Science.gov

Sample records for 1-d reactive transport

  1. Column Testing and 1D Reactive Transport Modeling to Evaluate Uranium Plume Persistence Processes

    NASA Astrophysics Data System (ADS)

    Johnson, R. H.; Morrison, S.; Morris, S.; Tigar, A.; Dam, W. L.; Dayvault, J.

    2015-12-01

    At many U.S. Department of Energy Office of Legacy Management sites, 100 year natural flushing was selected as a remedial option for groundwater uranium plumes. However, current data indicate that natural flushing is not occurring as quickly as expected and solid-phase and aqueous uranium concentrations are persistent. At the Grand Junction, Colorado office site, column testing was completed on core collected below an area where uranium mill tailings have been removed. The total uranium concentration in this core was 13.2 mg/kg and the column was flushed with laboratory-created water with no uranium and chemistry similar to the nearby Gunnison River. The core was flushed for a total of 91 pore volumes producing a maximum effluent uranium concentration of 6,110 μg/L at 2.1 pore volumes and a minimum uranium concentration of 36.2 μg/L at the final pore volume. These results indicate complex geochemical reactions at small pore volumes and a long tailing affect at greater pore volumes. Stop flow data indicate the occurrence of non-equilibrium processes that create uranium concentration rebound. These data confirm the potential for plume persistence, which is occurring at the field scale. 1D reactive transport modeling was completed using PHREEQC (geochemical model) and calibrated to the column test data manually and using PEST (inverse modeling calibration routine). Processes of sorption, dual porosity with diffusion, mineral dissolution, dispersion, and cation exchange were evaluated separately and in combination. The calibration results indicate that sorption and dual porosity are major processes in explaining the column test data. These processes are also supported by fission track photographs that show solid-phase uranium residing in less mobile pore spaces. These procedures provide valuable information on plume persistence and secondary source processes that may be used to better inform and evaluate remedial strategies, including natural flushing.

  2. Reactive Transport Modeling of Microbially-Mediated Chromate Reduction in 1-D Soil Columns

    NASA Astrophysics Data System (ADS)

    Qiu, H.; Viamajala, S.; Alam, M. M.; Peyton, B. M.; Petersen, J. N.; Yonge, D. R.

    2002-12-01

    Cr(VI) reduction tests were performed with the well known metal reducing bacterium Shewanella oneidensis MR-1 in liquid phase batch reactors and continuous flow soil columns under anaerobic conditions. In the batch tests, the cultures were grown with fumarate as the terminal electron acceptor and lactate as the electron donor in a simulated groundwater medium to determine yield coefficients and specific growth rates. The bench-scale soil column experiments were carried out with MR-1 to test the hypothesis that the kinetic parameters obtained in batch studies, combined with microbial attachment /detachment processes, will accurately predict reactive transport of Cr(VI) during bacterial Cr(VI) reduction in a soil matrix. Cr(VI)-free simulated groundwater media containing fumarate as the limiting substrate and lactate was supplied to a 2.1cm (ID) x 15 cm soil column inoculated with MR-1 for a duration of 9 residence times to allow for biomass to build-up in the column. Thereafter the column was supplied with both Cr(VI) and substrate. The concentrations of effluent substrate, biomass and Cr(VI) were monitored on a periodic basis and attached biomass in the column was measured in the termination of each column test. A reactive transport model was developed in which 6 governing equations deal with Cr(VI) bioreaction, fumarate (as electron donor) consumption, aqueous biomass growth and transport, solid biomass detachment and attachment kinetics, aqueous and solid phase enzyme reaction and transport, respectively. The model incorporating the enzyme reaction kinetics for Cr(VI) reduction, Monod kinetic expressions for substrate depletion, nonlinear attachment and detachment kinetics for aqueous and solid phase microorganism concentration, was solved by a fully implicit, finite-difference procedure using RT3D (A Modular Computer Code for Reactive Multi-species Transport in 3-Dimensional Groundwater Systems) platform in one dimension. Cr(VI)-free column data was used to

  3. Comprehensive 1D Modelling of Reactive Chemical Transport in Unsaturated Soil

    NASA Astrophysics Data System (ADS)

    Wissmeier, L.; Barry, D. A.

    2007-12-01

    Computer models for simulating environmental processes of water flow, solute transport and geochemical reactions have greatly advanced during recent years. However, there is still demand for the development of programs that a capable of simulating the numerous interactions between physical transport processes and biogeochemical reactions in natural soils. We present a new tool for simulating transient vadose zone flow and solute transport according to the moisture- based form of Richards' equation within the widely used geochemical software PHREEQC. The direct implementation into the geochemical framework provides access to comprehensive geochemical models, giving capabilities beyond existing software for coupled unsaturated flow and reaction. Possible reactions include complex aqueous speciation, cation exchange, equilibrium phase dissolution and precipitation, formation of solid solutions, redox reactions, gas phase exchange, surface adsorption considering electrostatics and kinetic reactions with user-defined rate equations, among others. As a result of the close coupling procedure, the influence of geochemical reactions on water content, e.g., through dissolution or precipitation of water-containing phases, can be investigated. For the solution of the partial differential equations of flow and transport, an explicit finite-difference formulation with a second-order space discretization and first-order time discretization was employed. The use of integrated diffusivities transforms Richards' equation into a simple advection-diffusion equation. Changes in water content and solute concentration were conceptualized as local kinetic reactions of individual elements where changes in moisture content result from fluxes of oxygen and hydrogen across cell boundaries. Reactions and chemical element transport are coupled via sequential two-step operator splitting. The scheme was implemented into PHREEQC without any source code modification such that it can be applied by

  4. 1D Thermal-Hydraulic-Chemical (THC) Reactive transport modeling for deep geothermal systems: A case study of Groß Schönebeck reservoir, Germany

    NASA Astrophysics Data System (ADS)

    Driba, D. L.; De Lucia, M.; Peiffer, S.

    2014-12-01

    Fluid-rock interactions in geothermal reservoirs are driven by the state of disequilibrium that persists among solid and solutes due to changing temperature and pressure. During operation of enhanced geothermal systems, injection of cooled water back into the reservoir disturbs the initial thermodynamic equilibrium between the reservoir and its geothermal fluid, which may induce modifications in permeability through changes in porosity and pore space geometry, consequently bringing about several impairments to the overall system.Modeling of fluid-rock interactions induced by injection of cold brine into Groß Schönebeck geothermal reservoir system situated in the Rotliegend sandstone at 4200m depth have been done by coupling geochemical modeling Code Phreeqc with OpenGeoSys. Through batch modeling the re-evaluation of the measured hydrochemical composition of the brine has been done using Quintessa databases, the results from the calculation indicate that a mineral phases comprising of K-feldspar, hematite, Barite, Calcite and Dolomite was found to match the hypothesis of equilibrium with the formation fluid, Reducing conditions are presumed in the model (pe = -3.5) in order to match the amount of observed dissolved Fe and thus considered as initial state for the reactive transport modeling. based on a measured composition of formation fluids and the predominant mineralogical assemblage of the host rock, a preliminary 1D Reactive transport modeling (RTM) was run with total time set to 30 years; results obtained for the initial simulation revealed that during this period, no significant change is evident for K-feldspar. Furthermore, the precipitation of calcite along the flow path in the brine results in a drop of pH from 6.2 to a value of 5.2 noticed over the simulated period. The circulation of cooled fluid in the reservoir is predicted to affect the temperature of the reservoir within the first 100 -150m from the injection well. Examination of porosity change in

  5. Polar molecule reactive collisions in quasi-1D systems

    NASA Astrophysics Data System (ADS)

    Simoni, A.; Srinivasan, S.; Launay, J.-M.; Jachymski, K.; Idziaszek, Z.; Julienne, P. S.

    2015-01-01

    We study polar molecule scattering in quasi-one-dimensional geometries. Elastic and reactive collision rates are computed as a function of collision energy and electric dipole moment for different confinement strengths. The numerical results are interpreted in terms of first order scattering and of adiabatic models. Universal dipolar scattering is also discussed. Our results are relevant to experiments where control of the collision dynamics through one-dimensional confinement and an applied electric field is envisioned.

  6. Interaction of environmental contaminants with zebrafish organic anion transporting polypeptide, Oatp1d1 (Slco1d1)

    SciTech Connect

    Popovic, Marta; Zaja, Roko; Fent, Karl; Smital, Tvrtko

    2014-10-01

    Polyspecific transporters from the organic anion transporting polypeptide (OATP/Oatp) superfamily mediate the uptake of a wide range of compounds. In zebrafish, Oatp1d1 transports conjugated steroid hormones and cortisol. It is predominantly expressed in the liver, brain and testes. In this study we have characterized the transport of xenobiotics by the zebrafish Oatp1d1 transporter. We developed a novel assay for assessing Oatp1d1 interactors using the fluorescent probe Lucifer yellow and transient transfection in HEK293 cells. Our data showed that numerous environmental contaminants interact with zebrafish Oatp1d1. Oatp1d1 mediated the transport of diclofenac with very high affinity, followed by high affinity towards perfluorooctanesulfonic acid (PFOS), nonylphenol, gemfibrozil and 17α-ethinylestradiol; moderate affinity towards carbaryl, diazinon and caffeine; and low affinity towards metolachlor. Importantly, many environmental chemicals acted as strong inhibitors of Oatp1d1. A strong inhibition of Oatp1d1 transport activity was found by perfluorooctanoic acid (PFOA), chlorpyrifos-methyl, estrone (E1) and 17β-estradiol (E2), followed by moderate to low inhibition by diethyl phthalate, bisphenol A, 7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4 tetrahydronapthalene and clofibrate. In this study we identified Oatp1d1 as a first Solute Carrier (SLC) transporter involved in the transport of a wide range of xenobiotics in fish. Considering that Oatps in zebrafish have not been characterized before, our work on zebrafish Oatp1d1 offers important new insights on the understanding of uptake processes of environmental contaminants, and contributes to the better characterization of zebrafish as a model species. - Highlights: • We optimized a novel assay for determination of Oatp1d1 interactors • Oatp1d1 is the first SLC characterized fish xenobiotic transporter • PFOS, nonylphenol, diclofenac, EE2, caffeine are high affinity Oatp1d1substrates • PFOA, chlorpyrifos

  7. Interaction of environmental contaminants with zebrafish organic anion transporting polypeptide, Oatp1d1 (Slco1d1).

    PubMed

    Popovic, Marta; Zaja, Roko; Fent, Karl; Smital, Tvrtko

    2014-10-01

    Polyspecific transporters from the organic anion transporting polypeptide (OATP/Oatp) superfamily mediate the uptake of a wide range of compounds. In zebrafish, Oatp1d1 transports conjugated steroid hormones and cortisol. It is predominantly expressed in the liver, brain and testes. In this study we have characterized the transport of xenobiotics by the zebrafish Oatp1d1 transporter. We developed a novel assay for assessing Oatp1d1 interactors using the fluorescent probe Lucifer yellow and transient transfection in HEK293 cells. Our data showed that numerous environmental contaminants interact with zebrafish Oatp1d1. Oatp1d1 mediated the transport of diclofenac with very high affinity, followed by high affinity towards perfluorooctanesulfonic acid (PFOS), nonylphenol, gemfibrozil and 17α-ethinylestradiol; moderate affinity towards carbaryl, diazinon and caffeine; and low affinity towards metolachlor. Importantly, many environmental chemicals acted as strong inhibitors of Oatp1d1. A strong inhibition of Oatp1d1 transport activity was found by perfluorooctanoic acid (PFOA), chlorpyrifos-methyl, estrone (E1) and 17β-estradiol (E2), followed by moderate to low inhibition by diethyl phthalate, bisphenol A, 7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4 tetrahydronapthalene and clofibrate. In this study we identified Oatp1d1 as a first Solute Carrier (SLC) transporter involved in the transport of a wide range of xenobiotics in fish. Considering that Oatps in zebrafish have not been characterized before, our work on zebrafish Oatp1d1 offers important new insights on the understanding of uptake processes of environmental contaminants, and contributes to the better characterization of zebrafish as a model species. PMID:25088042

  8. Quadratic Finite Element Method for 1D Deterministic Transport

    SciTech Connect

    Tolar, Jr., D R; Ferguson, J M

    2004-01-06

    In the discrete ordinates, or SN, numerical solution of the transport equation, both the spatial ({und r}) and angular ({und {Omega}}) dependences on the angular flux {psi}{und r},{und {Omega}}are modeled discretely. While significant effort has been devoted toward improving the spatial discretization of the angular flux, we focus on improving the angular discretization of {psi}{und r},{und {Omega}}. Specifically, we employ a Petrov-Galerkin quadratic finite element approximation for the differencing of the angular variable ({mu}) in developing the one-dimensional (1D) spherical geometry S{sub N} equations. We develop an algorithm that shows faster convergence with angular resolution than conventional S{sub N} algorithms.

  9. Inter-annual variability of dissolved inorganic nitrogen in the Biobío River, Central Chile: an analysis base on a decadal database along with 1-D reactive transport modeling

    NASA Astrophysics Data System (ADS)

    Yévenes, M.; Figueroa, R.; Parra, O.; Farías, L.

    2015-01-01

    Rivers may act as important sinks (filters) or sources for inorganic nutrients between the land and the sea, depending on the biogeochemical processes and nutrient inputs along the river. This study examines the inter-annual variability of dissolved inorganic nitrogen (DIN) seasonal (wet-dry) cycle for the Biobío River, one of the largest and most industrialized rivers of Central Chile (36°45'-38°49' S and 71°00'-73°20' W). Long-term water flow (1990-2012) and water quality datasets (2004-2012) were used along with a one-dimensional reactive transport ecosystem model to evaluate the effects of water flow and N inputs on seasonal pattern of DIN. From 2004 to 2012, annual average nitrate levels significantly increased from 1.73 ± 2.17 μmol L-1 (upstream of the river) to 18.4 ± 12.7 μmol L-1 (in the river mouth); while the annual average oxygen concentration decreased from 348 ± 22 to 278 ± 42 μmol L-1 between upstream and downstream, indicating an additional oxygen consumption. Variability in the mid-section of the river (station BB8) was identified as a major influence on the inter-annual variability and appeared to be the site of a major anthropogenic disturbance. However, there was also an influence of climate on riverine DIN concentrations; high DIN production occurred during wet years, whereas high consumption proceeded during dry years. Extremely reduced river flow and drought during summer also strongly affected the annual DIN concentration, reducing the DIN production. Additionally, summer storm events during drought periods appeared to cause significant runoff resulting in nitrate inputs to the river. The total DIN input reaching the river mouth was 0.159 Gmol yr-1, implying that internal production exceeds consumption processes, and identifying nitrification as one of the predominant processes occurring in the estuary. In the following, the impact on the river of DIN increases as a nutrient source, as well as climate and biogeochemical factors

  10. Validation of 1-D transport and sawtooth models for ITER

    SciTech Connect

    Connor, J.W.; Turner, M.F.; Attenberger, S.E.; Houlberg, W.A.

    1996-12-31

    In this paper the authors describe progress on validating a number of local transport models by comparing their predictions with relevant experimental data from a range of tokamaks in the ITER profile database. This database, the testing procedure and results are discussed. In addition a model for sawtooth oscillations is used to investigate their effect in an ITER plasma with alpha-particles.

  11. Morphodynamics and sediment tracers in 1-D (MAST-1D): 1-D sediment transport that includes exchange with an off-channel sediment reservoir

    NASA Astrophysics Data System (ADS)

    Lauer, J. Wesley; Viparelli, Enrica; Piégay, Hervé

    2016-07-01

    Bed material transported in geomorphically active gravel bed rivers often has a local source at nearby eroding banks and ends up sequestered in bars not far downstream. However, most 1-D numerical models for gravel transport assume that gravel originates from and deposits on the channel bed. In this paper, we present a 1-D framework for simulating morphodynamic evolution of bed elevation and size distribution in a gravel-bed river that actively exchanges sediment with its floodplain, which is represented as an off-channel sediment reservoir. The model is based on the idea that sediment enters the channel at eroding banks whose elevation depends on total floodplain sediment storage and on the average elevation of the floodplain relative to the channel bed. Lateral erosion of these banks occurs at a specified rate that can represent either net channel migration or channel widening. Transfer of material out of the channel depends on a typical bar thickness and a specified lateral exchange rate due either to net channel migration or narrowing. The model is implemented using an object oriented framework that allows users to explore relationships between bank supply, bed structure, and lateral change rates. It is applied to a ∼50-km reach of the Ain River, France, that experienced significant reduction in sediment supply due to dam construction during the 20th century. Results are strongly sensitive to lateral exchange rates, showing that in this reach, the supply of sand and gravel at eroding banks and the sequestration of gravel in point bars can have strong influence on overall reach-scale sediment budgets.

  12. XCHEM-1D: A Heat Transfer/Chemical Kinetics Computer Program for multilayered reactive materials

    SciTech Connect

    Gross, R.J.; Baer, M.R.; Hobbs, M.L.

    1993-10-01

    An eXplosive CHEMical kinetics code, XCHEM, has been developed to solve the reactive diffusion equations associated with thermal ignition of energetic materials. This method-of-lines code uses stiff numerical methods and adaptive meshing to resolve relevant combustion physics. Solution accuracy is maintained between multilayered materials consisting of blends of reactive components and/or inert materials. Phase change and variable properties are included in one-dimensional slab, cylindrical and spherical geometries. Temperature-dependent thermal properties have been incorporated and the modification of thermal conductivities to include decomposition effects are estimated using solid/gas volume fractions determined by species fractions. Gas transport properties, including high pressure corrections, have also been included. Time varying temperature, heat flux, convective and thermal radiation boundary conditions, and layer to layer contact resistances have also been implemented.

  13. MULTICOMPONENT GEOCHEMICAL TRANSPORT MODELING USING HYDRUS-1D AND HP1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The transport of reactive contaminants in the subsurface is generally affected by a large number of nonlinear and often interactive physical, chemical, and biological processes. Simulating these processes requires a comprehensive reactive transport code that couples the physical processes of water f...

  14. MULTICOMPONENT GEOCHEMICAL TRANSPORT MODELING USING THE HYDRUS-1D COMPUTER SOFTWARE PACKAGE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ABSTRACT: The transport of reactive contaminants in the subsurface is generally affected by a large number of nonlinear and often interactive physical, chemical and biological processes. Simulating these processes requires a coupled reactive transport code that couples the physical processes of wate...

  15. Reactive transport modeling of Li isotope fractionation

    NASA Astrophysics Data System (ADS)

    Wanner, C.; Sonnenthal, E. L.

    2013-12-01

    The fractionation of Li isotopes has been used as a proxy for interaction processes between silicate rocks and any kind of fluids. In particular, Li isotope measurements are powerful because Li is almost exclusively found in silicate minerals. Moreover, the two stable Li isotopes, 6Li and 7Li, differ by 17% in mass introducing a large mass dependent isotope fractionation even at high temperature. Typical applications include Li isotope measurements along soil profiles and of river waters to track silicate weathering patterns and Li isotope measurements of geothermal wells and springs to assess water-rock interaction processes in geothermal systems. For this contribution we present a novel reactive transport modeling approach for the simulation of Li isotope fractionation using the code TOUGHREACT [1]. It is based on a 6Li-7Li solid solution approach similar to the one recently described for simulating Cr isotope fractionation [2]. Model applications include the simulation of granite weathering along a 1D flow path as well as the simulation of a column experiment related to an enhanced geothermal system. Results show that measured δ7Li values are mainly controlled by (i) the degree of interaction between Li bearing primary silicate mineral phases (e.g., micas, feldspars) and the corresponding fluid, (ii) the Li isotope fractionation factor during precipitation of secondary mineral phases (e.g., clays), (iii) the Li concentration in primary and secondary Li bearing mineral phases and (iv) the proportion of dissolved Li that adsorbs to negatively charged surfaces (e.g., clays, Fe/Al-hydroxides). To date, most of these parameters are not very well constrained. Reactive transport modeling thus currently has to rely on many assumptions. Nevertheless, such models are powerful because they are the only viable option if individual contributions of all potential processes on the resulting (i.e., measured) Li isotopic ratio have to be quantitatively assessed. Accordingly, we

  16. TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport.

    PubMed

    Schmidts, Miriam; Hou, Yuqing; Cortés, Claudio R; Mans, Dorus A; Huber, Celine; Boldt, Karsten; Patel, Mitali; van Reeuwijk, Jeroen; Plaza, Jean-Marc; van Beersum, Sylvia E C; Yap, Zhi Min; Letteboer, Stef J F; Taylor, S Paige; Herridge, Warren; Johnson, Colin A; Scambler, Peter J; Ueffing, Marius; Kayserili, Hulya; Krakow, Deborah; King, Stephen M; Beales, Philip L; Al-Gazali, Lihadh; Wicking, Carol; Cormier-Daire, Valerie; Roepman, Ronald; Mitchison, Hannah M; Witman, George B

    2015-01-01

    The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions. PMID:26044572

  17. TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport

    PubMed Central

    Schmidts, Miriam; Hou, Yuqing; Cortés, Claudio R.; Mans, Dorus A.; Huber, Celine; Boldt, Karsten; Patel, Mitali; van Reeuwijk, Jeroen; Plaza, Jean-Marc; van Beersum, Sylvia E. C.; Yap, Zhi Min; Letteboer, Stef J. F.; Taylor, S. Paige; Herridge, Warren; Johnson, Colin A.; Scambler, Peter J.; Ueffing, Marius; Kayserili, Hulya; Krakow, Deborah; King, Stephen M.; Beales, Philip L.; Al-Gazali, Lihadh; Wicking, Carol; Cormier-Daire, Valerie; Roepman, Ronald; Mitchison, Hannah M.; Witman, George B.; Al-Turki, Saeed; Anderson, Carl; Anney, Richard; Antony, Dinu; Asimit, Jennifer; Ayub, Mohammad; Barrett, Jeff; Barroso, Inês; Bentham, Jamie; Bhattacharya, Shoumo; Blackwood, Douglas; Bobrow, Martin; Bochukova, Elena; Bolton, Patrick; Boustred, Chris; Breen, Gerome; Brion, Marie-Jo; Brown, Andrew; Calissano, Mattia; Carss, Keren; Chatterjee, Krishna; Chen, Lu; Cirak, Sebhattin; Clapham, Peter; Clement, Gail; Coates, Guy; Collier, David; Cosgrove, Catherine; Cox, Tony; Craddock, Nick; Crooks, Lucy; Curran, Sarah; Daly, Allan; Danecek, Petr; Smith, George Davey; Day-Williams, Aaron; Day, Ian; Durbin, Richard; Edkins, Sarah; Ellis, Peter; Evans, David; Farooqi, I. Sadaf; Fatemifar, Ghazaleh; Fitzpatrick, David; Flicek, Paul; Floyd, Jamie; Foley, A. Reghan; Franklin, Chris; Futema, Marta; Gallagher, Louise; Gaunt, Tom; Geschwind, Daniel; Greenwood, Celia; Grozeva, Detelina; Guo, Xiaosen; Gurling, Hugh; Hart, Deborah; Hendricks, Audrey; Holmans, Peter; Huang, Jie; Humphries, Steve E.; Hurles, Matt; Hysi, Pirro; Jackson, David; Jamshidi, Yalda; Jewell, David; Chris, Joyce; Kaye, Jane; Keane, Thomas; Kemp, John; Kennedy, Karen; Kent, Alastair; Kolb-Kokocinski, Anja; Lachance, Genevieve; Langford, Cordelia; Lee, Irene; Li, Rui; Li, Yingrui; Ryan, Liu; Lönnqvist, Jouko; Lopes, Margarida; MacArthur, Daniel G.; Massimo, Mangino; Marchini, Jonathan; Maslen, John; McCarthy, Shane; McGuffin, Peter; McIntosh, Andrew; McKechanie, Andrew; McQuillin, Andrew; Memari, Yasin; Metrustry, Sarah; Min, Josine; Moayyeri, Alireza; Morris, James; Muddyman, Dawn; Muntoni, Francesco; Northstone, Kate; O'Donovan, Michael; O'Rahilly, Stephen; Onoufriadis, Alexandros; Oualkacha, Karim; Owen, Michael; Palotie, Aarno; Panoutsopoulou, Kalliope; Parker, Victoria; Parr, Jeremy; Paternoster, Lavinia; Paunio, Tiina; Payne, Felicity; Perry, John; Pietilainen, Olli; Plagnol, Vincent; Quail, Michael A.; Quaye, Lydia; Raymond, Lucy; Rehnström, Karola; Brent Richards, J.; Ring, Sue; Ritchie, Graham R S; Savage, David B.; Schoenmakers, Nadia; Semple, Robert K.; Serra, Eva; Shihab, Hashem; Shin, So-Youn; Skuse, David; Small, Kerrin; Smee, Carol; Soler, Artigas María; Soranzo, Nicole; Southam, Lorraine; Spector, Tim; St Pourcain, Beate; St. Clair, David; Stalker, Jim; Surdulescu, Gabriela; Suvisaari, Jaana; Tachmazidou, Ioanna; Tian, Jing; Timpson, Nic; Tobin, Martin; Valdes, Ana; van Kogelenberg, Margriet; Vijayarangakannan, Parthiban; Wain, Louise; Walter, Klaudia; Wang, Jun; Ward, Kirsten; Wheeler, Ellie; Whittall, Ros; Williams, Hywel; Williamson, Kathy; Wilson, Scott G.; Wong, Kim; Whyte, Tamieka; ChangJiang, Xu; Zeggini, Eleftheria; Zhang, Feng; Zheng, Hou-Feng

    2015-01-01

    The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions. PMID:26044572

  18. A New 2D-Transport, 1D-Diffusion Approximation of the Boltzmann Transport equation

    SciTech Connect

    Larsen, Edward

    2013-06-17

    The work performed in this project consisted of the derivation, implementation, and testing of a new, computationally advantageous approximation to the 3D Boltz- mann transport equation. The solution of the Boltzmann equation is the neutron flux in nuclear reactor cores and shields, but solving this equation is difficult and costly. The new “2D/1D” approximation takes advantage of a special geometric feature of typical 3D reactors to approximate the neutron transport physics in a specific (ax- ial) direction, but not in the other two (radial) directions. The resulting equation is much less expensive to solve computationally, and its solutions are expected to be sufficiently accurate for many practical problems. In this project we formulated the new equation, discretized it using standard methods, developed a stable itera- tion scheme for solving the equation, implemented the new numerical scheme in the MPACT code, and tested the method on several realistic problems. All the hoped- for features of this new approximation were seen. For large, difficult problems, the resulting 2D/1D solution is highly accurate, and is calculated about 100 times faster than a 3D discrete ordinates simulation.

  19. Epitaxial 1D electron transport layers for high-performance perovskite solar cells.

    PubMed

    Han, Gill Sang; Chung, Hyun Suk; Kim, Dong Hoe; Kim, Byeong Jo; Lee, Jin-Wook; Park, Nam-Gyu; Cho, In Sun; Lee, Jung-Kun; Lee, Sangwook; Jung, Hyun Suk

    2015-10-01

    We demonstrate high-performance perovskite solar cells with excellent electron transport properties using a one-dimensional (1D) electron transport layer (ETL). The 1D array-based ETL is comprised of 1D SnO2 nanowires (NWs) array grown on a F:SnO2 transparent conducting oxide substrate and rutile TiO2 nanoshells epitaxially grown on the surface of the 1D SnO2 NWs. The optimized devices show more than 95% internal quantum yield at 750 nm, and a power conversion efficiency (PCE) of 14.2%. The high quantum yield is attributed to dramatically enhanced electron transport in the epitaxial TiO2 layer, compared to that in conventional nanoparticle-based mesoporous TiO2 (mp-TiO2) layers. In addition, the open space in the 1D array-based ETL increases the prevalence of uniform TiO2/perovskite junctions, leading to reproducible device performance with a high fill factor. This work offers a method to achieve reproducible, high-efficiency perovskite solar cells with high-speed electron transport. PMID:26324759

  20. Significance of flow clustering and sequencing on sediment transport: 1D sediment transport modelling

    NASA Astrophysics Data System (ADS)

    Hassan, Kazi; Allen, Deonie; Haynes, Heather

    2016-04-01

    This paper considers 1D hydraulic model data on the effect of high flow clusters and sequencing on sediment transport. Using observed flow gauge data from the River Caldew, England, a novel stochastic modelling approach was developed in order to create alternative 50 year flow sequences. Whilst the observed probability density of gauge data was preserved in all sequences, the order in which those flows occurred was varied using the output from a Hidden Markov Model (HMM) with generalised Pareto distribution (GP). In total, one hundred 50 year synthetic flow series were generated and used as the inflow boundary conditions for individual flow series model runs using the 1D sediment transport model HEC-RAS. The model routed graded sediment through the case study river reach to define the long-term morphological changes. Comparison of individual simulations provided a detailed understanding of the sensitivity of channel capacity to flow sequence. Specifically, each 50 year synthetic flow sequence was analysed using a 3-month, 6-month or 12-month rolling window approach and classified for clusters in peak discharge. As a cluster is described as a temporal grouping of flow events above a specified threshold, the threshold condition used herein is considered as a morphologically active channel forming discharge event. Thus, clusters were identified for peak discharges in excess of 10%, 20%, 50%, 100% and 150% of the 1 year Return Period (RP) event. The window of above-peak flows also required cluster definition and was tested for timeframes 1, 2, 10 and 30 days. Subsequently, clusters could be described in terms of the number of events, maximum peak flow discharge, cumulative flow discharge and skewness (i.e. a description of the flow sequence). The model output for each cluster was analysed for the cumulative flow volume and cumulative sediment transport (mass). This was then compared to the total sediment transport of a single flow event of equivalent flow volume

  1. Epitaxial 1D electron transport layers for high-performance perovskite solar cells

    NASA Astrophysics Data System (ADS)

    Han, Gill Sang; Chung, Hyun Suk; Kim, Dong Hoe; Kim, Byeong Jo; Lee, Jin-Wook; Park, Nam-Gyu; Cho, In Sun; Lee, Jung-Kun; Lee, Sangwook; Jung, Hyun Suk

    2015-09-01

    We demonstrate high-performance perovskite solar cells with excellent electron transport properties using a one-dimensional (1D) electron transport layer (ETL). The 1D array-based ETL is comprised of 1D SnO2 nanowires (NWs) array grown on a F:SnO2 transparent conducting oxide substrate and rutile TiO2 nanoshells epitaxially grown on the surface of the 1D SnO2 NWs. The optimized devices show more than 95% internal quantum yield at 750 nm, and a power conversion efficiency (PCE) of 14.2%. The high quantum yield is attributed to dramatically enhanced electron transport in the epitaxial TiO2 layer, compared to that in conventional nanoparticle-based mesoporous TiO2 (mp-TiO2) layers. In addition, the open space in the 1D array-based ETL increases the prevalence of uniform TiO2/perovskite junctions, leading to reproducible device performance with a high fill factor. This work offers a method to achieve reproducible, high-efficiency perovskite solar cells with high-speed electron transport.We demonstrate high-performance perovskite solar cells with excellent electron transport properties using a one-dimensional (1D) electron transport layer (ETL). The 1D array-based ETL is comprised of 1D SnO2 nanowires (NWs) array grown on a F:SnO2 transparent conducting oxide substrate and rutile TiO2 nanoshells epitaxially grown on the surface of the 1D SnO2 NWs. The optimized devices show more than 95% internal quantum yield at 750 nm, and a power conversion efficiency (PCE) of 14.2%. The high quantum yield is attributed to dramatically enhanced electron transport in the epitaxial TiO2 layer, compared to that in conventional nanoparticle-based mesoporous TiO2 (mp-TiO2) layers. In addition, the open space in the 1D array-based ETL increases the prevalence of uniform TiO2/perovskite junctions, leading to reproducible device performance with a high fill factor. This work offers a method to achieve reproducible, high-efficiency perovskite solar cells with high-speed electron transport

  2. Benchmarks and models for 1-D radiation transport in stochastic participating media

    SciTech Connect

    Miller, D S

    2000-08-21

    Benchmark calculations for radiation transport coupled to a material temperature equation in a 1-D slab and 1-D spherical geometry binary random media are presented. The mixing statistics are taken to be homogeneous Markov statistics in the 1-D slab but only approximately Markov statistics in the 1-D sphere. The material chunk sizes are described by Poisson distribution functions. The material opacities are first taken to be constant and then allowed to vary as a strong function of material temperature. Benchmark values and variances for time evolution of the ensemble average of material temperature energy density and radiation transmission are computed via a Monte Carlo type method. These benchmarks are used as a basis for comparison with three other approximate methods of solution. One of these approximate methods is simple atomic mix. The second approximate model is an adaptation of what is commonly called the Levermore-Pomraning model and which is referred to here as the standard model. It is shown that recasting the temperature coupling as a type of effective scattering can be useful in formulating the third approximate model, an adaptation of a model due to Su and Pomraning which attempts to account for the effects of scattering in a stochastic context. This last adaptation shows consistent improvement over both the atomic mix and standard models when used in the 1-D slab geometry but shows limited improvement in the 1-D spherical geometry. Benchmark values are also computed for radiation transmission from the 1-D sphere without material heating present. This is to evaluate the performance of the standard model on this geometry--something which has never been done before. All of the various tests demonstrate the importance of stochastic structure on the solution. Also demonstrated are the range of usefulness and limitations of a simple atomic mix formulation.

  3. 2D/1D approximations to the 3D neutron transport equation. I: Theory

    SciTech Connect

    Kelley, B. W.; Larsen, E. W.

    2013-07-01

    A new class of '2D/1D' approximations is proposed for the 3D linear Boltzmann equation. These approximate equations preserve the exact transport physics in the radial directions x and y and diffusion physics in the axial direction z. Thus, the 2D/1D equations are more accurate approximations of the 3D Boltzmann equation than the conventional 3D diffusion equation. The 2D/1D equations can be systematically discretized, to yield accurate simulation methods for 3D reactor core problems. The resulting solutions will be more accurate than 3D diffusion solutions, and less expensive to generate than standard 3D transport solutions. In this paper, we (i) show that the simplest 2D/1D equation has certain desirable properties, (ii) systematically discretize this equation, and (iii) derive a stable iteration scheme for solving the discrete system of equations. In a companion paper [1], we give numerical results that confirm the theoretical predictions of accuracy and iterative stability. (authors)

  4. 2D/1D approximations to the 3D neutron transport equation. II: Numerical comparisons

    SciTech Connect

    Kelley, B. W.; Collins, B.; Larsen, E. W.

    2013-07-01

    In a companion paper [1], (i) several new '2D/1D equations' are introduced as accurate approximations to the 3D Boltzmann transport equation, (ii) the simplest of these approximate equations is systematically discretized, and (iii) a theoretically stable iteration scheme is developed to solve the discrete equations. In this paper, numerical results are presented that confirm the theoretical predictions made in [1]. (authors)

  5. Discontinuous Galerkin finite element method applied to the 1-D spherical neutron transport equation

    SciTech Connect

    Machorro, Eric . E-mail: machorro@amath.washington.edu

    2007-04-10

    Discontinuous Galerkin finite element methods are used to estimate solutions to the non-scattering 1-D spherical neutron transport equation. Various trial and test spaces are compared in the context of a few sample problems whose exact solution is known. Certain trial spaces avoid unphysical behaviors that seem to plague other methods. Comparisons with diamond differencing and simple corner-balancing are presented to highlight these improvements.

  6. Comparative effects of nodularin and microcystin-LR in zebrafish: 1. Uptake by organic anion transporting polypeptide Oatp1d1 (Slco1d1).

    PubMed

    Faltermann, Susanne; Prétôt, René; Pernthaler, Jakob; Fent, Karl

    2016-02-01

    Microcystin-LR (MC-LR) and nodularin are hepatotoxins produced by several cyanobacterial species. Their toxicity is based on active cellular uptake and subsequent inhibition of protein phosphatases PP1/2A, leading to hyperphosphorylation and cell death. To date, uptake of MC-LR and nodularin in fish is poorly understood. Here, we investigated the role of the organic anion transporting polypeptide Oatp1d1 in zebrafish (drOatp1d1, Slco1d1) in cellular uptake in zebrafish. We stably transfected CHO and HEK293 cell lines expressing drOatp1d1. In both transfectants, uptake of MC-LR and nodularin was demonstrated by competitive inhibition of uptake with fluorescent substrate lucifer yellow. Direct uptake of MC-LR was demonstrated by immunostaining, and indirectly by the high cytotoxicity in stable transfectants. By means of a synthesized fluorescent labeled MC-LR derivative, direct uptake was further confirmed in HEK293 cells expressing drOatp1d1. Additionally, uptake and toxicity was investigated in the permanent zebrafish liver cell line ZFL. These cells had only a low relative abundance of drOatp1d1, drOatp2b1 and drOatp1f transcripts, which correlated with the lack of MC-LR induced cytotoxicity and transcriptional changes of genes indicative of endoplasmic reticulum stress, a known effect of this toxin. Our study demonstrates that drOatp1d1 functions as an uptake transporter for both MC-LR and nodularin in zebrafish. PMID:26769064

  7. Electronic and Transport Properties of Quasi-1D Wires of Biological Molecules

    NASA Astrophysics Data System (ADS)

    Oetzel, Björn; Matthes, Lars; Tandetzky, Falk; Ortmann, Frank; Bechstedt, Friedhelm; Hannewald, Karsten

    2010-03-01

    In the search for organic materials with good charge-transport properties, artificial stacks of biological molecules are considered attractive candidates [1,2]. In this spirit, we present ab-initio DFT calculations of the structural, electronic, and quantum-transport properties of quasi-1D wires based on guanine and eumelanin molecules [3]. Hereby, a special focus is put on the results for the electronic bandwidths and the consequences for potential applications. [4pt] [1] R. di Felice et al., Phys. Rev. B 65, 045104 (2001) [0pt] [2] P. Meredith et al., Pigment Cell Res. 19, 572 (2006) [0pt] [3] B. Oetzel et al. (unpublished)

  8. Exponentially-convergent Monte Carlo for the 1-D transport equation

    SciTech Connect

    Peterson, J. R.; Morel, J. E.; Ragusa, J. C.

    2013-07-01

    We define a new exponentially-convergent Monte Carlo method for solving the one-speed 1-D slab-geometry transport equation. This method is based upon the use of a linear discontinuous finite-element trial space in space and direction to represent the transport solution. A space-direction h-adaptive algorithm is employed to restore exponential convergence after stagnation occurs due to inadequate trial-space resolution. This methods uses jumps in the solution at cell interfaces as an error indicator. Computational results are presented demonstrating the efficacy of the new approach. (authors)

  9. quantifying and Predicting Reactive Transport

    SciTech Connect

    Peter C. Burns, Department of Civil Engineering and Geological Sciences, University of Notre Dame

    2009-12-04

    This project was led by Dr. Jiamin Wan at Lawrence Berkeley National Laboratory. Peter Burns provided expertise in uranium mineralogy and in identification of uranium minerals in test materials. Dr. Wan conducted column tests regarding uranium transport at LBNL, and samples of the resulting columns were sent to Dr. Burns for analysis. Samples were analyzed for uranium mineralogy by X-ray powder diffraction and by scanning electron microscopy, and results were provided to Dr. Wan for inclusion in the modeling effort. Full details of the project can be found in Dr. Wan's final reports for the associated effort at LBNL.

  10. Multicomponent Transport in Polyatomic Reactive Gas Mixtures

    NASA Astrophysics Data System (ADS)

    Giovangigli, Vincent

    2011-05-01

    We investigate multicomponent reactive flow models derived from the kinetic theory of gases. We discuss in particular the conservation equations, the transport fluxes and the transport coefficients in weak and strong magnetic fields. The mathematical properties of the resulting hyperbolic-parabolic systems of partial differential equations modeling multicomponent flows are deduced from the underlying kinetic framework. The structure and solution of the transport linear systems associated with the evaluation of transport coefficients are also addressed. In particular, the convergence of iterative techniques is deduced from the properties of the linearized Boltzmann collision operator. The impact of multicomponent transport is also discussed, notably the importance of Soret effects in various flows and the impact of volume viscosity.

  11. Multicomponent Transport in Polyatomic Reactive Gas Mixtures

    SciTech Connect

    Giovangigli, Vincent

    2011-05-20

    We investigate multicomponent reactive flow models derived from the kinetic theory of gases. We discuss in particular the conservation equations, the transport fluxes and the transport coefficients in weak and strong magnetic fields. The mathematical properties of the resulting hyperbolic-parabolic systems of partial differential equations modeling multicomponent flows are deduced from the underlying kinetic framework. The structure and solution of the transport linear systems associated with the evaluation of transport coefficients are also addressed. In particular, the convergence of iterative techniques is deduced from the properties of the linearized Boltzmann collision operator. The impact of multicomponent transport is also discussed, notably the importance of Soret effects in various flows and the impact of volume viscosity.

  12. Scale up tools in reactive extrusion and compounding processes. Could 1D-computer modeling be helpful?

    NASA Astrophysics Data System (ADS)

    Pradel, J.-L.; David, C.; Quinebèche, S.; Blondel, P.

    2014-05-01

    Industrial scale-up (or scale down) in Compounding and Reactive Extrusion processes is one of the most critical R&D challenges. Indeed, most of High Performances Polymers are obtained within a reactive compounding involving chemistry: free radical grafting, in situ compatibilization, rheology control... but also side reactions: oxidation, branching, chain scission... As described by basic Arrhenius and kinetics laws, the competition between all chemical reactions depends on residence time distribution and temperature. Then, to ensure the best possible scale up methodology, we need tools to match thermal history of the formulation along the screws from a lab scale twin screw extruder to an industrial one. This paper proposes a comparison between standard scale-up laws and the use of Computer modeling Software such as Ludovic® applied and compared to experimental data. Scaling data from a compounding line to another one, applying general rules (for example at constant specific mechanical energy), shows differences between experimental and computed data, and error depends on the screw speed range. For more accurate prediction, 1D-Computer Modeling could be used to optimize the process conditions to ensure the best scale-up product, especially in temperature sensitive reactive extrusion processes. When the product temperature along the screws is the key, Ludovic® software could help to compute the temperature profile along the screws and extrapolate conditions, even screw profile, on industrial extruders.

  13. Dual Diagonalization of Reactive Transport Equations

    NASA Astrophysics Data System (ADS)

    Yeh, G.; Tsai, C.

    2013-12-01

    One solves a system of species transport equations in the primitive approach to reactive transport modeling. This approach is not able to decouple equilibrium reaction rates from species concentrations. This problem has been overcome with the approach to diagonalizing the reaction matrix since mid 1990's, which yields the same number of transport equations for reaction-extents. In the diagonalization approach, first, a subset of reaction- extent transport equations is solved for concentrations of components and kinetic-variables. Then, the component, kinetic-variable, and mass action equations are solved for all species concentrations. Finally, the equilibrium reaction rates are posterior computed. The difficulty in this approach is that the solution of species concentrations in the second step is a stiff problem when the concentrations of master species are small compared to those of equilibrium species. To overcome the problem of stiffness, we propose a dual diagonalization approach. Here, a second diagonalization is performed on the decomposed unit matrix to yield species concentrations, each as a linear function of reaction extents. In this dual diagonalization approach, four steps are needed to complete the modeling. First, component and kinetic-variable transport equations are solved for the concentrations of components (a subset of reaction-extents) and kinetic-variables (another subset of reaction-extents). Second, the set of mass action equations written in terms of reaction extents are solved for equilibrium-variables (yet another subset of reaction-extents). Third, species concentrations are posterior obtained by solving the set of linear equations defining reaction-extents. Fourth, equilibrium rates are posterior calculated with transport equations for equilibrium-variables. Several example problems will be used to demonstrate the efficiency of this approach. Keywords: Reactive Transport, Reaction-Extent, Component, Kinetic-Variable, Equilibrium

  14. Periodic solutions for a 1D-model with nonlocal velocity via mass transport

    NASA Astrophysics Data System (ADS)

    Ferreira, Lucas C. F.; Valencia-Guevara, Julio C.

