermal hydraulic phenomena of fast reactors including inter-wrapper flow under various reactor operation conditions. In this work, the core module as a main part of the ACT developed last year, which simulates thermal-hydraulics in the subassemblies and the inter-subassembly gaps, was coupled with an one dimensional plant system thermal-hydraulic analysis code LEDHER to simulate transients in the primary heat transport system and to give appropriate boundary conditions to the core model. The effective algorithm to couple these two calculation modules was developed, which required minimum modification of them. In order to couple these two calculation modules on the computing system, parallel computing technique using PVM (Parallel Virtual Machine) programming environment was applied. The code system was applied to analyze an out-of-pile sodium experiment simulating core with 7 subassemblies under transient condition for code verification. It was confirmed that the analytical results show a similar tendency of experimental results. (author)

  2. Semiclassical treatment of transport and spin relaxation in spin-orbit coupled systems

    Energy Technology Data Exchange (ETDEWEB)

    Lueffe, Matthias Clemens

    2012-02-10

    The coupling of orbital motion and spin, as derived from the relativistic Dirac equation, plays an important role not only in the atomic spectra but as well in solid state physics. Spin-orbit interactions are fundamental for the young research field of semiconductor spintronics, which is inspired by the idea to use the electron's spin instead of its charge for fast and power saving information processing in the future. However, on the route towards a functional spin transistor there is still some groundwork to be done, e.g., concerning the detailed understanding of spin relaxation in semiconductors. The first part of the present thesis can be placed in this context. We have investigated the processes contributing to the relaxation of a particularly long-lived spin-density wave, which can exist in semiconductor heterostructures with Dresselhaus and Rashba spin-orbit coupling of precisely the same magnitude. We have used a semiclassical spindiffusion equation to study the influence of the Coulomb interaction on the lifetime of this persistent spin helix. We have thus established that, in the presence of perturbations that violate the special symmetry of the problem, electron-electron scattering can have an impact on the relaxation of the spin helix. The resulting temperature-dependent lifetime reproduces the experimentally observed one in a satisfactory manner. It turns out that cubic Dresselhaus spin-orbit coupling is the most important symmetry-breaking element. The Coulomb interaction affects the dynamics of the persistent spin helix also via an Hartree-Fock exchange field. As a consequence, the individual spins precess about the vector of the surrounding local spin density, thus causing a nonlinear dynamics. We have shown that, for an experimentally accessible degree of initial spin polarization, characteristic non-linear effects such as a dramatic increase of lifetime and the appearance of higher harmonics can be expected. Another fascinating solid

  3. Modelling for reactor-style aerobic composting based on coupling theory of mass-heat-momentum transport and Contois equation.

    Science.gov (United States)

    He, Xueqin; Han, Lujia; Ge, Jinyi; Huang, Guangqun

    2018-04-01

    This study establishes an optimal mathematical modelling to rationally describe the dynamic changes and spatial distribution of temperature and oxygen concentration in the aerobic composting process using coupling mass-heat-momentum transfer based on the microbial mechanism. Two different conditional composting experiments, namely continuous aeration and intermittent aeration, were performed to verify the proposed model. The results show that the model accurately predicted the dynamic changes in temperature (case I: R 2  = 0.93, RMSE = 1.95 K; case II: R 2  = 0.86, RMSE = 4.69 K) and oxygen concentration (case I: R 2  = 0.90, RMSE = 1.26%; case II: R 2  = 0.75, RMSE = 2.93%) in the central point of compost substrates. It also systematically simulated fluctuations in oxygen concentration caused by boundary conditions and the spatial distribution of the actual temperature and oxygen concentration. The proposed model exhibits good applicability in simulating the actual working conditions of aerobic composting process. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. Coupled light transport-heat diffusion model for laser dosimetry with dynamic optical properties

    International Nuclear Information System (INIS)

    London, R.A.; Glinsky, M.E.; Zimmerman, G.B.; Eder, D.C.; Jacques, S.L.

    1995-01-01

    The effect of dynamic optical properties on the spatial distribution of light in laser therapy is studied via numerical simulations. A two-dimensional, time dependent computer program called LATIS is used. Laser light transport is simulated with a Monte Carlo technique including anisotropic scattering and absorption. Thermal heat transport is calculated with a finite difference algorithm. Material properties are specified on a 2-D mesh and can be arbitrary functions of space and time. Arrhenius rate equations are solved for tissue damage caused by elevated temperatures. Optical properties are functions of tissue damage, as determined by previous measurements. Results are presented for the time variation of the light distribution and damage within the tissue as the optical properties of the tissue are altered

  5. Transport from diffuse sources of contamination and its application to a coupled unsaturated - saturated system

    OpenAIRE

    Ommen, van, H.C.

    1988-01-01

    A simple theory to predict groundwater quality upon contamination from diffuse sources was developed. It appeared that an analogy exists between the predominant transport phenomena and the reaction of a reservoir, in which perfect mixing takes place. Such an analogy enables a simple incorporation of physico-chemical processes (decomposition, adsorption), as was shown by an illustrative response of the quality of groundwater to an input of a radio-active decaying solute (and its decay...

  6. Anomalous convection diffusion and wave coupling transport of cells on comb frame with fractional Cattaneo-Christov flux

    Science.gov (United States)

    Liu, Lin; Zheng, Liancun; Liu, Fawang; Zhang, Xinxin

    2016-09-01

    An improved Cattaneo-Christov flux model is proposed which can be used to capture the effects of the time and spatial relaxations, the time and spatial inhomogeneous diffusion and the spatial transition probability of cell transport in a highly non-homogeneous medium. Solutions are obtained by numerical discretization method where the time and spatial fractional derivative are discretized by the L1-approximation and shifted Grünwald definition, respectively. The solvability, stability and convergence of the numerical method for the special case of the Cattaneo-Christov equation are proved. Results indicate that the fractional convection diffusion-wave equation is an evolution equation which displays the coexisting characteristics of parabolicity and hyperbolicity. In other words, for α in (0, 1), the cells transport occupies the characteristics of coupling convection diffusion and wave spreading. Moreover, the effects of pertinent time parameter, time and spatial fractional derivative parameters, relaxation parameter, weight coefficient and the convection velocity on the anomalous transport of cells are shown graphically and analyzed in detail.

  7. The understanding of the R7T7 glass blocks long term behavior: chemical and transport coupling in fractured media

    International Nuclear Information System (INIS)

    Chomat, L.

    2008-04-01

    The long term behavior of nuclear waste glass blocks depends highly on chemical reactions which occur at the surface in contact with water. Studies carried out on inactive fractured glass blocks show that fracture networks play a significant part in reactive surface area. Nevertheless, the complexity of results interpretation, due to a weak knowledge of fracture networks and local lixiviation conditions, does not allow us to comprehend the physical and chemical mechanisms involved. Model cracks are a key step to study chemical and transport coupling in fractured media. Crack lixiviation in aggressive conditions (pH≥11) show that the crack's position (horizontal or vertical) determines the dominant transport mechanism (respectively diffusion or convection induced by gravity). This gravity driven flow seems to be negligible in lower pH conditions. The convective velocity is estimated by a 1D model of reactive transport. Two other parameters are studied: the influence of thermal gradient and the influence of interconnected cracks on alteration. A strong retroactive effect of convection, due to thermal gradient, on the alteration kinetic is observed inside the crack. These works lead to a complete alteration experiment of a 163 crack network subject to a thermal gradient. The use of the geochemical software, HYTEC, within the framework of this study shows the potential of the software which is however limited by the kinetics law used. (author)

  8. Beta-adrenergic activation of solute coupled water uptake by toad skin epithelium results in near-isosmotic transport

    DEFF Research Database (Denmark)

    Nielsen, Robert; Larsen, Erik Hviid

    2007-01-01

    (V) with a [Na+] of the transported fluid of 130+/-24 mM ([Na+]Ringer's solution = 117.4 mM). Addition of bumetanide to the inside solution reduced J(V). Water was transported uphill and J(V) reversed at an excess outside osmotic concentration, deltaC(S,rev) = 28.9+/-3.9 mOsm, amiloride decreased delta......C(S,rev) to 7.5+/-1.5 mOsm. It is concluded that water uptake is accomplished by osmotic coupling in the lateral intercellular space (lis), and hypothesized that a small fraction of the Na+ flux pumped into lis is recirculated via basolateral NKCC transporters.......Transepithelial potential (V(T)), conductance (G(T)), and water flow (J(V)) were measured simultaneously with good time resolution (min) in isolated toad (Bufo bufo) skin epithelium with Ringer on both sides. Inside application of 5 microM isoproterenol resulted in the fast increase in G(T) from 1...

  9. Function and expression of the proton-coupled amino acid transporter Slc36a1 along the rat gastrointestinal tract

    DEFF Research Database (Denmark)

    Broberg, M. L.; Holm, Rasmus Koldborg; Tønsberg, H

    2012-01-01

    BACKGROUND AND PURPOSE: Intestinal absorption via membrane transporters may determine the pharmacokinetics of drug compounds. The hypothesis is that oral absorption of gaboxadol (4, 5, 6, 7-tetrahydroisoxazolo [5,4-c] pyridine-3-ol) in rats occurs via the proton-coupled amino acid transporter, r....... The intestinal expression of rSlc36a1 mRNA was measured by quantitative real-time PCR (q-RT-PCR). Furthermore, the hPAT1-/rPAT1-mediated transport of gaboxadol or L-proline was studied in hPAT1-expressing X. laevis oocytes, Caco-2 cell monolayers and excised segments of the rat intestine. KEY RESULTS......). The in vitro carrier-mediated uptake rate of L-proline in the excised intestinal segments was highest in the mid jejunum and low in the colon. The in vitro uptake and the in vivo absorption correlated with the expression of rSlc36a1 mRNA along the rat intestine. CONCLUSIONS AND IMPLICATIONS: The results...

  10. The proton-coupled amino acid transporter hPAT1 is the main transporter involved in vigabatrin uptake in intestinal Caco-2 cells

    DEFF Research Database (Denmark)

    Nøhr, Martha Kampp; Hansen, Steen Honore'; Brodin, Birger

    2012-01-01

    transporter hPAT1. The aim of the project was to identify if transporters are involved in cellular uptake of vigabatrin in Caco-2 cells. Methods: The uptake rate of vigabatrin was measured in Caco-2 cells at pH 6.0 or 7.4 for 15 min after application of 0.1 – 25.0 mM vigabatrin. The inhibitory effect...... of selected amino acids and -derivatives on the apical vigabatrin uptake in Caco-2 cells was investigated. Vigabatrin samples were analyzed using liquid chromatography (LC) coupled to a mass selective detector (MSD). Results: The uptake rate of vigabatrin in Caco-2 cells was pH-dependent. The uptake...... of vigabatrin was saturable at pH 6.0 with a Michaelis constant, Km of 12.7 ± 3.7 mM and a maximal flux, Jmax of 3.7 ± 0.5 nmol•min-1•cm-2. The presences of hPAT1 ligands significantly inhibited the uptake of vigabatrin in Caco-2 cells at pH 6.0, whereas hPAT1 non-ligands did not. Discussion: The saturability...

  11. Transport-diffusion coupling for Candu reactor core follow-Up

    International Nuclear Information System (INIS)

    Varin, E.; Marleau, G.; Chambon, R.

    2003-01-01

    We couple the finite reactor diffusion code DONJON and the lattice code DRAGON, called for simplicity DD, to perform reactor follow-up calculations using a history-based approach. In order to do this, a new DD module is developed. This module manages the transfer of information between standard DONJON and DRAGON data structures. Moreover, it stores in a history data structure the global and local parameters required for cell calculations as well as the isotopic composition of the various materials present in each cell of the reactor. We then implement in DD a parallel algorithm to perform history-based Candu reactor calculations. Here, we assign to each processor a specific number of fuel channels to be analyzed. The DRAGON cell calculations for each of the fuel bundles associated with the specified channels are performed on the same processor in order to minimize communication time. Only the macroscopic cross section libraries are exchanged between the processor. Since the amount of data exchanged is relatively small, we expect to obtain an ideal speed-up. The coupling is tested for the analysis of a simplified Candu reactor model with 4 x 4 channels each containing 4 bundles. A 100 full-power days core tracking sequence with 16 refueling steps is studied. Results are coherent with those obtained using more approximate approaches. Parallel speed-up is near optimal indicating that the use of this approach for more realistic reactor calculations should be pursued. (authors)

  12. A faster numerical scheme for a coupled system modeling soil erosion and sediment transport

    Science.gov (United States)

    Le, M.-H.; Cordier, S.; Lucas, C.; Cerdan, O.

    2015-02-01

    Overland flow and soil erosion play an essential role in water quality and soil degradation. Such processes, involving the interactions between water flow and the bed sediment, are classically described by a well-established system coupling the shallow water equations and the Hairsine-Rose model. Numerical approximation of this coupled system requires advanced methods to preserve some important physical and mathematical properties; in particular, the steady states and the positivity of both water depth and sediment concentration. Recently, finite volume schemes based on Roe's solver have been proposed by Heng et al. (2009) and Kim et al. (2013) for one and two-dimensional problems. In their approach, an additional and artificial restriction on the time step is required to guarantee the positivity of sediment concentration. This artificial condition can lead the computation to be costly when dealing with very shallow flow and wet/dry fronts. The main result of this paper is to propose a new and faster scheme for which only the CFL condition of the shallow water equations is sufficient to preserve the positivity of sediment concentration. In addition, the numerical procedure of the erosion part can be used with any well-balanced and positivity preserving scheme of the shallow water equations. The proposed method is tested on classical benchmarks and also on a realistic configuration.

  13. Linking the Power and Transport Sectors—Part 2: Modelling a Sector Coupling Scenario for Germany

    Directory of Open Access Journals (Sweden)

    Martin Robinius

    2017-07-01

    Full Text Available “Linking the power and transport sectors—Part 1” describes the general principle of “sector coupling” (SC, develops a working definition intended of the concept to be of utility to the international scientific community, contains a literature review that provides an overview of relevant scientific papers on this topic and conducts a rudimentary analysis of the linking of the power and transport sectors on a worldwide, EU and German level. The aim of this follow-on paper is to outline an approach to the modelling of SC. Therefore, a study of Germany as a case study was conducted. This study assumes a high share of renewable energy sources (RES contributing to the grid and significant proportion of fuel cell vehicles (FCVs in the year 2050, along with a dedicated hydrogen pipeline grid to meet hydrogen demand. To construct a model of this nature, the model environment “METIS” (models for energy transformation and integration systems we developed will be described in more detail in this paper. Within this framework, a detailed model of the power and transport sector in Germany will be presented in this paper and the rationale behind its assumptions described. Furthermore, an intensive result analysis for the power surplus, utilization of electrolysis, hydrogen pipeline and economic considerations has been conducted to show the potential outcomes of modelling SC. It is hoped that this will serve as a basis for researchers to apply this framework in future to models and analysis with an international focus.

  14. Uncertanity Analysis in Parameter Estimation of Coupled Bacteria-Sediment Fate and Transport in Streams

    Science.gov (United States)

    Massoudieh, A.; Le, T.; Pachepsky, Y. A.

    2014-12-01

    E. coli is widely used as an fecal indicator bacteria in streams. It has been shown that the interaction between sediments and the bacteria is an important factor in determining its fate and transport in water bodies. In this presentation parameter estimation and uncertainty analysis of a mechanistic model of bacteria-sediment interaction respectively using a hybrid genetic algorithm and Makov-Chain Monte Carlo (MCMC) approach will be presented. The physically-based model considers the advective-dispersive transport of sediments as well as both free-floating and sediment-associated bacteria in the water column and also the fate and transport of bacteria in the bed sediments in a small stream. The bed sediments are treated as a distributed system which allows modeling the evolution of the vertical distribution of bacteria as a result of sedimentation and resuspension, diffusion and bioturbation in the sediments. One-dimensional St. Venant's equation is used to model flow in the stream. The model is applied to sediment and E. coli concentration data collected during a high flow event in a small stream historically receiving agricultural runoff. Measured total suspended sediments and total E. coli concentrations in the water column at three sections of the stream are used for the parameter estimation. The data on the initial distribution of E. coli in the sediments was available and was used as the initial conditions. The MCMC method is used to estimate the joint probability distribution of model parameters including sediment deposition and erosion rates, critical shear stress for deposition and erosion, attachment and detachment rate constants of E. coli to/from sediments and also the effective diffusion coefficients of E. coli in the bed sediments. The uncertainties associated with the estimated parameters are quantified via the MCMC approach and the correlation between the posterior distribution of parameters have been used to assess the model adequacy and

  15. Spatial and thickness dependence of coupling interaction of surface states and influence on transport and optical properties of few-layer Bi2Se3

    Science.gov (United States)

    Li, Zhongjun; Chen, Shi; Sun, Jiuyu; Li, Xingxing; Qiu, Huaili; Yang, Jinlong

    2018-02-01

    Coupling interaction between the bottom and top surface electronic states and the influence on transport and optical properties of Bi2Se3 thin films with 1-8 quintuple layers (QLs) have been investigated by first principles calculations. Obvious spatial and thickness dependences of coupling interaction are found by analyzing hybridization of two surface states. In the thin film with a certain thickness, from the outer to inner atomic layers, the coupling interaction exhibits an increasing trend. On the other hand, as thickness increases, the coupling interaction shows a disproportionate decrease trend. Moreover, the system with 3 QLs exhibits stronger interaction than that with 2 QLs. The presence of coupling interaction would suppress destructive interference of surface states and enhance resistance in various degrees. In view of the inversely proportional relation to transport channel width, the resistance of thin films should show disproportionate thickness dependence. This prediction is qualitatively consistent with the transport measurements at low temperature. Furthermore, the optical properties also exhibit obvious thickness dependence. Especially as the thickness increases, the coupling interaction results in red and blue shifts of the multiple-peak structures in low and high energy regions of imaginary dielectric function, respectively. The red shift trend is in agreement with the recent experimental observation and the blue shift is firstly predicted by the present calculation. The present results give a concrete understanding of transport and optical properties in devices based on Bi2Se3 thin films with few QLs.

  16. A midway forward-adjoint coupling method for neutron and photon Monte Carlo transport

    International Nuclear Information System (INIS)

    Serov, I.V.; John, T.M.; Hoogenboom, J.E.

    1999-01-01

    The midway Monte Carlo method for calculating detector responses combines a forward and an adjoint Monte Carlo calculation. In both calculations, particle scores are registered at a surface to be chosen by the user somewhere between the source and detector domains. The theory of the midway response determination is developed within the framework of transport theory for external sources and for criticality theory. The theory is also developed for photons, which are generated at inelastic scattering or capture of neutrons. In either the forward or the adjoint calculation a so-called black absorber technique can be applied; i.e., particles need not be followed after passing the midway surface. The midway Monte Carlo method is implemented in the general-purpose MCNP Monte Carlo code. The midway Monte Carlo method is demonstrated to be very efficient in problems with deep penetration, small source and detector domains, and complicated streaming paths. All the problems considered pose difficult variance reduction challenges. Calculations were performed using existing variance reduction methods of normal MCNP runs and using the midway method. The performed comparative analyses show that the midway method appears to be much more efficient than the standard techniques in an overwhelming majority of cases and can be recommended for use in many difficult variance reduction problems of neutral particle transport

  17. Two-dimensional model of coupled heat and moisture transport in frost-heaving soils

    International Nuclear Information System (INIS)

    Guymon, G.L.; Berg, R.L.; Hromadka, T.V.

    1984-01-01

    A two-dimensional model of coupled heat and moisture flow in frost-heaving soils is developed based upon well known equations of heat and moisture flow in soils. Numerical solution is by the nodal domain integration method which includes the integrated finite difference and the Galerkin finite element methods. Solution of the phase change process is approximated by an isothermal approach and phenomenological equations are assumed for processes occurring in freezing or thawing zones. The model has been verified against experimental one-dimensional freezing soil column data and experimental two-dimensional soil thawing tank data as well as two-dimensional soil seepage data. The model has been applied to several simple but useful field problems such as roadway embankment freezing and frost heaving

  18. Nutrient and physical profile data from four Microbial Exchanges and Coupling in Coastal Atlantic Systems (MECCAS) cruises collected aboard the R/V Gyre at the mouth of the Chesapeake Bay and northern Atlantic Ocean from February 17, 1985 to September 7, 1986 (NODC Accession 8800324)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Microbial Exchanges and Coupling in Coastal Atlantic Systems (MECCAS) cruise data collected aboard the R/V Gyre at the mouth of the Chesapeake Bay and northern...

  19. Upscaling the Coupled Water and Heat Transport in the Shallow Subsurface

    Science.gov (United States)

    Sviercoski, R. F.; Efendiev, Y.; Mohanty, B. P.

    2018-02-01

    Predicting simultaneous movement of liquid water, water vapor, and heat in the shallow subsurface has many practical interests. The demand for multidimensional multiscale models for this region is important given: (a) the critical role that these processes play in the global water and energy balances, (b) that more data from air-borne and space-borne sensors are becoming available for parameterizations of modeling efforts. On the other hand, numerical models that consider spatial variations of the soil properties, termed here as multiscale, are prohibitively expensive. Thus, there is a need for upscaled models that take into consideration these features, and be computationally affordable. In this paper, a multidimensional multiscale model coupling the water flow and heat transfer and its respective upscaled version are proposed. The formulation is novel as it describes the multidimensional and multiscale tensorial versions of the hydraulic conductivity and the vapor diffusivity, taking into account the tortuosity and porosity properties of the medium. It also includes the coupling with the energy balance equation as a boundary describing atmospheric influences at the shallow subsurface. To demonstrate the accuracy of both models, comparisons were made between simulation and field experiments for soil moisture and temperature at 2, 7, and 12 cm deep, during 11 days. The root-mean-square errors showed that the upscaled version of the system captured the multiscale features with similar accuracy. Given the good matching between simulated and field data for near-surface soil temperature, the results suggest that it can be regarded as a 1-D variable.

  20. Down-Regulation of the Na+-Coupled Phosphate Transporter NaPi-IIa by AMP-Activated Protein Kinase

    Directory of Open Access Journals (Sweden)

    Miribane Dërmaku-Sopjani

    2013-11-01

    Full Text Available Background/Aims: The Na+-coupled phosphate transporter NaPi-IIa is the main carrier accomplishing renal tubular phosphate reabsorption. It is driven by the electrochemical Na+ gradient across the apical cell membrane, which is maintained by Na+ extrusion across the basolateral cell membrane through the Na+/K+ ATPase. The operation of NaPi-IIa thus requires energy in order to avoid cellular Na+ accumulation and K+ loss with eventual decrease of cell membrane potential, Cl- entry and cell swelling. Upon energy depletion, early inhibition of Na+-coupled transport processes may delay cell swelling and thus foster cell survival. Energy depletion is sensed by the AMP-activated protein kinase (AMPK, a serine/threonine kinase stimulating several cellular mechanisms increasing energy production and limiting energy utilization. The present study explored whether AMPK influences the activity of NAPi-IIa. Methods: cRNA encoding NAPi-IIa was injected into Xenopus oocytes with or without additional expression of wild-type AMPK (AMPKα1-HA+AMPKβ1-Flag+AMPKγ1-HA, of inactive AMPKαK45R (AMPKα1K45R+AMPKβ1-Flag+AMPKγ1-HA or of constitutively active AMPKγR70Q (AMPKα1-HA+AMPKβ1-Flag+AMPKγ1R70Q. NaPi-IIa activity was estimated from phosphate-induced current in dual electrode voltage clamp experiments. Results: In NaPi-IIa-expressing, but not in water-injected Xenopus oocytes, the addition of phosphate (1 mM to the extracellular bath solution generated a current (Ip, which was significantly decreased by coexpression of wild-type AMPK and of AMPKγR70Q but not of AMPKαK45R. The phosphate-induced current in NaPi-IIa- and AMPK-expressing Xenopus ooocytes was significantly increased by AMPK inhibitor Compound C (20 µM. Kinetic analysis revealed that AMPK significantly decreased the maximal transport rate. Conclusion: The AMP-activated protein kinase AMPK is a powerful regulator of NaPi-IIa and thus of renal tubular phosphate transport.

  1. The effect of interstitial pressure on therapeutic agent transport: coupling with the tumor blood and lymphatic vascular systems.

    Science.gov (United States)

    Wu, Min; Frieboes, Hermann B; Chaplain, Mark A J; McDougall, Steven R; Cristini, Vittorio; Lowengrub, John S

    2014-08-21

    Vascularized tumor growth is characterized by both abnormal interstitial fluid flow and the associated interstitial fluid pressure (IFP). Here, we study the effect that these conditions have on the transport of therapeutic agents during chemotherapy. We apply our recently developed vascular tumor growth model which couples a continuous growth component with a discrete angiogenesis model to show that hypertensive IFP is a physical barrier that may hinder vascular extravasation of agents through transvascular fluid flux convection, which drives the agents away from the tumor. This result is consistent with previous work using simpler models without blood flow or lymphatic drainage. We consider the vascular/interstitial/lymphatic fluid dynamics to show that tumors with larger lymphatic resistance increase the agent concentration more rapidly while also experiencing faster washout. In contrast, tumors with smaller lymphatic resistance accumulate less agents but are able to retain them for a longer time. The agent availability (area-under-the curve, or AUC) increases for less permeable agents as lymphatic resistance increases, and correspondingly decreases for more permeable agents. We also investigate the effect of vascular pathologies on agent transport. We show that elevated vascular hydraulic conductivity contributes to the highest AUC when the agent is less permeable, but to lower AUC when the agent is more permeable. We find that elevated interstitial hydraulic conductivity contributes to low AUC in general regardless of the transvascular agent transport capability. We also couple the agent transport with the tumor dynamics to simulate chemotherapy with the same vascularized tumor under different vascular pathologies. We show that tumors with an elevated interstitial hydraulic conductivity alone require the strongest dosage to shrink. We further show that tumors with elevated vascular hydraulic conductivity are more hypoxic during therapy and that the response

  2. TART 2000: A Coupled Neutron-Photon, 3-D, Combinatorial Geometry, Time Dependent, Monte Carlo Transport Code

    International Nuclear Information System (INIS)

    Cullen, D.E

    2000-01-01

    TART2000 is a coupled neutron-photon, 3 Dimensional, combinatorial geometry, time dependent Monte Carlo radiation transport code. This code can run on any modern computer. It is a complete system to assist you with input Preparation, running Monte Carlo calculations, and analysis of output results. TART2000 is also incredibly FAST; if you have used similar codes, you will be amazed at how fast this code is compared to other similar codes. Use of the entire system can save you a great deal of time and energy. TART2000 is distributed on CD. This CD contains on-line documentation for all codes included in the system, the codes configured to run on a variety of computers, and many example problems that you can use to familiarize yourself with the system. TART2000 completely supersedes all older versions of TART, and it is strongly recommended that users only use the most recent version of TART2000 and its data files

  3. TART 2000 A Coupled Neutron-Photon, 3-D, Combinatorial Geometry, Time Dependent, Monte Carlo Transport Code

    CERN Document Server

    Cullen, D

    2000-01-01

    TART2000 is a coupled neutron-photon, 3 Dimensional, combinatorial geometry, time dependent Monte Carlo radiation transport code. This code can run on any modern computer. It is a complete system to assist you with input Preparation, running Monte Carlo calculations, and analysis of output results. TART2000 is also incredibly FAST; if you have used similar codes, you will be amazed at how fast this code is compared to other similar codes. Use of the entire system can save you a great deal of time and energy. TART2000 is distributed on CD. This CD contains on-line documentation for all codes included in the system, the codes configured to run on a variety of computers, and many example problems that you can use to familiarize yourself with the system. TART2000 completely supersedes all older versions of TART, and it is strongly recommended that users only use the most recent version of TART2000 and its data files.

  4. Mathematical modeling of coupled drug and drug-encapsulated nanoparticle transport in patient-specific coronary artery walls

    KAUST Repository

    Hossain, Shaolie S.

    2011-08-20

    The majority of heart attacks occur when there is a sudden rupture of atherosclerotic plaque, exposing prothrombotic emboli to coronary blood flow, forming clots that can cause blockages of the arterial lumen. Diseased arteries can be treated with drugs delivered locally to vulnerable plaques. The objective of this work was to develop a computational tool-set to support the design and analysis of a catheter-based nanoparticulate drug delivery system to treat vulnerable plaques and diffuse atherosclerosis. A threedimensional mathematical model of coupled mass transport of drug and drug-encapsulated nanoparticles was developed and solved numerically utilizing isogeometric finite element analysis. Simulations were run on a patient-specific multilayered coronary artery wall segment with a vulnerable plaque and the effect of artery and plaque inhomogeneity was analyzed. The method captured trends observed in local drug delivery and demonstrated potential for optimizing drug design parameters, including delivery location, nanoparticle surface properties, and drug release rate. © Springer-Verlag 2011.

  5. Phase-coherent transport and spin-orbit-coupling in III/V-semiconductor nanowires; Phasenkohaerenter Transport und Spin-Bahn-Wechselwirkung in III/V-Halbleiternanodraehten

    Energy Technology Data Exchange (ETDEWEB)

    Estevez Hernandez, Sergio

    2009-10-16

    Semiconductor nanowires fabricated by a bottom-up approach are not only interesting for the realization of future nanoscaled devices but also appear to be very attractive model systems to tackle fundamental questions concerning the transport in strongly confined systems. In order to avoid the problem connected with carrier depletion, narrowband gap semiconductors, i.e., InAs or InN, or core-shell Nanowires, i.e., GaAs/AlGaAs, are preferred. The underlying reason is that in InAs or InN the Fermi-level pinning in the conduction band results in a carrier accumulation at the surface. In fact, the tubular topology of the surface electron gas opens up the possibility to observe unconventional quantum transport phenomena. When the phase-coherence length in the nanowire is comparable to its dimensions the conductance fluctuates if a magnetic field is applied or if the electron concentration is changed by means of a gate electrode. These so-called universal conductance fluctuations being in the order of e{sup 2}/h originate from the fact that in small disordered samples, electron interference effects are not averaged out. In this work are analyzed universal conductance fluctuations to study the quantum transport properties in InN, InAs and GaAs/AlGaAs nanowires. With the use of a magnetic field and a back-gate electrode the universal conductance fluctuations and localizations effects were analyzed. Since InN and InAs are narrow band gap semiconductors, one naturally expects spin-orbit coupling effects. Because this phenomena is of importance for spin electronic applications. However, owing to the cylindrical symmetry of the InN and InAs nanowires, the latter effect was observable and actually be used to determine the strength of spin-orbit coupling. In order to clearly separate the weak antilocalization effect from the conductance fluctuations, the averaging of the magnetoconductance at different gate voltages was essential. The low-temperature quantum transport properties

  6. Report on stages 3 and 4: testing of coupled chemical transport models

    International Nuclear Information System (INIS)

    Read, D.

    1991-01-01

    Chemval is an international exercise aimed at the verification and validation of predictive models describing groundwater speciation and geochemical transport. As a component of the CEC Mirage project (Migration of radionuclides in the geosphere) - second phase, Chemval is being carried out within the framework of the third Community R and D programme on radioactive waste management and storage (1985-89). This report describes the methodology employed and results obtained for 15 verification tests of varying complexity. The outcome of validation studies against two well-characterized experimental systems is also assessed in terms of the requirements for radiological risk assessment. Chemval is funded jointly by the Commission of the European Communities and Her majesty's Inspectorate of Pollution - UK Department of the Environment. 75 refs., 67 figs; 21 tabs

  7. Analysis of PBMR transients using a coupled neutron transport/thermal-hydraulics code DORT-TD/thermix

    International Nuclear Information System (INIS)

    Tyobeka, B.; Ivanov, K.; Pautz, A.

    2007-01-01

    In the advent of increased demand for safety and economics of nuclear power plants, nuclear engineers and designers are called upon to develop advanced computation tools. In these developments, space-time effects in the dynamics of nuclear reactors must be considered within the framework of a full 3-dimensional treatment of both neutron kinetics and thermal hydraulics. In a recent effort at the Pennsylvania State University, a time-dependent version of the discrete ordinates transport code DORT, DORT-TD was coupled to a 2-dimensional core thermal hydraulics code THERMIX-DIREKT. In the coupling process, a feedback model was developed to account for the feedback effects and was implemented into DORT-TD. During the calculation process for each spatial node of the DORT-TD core model, feedback parameters representative of this node are passed to the feedback module. Using these values, cross section tables are then interpolated for the appropriate macroscopic cross section values. The updated macroscopic cross sections are passed back to DORT-TD to perform transport core calculations, and the power distribution is transferred to THERMIX-DIREKT to obtain the relevant thermal-hydraulics data in turn, and this calculation loop continues. In this paper, DORT-TD/THERMIX is used to simulate transients of interest in the PBMR (Pebble Bed Modular Reactor) safety using established benchmark problems: load change from 100% to 40% power and fast control rod ejection (PBMR-268 benchmark problem). The results obtained are compared with those obtained using the diffusion-based module of the code. The results are only preliminary and so far show that diffusion theory is not such a bad approximation for PBMR for the prediction of integral parameters

  8. Bioenergetic coupling between membrane transport systems and biosynthetic pathways essential for cell cycle progression

    International Nuclear Information System (INIS)

    Leister, K.J.; Cutry, A.F.; Wenner, C.E.

    1986-01-01

    Recently, it has been shown that there exists a point in the cell cycle (approximately 2 h prior to S phase entry) when (Na + /K + )ATPase pump activity is no longer needed for progression through the cycle. These data suggests that pump activity is critical in the biosynthetic processes which enables the cell to proceed through the G 1 phase. A scheme is proposed which is currently being tested that (Na + /K + )ATPase pump activity serves as the driving force in the regulation of other membrane transport processes critical for cell proliferation. For example, in post-confluent quiescent C3H-10T1/2 fibroblasts, when [K + ]/sub o/ is lowered just below the K/sub m/ of the pump for K + there is a 10-fold increase in 3 H-uridine uptake into both acid soluble and insoluble cell fractions. By modulation of the pump in this manner, glucose utilization is enhanced whereas inhibition of the pump by ouabain suppresses glucose utilization. In both methods of affecting the pump, 3 H-leucine incorporation is inhibited. Electron acceptors that influence the redox state of the cell have been shown to both stimulate or inhibit cell cycle progression. Under conditions where [K + ]/sub o/ is lowered, the nucleoside uptake responses observed were modified by electron acceptors depending on the ability to oxidize NAD(P)H directly or to interact with a cytochrome-like component, (e.g. phenazine methosulfate) reversed the enhanced uridine uptake and p-phenylene diamine further enhanced the uridine uptake response. These findings suggest that a plasma membrane redox system (presumably cyt-c like) is linked to nucleoside transport which is subject to (Na + /K + )ATPase activity

  9. A simplified spherical harmonic method for coupled electron-photon transport calculations

    International Nuclear Information System (INIS)

    Josef, J.A.