    2016-05-01

    This paper concerns periodic solutions for a 1D-model with nonlocal velocity given by the periodic Hilbert transform. There is a rich literature showing, via numerics and rigorous analysis, that this model presents singular behavior of solutions. For instance, they can blow up by forming mass-concentration. We develop a global well-posedness theory for periodic measure initial data that allows, in particular, to analyze how the model evolves from those singularities. Our results are based on periodic mass transport theory and the abstract gradient flow theory in metric spaces developed by Ambrosio et al. (2005). A viscous version of the model is also analyzed and inviscid limit properties are obtained.

  15. Equilibrium, kinetic, and reactive transport models for plutonium

    NASA Astrophysics Data System (ADS)

    Schwantes, Jon Michael

    Equilibrium, kinetic, and reactive transport models for plutonium (Pu) have been developed to help meet environmental concerns posed by past war-related and present and future peacetime nuclear technologies. A thorough review of the literature identified several hurdles that needed to be overcome in order to develop capable predictive tools for Pu. These hurdles include: (1) missing or ill-defined chemical equilibrium and kinetic constants for environmentally important Pu species; (2) no adequate conceptual model describing the formation of Pu oxy/hydroxide colloids and solids; and (3) an inability of two-phase reactive transport models to adequately simulate Pu behavior in the presence of colloids. A computer program called INVRS K was developed that integrates the geochemical modeling software of PHREEQC with a nonlinear regression routine. This program provides a tool for estimating equilibrium and kinetic constants from experimental data. INVRS K was used to regress on binding constants for Pu sorbing onto various mineral and humic surfaces. These constants enhance the thermodynamic database for Pu and improve the capability of current predictive tools. Time and temperature studies of the Pu intrinsic colloid were also conducted and results of these studies were presented here. Formation constants for the fresh and aged Pu intrinsic colloid were regressed upon using INVRS K. From these results, it was possible to develop a cohesive diagenetic model that describes the formation of Pu oxy/hydroxide colloids and solids. This model provides for the first time a means of deciphering historically unexplained observations with respect to the Pu intrinsic colloid, as well as a basis for simulating the behavior within systems containing these solids. Discussion of the development and application of reactive transport models is also presented and includes: (1) the general application of a 1-D in flow, three-phase (i.e., dissolved, solid, and colloidal), reactive

  16. Modeling multispecies reactive transport in ground water

    SciTech Connect

    Clement, T.P.; Sun, Y.; Hooker, B.S.; Petersen, J.N.

    1998-12-31

    In this paper, the details of RT3D, a general purpose, multispecies, reactive transport code, are presented. The code uses MODFLOW to simulate flow and several MT3D sub-programs to simulate advection and dispersion. A set of reaction modules were developed and incorporated into RT3D to simulate various types of multispecies reactive transport. This new computer model can be used for analyzing different types of subsurface contaminant reactions, microbial metabolisms, and microbial transport kinetics. Details of the model and numerical solution procedure are presented. The numerical formulation of the code is general enough to allow description of any type of reaction with any number of mobile/immobile species. Several example problems are presented to test the performance of the code, and to illustrate its features. The presented numerical model is shown to be a useful tool for analyzing different types of subsurface bioremediation systems. Prediction based on this model can be used for screening remediation alternatives including natural attenuation and/or for forecasting contaminant exposure levels and environmental risks at sensitive, downgradient receptors.

  17. Reactive solute transport in acidic streams

    USGS Publications Warehouse

    Broshears, R.E.

    1996-01-01

    Spatial and temporal profiles of Ph and concentrations of toxic metals in streams affected by acid mine drainage are the result of the interplay of physical and biogeochemical processes. This paper describes a reactive solute transport model that provides a physically and thermodynamically quantitative interpretation of these profiles. The model combines a transport module that includes advection-dispersion and transient storage with a geochemical speciation module based on MINTEQA2. Input to the model includes stream hydrologic properties derived from tracer-dilution experiments, headwater and lateral inflow concentrations analyzed in field samples, and a thermodynamic database. Simulations reproduced the general features of steady-state patterns of observed pH and concentrations of aluminum and sulfate in St. Kevin Gulch, an acid mine drainage stream near Leadville, Colorado. These patterns were altered temporarily by injection of sodium carbonate into the stream. A transient simulation reproduced the observed effects of the base injection.

  18. Global analytical ab initio ground-state potential energy surface for the C((1)D)+H2 reactive system.

    PubMed

    Zhang, Chunfang; Fu, Mingkai; Shen, Zhitao; Ma, Haitao; Bian, Wensheng

    2014-06-21

    A new global ab initio potential energy surface (called ZMB-a) for the 1(1)A' state of the C((1)D)+H2 reactive system has been constructed. This is based upon ab initio calculations using the internally contracted multireference configuration interaction approach with the aug-cc-pVQZ basis set, performed at about 6300 symmetry unique geometries. Accurate analytical fits are generated using many-body expansions with the permutationally invariant polynomials, except that the fit of the deep well region is taken from our previous fit. The ZMB-a surface is unique in the accurate description of the regions around conical intersections (CIs) and of van der Waals (vdW) interactions. The CIs between the 1(1)A' and 2(1)A' states cause two kinds of barriers on the ZMB-a surface: one is in the linear H-CH dissociation direction with a barrier height of 9.07 kcal/mol, which is much higher than those on the surfaces reported before; the other is in the C((1)D) collinearly attacking H2 direction with a barrier height of 12.39 kcal/mol. The ZMB-a surface basically reproduces our ab initio calculations in the vdW interaction regions, and supports a linear C-HH vdW complex in the entrance channel, and two vdW complexes in the exit channel, at linear CH-H and HC-H geometries, respectively. PMID:24952535

  19. A Uranium Bioremediation Reactive Transport Benchmark

    SciTech Connect

    Yabusaki, Steven B.; Sengor, Sevinc; Fang, Yilin

    2015-06-01

    A reactive transport benchmark problem set has been developed based on in situ uranium bio-immobilization experiments that have been performed at a former uranium mill tailings site in Rifle, Colorado, USA. Acetate-amended groundwater stimulates indigenous microorganisms to catalyze the reduction of U(VI) to a sparingly soluble U(IV) mineral. The interplay between the flow, acetate loading periods and rates, microbially-mediated and geochemical reactions leads to dynamic behavior in metal- and sulfate-reducing bacteria, pH, alkalinity, and reactive mineral surfaces. The benchmark is based on an 8.5 m long one-dimensional model domain with constant saturated flow and uniform porosity. The 159-day simulation introduces acetate and bromide through the upgradient boundary in 14-day and 85-day pulses separated by a 10 day interruption. Acetate loading is tripled during the second pulse, which is followed by a 50 day recovery period. Terminal electron accepting processes for goethite, phyllosilicate Fe(III), U(VI), and sulfate are modeled using Monod-type rate laws. Major ion geochemistry modeled includes mineral reactions, as well as aqueous and surface complexation reactions for UO2++, Fe++, and H+. In addition to the dynamics imparted by the transport of the acetate pulses, U(VI) behavior involves the interplay between bioreduction, which is dependent on acetate availability, and speciation-controlled surface complexation, which is dependent on pH, alkalinity and available surface complexation sites. The general difficulty of this benchmark is the large number of reactions (74), multiple rate law formulations, a multisite uranium surface complexation model, and the strong interdependency and sensitivity of the reaction processes. Results are presented for three simulators: HYDROGEOCHEM, PHT3D, and PHREEQC.

  20. Box model and 1D longitudinal model of flow and transport in Bosten Lake, China

    NASA Astrophysics Data System (ADS)

    Li, Ning; Kinzelbach, Wolfgang; Li, WenPeng; Dong, XinGuang

    2015-05-01

    Bosten Lake in the southeast of Yanqi Catchment, China, supports the downstream agricultural and natural environments. Over the last few decades the intensive agricultural activities in Yanqi Catchment resulted in decreased lake levels and deteriorated lake water quality. A two-box model is constructed to understand the evolution of lake level and salinity between 1958 and 2008. The two-box model of the lake indicates that the evaporation does have the same trend as the observed lake area and the annual average evaporation agrees with the value obtained from the Penman-Monteith approach. To achieve a correct salt balance, the ratio of outflow concentration and average lake concentration has to be around 0.7. This is due to the incomplete mixing of the lake caused by short-circuiting between tributary inflow and the main outflow via the pump stations abstracting water from the lake. This short-circuiting is investigated in more detail by a 1D numerical flow and transport model of the lake calibrated with observations of lake level and lake concentrations. The distributed model reproduces the correct time-varying outflow concentration. It is used for the assessment of two basic management options: increasing river discharge (by water saving irrigation, reduction of phreatic evaporation or reduction of agricultural area) and diverting saline drainage water to the desert. Increasing river discharge to the lake by 20% reduces the east basin salt concentration by 0.55 kg/m3, while capturing all the drainage water and discharging it to depressions instead of the lake reduces the east basin salt concentration by 0.63 kg/m3. A combination of increasing river inflow and decreasing drainage salt flux is sufficient to bring future lake TDS below the required 1 kg/m3, to keep a lake level that sustains the lake ecosystem, and to supply more water for downstream development and ecosystem rehabilitation.

  1. Reactive transport benchmarks for subsurface environmental simulation

    SciTech Connect

    Steefel, Carl I.; Yabusaki, Steven B.; Mayer, K. U.

    2015-06-01

    Over the last 20 years, we have seen firsthand the evolution of multicomponent reactive transport modeling and the expanding range and increasing complexity of subsurface applications it is being used to address. There is a growing reliance on reactive transport modeling (RTM) to address some of the most compelling issues facing our planet: climate change, nuclear waste management, contaminant remediation, and pollution prevention. While these issues are motivating the development of new and improved capabilities for subsurface environmental modeling using RTM (e.g., biogeochemistry from cell-scale physiology to continental-scale terrestrial ecosystems, nonisothermal multiphase conditions, coupled geomechanics), there remain longstanding challenges in characterizing the natural variability of hydrological, biological, and geochemical properties in subsurface environments and limited success in transferring models between sites and across scales. An equally important trend over the last 20 years is the evolution of modeling from a service sought out after data has been collected to a multifaceted research approach that provides (1) an organizing principle for characterization and monitoring activities; (2) a systematic framework for identifying knowledge gaps, developing and integrating new knowledge; and (3) a mechanistic understanding that represents the collective wisdom of the participating scientists and engineers. There are now large multidisciplinary projects where the research approach is model-driven, and the principal product is a holistic predictive simulation capability that can be used as a test bed for alternative conceptualizations of processes, properties, and conditions. Much of the future growth and expanded role for RTM will depend on its continued ability to exploit technological advancements in the earth and environmental sciences. Advances in measurement technology, particularly in molecular biology (genomics), isotope fractionation, and high

  2. Quantum and semi-classical transport in RTDs using NEMO 1-D

    NASA Technical Reports Server (NTRS)

    Klimeck, G.; Stout, P.; Bowen, R. C.

    2003-01-01

    NEMO 1-D has been developed primarily for the simulation of resonant tunneling diodes, and quantitative and predictive agreements with experimental high performance, high current density devices have been achieved in the past.

  3. GIS-based channel flow and sediment transport simulation using CCHE1D coupled with AnnAGNPS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    CCHE1D (Center for Computational Hydroscience and Engineering 1-Dimensional model) simulates unsteady free-surface flows with nonequilibrium, nonuniform sediment transport in dendritic channel networks. Since early 1990’s, the model and its software packages have been developed and continuously main...

  4. Benchmarking a Visual-Basic based multi-component one-dimensional reactive transport modeling tool

    NASA Astrophysics Data System (ADS)

    Torlapati, Jagadish; Prabhakar Clement, T.

    2013-01-01

    We present the details of a comprehensive numerical modeling tool, RT1D, which can be used for simulating biochemical and geochemical reactive transport problems. The code can be run within the standard Microsoft EXCEL Visual Basic platform, and it does not require any additional software tools. The code can be easily adapted by others for simulating different types of laboratory-scale reactive transport experiments. We illustrate the capabilities of the tool by solving five benchmark problems with varying levels of reaction complexity. These literature-derived benchmarks are used to highlight the versatility of the code for solving a variety of practical reactive transport problems. The benchmarks are described in detail to provide a comprehensive database, which can be used by model developers to test other numerical codes. The VBA code presented in the study is a practical tool that can be used by laboratory researchers for analyzing both batch and column datasets within an EXCEL platform.

  5. Geothermal Fluid Interaction with Mafic Rocks in Porous Media - AN Experimental and Reactive Transport Modeling Study

    NASA Astrophysics Data System (ADS)

    Stefansson, A.

    2013-12-01

    Reaction and reactive transport modeling is becoming an increasingly popular method to study fluid-rock interaction and fluid transport on small to large scales. In this study, fluid-rock experiments were carried out and the observations compared with the results of reaction and reactive transport models. The systems studied included fluid-rock interaction of olivine on one hand and basaltic glass on the other hand with dilute aqueous solutions containing CO2 at acid to neutral pH and temperatures from ambient to 250 °C. The experiments were conducted using batch type experiments in closed reactors and 1-D plug experiments in flow-through reactors and the solution chemistry, the reaction progress, secondary mineralization and porosity changes analyzed as a function of time. The reaction and 1-D reactive transport simulations were conducted with the aid of the PHREEQC program. For the simulations the thermodynamic database for mineral reactions was largely updated and the kinetics of mineral dissolution as well as mineral nucleation and crystal growth was incorporated. According to the experimental results and the reactive transport simulations, olivine and basaltic glass progressively dissolves forming secondary minerals and solutes that are partially transported out of them column (system). The exact reaction path was found to depend on solution composition and pH and reaction progress (time). The mass movement of the system at a particular steady state as well as porosity changes may be divided into three stages. Stage I is characterized by initial olivine or basaltic glass leaching, stage II is characterized by progressive mineral formation and decrease in porosity and stage III is characterized by remobilization of the previously formed secondary minerals and eventual increase in porosity. The reaction and reactive transport modeling was found to simulate reasonable the reaction path as a function of reaction time. However, exact mass movement and time

  6. EFDC1D - A ONE DIMENSIONAL HYDRODYNAMIC AND SEDIMENT TRANSPORT MODEL FOR RIVER AND STREAM NETWORKS: MODEL THEORY AND USERS GUIDE

    EPA Science Inventory

    This technical report describes the new one-dimensional (1D) hydrodynamic and sediment transport model EFDC1D. This model that can be applied to stream networks. The model code and two sample data sets are included on the distribution CD. EFDC1D can simulate bi-directional unstea...

  7. Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

    NASA Astrophysics Data System (ADS)

    Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

    2014-12-01

    Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

  8. Complementing Graphenes: 1D Interplanar Charge Transport in Polymeric Graphitic Carbon Nitrides.

    PubMed

    Merschjann, Christoph; Tschierlei, Stefanie; Tyborski, Tobias; Kailasam, Kamalakannan; Orthmann, Steven; Hollmann, Dirk; Schedel-Niedrig, Thomas; Thomas, Arne; Lochbrunner, Stefan

    2015-12-22

    Charge transport in polymeric graphitic carbon nitrides is shown to proceed via diffusive hopping of electron and hole polarons with reasonably high mobilities >10(-5) cm(2) V(-1) s(-1). The power-law behavior of the ultrafast luminescence decay exhibits that the predominant transport direction is perpendicular to the graphitic polymer sheets, thus complementing 2D materials like graphene. PMID:26543003

  9. Detection and characterization of uranium-humic complexes during 1D transport studies

    SciTech Connect

    Lesher, Emily K.; Honeyman, Bruce D.; Ranville, James F.

    2013-05-01

    The speciation and transport of uranium (VI) through porous media is highly dependent on solution conditions, the presence of complexing ligands, and the nature of the porous media. The dependency on many variables makes prediction of U transport in bench-scale experiments and in the field difficult. In particular, the identification of colloidal U phases poses a technical challenge. Transport of U in the presence and absence of natural organic matter (Suwannee River humic acid, SRHA) through silica sand and hematite coated silica sand was tested at pH 4 and 5 using static columns, where flow is controlled by gravity and residence time between advective pore volume exchanges can be strictly controlled. The column effluents were characterized by traditional techniques including ICPMS quantification of total [U] and [Fe], TOC analysis of [DOC], and pH analysis, and also by non-traditional techniques: flow field flow fractionation with online ICPMS detection (FlFFF-ICPMS) and specific UV absorbance (SUVA) characterization of effluent fractions. Key results include that the transport of U through the columns was enhanced by pre-equilibration with SRHA, and previously deposited U was remobilized by the addition of SRHA. The advanced techniques yielded important insights on the mechanisms of transport: FlFFF-ICPMS identified a U-SRHA complex as the mobile U species and directly quantified relative amounts of the complex, while specific UV absorbance (SUVA) measurements indicated a composition-based fractionation onto the porous media.

  10. Linear transport of domain walls confined to propagating 1-D potential wells

    NASA Astrophysics Data System (ADS)

    Negotia, M.; Hodges, M. P. P.; Bryan, M. T.; Fry, P. W.; Im, M.-Y.; Fischer, P.; Allwood, D. A.; Hayward, T. J.

    2013-10-01

    We present a method of controllably propagating domain walls (DWs) in magnetic nanowires over extended linear distances by confining them to geometrically defined energy minima. Using simple models, magnetic transmission soft x-ray microscopy and magneto-optic Kerr effect measurements, we show that the technique allows DWs to be moved at arbitrary, user-defined velocities and be positioned with micrometer precision. Our approach is expected to be of utility in applications where the precise transport and positioning of DWs take precedent over the absolute speed of propagation, for example, where the fields produced by DWs are used to trap and transport magnetized particles.

  11. 1D momentum-conserving systems: the conundrum of anomalous versus normal heat transport

    NASA Astrophysics Data System (ADS)

    Li, Yunyun; Liu, Sha; Li, Nianbei; Hänggi, Peter; Li, Baowen

    2015-04-01

    Transport and the spread of heat in Hamiltonian one dimensional momentum conserving nonlinear systems is commonly thought to proceed anomalously. Notable exceptions, however, do exist of which the coupled rotator model is a prominent case. Therefore, the quest arises to identify the origin of manifest anomalous energy and momentum transport in those low dimensional systems. We develop the theory for both, the statistical densities for momentum- and energy-spread and particularly its momentum-/heat-diffusion behavior, as well as its corresponding momentum/heat transport features. We demonstrate that the second temporal derivative of the mean squared deviation of the momentum spread is proportional to the equilibrium correlation of the total momentum flux. Subtracting the part which corresponds to a ballistic momentum spread relates (via this integrated, subleading momentum flux correlation) to an effective viscosity, or equivalently, to the underlying momentum diffusivity. We next put forward the intriguing hypothesis: normal spread of this so adjusted excess momentum density causes normal energy spread and alike normal heat transport (Fourier Law). Its corollary being that an anomalous, superdiffusive broadening of this adjusted excess momentum density in turn implies an anomalous energy spread and correspondingly anomalous, superdiffusive heat transport. This hypothesis is successfully corroborated within extensive molecular dynamics simulations over large extended time scales. Our numerical validation of the hypothesis involves four distinct archetype classes of nonlinear pair-interaction potentials: (i) a globally bounded pair interaction (the noted coupled rotator model), (ii) unbounded interactions acting at large distances (the coupled rotator model amended with harmonic pair interactions), (iii) the case of a hard point gas with unbounded square-well interactions and (iv) a pair interaction potential being unbounded at short distances while displaying an

  12. Transport of an interacting Bose gas in 1D disordered lattices

    SciTech Connect

    D'Errico, C.; Chaudhuri, S.; Gori, L.; Kumar, A.; Lucioni, E.; Tanzi, L.; Inguscio, M.; Modugno, G.

    2014-08-20

    We use ultracold atoms in a quasiperiodic lattice to study two outstanding problems in the physics of disordered systems: a) the anomalous diffusion of a wavepacket in the presence of disorder, interactions and noise; b) the transport of a disordered superfluid. a) Our results show that the subdiffusion, observed when interaction alone is present, can be modelled with a nonlinear diffusion equation and the peculiar shape of the expanding density profiles can be connected to the microscopic nonlinear diffusion coefficients. Also when noise alone is present we can describe the observed normal diffusion dynamics by existing microscopic models. In the unexplored regime in which noise and interaction are combined, instead, we observe an anomalous diffusion, that we model with a generalized diffusion equation, where noise- and interaction-induced contributions add each other. b) We find that an instability appearing at relatively large momenta can be employed to locate the fluid-insulator crossover driven by disorder. By investigating the momentum-dependent transport, we observe a sharp crossover from a weakly dissipative regime to a strongly unstable one at a disorder-dependent critical momentum. The set of critical disorder and interaction strengths for which such critical momentum vanishes, can be identified with the separation between a fluid regime and an insulating one and can be related to the predicted zero-temperature superfluid-Bose glass transition.

  13. Lessons learned from reactive transport modeling of a low-activity waste glass disposal system

    NASA Astrophysics Data System (ADS)

    Bacon, Diana H.; Peter McGrail, B.

    2003-04-01

    A set of reactive chemical transport calculations were conducted with the Subsurface Transport Over Reactive Multi-phases (STORM) code to evaluate the long-term performance of a representative low-activity waste glass in a shallow subsurface disposal system located on the Hanford site. Two different trench designs were considered, one with four rows of small waste packages (old design), the other with three layers of larger waste packages (new design). One-dimensional (1D) simulations were carried out to 20,000 yr, whereas two-dimensional (2D) simulations could only be carried out for 10,000 yr due to constraints on computational time. Both the 1D and 2D simulations predicted that the technetium release rate from the waste packages would be lower for the new trench design at times greater than 1 yr. Having fewer, larger waste packages decreases the glass surface area exposed to reaction with pore water. In the 2D simulations, water can flow around the waste packages, which causes a decrease in the water flux through the waste packages and lower release rates than predicted in the 1D simulations. This result reinforces the importance of performing multi-dimensional waste form release simulations.

  14. Sensitivity Analysis and Parameter Estimation for a Reactive Transport Model of Uranium Bioremediation

    NASA Astrophysics Data System (ADS)

    Meyer, P. D.; Yabusaki, S.; Curtis, G. P.; Ye, M.; Fang, Y.

    2011-12-01

    A three-dimensional, variably-saturated flow and multicomponent biogeochemical reactive transport model of uranium bioremediation was used to generate synthetic data . The 3-D model was based on a field experiment at the U.S. Dept. of Energy Rifle Integrated Field Research Challenge site that used acetate biostimulation of indigenous metal reducing bacteria to catalyze the conversion of aqueous uranium in the +6 oxidation state to immobile solid-associated uranium in the +4 oxidation state. A key assumption in past modeling studies at this site was that a comprehensive reaction network could be developed largely through one-dimensional modeling. Sensitivity analyses and parameter estimation were completed for a 1-D reactive transport model abstracted from the 3-D model to test this assumption, to identify parameters with the greatest potential to contribute to model predictive uncertainty, and to evaluate model structure and data limitations. Results showed that sensitivities of key biogeochemical concentrations varied in space and time, that model nonlinearities and/or parameter interactions have a significant impact on calculated sensitivities, and that the complexity of the model's representation of processes affecting Fe(II) in the system may make it difficult to correctly attribute observed Fe(II) behavior to modeled processes. Non-uniformity of the 3-D simulated groundwater flux and averaging of the 3-D synthetic data for use as calibration targets in the 1-D modeling resulted in systematic errors in the 1-D model parameter estimates and outputs. This occurred despite using the same reaction network for 1-D modeling as used in the data-generating 3-D model. Predictive uncertainty of the 1-D model appeared to be significantly underestimated by linear parameter uncertainty estimates.

  15. Multiple species reactive chemical transport in groundwater: A verification exercise

    SciTech Connect

    Narasimhan, T.N.; Apps, J.A.; Zhu, Ming.

    1991-04-01

    Two multiple-species reactive chemical transport models (FASTCHEM and DYNAMIX) were tested against each other to check for consistency of solutions. For the particular problem studied, FASTCHEM and DYNAMIX led to differences in aqueous concentrations and mineral assemblages primarily because FASTCHEM ignores redox reactions in the transport phase of the calculations. Also, the spatial concentration profiles generated by FASTCHEM tend to be sharper than those generated by DYNAMIX because FASTCHEM is particularly designed to handle advection-dominated transport systems.

  16. Development of a 3D to 1D Particle Transport Model to Predict Deposition in the Lungs

    NASA Astrophysics Data System (ADS)

    Oakes, Jessica M.; Grandmont, Celine; Shadden, Shawn C.; Vignon-Clementel, Irene E.

    2014-11-01

    Aerosolized particles are commonly used for therapeutic drug delivery as they can be delivered to the body systemically or be used to treat lung diseases. Recent advances in computational resources have allowed for sophisticated pulmonary simulations, however it is currently impossible to solve for airflow and particle transport for all length and time scales of the lung. Instead, multi-scale methods must be used. In our recent work, where computational methods were employed to solve for airflow and particle transport in the rat airways (Oakes et al. (2014), Annals of Biomedical Engineering 42, 899), the number of particles to exit downstream of the 3D domain was determined. In this current work, the time-dependent Lagrangian description of particles was used to numerically solve a 1D convection-diffusion model (trumpet model, Taulbee and Yu (1975), Journal of Applied Physiology, 38, 77) parameterized specifically for the lung. The expansion of the airway dimensions was determined based on data collected from our aerosol exposure experiments (Oakes et al. (2014), Journal of Applied Physiology, 116, 1561). This 3D-1D framework enables us to predict the fate of particles in the whole lung. This work was supported by the Whitaker Foundation at the IIE, a INRIA Associated Team Postdoc Grant, and a UC Presidential Fellowship.

  17. Analytic structure of two 1D-transport equations with nonlocal fluxes

    NASA Astrophysics Data System (ADS)

    Baker, Gregory R.; Li, Xiao; Morlet, Anne C.

    We replace the flux term in Burger's equation by two simple alternates that contain contributions depending globally on the solution. In one case, the term is in the form of a hyperbolic equation where the characteristic speed is nonlocal, and in the other the term is in conservation form. In both cases, the nonanalytic is due to the presence of the Hilbert transform. The equations have a loose analogy to the motion of vortex sheets. In particular, they both form singularities in finite time in the absence of viscous effects. Our motivation then is to study the influence of viscosity. In one case, viscosity does not prevent singularity formation. In the other, we can prove solutions exist for all time, and determine the likely weak solution as viscosity vanishes. An interesting aspect of our work is that singularity formation can be viewed as the motion of singularities in the complex physical plane that reach the real axis in finite time. In one case, the singularity is a pole and causes the solution to blow up when it reaches the real axis. In the other, numerical solutions and an asymptotic analysis suggest that the weak solution contains a square root singularity that reaches the real axis in finite time, and then propagates along it. We hope our results will spur further interest in the role of singularities in the complex spatial plane in solutions to transport equations.

  18. Upscaling of reaction rates in reactive transport using pore-scale reactive transport model

    NASA Astrophysics Data System (ADS)

    Yoon, H.; Dewers, T. A.; Arnold, B. W.; Major, J. R.; Eichhubl, P.; Srinivasan, S.

    2013-12-01

    Dissolved CO2 during geological CO2 storage may react with minerals in fractured rocks, confined aquifers, or faults, resulting in mineral precipitation and dissolution. The overall rate of reaction can be affected by coupled processes among hydrodynamics, transport, and reactions at the (sub) pore-scale. In this research pore-scale modeling of coupled fluid flow, reactive transport, and heterogeneous reaction at the mineral surface is applied to account for permeability alterations caused by precipitation-induced pore-blocking. This work is motivated by the observed CO2 seeps from a natural analog to geologic CO2 sequestration at Crystal Geyser, Utah. A key observation is the lateral migration of CO2 seep sites at a scale of ~ 100 meters over time. A pore-scale model provides fundamental mechanistic explanations of how calcite precipitation alters flow paths by pore plugging under different geochemical compositions and pore configurations. In addition, response function of reaction rates will be constructed from pore-scale simulations which account for a range of reaction regimes characterized by the Damkohler and Peclet numbers. Newly developed response functions will be used in a continuum scale model that may account for large-scale phenomena mimicking lateral migration of surface CO2 seeps. Comparison of field observations and simulations results will provide mechanistic explanations of the lateral migration and enhance our understanding of subsurface processes associated with the CO2 injection. This work is supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security

  19. Modeling variably saturated multispecies reactive groundwater solute transport with MODFLOW-UZF and RT3D

    USGS Publications Warehouse

    Bailey, Ryan T.; Morway, Eric D.; Niswonger, Richard G.; Gates, Timothy K.

    2013-01-01

    A numerical model was developed that is capable of simulating multispecies reactive solute transport in variably saturated porous media. This model consists of a modified version of the reactive transport model RT3D (Reactive Transport in 3 Dimensions) that is linked to the Unsaturated-Zone Flow (UZF1) package and MODFLOW. Referred to as UZF-RT3D, the model is tested against published analytical benchmarks as well as other published contaminant transport models, including HYDRUS-1D, VS2DT, and SUTRA, and the coupled flow and transport modeling system of CATHY and TRAN3D. Comparisons in one-dimensional, two-dimensional, and three-dimensional variably saturated systems are explored. While several test cases are included to verify the correct implementation of variably saturated transport in UZF-RT3D, other cases are included to demonstrate the usefulness of the code in terms of model run-time and handling the reaction kinetics of multiple interacting species in variably saturated subsurface systems. As UZF1 relies on a kinematic-wave approximation for unsaturated flow that neglects the diffusive terms in Richards equation, UZF-RT3D can be used for large-scale aquifer systems for which the UZF1 formulation is reasonable, that is, capillary-pressure gradients can be neglected and soil parameters can be treated as homogeneous. Decreased model run-time and the ability to include site-specific chemical species and chemical reactions make UZF-RT3D an attractive model for efficient simulation of multispecies reactive transport in variably saturated large-scale subsurface systems.

  20. Modeling variably saturated multispecies reactive groundwater solute transport with MODFLOW-UZF and RT3D.

    PubMed

    Bailey, Ryan T; Morway, Eric D; Niswonger, Richard G; Gates, Timothy K

    2013-01-01

    A numerical model was developed that is capable of simulating multispecies reactive solute transport in variably saturated porous media. This model consists of a modified version of the reactive transport model RT3D (Reactive Transport in 3 Dimensions) that is linked to the Unsaturated-Zone Flow (UZF1) package and MODFLOW. Referred to as UZF-RT3D, the model is tested against published analytical benchmarks as well as other published contaminant transport models, including HYDRUS-1D, VS2DT, and SUTRA, and the coupled flow and transport modeling system of CATHY and TRAN3D. Comparisons in one-dimensional, two-dimensional, and three-dimensional variably saturated systems are explored. While several test cases are included to verify the correct implementation of variably saturated transport in UZF-RT3D, other cases are included to demonstrate the usefulness of the code in terms of model run-time and handling the reaction kinetics of multiple interacting species in variably saturated subsurface systems. As UZF1 relies on a kinematic-wave approximation for unsaturated flow that neglects the diffusive terms in Richards equation, UZF-RT3D can be used for large-scale aquifer systems for which the UZF1 formulation is reasonable, that is, capillary-pressure gradients can be neglected and soil parameters can be treated as homogeneous. Decreased model run-time and the ability to include site-specific chemical species and chemical reactions make UZF-RT3D an attractive model for efficient simulation of multispecies reactive transport in variably saturated large-scale subsurface systems. PMID:23131109

  1. Transport equations for partially ionized reactive plasma in magnetic field

    NASA Astrophysics Data System (ADS)

    Zhdanov, V. M.; Stepanenko, A. A.

    2016-06-01

    Transport equations for partially ionized reactive plasma in magnetic field taking into account the internal degrees of freedom and electronic excitation of plasma particles are derived. As a starting point of analysis the kinetic equation with a binary collision operator written in the Wang-Chang and Uhlenbeck form and with a reactive collision integral allowing for arbitrary chemical reactions is used. The linearized variant of Grad's moment method is applied to deduce the systems of moment equations for plasma and also full and reduced transport equations for plasma species nonequilibrium parameters.

  2. Vectorization of a 2D-1D Iterative Algorithm for the 3D Neutron Transport Problem in Prismatic Geometries

    NASA Astrophysics Data System (ADS)

    Moustafa, Salli; Févotte, François; Lathuilière, Bruno; Plagne, Laurent

    2014-06-01

    The past few years have been marked by a noticeable increase in the interest in 3D whole-core heterogeneous deterministic neutron transport solvers for reference calculations. Due to the extremely large problem sizes tackled by such solvers, they need to use adapted numerical methods and need to be efficiently implemented to take advantage of the full computing power of modern systems. As for numerical methods, one possible approach consists in iterating over resolutions of 2D and 1D MOC problems by taking advantage of prismatic geometries. The MICADO solver, developed at EDF R&D, is a parallel implementation of such a method in distributed and shared memory systems. However it is currently unable to use SIMD vectorization to leverage the full computing power of modern CPUs. In this paper, we describe our first effort to support vectorization in MICADO, typically targeting Intel© SSE CPUs. Both the 2D and 1D algorithms are vectorized, allowing for high expected speedups for the whole spatial solver. We present benchmark computations, which show nearly optimal speedups for our vectorized implementation on the TAKEDA case.

  3. Interpretation of MSL REMS data using 1D coupled heat and water vapor transport model of Mars subsurface

    NASA Astrophysics Data System (ADS)

    Gloesener, Elodie; Karatekin, Özgür; Dehant, Véronique

    2016-04-01

    MSL Rover Environmental Monitoring Station (REMS) performed high-resolution measurements of temperature and relative humidity during more than one Martian year. In this work, a 1D subsurface model is used to study water vapor exchange between the atmosphere and the subsurface at Gale crater using REMS data. The thermal model used includes several layers of varying thickness with depth and properties that can be changed to correspond to those of Martian rocks at locations studied. It also includes the transport of water vapor through porous Martian regolith and the different phases considered are vapor, ice and adsorbed H2O. The total mass flux is given by the sum of diffusive and advective transport. The role of an adsorbing regolith on water transfer as well as the range of parameters with significant effect on water transport in Martian conditions are investigated. In addition, kinetics of the adsorption process is considered to examine its influence on the water vapor exchange between the subsurface and the atmosphere.

  4. A 1-D Size Specific Numerical Model for Gravel Transport That Includes Sediment Exchange with a Floodplain

    NASA Astrophysics Data System (ADS)

    Lauer, Wesley; Viparelli, Enrica; Piegay, Herve

    2014-05-01

    Sedimentary deposits adjacent to rivers can represent important sources and sinks for bed material sediment, particularly on decadal and longer timescales. The Morphodynamics and Sediment Tracers in 1-D model (MAST-1D) is a size-specific sediment transport model that allows for active exchange between channel and floodplain sediment on river reaches of tens to hundreds of kilometers in length. The model is intended to provide a mechanism for performing a first-order assessment of the likely importance of off-channel sediment exchange in controlling decadal-scale geomorphic trends, thereby helping plan and/or prioritize field data collection and higher resolution modeling work. The model develops a sediment budget for short segments of an alluvial valley. Each segment encompasses several active river bends. In each segment, a sediment transport capacity computation is performed to determine the downstream flux of bed material sediment, following the approach of most other 1-D sediment transport models. However, the model differs from most other bed evolution models in that sediment can be exchanged with the floodplain in each segment, and mass conservation is applied to both the active layer and floodplain sediment storage reservoirs. The potential for net imbalances in overall exchange as well as the size specific nature of the computations allows the model to simulate reach-scale aggradation/degradation and/or changes in bed texture. The inclusion of fine sediment in the model allows it to track geochemical tracer material and also provides a mechanism to simulate, to first order, the effects of changes in the supply of silt and clay on overall channel hydraulic capacity. The model is applied to a ~40 km reach of the Ain River, a tributary of the Rhône River in eastern France that has experienced a significant sediment deficit as a result of the construction of several dams between 1920 and 1970. MAST-1D simulations result in both incision and the formation of a

  5. Assessment of phenol infiltration resilience in soil media by HYDRUS-1D transport model for a waste discharge site.

    PubMed

    Adhikari, K; Pal, S; Chakraborty, B; Mukherjee, S N; Gangopadhyay, A

    2014-10-01

    The movement of contaminants through soil imparts a variety of geo-environmental problem inclusive of lithospheric pollution. Near-surface aquifers are often vulnerable to contamination from surface source if overlying soil possesses poor resilience or contaminant attenuation capacity. The prediction of contaminant transport through soil is urged to protect groundwater from sources of pollutants. Using field simulation through column experiments and mathematical modeling like HYDRUS-1D, assessment of soil resilience and movement of contaminants through the subsurface to reach aquifers can be predicted. An outfall site of effluents of a coke oven plant comprising of alarming concentration of phenol (4-12.2 mg/L) have been considered for studying groundwater condition and quality, in situ soil characterization, and effluent characterization. Hydrogeological feature suggests the presence of near-surface aquifers at the effluent discharge site. Analysis of groundwater of nearby locality reveals the phenol concentration (0.11-0.75 mg/L) exceeded the prescribed limit of WHO specification (0.002 mg/L). The in situ soil, used in column experiment, possess higher saturated hydraulic conductivity (KS  = 5.25 × 10(-4) cm/s). The soil containing 47 % silt, 11 % clay, and 1.54% organic carbon content was found to be a poor absorber of phenol (24 mg/kg). The linear phenol adsorption isotherm model showed the best fit (R(2) = 0.977, RMSE = 1.057) to the test results. Column experiments revealed that the phenol removal percent and the length of the mass transfer zone increased with increasing bed heights. The overall phenol adsorption efficiency was found to be 42-49%. Breakthrough curves (BTCs) predicted by HYDRUS-1D model appears to be close fitting with the BTCs derived from the column experiments. The phenol BTC predicted by the HYDRUS-1D model for 1.2 m depth subsurface soil, i.e., up to the depth of groundwater in the study area, showed that the exhaustion

  6. Surrogate model approach for improving the performance of reactive transport simulations

    NASA Astrophysics Data System (ADS)

    Jatnieks, Janis; De Lucia, Marco; Sips, Mike; Dransch, Doris

    2016-04-01

    Reactive transport models can serve a large number of important geoscientific applications involving underground resources in industry and scientific research. It is common for simulation of reactive transport to consist of at least two coupled simulation models. First is a hydrodynamics simulator that is responsible for simulating the flow of groundwaters and transport of solutes. Hydrodynamics simulators are well established technology and can be very efficient. When hydrodynamics simulations are performed without coupled geochemistry, their spatial geometries can span millions of elements even when running on desktop workstations. Second is a geochemical simulation model that is coupled to the hydrodynamics simulator. Geochemical simulation models are much more computationally costly. This is a problem that makes reactive transport simulations spanning millions of spatial elements very difficult to achieve. To address this problem we propose to replace the coupled geochemical simulation model with a surrogate model. A surrogate is a statistical model created to include only the necessary subset of simulator complexity for a particular scenario. To demonstrate the viability of such an approach we tested it on a popular reactive transport benchmark problem that involves 1D Calcite transport. This is a published benchmark problem (Kolditz, 2012) for simulation models and for this reason we use it to test the surrogate model approach. To do this we tried a number of statistical models available through the caret and DiceEval packages for R, to be used as surrogate models. These were trained on randomly sampled subset of the input-output data from the geochemical simulation model used in the original reactive transport simulation. For validation we use the surrogate model to predict the simulator output using the part of sampled input data that was not used for training the statistical model. For this scenario we find that the multivariate adaptive regression splines

  7. High-resolution reactive transport: A coupled parallel hydrogeochemical model

    NASA Astrophysics Data System (ADS)

    Beisman, J. J.; Maxwell, R. M.; Steefel, C. I.; Sitchler, A.; Molins, S.

    2013-12-01

    Subsurface hydrogeochemical systems are an especially complex component of the terrestrial environment and play host to a multitude of interactions. Parameterizations of these interactions are perhaps the least understood component of terrestrial systems, presenting uncertainties in the predictive understanding of biogeochemical cycling and transport. Thorough knowledge of biogeochemical transport processes is critical to the quantification of carbon/nutrient fluxes in the subsurface, and to the development of effective contaminant remediation techniques. Here we present a coupled parallel hydrogeochemical model, ParCrunchFlow, as a tool to further our understanding of governing processes and interactions in natural hydrogeochemical systems. ParCrunchFlow is a coupling of the reactive transport simulator CrunchFlow with the hydrologic model ParFlow. CrunchFlow is a multicomponent reactive flow and transport code that can be used to simulate a range of important processes and environments, including reactive contaminant transport, chemical weathering, carbon sequestration, biogeochemical cycling, and water-rock interaction. ParFlow is a parallel, three-dimensional, variably-saturated, coupled surface-subsurface flow and transport code with the ability to simulate complex topography, geology, and heterogeneity. ParCrunchflow takes advantage of the efficient parallelism built into Parflow, allowing the numerical simulation of reactive transport processes in chemically and physically heterogeneous media at high spatial resolutions. This model provides an ability to further examine the interactions and feedbacks between biogeochemical systems and complex subsurface flow fields. In addition to the details of model construction, results will be presented that show floodplain nutrient cycling and the effects of heterogeneity on small-scale mixing reactions at the Department of Energy's Old Rifle Legacy site.

  8. Multi-phase reactive transport theory

    SciTech Connect

    Lichtner, P.C.

    1995-07-01

    Physicochemical processes in the near-field region of a high-level waste repository may involve a diverse set of phenomena including flow of liquid and gas, gaseous diffusion, and chemical reaction of the host rock with aqueous solutions at elevated temperatures. This report develops some of the formalism for describing simultaneous multicomponent solute and heat transport in a two-phase system for partially saturated porous media. Diffusion of gaseous species is described using the Dusty Gas Model which provides for simultaneous Knudsen and Fickian diffusion in addition to Darcy flow. A new form of the Dusty Gas Model equations is derived for binary diffusion which separates the total diffusive flux into segregative and nonsegregative components. Migration of a wetting front is analyzed using the quasi-stationary state approximation to the Richards` equation. Heat-pipe phenomena are investigated for both gravity- and capillary-driven reflux of liquid water. An expression for the burnout permeability is derived for a gravity-driven heat-pipe. Finally an estimate is given for the change in porosity and permeability due to mineral dissolution which could occur in the region of condensate formation in a heat-pipe.

  9. Assessment of parametric uncertainty for groundwater reactive transport modeling,

    USGS Publications Warehouse

    Shi, Xiaoqing; Ye, Ming; Curtis, Gary P.; Miller, Geoffery L.; Meyer, Philip D.; Kohler, Matthias; Yabusaki, Steve; Wu, Jichun

    2014-01-01

    The validity of using Gaussian assumptions for model residuals in uncertainty quantification of a groundwater reactive transport model was evaluated in this study. Least squares regression methods explicitly assume Gaussian residuals, and the assumption leads to Gaussian likelihood functions, model parameters, and model predictions. While the Bayesian methods do not explicitly require the Gaussian assumption, Gaussian residuals are widely used. This paper shows that the residuals of the reactive transport model are non-Gaussian, heteroscedastic, and correlated in time; characterizing them requires using a generalized likelihood function such as the formal generalized likelihood function developed by Schoups and Vrugt (2010). For the surface complexation model considered in this study for simulating uranium reactive transport in groundwater, parametric uncertainty is quantified using the least squares regression methods and Bayesian methods with both Gaussian and formal generalized likelihood functions. While the least squares methods and Bayesian methods with Gaussian likelihood function produce similar Gaussian parameter distributions, the parameter distributions of Bayesian uncertainty quantification using the formal generalized likelihood function are non-Gaussian. In addition, predictive performance of formal generalized likelihood function is superior to that of least squares regression and Bayesian methods with Gaussian likelihood function. The Bayesian uncertainty quantification is conducted using the differential evolution adaptive metropolis (DREAM(zs)) algorithm; as a Markov chain Monte Carlo (MCMC) method, it is a robust tool for quantifying uncertainty in groundwater reactive transport models. For the surface complexation model, the regression-based local sensitivity analysis and Morris- and DREAM(ZS)-based global sensitivity analysis yield almost identical ranking of parameter importance. The uncertainty analysis may help select appropriate likelihood

  10. A 2D/1D coupling neutron transport method based on the matrix MOC and NEM methods

    SciTech Connect

    Zhang, H.; Zheng, Y.; Wu, H.; Cao, L.