    1996-12-01

    In this thesis we have developed a simplified spherical harmonic method (SP N method) and associated efficient solution techniques for 2-D multigroup electron-photon transport calculations. The SP N method has never before been applied to charged-particle transport. We have performed a first time Fourier analysis of the source iteration scheme and the P 1 diffusion synthetic acceleration (DSA) scheme applied to the 2-D SP N equations. Our theoretical analyses indicate that the source iteration and P 1 DSA schemes are as effective for the 2-D SP N equations as for the 1-D S N equations. Previous analyses have indicated that the P 1 DSA scheme is unstable (with sufficiently forward-peaked scattering and sufficiently small absorption) for the 2-D S N equations, yet is very effective for the 1-D S N equations. In addition, we have applied an angular multigrid acceleration scheme, and computationally demonstrated that it performs as well for the 2-D SP N equations as for the 1-D S N equations. It has previously been shown for 1-D S N calculations that this scheme is much more effective than the DSA scheme when scattering is highly forward-peaked. We have investigated the applicability of the SP N approximation to two different physical classes of problems: satellite electronics shielding from geomagnetically trapped electrons, and electron beam problems. In the space shielding study, the SP N method produced solutions that are accurate within 10% of the benchmark Monte Carlo solutions, and often orders of magnitude faster than Monte Carlo. We have successfully modeled quasi-void problems and have obtained excellent agreement with Monte Carlo. We have observed that the SP N method appears to be too diffusive an approximation for beam problems. This result, however, is in agreement with theoretical expectations

  10. Coupling Flow & Transport Modeling with Electromagnetic Geophysics to Better Understand Crustal Permeability

    Science.gov (United States)

    Pepin, J.; Folsom, M.; Person, M. A.; Kelley, S.; Gomez-Velez, J. D.; Peacock, J.

    2016-12-01

    Over the last 30 years, considerable effort has focused on understanding the distribution of permeability within the earth's crust and its implications for flow and transport. The scarcity of direct observations makes the description of permeabilities beyond depths of about 3 km particularly challenging. Numerous studies have defined depth-decay relationships for basement permeability, while others note that it is too complex to be characterized by a general relationship. Hydrothermal modeling studies focusing on two geothermal systems within the tectonically active Rio Grande rift of New Mexico suggest that there may be laterally extensive regions of highly permeable (10-14 to 10-12 m2) basement rocks at depths ranging between 4 and 8 km. The NaCl groundwater signature, elevated fracture density, and secondary mineralization of fractured basement outcrops associated with these geothermal systems indicate that there may indeed be significant groundwater flow within the basement rocks of the rift. We hypothesize that there are extensive regions of highly permeable crystalline basement rocks at depths greater than 3 km within the Rio Grande rift. These fractured zones serve as large conduits for geothermal fluids before they ascend to shallow depths through gaps in overlying confining sediments or along faults. To test these hypotheses, we use a combination of geophysical observations and flow and transport modeling. We used electromagnetic geophysics (TEM & MT) to image resistivity in one of the hypothesized deep circulation geothermal systems near Truth or Consequences, NM. The resistivity dataset, in tandem with geochemical and thermal observations, is then used to calibrate a hydrothermal model of the system. This new calibration methodology has the potential to change the way researchers study crustal fluid flow and geothermal systems; thereby providing a tool to explore depths greater than 3 km where minimal data is available. In addition, it has the advantage

  11. Preliminary study on performance of a coupled hydrodynamic and sediment transport model on small domain

    Science.gov (United States)

    Rasyif, Teuku M.; Kato, Shigeru; Syamsidik, Okabe, Takumi

    2017-10-01

    Numerical simulation is one of the useful tools to analyze natural phenomena in the earth such as the tsunami disaster. Several numerical models can simulate the tsunami wave from its generation, propagation, and inundation. However, most tsunami models do not include the sediment transport module. The tsunami wave actually induces a lot of sediment during the propagation in the coastal area. In the case of Indian Ocean Tsunami in 2004, massive morphological changes were caused by the tsunami waves around Sumatra coast. In Aceh, some areas eroded by the tsunami wave were living place for a local community. It is indispensable for the resident in the coastal area to estimate the risk of morphological changes due to a tsunami wave. Therefore, a model that can investigate the morphological changes due tsunami wave is necessary. The result of this model can be used to consider a countermeasure for tsunami wave impact in the coastal area, such as land-use management and planning. The COMCOT-SED model had been developed by several researchers. This model combines the hydrodynamic module and the sediment module. The aim of this study is to get general information about performance of the COMCOT-SED model and to modify the model for more accurate results. Firstly, the model was demonstrated in the ideal condition to confirm the model validity. Then, we evaluated the model performance comparing the model results and the laboratory experiment data which was conducted by other researcher. The authors found that the results of water level and bottom profile by the original model in the ideal condition are not suitable. The model modification will give us more suitable results. The modified model will be applied to simulate the tsunami wave and sediment transport in the small area.

  12. Combined Study of Titanium Dioxide Nanoparticle Transport and Toxicity on Microbial Nitrifying Communities under Single and Repeated Exposures in Soil Columns.

    Science.gov (United States)

    Simonin, Marie; Martins, Jean M F; Uzu, Gaëlle; Vince, Erwann; Richaume, Agnès

    2016-10-04

    Soils are exposed to nanoparticles (NPs) as a result of their increasing use in many commercial products. Adverse effects of NPs on soil microorganisms have been reported in several ecotoxicological studies using microcosms. Although repeated exposures are more likely to occur in soils, most of these previous studies were performed as a single exposure to NPs. Contrary to single contamination, the study of multiple NP contaminations in soils requires the use of specialized setups. Using a soil column experiment, we compared the influence of single and repeated exposures (one, two, or three exposures that resulted in the same final concentration applied) on the transport of titanium dioxide (TiO 2 ) NPs through soil and the effect of these different exposure scenarios on the abundance and activity of soil nitrifying microbial communities after a 2 month incubation. The transport of TiO 2 NPs was very limited under both single and repeated exposures and was highest for the lowest concentration injected during the first application. Significant decreases in nitrification activity and ammonia-oxidizing archaea and bacteria populations were observed only for the repeated exposure scenario (three TiO 2 NP contaminations). These results suggest that, under repeated exposures, the transport of TiO 2 NPs to deep soil layers and groundwater is limited and that a chronic contamination is more harmful for the soil microbiological functioning than a single exposure.

  13. On the modeling of bubble evolution and transport using coupled level-set/CFD method

    International Nuclear Information System (INIS)

    Bartlomiej Wierzbicki; Steven P Antal; Michael Z Podowski

    2005-01-01

    Full text of publication follows: The ability to predict the shape of the gas/liquid/solid interfaces is important for various multiphase flow and heat transfer applications. Specific issues of interest to nuclear reactor thermal-hydraulics, include the evolution of the shape of bubbles attached to solid surfaces during nucleation, bubble surface interactions in complex geometries, etc. Additional problems, making the overall task even more complicated, are associated with the effect of material properties that may be significantly altered by the addition of minute amounts of impurities, such as surfactants or nano-particles. The present paper is concerned with the development of an innovative approach to model time-dependent shape of gas/liquid interfaces in the presence of solid walls. The proposed approach combines a modified level-set method with an advanced CFD code, NPHASE. The coupled numerical solver can be used to simulate the evolution of gas/liquid interfaces in two-phase flows for a variety of geometries and flow conditions, from individual bubbles to free surfaces (stratified flows). The issues discussed in the full paper will include: a description of the novel aspects of the proposed level-set concept based method, an overview of the NPHASE code modeling framework and a description of the coupling method between these two elements of the overall model. A particular attention will be give to the consistency and completeness of model formulation for the interfacial phenomena near the liquid/gas/solid triple line, and to the impact of the proposed numerical approach on the accuracy and consistency of predictions. The accuracy will be measured in terms of both the calculated shape of the interfaces and the gas and liquid velocity fields around the interfaces and in the entire computational domain. The results of model testing and validation will also be shown in the full paper. The situations analyzed will include: bubbles of different sizes and varying

  14. Bonding Strength Effects in Hydro-Mechanical Coupling Transport in Granular Porous Media by Pore-Scale Modeling

    Directory of Open Access Journals (Sweden)

    Zhiqiang Chen

    2016-03-01

    Full Text Available The hydro-mechanical coupling transport process of sand production is numerically investigated with special attention paid to the bonding effect between sand grains. By coupling the lattice Boltzmann method (LBM and the discrete element method (DEM, we are able to capture particles movements and fluid flows simultaneously. In order to account for the bonding effects on sand production, a contact bond model is introduced into the LBM-DEM framework. Our simulations first examine the experimental observation of “initial sand production is evoked by localized failure” and then show that the bonding or cement plays an important role in sand production. Lower bonding strength will lead to more sand production than higher bonding strength. It is also found that the influence of flow rate on sand production depends on the bonding strength in cemented granular media, and for low bonding strength sample, the higher the flow rate is, the more severe the erosion found in localized failure zone becomes.

  15. Modeling of radiation transport in coupled atmosphere-snow-ice-ocean systems

    International Nuclear Information System (INIS)

    Stamnes, K.; Hamre, B.; Stamnes, J.J.; Ryzhikov, G.; Biryulina, M.; Mahoney, R.; Hauss, B.; Sei, A.

    2011-01-01

    A radiative transfer model for coupled atmosphere-snow-ice-ocean systems (CASIO-DISORT) is used to develop accurate and efficient tools for computing the bidirectional reflectance distribution function (BRDF) of sea ice for a wide range of situations occurring in nature. These tools include a method to generate sea ice inherent optical properties (IOPs: single-scattering albedo, extinction optical depth, and scattering asymmetry parameter) for any wavelength between 300 and 4000 nm as a function of sea ice physical parameters including real and imaginary parts of the sea ice refractive index, brine pocket concentration and effective brine pocket size, air bubble concentration and effective air bubble size, volume fraction of ice impurities and impurity absorption coefficient, and sea ice thickness. The CASIO-DISORT code was used to compute look-up tables (LUTs) of the Fourier expansion coefficients of the BRDF as a function of angles of illumination and observation, sea ice IOPs, and ocean albedo. By interpolation in the LUTs one efficiently obtains accurate BRDF values. To include snow on the ice we modified DISORT2 to accept Fourier expansion coefficients for the BDRF as input instead of the BRDF itself, thereby reducing the computation time by a factor of about 60. The BRDF computed by CASIO-DISORT or retrieved from the LUTs applies to diffuse light only. To remedy this shortcoming we added a specular Gaussian beam component to the new BRDF tool and verified that it works well for BRDFs for bare and snow-covered sea ice.

  16. Coupling External Radiation Transport Code Results to the GADRAS Detector Response Function

    International Nuclear Information System (INIS)

    Mitchell, Dean J.; Thoreson, Gregory G.; Horne, Steven M.

    2014-01-01

    Simulating gamma spectra is useful for analyzing special nuclear materials. Gamma spectra are influenced not only by the source and the detector, but also by the external, and potentially complex, scattering environment. The scattering environment can make accurate representations of gamma spectra difficult to obtain. By coupling the Monte Carlo Nuclear Particle (MCNP) code with the Gamma Detector Response and Analysis Software (GADRAS) detector response function, gamma spectrum simulations can be computed with a high degree of fidelity even in the presence of a complex scattering environment. Traditionally, GADRAS represents the external scattering environment with empirically derived scattering parameters. By modeling the external scattering environment in MCNP and using the results as input for the GADRAS detector response function, gamma spectra can be obtained with a high degree of fidelity. This method was verified with experimental data obtained in an environment with a significant amount of scattering material. The experiment used both gamma-emitting sources and moderated and bare neutron-emitting sources. The sources were modeled using GADRAS and MCNP in the presence of the external scattering environment, producing accurate representations of the experimental data.

  17. Spin-orbit coupling and transport in strongly correlated two-dimensional systems

    Science.gov (United States)

    Huang, Jian; Pfeiffer, L. N.; West, K. W.

    2017-05-01

    Measuring the magnetoresistance (MR) of ultraclean GaAs two-dimensional holes for a large rs range of 20-50, two striking behaviors in relation to the spin-orbit coupling (SOC) emerge in response to strong electron-electron interaction. First, in exact correspondence to the zero-field metal-to-insulator transition (MIT), the sign of the MR switches from being positive in the metallic regime to being negative in the insulating regime when the carrier density crosses the critical density pc of MIT (rs˜39 ). Second, as the SOC-driven correction Δ ρ to the MR decreases with reducing carrier density (or the in-plane wave vector), it exhibits an upturn in the close proximity just above pc where rs is beyond 30, indicating a substantially enhanced SOC effect. This peculiar behavior echoes with a trend of delocalization long suspected for the SOC-interaction interplay. Meanwhile, for p 40 , in contrast to the common belief that a magnet field enhances Wigner crystallization, the negative MR is likely linked to enhanced interaction.

  18. Human proton coupled folic acid transporter is a monodisperse oligomer in the lauryl maltose neopentyl glycol solubilized state.

    Science.gov (United States)

    Aduri, Nanda G; Ernst, Heidi A; Prabhala, Bala K; Bhatt, Shweta; Boesen, Thomas; Gajhede, Michael; Mirza, Osman

    2018-01-08

    The human proton coupled folic acid transporter PCFT is the major import route for dietary folates. Mutations in the gene encoding PCFT cause hereditary folic acid malabsorption, which manifests itself by compromised folate absorption from the intestine and also in impaired folate transport into the central nervous system. Since its recent discovery, PCFT has been the subject of numerous biochemical studies aiming at understanding its structure and mechanism. One major focus has been its oligomeric state, with some reports supporting oligomers and others a monomer. Here, we report the overexpression and purification of recombinant PCFT. Following detergent screening, n-Dodecyl β-D-maltoside (DDM) and lauryl maltose neopentyl glycol (LMNG) were chosen for further work as they exhibited the most optimal solubilization. We found that purified detergent solubilized PCFT was able to bind folic acid, thus indicating a functionally active protein. Size exclusion chromatography showed that PCFT in DDM was polydisperse; the LMNG preparation was clearly monodisperse but with shorter retention time than the major DDM peak. To assess the oligomeric state negative stain electron microscopy was performed which showed a particle with the size of a PCFT dimer. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Mathematical modeling of the coupled transport and electrochemical reactions in solid oxide steam electrolyzer for hydrogen production

    International Nuclear Information System (INIS)

    Ni, Meng; Leung, Michael K.H.; Leung, Dennis Y.C.

    2007-01-01

    A mathematical model was developed to simulate the coupled transport/electrochemical reaction phenomena in a solid oxide steam electrolyzer (SOSE) at the micro-scale level. Ohm's law, dusty gas model (DGM), Darcy's law, and the generalized Butler Volmer equation were employed to determine the transport of electronic/ionic charges and gas species as well as the electrochemical reactions. Parametric analyses were performed to investigate the effects of operating parameters and micro-structural parameters on SOSE potential. The results substantiated the fact that SOSE potential could be effectively decreased by increasing the operating temperature. In addition, higher steam molar fraction would enhance the operation of SOSE with lower potential. The effect of particle sizes on SOSE potential was studied with due consideration on the SOSE activation and concentration overpotentials. Optimal particle sizes that could minimize the SOSE potential were obtained. It was also found that decreasing electrode porosity could monotonically decrease the SOSE potential. Besides, optimal values of volumetric fraction of electronic particles were found to minimize electrode total overpotentials. In order to optimize electrode microstructure to minimize SOSE electricity consumption, the concept of 'functionally graded materials (FGM)' was introduced to lower the SOSE potential. The advanced design of particle size graded SOSE was found effective for minimizing electrical energy consumption resulting in efficient SOSE hydrogen production. The micro-scale model was capable of predicting SOSE hydrogen production performance and would be a useful tool for design optimization

  20. Electrical and thermoelectric transport properties of two-dimensional fermionic systems with k-cubic spin-orbit coupling.

    Science.gov (United States)

    Mawrie, Alestin; Verma, Sonu; Ghosh, Tarun Kanti

    2017-09-01

    We investigate effect of k-cubic spin-orbit interaction on electrical and thermoelectric transport properties of two-dimensional fermionic systems. We obtain exact analytical expressions of the inverse relaxation time (IRT) and the Drude conductivity for long-range Coulomb and short-range delta scattering potentials. The IRT reveals that the scattering is completely suppressed along the three directions θ = (2n+1)π/3 with n=1,2,3. We also obtain analytical results of the thermopower and thermal conductivity at low temperature. The thermoelectric transport coefficients obey the Wiedemann-Franz law, even in the presence of k-cubic Rashba spin-orbit interaction (RSOI) at low temperature. In the presence of quantizing magnetic field, the signature of the RSOI is revealed through the appearance of the beating pattern in the Shubnikov-de Haas (SdH) oscillations of thermopower and thermal conductivity in low magnetic field regime. The empirical formulae for the SdH oscillation frequencies accurately describe the locations of the beating nodes. The beating pattern in magnetothermoelectric measurement can be used to extract the spin-orbit coupling constant. © 2017 IOP Publishing Ltd.

  1. Electrical and thermoelectric transport properties of two-dimensional fermionic systems with k-cubic spin-orbit coupling

    Science.gov (United States)

    Mawrie, Alestin; Verma, Sonu; Kanti Ghosh, Tarun

    2017-11-01

    We investigate the effect of k-cubic spin-orbit interaction on the electrical and thermoelectric transport properties of two-dimensional fermionic systems. We obtain exact analytical expressions of the inverse relaxation time (IRT) and the Drude conductivity for long-range Coulomb and short-range delta scattering potentials. The IRT reveals that the scattering is completely suppressed along the three directions θ^\\prime = (2n+1)π/3 with n=1, 2, 3 . We also obtain analytical results of the thermopower and thermal conductivity at low temperature. The thermoelectric transport coefficients obey the Wiedemann-Franz law, even in the presence of k-cubic Rashba spin-orbit interaction (RSOI) at low temperature. In the presence of a quantizing magnetic field, the signature of the RSOI is revealed through the appearance of the beating pattern in the Shubnikov-de Haas (SdH) oscillations of thermopower and thermal conductivity in the low magnetic field regime. The empirical formulae for the SdH oscillation frequencies accurately describe the locations of the beating nodes. The beating pattern in magnetothermoelectric measurement can be used to extract the spin-orbit coupling constant.

  2. Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB.

    Science.gov (United States)

    Eicher, Thomas; Seeger, Markus A; Anselmi, Claudio; Zhou, Wenchang; Brandstätter, Lorenz; Verrey, François; Diederichs, Kay; Faraldo-Gómez, José D; Pos, Klaas M

    2014-09-19

    Membrane transporters of the RND superfamily confer multidrug resistance to pathogenic bacteria, and are essential for cholesterol metabolism and embryonic development in humans. We use high-resolution X-ray crystallography and computational methods to delineate the mechanism of the homotrimeric RND-type proton/drug antiporter AcrB, the active component of the major efflux system AcrAB-TolC in Escherichia coli, and one most complex and intriguing membrane transporters known to date. Analysis of wildtype AcrB and four functionally-inactive variants reveals an unprecedented mechanism that involves two remote alternating-access conformational cycles within each protomer, namely one for protons in the transmembrane region and another for drugs in the periplasmic domain, 50 Å apart. Each of these cycles entails two distinct types of collective motions of two structural repeats, coupled by flanking α-helices that project from the membrane. Moreover, we rationalize how the cross-talk among protomers across the trimerization interface might lead to a more kinetically efficient efflux system.

  3. Coupled Vortex-Lattice Flight Dynamic Model with Aeroelastic Finite-Element Model of Flexible Wing Transport Aircraft with Variable Camber Continuous Trailing Edge Flap for Drag Reduction

    Science.gov (United States)

    Nguyen, Nhan; Ting, Eric; Nguyen, Daniel; Dao, Tung; Trinh, Khanh

    2013-01-01

    This paper presents a coupled vortex-lattice flight dynamic model with an aeroelastic finite-element model to predict dynamic characteristics of a flexible wing transport aircraft. The aircraft model is based on NASA Generic Transport Model (GTM) with representative mass and stiffness properties to achieve a wing tip deflection about twice that of a conventional transport aircraft (10% versus 5%). This flexible wing transport aircraft is referred to as an Elastically Shaped Aircraft Concept (ESAC) which is equipped with a Variable Camber Continuous Trailing Edge Flap (VCCTEF) system for active wing shaping control for drag reduction. A vortex-lattice aerodynamic model of the ESAC is developed and is coupled with an aeroelastic finite-element model via an automated geometry modeler. This coupled model is used to compute static and dynamic aeroelastic solutions. The deflection information from the finite-element model and the vortex-lattice model is used to compute unsteady contributions to the aerodynamic force and moment coefficients. A coupled aeroelastic-longitudinal flight dynamic model is developed by coupling the finite-element model with the rigid-body flight dynamic model of the GTM.

  4. Model of the saltation transport by Discrete Element Method coupled with wind interaction

    Directory of Open Access Journals (Sweden)

    Oger Luc

    2017-01-01

    Full Text Available We study the Aeolian saltation transport problem by analysing the collision of incident energetic beads with granular packing. We investigate the collision process for the case where the incident bead and those from the packing have identical mechanical properties. We analyse the features of the consecutive collision process. We used a molecular dynamics method known as DEM (soft Discrete Element Method with 20000 particles (2D. The grains were displayed randomly in a box (250X60. A few incident disks are launched with a constant velocity and angle with high random position to initiate the flow. A wind velocity profile is applied on the flowing zone of the saltation. The velocity profile is obtained by the calculi of the counter-flow due to the local packing fraction induced by the granular flow. We analyse the evolution of the upper surface of the disk packing. In the beginning, the saltation process can be seen as the classical “splash function” in which one bead hits a fully static dense packing. Then, the quasi-fluidized upper layer of the packing creates a completely different behaviour of the “animated splash function”. The dilation of the upper surface due to the previous collisions is responsible for a need of less input energy for launching new ejected disks. This phenomenon permits to maintain a constant granular flow with a “small” wind velocity on the surface of the disk bed.

  5. A Generalized Boltzmann Fokker-Planck Method for Coupled Charged Particle Transport

    Energy Technology Data Exchange (ETDEWEB)

    Prinja, Anil K

    2012-01-09

    The goal of this project was to develop and investigate the performance of reduced-physics formulations of high energy charged particle (electrons, protons and heavier ions) transport that are computationally more efficient than not only analog Monte Carlo methods but also the established condensed history Monte Carlo technique. Charged particles interact with matter by Coulomb collisions with target nuclei and electrons, by bremsstrahlung radiation loss and by nuclear reactions such as spallation and fission. Of these, inelastic electronic collisions and elastic nuclear collisions are the dominant cause of energy-loss straggling and angular deflection or range straggling of a primary particle. These collisions are characterized by extremely short mean free paths (sub-microns) and highly peaked, near-singular differential cross sections about forward directions and zero energy loss, with the situation for protons and heavier ions more extreme than for electrons. For this reason, analog or truephysics single-event Monte Carlo simulation, while possible in principle, is computationally prohibitive for routine calculation of charged particle interaction phenomena.

  6. Subsurface Transport Over Reactive Multiphases (STORM): A general, coupled, nonisothermal multiphase flow, reactive transport, and porous medium alteration simulator, Version 2 user's guide

    International Nuclear Information System (INIS)

    Bacon, D.H.; White, M.D.; McGrail, B.P.

    2000-01-01

    The Hanford Site, in southeastern Washington State, has been used extensively to produce nuclear materials for the US strategic defense arsenal by the Department of Energy (DOE) and its predecessors, the US Atomic Energy Commission and the US Energy Research and Development Administration. A large inventory of radioactive and mixed waste has accumulated in 177 buried single- and double shell tanks. Liquid waste recovered from the tanks will be pretreated to separate the low-activity fraction from the high-level and transuranic wastes. Vitrification is the leading option for immobilization of these wastes, expected to produce approximately 550,000 metric tons of Low Activity Waste (LAW) glass. This total tonnage, based on nominal Na 2 O oxide loading of 20% by weight, is destined for disposal in a near-surface facility. Before disposal of the immobilized waste can proceed, the DOE must approve a performance assessment, a document that described the impacts, if any, of the disposal facility on public health and environmental resources. Studies have shown that release rates of radionuclides from the glass waste form by reaction with water determine the impacts of the disposal action more than any other independent parameter. This report describes the latest accomplishments in the development of a computational tool, Subsurface Transport Over Reactive Multiphases (STORM), Version 2, a general, coupled non-isothermal multiphase flow and reactive transport simulator. The underlying mathematics in STORM describe the rate of change of the solute concentrations of pore water in a variably saturated, non-isothermal porous medium, and the alteration of waste forms, packaging materials, backfill, and host rocks

  7. Stoichiometry of vectorial H+ movements coupled to electron transport and to ATP synthesis in mitochondria

    Science.gov (United States)

    Alexandre, Adolfo; Reynafarje, Baltazar; Lehninger, Albert L.

    1978-01-01

    In order to verify more directly our earlier measurements showing that, on the average, close to four vectorial H+ are rejected per pair of electrons passing each of the three energy-conserving sites of the mitochondrial electron transport chain, direct tests of the H+/2e- ratio for sites 2 and 3 were carried out in the presence of permeant charge-compensating cations. Site 2 was examined by utilizing succinate as electron donor and ferricyanide as electron acceptor from mitochondrial cytochrome c; the directly measured H+/2e- ratio was close to 4. Energy-conserving site 3 was isolated for study with ferrocyanide or ascorbate plus tetramethylphenylenediamine as electron donors to cytochrome c and with oxygen as electron acceptor. The directly measured H+/2e- ratio for site 3 was close to 4. The H+/ATP ratio (number of vectorial H+ ejected per ATP hydrolyzed) was determined with a new method in which the steady-state rates of both H+ ejection and ATP hydrolysis were measured in the presence of K+ + valinomycin. The H+/ATP ratio was found to approach 3.0. A proton cycle for oxidative phosphorylation is proposed, in which four electrochemical H+ equivalents are ejected per pair of electrons passing each energy-conserving site; three of the H+ equivalents pass inward to derive ATP synthesis from ADP and phosphate and the fourth H+ is used to bring about the energy-requiring electrogenic expulsion of ATP4- in exchange for extramitochondrial ADP3-, via the H+/H2PO4- symporter. PMID:31621

  8. Development and Implementation of Photonuclear Cross-Section Data for Mutually Coupled Neutron-Photon Transport Calculations in the Monte Carlo N-Particle (MCNP) Radiation Transport Code

    International Nuclear Information System (INIS)

    White, Morgan C.

    2000-01-01

    The fundamental motivation for the research presented in this dissertation was the need to development a more accurate prediction method for characterization of mixed radiation fields around medical electron accelerators (MEAs). Specifically, a model is developed for simulation of neutron and other particle production from photonuclear reactions and incorporated in the Monte Carlo N-Particle (MCNP) radiation transport code. This extension of the capability within the MCNP code provides for the more accurate assessment of the mixed radiation fields. The Nuclear Theory and Applications group of the Los Alamos National Laboratory has recently provided first-of-a-kind evaluated photonuclear data for a select group of isotopes. These data provide the reaction probabilities as functions of incident photon energy with angular and energy distribution information for all reaction products. The availability of these data is the cornerstone of the new methodology for state-of-the-art mutually coupled photon-neutron transport simulations. The dissertation includes details of the model development and implementation necessary to use the new photonuclear data within MCNP simulations. A new data format has been developed to include tabular photonuclear data. Data are processed from the Evaluated Nuclear Data Format (ENDF) to the new class ''u'' A Compact ENDF (ACE) format using a standalone processing code. MCNP modifications have been completed to enable Monte Carlo sampling of photonuclear reactions. Note that both neutron and gamma production are included in the present model. The new capability has been subjected to extensive verification and validation (V and V) testing. Verification testing has established the expected basic functionality. Two validation projects were undertaken. First, comparisons were made to benchmark data from literature. These calculations demonstrate the accuracy of the new data and transport routines to better than 25 percent. Second, the ability to

  9. Development and Implementation of Photonuclear Cross-Section Data for Mutually Coupled Neutron-Photon Transport Calculations in the Monte Carlo N-Particle (MCNP) Radiation Transport Code

    Energy Technology Data Exchange (ETDEWEB)

    White, Morgan C. [Univ. of Florida, Gainesville, FL (United States)

    2000-07-01

    The fundamental motivation for the research presented in this dissertation was the need to development a more accurate prediction method for characterization of mixed radiation fields around medical electron accelerators (MEAs). Specifically, a model is developed for simulation of neutron and other particle production from photonuclear reactions and incorporated in the Monte Carlo N-Particle (MCNP) radiation transport code. This extension of the capability within the MCNP code provides for the more accurate assessment of the mixed radiation fields. The Nuclear Theory and Applications group of the Los Alamos National Laboratory has recently provided first-of-a-kind evaluated photonuclear data for a select group of isotopes. These data provide the reaction probabilities as functions of incident photon energy with angular and energy distribution information for all reaction products. The availability of these data is the cornerstone of the new methodology for state-of-the-art mutually coupled photon-neutron transport simulations. The dissertation includes details of the model development and implementation necessary to use the new photonuclear data within MCNP simulations. A new data format has been developed to include tabular photonuclear data. Data are processed from the Evaluated Nuclear Data Format (ENDF) to the new class ''u'' A Compact ENDF (ACE) format using a standalone processing code. MCNP modifications have been completed to enable Monte Carlo sampling of photonuclear reactions. Note that both neutron and gamma production are included in the present model. The new capability has been subjected to extensive verification and validation (V&V) testing. Verification testing has established the expected basic functionality. Two validation projects were undertaken. First, comparisons were made to benchmark data from literature. These calculations demonstrate the accuracy of the new data and transport routines to better than 25 percent. Second

  10. Coupled nonequilibrium flow, energy and radiation transport for hypersonic planetary entry

    Science.gov (United States)

    Frederick, Donald Jerome

    An ever increasing demand for energy coupled with a need to mitigate climate change necessitates technology (and lifestyle) changes globally. An aspect of the needed change is a decrease in the amount of anthropogenically generated CO2 emitted to the atmosphere. The decrease needed cannot be expected to be achieved through only one source of change or technology, but rather a portfolio of solutions are needed. One possible technology is Carbon Capture and Storage (CCS), which is likely to play some role due to its combination of mature and promising emerging technologies, such as the burning of hydrogen in gas turbines created by pre-combustion CCS separation processes. Thus research on effective methods of burning turbulent hydrogen jet flames (mimicking gas turbine environments) are needed, both in terms of experimental investigation and model development. The challenge in burning (and modeling the burning of) hydrogen lies in its wide range of flammable conditions, its high diffusivity (often requiring a diluent such as nitrogen to produce a lifted turbulent jet flame), and its behavior under a wide range of pressures. In this work, numerical models are used to simulate the environment of a gas turbine combustion chamber. Concurrent experimental investigations are separately conducted using a vitiated coflow burner (which mimics the gas turbine environment) to guide the numerical work in this dissertation. A variety of models are used to simulate, and occasionally guide, the experiment. On the fundamental side, mixing and chemistry interactions motivated by a H2/N2 jet flame in a vitiated coflow are investigated using a 1-D numerical model for laminar flows and the Linear Eddy Model for turbulent flows. A radial profile of the jet in coflow can be modeled as fuel and oxidizer separated by an initial mixing width. The effects of species diffusion model, pressure, coflow composition, and turbulent mixing on the predicted autoignition delay times and mixture

  11. Coupling climate conditions, sediment sources and sediment transport in an alpine basin

    Science.gov (United States)

    Rainato, Riccardo; Picco, Lorenzo; Cavalli, Marco; Mao, Luca; Neverman, Andrew J.; Tarolli, Paolo

    2017-04-01

    -2006 period. In this sense, the sediment availability resulting from armour layer and bedform removal appears crucial to describing the sediment fluxes during this period, stressing the key role of the in-channel sediment supply. In the recent period 2007-2015 a marked climate warming accompanied by increased precipitation was observed. This climate forcing did not affect the landscape evolution, with sediment source extent remaining substantially in line between 2006 and 2016. The absence of a significant landscape response and the restoration of the channel armour layer can describe the limited sediment fluxes observed during the last decade. In particular, the increased temperature and precipitation were not accompanied by an increase in flood occurrence and magnitude, stressing the evident absence of hillslope-channel network coupling. This research was funded by the University of Padova Research Projects 'Sediment transfer processes in an Alpine basin: sediment cascades from hillslopes to the channel network-BIRD167919'.

  12. A coupling alternative to reactive transport simulations for long-term prediction of chemical reactions in heterogeneous CO2 storage systems

    Directory of Open Access Journals (Sweden)

    M. De Lucia

    2015-02-01

    Full Text Available Fully coupled, multi-phase reactive transport simulations of CO2 storage systems can be approximated by a simplified one-way coupling of hydrodynamics and reactive chemistry. The main characteristics of such systems, and hypotheses underlying the proposed alternative coupling, are (i that the presence of CO2 is the only driving force for chemical reactions and (ii that its migration in the reservoir is only marginally affected by immobilisation due to chemical reactions. In the simplified coupling, the exposure time to CO2 of each element of the hydrodynamic grid is estimated by non-reactive simulations and the reaction path of one single batch geochemical model is applied to each grid element during its exposure time. In heterogeneous settings, analytical scaling relationships provide the dependency of velocity and amount of reactions to porosity and gas saturation. The analysis of TOUGHREACT fully coupled reactive transport simulations of CO2 injection in saline aquifer, inspired to the Ketzin pilot site (Germany, both in homogeneous and heterogeneous settings, confirms that the reaction paths predicted by fully coupled simulations in every element of the grid show a high degree of self-similarity. A threshold value for the minimum concentration of dissolved CO2 considered chemically active is shown to mitigate the effects of the discrepancy between dissolved CO2 migration in non-reactive and fully coupled simulations. In real life, the optimal threshold value is unknown and has to be estimated, e.g. by means of 1-D or 2-D simulations, resulting in an uncertainty ultimately due to the process de-coupling. However, such uncertainty is more than acceptable given that the alternative coupling enables using grids of the order of millions of elements, profiting from much better description of heterogeneous reservoirs at a fraction of the calculation time of fully coupled models.

  13. Integration of prognostic aerosol-cloud interactions in a chemistry transport model coupled offline to a regional climate model

    Science.gov (United States)

    Thomas, M. A.; Kahnert, M.; Andersson, C.; Kokkola, H.; Hansson, U.; Jones, C.; Langner, J.; Devasthale, A.