    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)

  11. Imaging reactive minerals in the subsurface using inverse reactive transport modeling: an example relevant for arsenic mobilization

    NASA Astrophysics Data System (ADS)

    Fakhreddine, S.; Lee, J. H.; Kitanidis, P. K.; Fendorf, S. E.; Rolle, M.

    2014-12-01

    The spatial distribution of naturally occurring, arsenic-bearing minerals in the subsurface is a key factor for determining the fate and transport of arsenic in groundwater systems. However, the direct measurement and estimation of these heterogeneously distributed minerals are often costly and difficult to obtain. While previous studies have shown the utility of using indirect measurements combined with inverse modeling techniques for tomography of physical properties including hydraulic conductivity, these methods have seldom been used to image geochemical properties. In this study, we use synthetic applications to demonstrate the ability of inverse modeling techniques to image reactive mineral lenses in the subsurface and quantify estimation error using indirect, commonly measured groundwater parameters. Specifically, we simulate the mobilization of arsenic via kinetic oxidative dissolution of arsenopyrite due to dissolved oxygen in the ambient groundwater. The modeling investigation is carried out at various scales and considers different flow-through domains including (i) a 1D lab-scale column (80 cm), (ii) a 2D lab-scale setup (30 cm x 60 cm) and (iii) a 2D field-scale domain (4 m x 20 m). Next, the simulated dissolved oxygen data and forward reactive transport model are used to image the spatial distribution of arsenopyrite using the Principal Component Geostatistical Approach (PCGA) for inverse modeling. The PCGA is a matrix-free geostatistical inversion approach that uses the leading principal components of the prior information to save computational costs and can be easily linked with any simulation software. Our results show that the PCGA can be used to image randomly distributed arsenopyrite lenses at various scales and has the potential to be employed at the field-scale to map complex distributions of reactive minerals in the subsurface based on the measurement of dissolved constituents in groundwater.

  12. Geophysical Characterization and Reactive Transport Modeling to Quantify Plume Behavior

    NASA Astrophysics Data System (ADS)

    Hubbard, S. S.; Wainwright, H.; Bea, S. A.; Spycher, N.; Li, L.; Sassen, D.; Chen, J.

    2012-12-01

    Predictions of subsurface contaminant plume mobility and remediation often fail due to the inability to tractably characterize heterogeneous flow-and-transport properties and monitor critical geochemical transitions over plume-relevant scales. This study presents two recently developed strategies to quantify and predict states and processes across scales that govern plume behavior. Development of both strategies takes advantage of multi-scale and disparate datasets and has involved the use of reactive transport models, geophysical methods, and stochastic integration approaches. The first approach, called reactive facies, exploits coupled physiochemical heterogeneity to characterize subsurface flow and transport properties that impact plume sorption and thus mobility. We develop and test the reactive facies concept within uranium contaminated Atlantic Coastal Plain sediments that underlie the U.S. Department of Energy Savannah River Site, F-Area, South Carolina. Through analysis of field data (core samples, geophysical well logs, and cross-hole ground penetrating radar and seismic datasets) coupled with laboratory sorption studies, we have identified two reactive facies that have unique distributions of mineralogy, texture, porosity, hydraulic conductivity and geophysical attributes. We develop and use facies-based relationships with geophysical data in a Bayesian framework to spatially distribute reactive facies and their associated transport properties and uncertainties along local and plume-scale geophysical transects. To illustrate the value of reactive facies, we used the geophysically-obtained reactive facies properties to parameterize reactive transport models and simulate the migration of an acidic-U(VI) plume through the 2D domains. Modeling results suggest that each identified reactive facies exerts control on plume evolution, highlighting the usefulness of the reactive facies concept and approach for spatially distributing properties that control flow and

  13. Anomalous reactive transport in porous media: Experiments and modeling

    NASA Astrophysics Data System (ADS)

    Edery, Yaniv; Dror, Ishai; Scher, Harvey; Berkowitz, Brian

    2015-05-01

    We analyze dynamic behavior of chemically reactive species in a porous medium, subject to anomalous transport. In this context, we present transport experiments in a refraction-index-matched, three-dimensional, water-saturated porous medium. A pH indicator (Congo red) was used as either a conservative or a reactive tracer, depending on the tracer solution pH relative to that of the background solution. The porous medium consisted of an acrylic polymer material formed as spherical beads that have pH-buffering capacity. The magnitude of reaction during transport through the porous medium was related to the color change of the Congo red, via image analysis. Here, we focused on point injection of the tracer into a macroscopically uniform flow field containing water at a pH different from that of the injected tracer. The setup yielded measurements of the temporally evolving spatial (local-in-space) concentration field. Parallel experiments with the same tracer, but without reactions (no changes in pH), enabled identification of the transport itself to be anomalous (non-Fickian); this was quantified by a continuous time random walk (CTRW) formulation. A CTRW particle tracking model was then used to quantify the spatial and temporal migration of both the conservative and reactive tracer plumes. Model parameters related to the anomalous transport were determined from the conservative tracer experiments. An additional term accounting for chemical reaction was established solely from analysis of the reactant concentrations, and significantly, no other fitting parameters were required. The measurements and analysis emphasized the localized nature of reaction, caused by small-scale concentration fluctuations and preferential pathways. In addition, a threshold radius for pH-controlled reactive transport processes was defined under buffering conditions, which delineated the region in which reactions occurred rapidly.

  14. Simulations of reactive transport and precipitation with smoothed particle hydrodynamics

    NASA Astrophysics Data System (ADS)

    Tartakovsky, Alexandre M.; Meakin, Paul; Scheibe, Timothy D.; Eichler West, Rogene M.

    2007-03-01

    A numerical model based on smoothed particle hydrodynamics (SPH) was developed for reactive transport and mineral precipitation in fractured and porous materials. Because of its Lagrangian particle nature, SPH has several advantages for modeling Navier-Stokes flow and reactive transport including: (1) in a Lagrangian framework there is no non-linear term in the momentum conservation equation, so that accurate solutions can be obtained for momentum dominated flows and; (2) complicated physical and chemical processes such as surface growth due to precipitation/dissolution and chemical reactions are easy to implement. In addition, SPH simulations explicitly conserve mass and linear momentum. The SPH solution of the diffusion equation with fixed and moving reactive solid-fluid boundaries was compared with analytical solutions, Lattice Boltzmann [Q. Kang, D. Zhang, P. Lichtner, I. Tsimpanogiannis, Lattice Boltzmann model for crystal growth from supersaturated solution, Geophysical Research Letters, 31 (2004) L21604] simulations and diffusion limited aggregation (DLA) [P. Meakin, Fractals, scaling and far from equilibrium. Cambridge University Press, Cambridge, UK, 1998] model simulations. To illustrate the capabilities of the model, coupled three-dimensional flow, reactive transport and precipitation in a fracture aperture with a complex geometry were simulated.

  15. Kinetic theory of transport processes in partially ionized reactive plasma, I: General transport equations

    NASA Astrophysics Data System (ADS)

    Zhdanov, V. M.; Stepanenko, A. A.

    2016-03-01

    In this paper we derive the set of general transport equations for multicomponent partially ionized reactive plasma in the presence of electric and magnetic fields taking into account the internal degrees of freedom and electronic excitation of plasma particles. Our starting point is a generalized Boltzmann equation with the collision integral in the Wang-Chang and Uhlenbeck form and a reactive collision integral. We obtain a set of conservation equations for such plasma and employ a linearized variant of Grad's moment method to derive the system of moment (or transport) equations for the plasma species nonequilibrium parameters. Full and reduced transport equations, resulting from the linearized system of moment equations, are presented, which can be used to obtain transport relations and expressions for transport coefficients of electrons and heavy plasma particles (molecules, atoms and ions) in partially ionized reactive plasma.

  16. Analytical model of reactive transport processes with spatially variable coefficients.

    PubMed

    Simpson, Matthew J; Morrow, Liam C

    2015-05-01

    Analytical solutions of partial differential equation (PDE) models describing reactive transport phenomena in saturated porous media are often used as screening tools to provide insight into contaminant fate and transport processes. While many practical modelling scenarios involve spatially variable coefficients, such as spatially variable flow velocity, v(x), or spatially variable decay rate, k(x), most analytical models deal with constant coefficients. Here we present a framework for constructing exact solutions of PDE models of reactive transport. Our approach is relevant for advection-dominant problems, and is based on a regular perturbation technique. We present a description of the solution technique for a range of one-dimensional scenarios involving constant and variable coefficients, and we show that the solutions compare well with numerical approximations. Our general approach applies to a range of initial conditions and various forms of v(x) and k(x). Instead of simply documenting specific solutions for particular cases, we present a symbolic worksheet, as supplementary material, which enables the solution to be evaluated for different choices of the initial condition, v(x) and k(x). We also discuss how the technique generalizes to apply to models of coupled multispecies reactive transport as well as higher dimensional problems. PMID:26064648

  17. Analytical model of reactive transport processes with spatially variable coefficients

    PubMed Central

    Simpson, Matthew J.; Morrow, Liam C.

    2015-01-01

    Analytical solutions of partial differential equation (PDE) models describing reactive transport phenomena in saturated porous media are often used as screening tools to provide insight into contaminant fate and transport processes. While many practical modelling scenarios involve spatially variable coefficients, such as spatially variable flow velocity, v(x), or spatially variable decay rate, k(x), most analytical models deal with constant coefficients. Here we present a framework for constructing exact solutions of PDE models of reactive transport. Our approach is relevant for advection-dominant problems, and is based on a regular perturbation technique. We present a description of the solution technique for a range of one-dimensional scenarios involving constant and variable coefficients, and we show that the solutions compare well with numerical approximations. Our general approach applies to a range of initial conditions and various forms of v(x) and k(x). Instead of simply documenting specific solutions for particular cases, we present a symbolic worksheet, as supplementary material, which enables the solution to be evaluated for different choices of the initial condition, v(x) and k(x). We also discuss how the technique generalizes to apply to models of coupled multispecies reactive transport as well as higher dimensional problems. PMID:26064648

  18. Reactive solute transport in physically and chemically heterogeneous porous media with multimodal reactive mineral facies: the Lagrangian approach.

    PubMed

    Soltanian, Mohamad Reza; Ritzi, Robert W; Dai, Zhenxue; Huang, Chao Cheng

    2015-03-01

    Physical and chemical heterogeneities have a large impact on reactive transport in porous media. Examples of heterogeneous attributes affecting reactive mass transport are the hydraulic conductivity (K), and the equilibrium sorption distribution coefficient (Kd). This paper uses the Deng et al. (2013) conceptual model for multimodal reactive mineral facies and a Lagrangian-based stochastic theory in order to analyze the reactive solute dispersion in three-dimensional anisotropic heterogeneous porous media with hierarchical organization of reactive minerals. An example based on real field data is used to illustrate the time evolution trends of reactive solute dispersion. The results show that the correlation between the hydraulic conductivity and the equilibrium sorption distribution coefficient does have a significant effect on reactive solute dispersion. The anisotropy ratio does not have a significant effect on reactive solute dispersion. Furthermore, through a sensitivity analysis we investigate the impact of changing the mean, variance, and integral scale of K and Kd on reactive solute dispersion. PMID:25532767

  19. Quantification of sequential chlorinated ethene degradation by use of a reactive transport model incorporating isotope fractionation.

    PubMed

    Van Breukelen, Boris M; Hunkeler, Daniel; Volkering, Frank

    2005-06-01

    Compound-specific isotope analysis (CSIA) enables quantification of biodegradation by use of the Rayleigh equation. The Rayleigh equation fails, however, to describe the sequential degradation of chlorinated aliphatic hydrocarbons (CAHs) involving various intermediates that are controlled by simultaneous degradation and production. This paper shows how isotope fractionation during sequential degradation can be simulated in a 1D reactive transport code (PHREEQC-2). 12C and 13C isotopes of each CAH were simulated as separate species, and the ratio of the rate constants of the heavy to light isotope equaled the kinetic isotope fractionation factor for each degradation step. The developed multistep isotope fractionation reactive transport model (IF-RTM) adequately simulated reductive dechlorination of tetrachloroethene (PCE) to ethene in a microcosm experiment. Transport scenarios were performed to evaluate the effect of sorption and of different degradation rate constant ratios among CAH species on the downgradient isotope evolution. The power of the model to quantify degradation is illustrated for situations where mixed sources degrade and for situations where daughter products are removed by oxidative processes. Finally, the model was used to interpret the occurrence of reductive dechlorination at a field site. The developed methodology can easily be incorporated in 3D solute transport models to enable quantification of sequential CAH degradation in the field by CSIA. PMID:15984799

  20. Evaluating Conceptual Site Models with Multicomponent Reactive Transport Modeling

    NASA Astrophysics Data System (ADS)

    Dai, Z.; Heffner, D.; Price, V.; Temples, T. J.; Nicholson, T. J.

    2005-05-01

    Modeling ground-water flow and multicomponent reactive chemical transport is a useful approach for testing conceptual site models and assessing the design of monitoring networks. A graded approach with three conceptual site models is presented here with a field case of tetrachloroethene (PCE) transport and biodegradation near Charleston, SC. The first model assumed a one-layer homogeneous aquifer structure with semi-infinite boundary conditions, in which an analytical solution of the reactive solute transport can be obtained with BIOCHLOR (Aziz et al., 1999). Due to the over-simplification of the aquifer structure, this simulation cannot reproduce the monitoring data. In the second approach we used GMS to develop the conceptual site model, a layer-cake multi-aquifer system, and applied a numerical module (MODFLOW and RT3D within GMS) to solve the flow and reactive transport problem. The results were better than the first approach but still did not fit the plume well because the geological structures were still inadequately defined. In the third approach we developed a complex conceptual site model by interpreting log and seismic survey data with Petra and PetraSeis. We detected a major channel and a younger channel, through the PCE source area. These channels control the local ground-water flow direction and provide a preferential chemical transport pathway. Results using the third conceptual site model agree well with the monitoring concentration data. This study confirms that the bias and uncertainty from inadequate conceptual models are much larger than those introduced from an inadequate choice of model parameter values (Neuman and Wierenga, 2003; Meyer et al., 2004). Numerical modeling in this case provides key insight into the hydrogeology and geochemistry of the field site for predicting contaminant transport in the future. Finally, critical monitoring points and performance indicator parameters are selected for future monitoring to confirm system

  1. Constraining kinetic rates of mineral reactions using reactive transport models

    NASA Astrophysics Data System (ADS)

    Bolton, E. W.; Wang, Z.; Ague, J.; Bercovici, D.; Cai, Z.; Karato, S.; Oristaglio, M. L.; Qiu, L.

    2012-12-01

    We use a reactive transport model to better understand results of experiments to obtain kinetic rates of mineral reactions in closed systems. Closed system experiments pose special challenges in that secondary minerals may form that modify the fluid composition evolution and may grow on the dissolving minerals thus armoring the surface. Even so, such closed system experiments provide critical data for what minerals would actually form in field applications and how coupled dissolution and precipitation mineral reactions are strongly linked. Comparing to experimental observations can test the reactive transport model, and the experimental observations can be better understood by comparing the results to the modeling. We apply a 0D end member of the model to understand the dissolution of single crystals of forsterite in a variety of settings (low pH, high pH, or NaHCO3 initial fluids, at 100 C and 1 bar, or 200 C and 150 bar). Depending on the initial conditions, we observe the precipitation of talc, brucite, amorphous silica, chrysotile, or magnesite, in various combinations. We compare simulation results to fluid compositions and the presence of secondary minerals experimentally sampled at various times. Insight from the simulations helped create an inverse model to extract the rates of forsterite dissolution and to create a simple forward model useful for exploring the influence of system size, secondary mineral surface areas, etc. Our reactive transport model allows secondary minerals to armor the forsterite surface, which can strongly decrease the dissolution rate as the system evolves. Tuning our model with experimentally derived rates and assuring relevant processes are included so as to reproduce experimental observations is necessary before upscaling to heterogeneous field conditions. The reactive transport model will be used for field-scale sequestration simulations and coupled with a geomechanical model that includes the influence of deformation.

  2. Validation of a coupled reactive transport code in porous media

    NASA Astrophysics Data System (ADS)

    Mugler, C.; Montarnal, P.; Dimier, A.

    2003-04-01

    The safety assessment of nuclear waste disposals needs to predict the migration of radionuclides and chemical species through a geological medium. It is therefore necessary to develop and assess qualified and validated tools which integrate both the transport mechanisms through the geological media and the chemical mechanisms governing the mobility of radionuclides. In this problem, both geochemical and hydrodynamic phenomena are tightly linked together. That is the reason why the French Nuclear Energy Agency (CEA) and the French Agency for the Management of Radioactive Wastes (ANDRA) are conjointly developping a coupled reactive transport code that solves simultaneously a geochemical model and a transport model. This code, which is part of the software project ALLIANCES, leans on the libraries of two geochemical codes solving the complex ensemble of reacting chemical species: CHESS and PHREEQC. Geochemical processes considered here include ion exchange, redox reactions, acid-base reactions, surface complexation and mineral dissolution and/or precipitation. Transport is simulated using the mixed-hybrid finite element scheme CAST3M or the finite volume scheme MT3D. All together solve Darcy's law and simulate several hydrological processes such as advection, diffusion and dispersion. The coupling algorithm is an iterative sequential algorithm. Several analytical test cases have been defined and used to validate the reactive transport code. Numerical results can be compared to analytical solutions.

  3. Anthropogenic contamination of a phreatic drinking water winning: 3-dimensional reactive transport modelling

    NASA Astrophysics Data System (ADS)

    Griffioen, J.; van der Grift, B.; Maas, D.; van den Brink, C.; Zaadnoordijk, J. W.

    2003-04-01

    Groundwater is contaminated at the regional scale by agricultural activities and atmospheric deposition. A 3-D transport model was set-up for a phreatic drinking water winning, where the groundwater composition was monitored accurately. The winning is situated at an area with unconsolidated Pleistocene deposits. The land use is nature and agriculture. Annual mass-balances were determined using a wide range of historic data. The modelling approach for the unsaturated zone was either simple box models (Cl, NO_3 and SO_4) or 1-D transport modelling using HYDRUS (Cd). The modelling approach for the saturated zone used a multiple solute version of MT3D, where denitrification associated with pyrite oxidation and sorption of Cd were included. The solute transport calculations were performed for the period 1950--2030. The results obtained for the year 2000 were used as input concentration for the period 2000--2030. A comparison between the calculated and the measured concentrations of groundwater abstracted for Cl, NO_3 and SO_4 yields the following. First, the input at the surface is rather well estimated. Second, the redox reactivity of the first two aquifers is negligible around the winning, which is confirmed by respiration experiments using anaerobically sampled aquifer sediments. The reactivity of the third aquifer, which is a marine deposit and lies at least 30 meters below surface, is considerable. The discrepancies between modelled and measured output are explained by lack of knowledge about the subsurface reactivity and/or wrong estimates of surface loading and leaching from the unsaturated zone. The patterns for other hydrogeochemical variables such as Ca, HCO_3 may further constrain this lack of knowledge. The results for Cd indicate that Cd becomes strongly retarded, despite the low reactivity of the sandy sediments. The winning is rather insensitive to Cd contamination (but the surface water drainage network is not). Two major uncertainties for input of Cd

  4. Modeling Reactive Transport in Coupled Groundwater-Conduit Systems

    NASA Astrophysics Data System (ADS)

    Spiessl, S. M.; Sauter, M.; Zheng, C.; Viswanathan, H. S.

    2002-05-01

    Modeling reactive transport in coupled groundwater-conduit systems requires consideration of two transport time scales in the flow and transport models. Consider for example a subsurface mine consisting of a network of highly conductive shafts, drifts or ventilation raises (i.e., conduits) within the considerably less permeable ore material (i.e., matrix). In the conduits, potential contaminants can travel much more rapidly than in the background aquifer (matrix). Since conduits cannot necessarily be regarded as a continuum, double continuum models are only of limited use for simulation of contaminant transport in such coupled groundwater-conduit systems. This study utilizes a "hybrid" flow and transport model in which contaminants can in essence be transported at a slower time scale in the matrix and at a faster time scale in the conduits. The hybrid flow model uses an approach developed by Clemens et al. (1996), which is based on the modelling of flow in a discrete pipe network, coupled to a continuum representing the low-permeability inter-conduit matrix blocks. Laminar or turbulent flow can be simulated in the different pipes depending on the flow conditions in the model domain. The three-dimensional finite-difference groundwater flow model MODFLOW (Harbaugh and McDonald, 1996) is used to simulate flow in the continuum. Contaminant transport within the matrix is simulated with a continuum approach using the three-dimensional multi-species solute transport model MT3DMS (Zheng and Wang, 1999), while that in the conduit system is simulated with a one-dimensional advective transport model. As a first step for reactive transport modeling in such systems, only equilibrium reactions among multiple species are considered by coupling the hybrid transport model to a geochemical speciation package. An idealized mine network developed by Viswanathan and Sauter (2001) is used as a test problem in this study. The numerical experiment is based on reference date collected from

  5. Fluid-rock interaction: A reactive transport approach

    SciTech Connect

    Steefel, C.; Maher, K.

    2009-04-01

    Fluid-rock interaction (or water-rock interaction, as it was more commonly known) is a subject that has evolved considerably in its scope over the years. Initially its focus was primarily on interactions between subsurface fluids of various temperatures and mostly crystalline rocks, but the scope has broadened now to include fluid interaction with all forms of subsurface materials, whether they are unconsolidated or crystalline ('fluid-solid interaction' is perhaps less euphonious). Disciplines that previously carried their own distinct names, for example, basin diagenesis, early diagenesis, metamorphic petrology, reactive contaminant transport, chemical weathering, are now considered to fall under the broader rubric of fluid-rock interaction, although certainly some of the key research questions differ depending on the environment considered. Beyond the broadening of the environments considered in the study of fluid-rock interaction, the discipline has evolved in perhaps an even more important way. The study of water-rock interaction began by focusing on geochemical interactions in the absence of transport processes, although a few notable exceptions exist (Thompson 1959; Weare et al. 1976). Moreover, these analyses began by adopting a primarily thermodynamic approach, with the implicit or explicit assumption of equilibrium between the fluid and rock. As a result, these early models were fundamentally static rather than dynamic in nature. This all changed with the seminal papers by Helgeson and his co-workers (Helgeson 1968; Helgeson et al. 1969) wherein the concept of an irreversible reaction path was formally introduced into the geochemical literature. In addition to treating the reaction network as a dynamically evolving system, the Helgeson studies introduced an approach that allowed for the consideration of a multicomponent geochemical system, with multiple minerals and species appearing as both reactants and products, at least one of which could be

  6. Electrochemical reactivity and proton transport mechanisms in nanostructured ceria.

    PubMed

    Ding, J; Strelcov, E; Kalinin, S V; Bassiri-Gharb, N

    2016-08-26

    Electrochemical reactivity and ionic transport at the nanoscale are essential in many energy applications. In this study, time-resolved Kelvin probe force microscopy (tr-KPFM) is utilized for surface potential mapping of nanostructured ceria, in both space and time domains. The fundamental mechanisms of proton injection and transport are studied as a function of environmental conditions and the presence or absence of triple phase boundaries. Finite element modeling is used to extract physical parameters from the experimental data, allowing not only quantification of the observed processes, but also decoupling of their contributions to the measured signal. The constructed phase diagrams of the parameters demonstrate a thermally activated proton injection reaction at the triple phase boundary, and two transport processes that are responsible for the low-temperature proton conductivity of nanostructured ceria. PMID:27407076

  7. Electrochemical reactivity and proton transport mechanisms in nanostructured ceria

    NASA Astrophysics Data System (ADS)

    Ding, J.; Strelcov, E.; Kalinin, S. V.; Bassiri-Gharb, N.

    2016-08-01

    Electrochemical reactivity and ionic transport at the nanoscale are essential in many energy applications. In this study, time-resolved Kelvin probe force microscopy (tr-KPFM) is utilized for surface potential mapping of nanostructured ceria, in both space and time domains. The fundamental mechanisms of proton injection and transport are studied as a function of environmental conditions and the presence or absence of triple phase boundaries. Finite element modeling is used to extract physical parameters from the experimental data, allowing not only quantification of the observed processes, but also decoupling of their contributions to the measured signal. The constructed phase diagrams of the parameters demonstrate a thermally activated proton injection reaction at the triple phase boundary, and two transport processes that are responsible for the low-temperature proton conductivity of nanostructured ceria.

  8. Association between amygdala reactivity and a dopamine transporter gene polymorphism.

    PubMed

    Bergman, O; Åhs, F; Furmark, T; Appel, L; Linnman, C; Faria, V; Bani, M; Pich, E M; Bettica, P; Henningsson, S; Manuck, S B; Ferrell, R E; Nikolova, Y S; Hariri, A R; Fredrikson, M; Westberg, L; Eriksson, E

    2014-01-01

    Essential for detection of relevant external stimuli and for fear processing, the amygdala is under modulatory influence of dopamine (DA). The DA transporter (DAT) is of fundamental importance for the regulation of DA transmission by mediating reuptake inactivation of extracellular DA. This study examined if a common functional variable number tandem repeat polymorphism in the 3' untranslated region of the DAT gene (SLC6A3) influences amygdala function during the processing of aversive emotional stimuli. Amygdala reactivity was examined by comparing regional cerebral blood flow, measured with positron emission tomography and [(15)O]water, during exposure to angry and neutral faces, respectively, in a Swedish sample comprising 32 patients with social anxiety disorder and 17 healthy volunteers. In a separate US sample, comprising 85 healthy volunteers studied with blood oxygen level-dependent functional magnetic resonance imaging, amygdala reactivity was assessed by comparing the activity during exposure to threatening faces and neutral geometric shapes, respectively. In both the Swedish and the US sample, 9-repeat carriers displayed higher amygdala reactivity than 10-repeat homozygotes. The results suggest that this polymorphism contributes to individual variability in amygdala reactivity. PMID:25093598

  9. Association between amygdala reactivity and a dopamine transporter gene polymorphism

    PubMed Central

    Bergman, O; Åhs, F; Furmark, T; Appel, L; Linnman, C; Faria, V; Bani, M; Pich, E M; Bettica, P; Henningsson, S; Manuck, S B; Ferrell, R E; Nikolova, Y S; Hariri, A R; Fredrikson, M; Westberg, L; Eriksson, E

    2014-01-01

    Essential for detection of relevant external stimuli and for fear processing, the amygdala is under modulatory influence of dopamine (DA). The DA transporter (DAT) is of fundamental importance for the regulation of DA transmission by mediating reuptake inactivation of extracellular DA. This study examined if a common functional variable number tandem repeat polymorphism in the 3′ untranslated region of the DAT gene (SLC6A3) influences amygdala function during the processing of aversive emotional stimuli. Amygdala reactivity was examined by comparing regional cerebral blood flow, measured with positron emission tomography and [15O]water, during exposure to angry and neutral faces, respectively, in a Swedish sample comprising 32 patients with social anxiety disorder and 17 healthy volunteers. In a separate US sample, comprising 85 healthy volunteers studied with blood oxygen level-dependent functional magnetic resonance imaging, amygdala reactivity was assessed by comparing the activity during exposure to threatening faces and neutral geometric shapes, respectively. In both the Swedish and the US sample, 9-repeat carriers displayed higher amygdala reactivity than 10-repeat homozygotes. The results suggest that this polymorphism contributes to individual variability in amygdala reactivity. PMID:25093598

  10. Dopamine D1, D2, D3 Receptors, Vesicular Monoamine Transporter Type-2 (VMAT2) and Dopamine Transporter (DAT) Densities in Aged Human Brain

    PubMed Central

    Sun, Jianjun; Xu, Jinbin; Cairns, Nigel J.; Perlmutter, Joel S.; Mach, Robert H.

    2012-01-01

    The dopamine D1, D2, D3 receptors, vesicular monoamine transporter type-2 (VMAT2), and dopamine transporter (DAT) densities were measured in 11 aged human brains (aged 77–107.8, mean: 91 years) by quantitative autoradiography. The density of D1 receptors, VMAT2, and DAT was measured using [3H]SCH23390, [3H]dihydrotetrabenazine, and [3H]WIN35428, respectively. The density of D2 and D3 receptors was calculated using the D3-preferring radioligand, [3H]WC-10 and the D2-preferring radioligand [3H]raclopride using a mathematical model developed previously by our group. Dopamine D1, D2, and D3 receptors are extensively distributed throughout striatum; the highest density of D3 receptors occurred in the nucleus accumbens (NAc). The density of the DAT is 10–20-fold lower than that of VMAT2 in striatal regions. Dopamine D3 receptor density exceeded D2 receptor densities in extrastriatal regions, and thalamus contained a high level of D3 receptors with negligible D2 receptors. The density of dopamine D1 linearly correlated with D3 receptor density in the thalamus. The density of the DAT was negligible in the extrastriatal regions whereas the VMAT2 was expressed in moderate density. D3 receptor and VMAT2 densities were in similar level between the aged human and aged rhesus brain samples, whereas aged human brain samples had lower range of densities of D1 and D2 receptors and DAT compared with the aged rhesus monkey brain. The differential density of D3 and D2 receptors in human brain will be useful in the interpretation of PET imaging studies in human subjects with existing radiotracers, and assist in the validation of newer PET radiotracers having a higher selectivity for dopamine D2 or D3 receptors. PMID:23185343

  11. Parameterized isoprene and monoterpene emissions from the boreal forest floor: Implementation into a 1D chemistry-transport model and investigation of the influence on atmospheric chemistry

    NASA Astrophysics Data System (ADS)

    Mogensen, Ditte; Aaltonen, Hermanni; Aalto, Juho; Bäck, Jaana; Kieloaho, Antti-Jussi; Gierens, Rosa; Smolander, Sampo; Kulmala, Markku; Boy, Michael

    2015-04-01

    Volatile organic compounds (VOCs) are emitted from the biosphere and can work as precursor gases for aerosol particles that can affect the climate (e.g. Makkonen et al., ACP, 2012). VOC emissions from needles and leaves have gained the most attention, however other parts of the ecosystem also have the ability to emit a vast amount of VOCs. This, often neglected, source can be important e.g. at periods where leaves are absent. Both sources and drivers related to forest floor emission of VOCs are currently limited. It is thought that the sources are mainly due to degradation of organic matter (Isidorov and Jdanova, Chemosphere, 2002), living roots (Asensio et al., Soil Biol. Biochem., 2008) and ground vegetation. The drivers are biotic (e.g. microbes) and abiotic (e.g. temperature and moisture). However, the relative importance of the sources and the drivers individually are currently poorly understood. Further, the relative importance of these factors is highly dependent on the tree species occupying the area of interest. The emission of isoprene and monoterpenes where measured from the boreal forest floor at the SMEAR II station in Southern Finland (Hari and Kulmala, Boreal Env. Res., 2005) during the snow-free period in 2010-2012. We used a dynamic method with 3 automated chambers analyzed by Proton Transfer Reaction - Mass Spectrometer (Aaltonen et al., Plant Soil, 2013). Using this data, we have developed empirical parameterizations for the emission of isoprene and monoterpenes from the forest floor. These parameterizations depends on abiotic factors, however, since the parameterizations are based on field measurements, biotic features are captured. Further, we have used the 1D chemistry-transport model SOSAA (Boy et al., ACP, 2011) to test the seasonal relative importance of inclusion of these parameterizations of the forest floor compared to the canopy crown emissions, on the atmospheric reactivity throughout the canopy.

  12. Expanding the Role of Reactive Transport Modeling in Biogeochemical Sciences

    NASA Astrophysics Data System (ADS)

    Li, Li; Maher, Katherine M.; Navarre-Sitchler, Alexis

    2014-09-01

    Earth systems are complex due to the intimate coupling of physical, chemical, and biological processes in the subsurface. Field observation and data analysis have provided significant insights into the coupling of these processes. However, mechanistic understanding often requires advanced modeling tools to quantify the role of individual processes while maintaining the process coupling that determines the overall system behavior. As a result, reactive transport modeling (RTM) has been used extensively to interrogate complex subsurface processes relevant to energy and the environment. Existing work has shown the significant research and educational advantages of RTM in elucidating mechanisms, integrating large data sets, testing hypotheses, and guiding the stewardship and management of water and energy resources.

  13. Representing Microbial Processes in Environmental Reactive Transport Models

    NASA Astrophysics Data System (ADS)

    van Cappellen, P.

    2009-04-01

    The activities of microorganisms profoundly impact the chemical structure and biogeochemical dynamics of surface and subsurface environments. In the context of reactive transport modeling, a major challenge is to derive, calibrate and validate rate expressions for microbially-mediated reaction processes. This challenge is best met by combining field observations, laboratory experiments and theory. In my presentation, I will illustrate such an integrated approach for the case of microbial respiration in aquatic sediments. Topics that will be dealt with are model consistency, interpretation of experimental data, bioenergetics, transient behavior and model performance.

  14. Representing Microbial Processes in Environmental Reactive Transport Models

    NASA Astrophysics Data System (ADS)

    van Cappellen, P.

    2009-04-01

    Microorganisms play a key role in the biogeochemical functioning of the earth's surface and shallow subsurface. In the context of reactive transport modeling, a major challenge is to derive, parameterize, calibrate and verify mathematical expressions for microbially-mediated reactions in the environmental. This is best achieved by combining field observations, laboratory experiments, theoretical principles and modeling. Here, I will illustrate such an integrated approach for the case of microbial respiration processes in aquatic sediments. Important issues that will be covered include experimental design, model consistency and performance, as well as the bioenergetics and transient behavior of geomicrobial reaction systems.

  15. Modeling biogechemical reactive transport in a fracture zone

    SciTech Connect

    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.

  16. A Coupled Model of Multiphase Flow, Reactive Biogeochemical Transport, Thermal Transport and Geo-Mechanics.

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    In this investigation, a coupled model of multiphase flow, reactive biogeochemical transport, thermal transport and geo-mechanics in subsurface media is presented. It iteratively solves the mass conservation equation for fluid flow, thermal transport equation for temperature, reactive biogeochemical transport equations for concentration distributions, and solid momentum equation for displacement with successive linearization algorithm. With species-based equations of state, density of a phase in the system is obtained by summing up concentrations of all species. This circumvents the problem of having to use empirical functions. Moreover, reaction rates of all species are incorporated in mass conservation equation for fluid flow. Formation enthalpy of all species is included in the law of energy conservation as a source-sink term. Finite element methods are used to discretize the governing equations. Numerical experiments are presented to examine the accuracy and robustness of the proposed model. The results demonstrate the feasibility and capability of present model in subsurface media.

  17. Reactive transport studies at the Raymond Field Site

    SciTech Connect

    Freifeld, B.; Karasaki, K.; Solbau, R.; Cohen, A.

    1995-12-01

    To ensure the safety of a nuclear waste repository, an understanding of the transport of radionuclides from the repository nearfield to the biosphere is necessary. At the Raymond Field Site, in Raymond, California, tracer tests are being conducted to test characterization methods for fractured media and to evaluate the equipment and tracers that will be used for Yucca Mountain`s fracture characterization. Recent tracer tests at Raymond have used reactive cations to demonstrate transport with sorption. A convective-dispersive model was used to simulate a two-well recirculating test with reasonable results. However, when the same model was used to simulate a radially convergent tracer test, the model poorly predicted the actual test data.

  18. 1D and 3D anthropometric data application on public transport vehicle layout and on oil and gas laboratories work environment design.

    PubMed

    Pastura, F C H; Guimarães, C P; Zamberlan, M C P; Cid, G L; Santos, V S; Streit, P; Paranhos, A G; Cobbe, R T; Cobbe, K T; Batista, D S

    2012-01-01

    The goal of this paper is to present 1D and 3D anthropometric data applied to two distinct design situations: one related to the interior layout of a public transport vehicle and another one related to oil and gas laboratories work environment design. On this study, the 1D anthropometric data were extracted from the Brazilian anthropometric database developed by INT and the 3D anthropometric data were obtained using a Cyberware 3D whole body scanner. A second purpose of this paper is to present the 3D human scanning data as a tool that can help designers on decision making. PMID:22317431

  19. Benchmarking reactive transport models at a hillslope scale

    NASA Astrophysics Data System (ADS)

    Kalbacher, T.; He, W.; Nixdorf, E.; Jang, E.; Fleckenstein, J. H.; Kolditz, O.

    2015-12-01

    The hillslope scale is an important transition between the field scale and the catchment scale. The water flow in the unsaturated zone of a hillslope can be highly dynamic, which can lead to dynamic changes of groundwater flow or stream outflow. Additionally, interactions among host rock formation, soil properties and recharge water from precipitation or anthropogenic activities (mining, agriculture etc.) can influence the water quality of groundwater and stream in the long term. To simulate reactive transport processes at such a scale is a challenging task. On the one hand, simulation of water flow in a coupled soil-aquifer system often involves solving of highly non-linear PDEs such as Richards equation; on the other hand, one has to consider complicated biogeochemical reactions (e.g. water-rock interactions, biological degradation, redox reactions). Both aspects are computationally expensive and have high requirements on the numerical precision and stabilities of the employed code. The primary goals of this study are as follows: i) Identify the bottlenecks and quantitatively analyse their influence on simulation of biogeochemical reactions at a hillslope scale; ii) find or suggest practical strategies to deal with these bottlenecks, thus to provide detailed hints for future improvements of reactive transport simulators. To achieve these goals, the parallelized reactive transport simulator OGS#IPhreeqc has been applied to simulate two benchmark examples. The first example is about uranium leaching based on Šimůnek et al. (2012), which considers the leaching of uranium from a mill tailing and accompanied mineral dissolution/precipitation. The geochemical system is then extended to include redox reactions in the second example. Based on these examples, the numerical stability and parallel performance of the tool is analysed. ReferenceŠimůnek, J., Jacques, D., Šejna, M., van Genuchten, M. T.: The HP2 program for HYDRUS (2D/3D), A coupled code for simulating two

  20. Connection between wave transport through disordered 1D waveguides and energy density inside the sample: A maximum-entropy approach

    NASA Astrophysics Data System (ADS)

    Mello, Pier A.; Shi, Zhou; Genack, Azriel Z.

    2015-11-01

    We study the average energy - or particle - density of waves inside disordered 1D multiply-scattering media. We extend the transfer-matrix technique that was used in the past for the calculation of the intensity beyond the sample to study the intensity in the interior of the sample by considering the transfer matrices of the two segments that form the entire waveguide. The statistical properties of the two disordered segments are found using a maximum-entropy ansatz subject to appropriate constraints. The theoretical expressions are shown to be in excellent agreement with 1D transfer-matrix simulations.

  1. Uranium transport in a crushed granodiorite: Experiments and reactive transport modeling

    SciTech Connect

    Dittrich, T. M.; Reimus, P. W.

    2015-02-12

    The primary objective of this study was to develop and demonstrate an experimental method to refine and better parameterize process models for reactive contaminant transport in aqueous subsurface environments and to reduce conservatism in such models without attempting to fully describe the geochemical system.

  2. End-Member Formulation of Solid Solutions and Reactive Transport

    SciTech Connect

    Lichtner, Peter C.

    2015-09-01

    A model for incorporating solid solutions into reactive transport equations is presented based on an end-member representation. Reactive transport equations are solved directly for the composition and bulk concentration of the solid solution. Reactions of a solid solution with an aqueous solution are formulated in terms of an overall stoichiometric reaction corresponding to a time-varying composition and exchange reactions, equivalent to reaction end-members. Reaction rates are treated kinetically using a transition state rate law for the overall reaction and a pseudo-kinetic rate law for exchange reactions. The composition of the solid solution at the onset of precipitation is assumed to correspond to the least soluble composition, equivalent to the composition at equilibrium. The stoichiometric saturation determines if the solid solution is super-saturated with respect to the aqueous solution. The method is implemented for a simple prototype batch reactor using Mathematica for a binary solid solution. Finally, the sensitivity of the results on the kinetic rate constant for a binary solid solution is investigated for reaction of an initially stoichiometric solid phase with an undersaturated aqueous solution.

  3. Conservative and reactive solute transport in constructed wetlands

    USGS Publications Warehouse

    Keefe, S.H.; Barber, L.B.; Runkel, R.L.; Ryan, J.N.; McKnight, Diane M.; Wass, R.D.

    2004-01-01

    The transport of bromide, a conservative tracer, and rhodamine WT (RWT), a photodegrading tracer, was evaluated in three wastewater-dependent wetlands near Phoenix, Arizona, using a solute transport model with transient storage. Coupled sodium bromide and RWT tracer tests were performed to establish conservative transport and reactive parameters in constructed wetlands with water losses ranging from (1) relatively impermeable (15%), (2) moderately leaky (45%), and (3) significantly leaky (76%). RWT first-order photolysis rates and sorption coefficients were determined from independent field and laboratory experiments. Individual wetland hydraulic profiles influenced the extent of transient storage interaction in stagnant water areas and consequently RWT removal. Solute mixing and transient storage interaction occurred in the impermeable wetland, resulting in 21% RWT mass loss from main channel and storage zone photolysis (10%) and sorption (11%) reactions. Advection and dispersion governed solute transport in the leaky wetland, limiting RWT photolysis removal (1.2%) and favoring main channel sorption (3.6%). The moderately leaky wetland contained islands parallel to flow, producing channel flow and minimizing RWT losses (1.6%).

  4. Treatment of reactive interfaces in pore-scale reactive transport with the phase-field method

    NASA Astrophysics Data System (ADS)

    Huber, C.; Di Palma, P. R.

    2014-12-01

    The two major challenges for continuum reactive transport models are the treatment of interfaces between different phases (multi-fluids like DNAPL-water, or solid-fluid) and the ability to model transient chemical gradients at the pore-scale. Pore-scale models allow us to deal naturally with chemical gradients at the discrete scale and they generally consider interfaces as boundary conditions that satisfy a local, but modified, mass balance equation. In other word grains do not take part in the mass balance of chemical species besides providing a boundary condition for the fluid. For instance, heterogeneous reactions at solid-fluid boundaries are framed as a balance between incoming chemical flux and reactions. Due to complex topology of interfaces in natural porous media, the treatment of heterogeneous reactions depends on the orientation of the interface and therefore requires a special care. It can become complicated and tedious especially when interfaces are allowed to evolve with time. Approaches such as the enthalpy method, which was developed for solving moving interfaces during melting processes, offer the advantage of a treatment that is independent of the shape of the moving interface. Similar methods have been used for modeling multiphase flows with diffuse interface successfully. Here, we expand on these approaches and introduce a phase-field approach to introduce heterogeneous reactions in single and multiphase reactive flows at the pore-scale. Mass conservation is solved in each phase and we introduce interface conditions as a source/sink term in the conservation equation rather than a boundary condition. The advantages are that the method becomes independent of the (time-dependent) topology of the interface and automatically enforces local mass conservation between the different constituents of the domain. We show validations of the model and applications to multispecies reactive transport, isotope fractionation during calcite growth and finally

  5. AN IN-SITU PERMEABLE REACTIVE BARRIER FOR THE TREATMENT OF HEXAVALENT CHROMIUM AND TRICHLOROETHYLENE IN GROUNDWATER: VOLUME 3 MULTICOMPONENT REACTIVE TRANSPORT MODELING

    EPA Science Inventory

    Reactive transport modeling has been conducted to describe the performance of the permeable reactive barrier at the Coast Guard Support Center near Elizabeth City, NC. The reactive barrier was installed to treat groundwater contaminated by hexavalent chromium and chlorinated org...