    2015-06-01

    To reduce uncertainties and hence to obtain a better estimate of aerosol (direct and indirect) radiative forcing, next generation climate models aim for a tighter coupling between chemistry transport models and regional climate models and a better representation of aerosol-cloud interactions. In this study, this coupling is done by first forcing the Rossby Center regional climate model (RCA4) with ERA-Interim lateral boundaries and sea surface temperature (SST) using the standard cloud droplet number concentration (CDNC) formulation (hereafter, referred to as the "stand-alone RCA4 version" or "CTRL" simulation). In the stand-alone RCA4 version, CDNCs are constants distinguishing only between land and ocean surface. The meteorology from this simulation is then used to drive the chemistry transport model, Multiple-scale Atmospheric Transport and Chemistry (MATCH), which is coupled online with the aerosol dynamics model, Sectional Aerosol module for Large Scale Applications (SALSA). CDNC fields obtained from MATCH-SALSA are then fed back into a new RCA4 simulation. In this new simulation (referred to as "MOD" simulation), all parameters remain the same as in the first run except for the CDNCs provided by MATCH-SALSA. Simulations are carried out with this model setup for the period 2005-2012 over Europe, and the differences in cloud microphysical properties and radiative fluxes as a result of local CDNC changes and possible model responses are analysed. Our study shows substantial improvements in cloud microphysical properties with the input of the MATCH-SALSA derived 3-D CDNCs compared to the stand-alone RCA4 version. This model setup improves the spatial, seasonal and vertical distribution of CDNCs with a higher concentration observed over central Europe during boreal summer (JJA) and over eastern Europe and Russia during winter (DJF). Realistic cloud droplet radii (CD radii) values have been simulated with the maxima reaching 13 μm, whereas in the stand

  14. Characterization of the ZAT1p zinc transporter from Arabidopsis thaliana in microbial model organisms and reconstituted proteoliposomes.

    Science.gov (United States)

    Bloss, Tanja; Clemens, Stephan; Nies, Dietrich H

    2002-03-01

    The ZAT1p zinc transporter from Arabidopsis thaliana (L.) Heynh. is a member of the cation diffusion facilitator (CDF) protein family. When heterologously expressed in Escherichia coli, ZAT1p bound zinc in a metal blot. Binding of zinc occurred mainly to the hydrophilic amino acid region from H182 to H232. A ZAT1p/ZAT1p*Delta(M1-I25) protein mixture was purified and reconstituted into proteoliposomes. Uptake of zinc into the proteoliposomes did not require a proton gradient across the liposomal membrane. ZAT1p did not transport cobalt, and transported cadmium at only 1% of the zinc transport rate. ZAT1p functioned as an uptake system for 65Zn2+ in two strains of the Gram-negative bacterium Ralstonia metallidurans, which were different in their content of zinc-efflux systems. The ZAT1 gene did not rescue increased zinc sensitivity of a Delta ZRC1single-mutant strain or of a Delta ZRC1 Delta COT1 double-mutant strain of Saccharomyces cerevisiae, but ZAT1 complemented this phenotype in a Delta SpZRC1 mutant strain of Schizosaccharomyces pombe.

  15. Effect of mass and charge transport speed and direction in porous anodes on microbial electrolysis cell performance

    NARCIS (Netherlands)

    Sleutels, T.H.J.A.; Hamelers, H.V.M.; Buisman, C.J.N.

    2011-01-01

    The use of porous electrodes like graphite felt as anode material has the potential of achieving high volumetric current densities. High volumetric current densities, however, may also lead to mass transport limitations within these porous materials. Therefore, in this study we investigated the mass

  16. Improved performance of porous bio-anodes in microbial electrolysis cells by enhancing mass and charge transport

    NARCIS (Netherlands)

    Sleutels, T.H.J.A.; Lodder, R.; Hamelers, H.V.M.; Buisman, C.J.N.

    2009-01-01

    To create an efficient MEC high current densities and high coulombic efficiencies are required. The aim of this study was to increase cur-rent densities and coulombic efficiencies by influencing mass and charge transport in porous electrodes by: (i) introduction of a forced flow through the anode to

  17. Stable "Waterbelt" climates controlled by tropical ocean heat transport: A nonlinear coupled climate mechanism of relevance to Snowball Earth

    Science.gov (United States)

    Rose, Brian E. J.

    2015-02-01

    Ongoing controversy about Neoproterozoic Snowball Earth events motivates a theoretical study of stability and hysteresis properties of very cold climates. A coupled atmosphere-ocean-sea ice general circulation model (GCM) has four stable equilibria ranging from 0% to 100% ice cover, including a "Waterbelt" state with tropical sea ice. All four states are found at present-day insolation and greenhouse gas levels and with two idealized ocean basin configurations. The Waterbelt is stabilized against albedo feedback by intense but narrow wind-driven ocean overturning cells that deliver roughly 100 W m-2 heating to the ice edges. This requires three-way feedback between winds, ocean circulation, and ice extent in which circulation is shifted equatorward, following the baroclinicity at the ice margins. The thermocline is much shallower and outcrops in the tropics. Sea ice is snow-covered everywhere and has a minuscule seasonal cycle. The Waterbelt state spans a 46 W m-2 range in solar constant, has a significant hysteresis, and permits near-freezing equatorial surface temperatures. Additional context is provided by a slab ocean GCM and a diffusive energy balance model, both with prescribed ocean heat transport (OHT). Unlike the fully coupled model, these support no more than one stable ice margin, the position of which is slaved to regions of rapid poleward decrease in OHT convergence. Wide ranges of different climates (including the stable Waterbelt) are found by varying the magnitude and spatial structure of OHT in both models. Some thermodynamic arguments for the sensitivity of climate, and ice extent to OHT are presented.

  18. Modeling of coupled heat transfer and reactive transport processes in porous media: Application to seepage studies at Yucca Mountain, Nevada

    International Nuclear Information System (INIS)

    Mukhopadhyay, Sumit; Sonnenthal, Eric L.; Spycher, Nicolas

    2007-01-01

    When hot radioactive waste is placed in subsurface tunnels, a series of complex changes occurs in the surrounding medium. The water in the pore space of the medium undergoes vaporization and boiling. Subsequently, vapor migrates out of the matrix pore space, moving away from the tunnel through the permeable fracture network. This migration is propelled by buoyancy, by the increased vapor pressure caused by heating and boiling, and through local convection. In cooler regions, the vapor condenses on fracture walls, where it drains through the fracture network. Slow imbibition of water thereafter leads to gradual rewetting of the rock matrix. These thermal and hydrological processes also bring about chemical changes in the medium. Amorphous silica precipitates from boiling and evaporation, and calcite from heating and CO2 volatilization. The precipitation of amorphous silica, and to a much lesser extent calcite, results in long-term permeability reduction. Evaporative concentration also results in the precipitation of gypsum (or anhydrite), halite, fluorite and other salts. These evaporative minerals eventually redissolve after the boiling period is over, however, their precipitation results in a significant temporary decrease in permeability. Reduction of permeability is also associated with changes in fracture capillary characteristics. In short, the coupled thermal-hydrological-chemical (THC) processes dynamically alter the hydrological properties of the rock. A model based on the TOUGHREACT reactive transport software is presented here to investigate the impact of THC processes on flow near an emplacement tunnel at Yucca Mountain, Nevada. We show how transient changes in hydrological properties caused by THC processes often lead to local flow channeling and saturation increases above the tunnel. For models that include only permeability changes to fractures, such local flow channeling may lead to seepage relative to models where THC effects are ignored. However

  19. Modeling of coupled heat transfer and reactive transport processes in porous media: Application to seepage studies at Yucca Mountain, Nevada

    International Nuclear Information System (INIS)

    Mukhopadhyay, S.; Sonnenthal, E.L.; Spycher, N.

    2007-01-01

    When hot radioactive waste is placed in subsurface tunnels, a series of complex changes occurs in the surrounding medium. The water in the pore space of the medium undergoes vaporization and boiling. Subsequently, vapor migrates out of the matrix pore space, moving away from the tunnel through the permeable fracture network. This migration is propelled by buoyancy, by the increased vapor pressure caused by heating and boiling, and through local convection. In cooler regions, the vapor condenses on fracture walls, where it drains through the fracture network. Slow imbibition of water thereafter leads to gradual rewetting of the rock matrix. These thermal and hydrological processes also bring about chemical changes in the medium. Amorphous silica precipitates from boiling and evaporation, and calcite from heating and CO 2 volatilization. The precipitation of amorphous silica, and to a much lesser extent calcite, results in long-term permeability reduction. Evaporative concentration also results in the precipitation of gypsum (or anhydrite), halite, fluorite and other salts. These evaporative minerals eventually redissolve after the boiling period is over, however, their precipitation results in a significant temporary decrease in permeability. Reduction of permeability is also associated with changes in fracture capillary characteristics. In short, the coupled thermal-hydrological-chemical (THC) processes dynamically alter the hydrological properties of the rock. A model based on the TOUGHREACT reactive transport software is presented here to investigate the impact of THC processes on flow near an emplacement tunnel at Yucca Mountain, Nevada. We show how transient changes in hydrological properties caused by THC processes often lead to local flow channeling and saturation increases above the tunnel. For models that include only permeability changes to fractures, such local flow channeling may lead to seepage relative to models where THC effects are ignored. However

  20. Modeling biogechemical reactive transport in a fracture zone

    Energy Technology Data Exchange (ETDEWEB)

    Molinero, Jorge; Samper, Javier; Yang, Chan Bing, and Zhang, Guoxiang; Guoxiang, Zhang

    2005-01-14

    A coupled model of groundwater flow, reactive solute transport and microbial processes for a fracture zone of the Aspo site at Sweden is presented. This is the model of the so-called Redox Zone Experiment aimed at evaluating the effects of tunnel construction on the geochemical conditions prevailing in a fracture granite. It is found that a model accounting for microbially-mediated geochemical processes is able to reproduce the unexpected measured increasing trends of dissolved sulfate and bicarbonate. The model is also useful for testing hypotheses regarding the role of microbial processes and evaluating the sensitivity of model results to changes in biochemical parameters.

  1. Modeling biogeochemical reactive transport in a fracture zone

    International Nuclear Information System (INIS)

    Molinero, Jorge; Samper, Javier; Yang, Chan Bing; Zhang, Guoxiang; Guoxiang, Zhang

    2005-01-01

    A coupled model of groundwater flow, reactive solute transport and microbial processes for a fracture zone of the Aspo site at Sweden is presented. This is the model of the so-called Redox Zone Experiment aimed at evaluating the effects of tunnel construction on the geochemical conditions prevailing in a fracture granite. It is found that a model accounting for microbially-mediated geochemical processes is able to reproduce the unexpected measured increasing trends of dissolved sulfate and bicarbonate. The model is also useful for testing hypotheses regarding the role of microbial processes and evaluating the sensitivity of model results to changes in biochemical parameters

  2. Dynamic combinatorial chemistry to identify binders of ThiT, an S-component of the energy-coupling factor transporter for thiamine

    NARCIS (Netherlands)

    Monjas, Leticia; Swier, Lotteke J Y M; Setyawati, Inda; Slotboom, Dirk Jan; Hirsch, Anna Katharina Herta

    2017-01-01

    We applied dynamic combinatorial chemistry (DCC) to identify ligands of ThiT, the S-component of the energy-coupling factor (ECF) transporter for thiamine in Lactococcus lactis. We used a pre-equilibrated dynamic combinatorial library (DCL) and saturation-transfer difference (STD) NMR spectroscopy

  3. Models for microtubule cargo transport coupling the Langevin equation to stochastic stepping motor dynamics: Caring about fluctuations.

    Science.gov (United States)

    Bouzat, Sebastián

    2016-01-01

    One-dimensional models coupling a Langevin equation for the cargo position to stochastic stepping dynamics for the motors constitute a relevant framework for analyzing multiple-motor microtubule transport. In this work we explore the consistence of these models focusing on the effects of the thermal noise. We study how to define consistent stepping and detachment rates for the motors as functions of the local forces acting on them in such a way that the cargo velocity and run-time match previously specified functions of the external load, which are set on the base of experimental results. We show that due to the influence of the thermal fluctuations this is not a trivial problem, even for the single-motor case. As a solution, we propose a motor stepping dynamics which considers memory on the motor force. This model leads to better results for single-motor transport than the approaches previously considered in the literature. Moreover, it gives a much better prediction for the stall force of the two-motor case, highly compatible with the experimental findings. We also analyze the fast fluctuations of the cargo position and the influence of the viscosity, comparing the proposed model to the standard one, and we show how the differences on the single-motor dynamics propagate to the multiple motor situations. Finally, we find that the one-dimensional character of the models impede an appropriate description of the fast fluctuations of the cargo position at small loads. We show how this problem can be solved by considering two-dimensional models.

  4. Coupling LaGrit unstructured mesh generation and model setup with TOUGH2 flow and transport: A case study

    Science.gov (United States)

    Sentís, Manuel Lorenzo; Gable, Carl W.

    2017-11-01

    There are many applications in science and engineering modeling where an accurate representation of a complex model geometry in the form of a mesh is important. In applications of flow and transport in subsurface porous media, this is manifest in models that must capture complex geologic stratigraphy, structure (faults, folds, erosion, deposition) and infrastructure (tunnels, boreholes, excavations). Model setup, defined as the activities of geometry definition, mesh generation (creation, optimization, modification, refine, de-refine, smooth), assigning material properties, initial conditions and boundary conditions requires specialized software tools to automate and streamline the process. In addition, some model setup tools will provide more utility if they are designed to interface with and meet the needs of a particular flow and transport software suite. A control volume discretization that uses a two point flux approximation is for example most accurate when the underlying control volumes are 2D or 3D Voronoi tessellations. In this paper we will present the coupling of LaGriT, a mesh generation and model setup software suite and TOUGH2 (Pruess et al., 1999) to model subsurface flow problems and we show an example of how LaGriT can be used as a model setup tool for the generation of a Voronoi mesh for the simulation program TOUGH2. To generate the MESH file for TOUGH2 from the LaGriT output a standalone module Lagrit2Tough2 was developed, which is presented here and will be included in a future release of LaGriT. In this paper an alternative method to generate a Voronoi mesh for TOUGH2 with LaGriT is presented and thanks to the modular and command based structure of LaGriT this method is well suited to generating a mesh for complex models.

  5. Development of a discrete-ordinate approximation of the neutron transport equation for coupled xy-R-geometry

    International Nuclear Information System (INIS)

    Maertens, H.D.

    1982-01-01

    The inhomogenious structure of modern heavy water reactor fuel elements result in a strong spacial dependence of the neutron flux. The flux distribution can be calculated in detail by numerical methods, which describe exactly the geometrical heterogeniety and take into account the neutron flux anisotropy by higher transport theoretical approximations. Starting from the discrete ordinate method an approximation of the neutron transport equation has been developed, allowing for a cylindrical representation of the fuel-elements in a rectangular array of rods. The discretisation of the space variables, is based on the finite-difference approximation, defining a rectangular lattice in a two-dimensional cartesian coordinate system, which can be cut and replaced by circular mesh elements of a partially one-dimensional cylindrical coordinate system at arbitrary space points. To couple the two spacial regions the outer circle line of a cylindrical geometry is approximated in the cartesian system by a polygon with n >= 8. A cylindrical geometry is approximated in the cartesian system by a polygon with n>=8. A cylindrical geometry is thus enclosed by a system of two-dimensional rectangular, triangular and trapezoid mesh elements. The directional distribution of the neutron flux is conserved when switching from the xy-system to the cylindrical coordinate system. The angle discretisation by balanced sets of squares (EQsub(n)) allows a simple definition of transfer-coefficients for the redistribution of the neutron flux due to coordinate transformations. The procedure is verified and tested by selected problems. Possible applications and limits are discussed. (orig.) [de

  6. Microphysics of mass-transport in coupled droplet-pairs at low Reynolds number and the role of convective dynamics

    Science.gov (United States)

    Dong, Qingming; Sau, Amalendu

    2016-06-01

    Interfacial mass-transport and redistribution in the micro-scale liquid droplets are important in diverse fields of research interest. The role of the "inflow" and the "outflow" type convective eddy-pairs in the entrainment of outer solute and internal relocation are examined for different homogeneous and heterogeneous water droplet pairs appearing in a tandem arrangement. Two micro-droplets of pure (rain) water interact with an oncoming outer air stream (Re ≤ 100) contaminated by uniformly distributed SO2. By virtue of separation/attachment induced non-uniform interfacial shear-stress gradient, the well-defined inflow/outflow type pairs of recirculating eddy-based convective motion quickly develops, and the eddies effectively attract/repel the accumulated outer solute and control the physical process of mass-transport in the droplet-pair. The non-uniformly shear-driven flow interaction and bifurcation of the circulatory internal flow lead to growth of important micro-scale "secondary" eddies which suitably regroup with the adjacent "primary" one to create the sustained inflow/outflow type convective dynamics. The presently derived flow characteristics and in-depth analysis help to significantly improve our understanding of the micro-droplet based transport phenomena in a wider context. By tuning "Re" (defined in terms of the droplet diameter and the average oncoming velocity of the outer air) and gap-ratio "α," the internal convective forcing and the solute entrainment efficiency could be considerably enhanced. The quantitative estimates for mass entrainment, convective strength, and saturation characteristics for different coupled micro-droplet pairs are extensively examined here for 0.2 ≤ α ≤ 2.0 and 30 ≤ Re ≤ 100. Interestingly, for the compound droplets, with suitably tuned radius-ratio "B" (of upstream droplet with respect to downstream one) the generated "inflow" type coherent convective dynamics helped to significantly augment the centre

  7. Considering a Threshold Energy in Reactive Transport Modeling of Microbially Mediated Redox Reactions in an Arsenic-Affected Aquifer

    Directory of Open Access Journals (Sweden)

    Marco Rotiroti

    2018-01-01

    Full Text Available The reductive dissolution of Fe-oxide driven by organic matter oxidation is the primary mechanism accepted for As mobilization in several alluvial aquifers. These processes are often mediated by microorganisms that require a minimum Gibbs energy available to conduct the reaction in order to sustain their life functions. Implementing this threshold energy in reactive transport modeling is rarely used in the existing literature. This work presents a 1D reactive transport modeling of As mobilization by the reductive dissolution of Fe-oxide and subsequent immobilization by co-precipitation in iron sulfides considering a threshold energy for the following terminal electron accepting processes: (a Fe-oxide reduction, (b sulfate reduction, and (c methanogenesis. The model is then extended by implementing a threshold energy on both reaction directions for the redox reaction pairs Fe(III reduction/Fe(II oxidation and methanogenesis/methane oxidation. The optimal threshold energy fitted in 4.50, 3.76, and 1.60 kJ/mol e− for sulfate reduction, Fe(III reduction/Fe(II oxidation, and methanogenesis/methane oxidation, respectively. The use of models implementing bidirectional threshold energy is needed when a redox reaction pair can be transported between domains with different redox potentials. This may often occur in 2D or 3D simulations.

  8. Reduced coupling of oxidative phosphorylation in vivo precedes electron transport chain defects due to mild oxidative stress in mice.

    Directory of Open Access Journals (Sweden)

    Michael P Siegel

    Full Text Available Oxidative stress and mitochondrial function are at the core of many degenerative conditions. However, the interaction between oxidative stress and in vivo mitochondrial function is unclear. We used both pharmacological (2 week paraquat (PQ treatment of wild type mice and transgenic (mice lacking Cu, Zn-superoxide dismutase (SOD1(-/- models to test the effect of oxidative stress on in vivo mitochondrial function in skeletal muscle. Magnetic resonance and optical spectroscopy were used to measure mitochondrial ATP and oxygen fluxes and cell energetic state. In both models of oxidative stress, coupling of oxidative phosphorylation was significantly lower (lower P/O at rest in vivo in skeletal muscle and was dose-dependent in the PQ model. Despite this reduction in efficiency, in vivo mitochondrial phosphorylation capacity (ATPmax was maintained in both models, and ex vivo mitochondrial respiration in permeabilized muscle fibers was unchanged following PQ treatment. In association with the reduced P/O, PQ treatment led to a dose-dependent reduction in PCr/ATP ratio and increased phosphorylation of AMPK. These results indicate that oxidative stress uncouples oxidative phosphorylation in vivo and results in energetic stress in the absence of defects in the mitochondrial electron transport chain.

  9. Coupled mechanical and chemo-transport model for the simulation of cementitious materials subjected to external sulfate attack

    International Nuclear Information System (INIS)

    Bary, B.; Le Bescop, P.; Leterrier, N.; Deville, E.

    2012-01-01

    We propose in this study to develop a chemo-transport-mechanical model for the simulation of external sulfate attack in cementitious materials. This degradation mainly consists in the hydrate decalcification/dissolution due to leaching, and in the reaction between the sulfate ions migrating within the material and mono-sulfate initially present to precipitate into ettringite. It may generate macroscopic expansions leading to severe microcracking. The key point in this study is the use of the integration numerical platform ALLIANCES which couples a code solving the chemical equations, the diffusion of ionic species into the porosity and the mechanical problem. The crystallization pressures resulting from the interaction between growing mono-sulfate crystals and the surrounding C-S-H matrix are assumed to cause the observed macroscopic swelling. A macroscopic bulk strain tensor calculated from the volume of formed ettringite is introduced for directly reproducing these expansions. Explicit up-scaling techniques applied on a simplified representation of the materials allow estimating both mechanical and diffusive properties of the evolving microstructure. The calculated macroscopic free expansions are in quite good agreement with experimental data, provided a correct calibration of the parameter involved in the expression of the bulk strain tensor. However, it is asserted that the model would lead to very high stress levels in the structures in the particular case of restrained displacements at its boundaries

  10. Removal of heavy-metal pollutants from ground water using a reverse-osmosis/coupled-transport hybrid system

    International Nuclear Information System (INIS)

    Edlund, D.J.; Friesen, D.T.; Ray, R.J.; Scholfield, R.W.

    1993-01-01

    Two membrane processes - reverse osmosis (RO) and coupled transport (CT) - are useful in removing heavy metals from aqueous solutions and producing purified water. Each process has advantages. RO produces clean water reliably and relatively inexpensively. However, the pollutants are removed nonselectively and cannot be appreciably concentrated. CT removes pollutants selectively and can concentrate them by several orders of magnitude, but CT suffers from limited reliability and performs poorly at low pollutant concentrations. By combining these two unit processes in a hybrid process, it is possible to capitalize on the advantages of each process and to minimize their disadvantages. The RO/CT hybrid process the authors are developing removes more than 98% of the uranium and chromium in a contaminated groundwater stream - reducing concentrations of each pollutant to less than 100 ppb. These pollutants are simultaneously recovered as a concentrate at metal-ion concentrations greater than 1 wt% in relatively pure form. The hybrid process promises to be reliable and to reduce treatment costs below that for costs if either CT or RO were used alone. Even more importantly, the high selectivity of the hybrid process minimizes the volume of waste requiring disposal

  11. Coupling of kinetic Monte Carlo simulations of surface reactions to transport in a fluid for heterogeneous catalytic reactor modeling

    International Nuclear Information System (INIS)

    Schaefer, C.; Jansen, A. P. J.

    2013-01-01

    We have developed a method to couple kinetic Monte Carlo simulations of surface reactions at a molecular scale to transport equations at a macroscopic scale. This method is applicable to steady state reactors. We use a finite difference upwinding scheme and a gap-tooth scheme to efficiently use a limited amount of kinetic Monte Carlo simulations. In general the stochastic kinetic Monte Carlo results do not obey mass conservation so that unphysical accumulation of mass could occur in the reactor. We have developed a method to perform mass balance corrections that is based on a stoichiometry matrix and a least-squares problem that is reduced to a non-singular set of linear equations that is applicable to any surface catalyzed reaction. The implementation of these methods is validated by comparing numerical results of a reactor simulation with a unimolecular reaction to an analytical solution. Furthermore, the method is applied to two reaction mechanisms. The first is the ZGB model for CO oxidation in which inevitable poisoning of the catalyst limits the performance of the reactor. The second is a model for the oxidation of NO on a Pt(111) surface, which becomes active due to lateral interaction at high coverages of oxygen. This reaction model is based on ab initio density functional theory calculations from literature.

  12. Hydro-mechanical coupling and transport in Meuse/Haute-Marne argillite: experimental and multi-scale approaches

    International Nuclear Information System (INIS)

    Cariou, S.

    2010-07-01

    This thesis deals with the hydro-mechanical behaviour of argillite. Classical Biot theory is shown to be badly adapted to the case of argillite. An original state equation is then built by use of homogenization tools, and takes into account the microstructure of argillite as well as physical phenomena happening inside the material, like the swelling overpressure inside the clay particles or the capillary effects in the porous network. This state equation explains some experiments which were not by the classical Biot theory. It is then improved by integrating the experimental data that are the dependency of the elasticity tensor with the saturation degree and the existence of a porosity surrounding the inclusions. Combined with the monitoring of length variation under hydric loading, this relevant state equation permits one to determine the Biot tensor of argillite. Since this state equation is coupled with the hydric state of the material, one is interested in modelling the variation of the saturation degree during a drying process. Two transport models are studied and compared, then a model for the porous network is proposed in order to explain the unusual permeability measurements. (author)

  13. Experimental evidence of two mechanisms coupling leaf-level C assimilation to rhizosphere CO2 release

    Science.gov (United States)

    Zachary Kayler; Claudia Keitel; Kirstin Jansen; Arthur Gessler

    2017-01-01

    The time span needed for carbon fixed by plants to induce belowground responses of root and rhizosphere microbial metabolic processing is of high importance for quantifying the coupling between plant canopy physiology and soil biogeochemistry, but recent observations of a rapid link cannot be explained by new assimilate transport by phloem mass flow alone. We performed...

  14. Quantitative microbial risk assessment for spray irrigation of dairy manure based on an empirical fate and transport model

    Science.gov (United States)

    Burch, Tucker R; Spencer, Susan K.; Stokdyk, Joel; Kieke, Burney A; Larson, Rebecca A; Firnstahl, Aaron; Rule, Ana M; Borchardt, Mark A.

    2017-01-01

    BACKGROUND: Spray irrigation for land-applying livestock manure is increasing in the United States as farms become larger and economies of scale make manure irrigation affordable. Human health risks from exposure to zoonotic pathogens aerosolized during manure irrigation are not well understood. OBJECTIVES: We aimed to a) estimate human health risks due to aerosolized zoonotic pathogens downwind of spray-irrigated dairy manure; and b) determine which factors (e.g., distance, weather conditions) have the greatest influence on risk estimates. METHODS: We sampled downwind air concentrations of manure-borne fecal indicators and zoonotic pathogens during 21 full-scale dairy manure irri- gation events at three farms. We fit these data to hierarchical empirical models and used model outputs in a quantitative microbial risk assessment (QMRA) to estimate risk [probability of acute gastrointestinal illness (AGI)] for individuals exposed to spray-irrigated dairy manure containing Campylobacter jejuni, enterohemorrhagic Escherichia coli (EHEC), or Salmonella spp. RESULTS: Median risk estimates from Monte Carlo simulations ranged from 10−5 to 10−2 and decreased with distance from the source. Risk estimates for Salmonella or EHEC-related AGI were most sensitive to the assumed level of pathogen prevalence in dairy manure, while risk estimates for C. jejuni were not sensitive to any single variable. Airborne microbe concentrations were negatively associated with distance and positively associated with wind speed, both of which were retained in models as a significant predictor more often than relative humidity, solar irradiation, or temperature. CONCLUSIONS: Our model-based estimates suggest that reducing pathogen prevalence and concentration in source manure would reduce the risk of AGI from exposure to manure irrigation, and that increasing the distance from irrigated manure (i.e., setbacks) and limiting irrigation to times of low wind speed may also reduce risk.

  15. Transportation

    National Research Council Canada - National Science Library

    Adams, James; Carr, Ron; Chebl, Maroun; Coleman, Robert; Costantini, William; Cox, Robert; Dial, William; Jenkins, Robert; McGovern, James; Mueller, Peter

    2006-01-01

    ...., trains, ships, etc.) and maximizing intermodal efficiency. A healthy balance must be achieved between the flow of international commerce and security requirements regardless of transportation mode...

  16. Metal/dielectric thermal interfacial transport considering cross-interface electron-phonon coupling: Theory, two-temperature molecular dynamics, and thermal circuit

    Science.gov (United States)

    Lu, Zexi; Wang, Yan; Ruan, Xiulin

    2016-02-01

    The standard two-temperature equations for electron-phonon coupled thermal transport across metal/nonmetal interfaces are modified to include the possible coupling between metal electrons with substrate phonons. The previous two-temperature molecular dynamics (TT-MD) approach is then extended to solve these equations numerically at the atomic scale, and the method is demonstrated using Cu/Si interface as an example. A key parameter in TT-MD is the nonlocal coupling distance of metal electrons and nonmetal phonons, and here we use two different approximations. The first is based on Overhauser's "joint-modes" concept, while we use an interfacial reconstruction region as the length scale of joint region rather than the phonon mean-free path as in Overhauser's original model. In this region, the metal electrons can couple to the joint phonon modes. The second approximation is the "phonon wavelength" concept where electrons couple to phonons nonlocally within the range of one phonon wavelength. Compared with the original TT-MD, including the cross-interface electron-phonon coupling can slightly reduce the total thermal boundary resistance. Whether the electron-phonon coupling within the metal block is nonlocal or not does not make an obvious difference in the heat transfer process. Based on the temperature profiles from TT-MD, we construct a new mixed series-parallel thermal circuit. We show that such a thermal circuit is essential for understanding metal/nonmetal interfacial transport, while calculating a single resistance without solving temperature profiles as done in most previous studies is generally incomplete. As a comparison, the simple series circuit that neglects the cross-interface electron-phonon coupling could overestimate the interfacial resistance, while the simple parallel circuit in the original Overhauser's model underestimates the total interfacial resistance.

  17. Several hPepT1-transported drugs are substrates of the Escherichia coli proton-coupled oligopeptide transporter YdgR

    DEFF Research Database (Denmark)

    Prabhala, Bala K; Aduri, Nanda G; Iqbal, Mazhar

    2017-01-01

    transported by hPepT1. The transport of these drugs was evaluated using the prototypical POT YdgR from E. coli. The transport studies were pursued through combining cell-based assays with liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis. These investigations revealed that YdgR from E. coli...

  18. Transportation

    International Nuclear Information System (INIS)

    Anon.

    1998-01-01

    Here is the decree of the thirtieth of July 1998 relative to road transportation, to trade and brokerage of wastes. It requires to firms which carry out a road transportation as well as to traders and to brokers of wastes to declare their operations to the prefect. The declaration has to be renewed every five years. (O.M.)

  19. Water transport by Na+-coupled cotransporters of glucose (SGLT1) and of iodide (NIS). The dependence of substrate size studied at high resolution

    DEFF Research Database (Denmark)

    Zeuthen, Thomas; Belhage, Bo; Zeuthen, Emil

    2005-01-01

    and osmosis at the membrane with diffusion in the cytoplasm. The combination of high resolution measurements and precise modelling showed that water transport across the membrane can be explained by cotransport of water in the membrane proteins and that intracellular unstirred layers effects are minute.......The relation between substrate and water transport was studied in Na+-coupled cotransporters of glucose (SGLT1) and of iodide (NIS) expressed in Xenopus oocytes. The water transport was monitored from changes in oocyte volume at a resolution of 20 pl, more than one order of magnitude better than...... previous investigations. The rate of cotransport was monitored as the clamp current obtained from two-electrode voltage clamp. The high resolution data demonstrated a fixed ratio between the turn-over of the cotransporter and the rate of water transport. This applied to experiments in which the rate...

  20. A model for coupled electro-hydro-mechanical processes in fine grained soils accounting for gas generation and transport

    Directory of Open Access Journals (Sweden)

    Claudio Tamagnini

    2010-03-01

    Full Text Available A theoretical and numerical model is developed for the quantitative analysis of coupled processes taking place in active waste containment systems, such as electrokinetic barriers or fences, in which alow intensity DC current is circulated across the clay barrier to move polar and non-polar contaminants. A novel feature of the proposed approach is the allowance for the presence of air in the pore space. Under unsaturated conditions, all transport coefficients involved in the electrokinetic process are strongly dependent on the degree of saturation of pore liquid. In order to assess the predictive capability of the proposed theory and to appreciate the impact of gas production at the electrodes, a series of numerical simulations of simple onedimensional electrokinetic tests have been performed. The results of the simulations compare reasonably well with data obtained from laboratory experiments performed on an illitic clayey silt. The numerical results indicate that the impact of gas production at the electrodes can be significant, even in low-intensity and short-duration treatments.Um modelo teórico e computacional é desenvolvido para a análise quantitativa de processos acoplados que tomam lugar em sistemas de contenção de lixo tais como barreiras ou grades eletrocinéticas no qual uma DC corrente de baixa intensidade é circulada através da barreira de argila para movimentar contaminantes polares e não polares. Uma nova característica da abordagem proposta é permitir a presença de ar nos poros. Sob condições não saturadas todos os coeficientes de transporte envolvidos nos processos eletrocinéticos são fortemente dependentes do grau de saturação do líquido. Com o objetivo de avaliar a capacidade do modelo proposto de predizer e de apreciar o impacto da produção de gás nos eletrodos uma série de simulações numéricas foi realizada em testes eletrocinéticos simples unidimensionais. Os resultados das simulações concordam

  1. Transporter Protein-Coupled DPCPX Nanoconjugates Induce Diaphragmatic Recovery after SCI by Blocking Adenosine A1 Receptors.

    Science.gov (United States)

    Minic, Zeljka; Zhang, Yanhua; Mao, Guangzhao; Goshgarian, Harry G

    2016-03-23

    Respiratory complications in patients with spinal cord injury (SCI) are common and have a negative impact on the quality of patients' lives. Systemic administration of drugs that improve respiratory function often cause deleterious side effects. The present study examines the applicability of a novel nanotechnology-based drug delivery system, which induces recovery of diaphragm function after SCI in the adult rat model. We developed a protein-coupled nanoconjugate to selectively deliver by transsynaptic transport small therapeutic amounts of an A1 adenosine receptor antagonist to the respiratory centers. A single administration of the nanoconjugate restored 75% of the respiratory drive at 0.1% of the systemic therapeutic drug dose. The reduction of the systemic dose may obviate the side effects. The recovery lasted for 4 weeks (the longest period studied). These findings have translational implications for patients with respiratory dysfunction after SCI. The leading causes of death in humans following SCI are respiratory complications secondary to paralysis of respiratory muscles. Systemic administration of methylxantines improves respiratory function but also leads to the development of deleterious side effects due to actions of the drug on nonrespiratory sites. The importance of the present study lies in the novel drug delivery approach that uses nanotechnology to selectively deliver recovery-inducing drugs to the respiratory centers exclusively. This strategy allows for a reduction in the therapeutic drug dose, which may reduce harmful side effects and markedly improve the quality of life for SCI patients. Copyright © 2016 the authors 0270-6474/16/363441-12$15.00/0.