  6. Modelling reactive transport in a phosphogypsum dump, Venezia, Italia

    NASA Astrophysics Data System (ADS)

    Calcara, Massimo; Borgia, Andrea; Cattaneo, Laura; Bartolo, Sergio; Clemente, Gianni; Glauco Amoroso, Carlo; Lo Re, Fabio; Tozzato, Elena

    2013-04-01

    We develop a reactive-transport porous media flow model for a phosphogypsum dump located on the intertidal deposits of the Venetian Lagoon: 1. we construct a complex conceptual and geologic model from field data using the GMS™ graphical user interface; 2. the geological model is mapped onto a rectangular MODFLOW grid; 3. using the TMT2 FORTRAN90 code we translate this grid into the MESH, INCON and GENER input files for the TOUGH2 series of codes; 4. we run TOUGH-REACT to model flow and reactive transport in the dump and the sediments below it. The model includes 3 different dump materials (phosphogypsum, bituminous and hazardous wastes) with the pores saturated by specific fluids. The sediments below the dump are formed by an intertidal sequence of calcareous sands and silts, in addition to clays and organic deposits, all of which are initially saturated with lagoon salty waters. The recharge rain-water dilutes the dump fluids. In turn, the percolates from the dump react with the underlying sediments and the sea water that saturates them. Simulation results have been compared with chemical sampled analyses. In fact, in spite of the simplicity of our model we are able to show how the pH becomes neutral at a short distance below the dump, a fact observed during aquifer monitoring. The spatial and temporal evolution of dissolution and precipitation reactions occur in our model much alike reality. Mobility of some elements, such as divalent iron, are reduced by specific and concurrent conditions of pH from near-neutrality to moderately high values and positive redox potential; opposite conditions favour mobility of potentially toxic metals such as Cr, As Cd and Pb. Vertical movement are predominant. Trend should be therefore heavily influenced by pH and Eh values. If conditions are favourable to mobility, concentration of these substances in the bottom strata could be high. However, simulation suggest that the sediments tend to reduce the transport potential of

  7. EVALUATING THE SENSITIVITY OF A SUBSURFACE MULTICOMPONENT REACTIVE TRANSPORT MODEL WITH RESPECT TO TRANSPORT AND REACTION PARAMETERS

    EPA Science Inventory

    The input variables for a numerical model of reactive solute transport in groundwater include both transport parameters, such as hydraulic conductivity and infiltration, and reaction parameters that describe the important chemical and biological processes in the system. These pa...

  8. Nonlocal reactive transport with physical, chemical, and biological heterogeneity

    NASA Astrophysics Data System (ADS)

    Hu, Bill X.; Cushman, John H.; Deng, Fei-Wen

    When a natural porous medium is viewed from an eulerian perspective, incomplete characterization of the hydraulic conductivity, chemical reactivity, and biological activity leads to nonlocal constitutive theories, irrespective of whether the medium has evolving heterogeneity with fluctuations over all scales. Within this framework a constitutive theory involving nonlocal dispersive and convective fluxes and nonlocal sources/sinks is developed for chemicals undergoing random linear nonequilibrium reactions and random equilibrium first-order decay in a random conductivity field. The resulting transport equations are solved exactly in Fourier-Laplace space and then numerically inverted to real space. Mean concentration contours and various spatial moments are presented graphically for several covariance structures. 1997 Published by Elsevier Science Ltd. All rights reserved

  9. Hybrid Models of Reactive Transport in Porous and Fractured Media

    SciTech Connect

    Battiato, Ilenia; Tartakovsky, Daniel M.; Tartakovsky, Alexandre M.; Scheibe, Timothy D.

    2011-02-02

    Darcy-scale models of flow and transport in porous media often fail to describe experimentally observed phenomena, while their pore-scale counterparts are accu- rate but can be computationally prohibitive. Most numerical multi-scale models, which seek to combine these two descriptions, require empirical closures and/or assumptions on the behavior of pore-scale quantities at the continuum (Darcy) scale. We present a general formulation of an iterative hybrid numerical method that links these two scales without resorting to such approximations. The algorithm treats the fluxes exchanged at the internal boundaries between the pore- and continuum-scale domains as unknown, and allows for iteratively determined boundary conditions to be applied at the pore-scale in order to guarantee their continuity. While the algorithm proposed is general, we use it to model Taylor dispersion in a fracture with chemically reactive walls. Results show significant improvement upon standard continuum-scale formulations.

  10. Modeling reactive geochemical transport of concentrated aqueous solutions

    NASA Astrophysics Data System (ADS)

    Zhang, Guoxiang; Zheng, Zuoping; Wan, Jiamin

    2005-02-01

    Aqueous solutions with ionic strength larger than 1 M are usually considered concentrated aqueous solutions. These solutions can be found in some natural systems and are also industrially produced and released into accessible natural environments, and as such, they pose a big environmental problem. Concentrated aqueous solutions have unique thermodynamic and physical properties. They are usually strongly acidic or strongly alkaline, with the ionic strength possibly reaching 30 M or higher. Chemical components in such solutions are incompletely dissociated. The thermodynamic activities of both ionic and molecular species in these solutions are determined by the ionic interactions. In geological media the problem is further complicated by the interactions between the solutions and sediments and rocks. The chemical composition of concentrated aqueous solutions when migrating through the geological media may be drastically altered by these strong fluid-rock interactions. To effectively model reactive transport of concentrated aqueous solutions, we must take into account the ionic interactions. For this purpose we substantially extended an existing reactive transport code, BIO-CORE2D©, by incorporating a Pitzer ion interaction model to calculate the ionic activity. In the present paper, the model and two test cases of the model are briefly introduced. We also simulate a laboratory column experiment in which the leakage of highly alkaline waste fluid stored at Hanford (a U.S. Department of Energy site, located in Washington State) was studied. Our simulation captures the measured pH evolution and indicates that all the reactions controlling the pH evolution, including cation exchanges and mineral dissolution/precipitation, are coupled.

  11. Absence of finite-temperature ballistic charge (and spin) transport in the 1D Hubbard model at half filling (and zero spin density)

    NASA Astrophysics Data System (ADS)

    Carmelo, J. M. P.; Gu, Shi-Jian; Sampaio, M. J.

    2014-06-01

    Finite-temperature T > 0 transport properties of integrable and nonintegrable one-dimensional (1D) many-particle quantum systems are rather different, showing ballistic and diffusive behavior, respectively. The repulsive 1D Hubbard model is a prominent example of an integrable correlated system. For electronic densities n ≠ 1 (and spin densities m ≠ 0) it is an ideal charge (and spin) conductor, with ballistic charge (and spin) transport for T ⩾ 0. In spite of the fact that it is solvable by the Bethe ansatz, at n = 1 (and m = 0) its T > 0 charge (and spin) transport properties are an issue that remains poorly understood. Here we combine this solution with symmetry and the explicit calculation of current-operator matrix elements between energy eigenstates to show that for on-site repulsion U > 0 and at n = 1 the charge stiffness Dη(T) vanishes for T > 0 in the thermodynamic limit. A similar behavior is found by such methods for the spin stiffness Ds(T) for U > 0 and T > 0, which vanishes at m = 0. This absence of finite temperature n = 1 ballistic charge transport and m = 0 ballistic spin transport are exact results that clarify long-standing open problems.

  12. Reactive transport modelling of biogeochemical processes and carbon isotope geochemistry inside a landfill leachate plume

    NASA Astrophysics Data System (ADS)

    van Breukelen, Boris M.; Griffioen, Jasper; Röling, Wilfred F. M.; van Verseveld, Henk W.

    2004-06-01

    The biogeochemical processes governing leachate attenuation inside a landfill leachate plume (Banisveld, the Netherlands) were revealed and quantified using the 1D reactive transport model PHREEQC-2. Biodegradation of dissolved organic carbon (DOC) was simulated assuming first-order oxidation of two DOC fractions with different reactivity, and was coupled to reductive dissolution of iron oxide. The following secondary geochemical processes were required in the model to match observations: kinetic precipitation of calcite and siderite, cation exchange, proton buffering and degassing. Rate constants for DOC oxidation and carbonate mineral precipitation were determined, and other model parameters were optimized using the nonlinear optimization program PEST by means of matching hydrochemical observations closely (pH, DIC, DOC, Na, K, Ca, Mg, NH 4, Fe(II), SO 4, Cl, CH 4, saturation index of calcite and siderite). The modelling demonstrated the relevance and impact of various secondary geochemical processes on leachate plume evolution. Concomitant precipitation of siderite masked the act of iron reduction. Cation exchange resulted in release of Fe(II) from the pristine anaerobic aquifer to the leachate. Degassing, triggered by elevated CO 2 pressures caused by carbonate precipitation and proton buffering at the front of the plume, explained the observed downstream decrease in methane concentration. Simulation of the carbon isotope geochemistry independently supported the proposed reaction network.

  13. Reactive transport modelling of biogeochemical processes and carbon isotope geochemistry inside a landfill leachate plume.

    PubMed

    van Breukelen, Boris M; Griffioen, Jasper; Röling, Wilfred F M; van Verseveld, Henk W

    2004-06-01

    The biogeochemical processes governing leachate attenuation inside a landfill leachate plume (Banisveld, the Netherlands) were revealed and quantified using the 1D reactive transport model PHREEQC-2. Biodegradation of dissolved organic carbon (DOC) was simulated assuming first-order oxidation of two DOC fractions with different reactivity, and was coupled to reductive dissolution of iron oxide. The following secondary geochemical processes were required in the model to match observations: kinetic precipitation of calcite and siderite, cation exchange, proton buffering and degassing. Rate constants for DOC oxidation and carbonate mineral precipitation were determined, and other model parameters were optimized using the nonlinear optimization program PEST by means of matching hydrochemical observations closely (pH, DIC, DOC, Na, K, Ca, Mg, NH4, Fe(II), SO4, Cl, CH4, saturation index of calcite and siderite). The modelling demonstrated the relevance and impact of various secondary geochemical processes on leachate plume evolution. Concomitant precipitation of siderite masked the act of iron reduction. Cation exchange resulted in release of Fe(II) from the pristine anaerobic aquifer to the leachate. Degassing, triggered by elevated CO2 pressures caused by carbonate precipitation and proton buffering at the front of the plume, explained the observed downstream decrease in methane concentration. Simulation of the carbon isotope geochemistry independently supported the proposed reaction network. PMID:15134877

  14. Modeling bimolecular irreversible reactive transport in porous media

    NASA Astrophysics Data System (ADS)

    Guadagnini, A.; Sanchez-Vila, X.; Fernandez-Garcia, D.

    2010-12-01

    We studied an irreversible bi-molecular reactive transport experiment performed by Gramling et al. [2002]. In this experiment, colorimetric reactions between CuSO4 and EDTA4- were measured in a laboratory column filled with cryolite. After pre-saturating the system with EDTA4- (denoted as species B), CuSO4 (denoted as A) was injected as a step input. Mixing of the injected species and the reaction region where the product CuEDTA4- (denoted as C) formed were measured and concentration profiles of species A, B, and C were offered at four observation times. The concentration of total product generated was measured as a function of displaced pore volumes. The authors then found that their observations could not be properly interpreted with an advection dispersion reaction equation (ADRE) assuming that the reaction was instantaneous, the actual measured total reaction rate being lower than predictions for all times. Data have been recently well reproduced by Edery et al. [2009, 2010] by means of a particle tracking approach in a Continuous Time Random Walk framework. These and other authors have questioned the use of partial differential equation (PDE) approaches to quantify reactive transport, because of the difficulty in capturing local scale mixing and reaction. Here, we interpret these experiments by means of a continuum-scale model based on the ADRE. Our modeling approach is based on the idea that micro-scale heterogeneity of the pore space causes the reactive solutes to experience differential diffusion. The latter develops on different time scales so that reactants cannot interact instantaneously and are controlled by mass transfer between regions associated with different pore velocities. We assume that the effects of incomplete mixing at the pore-scale can be embedded in a first-order kinetic reaction term and show that this model allows quantitative interpretation of the experiments in terms of both reaction product profiles and time-dependent global

  15. Multiple mobility edges in a 1D Aubry chain with Hubbard interaction in presence of electric field: Controlled electron transport

    NASA Astrophysics Data System (ADS)

    Saha, Srilekha; Maiti, Santanu K.; Karmakar, S. N.

    2016-09-01

    Electronic behavior of a 1D Aubry chain with Hubbard interaction is critically analyzed in presence of electric field. Multiple energy bands are generated as a result of Hubbard correlation and Aubry potential, and, within these bands localized states are developed under the application of electric field. Within a tight-binding framework we compute electronic transmission probability and average density of states using Green's function approach where the interaction parameter is treated under Hartree-Fock mean field scheme. From our analysis we find that selective transmission can be obtained by tuning injecting electron energy, and thus, the present model can be utilized as a controlled switching device.

  16. Modeling Biodegradation and Reactive Transport: Analytical and Numerical Models

    SciTech Connect

    Sun, Y; Glascoe, L

    2005-06-09

    The computational modeling of the biodegradation of contaminated groundwater systems accounting for biochemical reactions coupled to contaminant transport is a valuable tool for both the field engineer/planner with limited computational resources and the expert computational researcher less constrained by time and computer power. There exists several analytical and numerical computer models that have been and are being developed to cover the practical needs put forth by users to fulfill this spectrum of computational demands. Generally, analytical models provide rapid and convenient screening tools running on very limited computational power, while numerical models can provide more detailed information with consequent requirements of greater computational time and effort. While these analytical and numerical computer models can provide accurate and adequate information to produce defensible remediation strategies, decisions based on inadequate modeling output or on over-analysis can have costly and risky consequences. In this chapter we consider both analytical and numerical modeling approaches to biodegradation and reactive transport. Both approaches are discussed and analyzed in terms of achieving bioremediation goals, recognizing that there is always a tradeoff between computational cost and the resolution of simulated systems.

  17. Radial reactive solute transport in an aquifer-aquitard system

    NASA Astrophysics Data System (ADS)

    Wang, Quanrong; Zhan, Hongbin

    2013-11-01

    Radial reactive transport is investigated in an aquifer-aquitard system considering the important processes such as advection, radial and vertical dispersions for the aquifer, vertical advection and dispersion for the aquitards, and first-order biodegradation or radioactive decay. We solved the coupled governing equations of transport in the aquifer and the aquitards by honoring the continuity of concentration and mass flux across the aquifer-aquitard interfaces and recognizing the concentration variation along the aquifer thickness. This effort improved the averaged-approximation (AA) model, which dealt with radial dispersion in an aquifer-aquitard system by excluding the aquitard advection. To compare with our new solution, we expanded the AA model by including the aquitard advection. The expanded AA model considerably overestimated the mass in the upper aquitard when an upward advection existed there. The rates of mass change in the upper aquitard from the new solution and the AA model solution increased with time following sub-linear fashions. The times corresponding to the peak values of the residence time distributions for the AA model, the expanded AA model, and the new model were almost the same. The residence time distributions seemed to follow the Maxwell-Boltzmann distribution closely when plotting the time in logarithmic scale. In addition, we developed a finite-element COMSOL Multiphysics simulation of the problem, and found that the COMSOL solution agreed with the new solution well.

  18. Simulation of reactive processes related to biodegradation in aquifers. 1. Structure of the three-dimensional reactive transport model

    NASA Astrophysics Data System (ADS)

    Schäfer, Dirk; Schäfer, Wolfgang; Kinzelbach, Wolfgang

    1998-05-01

    The reactive transport model TBC (transport, biochemistry, and chemistry) numerically solves the equations for reactive transport in three-dimensional saturated groundwater flow. A finite element approximation and a standard Galerkin method are used. Solute transport is coupled to microbially mediated organic carbon degradation. Microbial growth is assumed to follow Monod-type kinetics. Substrate consumption and release of metabolic products is coupled to microbial growth via yield coefficients and stoichiometric relations. Additionally, the effects of microbial activity on selected inorganic chemical species in the aquifer can be considered. TBC allows the user to specify a wide range of possible biochemical and chemical reactions in the input file. This makes TBC a powerful and flexible simulation tool. It was developed to simulate reactive processes related to in situ bioremediation, but further fields of application are laboratory column studies on redox processes coupled to organic carbon degradation, field cases of intrinsic biodegradation, and early diagenetic processes in sediments.

  19. Imaging geochemical heterogeneities using inverse reactive transport modeling: An example relevant for characterizing arsenic mobilization and distribution

    NASA Astrophysics Data System (ADS)

    Fakhreddine, Sarah; Lee, Jonghyun; Kitanidis, Peter K.; Fendorf, Scott; Rolle, Massimo

    2016-02-01

    The spatial distribution of reactive minerals in the subsurface is often a primary factor controlling the fate and transport of contaminants in groundwater systems. However, direct measurement and estimation of heterogeneously distributed minerals are often costly and difficult to obtain. While previous studies have shown the utility of using hydrologic measurements combined with inverse modeling techniques for tomography of physical properties including hydraulic conductivity, these methods have seldom been used to image reactive geochemical heterogeneities. In this study, we focus on As-bearing reactive minerals as aquifer contaminants. We use synthetic applications to demonstrate the ability of inverse modeling techniques combined with mechanistic reactive transport models to image reactive mineral lenses in the subsurface and quantify estimation error using indirect, commonly measured groundwater parameters. Specifically, we simulate the mobilization of arsenic via kinetic oxidative dissolution of As-bearing pyrite due to dissolved oxygen in the ambient groundwater, which is an important mechanism for arsenic release in groundwater both under natural conditions and engineering applications such as managed aquifer recharge and recovery operations. The modeling investigation is carried out at various scales and considers different flow-through domains including (i) a 1D lab-scale column (80 cm), (ii) a 2D lab-scale setup (60 cm × 30 cm) and (iii) a 2D field-scale domain (20 m × 4 m). In these setups, synthetic dissolved oxygen data and forward reactive transport simulations are used to image the spatial distribution of As-bearing pyrite using the Principal Component Geostatistical Approach (PCGA) for inverse modeling.

  20. Filtered density function approach for reactive transport in groundwater

    NASA Astrophysics Data System (ADS)

    Suciu, Nicolae; Schüler, Lennart; Attinger, Sabine; Knabner, Peter

    2016-04-01

    Spatial filtering may be used in coarse-grained simulations (CGS) of reactive transport in groundwater, similar to the large eddy simulations (LES) in turbulence. The filtered density function (FDF), stochastically equivalent to a probability density function (PDF), provides a statistical description of the sub-grid, unresolved, variability of the concentration field. Besides closing the chemical source terms in the transport equation for the mean concentration, like in LES-FDF methods, the CGS-FDF approach aims at quantifying the uncertainty over the whole hierarchy of heterogeneity scales exhibited by natural porous media. Practically, that means estimating concentration PDFs on coarse grids, at affordable computational costs. To cope with the high dimensionality of the problem in case of multi-component reactive transport and to reduce the numerical diffusion, FDF equations are solved by particle methods. But, while trajectories of computational particles are modeled as stochastic processes indexed by time, the concentration's heterogeneity is modeled as a random field, with multi-dimensional, spatio-temporal sets of indices. To overcome this conceptual inconsistency, we consider FDFs/PDFs of random species concentrations weighted by conserved scalars and we show that their evolution equations can be formulated as Fokker-Planck equations describing stochastically equivalent processes in concentration-position spaces. Numerical solutions can then be approximated by the density in the concentration-position space of an ensemble of computational particles governed by the associated Itô equations. Instead of sequential particle methods we use a global random walk (GRW) algorithm, which is stable, free of numerical diffusion, and practically insensitive to the increase of the number of particles. We illustrate the general FDF approach and the GRW numerical solution for a reduced complexity problem consisting of the transport of a single scalar in groundwater

  1. Status of the solar and infrared radiation submodels in the LLNL 1-D and 2-D chemical-transport models

    SciTech Connect

    Grant, K.E.; Taylor, K.E.; Ellis, J.S.; Wuebbles, D.J.

    1987-07-01

    The authors have implemented a series of state of the art radiation transport submodels in previously developed one dimensional and two dimensional chemical transport models of the troposphere and stratosphere. These submodels provide the capability of calculating accurate solar and infrared heating rates. They are a firm basis for further radiation submodel development as well as for studying interactions between radiation and model dynamics under varying conditions of clear sky, clouds, and aerosols. 37 refs., 3 figs.

  2. PFLOTRAN: Recent Developments Facilitating Massively-Parallel Reactive Biogeochemical Transport

    NASA Astrophysics Data System (ADS)

    Hammond, G. E.

    2015-12-01

    With the recent shift towards modeling carbon and nitrogen cycling in support of climate-related initiatives, emphasis has been placed on incorporating increasingly mechanistic biogeochemistry within Earth system models to more accurately predict the response of terrestrial processes to natural and anthropogenic climate cycles. PFLOTRAN is an open-source subsurface code that is specialized for simulating multiphase flow and multicomponent biogeochemical transport on supercomputers. The object-oriented code was designed with modularity in mind and has been coupled with several third-party simulators (e.g. CLM to simulate land surface processes and E4D for coupled hydrogeophysical inversion). Central to PFLOTRAN's capabilities is its ability to simulate tightly-coupled reactive transport processes. This presentation focuses on recent enhancements to the code that enable the solution of large parameterized biogeochemical reaction networks with numerous chemical species. PFLOTRAN's "reaction sandbox" is described, which facilitates the implementation of user-defined reaction networks without the need for a comprehensive understanding of PFLOTRAN software infrastructure. The reaction sandbox is written in modern Fortran (2003-2008) and leverages encapsulation, inheritance, and polymorphism to provide the researcher with a flexible workspace for prototyping reactions within a massively parallel flow and transport simulation framework. As these prototypical reactions mature into well-accepted implementations, they can be incorporated into PFLOTRAN as native biogeochemistry capability. Users of the reaction sandbox are encouraged to upload their source code to PFLOTRAN's main source code repository, including the addition of simple regression tests to better ensure the long-term code compatibility and validity of simulation results.

  3. Modeling reactive transport with particle tracking and kernel estimators

    NASA Astrophysics Data System (ADS)

    Rahbaralam, Maryam; Fernandez-Garcia, Daniel; Sanchez-Vila, Xavier

    2015-04-01

    Groundwater reactive transport models are useful to assess and quantify the fate and transport of contaminants in subsurface media and are an essential tool for the analysis of coupled physical, chemical, and biological processes in Earth Systems. Particle Tracking Method (PTM) provides a computationally efficient and adaptable approach to solve the solute transport partial differential equation. On a molecular level, chemical reactions are the result of collisions, combinations, and/or decay of different species. For a well-mixed system, the chem- ical reactions are controlled by the classical thermodynamic rate coefficient. Each of these actions occurs with some probability that is a function of solute concentrations. PTM is based on considering that each particle actually represents a group of molecules. To properly simulate this system, an infinite number of particles is required, which is computationally unfeasible. On the other hand, a finite number of particles lead to a poor-mixed system which is limited by diffusion. Recent works have used this effect to actually model incomplete mix- ing in naturally occurring porous media. In this work, we demonstrate that this effect in most cases should be attributed to a defficient estimation of the concentrations and not to the occurrence of true incomplete mixing processes in porous media. To illustrate this, we show that a Kernel Density Estimation (KDE) of the concentrations can approach the well-mixed solution with a limited number of particles. KDEs provide weighting functions of each particle mass that expands its region of influence, hence providing a wider region for chemical reactions with time. Simulation results show that KDEs are powerful tools to improve state-of-the-art simulations of chemical reactions and indicates that incomplete mixing in diluted systems should be modeled based on alternative conceptual models and not on a limited number of particles.

  4. Modelling of reactive fluid transport in deformable porous rocks

    NASA Astrophysics Data System (ADS)

    Yarushina, V. M.; Podladchikov, Y. Y.

    2009-04-01

    One outstanding challenge in geology today is the formulation of an understanding of the interaction between rocks and fluids. Advances in such knowledge are important for a broad range of geologic settings including partial melting and subsequent migration and emplacement of a melt into upper levels of the crust, or fluid flow during regional metamorphism and metasomatism. Rock-fluid interaction involves heat and mass transfer, deformation, hydrodynamic flow, and chemical reactions, thereby necessitating its consideration as a complex process coupling several simultaneous mechanisms. Deformation, chemical reactions, and fluid flow are coupled processes. Each affects the others. Special effort is required for accurate modelling of the porosity field through time. Mechanical compaction of porous rocks is usually treated under isothermal or isoentropic simplifying assumptions. However, joint consideration of both mechanical compaction and reactive porosity alteration requires somewhat greater than usual care about thermodynamic consistency. Here we consider the modelling of multi-component, multi-phase systems, which is fundamental to the study of fluid-rock interaction. Based on the conservation laws for mass, momentum, and energy in the form adopted in the theory of mixtures, we derive a thermodynamically admissible closed system of equations describing the coupling of heat and mass transfer, chemical reactions, and fluid flow in a deformable solid matrix. Geological environments where reactive transport is important are located at different depths and accordingly have different rheologies. In the near surface, elastic or elastoplastic properties would dominate, whereas viscoplasticity would have a profound effect deeper in the lithosphere. Poorly understood rheologies of heterogeneous porous rocks are derived from well understood processes (i.e., elasticity, viscosity, plastic flow, fracturing, and their combinations) on the microscale by considering a

  5. Multicomponent reactive transport modeling of uranium bioremediation field experiments

    SciTech Connect

    Fang, Yilin; Yabusaki, Steven B.; Morrison, Stan J.; Amonette, James E.; Long, Philip E.

    2009-10-15

    Biostimulation field experiments with acetate amendment are being performed at a former uranium mill tailings site in Rifle, Colorado, to investigate subsurface processes controlling in situ bioremediation of uranium-contaminated groundwater. An important part of the research is identifying and quantifying field-scale models of the principal terminal electron-accepting processes (TEAPs) during biostimulation and the consequent biogeochemical impacts to the subsurface receiving environment. Integrating abiotic chemistry with the microbially mediated TEAPs in the reaction network brings into play geochemical observations (e.g., pH, alkalinity, redox potential, major ions, and secondary minerals) that the reactive transport model must recognize. These additional constraints provide for a more systematic and mechanistic interpretation of the field behaviors during biostimulation. The reaction network specification developed for the 2002 biostimulation field experiment was successfully applied without additional calibration to the 2003 and 2007 field experiments. The robustness of the model specification is significant in that 1) the 2003 biostimulation field experiment was performed with 3 times higher acetate concentrations than the previous biostimulation in the same field plot (i.e., the 2002 experiment), and 2) the 2007 field experiment was performed in a new unperturbed plot on the same site. The biogeochemical reactive transport simulations accounted for four TEAPs, two distinct functional microbial populations, two pools of bioavailable Fe(III) minerals (iron oxides and phyllosilicate iron), uranium aqueous and surface complexation, mineral precipitation, and dissolution. The conceptual model for bioavailable iron reflects recent laboratory studies with sediments from the Old Rifle Uranium Mill Tailings Remedial Action (UMTRA) site that demonstrated that the bulk (~90%) of Fe(III) bioreduction is associated with the phyllosilicates rather than the iron oxides

  6. Advanced Nodal P3/SP3 Axial Transport Solvers for the MPACT 2D/1D Scheme

    SciTech Connect

    Stimpson, Shane G; Collins, Benjamin S

    2015-01-01

    As part of its initiative to provide multiphysics simulations of nuclear reactor cores, the Consortium for Advanced Simulation of Light Water Reactors (CASL) is developing the Virtual Environment for Reactor Applications Core Simulator (VERA-CS). The MPACT code, which is the primary neutron transport solver of VERA-CS, employs the two-dimensional/one-dimensional (2D/1D) method to solve 3-dimensional neutron transport problems and provide sub-pin-level resolution of the power distribution. While 2D method of characteristics is used to solve for the transport effects within each plane, 1D-nodal methods are used axially. There have been extensive studies of the 2D/1D method with a variety nodal methods, and the P3/SP3 solver has proved to be an effective method of providing higher-fidelity solutions while maintaining a low computational burden.The current implementation in MPACT wraps a one-node nodal expansion method (NEM) kernel for each moment, iterating between them and performing multiple sweeps to resolve flux distributions. However, it has been observed that this approach is more sensitive to convergence problems. This paper documents the theory and application two new nodal P3/SP3 approaches to be used within the 2D/1D method in MPACT. These two approaches aim to provide enhanced stability compared with the pre-existing one-node approach. Results from the HY-NEM-SP3 solver show that the accuracy is consistent with the one-node formulations and provides improved convergence for some problems; but the solver has issues with cases in thin planes. Although the 2N-SENM-SP3 solver is still under development, it is intended to resolve the issues with HY-NEM-SP3 but it will incur some additional computational burden by necessitating an additional 1D-CMFD-P3 solver to generate the second moment cell-averaged scalar flux.

  7. Coupling WEPP and 3ST1D models for improved prediction of flow and sediment transport at watershed scales

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Watershed modeling is a key component of watershed management that involves the simulation of hydrological and fluvial processes for predicting flow and sediment transport within a watershed. For practical purposes, most numerical models have been developed to simulate either runoff and soil erosion...

  8. Reactive Transport Modeling of Acid Gas Generation and Condensation

    SciTech Connect

    G. Zhahg; N. Spycher; E. Sonnenthal; C. Steefel

    2005-01-25

    Pulvirenti et al. (2004) recently conducted a laboratory evaporation/condensation experiment on a synthetic solution of primarily calcium chloride. This solution represents one potential type of evaporated pore water at Yucca Mountain, Nevada, a site proposed for geologic storage of high-level nuclear waste. These authors reported that boiling this solution to near dryness (a concentration factor >75,000 relative to actual pore waters) leads to the generation of acid condensate (pH 4.5) presumably due to volatilization of HCl (and minor HF and/or HNO{sub 3}). To investigate the various processes taking place, including boiling, gas transport, and condensation, their experiment was simulated by modifying an existing multicomponent and multiphase reactive transport code (TOUGHREACT). This code was extended with a Pitzer ion-interaction model to deal with high ionic strength. The model of the experiment was set-up to capture the observed increase in boiling temperature (143 C at {approx}1 bar) resulting from high concentrations of dissolved salts (up to 8 m CaCl{sub 2}). The computed HCI fugacity ({approx} 10{sup -4} bars) generated by boiling under these conditions is not sufficient to lower the pH of the condensate (cooled to 80 and 25 C) down to observed values unless the H{sub 2}O mass fraction in gas is reduced below {approx}10%. This is because the condensate becomes progressively diluted by H{sub 2}O gas condensation. However, when the system is modeled to remove water vapor, the computed pH of instantaneous condensates decreases to {approx}1.7, consistent with the experiment (Figure 1). The results also show that the HCl fugacity increases, and calcite, gypsum, sylvite, halite, MgCl{sub 2}4H{sub 2}O and CaCl{sub 2} precipitate sequentially with increasing concentration factors.

  9. Reactive Nitrogen Compounds in the Troposphere: Observations, Transport, and Photochemistry

    NASA Astrophysics Data System (ADS)

    Luke, Winston Thomas

    Oxides of nitrogen critically control the photochemical production of ozone and account for approximately 1/3 of the total acid deposition in North America. This dissertation presents the results of three studies designed to enhance our knowledge of the distribution, transport, and photochemistry of reactive (or odd) nitrogen compounds in the troposphere. Concentrations of odd nitrogen were measured in both urban and rural air advected from the polluted east coast of North America to the western Atlantic ocean as part of the 1986 Western ATlantic Ocean eXperiment. On January 9, 1986, median (NOy) rose from 0.28 ppbv in the free troposphere (FT) to 1.38 ppbv in the marine boundary layer (MBL), and ratios of peroxyacetyl nitrate (PAN) to NOy were similar to those observed at a non-urban site in Colorado during autumn. The maximum gross flux of nitrogen through the FT and MBL between 31.5-44.1^ circN was estimated to be 25.6 kg N s ^{-1}. Reactive nitrogen compounds, carbon monoxide, and ozone were measured over the central United States in 1985 and 1986 from a twin-jet aircraft. Vertical profiles of reactive nitrogen compounds show dramatic perturbations due to the effects of violent convective activity. Measurements made in stable air dominated by high pressure contrast with those made near organized, isolated convective cells, which efficiently transport odd nitrogen to the upper troposphere. The layered lifting associated with episodes of cold frontal passage efficiently mixes both the upper and middle troposphere, however. Rapid injection of boundary layer air into the upper troposphere, where colder temperatures and higher wind velocities combine to extend both the lifetimes and range of influence of a variety of primary and secondary pollutants, will increase the rate of photochemical ozone production aloft and may thus exacerbate the greenhouse effect. Finally, the photolysis rate coefficients (j) of several alkyl nitrates (RONO_2) to NO_2 and the alkoxy

  10. On the behavior of approaches to simulate reactive transport.

    PubMed

    Saaltink, M W; Carrera, J; Ayora, C

    2001-04-01

    Two families of approaches exist to simulate reactive transport in groundwater: The Direct Substitution Approach (DSA), based on Newton-Raphson and the Picard or Sequential Iteration Approach (SIA). We applied basic versions of both methods to several test cases and compared both computational demands and quality of the solution for varying grid size. Results showed that the behavior of the two approaches is sensitive to both grid size and chemistry. As a general rule, the DSA is more robust than the SIA, in the sense that its convergence is less sensitive to time step size (any approach will converge given a sufficiently small time step). Moreover, the DSA leads to a better simulation of sharp fronts, which can only be reproduced with fine grids after many iterations when the SIA is used. As a consequence, the DSA runs faster than SIA in chemically difficult cases (i.e., highly non-linear and/or very retarded), because the SIA may require very small time steps to converge. On the other hand, the size of the system of equations is much larger for the DSA than for the SIA, so that its CPU time and memory requirements tend to be less favorable with increasing grid size. As a result, the SIA may become faster than the DSA for very large, chemically simple problems. The use of an iterative linear solver for the DSA makes its CPU time less sensitive to grid size. PMID:11285932

  11. Heptanoate as a neural fuel: energetic and neurotransmitter precursors in normal and glucose transporter I-deficient (G1D) brain

    PubMed Central

    Marin-Valencia, Isaac; Good, Levi B; Ma, Qian; Malloy, Craig R; Pascual, Juan M

    2013-01-01

    It has been postulated that triheptanoin can ameliorate seizures by supplying the tricarboxylic acid cycle with both acetyl-CoA for energy production and propionyl-CoA to replenish cycle intermediates. These potential effects may also be important in other disorders associated with impaired glucose metabolism because glucose supplies, in addition to acetyl-CoA, pyruvate, which fulfills biosynthetic demands via carboxylation. In patients with glucose transporter type I deficiency (G1D), ketogenic diet fat (a source only of acetyl-CoA) reduces seizures, but other symptoms persist, providing the motivation for studying heptanoate metabolism. In this work, metabolism of infused [5,6,7-13C3]heptanoate was examined in the normal mouse brain and in G1D by 13C-nuclear magnetic resonance spectroscopy, gas chromatography-mass spectrometry (GC-MS), and liquid chromatography-mass spectrometry (LC-MS). In both groups, plasma glucose was enriched in 13C, confirming gluconeogenesis from heptanoate. Acetyl-CoA and glutamine levels became significantly higher in the brain of G1D mice relative to normal mice. In addition, brain glutamine concentration and 13C enrichment were also greater when compared with glutamate in both animal groups, suggesting that heptanoate and/or C5 ketones are primarily metabolized by glia. These results enlighten the mechanism of heptanoate metabolism in the normal and glucose-deficient brain and encourage further studies to elucidate its potential antiepileptic effects in disorders of energy metabolism. PMID:23072752

  12. Heptanoate as a neural fuel: energetic and neurotransmitter precursors in normal and glucose transporter I-deficient (G1D) brain.

    PubMed

    Marin-Valencia, Isaac; Good, Levi B; Ma, Qian; Malloy, Craig R; Pascual, Juan M

    2013-02-01

    It has been postulated that triheptanoin can ameliorate seizures by supplying the tricarboxylic acid cycle with both acetyl-CoA for energy production and propionyl-CoA to replenish cycle intermediates. These potential effects may also be important in other disorders associated with impaired glucose metabolism because glucose supplies, in addition to acetyl-CoA, pyruvate, which fulfills biosynthetic demands via carboxylation. In patients with glucose transporter type I deficiency (G1D), ketogenic diet fat (a source only of acetyl-CoA) reduces seizures, but other symptoms persist, providing the motivation for studying heptanoate metabolism. In this work, metabolism of infused [5,6,7-(13)C(3)]heptanoate was examined in the normal mouse brain and in G1D by (13)C-nuclear magnetic resonance spectroscopy, gas chromatography-mass spectrometry (GC-MS), and liquid chromatography-mass spectrometry (LC-MS). In both groups, plasma glucose was enriched in (13)C, confirming gluconeogenesis from heptanoate. Acetyl-CoA and glutamine levels became significantly higher in the brain of G1D mice relative to normal mice. In addition, brain glutamine concentration and (13)C enrichment were also greater when compared with glutamate in both animal groups, suggesting that heptanoate and/or C5 ketones are primarily metabolized by glia. These results enlighten the mechanism of heptanoate metabolism in the normal and glucose-deficient brain and encourage further studies to elucidate its potential antiepileptic effects in disorders of energy metabolism. PMID:23072752

  13. CSDUST3 - A radiation transport code for a dusty medium with 1-D planar, spherical or cylindrical geometry

    NASA Technical Reports Server (NTRS)

    Egan, Michael P.; Leung, Chun Ming; Spagna, George F., Jr.

    1988-01-01

    The program solves the radiation transport problem in a dusty medium with one-dimensional planar, spherical or cylindrical geometry. It determines self-consistently the effects of multiple scattering, absorption, and re-emission of photons on the temperature of dust grains and the characteristics of the internal radiation field. The program can treat radiation field anisotropy, linear anisotropic scattering, and multi-grain components. The program output consists of the dust-temperature distribution, flux spectrum, surface brightness at each frequency and the observed intensities (involving a convolution with a telescope beam pattern).

  14. Modeling seawater intrusion and the associated reactive solute transport in fractured coastal aquifers

    NASA Astrophysics Data System (ADS)

    Nick, Hamid M.; Regnier, Pierre; Thullner, Martin

    2013-04-01

    In coastal aquifers seawater and terrestrial water get into contact and the reactive mixing between these water bodies controls the water quality of submarine groundwater discharge. The rates of such mixing controlled reactions are depending not only on the properties of the reactive species but also on the density driven flow dynamics and the resulting transport patterns. A prediction of these flow and transport processes and thus of the fate of reactive species is specifically challenged in fracture aquifers as it depends on the focusing of the flow and the local balance of viscous and gravitational forces. To study the influence of fractures on mixing and reactive transport in coastal aquifers we present a reactive discrete fracture and matrix (DFM) model using unstructured spatially adaptively refined finite-element meshes. This model is developed by coupling the Complex System Modelling Platform (CSMP++) utilizing a hybrid FEFV scheme, and a Biogeochemical Reaction Network Simulator (BRNS) capable of solving for kinetically and thermodynamically constrained biogeochemical reactions [1]. The model is applied to simulate the reactive transport in fracture networks embedded in a permeable rock matrix. For virtual coastal aquifers, different fracture data sets are employed to study the effect of fractures and their characteristics on the reactive mixing between fresh water and seawater in coastal aquifers. Obtained results show that the presence of fractures enhances reactive mixing for most cases due to the combined effect of fracture induced flow channeling and dispersion. The magnitude of this effect depends highly on fracture density, spacing and orientation. Furthermore the results indicate that reactive mixing in fractured aquifers is not well described using an effective parameterization of a homogeneous aquifer setup. This suggests that structural information on the fracture network is needed for a sufficient description of reactive transport processes in

  15. Alternate closures for radiation transport using Legendre polynomials in 1D and spherical harmonics in 2D

    NASA Astrophysics Data System (ADS)

    Olson, Gordon L.

    2012-04-01

    When using polynomial expansions for the angular variables in the radiation transport equation, the usual procedure is to truncate the series by setting all higher order terms to zero. At low order, such simple closures may not give the optimum solution. This work tests alternate closures that scale either the time- or spatial-derivatives in the highest order equation. These scale factors can be chosen such that waves propagate at exactly the speed of light in optically thin media. Alternatively, they may be chosen to significantly improve the accuracy of low-order solutions with no additional computational cost. The same scaling procedure and scale factors work in one- and multi-dimensions. In multidimensions, reducing the order of a solution can save significant amounts of computer time.

  16. Reactive Transport Modeling of Induced Calcite Precipitation Reaction Fronts in Porous Media Using A Parallel, Fully Coupled, Fully Implicit Approach

    NASA Astrophysics Data System (ADS)

    Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.

    2010-12-01

    Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs

  17. Transport of Energetic Electrons Produced from Two-Plasmon Decay in the 1-D Hydrodynamic Code LILAC

    NASA Astrophysics Data System (ADS)

    Delettrez, J. A.; Goncharov, V. N.; Radha, P. B.; Stoeckl, C.; Maximov, A. V.; Sangster, T. C.; Frenje, J. A.; Shvarts, D.

    2007-11-01

    The effect of two-plasmon-decay electrons on the implosion of cryogenic targets has been the subject of intense scrutiny at the Laboratory for Laser Energetics. Preheat of the fuel caused by these electrons can reduce the maximum areal density attainable at stagnation. The electrons are created at the quarter-critical surface when a threshold depending on laser intensity and local thermal electron scale length is attained. The fraction of laser energy absorbed is a parameter that depends exponentially on the threshold condition and saturates at laser intensities of 10^15 W/cm^2. The source distribution is Maxwellian with a temperature scaling inferred from the measurement of hard x rays. The electrons are transported with a multigroup diffusion model in which the free-streaming electrons are treated by a modified P2 model. Simulation results from warm plastic and cryogenic implosions are compared with the following experimental diagnostics: the hard-x-ray temporal and time-integrated emission, the fast-ion spectrum, and the neutron-averaged areal density at stagnation. This work was supported by the U.S. Department of Energy Office of Inertial Confinement Fusion under Cooperative Agreement DE-FC52-92SF19460.

  18. Transport of Energetic Electrons Produced from Two-Plasmon Decay in the 1-D Hydrodynamic Code LILAC

    NASA Astrophysics Data System (ADS)

    Delettrez, J. A.; Gocharov, V. N.; Radha, P. B.; Stoeckl, C.; Maximov, A. V.; Sangster, T. C.; Frenje, J. A.; Shvarts, D.

    2008-11-01

    The effect of two-plasmon-decay electrons on direct-drive cryogenic implosions on the OMEGA laser is modeled. The electrons are created at the quarter-critical surface when a threshold depending on laser intensity and local thermal-electron conditions is attained. The fraction of the absorbed laser energy is a parameter that depends exponentially on the threshold condition and saturates at laser intensities of 10^15 W/cm^2. The source distribution is a Maxwellian with a temperature scaling inferred from hard x-ray measurements. The electrons are transported with a multi-group diffusion model for the low energy electrons and a straight-line model for the high-energy electrons. Simulation results from warm plastic and cryogenic implosions are compared with the following diagnostics: the hard x-ray emission, the fast-ion spectrum, and the neutron-averaged areal density at stagnation. This work was supported by the U.S. Department of Energy Office of Inertial Confinement Fusion under Cooperative Agreement No. DE-FC52-08NA28302.

  19. Variably Saturated Flow and Multicomponent Biogeochemical Reactive Transport Modeling of a Uranium Bioremediation Field Experiment

    SciTech Connect

    Yabusaki, Steven B.; Fang, Yilin; Williams, Kenneth H.; Murray, Christopher J.; Ward, Anderson L.; Dayvault, Richard; Waichler, Scott R.; Newcomer, Darrell R.; Spane, Frank A.; Long, Philip E.