  2. The Coupled Photothermal Reaction and Transport in a Laser Additive Metal Nanolayer Simultaneous Synthesis and Pattering for Flexible Electronics

    Directory of Open Access Journals (Sweden)

    Song-Ling Tsai

    2016-01-01

    Full Text Available The Laser Direct Synthesis and Patterning (LDSP technology has advantages in terms of processing time and cost compared to nanomaterials-based laser additive microfabrication processes. In LDSP, a scanning laser on the substrate surface induces chemical reactions in the reactive liquid solution and selectively deposits target material in a preselected pattern on the substrate. In this study, we experimentally investigated the effect of the processing parameters and type and concentration of the additive solvent on the properties and growth rate of the resulting metal film fabricated by this LDSP technology. It was shown that reactive metal ion solutions with substantial viscosity yield metal films with superior physical properties. A numerical analysis was also carried out the first time to investigate the coupled opto-thermo-fluidic transport phenomena and the effects on the metal film growth rate. To complete the simulation, the optical properties of the LDSP deposited metal film with a variety of thicknesses were measured. The characteristics of the temperature field and the thermally induced flow associated with the moving heat source are discussed. It was shown that the processing temperature range of the LDSP is from 330 to 390 K. A semi-empirical model for estimating the metal film growth rate using this process was developed based on these results. From the experimental and numerical results, it is seen that, owing to the increased reflectivity of the silver film as its thickness increases, the growth rate decreases gradually from about 40 nm at initial to 10 nm per laser scan after ten scans. This self-controlling effect of LDSP process controls the thickness and improves the uniformity of the fabricated metal film. The growth rate and resulting thickness of the metal film can also be regulated by adjustment of the processing parameters, and thus can be utilized for controllable additive nano/microfabrication.

  3. Efficient C1-continuous phase-potential upwind (C1-PPU) schemes for coupled multiphase flow and transport with gravity

    Science.gov (United States)

    Jiang, Jiamin; Younis, Rami M.

    2017-10-01

    In the presence of counter-current flow, nonlinear convergence problems may arise in implicit time-stepping when the popular phase-potential upwinding (PPU) scheme is used. The PPU numerical flux is non-differentiable across the co-current/counter-current flow regimes. This may lead to cycles or divergence in the Newton iterations. Recently proposed methods address improved smoothness of the numerical flux. The objective of this work is to devise and analyze an alternative numerical flux scheme called C1-PPU that, in addition to improving smoothness with respect to saturations and phase potentials, also improves the level of scalar nonlinearity and accuracy. C1-PPU involves a novel use of the flux limiter concept from the context of high-resolution methods, and allows a smooth variation between the co-current/counter-current flow regimes. The scheme is general and applies to fully coupled flow and transport formulations with an arbitrary number of phases. We analyze the consistency property of the C1-PPU scheme, and derive saturation and pressure estimates, which are used to prove the solution existence. Several numerical examples for two- and three-phase flows in heterogeneous and multi-dimensional reservoirs are presented. The proposed scheme is compared to the conventional PPU and the recently proposed Hybrid Upwinding schemes. We investigate three properties of these numerical fluxes: smoothness, nonlinearity, and accuracy. The results indicate that in addition to smoothness, nonlinearity may also be critical for convergence behavior and thus needs to be considered in the design of an efficient numerical flux scheme. Moreover, the numerical examples show that the C1-PPU scheme exhibits superior convergence properties for large time steps compared to the other alternatives.

  4. Coupled magnetostructural transition in Ni-Mn-V-Ga Heusler alloys and its effect on the magnetocaloric and transport properties

    International Nuclear Information System (INIS)

    Devarajan, U; Kannan, M; Thiyagarajan, R; Arumugam, S; Manivel Raja, M; Rama Rao, N V; Singh, Sanjay; Venkateshwarlu, D; Ganesan, V; Ohashi, M

    2016-01-01

    In the present work, the magnetocaloric and transport properties of Ni 2.2 Mn 0.72−x V x Ga 1.08 (x  =  0.0, 0.04, 0.08, 0.12) magnetic shape memory alloys are investigated. The alloys show a coupled magnetostructural transition from paramagnetic austenite to ferromagnetic martensite in a composition range of 0  ⩽  x  ⩽  0.08. For higher V substitution (x  =  0.12), the martensite transition is lower than the conventional ferromagnetic transition. Large magnetic entropy change values of about 12.4, 16.2 and 19 J kg −1 K −1 and corresponding refrigeration capacities of 60.6, 82.5, and 103 J kg −1 were observed for x  =  0, 0.04 and 0.08 alloys, respectively. The above two parameters linearly increase with increasing magnetic field. The indirect adiabatic temperature change calculated from the heat capacity measurement is found to be at its maximum for x  =  0.12 at H  =  8 T. The magnetoresistance is observed to increase from 0% (x  =  0.12) to 28% (x  =  0) at the maximum field of 8 T. The Sommerfeld coefficients are almost the same for the parent and a V-doped sample, which reveals a low free electron density, and the Debye coefficients decrease with an increase in V doping, confirming the phenomenon of electron–phonon scattering. The critical exponents at second order magnetic transition for x  = 0.12 are calculated as β  =  0.482, γ  =  1.056, δ  =  3.021, which agrees closely with mean field theory. (paper)

  5. Coupled energy-drift and force-balance equations for high-field hot-carrier transport

    International Nuclear Information System (INIS)

    Huang, Danhong; Alsing, P.M.; Apostolova, T.; Cardimona, D.A.

    2005-01-01

    Coupled energy-drift and force-balance equations that contain a frictional force for the center-of-mass motion of electrons are derived for hot-electron transport under a strong dc electric field. The frictional force is found to be related to the net rate of phonon emission, which takes away the momentum of a phonon from an electron during each phonon-emission event. The net rate of phonon emission is determined by the Boltzmann scattering equation, which depends on the distribution of electrons interacting with phonons. The work done by the frictional force is included into the energy-drift equation for the electron-relative scattering motion and is found to increase the thermal energy of the electrons. The importance of the hot-electron effect in the energy-drift term under a strong dc field is demonstrated in reducing the field-dependent drift velocity and mobility. The Doppler shift in the energy conservation of scattering electrons interacting with impurities and phonons is found to lead to an anisotropic distribution of electrons in the momentum space along the field direction. The importance of this anisotropic distribution is demonstrated through a comparison with the isotropic energy-balance equation, from which we find that defining a state-independent electron temperature becomes impossible. To the leading order, the energy-drift equation is linearized with a distribution function by expanding it into a Fokker-Planck-type equation, along with the expansions of both the force-balance equation and the Boltzmann scattering equation for hot phonons

  6. Transportation

    National Research Council Canada - National Science Library

    Allshouse, Michael; Armstrong, Frederick Henry; Burns, Stephen; Courts, Michael; Denn, Douglas; Fortunato, Paul; Gettings, Daniel; Hansen, David; Hoffman, D. W; Jones, Robert

    2007-01-01

    .... The ability of the global transportation industry to rapidly move passengers and products from one corner of the globe to another continues to amaze even those wise to the dynamics of such operations...

  7. Several hPepT1-transported drugs are substrates of the Escherichia coli proton-coupled oligopeptide transporter YdgR.

    Science.gov (United States)

    Prabhala, Bala K; Aduri, Nanda G; Iqbal, Mazhar; Rahman, Moazur; Gajhede, Michael; Hansen, Paul R; Mirza, Osman

    2017-06-01

    Proton-dependent oligopeptide transporters (POTs) are secondary active transporters found in all kingdoms of life. POTs utilize the proton electrochemical gradient for the uptake of nutrient dipeptides and tripeptides. The human POT hPepT1 is known to transport a number of drugs. As part of ongoing studies on substrate specificities of POTs from Escherichia coli, our aim in this study was to investigate whether bacterial POTs could also transport these drugs. For this, we selected the common orally administered drugs sulpiride, bestatin, valacyclovir, ampicillin and oseltamivir, that are all transported by hPepT1. The transport of these drugs was evaluated using the prototypical POT YdgR from E. coli. The transport studies were pursued through combining cell-based assays with liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis. These investigations revealed that YdgR from E. coli is able to transport five (sulpiride, bestatin, valacyclovir, ampicillin and oseltamivir) drugs. Furthermore, cells not overexpressing YdgR were also able to transport these drugs in a POT-like manner. Orthologues of YdgR are found in several species in the gut microbiome; hence, our findings could have implications for further understanding about the interaction between gut microbes and orally administered drugs. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  8. The Effects of Different Electron-Phonon Couplings on the Spectral and Transport Properties of Small Molecule Single-Crystal Organic Semiconductors

    Directory of Open Access Journals (Sweden)

    Carmine Antonio Perroni

    2014-03-01

    Full Text Available Spectral and transport properties of small molecule single-crystal organic semiconductors have been theoretically analyzed focusing on oligoacenes, in particular on the series from naphthalene to rubrene and pentacene, aiming to show that the inclusion of different electron-phonon couplings is of paramount importance to interpret accurately the properties of prototype organic semiconductors. While in the case of rubrene, the coupling between charge carriers and low frequency inter-molecular modes is sufficient for a satisfactory description of spectral and transport properties, the inclusion of electron coupling to both low-frequency inter-molecular and high-frequency intra-molecular vibrational modes is needed to account for the temperature dependence of transport properties in smaller oligoacenes. For rubrene, a very accurate analysis in the relevant experimental configuration has allowed for the clarification of the origin of the temperature-dependent mobility observed in these organic semiconductors. With increasing temperature, the chemical potential moves into the tail of the density of states corresponding to localized states, but this is not enough to drive the system into an insulating state. The mobility along different crystallographic directions has been calculated, including vertex corrections that give rise to a transport lifetime one order of magnitude smaller than the spectral lifetime of the states involved in the transport mechanism. The mobility always exhibits a power-law behavior as a function of temperature, in agreement with experiments in rubrene. In systems gated with polarizable dielectrics, the electron coupling to interface vibrational modes of the gate has to be included in addition to the intrinsic electron-phonon interaction. While the intrinsic bulk electron-phonon interaction affects the behavior of mobility in the coherent regime below room temperature, the coupling with interface modes is dominant for the

  9. Simulation of Coupled Processes of Flow, Transport, and Storage of CO2 in Saline Aquifers

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Yu-Shu [Colorado School of Mines, Golden, CO (United States); Chen, Zizhong [Univ. of California, Riverside, CA (United States); Kazemi, Hossein [Colorado School of Mines, Golden, CO (United States); Yin, Xiaolong [Colorado School of Mines, Golden, CO (United States); Pruess, Karsten [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Oldenburg, Curt [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Winterfeld, Philip [Colorado School of Mines, Golden, CO (United States); Zhang, Ronglei [Colorado School of Mines, Golden, CO (United States)

    2014-09-30

    This report is the final scientific one for the award DE- FE0000988 entitled “Simulation of Coupled Processes of Flow, Transport, and Storage of CO2 in Saline Aquifers.” The work has been divided into six tasks. In task, “Development of a Three-Phase Non-Isothermal CO2 Flow Module,” we developed a fluid property module for brine-CO2 mixtures designed to handle all possible phase combinations of aqueous phase, sub-critical liquid and gaseous CO2, supercritical CO2, and solid salt. The thermodynamic and thermophysical properties of brine-CO2 mixtures (density, viscosity, and specific enthalpy of fluid phases; partitioning of mass components among the different phases) use the same correlations as an earlier fluid property module that does not distinguish between gaseous and liquid CO2-rich phases. We verified the fluid property module using two leakage scenarios, one that involves CO2 migration up a blind fault and subsequent accumulation in a secondary “parasitic” reservoir at shallower depth, and another investigating leakage of CO2 from a deep storage reservoir along a vertical fault zone. In task, “Development of a Rock Mechanical Module,” we developed a massively parallel reservoir simulator for modeling THM processes in porous media brine aquifers. We derived, from the fundamental equations describing deformation of porous elastic media, a momentum conservation equation relating mean stress, pressure, and temperature, and incorporated it alongside the mass and energy conservation equations from the TOUGH2 formulation, the starting point for the simulator. In addition, rock properties, namely permeability and porosity, are functions of effective stress and other variables that are obtained from the literature. We verified the simulator formulation and numerical implementation using analytical solutions and example problems from the literature. For

  10. Transport of the photodynamic therapy agent 5-aminolevulinic acid by distinct H+-coupled nutrient carriers coexpressed in the small intestine.

    Science.gov (United States)

    Anderson, Catriona M H; Jevons, Mark; Thangaraju, Muthusamy; Edwards, Noel; Conlon, Nichola J; Woods, Steven; Ganapathy, Vadivel; Thwaites, David T

    2010-01-01

    5-Aminolevulinic acid (ALA) is a prodrug used in photodynamic therapy, fluorescent diagnosis, and fluorescent-guided resection because it leads to accumulation of the photosensitizer protoporphyrin IX (PpIX) in tumor tissues. ALA has good oral bioavailability, but high oral doses are required to obtain selective PpIX accumulation in colonic tumors because accumulation is also observed in normal gut mucosa. Structural similarities between ALA and GABA led us to test the hypothesis that the H(+)-coupled amino acid transporter PAT1 (SLC36A1) will contribute to luminal ALA uptake. Radiolabel uptake and electrophysiological measurements identified PAT1-mediated H(+)-coupled ALA symport after heterologous expression in Xenopus oocytes. The selectivity of the nontransported inhibitors 5-hydroxytryptophan and 4-aminomethylbenzoic acid for, respectively, PAT1 and the H(+)-coupled di/tripeptide transporter PepT1 (SLC15A1) were examined. 5-Hydroxytryptophan selectively inhibited PAT1-mediated amino acid uptake across the brush-border membrane of the human intestinal (Caco-2) epithelium whereas 4-aminomethylbenzoic acid selectively inhibited PepT1-mediated dipeptide uptake. The inhibitory effects of 5-hydroxytryptophan and 4-aminomethylbenzoic acid were additive, demonstrating that both PAT1 and PepT1 contribute to intestinal transport of ALA. This is the first demonstration of overlap in substrate specificity between these distinct transporters for amino acids and dipeptides. PAT1 and PepT1 expression was monitored by reverse transcriptase-polymerase chain reaction using paired samples of normal and cancer tissue from human colon. mRNA for both transporters was detected. PepT1 mRNA was increased 2.3-fold in cancer tissues. Thus, increased PepT1 expression in colonic cancer could contribute to the increased PpIX accumulation observed. Selective inhibition of PAT1 could enhance PpIX loading in tumor tissue relative to that in normal tissue.

  11. Development and evaluation of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

    Science.gov (United States)

    Microbial contamination of waters in agricultural watershed is the critical public health issue. The watershed-scale model has been proven to be one of the candidate tools for predicting microbial water quality and evaluating management practices. The Agricultural Policy/Environmental eXtender (APEX...

  12. MCNP4C2, Coupled Neutron, Electron Gamma 3-D Time-Dependent Monte Carlo Transport Calculations

    International Nuclear Information System (INIS)

    2002-01-01

    1 - Description of program or function: MCNP is a general-purpose, continuous-energy, generalized geometry, time-dependent, coupled neutron-photon-electron Monte Carlo transport code system. MCNP4C2 is an interim release of MCNP4C with distribution restricted to the Criticality Safety community and attendees of the LANL MCNP workshops. The major new features of MCNP4C2 include: - Photonuclear physics; - Interactive plotting; - Plot superimposed weight window mesh; - Implement remaining macro-body surfaces; - Upgrade macro-bodies to surface sources and other capabilities; - Revised summary tables; - Weight window improvements. See the MCNP home page more information http://www-xdiv.lanl.gov/XCI/PROJECTS/MCNP with a link to the MCNP Forum. See the Electronic Notebook at http://www-rsicc.ornl.gov/rsic.html for information on user experiences with MCNP. 2 - Methods:MCNP treats an arbitrary three-dimensional configuration of materials in geometric cells bounded by first- and second-degree surfaces and some special fourth-degree surfaces. Pointwise continuous-energy cross section data are used, although multigroup data may also be used. Fixed-source adjoint calculations may be made with the multigroup data option. For neutrons, all reactions in a particular cross-section evaluation are accounted for. Both free gas and S(alpha, beta) thermal treatments are used. Criticality sources as well as fixed and surface sources are available. For photons, the code takes account of incoherent and coherent scattering with and without electron binding effects, the possibility of fluorescent emission following photoelectric absorption, and absorption in pair production with local emission of annihilation radiation. A very general source and tally structure is available. The tallies have extensive statistical analysis of convergence. Rapid convergence is enabled by a wide variety of variance reduction methods. Energy ranges are 0-60 MeV for neutrons (data generally only available up to

  13. RADHEAT-V3, a code system for generating coupled neutron and gamma-ray group constants and analyzing radiation transport

    International Nuclear Information System (INIS)

    Koyama, Kinji; Taji, Yukichi; Miyasaka, Shun-ichi; Minami, Kazuyoshi.

    1977-07-01

    The modular code system RADHEAT is for producing coupled multigroup neutron and gamma-ray cross section sets, analyzing the neutron and gamma-ray transport, and calculating the energy deposition and atomic displacements due to these radiations in a nuclear reactor or shield. The basic neutron cross sections and secondary gamma-ray production data are taken from ENDF/B and POPOP4 libraries respectively. The system (1) generates multigroup neutron cross sections, energy deposition coefficients and atomic displacement factors due to neutron reactions, (2) generates multigroup gamma-ray cross sections and energy transfer coefficients, (3) generates secondary gamma-ray production cross sections, (4) combines these cross sections into the coupled set, (5) outputs and updates the multigroup cross section libraries in convenient formats for other transport codes, (6) analyzes the neutron and gamma-ray transport and calculates the energy deposition and the number density of atomic displacements in a medium, (7) collapses the cross sections to a broad-group structure, by option, using the weighting functions obtained by one-dimensional transport calculation, and (8) plots, by option, multigroup cross sections, and neutron and gamma-ray distributions. Definitions of the input data required in various options of the code system are also given. (auth.)

  14. Modelling the coupled chemico-osmotic and advective-diffusive transport of nitrate salts in the Callovo-Oxfordian clay

    International Nuclear Information System (INIS)

    Baechler, S.; Croise, J.; Altmann, S.

    2010-01-01

    Document available in extended abstract form only. Fine-grained saturated porous materials can act as a semi-permeable osmotic membrane when exposed to a solute concentration gradient. The ions diffusion is hindered while water movement towards higher concentrations takes place in the semi-permeable membrane. The capacity of the fine-grained porous material to act as a semi permeable osmotic membrane is referred to as the osmotic efficiency (its value is 1 when the membranes is ideal, less than 1 when the membrane is leaky, allowing diffusion). The efficiency to retain ions in solution is dependent on the thickness of the diffuse double layer which itself depends on the solution concentration in the membrane. Clay rich formations have been shown to act as non-ideal semi-permeable membrane. Andra is investigating the Callovo-Oxfordian clay as a host rock for intermediate-level to high-level radioactive waste. In this context, it has been feared that osmotic water flows generated by the release of sodium nitrate salt in high concentrations, out of intermediate radioactive bituminous waste, could induce important over-pressures. The latest would eventually lead to fracturing of the host rock around the waste disposal drifts. The purpose of the present study was to develop a simulation code with the capacity to assess the potential impact of osmosis on: the re-saturation of the waste disposal drifts, the pressure evolution and the solute transport in and around a waste disposal drift. A chemo-osmotic coupled flow and transport model was implemented using the FlexPDE-finite element library. Our model is based on the chemo-osmotic formulation developed by Bader and Kooi, 2005. The model has been extended to highly concentrated solutions based on Pitzer's equation. In order to assess the impact of osmotic flow on the re-saturation time, the model was also designed to allow unsaturated flow modelling. The model configuration consists of an initially unsaturated 2D

  15. Regional coupling of unsaturated and saturated flow and transport modeling - implementation at an alpine foothill aquifer in Austria

    Science.gov (United States)

    Klammler, G.; Rock, G.; Kupfersberger, H.; Fank, J.

    2012-04-01

    interval of every hydrotope vertical profile until the lowest observed groundwater table is reached. The fluctuation range of the phreatic surface is also discretized in 10 cm intervals and used as outflow boundary condition. By this procedure, the influence of the groundwater table on the water and nitrate mass leaving the unsaturated can be considered taken into account varying soil horizons. To cover saturated flow in the WLF aquifer a 2-dimensional transient horizontal flow and solute transport model is set up. A sequential coupling between the two models is implemented, i.e. a unidirectional transfer of recharge and nitrate mass outflow from the hydrotopes to the saturated compartment. For this purpose, a one-time assignment between the spatial discretization of the hydrotopes and the finite element mesh has to be set up. The resulting groundwater table computed for a given time step with the input from SIMWASER/STOTRASIM is then used to extract the corresponding water and nitrate mass values from the look-up table to be used for the consecutive time step. This process is being repeated until the end of the simulation period. Within this approach there is no direct feedback between the unsaturated and the saturated aquifer compartment, i.e. there is no simultaneous (within the same time step) update of the pressure head - unsaturated head relationship at the soil and the phreatic surface (like is shown e.g. in Walsum and Groedendijk, 2008). For the dominating coarse sand conditions of the WLF aquifer we believe that this simplification is not of further relevance. For higher soil moisture contents (i.e. almost full saturation near the groundwater table) the curve returns to specific retention within a short vertical distance. Thus, there might only be mutual impact between soil and phreatic surface conditions for shallow groundwater tables. However, it should be mentioned here that all other processes in the two compartments (including capillary rise due to clay rich

  16. Coupling of discrete ordinates methods by transmission of boundary conditions in solving the neutron transport equation in slab geometry; Couplage de discretisations aux ordonnees discretes d`equations de transport 1D par passage de conditions frontieres

    Energy Technology Data Exchange (ETDEWEB)

    Bal, G. [Departement MMN, Service IMA, Direction des Etudes et Recherches, Electricite de France (EDF), 92 - Clamart (France)

    1995-10-01

    Neutron transport in nuclear reactors is quite well modelled by the linear Boltzmann transport equation. Its solution is relatively easy, but unfortunately too expensive to achieve whole core computations. Thus, we have to simplify it, for example by homogenizing some physical characteristics. However, the solution may then be inaccurate. Moreover, in strongly homogeneous areas, the error may be too big. Then we would like to deal with such an inconvenient by solving the equation accurately on this area, but more coarsely away from it, so that the computation is not too expensive. This problem is the subject of a thesis. We present here some results obtained for slab geometry. The couplings between the fine and coarse discretization regions could be conceived in a number of approaches. Here, we only deal with the coupling at crossing the interface between two sub-domains. In the first section, we present the coupling of discrete ordinate methods for solving the homogeneous, isotropic and mono-kinetic equation. Coupling operators are defined and shown to be optimal. The second and the third sections are devoted to an extension of the previous results when the equation is non-homogeneous, anisotropic and multigroup (under some restrictive assumptions). Some numerical results are given in the case of isotropic and mono-kinetic equations. (author) 15 refs.

  17. Microbial metabolomics with gas chromatography/mass spectrometry

    NARCIS (Netherlands)

    Koek, M.M.; Muilwijk, B.; Werf, M.J. van der; Hankemeier, T.

    2006-01-01

    An analytical method was set up suitable for the analysis of microbial metabolomes, consisting of an oximation and silylation derivatization reaction and subsequent analysis by gas chromatography coupled to mass spectrometry. Microbial matrixes contain many compounds that potentially interfere with

  18. A vector/parallel method for a three-dimensional transport model coupled with bio-chemical terms

    NARCIS (Netherlands)

    B.P. Sommeijer (Ben); J. Kok (Jan)

    1995-01-01

    textabstractA so-called fractional step method is considered for the time integration of a three-dimensional transport-chemical model in shallow seas. In this method, the transport part and the chemical part are treated separately by appropriate integration techniques. This separation is motivated

  19. Transportation

    Science.gov (United States)

    2007-01-01

    Faculty ii INDUSTRY TRAVEL Domestic Assistant Deputy Under Secretary of Defense (Transportation Policy), Washington, DC Department of...developed between the railroad and trucking industries. Railroads: Today’s seven Class I freight railroad systems move 42% of the nation’s intercity ...has been successfully employed in London to reduce congestion and observed by this industry study during its travels . It is currently being

  20. Effect of Freeze-Thaw Cycles on Soil Nitrogen Reactive Transport in a Polygonal Arctic Tundra Ecosystem at Barrow AK Using 3-D Coupled ALM-PFLOTRAN

    Science.gov (United States)

    Yuan, F.; Wang, G.; Painter, S. L.; Tang, G.; Xu, X.; Kumar, J.; Bisht, G.; Hammond, G. E.; Mills, R. T.; Thornton, P. E.; Wullschleger, S. D.

    2017-12-01

    In Arctic tundra ecosystem soil freezing-thawing is one of dominant physical processes through which biogeochemical (e.g., carbon and nitrogen) cycles are tightly coupled. Besides hydraulic transport, freezing-thawing can cause pore water movement and aqueous species gradients, which are additional mechanisms for soil nitrogen (N) reactive-transport in Tundra ecosystem. In this study, we have fully coupled an in-development ESM(i.e., Advanced Climate Model for Energy, ACME)'s Land Model (ALM) aboveground processes with a state-of-the-art massively parallel 3-D subsurface thermal-hydrology and reactive transport code, PFLOTRAN. The resulting coupled ALM-PFLOTRAN model is a Land Surface Model (LSM) capable of resolving 3-D soil thermal-hydrological-biogeochemical cycles. This specific version of PFLOTRAN has incorporated CLM-CN Converging Trophic Cascade (CTC) model and a full and simple but robust soil N cycle. It includes absorption-desorption for soil NH4+ and gas dissolving-degasing process as well. It also implements thermal-hydrology mode codes with three newly-modified freezing-thawing algorithms which can greatly improve computing performance in regarding to numerical stiffness at freezing-point. Here we tested the model in fully 3-D coupled mode at the Next Generation Ecosystem Experiment-Arctic (NGEE-Arctic) field intensive study site at the Barrow Environmental Observatory (BEO), AK. The simulations show that: (1) synchronous coupling of soil thermal-hydrology and biogeochemistry in 3-D can greatly impact ecosystem dynamics across polygonal tundra landscape; and (2) freezing-thawing cycles can add more complexity to the system, resulting in greater mobility of soil N vertically and laterally, depending upon local micro-topography. As a preliminary experiment, the model is also implemented for Pan-Arctic region in 1-D column mode (i.e. no lateral connection), showing significant differences compared to stand-alone ALM. The developed ALM-PFLOTRAN coupling

  1. Characterization of Charge-Carrier Transport in Semicrystalline Polymers: Electronic Couplings, Site Energies, and Charge-Carrier Dynamics in Poly(bithiophene- alt -thienothiophene) [PBTTT

    KAUST Repository

    Poelking, Carl

    2013-01-31

    We establish a link between the microscopic ordering and the charge-transport parameters for a highly crystalline polymeric organic semiconductor, poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT). We find that the nematic and dynamic order parameters of the conjugated backbones, as well as their separation, evolve linearly with temperature, while the side-chain dynamic order parameter and backbone paracrystallinity change abruptly upon the (also experimentally observed) melting of the side chains around 400 K. The distribution of site energies follows the behavior of the backbone paracrystallinity and can be treated as static on the time scale of a single-charge transfer reaction. On the contrary, the electronic couplings between adjacent backbones are insensitive to side-chain melting and vary on a much faster time scale. The hole mobility, calculated after time-averaging of the electronic couplings, reproduces well the value measured in a short-channel thin-film transistor. The results underline that to secure efficient charge transport in lamellar arrangements of conjugated polymers: (i) the electronic couplings should present high average values and fast dynamics, and (ii) the energetic disorder (paracrystallinity) should be small. © 2013 American Chemical Society.

  2. Characterization of Charge-Carrier Transport in Semicrystalline Polymers: Electronic Couplings, Site Energies, and Charge-Carrier Dynamics in Poly(bithiophene- alt -thienothiophene) [PBTTT

    KAUST Repository

    Poelking, Carl; Cho, Eunkyung; Malafeev, Alexander; Ivanov, Viktor; Kremer, Kurt; Risko, Chad; Bré das, Jean-Luc; Andrienko, Denis

    2013-01-01

    We establish a link between the microscopic ordering and the charge-transport parameters for a highly crystalline polymeric organic semiconductor, poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT). We find that the nematic and dynamic order parameters of the conjugated backbones, as well as their separation, evolve linearly with temperature, while the side-chain dynamic order parameter and backbone paracrystallinity change abruptly upon the (also experimentally observed) melting of the side chains around 400 K. The distribution of site energies follows the behavior of the backbone paracrystallinity and can be treated as static on the time scale of a single-charge transfer reaction. On the contrary, the electronic couplings between adjacent backbones are insensitive to side-chain melting and vary on a much faster time scale. The hole mobility, calculated after time-averaging of the electronic couplings, reproduces well the value measured in a short-channel thin-film transistor. The results underline that to secure efficient charge transport in lamellar arrangements of conjugated polymers: (i) the electronic couplings should present high average values and fast dynamics, and (ii) the energetic disorder (paracrystallinity) should be small. © 2013 American Chemical Society.

  3. Fully quantum-mechanical dynamic analysis of single-photon transport in a single-mode waveguide coupled to a traveling-wave resonator

    International Nuclear Information System (INIS)

    Hach, Edwin E. III; Elshaari, Ali W.; Preble, Stefan F.

    2010-01-01

    We analyze the dynamics of single-photon transport in a single-mode waveguide coupled to a micro-optical resonator by using a fully quantum-mechanical model. We examine the propagation of a single-photon Gaussian packet through the system under various coupling conditions. We review the theory of single-photon transport phenomena as applied to the system and we develop a discussion on the numerical technique we used to solve for dynamical behavior of the quantized field. To demonstrate our method and to establish robust single-photon results, we study the process of adiabatically lowering or raising the energy of a single photon trapped in an optical resonator under active tuning of the resonator. We show that our fully quantum-mechanical approach reproduces the semiclassical result in the appropriate limit and that the adiabatic invariant has the same form in each case. Finally, we explore the trapping of a single photon in a system of dynamically tuned, coupled optical cavities.

  4. Interaction between Polyketide Synthase and Transporter Suggests Coupled Synthesis and Export of Virulence Lipid in M. tuberculosis.

    Directory of Open Access Journals (Sweden)

    2005-09-01

    Full Text Available Virulent mycobacteria utilize surface-exposed polyketides to interact with host cells, but the mechanism by which these hydrophobic molecules are transported across the cell envelope to the surface of the bacteria is poorly understood. Phthiocerol dimycocerosate (PDIM, a surface-exposed polyketide lipid necessary for Mycobacterium tuberculosis virulence, is the product of several polyketide synthases including PpsE. Transport of PDIM requires MmpL7, a member of the MmpL family of RND permeases. Here we show that a domain of MmpL7 biochemically interacts with PpsE, the first report of an interaction between a biosynthetic enzyme and its cognate transporter. Overexpression of the interaction domain of MmpL7 acts as a dominant negative to PDIM synthesis by poisoning the interaction between synthase and transporter. This suggests that MmpL7 acts in complex with the synthesis machinery to efficiently transport PDIM across the cell membrane. Coordination of synthesis and transport may not only be a feature of MmpL-mediated transport in M. tuberculosis, but may also represent a general mechanism of polyketide export in many different microorganisms.

  5. A radiotracer study on the volatilization and transport effects of thermochemical reagents used in the analysis of alumina powders by slurry electrothermal vaporization inductively coupled plasma mass spectrometry

    International Nuclear Information System (INIS)

    Peschel, Birgit U.; Herdering, Wilhelm; Broekaert, Jose A.C.

    2007-01-01

    A neutron-activated Al 2 O 3 powder SRM 699 (NIST) containing the γ-radiation emitting radionuclides 51 Cr, 59 Fe, 60 Co and 65 Zn has been used to study the influence of thermochemical reagents on the volatilization and transport efficiency for these trace elements in electrothermal vaporization inductively coupled plasma mass spectrometry (ETV-ICP-MS) of Al 2 O 3 powders. From the signals in the γ-spectra for the radiotracers it has been found that less than 2% of the elements Cr, Fe, Co and Zn is left back in a graphite furnace from Al 2 O 3 powders at 2200 deg. C even without addition of a thermochemical reagent and the latter even was found to decrease the volatilization efficiencies. The recovery for the radiotracers on filters at the end of the transport tube as measured from the signals in the γ-spectra, however, was found to increase in most cases (i.e. from about 10% to more than 20%) when Pd(NO 3 ) 2 , Pd(NO 3 ) 2 + Mg(NO 3 ) 2 , PdCl 2 , IrCl 3 , SnCl 2 , AgCl, NaF, NH 4 Cl and NH 4 F were added at amounts generally used in electrothermal vaporization inductively coupled plasma mass spectrometry. However, when adding higher amounts as stoichiometrically required for a complete halogenation of the sample matrix in the case of AgCl, C 8 F 15 O 2 Na, IrCl 3 or PdCl 2 the transport efficiencies considerably decrease again. As shown in the case of NH 4 Cl the amount of thermochemical reagent used has to be optimized so as to obtain maximum analyte transport efficiencies. A comparison of the influence of NH 4 Cl on the transport efficiencies with its influence on the ETV-ICP-MS signals for Fe demonstrates the importance of transport efficiency changes for the effects of thermochemical reagents in electrothermal vaporization inductively coupled plasma mass spectrometry

  6. Deep subsurface microbial processes

    Science.gov (United States)

    Lovley, D.R.; Chapelle, F.H.

    1995-01-01

    Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

  7. Coupling between reactions and transport for the modelling and simulation of CO{sub 2} geological storage; Couplage reactions-transport pour la modelisation et la simulation du stockage geologique de CO{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Tillier, E

    2007-09-15

    In this work, we present some results about the coupling between transport and geochemistry for the modelling and the simulation of CO{sub 2} geological storage. We present a multiphase flow model and a geochemical model which enables to describe a coupled reactive multiphase flow problem. We then propose two methods of resolution, the first one is a global method, the other one is a splitting method which is used at the IFP in the software COORES. The splitting is based on physical assumptions. The coupling method used is a non iterative method,