    2011-11-01

    Field experiments at a former uranium mill tailings site have identified the potential for stimulating indigenous bacteria to catalyze the conversion of aqueous uranium in the +6 oxidation state to immobile solid-associated uranium in the +4 oxidation state. This effectively removes uranium from solution resulting in groundwater concentrations below actionable standards. Three-dimensional, coupled variably-saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport rates and biogeochemical reaction rates that determine the location and magnitude of key reaction products. A comprehensive reaction network, developed largely through previous 1-D modeling studies, was used to simulate the impacts on uranium behavior of pulsed acetate amendment, seasonal water table variation, spatially-variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. A principal challenge is the mechanistic representation of biologically-mediated terminal electron acceptor process (TEAP) reactions whose products significantly alter geochemical controls on uranium mobility through increases in pH, alkalinity, exchangeable cations, and highly reactive reduction products. In general, these simulations of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado confirmed previously identified behaviors including (1) initial dominance by iron reducing bacteria that concomitantly reduce aqueous U(VI), (2) sulfate reducing bacteria that become dominant after {approx}30 days and outcompete iron reducers for the acetate electron donor, (3) continuing iron-reducer activity and U(VI) bioreduction during dominantly sulfate reducing conditions, and (4) lower apparent U(VI) removal from groundwater during dominantly sulfate reducing conditions. New knowledge on simultaneously active metal and sulfate reducers has been

  20. OS3D/GIMRT software for modeling multicomponent-multidimensional reactive transport

    SciTech Connect

    CI Steefel; SB Yabusaki

    2000-05-17

    OS3D/GIMRT is a numerical software package for simulating multicomponent reactive transport in porous media. The package consists of two principal components: (1) the code OS3D (Operator Splitting 3-Dimensional Reactive Transport) which simulates reactive transport by either splitting the reaction and transport steps in time, i.e., the classic time or operator splitting approach, or by iterating sequentially between reactions and transport, and (2) the code GIMRT (Global Implicit Multicomponent Reactive Transport) which treats up to two dimensional reactive transport with a one step or global implicit approach. Although the two codes do not yet have totally identical capabilities, they can be run from the same input file, allowing comparisons to be made between the two approaches in many cases. The advantages and disadvantages of the two approaches are discussed more fully below, but in general OS3D is designed for simulation of transient concentration fronts, particularly under high Peclet number transport conditions, because of its use of a total variation diminishing or TVD transport algorithm. GIMRT is suited for simulating water-rock alteration over long periods of time where the aqueous concentration field is at or close to a quasi-stationary state and the numerical transport errors are less important. Where water-rock interaction occurs over geological periods of time, GIMRT may be preferable to OS3D because of its ability to take larger time steps.

  1. Modification of the finite element heat and mass transfer code (FEHMN) to model multicomponent reactive transport

    SciTech Connect

    Viswanathan, H.S.

    1995-12-31

    The finite element code FEHMN is a three-dimensional finite element heat and mass transport simulator that can handle complex stratigraphy and nonlinear processes such as vadose zone flow, heat flow and solute transport. Scientists at LANL have been developed hydrologic flow and transport models of the Yucca Mountain site using FEHMN. Previous FEHMN simulations have used an equivalent K{sub d} model to model solute transport. In this thesis, FEHMN is modified making it possible to simulate the transport of a species with a rigorous chemical model. Including the rigorous chemical equations into FEHMN simulations should provide for more representative transport models for highly reactive chemical species. A fully kinetic formulation is chosen for the FEHMN reactive transport model. Several methods are available to computationally implement a fully kinetic formulation. Different numerical algorithms are investigated in order to optimize computational efficiency and memory requirements of the reactive transport model. The best algorithm of those investigated is then incorporated into FEHMN. The algorithm chosen requires for the user to place strongly coupled species into groups which are then solved for simultaneously using FEHMN. The complete reactive transport model is verified over a wide variety of problems and is shown to be working properly. The simulations demonstrate that gas flow and carbonate chemistry can significantly affect {sup 14}C transport at Yucca Mountain. The simulations also provide that the new capabilities of FEHMN can be used to refine and buttress already existing Yucca Mountain radionuclide transport studies.

  2. A non-negative moment-preserving spatial discretization scheme for the linearized Boltzmann transport equation in 1-D and 2-D Cartesian geometries

    NASA Astrophysics Data System (ADS)

    Maginot, Peter G.; Morel, Jim E.; Ragusa, Jean C.

    2012-08-01

    We present a new nonlinear spatial finite-element method for the linearized Boltzmann transport equation with Sn angular discretization in 1-D and 2-D Cartesian geometries. This method has two central characteristics. First, it is equivalent to the linear-discontinuous (LD) Galerkin method whenever that method yields a strictly non-negative solution. Second, it always satisfies both the zeroth and first spatial moment equations. Because it yields the LD solution when that solution is non-negative, one might interpret our method as a classical fix-up to the LD scheme. However, fix-up schemes for the LD equations derived in the past have given up solution of the first moment equations when the LD solution is negative in order to satisfy positivity in a simple manner. We present computational results comparing our method in 1-D to the strictly non-negative linear exponential-discontinuous method and to the LD method. We present computational results in 2-D comparing our method to a recently developed LD fix-up scheme and to the LD scheme. It is demonstrated that our method is a valuable alternative to existing methods.

  3. CALIBRATION OF SUBSURFACE BATCH AND REACTIVE-TRANSPORT MODELS INVOLVING COMPLEX BIOGEOCHEMICAL PROCESSES

    EPA Science Inventory

    In this study, the calibration of subsurface batch and reactive-transport models involving complex biogeochemical processes was systematically evaluated. Two hypothetical nitrate biodegradation scenarios were developed and simulated in numerical experiments to evaluate the perfor...

  4. SELECTION AND CALIBRATION OF SUBSURFACE REACTIVE TRANSPORT MODELS USING A SURROGATE-MODEL APPROACH

    EPA Science Inventory

    While standard techniques for uncertainty analysis have been successfully applied to groundwater flow models, extension to reactive transport is frustrated by numerous difficulties, including excessive computational burden and parameter non-uniqueness. This research introduces a...

  5. Influence of calcite on uranium(VI) reactive transport in the groundwater–river mixing zone

    SciTech Connect

    Ma, Rui; Liu, Chongxuan; Greskowiak, Janek; Prommer, Henning; Zachara, John M.; Zheng, Chunmiao

    2014-01-23

    Calcite is an important mineral that can affect uranyl reactive transport in subsurface sediments. This study investigated the distribution of calcite and its influence on uranyl adsorption and reactive transport in the groundwater-river mixing zone at US Hanford 300A, Washington State. Simulations using a 2D reactive transport model under field-relevant hydrogeochemical conditions revealed a complex distribution of calcite concentration as a result of dynamic groundwater-river interactions. The calcite concentration distribution in turn affected the spatial and temporal changes in aqueous carbonate, calcium, and pH, which subsequently influenced U(VI) mobility and discharge rates into the river. The results implied that calcite distribution and its concentration dynamics is an important consideration for field characterization, monitoring, and reactive transport prediction.

  6. Constraining chemical geothermometry with reactive transport models: An example study of the Dixie Valley geothermal area

    NASA Astrophysics Data System (ADS)

    Wanner, C.; Peiffer, L.; Spycher, N.; Sonnenthal, E. L.; Iovenitti, J. L.; Kennedy, B. M.

    2012-12-01

    In this study, 1D and 2D reactive transport simulations of the Dixie Valley geothermal area (Nevada, USA) were performed using Toughreact [1] to evaluate the fluid flow pathways and rates of equilibration of hydrothermal fluids. Modeling studies were combined with new multicomponent geothermometry, which is being used to estimate the temperature of geothermal reservoirs based on chemical analysis of geothermal springs. The concept is based on the assumption of chemical equilibrium between the thermal fluid and minerals of the reservoir rock [2]. If re-equilibration occurs between the reservoir at depth and the surface, then the 'deep' chemical signature of the fluid is lost and the obtained reservoir temperature is underestimated. The simulations were run for a vertical cross-section that has been structurally and geologically characterized. Model calibration was performed using available site information such as chemical analysis of geothermal springs, isotherms inferred from geothermal wells and results of a previous flow simulation study [3]. Model runs included the simulation of typical near-surface processes such as dilution, mixing and salt leaching occurring at the Dixie Valley geothermal area. Each reactive transport model produced 'synthetic' waters that were processed using the multicomponent chemical geothermometer code GeoT [4]. This code computes the saturation indices of reservoir minerals as a function of the temperature. Reservoir temperature is inferred when mineral saturation indices all cluster around zero. GeoT results were also compared with classical solute geothermometers (silica, Na-K-(Ca), K-Mg) [5]. Simulation results reveal that a minimum vertical fluid velocity on the order of a meter per day is needed to preserve the geochemical signature of a geothermal reservoir and to predict its temperature. The simulations also show that deep geochemical signatures are well preserved if fracture surfaces are partially coated by secondary minerals

  7. Recent Advances in the Modeling of the Transport of Two-Plasmon-Decay Electrons in the 1-D Hydrodynamic Code LILAC

    NASA Astrophysics Data System (ADS)

    Delettrez, J. A.; Myatt, J. F.; Yaakobi, B.

    2015-11-01

    The modeling of the fast-electron transport in the 1-D hydrodynamic code LILAC was modified because of the addition of cross-beam-energy-transfer (CBET) in implosion simulations. Using the old fast-electron with source model CBET results in a shift of the peak of the hard x-ray (HXR) production from the end of the laser pulse, as observed in experiments, to earlier in the pulse. This is caused by a drop in the laser intensity of the quarter-critical surface from CBET interaction at lower densities. Data from simulations with the laser plasma simulation environment (LPSE) code will be used to modify the source algorithm in LILAC. In addition, the transport model in LILAC has been modified to include deviations from the straight-line algorithm and non-specular reflection at the sheath to take into account the scattering from collisions and magnetic fields in the corona. Simulation results will be compared with HXR emissions from both room-temperature plastic and cryogenic target experiments. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

  8. Uranium transport in a crushed granodiorite: Experiments and reactive transport modeling

    NASA Astrophysics Data System (ADS)

    Dittrich, T. M.; Reimus, P. W.

    2015-04-01

    The primary objective of this study was to develop and demonstrate an experimental method to refine and better parameterize process models for reactive contaminant transport in aqueous subsurface environments and to reduce conservatism in such models without attempting to fully describe the geochemical system. Uranium was used as an example of a moderately adsorbing contaminant because of its relevance in geologic disposal of spent nuclear fuel. A fractured granodiorite from the Grimsel Test Site (GTS) in Switzerland was selected because this system has been studied extensively and field experiments have been conducted with radionuclides including uranium. We evaluated the role of pH, porous media size fraction, and flow interruptions on uranium transport. Rock cores drilled from the GTS were shipped to Los Alamos National Laboratory, characterized by x-ray diffraction and optical microscopy, and used in uranium batch sorption and column breakthrough experiments. A synthetic water was prepared that represented the porewater that would be present after groundwater interacts with bentonite backfill material near a nuclear waste package. Uranium was conservatively transported at pH 8.8. Significant adsorption and subsequent desorption was observed at pH ~ 7, with long desorption tails resulting after switching the column injection solution to uranium-free groundwater. Our experiments were designed to better interrogate this slow desorption behavior. A three-site model predicted sorption rate constants for a pH 7.2 solution with a 75-150 μm granodiorite fraction to be 3.5, 0.012, and 0.012 mL/g-h for the forward reactions and 0.49, 0.0025, and 0.001 h- 1 for the reverse reactions. Surface site densities were 1.3, 0.042, and 0.042 μmol/g for the first, second, and third sites, respectively. 10-year simulations show that including a slow binding site increases the arrival time of a uranium pulse by ~ 70%.

  9. OpenGeoSys-GEMS: Hybrid parallelization of a reactive transport code with MPI and threads

    NASA Astrophysics Data System (ADS)

    Kosakowski, G.; Kulik, D. A.; Shao, H.

    2012-04-01

    OpenGeoSys-GEMS is a generic purpose reactive transport code based on the operator splitting approach. The code couples the Finite-Element groundwater flow and multi-species transport modules of the OpenGeoSys (OGS) project (http://www.ufz.de/index.php?en=18345) with the GEM-Selektor research package to model thermodynamic equilibrium of aquatic (geo)chemical systems utilizing the Gibbs Energy Minimization approach (http://gems.web.psi.ch/). The combination of OGS and the GEM-Selektor kernel (GEMS3K) is highly flexible due to the object-oriented modular code structures and the well defined (memory based) data exchange modules. Like other reactive transport codes, the practical applicability of OGS-GEMS is often hampered by the long calculation time and large memory requirements. • For realistic geochemical systems which might include dozens of mineral phases and several (non-ideal) solid solutions the time needed to solve the chemical system with GEMS3K may increase exceptionally. • The codes are coupled in a sequential non-iterative loop. In order to keep the accuracy, the time step size is restricted. In combination with a fine spatial discretization the time step size may become very small which increases calculation times drastically even for small 1D problems. • The current version of OGS is not optimized for memory use and the MPI version of OGS does not distribute data between nodes. Even for moderately small 2D problems the number of MPI processes that fit into memory of up-to-date workstations or HPC hardware is limited. One strategy to overcome the above mentioned restrictions of OGS-GEMS is to parallelize the coupled code. For OGS a parallelized version already exists. It is based on a domain decomposition method implemented with MPI and provides a parallel solver for fluid and mass transport processes. In the coupled code, after solving fluid flow and solute transport, geochemical calculations are done in form of a central loop over all finite

  10. The effect of modafinil on the rat dopamine transporter and dopamine receptors D1-D3 paralleling cognitive enhancement in the radial arm maze.

    PubMed

    Karabacak, Yasemin; Sase, Sunetra; Aher, Yogesh D; Sase, Ajinkya; Saroja, Sivaprakasam R; Cicvaric, Ana; Höger, Harald; Berger, Michael; Bakulev, Vasiliy; Sitte, Harald H; Leban, Johann; Monje, Francisco J; Lubec, Gert

    2015-01-01

    A series of drugs have been reported to increase memory performance modulating the dopaminergic system and herein modafinil was tested for its working memory (WM) enhancing properties. Reuptake inhibition of dopamine, serotonin (SERT) and norepinephrine (NET) by modafinil was tested. Sixty male Sprague-Dawley rats were divided into six groups (modafinil-treated 1-5-10 mg/kg body weight, trained and untrained and vehicle treated trained and untrained rats; daily injected intraperitoneally for a period of 10 days) and tested in a radial arm maze (RAM), a paradigm for testing spatial WM. Hippocampi were taken 6 h following the last day of training and complexes containing the unphosphorylated or phosphorylated dopamine transporter (DAT-CC and pDAT-CC) and complexes containing the D1-3 dopamine receptor subunits (D1-D3-CC) were determined. Modafinil was binding to the DAT but insignificantly to SERT or NET and dopamine reuptake was blocked specifically (IC50 = 11.11 μM; SERT 1547 μM; NET 182 μM). From day 8 (day 9 for 1 mg/kg body weight) modafinil was decreasing WM errors (WMEs) in the RAM significantly and remarkably at all doses tested as compared to the vehicle controls. WMEs were linked to the D2R-CC and the pDAT-CC. pDAT and D1-D3-CC levels were modulated significantly and modafinil was shown to enhance spatial WM in the rat in a well-documented paradigm at all the three doses and dopamine reuptake inhibition with subsequent modulation of D1-3-CC is proposed as a possible mechanism of action. PMID:26347626

  11. PHT3D-UZF: A reactive transport model for variably-saturated porous media

    USGS Publications Warehouse

    Wu, Ming Zhi; Post, Vincent E. A.; Salmon, S. Ursula; Morway, Eric; Prommer, H.

    2016-01-01

    A modified version of the MODFLOW/MT3DMS-based reactive transport model PHT3D was developed to extend current reactive transport capabilities to the variably-saturated component of the subsurface system and incorporate diffusive reactive transport of gaseous species. Referred to as PHT3D-UZF, this code incorporates flux terms calculated by MODFLOW's unsaturated-zone flow (UZF1) package. A volume-averaged approach similar to the method used in UZF-MT3DMS was adopted. The PHREEQC-based computation of chemical processes within PHT3D-UZF in combination with the analytical solution method of UZF1 allows for comprehensive reactive transport investigations (i.e., biogeochemical transformations) that jointly involve saturated and unsaturated zone processes. Intended for regional-scale applications, UZF1 simulates downward-only flux within the unsaturated zone. The model was tested by comparing simulation results with those of existing numerical models. The comparison was performed for several benchmark problems that cover a range of important hydrological and reactive transport processes. A 2D simulation scenario was defined to illustrate the geochemical evolution following dewatering in a sandy acid sulfate soil environment. Other potential applications include the simulation of biogeochemical processes in variably-saturated systems that track the transport and fate of agricultural pollutants, nutrients, natural and xenobiotic organic compounds and micropollutants such as pharmaceuticals, as well as the evolution of isotope patterns.

  12. PHT3D-UZF: A Reactive Transport Model for Variably-Saturated Porous Media.

    PubMed

    Wu, Ming Zhi; Post, Vincent E A; Salmon, S Ursula; Morway, Eric D; Prommer, Henning

    2016-01-01

    A modified version of the MODFLOW/MT3DMS-based reactive transport model PHT3D was developed to extend current reactive transport capabilities to the variably-saturated component of the subsurface system and incorporate diffusive reactive transport of gaseous species. Referred to as PHT3D-UZF, this code incorporates flux terms calculated by MODFLOW's unsaturated-zone flow (UZF1) package. A volume-averaged approach similar to the method used in UZF-MT3DMS was adopted. The PHREEQC-based computation of chemical processes within PHT3D-UZF in combination with the analytical solution method of UZF1 allows for comprehensive reactive transport investigations (i.e., biogeochemical transformations) that jointly involve saturated and unsaturated zone processes. Intended for regional-scale applications, UZF1 simulates downward-only flux within the unsaturated zone. The model was tested by comparing simulation results with those of existing numerical models. The comparison was performed for several benchmark problems that cover a range of important hydrological and reactive transport processes. A 2D simulation scenario was defined to illustrate the geochemical evolution following dewatering in a sandy acid sulfate soil environment. Other potential applications include the simulation of biogeochemical processes in variably-saturated systems that track the transport and fate of agricultural pollutants, nutrients, natural and xenobiotic organic compounds and micropollutants such as pharmaceuticals, as well as the evolution of isotope patterns. PMID:25628017

  13. A transport based one-dimensional perturbation code for reactivity calculations in metal systems

    SciTech Connect

    Wenz, T.R.

    1995-02-01

    A one-dimensional reactivity calculation code is developed using first order perturbation theory. The reactivity equation is based on the multi-group transport equation using the discrete ordinates method for angular dependence. In addition to the first order perturbation approximations, the reactivity code uses only the isotropic scattering data, but cross section libraries with higher order scattering data can still be used with this code. The reactivity code obtains all the flux, cross section, and geometry data from the standard interface files created by ONEDANT, a discrete ordinates transport code. Comparisons between calculated and experimental reactivities were done with the central reactivity worth data for Lady Godiva, a bare uranium metal assembly. Good agreement is found for isotopes that do not violate the assumptions in the first order approximation. In general for cases where there are large discrepancies, the discretized cross section data is not accurately representing certain resonance regions that coincide with dominant flux groups in the Godiva assembly. Comparing reactivities calculated with first order perturbation theory and a straight {Delta}k/k calculation shows agreement within 10% indicating the perturbation of the calculated fluxes is small enough for first order perturbation theory to be applicable in the modeled system. Computation time comparisons between reactivities calculated with first order perturbation theory and straight {Delta}k/k calculations indicate considerable time can be saved performing a calculation with a perturbation code particularly as the complexity of the modeled problems increase.

  14. Investigating dominant processes in ZVI permeable reactive barriers using reactive transport modeling.

    PubMed

    Weber, Anne; Ruhl, Aki S; Amos, Richard T

    2013-08-01

    The reactive and hydraulic efficacy of zero valent iron permeable reactive barriers (ZVI PRBs) is strongly affected by geochemical composition of the groundwater treated. An enhanced version of the geochemical simulation code MIN3P was applied to simulate dominating processes in chlorinated hydrocarbons (CHCs) treating ZVI PRBs including geochemical dependency of ZVI reactivity, gas phase formation and a basic formulation of degassing. Results of target oriented column experiments with distinct chemical conditions (carbonate, calcium, sulfate, CHCs) were simulated to parameterize the model. The simulations demonstrate the initial enhancement of anaerobic iron corrosion due to carbonate and long term inhibition by precipitates (chukanovite, siderite, iron sulfide). Calcium was shown to enhance long term corrosion due to competition for carbonate between siderite, chukanovite, and aragonite, with less inhibition of iron corrosion by the needle like aragonite crystals. Application of the parameterized model to a field site (Bernau, Germany) demonstrated that temporarily enhanced groundwater carbonate concentrations caused an increase in gas phase formation due to the acceleration of anaerobic iron corrosion. PMID:23743511

  15. Modification of the finite element heat and mass transfer code (FEHM) to model multicomponent reactive transport

    SciTech Connect

    Viswanathan, H.S.

    1996-08-01

    The finite element code FEHMN, developed by scientists at Los Alamos National Laboratory (LANL), is a three-dimensional finite element heat and mass transport simulator that can handle complex stratigraphy and nonlinear processes such as vadose zone flow, heat flow and solute transport. Scientists at LANL have been developing hydrologic flow and transport models of the Yucca Mountain site using FEHMN. Previous FEHMN simulations have used an equivalent Kd model to model solute transport. In this thesis, FEHMN is modified making it possible to simulate the transport of a species with a rigorous chemical model. Including the rigorous chemical equations into FEHMN simulations should provide for more representative transport models for highly reactive chemical species. A fully kinetic formulation is chosen for the FEHMN reactive transport model. Several methods are available to computationally implement a fully kinetic formulation. Different numerical algorithms are investigated in order to optimize computational efficiency and memory requirements of the reactive transport model. The best algorithm of those investigated is then incorporated into FEHMN. The algorithm chosen requires for the user to place strongly coupled species into groups which are then solved for simultaneously using FEHMN. The complete reactive transport model is verified over a wide variety of problems and is shown to be working properly. The new chemical capabilities of FEHMN are illustrated by using Los Alamos National Laboratory`s site scale model of Yucca Mountain to model two-dimensional, vadose zone {sup 14}C transport. The simulations demonstrate that gas flow and carbonate chemistry can significantly affect {sup 14}C transport at Yucca Mountain. The simulations also prove that the new capabilities of FEHMN can be used to refine and buttress already existing Yucca Mountain radionuclide transport studies.

  16. Contaminant transport through a coal washery discard reactive wall

    SciTech Connect

    Gray, S.C.; Indraratna, B.; Yassini, I.

    1999-07-01

    This study examines the utilization of coal washery discard (CWD) as an inexpensive and readily available reactive wall material for the treatment of contaminated groundwater within the Illawarra region of New South Wales, Australia. The technology has been applied to a blast furnace slag (BFS) emplacement to attenuate an alkaline plume migrating towards a sensitive marine water body. Preliminary field performance data indicates that the CWD wall is reducing the pH of the plume to acceptable levels for marine ecosystems. The primary removal mechanisms within the CWD have been identified, however, have not be quantified at this stage.

  17. Visualization and Model Quantification of pH-Controlled Reactive Transport in Porous Media

    NASA Astrophysics Data System (ADS)

    Berkowitz, B.; Edery, Y.; Dror, I.

    2014-12-01

    We present conservative and reactive transport experiments in a refraction index-matched, three-dimensional, water-saturated porous medium, using a pH indicator as the reactant to follow chemical reactions. The measurements were matched with a particle tracking (PT) modeling approach requiring a minimal set of fitting parameters. The magnitude of reaction during transport through the porous medium can be related to the color change of the pH indicator, via detailed high resolution image analysis, with sequential imaging of the flow cell. The setup yields measurements of the temporally evolving spatial (local) concentration field. The current experiments focused on point injection of a pH-sensitive reactive tracer into a macroscopically uniform flow field containing water at a pH different from that of the injected tracer. Parallel experiments employing a conservative tracer demonstrated the transport to be mildly non-Fickian. A PT model was then used to quantify the spatial and temporal migration of both the conservative and reactive tracer plumes. The PT simulations account for non-Fickian transport within a continuous time random walk framework; model parameters related to the non-Fickian transport were determined from the conservative tracer experiments. An additional term accounting for chemical reaction was established solely from analysis of the reactant concentrations, and significantly, no other fitting parameters were used to quantify the reactive transport experiment. The measurements and analysis emphasize the localized nature of transport and reaction, caused by small-scale concentration fluctuations. In particular, an "extinction radius" for pH-controlled reactive transport processes was defined, which delineates the region in which reactions occur rapidly. The small-scale preferential flows, their relation to the non-Fickian transport, and their influence on reaction dynamics in the system, were also identified.

  18. Analytical Solutions for Sequentially Reactive Transport with Different Retardation Factors

    SciTech Connect

    Sun, Y; Buscheck, T A; Mansoor, K; Lu, X

    2001-08-01

    Integral transforms have been widely used for deriving analytical solutions for solute transport systems. Often, analytical solutions can only be written in closed form in frequency domains and numerical inverse-transforms have to be involved to obtain semi-analytical solutions in the time domain. For this reason, previously published closed form solutions are restricted either to a small number of species or to the same retardation assumption. In this paper, we applied the solution scheme proposed by Bauer et al. in the time domain. Using available analytical solutions of a single species transport with first-order decay without coupling with its parent species concentration as fundamental solutions, a daughter species concentration can be expressed as a linear function of those fundamental solutions. The implementation of the solution scheme is straight forward and exact analytical solutions are derived for one- and three-dimensional transport systems.

  19. Coupled Reactive Transport Modeling of CO2 Injection in Mt. Simon Sandstone Formation, Midwest USA

    NASA Astrophysics Data System (ADS)

    Liu, F.; Lu, P.; Zhu, C.; Xiao, Y.

    2009-12-01

    CO2 sequestration in deep geological formations is one of the promising options for CO2 emission reduction. While several large scale CO2 injections in saline aquifers have shown to be successful for the short-term, there is still a lack of fundamental understanding on key issues such as CO2 storage capacity, injectivity, and security over multiple spatial and temporal scales that need to be addressed. To advance these understandings, we applied multi-phase coupled reactive mass transport modeling to investigate the fate of injected CO2 and reservoir responses to the injection into Mt. Simon Formation. We developed both 1-D and 2-D reactive transport models in a radial region of 10,000 m surrounding a CO2 injection well to represent the Mt. Simon sandstone formation, which is a major regional deep saline reservoir in the Midwest, USA. Supercritical CO2 is injected into the formation for 100 years, and the modeling continues till 10,000 years to monitor both short-term and long-term behavior of injected CO2 and the associated rock-fluid interactions. CO2 co-injection with H2S and SO2 is also simulated to represent the flue gases from coal gasification and combustion in the Illinois Basin. The injection of CO2 results in acidified zones (pH ~3 and 5) adjacent to the wellbore, causing progressive water-rock interactions in the surrounding region. In accordance with the extensive dissolution of authigenic K-feldspar, sequential precipitations of secondary carbonates and clay minerals are predicted in this zone. The vertical profiles of CO2 show fingering pattern from the top of the reservoir to the bottom due to the density variation of CO2-impregnated brine, which facilitate convection induced mixing and solubility trapping. Most of the injected CO2 remains within a radial distance of 2500 m at the end of 10,000 years and is sequestered and immobilized by solubility and residual trapping. Mineral trapping via secondary carbonates, including calcite, magnesite

  20. Modeling water flow and bacterial transport in undisturbed lysimeters under irrigations of dairy shed effluent and water using HYDRUS-1D.

    PubMed

    Jiang, Shuang; Pang, Liping; Buchan, Graeme D; Simůnek, Jirí; Noonan, Mike J; Close, Murray E

    2010-02-01

    HYDRUS-1D was used to simulate water flow and leaching of fecal coliforms and bromide (Br) through six undisturbed soil lysimeters (70 cm depth by 50 cm diameter) under field conditions. Dairy shed effluent (DSE) spiked with Br was applied to the lysimeters, which contained fine sandy loam layers. This application was followed by fortnightly spray or flood water irrigation. Soil water contents were measured at four soil depths over 171 days, and leachate was collected from the bottom. The post-DSE period simulations yielded a generally decreased saturated water content compared to the pre-DSE period, and an increased saturated hydraulic conductivity and air-entry index, suggesting that changes in soil hydraulic properties (e.g. via changes in structure) can be induced by irrigation and seasonal effects. The single-porosity flow model was successful in simulating water flow under natural climatic conditions and spray irrigation. However, for lysimeters under flood irrigation, when the effect of preferential flow paths becomes more significant, the good agreement between predicted and observed water contents could only be achieved by using a dual-porosity flow model. Results derived from a mobile-immobile transport model suggest that compared to Br, bacteria were transported through a narrower pore-network with less mass exchange between mobile and immobile water zones. Our study suggests that soils with higher topsoil clay content and soils under flood irrigation are at a high risk of bacteria leaching through preferential flow paths. Irrigation management strategies must minimize the effect of preferential flow to reduce bacterial leaching from land applications of effluent. PMID:19775719

  1. MICADO: Parallel implementation of a 2D-1D iterative algorithm for the 3D neutron transport problem in prismatic geometries

    SciTech Connect

    Fevotte, F.; Lathuiliere, B.

    2013-07-01

    The large increase in computing power over the past few years now makes it possible to consider developing 3D full-core heterogeneous deterministic neutron transport solvers for reference calculations. Among all approaches presented in the literature, the method first introduced in [1] seems very promising. It consists in iterating over resolutions of 2D and ID MOC problems by taking advantage of prismatic geometries without introducing approximations of a low order operator such as diffusion. However, before developing a solver with all industrial options at EDF, several points needed to be clarified. In this work, we first prove the convergence of this iterative process, under some assumptions. We then present our high-performance, parallel implementation of this algorithm in the MICADO solver. Benchmarking the solver against the Takeda case shows that the 2D-1D coupling algorithm does not seem to affect the spatial convergence order of the MOC solver. As for performance issues, our study shows that even though the data distribution is suited to the 2D solver part, the efficiency of the ID part is sufficient to ensure a good parallel efficiency of the global algorithm. After this study, the main remaining difficulty implementation-wise is about the memory requirement of a vector used for initialization. An efficient acceleration operator will also need to be developed. (authors)

  2. Uranium transport in a crushed granodiorite: experiments and reactive transport modeling.

    PubMed

    Dittrich, T M; Reimus, P W

    2015-01-01

    The primary objective of this study was to develop and demonstrate an experimental method to refine and better parameterize process models for reactive contaminant transport in aqueous subsurface environments and to reduce conservatism in such models without attempting to fully describe the geochemical system. Uranium was used as an example of a moderately adsorbing contaminant because of its relevance in geologic disposal of spent nuclear fuel. A fractured granodiorite from the Grimsel Test Site (GTS) in Switzerland was selected because this system has been studied extensively and field experiments have been conducted with radionuclides including uranium. We evaluated the role of pH, porous media size fraction, and flow interruptions on uranium transport. Rock cores drilled from the GTS were shipped to Los Alamos National Laboratory, characterized by x-ray diffraction and optical microscopy, and used in uranium batch sorption and column breakthrough experiments. A synthetic water was prepared that represented the porewater that would be present after groundwater interacts with bentonite backfill material near a nuclear waste package. Uranium was conservatively transported at pH8.8. Significant adsorption and subsequent desorption was observed at pH ~7, with long desorption tails resulting after switching the column injection solution to uranium-free groundwater. Our experiments were designed to better interrogate this slow desorption behavior. A three-site model predicted sorption rate constants for a pH7.2 solution with a 75-150 μm granodiorite fraction to be 3.5, 0.012, and 0.012 mL/g-h for the forward reactions and 0.49, 0.0025, and 0.001 h(-1) for the reverse reactions. Surface site densities were 1.3, 0.042, and 0.042 μmol/g for the first, second, and third sites, respectively. 10-year simulations show that including a slow binding site increases the arrival time of a uranium pulse by ~70%. PMID:25727688

  3. Reactive transport modeling of ⁹⁰Sr sorption in reactive sandpacks.

    PubMed

    Yin, Jun; Jeen, Sung-Wook; Lee, David R; Mayer, K Ulrich

    2014-09-15

    Strontium-90 ((90)Sr) is one of the most problematic radioactive contaminants in groundwater at nuclear sites. Although (90)Sr is retarded relative to groundwater flow, it is sufficiently mobile and long-lived to require treatment in many hydrogeological settings. A detailed study was performed on the practicality of using granular clinoptilolite as a sandpack around groundwater wells where groundwater is contaminated with (90)Sr and the water table must be lowered. The effectiveness of the reactive sandpack concept and the mechanisms controlling (90)Sr attenuation was investigated by numerical analysis of data obtained from four in situ column experiments. The experiments spanned the range of pore-water velocities that would occur during radial flow through granular clinoptilolite sandpacks. A kinetic sorption model was required to adequately reproduce the experimentally observed (90)Sr behavior. Calibrated first-order kinetic rates were correlated with pore-water velocities. After calibration, three sorption models were used to simulate (90)Sr attenuation for four hypothetical pumping scenarios. Results show that a velocity-dependent kinetic model accurately simulates the observed early breakthrough for high pore-water velocities. The results indicate (1) that reactive sandpacks have good potential for in situ remediation and construction dewatering and (2) that quantitative modeling can aid in the design and application of this novel technique. PMID:25232651

  4. Pore scale modeling of reactive transport involved in geologic CO2 sequestration

    SciTech Connect

    Kang, Qinjin; Lichtner, Peter C; Viswanathan, Hari S; Abdel-fattah, Amr I

    2009-01-01

    We apply a multi-component reactive transport lattice Boltzmann model developed in previolls studies to modeling the injection of a C02 saturated brine into various porous media structures at temperature T=25 and 80 C. The porous media are originally consisted of calcite. A chemical system consisting of Na+, Ca2+, Mg2+, H+, CO2(aq), and CI-is considered. The fluid flow, advection and diHusion of aqueous species, homogeneous reactions occurring in the bulk fluid, as weB as the dissolution of calcite and precipitation of dolomite are simulated at the pore scale. The effects of porous media structure on reactive transport are investigated. The results are compared with continuum scale modeling and the agreement and discrepancy are discussed. This work may shed some light on the fundamental physics occurring at the pore scale for reactive transport involved in geologic C02 sequestration.

  5. Effective reaction rates for transport of particles to heterogeneous reactive (or porous) surfaces under shear

    NASA Astrophysics Data System (ADS)

    Shah, Preyas; Shaqfeh, Eric S. G.

    2015-11-01

    Mass transfer to heterogeneous reactive (or porous) surfaces is common in applications like heterogeneous catalysis, and biological porous media transport like drug delivery. This is modeled as advection-diffusion in a shear flow to an inert surface with first order reactive patches. We study transport of point particles using boundary element simulations. We show that the heterogeneous surface can be replaced with a uniform-flux boundary condition related to the Sherwood number (S), aka, the dimensionless flux to the reactive region. In the dilute limit of reactive regions, large-scale interaction between the reactive patches is important. In the dilute limit of inert regions, [S] grows as the reciprocal of the inert area fraction. Based on the method of resistances and numerical results, we provide correlations for [S] for general reactive surfaces and flow conditions. We model finite sized particles as general spheroids, specifically for biological applications. We do Brownian Dynamics simulations to account for hydrodynamic and steric interactions with the flow field and the domain geometry, and compare to the point particle results. We observe that anisotropic particles gave a higher pore transport flux compared to spherical particles at all flow conditions.

  6. A reactive transport modelling approach to assess the leaching potential of hydraulic fracturing fluids associated with coal seam gas extraction

    NASA Astrophysics Data System (ADS)

    Mallants, Dirk; Simunek, Jirka; Gerke, Kirill

    2015-04-01

    Coal Seam Gas production generates large volumes of "produced" water that may contain compounds originating from the use of hydraulic fracturing fluids. Such produced water also contains elevated concentrations of naturally occurring inorganic and organic compounds, and usually has a high salinity. Leaching of produced water from storage ponds may occur as a result of flooding or containment failure. Some produced water is used for irrigation of specific crops tolerant to elevated salt levels. These chemicals may potentially contaminate soil, shallow groundwater, and groundwater, as well as receiving surface waters. This paper presents an application of scenario modelling using the reactive transport model for variably-saturated media HP1 (coupled HYDRUS-1D and PHREEQC). We evaluate the fate of hydraulic fracturing chemicals and naturally occurring chemicals in soil as a result of unintentional release from storage ponds or when produced water from Coal Seam Gas operations is used in irrigation practices. We present a review of exposure pathways and relevant hydro-bio-geo-chemical processes, a collation of physico-chemical properties of organic/inorganic contaminants as input to a set of generic simulations of transport and attenuation in variably saturated soil profiles. We demonstrate the ability to model the coupled processes of flow and transport in soil of contaminants associated with hydraulic fracturing fluids and naturally occurring contaminants.

  7. Predicting Upscaling Relationships for Heterogeneous Flow and Reactive Transport at the Savannah River Site

    NASA Astrophysics Data System (ADS)

    Arora, B.; Wainwright, H. M.; Spycher, N.

    2013-12-01

    This study aims at understanding key hydrogeochemical processes dictating pH behavior and U transport at the Savannah River Site (SRS) F-Area, South Carolina, with particular focus on the impact of chemical and physical heterogeneities. Acidic waste solutions containing low level radioactivity from numerous isotopes were discharged to a series of unlined seepage basins at the F-Area, from 1955 through 1989, which resulted in a nearly 1 km long acidic uranium plume. Reactive facies is a new approach that spatially characterizes linked flow and geochemical properties over large domains, where it is typically challenging to obtain parameters with sufficient resolution for reactive transport modeling. This approach - based on the hypothesis that we can identify geological units that have unique distributions of reactive transport properties - allows us to integrate various types of datasets (e.g., historical data, laboratory analysis, crosshole and surface geophysics) for estimating heterogeneous reactive transport parameters. At the SRS F-Area, data mining and iteration with laboratory analysis identified two reactive facies coincident with the depositional facies, which have distinct distributions of reactive transport properties: %fines, permeability, and Al:Fe ratio (proxy for kaolinite:geothite ratio). The reactive facies over the plume-scale domain was estimated based on measured data (foot-by-foot core analysis, cone penetrometer, crosshole seismic and surface seismic data) and integrated using the Bayesian framework. In parallel, a numerical reactive transport model was developed including saturated and unsaturated flow, and complex geochemical processes such as U(VI) and H+ adsorption (surface complexation) onto sediments and dissolution and precipitation of Al and Fe minerals. By combining the developed reactive transport model with the estimated spatial distribution of reactive transport parameters, we perform stochastic simulations of U and pH plume

  8. Transport of reactive chemicals in sediment-laden streams

    NASA Astrophysics Data System (ADS)

    Revelli, R.; Ridolfi, L.

    This paper deals with the transport of chemicals in a turbulent stream when both sorbing suspended load and decay reactions are present. These conditions, which can be found quite commonly in rivers, give rise to interesting behaviour. Important and not trivial processes are added and interact with the classical diffusive, advective, and dispersive mechanisms. Due to the sorption process, the chemical divides into an aqueous and a sorbed phase which follow different evolutions: the aqueous phase is regulated by turbulent diffusion, advection and shear, while the sorbed one undergoes the same fluid dynamic mechanisms but through the evolution of suspended sediment, which is also subjected to sedimentation. The evolutions of the two phases are not separate, as the sorption-desorption exchanges between the aqueous and sorbed phases connect their dynamics. In turn, the decay reactions, being able to modify the concentrations in the two phases, influence the sorption process and therefore the entire transport dynamics. A complex picture results where several nonlinear interactions occur. The main objective of the work is to obtain the one-dimensional partial differential equation that describes the temporal and spatial dynamics of the depth-averaged concentration of the chemical. Due to the existence of three well separated time scales in the whole transport process, the mathematical homogenization theory is adopted to average the two-dimensional model, and the most general case is dealt with in which sediment transport is unsteady while the reactions are nonlinear and different for the aqueous and sorbed phases. Finally, some examples of real cases are discussed where the influence of unsteady suspended sediment dynamics and the nonlinearity of reactions is analyzed, while the role of the several nonlinear differential terms in the model is highlighted.

  9. STOMP-ECKEChem: An Engineering Perspective on Reactive Transport in Geologic Media

    SciTech Connect

    White, Mark D.; Fang, Yilin

    2012-04-04

    ECKEChem (Equilibrium, Conservation, Kinetic Equation Chemistry) is a reactive transport module for the STOMP suite of multifluid subsurface flow and transport simulators that was developed from an engineering perspective. STOMP comprises a suite of operational modes that are distinguished by the solved coupled conservation equations with capabilities for a variety of subsurface applications (e.g., environmental remediation and stewardship, geologic sequestration of greenhouse gases, gas hydrate production, and oil shale production). The ECKEChem module was designed to provide integrated reactive transport capabilities across the suite of STOMP simulator operational modes. The initial application for the ECKEChem module was in the simulation of the mineralization reactions that occurred with the injection of supercritical carbon dioxide into deep Columbia River basalt formations, where it was implemented in the STOMP-CO2 simulator. The STOMP-ECKEChem solution approach to modeling reactive transport in multifluid geologic media is founded on an engineering perspective: (1) sequential non-iterative coupling between the flow and reactive transport is sufficient, (2) reactive transport can be modeled by operator splitting with local geochemistry and global transport, (3) geochemistry can be expressed as a system of coupled nonlinear equilibrium, conservation and kinetic equations, (4) a limited number of kinetic equation forms are used in geochemical practice. This chapter describes the conceptual approach to converting a geochemical reaction network into a series of equilibrium, conservation and kinetic equations, the implementation of ECKEChem in STOMP, the numerical solution approach, and a demonstration of the simulator on a complex application involving desorption of uranium from contaminated field-textured sediments.

  10. Reactive Transport Modeling: An Essential Tool and a New ResearchApproach for the Earth Sciences

    SciTech Connect

    Steefel, Carl I.; DePaolo, Donald J.; Lichtner, Peter C.

    2005-08-25

    Reactive transport modeling is an essential tool for the analysis of coupled physical, chemical, and biological processes in Earth systems, and has additional potential to better integrate the results from focused fundamental research on Earth materials. Appropriately designed models can describe the interactions of competing processes at a range of spatial and time scales, and hence are critical for connecting the advancing capabilities for materials characterization at the atomic scale with the macroscopic behavior of complex Earth systems. Reactive transport modeling has had a significant impact on the treatment of contaminant retardation in the subsurface, the description of elemental and nutrient fluxes between major Earth reservoirs, and in the treatment of deep Earth processes such as metamorphism and magma transport. Active topics of research include the development of pore scale and hybrid, or multiple continua, models to capture the scale dependence of coupled reactive transport processes. Frontier research questions, that are only now being addressed, include the effects of chemical microenvironments, coupled thermal mechanical chemical processes, controls on mineral fluid reaction rates in natural media, and scaling of reactive transport processes from the microscopic to pore to field scale.

  11. Reactive Gas transport in soil: Kinetics versus Local Equilibrium Approach

    NASA Astrophysics Data System (ADS)

    Geistlinger, Helmut; Jia, Ruijan

    2010-05-01

    Gas transport through the unsaturated soil zone was studied using an analytical solution of the gas transport model that is mathematically equivalent to the Two-Region model. The gas transport model includes diffusive and convective gas fluxes, interphase mass transfer between the gas and water phase, and biodegradation. The influence of non-equilibrium phenomena, spatially variable initial conditions, and transient boundary conditions are studied. The objective of this paper is to compare the kinetic approach for interphase mass transfer with the standard local equilibrium approach and to find conditions and time-scales under which the local equilibrium approach is justified. The time-scale of investigation was limited to the day-scale, because this is the relevant scale for understanding gas emission from the soil zone with transient water saturation. For the first time a generalized mass transfer coefficient is proposed that justifies the often used steady-state Thin-Film mass transfer coefficient for small and medium water-saturated aggregates of about 10 mm. The main conclusion from this study is that non-equilibrium mass transfer depends strongly on the temporal and small-scale spatial distribution of water within the unsaturated soil zone. For regions with low water saturation and small water-saturated aggregates (radius about 1 mm) the local equilibrium approach can be used as a first approximation for diffusive gas transport. For higher water saturation and medium radii of water-saturated aggregates (radius about 10 mm) and for convective gas transport, the non-equilibrium effect becomes more and more important if the hydraulic residence time and the Damköhler number decrease. Relative errors can range up to 100% and more. While for medium radii the local equilibrium approach describes the main features both of the spatial concentration profile and the time-dependence of the emission rate, it fails completely for larger aggregates (radius about 100 mm

  12. A COMSOL-GEMS interface for modeling coupled reactive-transport geochemical processes

    NASA Astrophysics Data System (ADS)

    Azad, Vahid Jafari; Li, Chang; Verba, Circe; Ideker, Jason H.; Isgor, O. Burkan

    2016-07-01

    An interface was developed between COMSOL MultiphysicsTM finite element analysis software and (geo)chemical modeling platform, GEMS, for the reactive-transport modeling of (geo)chemical processes in variably saturated porous media. The two standalone software packages are managed from the interface that uses a non-iterative operator splitting technique to couple the transport (COMSOL) and reaction (GEMS) processes. The interface allows modeling media with complex chemistry (e.g. cement) using GEMS thermodynamic database formats. Benchmark comparisons show that the developed interface can be used to predict a variety of reactive-transport processes accurately. The full functionality of the interface was demonstrated to model transport processes, governed by extended Nernst-Plank equation, in Class H Portland cement samples in high pressure and temperature autoclaves simulating systems that are used to store captured carbon dioxide (CO2) in geological reservoirs.

  13. Uncertainties in vertical groundwater fluxes from 1-D steady state heat transport analyses caused by heterogeneity, multidimensional flow, and climate change

    NASA Astrophysics Data System (ADS)

    Irvine, Dylan J.; Cartwright, Ian; Post, Vincent E. A.; Simmons, Craig T.; Banks, Eddie W.

    2016-02-01

    Steady state 1-D analytical solutions to estimate groundwater fluxes from temperature profiles are an attractive option because they are simple to apply, with no complex boundary or initial conditions. Steady state solutions have been applied to estimate both aquifer scale fluxes as well as to estimate groundwater discharge to streams. This study explores the sources of uncertainty in flux estimates from regional scale aquifers caused by sensor precision, aquifer heterogeneity, multidimensional flow and variations in surface temperature due to climate change. Synthetic temperature profiles were generated using 2-D groundwater flow and heat transport models with homogeneous and heterogeneous hydraulic and thermal properties. Temperature profiles were analyzed assuming temperature can be determined with a precision between 0.1°C and 0.001°C. Analysis of synthetic temperature profiles show that the Bredehoeft and Papadopulos (1965) method can provide good estimates of the mean vertical Darcy flux over the length of the temperature profile. Reliable flux estimates were obtained when the ratio of vertical to horizontal flux was as low as 0.1, and in heterogeneous media, providing that temperature at the upper boundary was constant in time. However, temporal increases in surface temperature led to over-estimation of fluxes. Overestimates increased with time since the onset of, and with the rate of surface warming. Overall, the Bredehoeft and Papadopulos (1965) method may be more robust for the conditions with constant temperature distributions than previously thought, but that transient methods that account for surface warming should be used to determine fluxes in shallow aquifers.

  14. Multi-scale modeling of multi-component reactive transport in geothermal aquifers

    NASA Astrophysics Data System (ADS)

    Nick, Hamidreza M.; Raoof, Amir; Wolf, Karl-Heinz; Bruhn, David

    2014-05-01

    In deep geothermal systems heat and chemical stresses can cause physical alterations, which may have a significant effect on flow and reaction rates. As a consequence it will lead to changes in permeability and porosity of the formations due to mineral precipitation and dissolution. Large-scale modeling of reactive transport in such systems is still challenging. A large area of uncertainty is the way in which the pore-scale information controlling the flow and reaction will behave at a larger scale. A possible choice is to use constitutive relationships relating, for example the permeability and porosity evolutions to the change in the pore geometry. While determining such relationships through laboratory experiments may be limited, pore-network modeling provides an alternative solution. In this work, we introduce a new workflow in which a hybrid Finite-Element Finite-Volume method [1,2] and a pore network modeling approach [3] are employed. Using the pore-scale model, relevant constitutive relations are developed. These relations are then embedded in the continuum-scale model. This approach enables us to study non-isothermal reactive transport in porous media while accounting for micro-scale features under realistic conditions. The performance and applicability of the proposed model is explored for different flow and reaction regimes. References: 1. Matthäi, S.K., et al.: Simulation of solute transport through fractured rock: a higher-order accurate finite-element finite-volume method permitting large time steps. Transport in porous media 83.2 (2010): 289-318. 2. Nick, H.M., et al.: Reactive dispersive contaminant transport in coastal aquifers: Numerical simulation of a reactive Henry problem. Journal of contaminant hydrology 145 (2012), 90-104. 3. Raoof A., et al.: PoreFlow: A Complex pore-network model for simulation of reactive transport in variably saturated porous media, Computers & Geosciences, 61, (2013), 160-174.

  15. A Reactive Transport Simulator for Biogeochemical Processes in Subsurface System

    2003-04-01

    BIOGEOCHEM is a Fortran code that mumerically simulates the coupled processes of solute transport, microbial population dynamics, microbial metabolism, and geochemical reactions. The potential applications of the code include, but not limited to, (a) sensitivity and uncertainty analyses for assessing the impact of microbial activity on subsurface geochemical systems; (b) extraction of biogeochemical parameter values from field observations or laboratory measurements, (c) helping to design and optimize laboratory biogeochemical experiments, and (d) data integration. Methodmore » of Solution: A finite difference method and a Newton-Raphson technique are used to solve a set of coupled nonlinear partial differential equations and algebraic equations. Practical Application: Environmental analysis, bioremediation performance assessments of radioactive or non-radioactive wase disposal, and academic research.« less

  16. Simulating MODFLOW-based reactive transport under radially symmetric flow conditions.

    PubMed

    Wallis, Ilka; Prommer, Henning; Post, Vincent; Vandenbohede, Alexander; Simmons, Craig T

    2013-01-01

    Radially symmetric flow and solute transport around point sources and sinks is an important specialized topic of groundwater hydraulics. Analysis of radial flow fields is routinely used to determine heads and flows in the vicinity of point sources or sinks. Increasingly, studies also consider solute transport, biogeochemical processes, and thermal changes that occur in the vicinity of point sources/sinks. Commonly, the analysis of hydraulic processes involves numerical or (semi-) analytical modeling methods. For the description of solute transport, analytical solutions are only available for the most basic transport phenomena. Solving advanced transport problems numerically is often associated with a significant computational burden. However, where axis-symmetry applies, computational cost can be decreased substantially in comparison with full three-dimensional (3D) solutions. In this study, we explore several techniques of simulating conservative and reactive transport within radial flow fields using MODFLOW as the flow simulator, based on its widespread use and ability to be coupled with multiple solute and reactive transport codes of different complexity. The selected transport simulators are MT3DMS and PHT3D. Computational efficiency and accuracy of the approaches are evaluated through comparisons with full 2D/3D model simulations, analytical solutions, and benchmark problems. We demonstrate that radial transport models are capable of accurately reproducing a wide variety of conservative and reactive transport problems provided that an adequate spatial discretization and advection scheme is selected. For the investigated test problems, the computational load was substantially reduced, with the improvement varying, depending on the complexity of the considered reaction network. PMID:22900478

  17. Phase behavior and reactive transport of partial melt in heterogeneous mantle model

    NASA Astrophysics Data System (ADS)

    Jordan, J.; Hesse, M. A.

    2013-12-01

    The reactive transport of partial melt is the key process that leads to the chemical and physical differentiation of terrestrial planets and smaller celestial bodies. The essential role of the lithological heterogeneities during partial melting of the mantle is increasingly recognized. How far can enriched melts propagate while interacting with the ambient mantle? Can the melt flow emanating from a fertile heterogeneity be localized through a reactive infiltration feedback in a model without exogenous factors or contrived initial conditions? A full understanding of the role of heterogeneities requires reactive melt transport models that account for the phase behavior of major elements. Previous work on reactive transport in the mantle focuses on trace element partitioning; we present the first nonlinear chromatographic analysis of reactive melt transport in systems with binary solid solution. Our analysis shows that reactive melt transport in systems with binary solid solution leads to the formation of two separate reaction fronts: a slow melting/freezing front along which enthalpy change is dominant and a fast dissolution/precipitation front along which compositional changes are dominated by an ion-exchange process over enthalpy change. An intermediate state forms between these two fronts with a bulk-rock composition and enthalpy that are not necessarily bounded by the bulk-rock composition and enthalpy of either the enriched heterogeneity or the depleted ambient mantle. The formation of this intermediate state makes it difficult to anticipate the porosity changes and hence the stability of reaction fronts. Therefore, we develop a graphical representation for the solution that allows identification of the intermediate state by inspection, for all possible bulk-rock compositions and enthalpies of the heterogeneity and the ambient mantle. We apply the analysis to the partial melting of an enriched heterogeneity. This leads to the formation of moving precipitation

  18. Core-flood experiment for transport of reactive fluids in rocks

    NASA Astrophysics Data System (ADS)

    Ott, H.; de Kloe, K.; van Bakel, M.; Vos, F.; van Pelt, A.; Legerstee, P.; Bauer, A.; Eide, K.; van der Linden, A.; Berg, S.; Makurat, A.

    2012-08-01

    Investigation of the transport of reactive fluids in porous rocks is an intriguing but challenging task and relevant in several areas of science and engineering such as geology, hydrogeology, and petroleum engineering. We designed and constructed an experimental setup to investigate physical and chemical processes caused by the flow of reactive and volatile fluids such as supercritical CO2 and/or H2S in geological formations. Potential applications are geological sequestration of CO2 in the frame of carbon capture and storage and acid-gas injection for sulfur disposal and/or enhanced oil recovery. The present paper outlines the design criteria and the realization of reactive transport experiments on the laboratory scale. We focus on the spatial and time evolution of rock and fluid composition as a result of chemical rock fluid interaction and the coupling of chemistry and fluid flow in porous rocks.

  19. Influence of calcite on uranium(VI) reactive transport in the groundwate-river mixing zone

    NASA Astrophysics Data System (ADS)

    Ma, Rui; Liu, Chongxuan; Greskowiak, Janek; Prommer, Henning; Zachara, John; Zheng, Chunmiao

    2014-01-01

    Calcite is an important, relatively soluble mineral phase that can affect uranium reactive transport in subsurface sediments. This study was conducted to investigate the distribution of calcite and its influence on uranium adsorption and reactive transport in the groundwate-river mixing zone of the Hanford 300A site, Washington State. Simulations using a two-dimensional (2D) reactive transport model under field-relevant hydrological and hydrogeochemical conditions revealed the development of a calcite reaction front through the mixing zone as a result of dynamic groundwate-river interactions. The calcite concentration distribution, in turn, affected the concentrations of aqueous carbonate and calcium, and pH through dissolution, as river waters intruded and receded from the site at different velocities in response to stage changes. The composition variations in groundwater subsequently influenced uranium mobility and discharge rates into the river in a complex fashion. The results implied that calcite distribution and concentration are important variables that need to be quantified for accurate reactive transport predictions of uranium, especially in dynamic groundwate-river mixing zones.

  20. Influence of calcite on uranium(VI) reactive transport in the groundwater-river mixing zone.

    PubMed

    Ma, Rui; Liu, Chongxuan; Greskowiak, Janek; Prommer, Henning; Zachara, John; Zheng, Chunmiao

    2014-01-01

    Calcite is an important, relatively soluble mineral phase that can affect uranium reactive transport in subsurface sediments. This study was conducted to investigate the distribution of calcite and its influence on uranium adsorption and reactive transport in the groundwater-river mixing zone of the Hanford 300A site, Washington State. Simulations using a two-dimensional (2D) reactive transport model under field-relevant hydrological and hydrogeochemical conditions revealed the development of a calcite reaction front through the mixing zone as a result of dynamic groundwater-river interactions. The calcite concentration distribution, in turn, affected the concentrations of aqueous carbonate and calcium, and pH through dissolution, as river waters intruded and receded from the site at different velocities in response to stage changes. The composition variations in groundwater subsequently influenced uranium mobility and discharge rates into the river in a complex fashion. The results implied that calcite distribution and concentration are important variables that need to be quantified for accurate reactive transport predictions of uranium, especially in dynamic groundwater-river mixing zones. PMID:24240103

  1. Modeling two-dimensional reactive transport using a Godunov-mixed finite element method

    NASA Astrophysics Data System (ADS)

    James, Andrew I.; Jawitz, James W.

    2007-05-01

    SummaryThe development of a model to simulate transport of materials in variable-depth flows is discussed. The model numerically approximates solutions to the advection-dispersion-reaction equation using a time-splitting technique where the advective, dispersive, and reactive parts of the equation are solved separately. An explicit finite-volume Godunov method is used to approximate the advective part while a hybridized mixed finite element method is used to solve for the dispersive step. A backward Euler method is used to solve the reactive component. Rather than solving each component once at each time step, the advective and reactive steps are fractionally and symmetrically split around the dispersive step, so that half of a reactive and advective step are solved before and after each dispersive step. Since the dispersive step is implicit, but computationally expensive, while the advective step is explicit but has time step constraints, this allows stable and more efficient schemes to be implemented in contrast to non-split or simple time-split algorithms. This technique allows problems with high grid Peclet numbers, such as transport problems with sharp solute fronts, to be solved without oscillations in the solution and with virtually no artificial diffusion. By applying the technique to variable depth flows, a variety of applications to transport and reaction problems in surface water and unconfined aquifers can be undertaken. Numerical results for several non-reactive and reactive transport problems in one- and two-dimensions are presented. Observed convergence rates are up to second-order for these simulations.

  2. Triheptanoin for glucose transporter type I deficiency (G1D): Modulation of human ictogenesis, cerebral metabolic rate and cognitive indices by a food supplement

    PubMed Central

    Pascual, Juan M.; Liu, Peiying; Mao, Deng; Kelly, Dorothy; Hernandez, Ana; Sheng, Min; Good, Levi B.; Ma, Qian; Marin-Valencia, Isaac; Zhang, Xuchen; Park, Jason Y.; Hynan, Linda S.; Stavinoha, Peter; Roe, Charles R.; Lu, Hanzhang

    2015-01-01

    Objective G1D is commonly associated with electrographic spike-wave and - less-noticeably – with absence seizures. The G1D syndrome has long been attributed to energy (i.e., ATP-synthetic) failure, as have experimental, toxic-rodent epilepsies to impaired brain metabolism and tricarboxylic acid (TCA) cycle intermediate depletion. Indeed, a (seldom-acknowledged) function of glucose and other substrates is the generation of brain TCAs via carbon-donor reactions collectively named anaplerosis. However, TCAs are preserved in murine G1D. This renders inferences about energy failure premature and suggests a different hypothesis, also grounded on our findings, that consumption of alternate TCA precursors is stimulated, potentially detracting from other functions. Second, common ketogenic diets can ameliorate G1D seizures, but lead to a therapeutically-counterintuitive reduction in blood glucose available to the brain, and they can prove ineffective in 1/3 of cases. While developing G1D treatments, all of this motivated us to: a) uphold (rather than attenuate) the residual brain glucose flux that all G1D patients possess; and b) stimulate the TCA cycle, including anaplerosis. Therefore, we tested the medium-chain triglyceride triheptanoin, a widely-used medical food supplement that can fulfill both of these metabolic roles. The rationale is that ketone bodies derived from ketogenic diets are not anaplerotic, in contrast with triheptanoin metabolites, as we have shown in the G1D mouse brain. Design We supplemented the regular diet of a case series of G1D patients with food-grade triheptanoin. First we confirmed that, despite their frequent electroencephalographic (EEG) presence as spike-waves, most seizures are rarely visible, such that perceptions by patients or others are inadequate for treatment evaluation. Thus, we used EEG, quantitative neuropsychological, blood analytical, and MRI cerebral metabolic rate measurements as main outcomes. Setting Academic and

  3. Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

    NASA Astrophysics Data System (ADS)

    Lu, Dan; Ye, Ming; Curtis, Gary P.

    2015-10-01

    While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. This study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict the reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. These reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Limitations of applying MLBMA to the

  4. Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

    USGS Publications Warehouse

    Curtis, Gary P.; Lu, Dan; Ye, Ming

    2015-01-01

    While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. This study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict the reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. These reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Limitations of applying MLBMA to the

  5. Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

    SciTech Connect

    Lu, Dan; Ye, Ming; Curtis, Gary P.

    2015-08-01

    While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. Our study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict the reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. Moreover, these reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Finally, limitations of

  6. Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

    DOE PAGESBeta

    Lu, Dan; Ye, Ming; Curtis, Gary P.

    2015-08-01

    While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. Our study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict themore » reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. Moreover, these reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Finally

  7. An alternative to fully coupled reactive transport simulations for long-term prediction of chemical reactions in complex geological systems

    NASA Astrophysics Data System (ADS)

    De Lucia, Marco; Kempka, Thomas; Kühn, Michael

    2014-05-01

    Fully-coupled reactive transport simulations involving multiphase hydrodynamics and chemical reactions in heterogeneous settings are extremely challenging from a computational point of view. This often leads to oversimplification of the investigated system: coarse spatial discretization, to keep the number of elements in the order of few thousands; simplified chemistry, disregarding many potentially important reactions. A novel approach for coupling non-reactive hydrodynamic simulations with the outcome of single batch geochemical simulations was therefore introduced to assess the potential long-term mineral trapping at the Ketzin pilot site for underground CO2 storage in Germany [1],[2]. The advantage of the coupling is the ability to use multi-million grid non-reactive hydrodynamics simulations on one side and few batch 0D geochemical simulations on the other, so that the complexity of both systems does not need to be reduced. This contribution shows the approach which was taken to validate this simplified coupling scheme. The procedure involved batch simulations of the reference geochemical model, then performing both non-reactive and fully coupled 1D and 3D reactive transport simulations and finally applying the simplified coupling scheme based on the non-reactive and geochemical batch model. The TOUGHREACT/ECO2N [3] simulator was adopted for the validation. The degree of refinement of the spatial grid and the complexity and velocity of the mineral reactions, along with a cut-off value for the minimum concentration of dissolved CO2 allowed to originate precipitates in the simplified approach were found out to be the governing parameters for the convergence of the two schemes. Systematic discrepancies between the approaches are not reducible, simply because there is no feedback between chemistry and hydrodynamics, and can reach 20 % - 30 % in unfavourable cases. However, even such discrepancy is completely acceptable, in our opinion, given the amount of

  8. Multicomponent reactive transport in an in situ zero-valent iron cell

    SciTech Connect

    Yabusaki, Steven B. ); Cantrell, Kirk J. ); Sass, Bruce; Steefel, Carl

    2000-12-01

    Data collected from a field study of in situ zero-valent iron treatment for TCE were analyzed in the context of coupled transport and reaction processes. The focus of this analysis was to understand the behavior of chemical components, including contaminants, in groundwater transported through the iron cell of a pilot-scale funnel and gate treatment system. A multicomponent reactive transport simulator was used to simultaneously model mobile and nonmobile components undergoing equilibrium and kinetic reactions including TCE degradation, parallel iron dissolution reactions, precipitation of secondary minerals, and complexation reactions. The resulting mechanistic model of coupled processes reproduced solution chemistry behavior observed in the iron cell with a minimum of calibration. These observations included the destruction of TCE and cis-1,2-DCE; increases in pH and hydrocarbons; and decreases in EH, alkalinity, dissolved O2 and CO2, and major ions (i.e., Ca, Mg, Cl, sulfate, nitrate). Mineral precipitation in the iron zone was critical to correctly predicting these behaviors. The dominant precipitation products were ferrous hydroxide, siderite, aragonite, brucite, and iron sulfide. In the first few centimeters of the reactive iron cell, these precipitation products are predicted to account for a 3% increase in mineral volume per year, which could have implications for the longevity of favorable barrier hydraulics and reactivity. The inclusion of transport was key to understanding the interplay between rates of transport and rates of reaction in the field.

  9. Coupling Isotopic Fractionation to Multiple-Continuum Reactive Transport Models of Biogeochemical Systems

    NASA Astrophysics Data System (ADS)

    Sonnenthal, E. L.; Wanner, C.

    2014-12-01

    Stable isotopic systems often show an unexpected range in observed fractionation factors associated with biogeochemical systems. In particular, the ranges in such isotopic systems as Cr, Ca, Li, and C have often been attributed to kinetic effects as well as different biogeochemical mechanisms. Reactive transport models developed to capture the sub-micron-scale transport and reaction processes within the macroscale system (e.g., biofilm to cm-scale) have been successful in simulating the biogeochemical processes associated with bacterial growth and the resultant changes in pore-fluid chemistry and redox conditions. Once such multicontinuum reactive transport models are extended to include equilibrium and kinetic isotopic fractionation, diffusive transport, and fluid-gas equilibria, it becomes possible to quantitatively interpret the isotopic changes observed in experimental and natural or engineered biogeochemical systems. We combine a solid-solution approach for isotopic substitution in minerals with the multiple-continuum reactive-transport approach to interpret the effective fractionation factor observed in experimental systems. Although such systems often have poorly constrained inputs (such as the equilibrium fractionation factor and many of the parameters associated with bacterial growth), by combining several independent contraints on reaction rates (such as lactate consumption, 13C/12C and 87Sr/86Sr in calcite), the range of possible interpretations can often be greatly narrowed. Here we present examples of the modeling approaches and their application to experimental systems to examine why the observed fractionation factors are often different from the theoretical values.

  10. Application of a data assimilation method via an ensemble Kalman filter to reactive urea hydrolysis transport modeling

    SciTech Connect

    Juxiu Tong; Bill X. Hu; Hai Huang; Luanjin Guo; Jinzhong Yang

    2014-03-01

    With growing importance of water resources in the world, remediations of anthropogenic contaminations due to reactive solute transport become even more important. A good understanding of reactive rate parameters such as kinetic parameters is the key to accurately predicting reactive solute transport processes and designing corresponding remediation schemes. For modeling reactive solute transport, it is very difficult to estimate chemical reaction rate parameters due to complex processes of chemical reactions and limited available data. To find a method to get the reactive rate parameters for the reactive urea hydrolysis transport modeling and obtain more accurate prediction for the chemical concentrations, we developed a data assimilation method based on an ensemble Kalman filter (EnKF) method to calibrate reactive rate parameters for modeling urea hydrolysis transport in a synthetic one-dimensional column at laboratory scale and to update modeling prediction. We applied a constrained EnKF method to pose constraints to the updated reactive rate parameters and the predicted solute concentrations based on their physical meanings after the data assimilation calibration. From the study results we concluded that we could efficiently improve the chemical reactive rate parameters with the data assimilation method via the EnKF, and at the same time we could improve solute concentration prediction. The more data we assimilated, the more accurate the reactive rate parameters and concentration prediction. The filter divergence problem was also solved in this study.

  11. Reactive transport in unsaturated soil: Comprehensive modelling of the dynamic spatial and temporal mass balance of water and chemical components

    NASA Astrophysics Data System (ADS)

    Wissmeier, L.; Barry, D. A.

    2008-05-01

    By implementing the moisture-based form of Richards' equation into the geochemical modelling framework PHREEQC, a generic tool for the simulation of one-dimensional flow and solute transport in the vadose zone undergoing complex geochemical reactions was developed. A second-order, cell-centred, explicit finite difference scheme was employed for the numerical solution of the partial differential equations of flow and transport. In this scheme, the charge-balanced soil solution is treated as an assembly of elements, where changes in water and solute contents result from fluxes of elements across cell boundaries. Therefore, water flow is considered in terms of oxygen and hydrogen transport. The direct implementation into the geochemical framework provides access to the full set of reactions available in PHREEQC, giving capabilities beyond existing software for unsaturated flow and reaction. Possible reactions include complex aqueous speciation, cation exchange, equilibrium phase dissolution and precipitation, formation of solid solutions, redox reactions, gas phase exchange, surface adsorption considering electrostatics and kinetic reactions with user-defined rate equations, among others. Geochemical reactions were coupled to transport processes by non-iterative sequential operator splitting. The scheme is currently limited to cases where changes in physical fluid properties and hydraulic flow characteristics due to geochemical reactions are negligible. Results from extensive code verification with analytical and accurate numerical solutions as well as HYDRUS-1D show the excellent performance of the scheme for a variety of hydraulic models including the Brooks and Corey model and the van Genuchten model. High accuracy was gained by the use of integrated diffusivities in the finite difference formulation. The integration of complex geochemical reactions was verified with HP1 by simulating the infiltration of a hyperalkaline solution into a clay soil involving aqueous

  12. Moving from Batch to Field Using the RT3D Reactive Transport Modeling System

    NASA Astrophysics Data System (ADS)

    Clement, T. P.; Gautam, T. R.

    2002-12-01

    The public domain reactive transport code RT3D (Clement, 1997) is a general-purpose numerical code for solving coupled, multi-species reactive transport in saturated groundwater systems. The code uses MODFLOW to simulate flow and several modules of MT3DMS to simulate the advection and dispersion processes. RT3D employs the operator-split strategy which allows the code solve the coupled reactive transport problem in a modular fashion. The coupling between reaction and transport is defined through a separate module where the reaction equations are specified. The code supports a versatile user-defined reaction option that allows users to define their own reaction system through a Fortran-90 subroutine, known as the RT3D-reaction package. Further a utility code, known as BATCHRXN, allows the users to independently test and debug their reaction package. To analyze a new reaction system at a batch scale, users should first run BATCHRXN to test the ability of their reaction package to model the batch data. After testing, the reaction package can simply be ported to the RT3D environment to study the model response under 1-, 2-, or 3-dimensional transport conditions. This paper presents example problems that demonstrate the methods for moving from batch to field-scale simulations using BATCHRXN and RT3D codes. The first example describes a simple first-order reaction system for simulating the sequential degradation of Tetrachloroethene (PCE) and its daughter products. The second example uses a relatively complex reaction system for describing the multiple degradation pathways of Tetrachloroethane (PCA) and its daughter products. References 1) Clement, T.P, RT3D - A modular computer code for simulating reactive multi-species transport in 3-Dimensional groundwater aquifers, Battelle Pacific Northwest National Laboratory Research Report, PNNL-SA-28967, September, 1997. Available at: http://bioprocess.pnl.gov/rt3d.htm.

  13. Upscaling multi-component reactive transport in presence of connected subsurface structures

    NASA Astrophysics Data System (ADS)

    Willmann, M.; Mañé, R.; Tyukhova, A.

    2015-12-01

    Heterogeneity in hydraulic conductivity leads to incomplete mixing. Upscaling using the dispersion tensor in the advection-dispersion equation overestimates local mixing. Modelling multi-component reactive transport leads to an overestimation of reaction rates and overall reactions. Multi-rate mass transfer was shown previously to better represent mixing. But it is still unclear under what conditions this linear model is able to represent the underlying non-linear process. We study explicit multi-component transport in heterogeneous aquifers for the example of calcite-dissolution. We compare different types of heterogeneity from intermediately well connected (multigaussian) fields to very well connected fields. The fundamental difference stems from their connectivity structure. We observe for the well connected field different dominating channels with an almost uniform advective velocity while the multigaussian fields show dominating channels with a varying advective velocity. Then, we compare our results with an effective reactive mass transfer model where the distribution of exchanges rates or the memory function are derived from information of the hydraulic conductivity field only. We see that reactive multi-rate models show a good agreement for the well connected fields where the connected channels are more or less homogeneous and the immobile inclusions are of more or less equal size. We find connectivity important for upscaling reactive transport in highly heterogeneous conductivity fields.

  14. Analytical solutions of one-dimensional multispecies reactive transport in a permeable reactive barrier-aquifer system.

    PubMed

    Mieles, John; Zhan, Hongbin

    2012-06-01

    The permeable reactive barrier (PRB) remediation technology has proven to be more cost-effective than conventional pump-and-treat systems, and has demonstrated the ability to rapidly reduce the concentrations of specific chemicals of concern (COCs) by up to several orders of magnitude in some scenarios. This study derives new steady-state analytical solutions to multispecies reactive transport in a PRB-aquifer (dual domain) system. The advantage of the dual domain model is that it can account for the potential existence of natural degradation in the aquifer, when designing the required PRB thickness. The study focuses primarily on the steady-state analytical solutions of the tetrachloroethene (PCE) serial degradation pathway and secondly on the analytical solutions of the parallel degradation pathway. The solutions in this study can also be applied to other types of dual domain systems with distinct flow and transport properties. The steady-state analytical solutions are shown to be accurate and the numerical program RT3D is selected for comparison. The results of this study are novel in that the solutions provide improved modeling flexibility including: 1) every species can have unique first-order reaction rates and unique retardation factors, and 2) daughter species can be modeled with their individual input concentrations or solely as byproducts of the parent species. The steady-state analytical solutions exhibit a limitation that occurs when interspecies reaction rate factors equal each other, which result in undefined solutions. Excel spreadsheet programs were created to facilitate prompt application of the steady-state analytical solutions, for both the serial and parallel degradation pathways. PMID:22579667

  15. Quantifying Fluxes of Chemical and Biological Species in Great Lakes Watersheds: A Reactive Transport Modeling Framework

    NASA Astrophysics Data System (ADS)

    Niu, J.; Phanikumar, M. S.

    2012-12-01

    Understanding and quantifying the interactions between hydro-climatic processes and the fate and transport of aquatic pollutants and the resultant threats to human and ecosystem health is a high priority research area in many parts of the world. In the Great Lakes region, harmful algal blooms, increased beach closures due to microbiological pollution and drinking water related issues continue to be causes for concern in recent years highlighting the need for accurate transport models. In this presentation we describe the development of a watershed-scale multi-component reactive transport modeling framework to describe fluxes of nutrients and bacteria exported to the Great Lakes. We describe an operator-splitting strategy combined with a particle transport modeling approach with reactions to describe transport in different hydrologic units with interactions between domains. The algorithms are tested using analytical solutions (where available), data from plot-scale experiments and monitoring data from watersheds in the Great Lakes region.

  16. Reprint of : Connection between wave transport through disordered 1D waveguides and energy density inside the sample: A maximum-entropy approach

    NASA Astrophysics Data System (ADS)

    Mello, Pier A.; Shi, Zhou; Genack, Azriel Z.

    2016-08-01

    We study the average energy - or particle - density of waves inside disordered 1D multiply-scattering media. We extend the transfer-matrix technique that was used in the past for the calculation of the intensity beyond the sample to study the intensity in the interior of the sample by considering the transfer matrices of the two segments that form the entire waveguide. The statistical properties of the two disordered segments are found using a maximum-entropy ansatz subject to appropriate constraints. The theoretical expressions are shown to be in excellent agreement with 1D transfer-matrix simulations.

  17. Computational methods for reactive transport modeling: A Gibbs energy minimization approach for multiphase equilibrium calculations

    NASA Astrophysics Data System (ADS)

    Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg

    2016-02-01

    We present a numerical method for multiphase chemical equilibrium calculations based on a Gibbs energy minimization approach. The method can accurately and efficiently determine the stable phase assemblage at equilibrium independently of the type of phases and species that constitute the chemical system. We have successfully applied our chemical equilibrium algorithm in reactive transport simulations to demonstrate its effective use in computationally intensive applications. We used FEniCS to solve the governing partial differential equations of mass transport in porous media using finite element methods in unstructured meshes. Our equilibrium calculations were benchmarked with GEMS3K, the numerical kernel of the geochemical package GEMS. This allowed us to compare our results with a well-established Gibbs energy minimization algorithm, as well as their performance on every mesh node, at every time step of the transport simulation. The benchmark shows that our novel chemical equilibrium algorithm is accurate, robust, and efficient for reactive transport applications, and it is an improvement over the Gibbs energy minimization algorithm used in GEMS3K. The proposed chemical equilibrium method has been implemented in Reaktoro, a unified framework for modeling chemically reactive systems, which is now used as an alternative numerical kernel of GEMS.

  18. Enhancing the design of in situ chemical barriers with multicomponent reactive transport modeling

    SciTech Connect

    Sevougian, S.D.; Steefel, C.I.; Yabusaki, S.B.

    1994-11-01

    This paper addresses the need for systematic control of field-scale performance in the emplacement and operation of in situ chemical treatment barriers; in particular, it addresses the issue of how the local coupling of reaction kinetics and material heterogeneities at the laboratory or bench scale can be accurately upscaled to the field. The authors have recently developed modeling analysis tools that can explicitly account for all relevant chemical reactions that accompany the transport of reagents and contaminants through a chemically and physically heterogeneous subsurface rock or soil matrix. These tools are incorporated into an enhanced design methodology for in situ chemical treatment technologies, and the new methodology is demonstrated in the ongoing design of a field experiment for the In Situ Redox Manipulation (ISRM) project at the U.S. Department of Energy (DOE) Hanford Site. The ISRM design approach, which systematically integrates bench-scale and site characterization information, provides an ideal test for the new reactive transport techniques. The need for the enhanced chemistry capability is demonstrated by an example that shows how intra-aqueous redox kinetics can affect the transport of reactive solutes. Simulations are carried out on massively parallel computer architectures to resolve the influence of multiscale heterogeneities on multicomponent, multidimensional reactive transport. The technology will soon be available to design larger-scale remediation schemes.

  19. Reactive Transport Modeling of Microbe-mediated Fe (II) Oxidation for Enhanced Oil Recovery

    NASA Astrophysics Data System (ADS)

    Surasani, V.; Li, L.

    2011-12-01

    Microbially Enhanced Oil Recovery (MEOR) aims to improve the recovery of entrapped heavy oil in depleted reservoirs using microbe-based technology. Reservoir ecosystems often contain diverse microbial communities those can interact with subsurface fluids and minerals through a network of nutrients and energy fluxes. Microbe-mediated reactions products include gases, biosurfactants, biopolymers those can alter the properties of oil and interfacial interactions between oil, brine, and rocks. In addition, the produced biomass and mineral precipitates can change the reservoir permeability profile and increase sweeping efficiency. Under subsurface conditions, the injection of nitrate and Fe (II) as the electron acceptor and donor allows bacteria to grow. The reaction products include minerals such as Fe(OH)3 and nitrogen containing gases. These reaction products can have large impact on oil and reservoir properties and can enhance the recovery of trapped oil. This work aims to understand the Fe(II) oxidation by nitrate under conditions relevant to MEOR. Reactive transport modeling is used to simulate the fluid flow, transport, and reactions involved in this process. Here we developed a complex reactive network for microbial mediated nitrate-dependent Fe (II) oxidation that involves both thermodynamic controlled aqueous reactions and kinetic controlled Fe (II) mineral reaction. Reactive transport modeling is used to understand and quantify the coupling between flow, transport, and reaction processes. Our results identify key parameter controls those are important for the alteration of permeability profile under field conditions.

  20. Reactive transport LBM model for CO2 injection in fractured reservoirs

    NASA Astrophysics Data System (ADS)

    Tian, Zhiwei; Xing, Huilin; Tan, Yunliang; Gu, Sai; Golding, Suzanne D.

    2016-01-01

    A geochemical LBM model has been developed to simulate the CO2 injection in homogeneous porous media in our previous work. That model has the ability to investigate the coupled reactive transport processes with reactants and products ions transport, matrix dissolution, and dissolution induced porosity change. In the present work, the model is extended to study the reactive transport properties in "fractured" media. Two kinds of fractures are investigated: one is straightforward along the centerline, and the other is inclined. The reaction rate distribution and evolution are analyzed at different time steps. The dissolution property of fracture edges is also studied, the bottom edge dissolution rate is generally higher than that of the upper edge in inclined fractured media. The porosity change becomes more and more obvious with the increase of time steps, as well as the edge porosity profiles. For the different fracture width, the dissolution rate and edge porosity become higher with the increase of fracture width. All the results show that the present model has the capability to numerically investigate CO2 injection and reactive transport in fractured reservoirs.

  1. Efficient chemical equilibrium calculations for geochemical speciation and reactive transport modelling

    NASA Astrophysics Data System (ADS)

    Leal, Allan M. M.; Blunt, Martin J.; LaForce, Tara C.

    2014-04-01

    Chemical equilibrium calculations are essential for many environmental problems. It is also a fundamental tool for chemical kinetics and reactive transport modelling, since these applications may require hundreds to billions equilibrium calculations in a single simulation. Therefore, an equilibrium method for such critical applications must be very efficient, robust and accurate. In this work we demonstrate the potential effectiveness of a novel Gibbs energy minimisation algorithm for reactive transport simulations. The algorithm includes strategies to converge from poor initial guesses; capabilities to specify non-linear equilibrium constraints such as pH of an aqueous solution and activity or fugacity of a species; a rigorous phase stability test to determine the unstable phases; and a strategy to boost the convergence speed of the calculations to quadratic rates, requiring only few iterations to converge. We use this equilibrium method to solve geochemical problems relevant to carbon storage in saline aquifers, where aqueous, gaseous and minerals phases are present. The problems are formulated to mimic the ones found in kinetics and transport simulations, where a sequence of equilibrium calculations are performed, each one using the previous solution as the initial guess. The efficiency and convergence rates of the calculations are presented, which require an average of 1-2 iterations. These results indicate that critical applications such as chemical kinetics and reactive transport modelling can potentially benefit by using this multiphase equilibrium algorithm.

  2. Reactive transport in a partially molten system with binary solid solution

    NASA Astrophysics Data System (ADS)

    Jordan, Jacob S.; Hesse, Marc A.

    2015-12-01

    Melt extraction from the Earth's mantle through high-porosity channels is required to explain the composition of the oceanic crust. Feedbacks from reactive melt transport are thought to localize melt into a network of high-porosity channels. Recent studies invoke lithological heterogeneities in the Earth's mantle to seed the localization of partial melts. Therefore, it is necessary to understand the reaction fronts that form as melt flows across the lithological interface between the heterogeneity and the ambient mantle. Here we present a chromatographic analysis of reactive melt transport across lithological boundaries, using the theory of hyperbolic conservation laws. This is an extension of linear trace element chromatography to the coupling of major elements and energy transport. Our analysis allows the prediction of the nonlinear feedbacks that arise in reactive melt transport due to changes in porosity. This study considers the special case of a partially molten porous medium with binary solid solution. As melt traverses a lithological contact, binary solid solution leads to the formation of a reacted zone between an advancing reaction front and the initial contact. The analysis also shows that the behavior of a fertile heterogeneity depends on its absolute concentration, in addition to compositional differences between itself and the refractory background. We present a regime diagram that predicts if melt emanating from a fertile heterogeneity localizes into high-porosity channels or develops a zero porosity shell. The theoretical framework presented here provides a useful tool for understanding nonlinear feedbacks in reactive melt transport, because it can be extended to more complex and realistic phase behaviors.

  3. Illuminating reactive microbial transport in saturated porous media: Demonstration of a visualization method and conceptual transport model

    NASA Astrophysics Data System (ADS)

    Oates, Peter M.; Castenson, Catherine; Harvey, Charles F.; Polz, Martin; Culligan, Patricia

    2005-05-01

    We demonstrate a method to study reactive microbial transport in saturated translucent porous media using the bacteria Pseudomonas fluorescens 5RL genetically engineered to carry a plasmid with bioluminescence genes inducible by salicylate. Induced bacteria were injected into a cryolite grain filled chamber saturated with a sterile non-growth-promoting (phosphorus limited) chemical mixture containing salicylate as an aromatic hydrocarbon analogue. The amount of light produced by the bacteria serves as an estimator of the relative efficiency of aerobic biodegradation since bioluminescence is dependent on both salicylate and oxygen but only consumes oxygen. Bioluminescence was captured with a digital camera and analyzed to study the evolving spatial pattern of the bulk oxygen consuming reactions. As fluid flow transported the bacteria through the chamber, bioluminescence was observed to initially increase until an oxygen depletion zone developed behind the advective front. Bacterial transport was modeled with the advection dispersion equation and oxygen concentration was modeled assuming bacterial consumption via Monod kinetics with consideration of additional effects of rate-limited mass transfer from residual gas bubbles. Consistent with previous measurements, bioluminescence was considered proportional to oxygen consumed. Using the observed bioluminescence, model parameters were fit that were consistent with literature values and produced results in good agreement with the experimental data. These findings demonstrate potential for using this method to investigate the complex spatial and temporal dynamics of reactive microbial transport in saturated porous media.

  4. Illuminating reactive microbial transport in saturated porous media: demonstration of a visualization method and conceptual transport model.

    PubMed

    Oates, Peter M; Castenson, Catherine; Harvey, Charles F; Polz, Martin; Culligan, Patricia

    2005-05-01

    We demonstrate a method to study reactive microbial transport in saturated translucent porous media using the bacteria Pseudomonas fluorescens 5RL genetically engineered to carry a plasmid with bioluminescence genes inducible by salicylate. Induced bacteria were injected into a cryolite grain filled chamber saturated with a sterile non-growth-promoting (phosphorus limited) chemical mixture containing salicylate as an aromatic hydrocarbon analogue. The amount of light produced by the bacteria serves as an estimator of the relative efficiency of aerobic biodegradation since bioluminescence is dependent on both salicylate and oxygen but only consumes oxygen. Bioluminescence was captured with a digital camera and analyzed to study the evolving spatial pattern of the bulk oxygen consuming reactions. As fluid flow transported the bacteria through the chamber, bioluminescence was observed to initially increase until an oxygen depletion zone developed behind the advective front. Bacterial transport was modeled with the advection dispersion equation and oxygen concentration was modeled assuming bacterial consumption via Monod kinetics with consideration of additional effects of rate-limited mass transfer from residual gas bubbles. Consistent with previous measurements, bioluminescence was considered proportional to oxygen consumed. Using the observed bioluminescence, model parameters were fit that were consistent with literature values and produced results in good agreement with the experimental data. These findings demonstrate potential for using this method to investigate the complex spatial and temporal dynamics of reactive microbial transport in saturated porous media. PMID:15854718

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

    USGS Publications Warehouse

    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.

  6. Reactive Transport Modeling Approach and its Initial Saltcake Dilution Chemical Modeling

    SciTech Connect

    Onishi, Yasuo

    2002-11-29

    During waste retrieval, chemical reactions, waste property changes, and waste movements/mixing interact. Thus,to be accurate, a waste process assessment methodology must account for these physical and chemical waste characteristics and mechanisms. This study provides suggestions for column tests and simulation modeling efforts to investigate saltwell pumping of Hanford Tank S-112. In addition, GMIN chemical modeling was initiated for S-112 saltcake dilution with 50% and 100% water as the first step of evaluating the feasibility of the reactive transport code ARIEL as a waste retrieval assessment methodology. The chemical modeling predicted the S-112 saltcake chemistry reasonably well. Although it is too early to conclude the usefulness of this reactive transport modeling approach, it is worth further evaluating its applicability to the waste retrieval process.

  7. Coupling lattice Boltzmann and continuum equations for flow and reactive transport in porous media.

    SciTech Connect

    Coon, Ethan; Porter, Mark L.; Kang, Qinjun; Moulton, John D.; Lichtner, Peter C.

    2012-06-18

    In spatially and temporally localized instances, capturing sub-reservoir scale information is necessary. Capturing sub-reservoir scale information everywhere is neither necessary, nor computationally possible. The lattice Boltzmann Method for solving pore-scale systems. At the pore-scale, LBM provides an extremely scalable, efficient way of solving Navier-Stokes equations on complex geometries. Coupling pore-scale and continuum scale systems via domain decomposition. By leveraging the interpolations implied by pore-scale and continuum scale discretizations, overlapping Schwartz domain decomposition is used to ensure continuity of pressure and flux. This approach is demonstrated on a fractured medium, in which Navier-Stokes equations are solved within the fracture while Darcy's equation is solved away from the fracture Coupling reactive transport to pore-scale flow simulators allows hybrid approaches to be extended to solve multi-scale reactive transport.

  8. Inverse modeling of multicomponent reactive transport through single and dual porosity media.

    PubMed

    Samper, Javier; Zheng, Liange; Fernández, Ana María; Montenegro, Luis

    2008-06-01

    Compacted bentonite is foreseen as buffer material for high-level radioactive waste in deep geological repositories because it provides hydraulic isolation, chemical stability, and radionuclide sorption. A wide range of laboratory tests were performed within the framework of FEBEX (Full-scale Engineered Barrier EXperiment) project to characterize buffer properties and develop numerical models for FEBEX bentonite. Here we present inverse single and dual-continuum multicomponent reactive transport models of a long-term permeation test performed on a 2.5 cm long sample of FEBEX bentonite. Initial saline bentonite porewater was flushed with 5.5 pore volumes of fresh granitic water. Water flux and chemical composition of effluent waters were monitored during almost 4 years. The model accounts for solute advection and diffusion and geochemical reactions such as aqueous complexation, acid-base, cation exchange, protonation/deprotonation by surface complexation and dissolution/precipitation of calcite, chalcedony and gypsum. All of these processes are assumed at local equilibrium. Similar to previous studies of bentonite porewater chemistry on batch systems which attest the relevance of protonation/deprotonation on buffering pH, our results confirm that protonation/deprotonation is a key process in maintaining a stable pH under dynamic transport conditions. Breakthrough curves of reactive species are more sensitive to initial porewater concentration than to effective diffusion coefficient. Optimum estimates of initial porewater chemistry of saturated compacted FEBEX bentonite are obtained by solving the inverse problem of multicomponent reactive transport. While the single-continuum model reproduces the trends of measured data for most chemical species, it fails to match properly the long tails of most breakthrough curves. Such limitation is overcome by resorting to a dual-continuum reactive transport model. PMID:18468720

  9. Coupled inverse geochemical and microbial reactive transport models in porous media

    NASA Astrophysics Data System (ADS)

    Samper, J.; Yang, C.

    2007-12-01

    Microbial processes play a major role in controlling geochemical conditions in subsurface systems. Various laboratory and in situ experiments have been performed to evaluate the relevance of microbial processes and derive key microbial parameters. Such experiments are often interpreted by suboptimal trial-and-error curve fitting. Here we present an inverse model for coupled flow, reactive solute transport, geochemical and microbial processes which overcomes the limitations of trial-and-error methods by making data interpretation in a systematic, objective, and efficient manner. It extends the capabilities of existing inverse models which deal mostly with flow and chemically-reactive solute transport. Our inverse model relies on the microbial reactive transport code BIOCORE of Samper et al. (2006a) and improves the inverse reactive transport model INVERSE- CORE of Dai and Samper (2004) by allowing the simultaneous estimation of geochemical and microbial parameters. The inverse model has been implemented in a finite element code, INVERSE-BIOCORE2D and its capabilities have been verified and tested with a synthetic experiment involving equilibrium speciation, kinetic sorption/desorption and kinetic biodegradation reactions. Model results indicate that both chemical and microbial parameters can be estimated accurately for error-free data. Estimation errors of microbial parameters are larger than those of kinetic sorption parameters and generally increase with increasing standard deviation of data noise. Estimation error of yield coefficient is the smallest among all microbial parameter and which does not depend on data noise. The inverse model has been used also to estimate microbial parameters of a laboratory experiment involving sucrose fermentation by yeast. Inverse estimation improves significantly the fit to measured data.

  10. Reactive transport modeling at uranium in situ recovery sites: uncertainties in uranium sorption on iron hydroxides

    USGS Publications Warehouse

    Johnson, Raymond H.; Tutu, Hlanganani

    2013-01-01

    Geochemical changes that can occur down gradient from uranium in situ recovery (ISR) sites are important for various stakeholders to understand when evaluating potential effects on surrounding groundwater quality. If down gradient solid-phase material consists of sandstone with iron hydroxide coatings (no pyrite or organic carbon), sorption of uranium on iron hydroxides can control uranium mobility. Using one-dimensional reactive transport models with PHREEQC, two different geochemical databases, and various geochemical parameters, the uncertainties in uranium sorption on iron hydroxides are evaluated, because these oxidized zones create a greater risk for future uranium transport than fully reduced zones where uranium generally precipitates.

  11. Development of a New and Fast Linear Solver for Multi-component Reactive Transport Simulation

    NASA Astrophysics Data System (ADS)

    Qiao, C.; Li, L.; Bao, C.; Hu, X.; Johns, R.; Xu, J.

    2013-12-01

    Reactive transport models (RTM) have been extensively used to understand the coupling between solute transport and (bio) geochemical reactions in complex earth systems. RTM typically involves a large number of primary and secondary species with a complex reaction network in large domains. The computational expenses increase significantly with the number of grid blocks and the number of chemical species. Within both the operator splitting approach (OS) and the global implicit approach (GI) that are commonly used, the steps that involve Newton-Raphson method are typically one of the most time-consuming parts (up to 80% to 90% of CPU times). Under such circumstances, accelerating reactive transport simulation is very essential. In this research, we present a physics-based linear system solution strategy for general reactive transport models with many species. We observed up to five times speed up for the linear solver portion of the simulations in our test cases. Our new linear solver takes advantage of the sparsity of the Jacobian matrix arising from the reaction network. The Jacobian matrix for the speciation problem is typically considered as a dense matrix and solved with a direct method such as Gaussian elimination. For the reactive transport problem, the graph of the local Jacobian matrix has a one-to-one correspondence to the reaction network graph. The Jacobian matrix is commonly sparse and has the same sparsity structure for the same reaction network. We developed a strategy that performs a minimum degree of reordering and symbolic factorization to determine the non-zero pattern at the beginning of the OS and GI simulation. During the speciation calculation in OS, we calculate the L and U factors and solve the triangular matrices according to the non-zero pattern. For GI, our strategy can be applied to inverse the diagonal blocks in the block-Jacobi preconditioner and smoothers of the multigrid preconditioners in iterative solvers. Our strategy is naturally

  12. Modeling non-isothermal multiphase multi-species reactive chemical transport in geologic media

    SciTech Connect

    Tianfu Xu; Gerard, F.; Pruess, K.; Brimhall, G.

    1997-07-01

    The assessment of mineral deposits, the analysis of hydrothermal convection systems, the performance of radioactive, urban and industrial waste disposal, the study of groundwater pollution, and the understanding of natural groundwater quality patterns all require modeling tools that can consider both the transport of dissolved species as well as their interactions with solid (or other) phases in geologic media and engineered barriers. Here, a general multi-species reactive transport formulation has been developed, which is applicable to homogeneous and/or heterogeneous reactions that can proceed either subject to local equilibrium conditions or kinetic rates under non-isothermal multiphase flow conditions. Two numerical solution methods, the direct substitution approach (DSA) and sequential iteration approach (SIA) for solving the coupled complex subsurface thermo-physical-chemical processes, are described. An efficient sequential iteration approach, which solves transport of solutes and chemical reactions sequentially and iteratively, is proposed for the current reactive chemical transport computer code development. The coupled flow (water, vapor, air and heat) and solute transport equations are also solved sequentially. The existing multiphase flow code TOUGH2 and geochemical code EQ3/6 are used to implement this SIA. The flow chart of the coupled code TOUGH2-EQ3/6, required modifications of the existing codes and additional subroutines needed are presented.

  13. RAFT: A simulator for ReActive Flow and Transport of groundwater contaminants

    SciTech Connect

    Chilakapati, A

    1995-07-01

    This report documents the use of the simulator RAFT for the ReActive flow and Transport of groundwater contaminants. RAFT can be used as a predictive tool in the design and analysis of laboratory and field experiments or it can be used for the estimation of model/process parameters from experiments. RAFT simulates the reactive transport of groundwater contaminants in one, two-, or three-dimensions and it can model user specified source/link configurations and arbitrary injection strategies. A suite of solvers for transport, reactions and regression are employed so that a combination of numerical methods best suited for a problem can be chosen. User specified coupled equilibrium and kinetic reaction systems can be incorporated into RAFT. RAFT is integrated with a symbolic computational language MAPLE, to automate code generation for arbitrary reaction systems. RAFT is expected to be used as a simulator for engineering design for field experiments in groundwater remediation including bioremediation, reactive barriers and redox manipulation. As an integrated tool with both the predictive ability and the ability to analyze experimental data, RAFT can help in the development of remediation technologies, from laboratory to field.

  14. First-principles derivation of reactive transport modeling parameters for particle tracking and PDE approaches

    NASA Astrophysics Data System (ADS)

    Hansen, Scott K.; Scher, Harvey; Berkowitz, Brian

    2014-07-01

    Both Eulerian and Lagrangian reactive transport simulations in natural media require selection of a parameter that controls the “promiscuity” of the reacting particles. In Eulerian models, measurement of this parameter may be difficult because its value will generally differ between natural (diffusion-limited) systems and batch experiments, even though both are modeled by reaction terms of the same form. And in Lagrangian models, there previously has been no a priori way to compute this parameter. In both cases, then, selection is typically done by calibration, or ad hoc. This paper addresses the parameter selection problem for Fickian transport by deriving, from first principles and D (the diffusion constant) the reaction-rate-controlling parameters for particle tracking (PT) codes and for the diffusion-reaction equation (DRE). Using continuous time random walk analysis, exact reaction probabilities are derived for pairs of potentially reactive particles based on D and their probability of reaction provided that they collocate. Simultaneously, a second PT scheme directly employing collocation probabilities is derived. One-to-one correspondence between each of D, the reaction radius specified for a PT scheme, and the DRE decay constant are then developed. These results serve to ground reactive transport simulations in their underlying thermodynamics, and are confirmed by simulations.

  15. Multicomponent reactive transport modeling of acid neutralization reactions in mine tailings

    NASA Astrophysics Data System (ADS)

    Jurjovec, Jasna; Blowes, David W.; Ptacek, Carol J.; Mayer, K. Ulrich

    2004-11-01

    Multicomponent reactive transport modeling was conducted to analyze and quantify the acid neutralization reactions observed in a column experiment. Experimental results and the experimental procedures have been previously published. The pore water geochemistry was described by dissolution and precipitation reactions involving primary and secondary mineral phases. The initial amounts of the primary phases ankerite-dolomite, siderite, chlorite, and gypsum were constrained by mineralogical analyses of the tailings sample used in the experiment. Secondary gibbsite was incorporated into the model to adequately explain the changes in pH and concentration changes of Al in the column effluent water. The results of the reactive transport modeling show that the pH of the column effluent water can be explained by dissolution reactions of ankerite-dolomite, siderite, chlorite, and secondary gibbsite. The modeling results also show that changes in Eh can be explained by dissolution of ferrihydrite during the experiment. In addition, the modeling results show that the kinetically limited dissolution of chlorite contributes the largest mass of dissolved Mg and Fe (II) in the effluent water, followed by ankerite-dolomite, which contributes substantially less. In summary, reactive transport modeling based on detailed geochemical and mineralogical data was successful to quantitatively describe the changes in pH and major ions in the column effluent.

  16. Influence of Sedimentary Bedding on Reactive Transport Parameters under Unsaturated Conditions

    SciTech Connect

    Mayes, Melanie; Tang, Guoping; Jardine, Philip M; McKay, Larry Donald; Yin, Xiangping Lisa; Pace, M. N.; Parker, Jack C; Zhang, Fan; Mehlhorn, Tonia L; Dansby-Sparks, Royce N

    2009-01-01

    Moisture and contaminant transport in partially saturated, heterogeneous, layered sediments is typically anisotropic. Solute transport parameters, including dispersivity and the adsorption coefficient, and the modeled concentration of reactive minerals may depend on the direction of flow with respect to sedimentary layering. Reaction rates, in contrast, should be independent of flow direction. We determined the influence of flow direction on transport parameters for nonreactive (Br{sup -}) and reactive (cobalt ethylenediaminetetraacetic acid [Co(II)EDTA{sup 2-}]) solutes under partially saturated conditions by imposing flow either parallel to or across sedimentary bedding in 11 intact sediment cores of various textures. Higher dispersivity of nonreactive tracers in parallel-bed cores suggested fluid channeling through permeable layers, while low-conductivity layers dampened channeling in cross-bed samples. Rates of transformation of Co(II)EDTA{sup 2-} into Co(III)EDTA{sup -} and of disassociation of Co{sup 2+} and EDTA{sup 4-} were modeled assuming that the reaction rates were independent of the flow direction. The concentration of Mn oxides that was responsible for the transformation reaction was dependent on the flow direction, which governed the extent of contact between the solution and the solid phase. Similarly, the adsorption constants of Co(II)EDTA{sup 2-} and Co(III)EDTA{sup -} were dependent on the flow direction but were also unique for each experiment. The modeled concentration of reactive minerals was the most sensitive parameter describing the reaction and transformation of Co(II)EDTA{sup 2-}.

  17. THC-MP: High performance numerical simulation of reactive transport and multiphase flow in porous media

    NASA Astrophysics Data System (ADS)

    Wei, Xiaohui; Li, Weishan; Tian, Hailong; Li, Hongliang; Xu, Haixiao; Xu, Tianfu

    2015-07-01

    The numerical simulation of multiphase flow and reactive transport in the porous media on complex subsurface problem is a computationally intensive application. To meet the increasingly computational requirements, this paper presents a parallel computing method and architecture. Derived from TOUGHREACT that is a well-established code for simulating subsurface multi-phase flow and reactive transport problems, we developed a high performance computing THC-MP based on massive parallel computer, which extends greatly on the computational capability for the original code. The domain decomposition method was applied to the coupled numerical computing procedure in the THC-MP. We designed the distributed data structure, implemented the data initialization and exchange between the computing nodes and the core solving module using the hybrid parallel iterative and direct solver. Numerical accuracy of the THC-MP was verified through a CO2 injection-induced reactive transport problem by comparing the results obtained from the parallel computing and sequential computing (original code). Execution efficiency and code scalability were examined through field scale carbon sequestration applications on the multicore cluster. The results demonstrate successfully the enhanced performance using the THC-MP on parallel computing facilities.

  18. Toward Optimized Bioclogging and Biocementation Through Combining Advanced Geophysical Monitoring and Reactive Transport Modeling Approaches

    NASA Astrophysics Data System (ADS)

    Hubbard, C. G.; Hubbard, S. S.; Wu, Y.; Surasani, V.; Ajo Franklin, J. B.; Commer, M.; Dou, S.; Kwon, T.; Li, L.; Fouke, B. W.; Coates, J. D.

    2012-12-01

    Bioclogging and biocementation offer exciting opportunities for solutions to diverse problems ranging from soil stabilization to microbially enhanced hydrocarbon recovery. The effectiveness of bioclogging and biocementation strategies is governed by processes and properties ranging from microbial metabolism at the submicron scale, to changes in pore geometry at the pore scale, to geological heterogeneities at the field scale. Optimization of these strategies requires advances in mechanistic reactive transport modeling and geophysical monitoring methodologies. Our research focuses on (i) performing laboratory experiments to refine understanding of reaction networks and to quantify changes in hydrological properties (e.g. permeability), the evolution of biominerals and geophysical responses (focusing on seismic and electrical techniques); (ii) developing and using a reactive transport simulator capable of predicting the induced metabolic processes to numerically explore how to optimize the desired effect; and (iii) using loosely coupled reactive transport and geophysical simulators to explore detectability and resolvability of induced bioclogging and biocementation processes at the field scale using time-lapse geophysical methods. Here we present examples of our research focused on three different microbially-mediated methods to enhance hydrocarbon recovery through selective clogging of reservior thief zones, including: (a) biopolymer clogging through dextran production; (b) biomineral clogging through iron oxide precipitation; and (c) biomineral clogging through carbonate precipitation. We will compare the utility of these approaches for enhancing hydrocarbon recovery and will describe the utility of geophysical methods to remotely monitor associated field treatments.

  19. Semianalytical Solutions of Radioactive or Reactive Tracer Transport in Layered Fractured Media

    SciTech Connect

    G.J. Moridis; G. S. Bodvarsson

    2001-10-01

    In this paper, semianalytical solutions are developed for the problem of transport of radioactive or reactive tracers (solutes or colloids) through a layered system of heterogeneous fractured media with misaligned fractures. The tracer transport equations in the matrix account for (a) diffusion, (b) surface diffusion (for solutes only), (c) mass transfer between the mobile and immobile water fractions, (d) linear kinetic or equilibrium physical, chemical, or combined solute sorption or colloid filtration, and (e) radioactive decay or first order chemical reactions. Any number of radioactive decay daughter products (or products of a linear, first-order reaction chain) can be tracked. The tracer-transport equations in the fractures account for the same processes, in addition to advection and hydrodynamic dispersion. Additionally, the colloid transport equations account for straining and velocity adjustments related to the colloidal size. The solutions, which are analytical in the Laplace space, are numerically inverted to provide the solution in time and can accommodate any number of fractured and/or porous layers. The solutions are verified using analytical solutions for limiting cases of solute and colloid transport through fractured and porous media. The effect of important parameters on the transport of {sup 3}H, {sup 237}Np and {sup 239}Pu (and its daughters) is investigated in several test problems involving layered geological systems of varying complexity. {sup 239}Pu colloid transport problems in multilayered systems indicate significant colloid accumulations at straining interfaces but much faster transport of the colloid than the corresponding strongly sorbing solute species.

  20. Semianalytical solutions of radioactive or reactive tracer transport in layered fractured media

    SciTech Connect

    Moridis, G.J.; Bodvarsson, G.S.

    2001-10-10

    In this paper, semianalytical solutions are developed for the problem of transport of radioactive or reactive tracers (solutes or colloids) through a layered system of heterogeneous fractured media with misaligned fractures. The tracer transport equations in the matrix account for (a) diffusion, (b) surface diffusion (for solutes only), (c) mass transfer between the mobile and immobile water fractions, (d) linear kinetic or equilibrium physical, chemical, or combined solute sorption or colloid filtration, and (e) radioactive decay or first order chemical reactions. Any number of radioactive decay daughter products (or products of a linear, first-order reaction chain) can be tracked. The tracer-transport equations in the fractures account for the same processes, in addition to advection and hydrodynamic dispersion. Additionally, the colloid transport equations account for straining and velocity adjustments related to the colloidal size. The solutions, which are analytical in the Laplace space, are numerically inverted to provide the solution in time and can accommodate any number of fractured and/or porous layers. The solutions are verified using analytical solutions for limiting cases of solute and colloid transport through fractured and porous media. The effect of important parameters on the transport of {sup 3}H, {sup 237}Np and {sup 239}Pu (and its daughters) is investigated in several test problems involving layered geological systems of varying complexity. {sup 239}Pu colloid transport problems in multilayered systems indicate significant colloid accumulations at straining interfaces but much faster transport of the colloid than the corresponding strongly sorbing solute species.

  1. A coupling alternative to reactive transport simulations for long-term prediction of chemical reactions in heterogeneous CO2 storage systems

    NASA Astrophysics Data System (ADS)

    De Lucia, M.; Kempka, T.; Kühn, M.

    2015-02-01

    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.

  2. A coupling alternative to reactive transport simulations for long-term prediction of chemical reactions in heterogeneous CO2 storage systems

    NASA Astrophysics Data System (ADS)

    De Lucia, M.; Kempka, T.; Kühn, M.

    2014-09-01

    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 immobilization 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 showed 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 in the order of million elements, profiting from much better description of heterogeneous reservoirs at a fraction of the calculation time of fully coupled models.

  3. Assessment of controlling processes for field-scale uranium reactive transport under highly transient flow conditions

    NASA Astrophysics Data System (ADS)

    Ma, Rui; Zheng, Chunmiao; Liu, Chongxuan; Greskowiak, Janek; Prommer, Henning; Zachara, John M.

    2014-02-01

    This paper presents the results of a comprehensive model-based analysis of a uranyl [U(VI)] tracer test conducted at the U.S. DOE Hanford 300 Area (300A) IFRC. Despite the highly complex field conditions the numerical three-dimensional multicomponent reactive transport model was able to capture most of the spatiotemporal variations of the observed U(VI) concentrations. A multimodel analysis was performed to interrogate the relative importance of various processes and factors for controlling field-scale reactive transport during the uranyl tracer test. The results indicate that multirate sorption/desorption, surface complexation reactions, and initial concentration distributions were the most important processes and factors controlling U(VI) migration. On the other hand, cation exchange reactions, the choice of the surface complexation model, and dual-domain mass transfer processes played less important roles under the prevailing field-test conditions. Further analysis of the modeling results demonstrates that these findings are conditioned to the relatively stable groundwater chemistry and the selected length of the field experimental duration (16 days). The model analysis also revealed the crucial role of the intraborehole flow that occurred within the long-screened monitoring wells and thus affected both field measurements and simulated U(VI) concentrations as a combined effect of aquifer heterogeneity and dynamic flow conditions. This study provides the first highly data-constrained uranium transport simulations under highly dynamic flow conditions. It illustrates the value of reactive transport modeling for elucidating the relative importance of individual processes in controlling uranium transport under specific field-scale conditions.

  4. Reactive Transport Modeling of CO2-induced Porosity and Permeability Changes in Heterogeneous Carbonate Rocks

    NASA Astrophysics Data System (ADS)

    Hao, Y.; Smith, M. M.; Mason, H. E.; Carroll, S.

    2015-12-01

    It has long been appreciated that chemical interactions have a major effect on rock porosity and permeability evolution and may alter the behavior or performance of both natural and engineered reservoir systems. Such reaction-induced permeability evolution is of particular importance for geological CO2 sequestration and storage associated with enhanced oil recovery. In this study we used a three-dimensional Darcy scale reactive transport model to simulate CO2 core flood experiments in which the CO2-equilibrated brine was injected into dolostone cores collected from the Arbuckle carbonate reservoir, Wellington, Kansas. Heterogeneous distributions of macro pores, fractures, and mineral phases inside the cores were obtained from X-ray computed microtomography (XCMT) characterization data, and then used to construct initial model macroscopic properties including porosity, permeability, and mineral compositions. The reactive transport simulations were performed by using the Nonisothermal Unsaturated Flow and Transport (NUFT) code, and their results were compared with experimental data. It was observed both experimentally and numerically that the dissolution fronts became unstable in highly heterogeneous and less permeable formations, leading to the development of highly porous flow paths or wormholes. Our model results indicate that the continuum-scale reactive transport models are able to adequately capture the evolution of distinct dissolution fronts as observed in carbonate rocks at a core scale. The impacts of rock heterogeneity, chemical kinetics and porosity-permeability relationships were also examined in this study. The numerical model developed in this study will not only help improve understanding of coupled physical and chemical processes controlling carbonate dissolution, but also provide a useful basis for upscaling transport and reaction properties from core scale to field scale. This work was performed under the auspices of the U.S. Department of Energy

  5. A Dual Regime Reactive Transport Model for Simulation of High Level Waste Tank Closure Scenarios - 13375

    SciTech Connect

    Sarkar, Sohini; Kosson, David S.; Brown, Kevin; Garrabrants, Andrew C.; Meeussen, Hans; Van der Sloot, Hans

    2013-07-01

    A numerical simulation framework is presented in this paper for estimating evolution of pH and release of major species from grout within high-level waste tanks after closure. This model was developed as part of the Cementitious Barriers Partnership. The reactive transport model consists of two parts - (1) transport of species, and (2) chemical reactions. The closure grout can be assumed to have varying extents of cracking and composition for performance assessment purposes. The partially or completely degraded grouted tank is idealized as a dual regime system comprising of a mobile region having solid materials with cracks and macro-pores, and an immobile/stagnant region having solid matrix with micropores. The transport profiles of the species are calculated by incorporating advection of species through the mobile region, diffusion of species through the immobile/stagnant region, and exchange of species between the mobile and immobile regions. A geochemical speciation code in conjunction with the pH dependent test data for a grout material is used to obtain a mineral set that best describes the trends in the test data of the major species. The dual regime reactive transport model predictions are compared with the release data from an up-flow column percolation test. The coupled model is then used to assess effects of crack state of the structure, rate and composition of the infiltrating water on the pH evolution at the grout-waste interface. The coupled reactive transport model developed in this work can be used as part of the performance assessment process for evaluating potential risks from leaching of a cracked tank containing elements of human health and environmental concern. (authors)

  6. Influence of ACE I/D Polymorphism on Circulating Levels of Plasminogen Activator Inhibitor 1, D-Dimer, Ultrasensitive C-Reactive Protein and Transforming Growth Factor β1 in Patients Undergoing Hemodialysis

    PubMed Central

    de Carvalho, Sara Santos; Simões e Silva, Ana Cristina; Sabino, Adriano de Paula; Evangelista, Fernanda Cristina Gontijo; Gomes, Karina Braga; Dusse, Luci Maria SantAna; Rios, Danyelle Romana Alves

    2016-01-01

    Background There is substantial evidence that chronic renal and cardiovascular diseases are associated with coagulation disorders, endothelial dysfunction, inflammation and fibrosis. Angiotensin-Converting Enzyme Insertion/Deletion polymorphism (ACE I/D polymorphism) has also be linked to cardiovascular diseases. Therefore, this study aimed to compare plasma levels of ultrassensible C-reactive protein (usCRP), PAI-1, D-dimer and TGF-β1 in patients undergoing HD with different ACE I/D polymorphisms. Methods The study was performed in 138 patients at ESRD under hemodialysis therapy for more than six months. The patients were divided into three groups according to the genotype. Genomic DNA was extracted from blood cells (leukocytes). ACE I/D polymorphism was investigated by single polymerase chain reaction (PCR). Plasma levels of D-dimer, PAI-1 and TGF-β1 were measured by enzyme-linked immunosorbent assay (ELISA), and the determination of plasma levels of usCRP was performed by immunonephelometry. Data were analyzed by the software SigmaStat 2.03. Results Clinical characteristics were similar in patients with these three ACE I/D polymorphisms, except for interdialytic weight gain. I allele could be associated with higher interdialytic weight gain (P = 0.017). Patients genotyped as DD and as ID had significantly higher levels of PAI-1 than those with II genotype. Other laboratory parameters did not significantly differ among the three subgroups (P = 0.033). Despite not reaching statistical significance, plasma levels of usCRP were higher in patients carrying the D allele. Conclusion ACE I/D polymorphisms could be associated with changes in the regulation of sodium, fibrinolytic system, and possibly, inflammation. Our data showed that high levels of PAI-1 are detected when D allele is present, whereas greater interdialytic gain is associated with the presence of I allele. However, further studies with different experimental designs are necessary to elucidate the

  7. One-Dimensional Transport with Equilibrium Chemistry (OTEQ) - A Reactive Transport Model for Streams and Rivers

    USGS Publications Warehouse

    Runkel, Robert L.

    2010-01-01

    OTEQ is a mathematical simulation model used to characterize the fate and transport of waterborne solutes in streams and rivers. The model is formed by coupling a solute transport model with a chemical equilibrium submodel. The solute transport model is based on OTIS, a model that considers the physical processes of advection, dispersion, lateral inflow, and transient storage. The equilibrium submodel is based on MINTEQ, a model that considers the speciation and complexation of aqueous species, acid-base reactions, precipitation/dissolution, and sorption. Within OTEQ, reactions in the water column may result in the formation of solid phases (precipitates and sorbed species) that are subject to downstream transport and settling processes. Solid phases on the streambed may also interact with the water column through dissolution and sorption/desorption reactions. Consideration of both mobile (waterborne) and immobile (streambed) solid phases requires a unique set of governing differential equations and solution techniques that are developed herein. The partial differential equations describing physical transport and the algebraic equations describing chemical equilibria are coupled using the sequential iteration approach. The model's ability to simulate pH, precipitation/dissolution, and pH-dependent sorption provides a means of evaluating the complex interactions between instream chemistry and hydrologic transport at the field scale. This report details the development and application of OTEQ. Sections of the report describe model theory, input/output specifications, model applications, and installation instructions. OTEQ may be obtained over the Internet at http://water.usgs.gov/software/OTEQ.

  8. pH-dependent transport of metals through a reactive porous medium

    NASA Astrophysics Data System (ADS)

    Prigiobbe, V.; Bryant, S. L.

    2013-12-01

    Here we present a study on the effect of pH-dependent adsorption and hydrodynamic dispersion on metal transport through a reactive porous medium with hydrophilic surface. We investigate how the migration of a certain fraction of a metal can be facilitated by its competitive adsorption with protons. We performed laboratory experiments using a chromatographic column filled with silica beads coated with hydrous ferric oxide (HFO) and flooded initially with an acidic solution (pH 3) and then with an alkaline solution (pH > 7) containing either sodium, potassium, lithium, calcium, magnesium, strontium, or barium cations. Concentrations were chosen for which nonclassical transport is predicted. Highly resolved breakthrough curves measured with inline ion chromatography allowed us to observe in all cases the formation of a fast wave/pulse traveling at the interstitial fluid velocity and a retarded front. Classical theory of reactive transport through porous media predicts the formation of only the retarded front and assumes that hydrodynamic dispersion only smooths it without introducing an additional wave. Therefore, the fast wave is a notable exception to this theory. The mechanism responsible for this phenomenon is due to the interplay between hydrodynamic dispersion and pH-dependent adsorption. Hydrodynamic dispersion broadens the metal concentration front at the inlet of the column and creates a mixing zone where the high-pH solution containing the metal mixes with the low-pH solution initially present in the system. The resulting pH of the mixing zone spans a range where both the adsorption and the retardation of the metal are negligible. This leads to the formation of a metal plume, which then separates from the retarded front traveling at the interstitial fluid velocity as an isolated pulse. This fast transport phenomenon operates independently of other modes of rapid transport, such as colloid-facilitated transport and flow in fractures. A one

  9. Subsurface Transport Over Reactive Multiphases (STORM): A general, coupled, nonisothermal multiphase flow, reactive transport, and porous medium alteration simulator, Version 2 user's guide

    SciTech Connect

    DH Bacon; MD White; BP McGrail

    2000-03-07

    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{sub 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.

  10. Marine phages as excellent tracers for reactive colloidal transport in porous media

    NASA Astrophysics Data System (ADS)

    Ghanem, Nawras; Chatzinotas, Antonis; Harms, Hauke; Wick, Lukas Y.

    2016-04-01

    Question: Here we evaluate marine phages as specific markers of hydrological flow and reactive transport of colloidal particles in the Earth's critical zone (CZ). Marine phages and their bacterial hosts are naturally absent in the CZ, and can be detected with extremely high sensitivity. In the framework of the DFG Collaborative Research Center AquaDiva, we asked the following questions: (1) Are marine phages useful specific markers of hydrological flow and reactive transport in porous media? and (2) Which phage properties are relevant drivers for the transport of marine phages in porous media? Methods: Seven marine phages from different families (as well two commonly used terrestrial phages) were selected based on their morphology, size and physico-chemical surface properties (surface charge and hydrophobicity). Phage properties were assessed by electron microscopy, dynamic light scattering and water contact angle analysis (CA). Sand-filled laboratory percolation columns were used to study transport. The breakthrough curves of the phages were analyzed using the clean bed filtration theory and the XDLVO theory of colloid stability, respectively. Phages were quantified by a modified high- throughput plaque assay and a culture-independent particle counting method approach. Results: Our data show that most marine tested phages exhibited highly variable transport rates and deposition efficiency, yet generally high colloidal stability and viability. We find that size, morphology and hydrophobicity are key factors shaping the transport efficiency of phages. Differing deposition efficiencies of the phages were also supported by calculated XDLVO interaction energy profile. Conclusion: Marine phages have a high potential for the use as sensitive tracers in terrestrial habitats with their surface properties playing a crucial role for their transport. Marine phages however, exhibit differences in their deposition efficiency depending on their morphology, hydrophobicity and

  11. Coupled reactive mass transport and fluid flow: Issues in model verification

    SciTech Connect

    Freedman, Vicky L.; Ibaraki, Motomu

    2003-01-03

    Model verification and validation are both important steps in the development of reactive transport models. In this paper, a distinction is made between verification and validation, and the focus is on codifying the issues of verification for a numerical, reactive transport flow model. First, the conceptual basis of model verification is reviewed, which shows that verification should be understood as a first step in model development, and be followed by a protocol that assures that the model accurately represents system behavior. Second, commonly used procedures and methods of model verification are presented. In the third part of this paper, an intercomparison of models is used to demonstrate that model verification can be performed despite differences in hydrogeochemical transport code formulations. Results of an example simulation of transport are presented in which the numerical model is tested against other hydrogeochemical codes. Different kinetic formulations between solid and aqueous phases used among numerical models complicates model verification. This test problem involves uranium transport under conditions of varying pH and oxidation potential, with reversible precipitation of calcium uranate and coffinite. Results between the different hydrogeochemical transport codes show differences in oxidation potentials, but similarities in mineral assemblages and aqueous transport patterns. Because model verification can be further complicated by differences in the approach for solving redox problems, a comparison of a fugacity approach to both the external approach (based on hypothetical electron activity) and effective internal approach (based on conservation of electrons) is performed. The comparison demonstrates that the oxygen fugacity approach produces different redox potentials and mineral assemblages than both the effective internal and external approaches.

  12. Reactive species in non-equilibrium atmospheric-pressure plasmas: Generation, transport, and biological effects

    NASA Astrophysics Data System (ADS)

    Lu, X.; Naidis, G. V.; Laroussi, M.; Reuter, S.; Graves, D. B.; Ostrikov, K.

    2016-05-01

    Non-equilibrium atmospheric-pressure plasmas have recently become a topical area of research owing to their diverse applications in health care and medicine, environmental remediation and pollution control, materials processing, electrochemistry, nanotechnology and other fields. This review focuses on the reactive electrons and ionic, atomic, molecular, and radical species that are produced in these plasmas and then transported from the point of generation to the point of interaction with the material, medium, living cells or tissues being processed. The most important mechanisms of generation and transport of the key species in the plasmas of atmospheric-pressure plasma jets and other non-equilibrium atmospheric-pressure plasmas are introduced and examined from the viewpoint of their applications in plasma hygiene and medicine and other relevant fields. Sophisticated high-precision, time-resolved plasma diagnostics approaches and techniques are presented and their applications to monitor the reactive species and plasma dynamics in the plasma jets and other discharges, both in the gas phase and during the plasma interaction with liquid media, are critically reviewed. The large amount of experimental data is supported by the theoretical models of reactive species generation and transport in the plasmas, surrounding gaseous environments, and plasma interaction with liquid media. These models are presented and their limitations are discussed. Special attention is paid to biological effects of the plasma-generated reactive oxygen and nitrogen (and some other) species in basic biological processes such as cell metabolism, proliferation, survival, etc. as well as plasma applications in bacterial inactivation, wound healing, cancer treatment and some others. Challenges and opportunities for theoretical and experimental research are discussed and the authors' vision for the emerging convergence trends across several disciplines and application domains is presented to

  13. Role of reactive oxygen species in regulation of glucose transport in skeletal muscle during exercise.

    PubMed

    Katz, Abram

    2016-06-01

    Glucose derived from extracellular sources serves as an energy source in virtually all eukaryotic cells, including skeletal muscle. Its contribution to energy turnover increases with exercise intensity up to moderately heavy workloads. However, at very high workloads, the contribution of extracellular glucose to energy turnover is negligible, despite the high rate of glucose transport. Reactive oxygen species (ROS) are involved in the stimulation of glucose transport in isolated skeletal muscle preparations during intense repeated contractions. Consistent with this observation, heavy exercise is associated with significant production of ROS. However, during more mild to moderate stimulation or exercise conditions (in vitro, in situ and in vivo) antioxidants do not affect glucose transport. It is noteworthy that the production of ROS is limited or not observed under these conditions and that the concentration of the antioxidant used was extremely low. The results to date suggest that ROS involvement in activation of glucose transport occurs primarily during intense short-term exercise and that other mechanisms are involved during mild to moderate exercise. What remains puzzling is why ROS-mediated activation of glucose transport would occur under conditions where glucose transport is highest and utilization (i.e. phosphorylation of glucose by hexokinase) is low. Possibly ROS production is involved in priming glucose transport during heavy exercise to accelerate glycogen biogenesis during the initial recovery period after exercise, as well as altering other aspects of intracellular metabolism. PMID:26791627

  14. A reaction-based paradigm to model reactive chemical transport in groundwater with general kinetic and equilibrium reactions

    SciTech Connect

    Zhang, Fan; Yeh, Gour-Tsyh; Parker, Jack C; Brooks, Scott C; Pace, Molly; Kim, Young Jin; Jardine, Philip M; Watson, David B

    2007-01-01

    This paper presents a reaction-based water quality transport model in subsurface flow systems. Transport of chemical species with a variety of chemical and physical processes is mathematically described by M partial differential equations (PDEs). Decomposition via Gauss-Jordan column reduction of the reaction network transforms M species reactive transport equations into two sets of equations: a set of thermodynamic equilibrium equations representing NE equilibrium reactions and a set of reactive transport equations of M-NE kinetic-variables involving no equilibrium reactions (a kinetic-variable is a linear combination of species). The elimination of equilibrium reactions from reactive transport equations allows robust and efficient numerical integration. The model solves the PDEs of kinetic-variables rather than individual chemical species, which reduces the number of reactive transport equations and simplifies the reaction terms in the equations. A variety of numerical methods are investigated for solving the coupled transport and reaction equations. Simulation comparisons with exact solutions were performed to verify numerical accuracy and assess the effectiveness of various numerical strategies to deal with different application circumstances. Two validation examples involving simulations of uranium transport in soil columns are presented to evaluate the ability of the model to simulate reactive transport with complex reaction networks involving both kinetic and equilibrium reactions.

  15. A Modular Computer Code for Simulating Reactive Multi-Species Transport in 3-Dimensional Groundwater Systems

    SciTech Connect

    TP Clement

    1999-06-24

    RT3DV1 (Reactive Transport in 3-Dimensions) is computer code that solves the coupled partial differential equations that describe reactive-flow and transport of multiple mobile and/or immobile species in three-dimensional saturated groundwater systems. RT3D is a generalized multi-species version of the US Environmental Protection Agency (EPA) transport code, MT3D (Zheng, 1990). The current version of RT3D uses the advection and dispersion solvers from the DOD-1.5 (1997) version of MT3D. As with MT3D, RT3D also requires the groundwater flow code MODFLOW for computing spatial and temporal variations in groundwater head distribution. The RT3D code was originally developed to support the contaminant transport modeling efforts at natural attenuation demonstration sites. As a research tool, RT3D has also been used to model several laboratory and pilot-scale active bioremediation experiments. The performance of RT3D has been validated by comparing the code results against various numerical and analytical solutions. The code is currently being used to model field-scale natural attenuation at multiple sites. The RT3D code is unique in that it includes an implicit reaction solver that makes the code sufficiently flexible for simulating various types of chemical and microbial reaction kinetics. RT3D V1.0 supports seven pre-programmed reaction modules that can be used to simulate different types of reactive contaminants including benzene-toluene-xylene mixtures (BTEX), and chlorinated solvents such as tetrachloroethene (PCE) and trichloroethene (TCE). In addition, RT3D has a user-defined reaction option that can be used to simulate any other types of user-specified reactive transport systems. This report describes the mathematical details of the RT3D computer code and its input/output data structure. It is assumed that the user is familiar with the basics of groundwater flow and contaminant transport mechanics. In addition, RT3D users are expected to have some experience in

  16. Using Reactive Transport Modeling to Understand Changes in Electrical Conductivity Associated with Bacterial Growth and Respiration

    NASA Astrophysics Data System (ADS)

    Regberg, A. B.; Singha, K.; Picardal, F.; Brantley, S. L.

    2011-12-01

    Previous research has linked measured changes in the bulk electrical conductivity (σb) of water-saturated sediments to the respiration and growth of anaerobic bacteria. If the mechanism causing this signal is understood and characterized it could be used to identify and monitor zones of bacterial activity in the subsurface. The 1-D reactive transport model PHREEQC was used to understand σb signals by modeling chemical gradients within two column reactors and corresponding changes in effluent chemistry. The flow-through column reactors were packed with Fe(III)-bearing sediment from Oyster, VA and inoculated with an environmental consortia of microorganisms. Influent in the first reactor was amended with 1mM Na-acetate to encourage the growth of iron-reducing bacteria. Influent in the second reactor was amended with 0.1mM Na-Acetate and 2mM NaNO3 to encourage the growth of nitrate-reducing bacteria. While effluent concentrations of acetate, Fe(II), NO3-, NO2-, and NH4+ remained at steady state, we measured a 3-fold increase (0.055 S/m - 0.2 S/m) in σb in the iron-reducing column and a 10-fold increase in σb (0.07 S/m - 0.8 S/m) in the nitrate-reducing column over 198 days. The ionic strength in both reactors remained constant through time indicating that the measured increases in σb were not caused by changing effluent concentrations. PHREEQC successfully matched the measured changes in effluent concentrations for both columns when the reaction database was modified in the following manner. For the iron-reducing column, kinetic expressions governing the rate of iron reduction, the rate of bacterial growth, and the production of methane were added to the reaction database. Additionally, surface adsorption and cation exchange reactions were added so that the model was consistent with measured effluent chemistry. For the nitrate-reducing column, kinetic expressions governing nitrate reduction and bacterial growth were added to the reaction database. Additionally

  17. A Computer Program for the Calculation of Reactivity and Kinetic Parameters by Two-Dimensional Neutron Transport Perturbation Theory.

    1985-02-01

    Version 00 TP2 is a transport theory code, developed to determine reactivity effects and kinetic parameters such as effective delayed neutron fractions and mean generation time by applying the usual perturbation formalism for two-dimensional geometry.

  18. A Computer Code System for the Calculation of Reactivity and Kinetic Parameters by One-Dimensional Neutron Transport Perturbation Theory.

    1985-02-01

    Version 00 TP1 is a transport theory code, developed to determine reactivity effects and kinetic parameters such as effective delayed neutron fractions and mean generation time by applying the usual perturbation formalism for one-dimensional geometry.

  19. A Benchmarking Initiative for Reactive Transport Modeling Applied to Subsurface Environmental Applications

    NASA Astrophysics Data System (ADS)

    Steefel, C. I.

    2015-12-01

    Over the last 20 years, we have seen the evolution of multicomponent reactive transport modeling and the expanding range and increasing complexity of subsurface environmental applications it is being used to address. Reactive transport modeling is being asked to provide accurate assessments of engineering performance and risk for important issues with far-reaching consequences. As a result, the complexity and detail of subsurface processes, properties, and conditions that can be simulated have significantly expanded. Closed form solutions are necessary and useful, but limited to situations that are far simpler than typical applications that combine many physical and chemical processes, in many cases in coupled form. In the absence of closed form and yet realistic solutions for complex applications, numerical benchmark problems with an accepted set of results will be indispensable to qualifying codes for various environmental applications. The intent of this benchmarking exercise, now underway for more than five years, is to develop and publish a set of well-described benchmark problems that can be used to demonstrate simulator conformance with norms established by the subsurface science and engineering community. The objective is not to verify this or that specific code--the reactive transport codes play a supporting role in this regard—but rather to use the codes to verify that a common solution of the problem can be achieved. Thus, the objective of each of the manuscripts is to present an environmentally-relevant benchmark problem that tests the conceptual model capabilities, numerical implementation, process coupling, and accuracy. The benchmark problems developed to date include 1) microbially-mediated reactions, 2) isotopes, 3) multi-component diffusion, 4) uranium fate and transport, 5) metal mobility in mining affected systems, and 6) waste repositories and related aspects.

  20. Simulating variably-saturated reactive transport of selenium and nitrogen in agricultural groundwater systems

    NASA Astrophysics Data System (ADS)

    Bailey, Ryan T.; Gates, Timothy K.; Halvorson, Ardell D.

    2013-06-01

    Selenium (Se) contamination in environmental systems has become a major issue in many regions world-wide during the previous decades, with both elevated and deficient Se concentrations in groundwater, surface water, soils and associated cultivated crops reported. To provide a tool that can assess baseline conditions and explore remediation strategies, this paper presents a numerical model capable of simulating the reactive transport of Se species in large-scale variably-saturated groundwater systems influenced by agricultural practices. Developed by incorporating a Se reaction module into the multi-species, variably-saturated reactive transport model UZF-RT3D, model features include near-surface Se cycling due to agricultural practices, oxidation-reduction reactions, and the inclusion of a nitrogen (N) cycle and reaction module due to the dependence of Se transformation and speciation on the presence of nitrate (NO3). Although the primary motivation is applying the model to large-scale systems, this paper presents applications to agricultural soil profile systems to corroborate the near-surface module processes that are vital in estimating mass loadings to the saturated zone in large-scale fate and transport studies. The first application jointly tests the Se and N modules for corn test plots receiving varying loadings of fertilizer, whereas the second application tests the N module for fertilized and unfertilized test plots. Results indicate that the model is successful in reproducing observed measurements of Se and NO3 concentrations, particularly in lower soil layers and hence in regards to leaching. For the first application, the Ensemble Kalman Filter (EnKF) is used to condition model parameters, demonstrating the usefulness of the EnKF in real-world reactive transport systems.

  1. Post Audit of a Field Scale Reactive Transport Model of Uranium at a Former Mill Site

    NASA Astrophysics Data System (ADS)

    Curtis, G. P.

    2015-12-01

    Reactive transport of hexavalent uranium (U(VI)) in a shallow alluvial aquifer at a former uranium mill tailings site near Naturita CO has been monitored for nearly 30 years by the US Department of Energy and the US Geological Survey. Groundwater at the site has high concentrations of chloride, alkalinity and U(VI) as a owing to ore processing at the site from 1941 to 1974. We previously calibrated a multicomponent reactive transport model to data collected at the site from 1986 to 2001. A two dimensional nonreactive transport model used a uniform hydraulic conductivity which was estimated from observed chloride concentrations and tritium helium age dates. A reactive transport model for the 2km long site was developed by including an equilibrium U(VI) surface complexation model calibrated to laboratory data and calcite equilibrium. The calibrated model reproduced both nonreactive tracers as well as the observed U(VI), pH and alkalinity. Forward simulations for the period 2002-2015 conducted with the calibrated model predict significantly faster natural attenuation of U(VI) concentrations than has been observed by the persistent high U(VI) concentrations at the site. Alternative modeling approaches are being evaluating evaluated using recent data to determine if the persistence can be explained by multirate mass transfer models developed from experimental observations at the column scale(~0.2m), the laboratory tank scale (~2m), the field tracer test scale (~1-4m) or geophysical observation scale (~1-5m). Results of this comparison should provide insight into the persistence of U(VI) plumes and improved management options.

  2. In Situ Biostimulation at a Former Uranium Mill Tailings Site: Multicomponent Biogeochemical Reactive Transport Modeling

    NASA Astrophysics Data System (ADS)

    Yabusaki, S.; Fang, Y.; Long, P.

    2005-12-01

    In situ biostimulation at a Former Uranium Mill Tailings Site: Multicomponent Biogeochemical Reactive Transport Modeling Field experiments conducted at a former uranium mill tailings site in western Colorado are being used to investigate microbially mediated immobilization of uranium as a potential future remediation option for such sites. While the general principle of biostimulating microbial communities to reduce aqueous hexavalent uranium to immobile uraninite has been demonstrated in the laboratory and field, the ability to predictably engineer long lasting immobilization will require a more complete understanding of field-scale processes and properties. For this study, numerical simulation of the flow field, geochemical conditions, and micriobial communities is used to interpret field-scale biogeochemical reactive transport observed during experiments performed in 2002 to 2004. One key issue is identifying bioavailable Fe(III) oxide, which is the principal electron acceptor utilized by the acetate- oxidizing Geobacter sp. These organisms are responsible for uranium bioreduction that results in the removal of sufficient U(VI) to lower uranium groundwater concentrations to at or near applicable standards. The depletion of bioavailable Fe(III) leads to succession by sulfate reducers that are considerably less effective at uranium bioreduction. An important modeling consideration are the abiotic reactions (e.g., mineral precipitation and dissolution, aqueous and surface complexation) involving the Fe(II) and sulfide produced during biostimulation. These components, strongly associated with the solid phases, may play an important role in the evolving reactivity of the mineral surfaces that are likely to impact long-term uranium immobilization.

  3. Reactive transport in 3D models of irregularly fractured rock masses

    NASA Astrophysics Data System (ADS)

    Driesner, T.; Mindel, J. E.

    2014-12-01

    Reactive transport through irregularly fractured rock masses is a key phenomenon in ore-forming hydrothermal systems, geothermal systems, and many other geological processes and will affect the mechanical properties and hydraulic apertures of fractures. Realistic representations of such systems have so far been hampered by technical limitations of most hydrothermal reactive transport codes, namely the ability to represent discrete fracture networks in a porous rock matrix. We present the first three-dimensional simulation results obtained from coupling a combined finite element - finite volume scheme of the revised CSMP++ flow simulation platform (1) with the GEMIPM3K (2) chemical equilibration code. In these, we represented fracture zones as thin, porous zones of higher permeability. The simulations demonstrate the effects of fracture zone orientation relative to the pressure field and fracture zone intersections on the differential advance of reaction fronts. We outline our numerical approaches for testing and comparing the effect of various ways of representing fractures and fracture zones in irregular meshes, namely the possibility of using layers of prism elements to represent fractures of finite thickness with internally varying properties and the possibility to represent thin fractures as lower dimensional (=2D) elements. We intend to make use of the "split node" capabilities of CSMP++ (3) to maintain sharp interfaces at material boundaries in order to be able to study the transient influence of reactive flow on fracture and matrix permeability in irregularly fractured rock masses.

  4. Computational methods for multiphase equilibrium and kinetics calculations for geochemical and reactive transport applications

    NASA Astrophysics Data System (ADS)

    Leal, Allan; Saar, Martin

    2016-04-01

    Computational methods for geochemical and reactive transport modeling are essential for the understanding of many natural and industrial processes. Most of these processes involve several phases and components, and quite often requires chemical equilibrium and kinetics calculations. We present an overview of novel methods for multiphase equilibrium calculations, based on both the Gibbs energy minimization (GEM) approach and on the solution of the law of mass-action (LMA) equations. We also employ kinetics calculations, assuming partial equilibrium (e.g., fluid species in equilibrium while minerals are in disequilibrium) using automatic time stepping to improve simulation efficiency and robustness. These methods are developed specifically for applications that are computationally expensive, such as reactive transport simulations. We show how efficient the new methods are, compared to other algorithms, and how easy it is to use them for geochemical modeling via a simple script language. All methods are available in Reaktoro, a unified open-source framework for modeling chemically reactive systems, which we also briefly describe.

  5. Reactive transport simulations of the evolution of a cementitious repository in clay-rich host rocks

    NASA Astrophysics Data System (ADS)

    Kosakowski, Georg; Berner, Urs; Kulik, Dmitrii A.

    2010-05-01

    In Switzerland, the deep geological disposal in clay-rich rocks is foreseen not only for high-level radioactive waste, but also for intermediate-level (ILW) and low-level (LLW) radioactive waste. Typically, ILW and LLW repositories contain huge amounts of cementitious materials used for waste conditioning, confinement, and as backfill for the emplacement caverns. We are investigating the interactions of such a repository with the surrounding clay rocks and with other clay-rich materials such as sand/bentonite mixtures that are foreseen for backfilling the access tunnels. With the help of a numerical reactive transport model, we are comparing the evolution of cement/clay interfaces for different geochemical and transport conditions. In this work, the reactive transport of chemical components is simulated with the multi-component reactive transport code OpenGeoSys-GEM. It employs the sequential non-iterative approach to couple the mass transport code OpenGeoSys (http://www.ufz.de/index.php?en=18345) with the GEMIPM2K (http://gems.web.psi.ch/) code for thermodynamic modeling of aquatic geochemical systems which is using the Gibbs Energy Minimization (GEM) method. Details regarding code development and verification can be found in Shao et al. (2009). The mineral composition and the pore solution of a CEM I 52.5 N HTS hydrated cement as described by Lothenbach & Wieland (2006) are used as an initial state of the cement compartment. The setup is based on the most recent CEMDATA07 thermodynamic database which includes several ideal solid solutions for hydrated cement minerals and is consistent with the Nagra/PSI thermodynamic database 01/01. The smectite/montmorillonite model includes cation exchange processes and amphotheric≡SOH sites and was calibrated on the basis of data by Bradbury & Baeyens (2002). In other reactive transport codes based on the Law of Mass Action (LMA) for solving geochemical equilibria, cation exchange processes are usually calculated assuming

  6. Integration of field measurements and reactive transport modelling to evaluate contaminant transport at a sulfide mine tailings impoundment

    NASA Astrophysics Data System (ADS)

    Brookfield, A. E.; Blowes, D. W.; Mayer, K. U.

    2006-11-01

    Over a decade of field observations including geochemical, mineralogical and hydrological information are available on the generation of acid mine drainage from the Pistol Dam region of the P-area of Inco's tailings impoundment in Copper Cliff, Ontario. This work focuses on the integration and quantitative assessment of this data set using reactive transport modeling. The results of the reactive transport simulations are in general agreement with the field observations; however, exact agreement between the field and simulated results was not the objective of this study, and was not attained. Many factors contribute to the discrepancies between the field observations and simulation results including geochemical and hydrogeological complexities and necessary model simplifications. For example, fluctuating water levels observed at the site were averaged and described using a steady state flow system. In addition, the lack of representative thermodynamic and rate expression data contributed to the discrepancies between observations and simulation results, thus further research into the applicability of laboratory-derived thermodynamic and rate expression data to field conditions could minimize these discrepancies. Despite the discrepancies between the field observations and simulated results, integrating field observations with numerical modelling of the P-area tailings impoundment allowed for a more complete understanding of what affects the complex geochemical reactions.

  7. Simulation of reactive transport of uranium(VI) in groundwater with variable chemical conditions

    USGS Publications Warehouse

    Curtis, G.P.; Davis, J.A.; Naftz, D.L.

    2006-01-01

    The reactive transport of U(VI) in a shallow alluvial aquifer beneath a former U(VI) mill located near Naturita, CO, was simulated using a surface complexation model (SCM) to describe U(VI) adsorption. The groundwater had variable U(VI) concentrations (0.01-20 ??M), variable alkalinity (2.5-18 meq/L), and a nearly constant pH equal to 7.1. U(VI) KD values decreased with increasing U(VI) and alkalinity, and these parameters were more important than sediment variability in controlling KD values. Reactive transport simulations were fit to the observed U(VI) and alkalinity by varying the concentration of U(VI) and alkalinity in recharge at the source area. Simulated KD values varied temporally and spatially because of the differential transport of U(VI) and alkalinity and the nonlinearity of U(VI) adsorption. The model also simulated the observed U(VI) tailing, which would not be expected from a constant KD model. The simulated U(VI) concentrations were sensitive to the recharge flux because of the increased flux of U(VI) to the aquifer. The geochemical behavior of U(VI) was most sensitive to the alkalinity and was relatively insensitive to pH.

  8. Simulation of geochemical localization using a multi-porosity reactive transport approach

    NASA Astrophysics Data System (ADS)

    Soler, Joaquim; Luquot, Linda; Martinez-Perez, Laura; Saaltink, Maarten; De Gaspari, Francesca; Carrera, Jesus

    2016-04-01

    Results of reactive transport laboratory experiments often suggest that pore scale heterogeneity induces localization of reactions (the generation of local micro environments favoring reactions that would not occur in a well-mixed Representative Elementary Volume, REV). Multi-Rate Mass Transfer (MRMT), which has been employed to reproduce hydrodynamic heterogeneity, may also be used to simulate geochemical localization. We extended the Water Mixing Approach (WMA) designed for single porosity media, to simulate chemical reactions caused by the mixing of mobile and immobile zones. The method is termed Multi-Rate Water Mixing (MRWM). The MRWM approach was employed to simulate laboratory experiments of CO2-rich brine transport through carbonate rich samples (Luquot et al. 2016). Chemical heterogeneity in space was reproduced by varying the mineral assemblages in immobile regions. This enabled us to reproduce the generally low pH environment while allowing for high pH local zones required for the localized precipitation of kaolinite, which has been observed in reality, but cannot be modeled with conventional reactive transport formulations. The resulting model is very rich, in that it can reproduce a broad range of pore scale processes in a Darcy scale model, and complex, in that the interaction between chemical kinetics and immobile zones physical parameters is non-trivial.

  9. A post audit and inverse modeling in reactive transport: 50 years of artificial recharge in the Amsterdam Water Supply Dunes

    NASA Astrophysics Data System (ADS)

    Karlsen, R. H.; Smits, F. J. C.; Stuyfzand, P. J.; Olsthoorn, T. N.; van Breukelen, B. M.

    2012-08-01

    SummaryThis article describes the post audit and inverse modeling of a 1-D forward reactive transport model. The model simulates the changes in water quality following artificial recharge of pre-treated water from the river Rhine in the Amsterdam Water Supply Dunes using the PHREEQC-2 numerical code. One observation dataset is used for model calibration, and another dataset for validation of model predictions. The total simulation time of the model is 50 years, from 1957 to 2007, with recharge composition varying on a monthly basis and the post audit is performed 26 years after the former model simulation period. The post audit revealed that the original model could reasonably predict conservative transport and kinetic redox reactions (oxygen and nitrate reduction coupled to the oxidation of soil organic carbon), but showed discrepancies in the simulation of cation exchange. Conceptualizations of the former model were inadequate to accurately simulate water quality changes controlled by cation exchange, especially concerning the breakthrough of potassium and magnesium fronts. Changes in conceptualization and model design, including the addition of five flow paths, to a total of six, and the use of parameter estimation software (PEST), resulted in a better model to measurement fit and system representation. No unique parameter set could be found for the model, primarily due to high parameter correlations, and an assessment of the predictive error was made using a calibration constrained Monte-Carlo method, and evaluated against field observations. The predictive error was found to be low for Na+ and Ca2+, except for greater travel times, while the K+ and Mg2+ error was restricted to the exchange fronts at some of the flow paths. Optimized cation exchange coefficients were relatively high, especially for potassium, but still within the observed range in literature. The exchange coefficient for potassium agrees with strong fixation on illite, a main clay mineral in

  10. Reactive transport models for mineral CO2 storage in basaltic rocks

    NASA Astrophysics Data System (ADS)

    Aradottir, E. S.; Sonnenthal, E. L.; Bjornsson, G.; Jonsson, H.

    2010-12-01

    CO2 mineral storage in basalts may provide a long lasting, thermodynamically stable and environmentally benign solution to reduce anthropogenic CO2 in the atmosphere. We present here development of reactive transport models of this process with focus on the CarbFix experiment at Hellisheidi geothermal power plant in Iceland. There, up to 2.2 tons/year of purified CO2 of volcanic origin will be dissolved in water and injected at intermediate depths (400-800 m) into relatively fresh basaltic lava. Plans call for a full-scale injection if the experiment is successful. Reactive transport modeling is an important factor in the CarbFix project, providing tools to predict and optimize long-term management of the injection site as well as to quantify the amount of CO2 that has the potential of being mineralized. TOUGHREACT and iTOUGH2 are used to develop reactive fluid flow models that simulate hydrology and mineral alteration associated with injecting dissolved CO2 into basalts. The mineral reactions database in TOUGHREACT has been revised and extended, providing an internally consistent database suitable for mineral reactions of interest for this study. A multiple interacting continua (MINC) dissolution model was developed to simulate the long and short-term dissolution of basaltic glass taking into account dissolution kinetics, leached layer formation and diffusion-limited dissolution rates. Our main focus has been on developing a three dimensional field model of the injection site at Hellisheidi. Hydrological parameters of the model were calibrated using iTOUGH2 to simulate tracer tests that have been ongoing since 2007. Modeling results indicate groundwater velocity in the reservoir to be significantly lower than expected. The slow groundwater velocity may necessitate increasing groundwater flow by producing downstream wells at low rates after CO2 injection has started. The three dimensional numerical model has proven to be a valuable tool in simulating different

  11. A sequential partly iterative approach for multicomponent reactive transport with CORE2D

    SciTech Connect

    Samper, J.; Xu, T.; Yang, C.

    2008-11-01

    CORE{sup 2D} V4 is a finite element code for modeling partly or fully saturated water flow, heat transport and multicomponent reactive solute transport under both local chemical equilibrium and kinetic conditions. It can handle coupled microbial processes and geochemical reactions such as acid-base, aqueous complexation, redox, mineral dissolution/precipitation, gas dissolution/exsolution, ion exchange, sorption via linear and nonlinear isotherms, sorption via surface complexation. Hydraulic parameters may change due to mineral precipitation/dissolution reactions. Coupled transport and chemical equations are solved by using sequential iterative approaches. A sequential partly-iterative approach (SPIA) is presented which improves the accuracy of the traditional sequential noniterative approach (SNIA) and is more efficient than the general sequential iterative approach (SIA). While SNIA leads to a substantial saving of computing time, it introduces numerical errors which are especially large for cation exchange reactions. SPIA improves the efficiency of SIA because the iteration between transport and chemical equations is only performed in nodes with a large mass transfer between solid and liquid phases. The efficiency and accuracy of SPIA are compared to those of SIA and SNIA using synthetic examples and a case study of reactive transport through the Llobregat Delta aquitard in Spain. SPIA is found to be as accurate as SIA while requiring significantly less CPU time. In addition, SPIA is much more accurate than SNIA with only a minor increase in computing time. A further enhancement of the efficiency of SPIA is achieved by improving the efficiency of the Newton-Raphson method used for solving chemical equations. Such an improvement is obtained by working with increments of log-concentrations and ignoring the terms of the Jacobian matrix containing derivatives of activity coefficients. A proof is given for the symmetry and non-singularity of the Jacobian matrix

  12. Challenges in reactive transport modeling for prediction of geometry evolution in fractured carbonate rocks

    NASA Astrophysics Data System (ADS)

    Peters, C. A.; Deng, H.; Guo, B.; Fitts, J. P.

    2014-12-01

    Carbonate minerals are common in sedimentary rocks including in formations that serve as caprock seals. These formations are intended to stop migration of injected fluids, such as CO2 in the context of geologic carbon sequestration, ensuring permanent isolation from the atmosphere. Fractures in caprocks may allow injected CO2 and pressurized brine to escape. If the caprock contains substantial amounts of carbonates, flow of acidified fluids may cause substantial mineral dissolution which would increase the leakiness over time. Our research seeks to understand this process with particular attention to the evolution of fracture geometry and the implications for flow permeability. Our work combines high-pressure core flow experiments, x-ray imaging methods, reactive transport modeling, and computational fluid dynamics simulations. We have found that fracture permeability can increase substantially as a result of calcite dissolution. However, the extent of permeability increase is affected by complex alterations in fracture geometry. Newly-formed surface roughness and microporosity diminishes flow relative to what would be predicted by conventional practical models such as the local cubic law model. In contrast, channelization could lead to higher-than-expected flow rates because such fractures would stabilize open flow paths against geomechanical closure forces. Modeling these processes requires fine-scale 2D, if not 3D, reactive transport flow models that simulate not only the increase in fracture aperture but also the evolution in fracture geometry. Development of computationally-tractable reactive transport models that accurately predict reaction-induced changes in fracture permeability is an ongoing research priority in our lab.

  13. Analytical solutions for reactive transport of N-member radionuclide chains in a single fracture.

    PubMed

    Sun, Yunwei; Buscheck, Thomas A

    2003-01-01

    Several numerical codes have been used to simulate radionuclide transport in fractured rock systems. The validation of such numerical codes can be accomplished by comparison of numerical simulations against appropriate analytical solutions. In this paper, we present analytical solutions for the reactive transport of N-member radionuclide chains (i.e., multiple species of radionuclides and their daughter species) through a discrete fracture in a porous rock matrix applying a system decomposition approach. We consider the transport of N-member radionuclide chains in a single-fracture-matrix system as a starting point to simulate more realistic and complex systems. The processes considered are advection along the fracture, lateral diffusion in the matrix, radioactive decay of multiple radionuclides, and adsorption in both the fracture and matrix. Different retardation factors can be specified for the fracture and matrix. However, all species are assumed to share the same retardation factors for the fracture and matrix, respectively. Although a daughter species may penetrate farther along the fracture than its parent species when a constant-concentration boundary condition is applied, our results indicate that all species retain the same transport speed in the fracture if a pulse of the first species is released into the fracture. This solution scheme provides a way to validate numerical computer codes of radionuclide transport in fractured rock, such as those being used to assess the performance of a potential nuclear-waste repository at Yucca Mountain. PMID:12714317

  14. Semianalytical solutions of radioactive or reactive transport invariably-fractured layered media: 1. Solutes

    SciTech Connect

    Moridis, George J.

    2001-10-10

    In this paper, semianalytical solutions are developed for the problem of transport of radioactive or reactive solute tracers through a layered system of heterogeneous fractured media with misaligned fractures. The tracer transport equations in the non-flowing matrix account for (a) diffusion, (b) surface diffusion, (c) mass transfer between the mobile and immobile water fractions, (d) linear kinetic or equilibrium physical, chemical, or combined solute sorption or colloid filtration, and (e) radioactive decay or first-order chemical reactions. The tracer-transport equations in the fractures account for the same processes, in addition to advection and hydrodynamic dispersion. Any number of radioactive decay daughter products (or products of a linear, first-order reaction chain) can be tracked. The solutions, which are analytical in the Laplace space, are numerically inverted to provide the solution in time and can accommodate any number of fractured and/or porous layers. The solutions are verified using analytical solutions for limiting cases of solute and colloid transport through fractured and porous media. The effect of important parameters on the transport of {sup 3}H, {sup 237}Np and {sup 239}Pu (and its daughters) is investigated in several test problems involving layered geological systems of varying complexity.

  15. Semianalytical Solutions of Radioactive or Reactive Transport in Variably-Fractured Layered Media: 1. Solutes

    SciTech Connect

    George J. Moridis

    2001-10-01

    In this paper, semianalytical solutions are developed for the problem of transport of radioactive or reactive solute tracers through a layered system of heterogeneous fractured media with misaligned fractures. The tracer transport equations in the non-flowing matrix account for (a) diffusion, (b) surface diffusion, (c) mass transfer between the mobile and immobile water fractions, (d) linear kinetic or equilibrium physical, chemical, or combined solute sorption or colloid filtration, and (e) radioactive decay or first-order chemical reactions. The tracer-transport equations in the fractures account for the same processes, in addition to advection and hydrodynamic dispersion. Any number of radioactive decay daughter products (or products of a linear, first-order reaction chain) can be tracked. The solutions, which are analytical in the Laplace space, are numerically inverted to provide the solution in time and can accommodate any number of fractured and/or porous layers. The solutions are verified using analytical solutions for limiting cases of solute and colloid transport through fractured and porous media. The effect of important parameters on the transport of {sup 3}H, {sup 237}Np and {sup 239}Pu (and its daughters) is investigated in several test problems involving layered geological systems of varying complexity.

  16. Coupling between geochemical reactions and multicomponent gas and solute transport in unsaturated media: A reactive transport modeling study

    NASA Astrophysics Data System (ADS)

    Molins, S.; Mayer, K. U.

    2007-05-01

    The two-way coupling that exists between biogeochemical reactions and vadose zone transport processes, in particular gas phase transport, determines the composition of soil gas. To explore these feedback processes quantitatively, multicomponent gas diffusion and advection are implemented into an existing reactive transport model that includes a full suite of geochemical reactions. Multicomponent gas diffusion is described on the basis of the dusty gas model, which accounts for all relevant gas diffusion mechanisms. The simulation of gas attenuation in partially saturated landfill soil covers, methane production, and oxidation in aquifers contaminated by organic compounds (e.g., an oil spill site) and pyrite oxidation in mine tailings demonstrate that both diffusive and advective gas transport can be affected by geochemical reactions. Methane oxidation in landfill covers reduces the existing upward pressure gradient, thereby decreasing the contribution of advective methane emissions to the atmosphere and enhancing the net flux of atmospheric oxygen into the soil column. At an oil spill site, methane oxidation causes a reversal in the direction of gas advection, which results in advective transport toward the zone of oxidation both from the ground surface and the deeper zone of methane production. Both diffusion and advection contribute to supply atmospheric oxygen into the subsurface, and methane emissions to the atmosphere are averted. During pyrite oxidation in mine tailings, pressure reduction in the reaction zone drives advective gas flow into the sediment column, enhancing the oxidation process. In carbonate-rich mine tailings, calcite dissolution releases carbon dioxide, which partly offsets the pressure reduction caused by O2 consumption.

  17. Convective transport of reactive constituents to the tropical and mid-latitude tropopause region: I. Observations

    NASA Technical Reports Server (NTRS)

    Ridley, B.; Atlas, E.; Selkirk, H.; Pfister, L.; Montzka, D.; Walega, J.; Donnelly, S.; Stroud, V.; Richard, E.; Kelly, K.

    2004-01-01

    Measurements of ozone, reactive carbon and nitrogen, and other trace constituents from flights of the NASA WB-57F aircraft in the upper troposphere and lower stratosphere reveal that convection in the tropics can present a complex mix of surface-emitted constituents right up to the altitude of the lapse rate tropopause. At higher latitudes over the southern US, the strongest transport signal, in terms of constituent mixing ratios, occurred in the potential temperature range of 340-350K or approximately over the altitude range of 9-11km. Weaker convective signals were also seen up to near the tropopause. There was no evidence of convective transport directly into the lower stratosphere from these flights. $CPY 2003 Elsevier Ltd. All rights reserved.

  18. A parallelization scheme to simulate reactive transport in the subsurface environment with OGS#IPhreeqc

    NASA Astrophysics Data System (ADS)

    He, W.; Beyer, C.; Fleckenstein, J. H.; Jang, E.; Kolditz, O.; Naumov, D.; Kalbacher, T.

    2015-03-01

    This technical paper presents an efficient and performance-oriented method to model reactive mass transport processes in environmental and geotechnical subsurface systems. The open source scientific software packages OpenGeoSys and IPhreeqc have been coupled, to combine their individual strengths and features to simulate thermo-hydro-mechanical-chemical coupled processes in porous and fractured media with simultaneous consideration of aqueous geochemical reactions. Furthermore, a flexible parallelization scheme using MPI (Message Passing Interface) grouping techniques has been implemented, which allows an optimized allocation of computer resources for the node-wise calculation of chemical reactions on the one hand, and the underlying processes such as for groundwater flow or solute transport on the other hand. The coupling interface and parallelization scheme have been tested and verified in terms of precision and performance.

  19. Assessing of Conceptual Models for Subsurface Reactive Transport of Inorganic Contaminants

    NASA Astrophysics Data System (ADS)

    Davis, James A.; Yabusaki, Steven B.; Steefel, Carl I.; Zachara, John M.; Curtis, Gary P.; Redden, George D.; Criscenti, Louise J.; Honeyman, Bruce D.

    2004-11-01

    In many subsurface situations where human health and environmental quality are at risk (e.g., contaminant hydrogeology, petroleum extraction, carbon sequestration, etc.), scientists and engineers are being asked by federal agency decision-makers to predict the fate of chemical species under conditions where both reactions and transport are processes of first-order importance. In 2002, a working group (WG) was formed by representatives of the U.S. Geological Survey, Environmental Protection Agency, Department of Energy, Nuclear Regulatory Commission, Department of Agriculture, and Army Engineer Research and Development Center to assess the role of reactive transport modeling (RTM) in addressing these situations. Specifically, the goals of the WG are to (1) evaluate the state of the art in conceptual model development and parameterization for RTM, as applied to soil, vadose zone, and groundwater systems, and (2) prioritize research directions that would enhance the practical utility of RTM.

  20. Development of reactive transport features within the OpenGeoSys project

    NASA Astrophysics Data System (ADS)

    Shao, H.; Zolfaghari, R.; Centler, F.; Maier, U.; He, W.; Jang, E.; Kalbacher, T.; Kolditz, O.

    2013-12-01

    The numerical modeling of reactive transport processes has wide applications in different disciplines of earth sciences. In contaminant hydrogeology, it was often utilized to predict the degradation of chemical pollutants in the groundwater. For the waste repositories, it is one of the tools to evaluate long term behaviors of hazardous materials' migration. In geothermal research, it is also helpful in the understanding of geochemical water-rock reactions and accessing its impact on the performance of deep geothermal reservoirs. To simulate the above mentioned reactive transport problems, the sequential non-iterative approach (SNIA) has been implemented. Previously, this approach has been adopted. In the resulting coupled codes, namely OGS-PhreeqC, OGS-GEMS and OGS-BRNS, the mass transport part is simulated by OGS in each time step, and a chemical solver is then employed to handle the local chemical systems. Recently, the Global Implicit Approach (GIA) with reduction scheme proposed by Kräutel et al (2010) has been implemented into OGS6. The new method allows a separation of linearly transported components and chemically coupled nonlinear ones. Through the separation, it reduces the number of primary unknowns in the nonlinearly coupled partial differential equation system, thus alleviated the memory and computational demand of the simulation. This newly developed reactive transport feature of OGS has been verified by a set of benchmarks. For mineral equilibrium reactions, the OGS6 code is verified against the OGS-PhreeqC result using the calcite example, in which calcite in a column slowly dissolves under the flushing of MgCl2 solution and dolomite is temporarily precipitated. For kinetic reactions, a sequential degradation benchmark has been simulated. In it, benzene is degraded through both aerobic oxidation and anaerobic sulfate reduction pathways. Three different codes, namely MIN3P, OGS-BRNS, and the newly implemented reduction scheme in OGS6 have produced

  1. A Computer Program for the Reactivity and Kinetic Parameters for Two-Dimensional Triangular Geometry by Transport Perturbation Theory.

    1990-04-25

    Version 00 TPTRIA calculates reactivity, effective delayed neutron fractions and mean generation time for two-dimensional triangular geometry on the basis of neutron transport perturbation theory. DIAMANT2 (also designated as CCC-414), is a multigroup two-dimensional discrete ordinates transport code system for triangular and hexagonal geometry which calculates direct and adjoint angular fluxes.

  2. Reactive Transport Modelling of Heterocyclic Hydrocarbons at a Former Gasworks Site

    NASA Astrophysics Data System (ADS)

    Herold, M.; Ptak, T.; Wendel, T.; Grathwohl, P.

    2007-12-01

    Highly mobile heterocyclic hydrocarbons constitute a persistent threat to groundwater at a former gasworks site in Southern Germany. This area is currently being used as a test site for novel subsurface investigation techniques, as well as for a site-specific enhanced natural attenuation (ENA) remediation approach. The subsurface investigation consisted of direct-push borings and monitoring well installations, tracer tests, and Integral Pumping Tests (IPTs) at multiple control planes, which were positioned at different distances downgradient of the source zone and perpendicular to the contaminant plume transport direction. The numerical inversion of groundwater concentration time series measured during the IPTs, in combination with a groundwater flow and transport model of the test site, leads to estimations of total mass flow rates of contaminants or other groundwater parameters relevant to NA, as well as of average concentrations and concentration distributions along the control planes. Following detailed investigations of the microbial and chemical conditions at the site, an in-situ ENA method involving a circulation well and the use of O2 as a terminal electron acceptor was devised to aid aerobic microbial degradation of the heterocyclic compounds in the otherwise anoxic surroundings. The aims of the study presented here were to verify the proposed conceptual model of interacting physical and biogeochemical processes and to assess the effectiveness of the in-situ remediation approach with the help of multi-component reactive transport modelling, focusing on the situations (i) prior to the implementation of the in- situ remediation scheme and (ii) following the operation of the circulation well with O2 injection. A finite-difference model was devised using the software PMWIN and PHT3D, utilizing the collected data to simulate the relevant processes in two and three dimensions, respectively. Instead of using interpolated point scale concentration measurements

  3. Testing hypotheses of soil organic matter dynamics in a mechanistic reactive transport model

    NASA Astrophysics Data System (ADS)

    Riley, W. J.; Maggi, F.; Guerry, N.; Torn, M. S.; Kleber, M.

    2012-12-01

    The range of processes hypothesized to be important for long-term soil organic matter dynamics far exceeds the capabilities of current land models integrated in regional- to global-scale climate models. Yet SOM stability and CO2 fluxes from soils to the atmosphere are critical for future projections of climate. Recent syntheses of processes that may influence the trajectory of future soil C storage emphasize mineral interactions, enzyme dynamics, microbial population dynamics, transport, and interactions with plants and nutrient cycles. We contend that evaluating the relative importance of these processes requires a numerical modelling structure that allows for consistent comparison with observations, uncertainty characterization, and as mechanistic as possible a representation of the processes. We will describe a detailed spatially-resolved 3-dimensional reactive transport solver (TOUGHREACT) that represents abiotic and biotic SOM transformations and multi-phase flows. The modelling framework allows for explicit representation of (1) SOM interactions with minerals and their temperature, pH, and redox dependencies; (2) multiple microbial groups with different survival strategies and environmental sensitivities; (3) aqueous, gaseous, and sorbed phases; and (4) disaggregation of litter inputs, depolymerisation productions, and microbial bodies into an arbitrary number of SOM functional groups. The model accurately represented vertically-resolved bulk SOM in grassland and forest ecosystems using a baseline set of parameters. After testing, we used the model to investigate the relative impact of various mechanisms affecting SOM storage. Model predictions highlight the importance of sorption, aqueous transport, and microbial dynamics for the slow turnover of SOM that is observed below the rooting zone. We will also describe (1) model structural and parametric uncertainty; (2) methods to extract low-order model representations from the detailed reactive transport

  4. Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment

    NASA Astrophysics Data System (ADS)

    Yabusaki, Steven B.; Fang, Yilin; Williams, Kenneth H.; Murray, Christopher J.; Ward, Andy L.; Dayvault, Richard D.; Waichler, Scott R.; Newcomer, Darrell R.; Spane, Frank A.; Long, Philip E.

    2011-11-01

    Three-dimensional, coupled variably saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport and biogeochemical reactions controlling uranium behavior under pulsed acetate amendment, seasonal water table variation, spatially variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. While the simulation of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado was generally consistent with behaviors identified in previous field experiments at the Rifle IFRC site, the additional process and property detail provided several new insights. A principal conclusion from this work is that uranium bioreduction is most effective when acetate, in excess of the sulfate-reducing bacteria demand, is available to the metal-reducing bacteria. The inclusion of an initially small population of slow growing sulfate-reducing bacteria identified in proteomic analyses led to an additional source of Fe(II) from the dissolution of Fe(III) minerals promoted by biogenic sulfide. The falling water table during the experiment significantly reduced the saturated thickness of the aquifer and resulted in reactants and products, as well as unmitigated uranium, in the newly unsaturated vadose zone. High permeability sandy gravel structures resulted in locally high flow rates in the vicinity of injection wells that increased acetate dilution. In downgradient locations, these structures created preferential flow paths for acetate delivery that enhanced local zones of TEAP reactivity and subsidiary reactions. Conversely, smaller transport rates associated with the lower permeability lithofacies (e.g., fine) and vadose zone were shown to limit acetate access and reaction. Once accessed by acetate, however, these same zones limited subsequent acetate dilution and provided longer residence times that resulted

  5. New Reactive Transport Challenges for Acidified Flows in Fractured Carbonate Rocks

    NASA Astrophysics Data System (ADS)

    Peters, C. A.; Deng, H.; Fitts, J. P.

    2013-12-01

    The single most important reactive mineral in the context of permeability evolution of fractures is calcite because it is highly soluble and fast-reacting, it is ubiquitous in sedimentary rocks, and is often sufficiently abundant that dissolution would lead to important porosity changes. Calcite dissolution is promoted not only by low pH such as from injected CO2 but also by low concentration of calcium such as in injection of hydrofracking fluids. Thus, for a calcite-containing rock, if a flow path exists or if a fresh fracture is created during fluid injection or hydrofracking, flows can alter the hydrodynamic properties of the fracture, a process that may or may not be favorable, depending on the application. We have investigated these reaction-induced permeability alterations using reactive transport modeling and fractured core flooding experiments. In all cases, the general finding is that fracture permeability can increase substantially as a result of calcite dissolution, but the extent of this change is dependent on a complex interplay of the initial fracture geometry, mineral spatial heterogeneity and variation, and fluid composition and flow rate. Model simulations show that even with simple geochemical models that account only for calcite as a reactive mineral, complex dynamics arise. The alkalinity increase that results from calcium release causes the calcite dissolution reaction to be self-limiting. This buffering can lead to counter-intuitive findings such as systems with larger volume fractions of calcite having smaller permeability change. Another example of the calcium buffering effect is that a far-from-equilibrium solution may produce less permeability change than a nearer-to-equilibrium solution at the same pH. In the lab, we have used a suite of imaging technologies to observe additional complexities relating to the reactive evolution of the 3D geometry of fractures. These effects are currently not accounted for in any reactive transport model

  6. Multiphase flow and multicomponent reactive transport model of the ventilation experiment in Opalinus clay

    SciTech Connect

    Zheng, L.; Samper, J.; Montenegro, L.; Major, J.C.

    2008-10-15

    During the construction and operational phases of a high-level radioactive waste (HLW) repository constructed in a clay formation, ventilation of underground drifts will cause desaturation and oxidation of the rock. The Ventilation Experiment (VE) was performed in a 1.3 m diameter unlined horizontal microtunnel on Opalinus clay at Mont Terri underground research laboratory in Switzerland to evaluate the impact of desaturation on rock properties. A multiphase flow and reactive transport model of VE is presented here. The model accounts for liquid, vapor and air flow, evaporation/condensation and multicomponent reactive solute transport with kinetic dissolution of pyrite and siderite and local-equilibrium dissolution/precipitation of calcite, ferrihydrite, dolomite, gypsum and quartz. Model results reproduce measured vapor flow, liquid pressure and hydrochemical data and capture the trends of measured relative humidities, although such data are slightly overestimated near the rock interface due to uncertainties in the turbulence factor. Rock desaturation allows oxygen to diffuse into the rock and triggers pyrite oxidation, dissolution of calcite and siderite, precipitation of ferrihydrite, dolomite and gypsum and cation exchange. pH in the unsaturated rock varies from 7.8 to 8 and is buffered by calcite. Computed changes in the porosity and the permeability of Opalinus clay in the unsaturated zone caused by oxidation and mineral dissolution/precipitation are smaller than 5%. Therefore, rock properties are not expected to be affected significantly by ventilation of underground drifts during construction and operational phases of a HLW repository in clay.

  7. Experimental Study and Reactive Transport Modeling of Boric Acid Leaching of Concrete

    NASA Astrophysics Data System (ADS)

    Pabalan, R. T.; Chiang, K.-T. K.

    2013-07-01

    Borated water leakage through spent fuel pools (SFPs) at pressurized water reactors is a concern because it could cause corrosion of reinforcement steel in the concrete structure, compromise the integrity of the structure, or cause unmonitored releases of contaminated water to the environment. Experimental data indicate that pH is a critical parameter that determines the corrosion susceptibility of rebar in borated water and the degree of concrete degradation by boric acid leaching. In this study, reactive transport modeling of concrete leaching by borated water was performed to provide information on the solution pH in the concrete crack or matrix and the degree of concrete degradation at different locations of an SFP concrete structure exposed to borated water. Simulations up to 100 years were performed using different boric acid concentrations, crack apertures, and solution flow rates. Concrete cylinders were immersed in boric acid solutions for several months and the mineralogical changes and boric acid penetration in the concrete cylinder were evaluated as a function of time. The depths of concrete leaching by boric acid solution derived from the reactive transport simulations were compared with the measured boric acid penetration depth.

  8. Characterizing biogeochemical processes in the hyporheic zone using flume experiments and reactive transport modeling

    NASA Astrophysics Data System (ADS)

    Quick, A. M.; Reeder, W. J.; Farrell, T. B.; Feris, K. P.; Tonina, D.; Benner, S. G.

    2015-12-01

    The hyporheic zones of streams are hotspots of biogeochemical cycling, where reactants from surface water and groundwater are continually brought into contact with microbial populations on the surfaces of stream sediments and reaction products are removed by hyporheic flow and degassing. Using large flume experiments we have documented the complex redox dynamics associated with dune-scale hyporheic flow. Observations, coupled with reactive transport modeling, provide insight into how flow dictates spatio-temporal distribution of redox reactions and the associated consumption and production of reactants and products. Dune hyporheic flow was experimentally produced by maintaining control over flow rates, slopes, sediment grain size, bedform geomorphology, and organic carbon content. An extensive in-situ monitoring array combined with sampling events over time elucidated redox-sensitive processes including constraints on the spatial distribution and magnitude of aerobic respiration, organic carbon consumption, sulfide deposition, and denitrification. Reactive transport modeling reveals further insight into the influence of system geometry and reaction rate. As an example application of the model, the relationship between residence times and reaction rates may be used to generate Damköhler numbers that are related to biogeochemical processes, such as the potential of streambed morphology and nitrate loading to influence production of the greenhouse gas nitrous oxide via incomplete denitrification.

  9. Reactive-transport modelling of gypsum dissolution in a coastal karst aquifer in Puglia, southern Italy

    NASA Astrophysics Data System (ADS)

    Campana, Claudia; Fidelibus, Maria Dolores

    2015-11-01

    The gypsum coastal aquifer of Lesina Marina (Puglia, southern Italy) has been affected by sinkhole formation in recent decades. Previous studies based on geomorphologic and hydrogeological data ascribed the onset of collapse phenomena to the erosion of material that fills palaeo-cavities (suffosion sinkholes). The change in the hydrodynamic conditions of groundwater induced by the excavation of a canal within the evaporite formation nearly 100 years ago was identified as the major factor in triggering the erosion, while the contribution of gypsum dissolution was considered negligible. A combined reactive-transport/density-dependent flow model was applied to the gypsum aquifer to evaluate whether gypsum dissolution rate is a dominant or insignificant factor in recent sinkhole formation under current hydrodynamic conditions. The conceptual model was first defined with a set of assumptions based on field and laboratory data along a two-dimensional transect of the aquifer, and then a density-dependent, tide-influenced flow model was set up and solved using the numerical code SEAWAT. Finally, the resulting transient flow field was used by the reactive multicomponent transport model PHT3D to estimate the gypsum dissolution rate. The validation tests show that the model accurately represents the real system, and the multi-disciplinary approach provides consistent information about the causes and evolution time of dissolution processes. The modelled porosity development rate is too low to represent a significant contribution to the recent sinkhole formation in the Lesina Marina area, although it justifies cavity formation and cavity position over geological time.

  10. Nitrate Biogeochemistry and Reactive Transport in California Groundwater: LDRD Final Report

    SciTech Connect

    Esser, B K; Beller, H; Carle, S; Cey, B; Hudson, G B; Leif, R; LeTain, T; Moody-Bartel, C; Moore, K; McNab, W; Moran, J; Tompson, A

    2006-02-24

    Nitrate is the number one drinking water contaminant in the United States. It is pervasive in surface and groundwater systems,and its principal anthropogenic sources have increased dramatically in the last 50 years. In California alone, one third of the public drinking-water wells has been lost since 1988 and nitrate contamination is the most common reason for abandonment. Effective nitrate management in groundwater is complicated by uncertainties related to multiple point and non-point sources, hydrogeologic complexity, geochemical reactivity, and quantification of denitrification processes. In this paper, we review an integrated experimental and simulation-based framework being developed to study the fate of nitrate in a 25 km-long groundwater subbasin south of San Jose, California, a historically agricultural area now undergoing rapid urbanization with increasing demands for groundwater. The modeling approach is driven by a need to integrate new and archival data that support the hypothesis that nitrate fate and transport at the basin scale is intricately related to hydrostratigraphic complexity, variability of flow paths and groundwater residence times, microbial activity, and multiple geochemical reaction mechanisms. This study synthesizes these disparate and multi-scale data into a three-dimensional and highly resolved reactive transport modeling framework.

  11. Simulation of Nitrate Biogeochemistry and Reactive Transport in a California Groundwater Basin

    SciTech Connect

    Tompson, A B; Kane, S R; Beller, H R; Hudson, G B; McNab, W W; Moran, J E; Carle, S F; Esser, B K

    2004-01-16

    Nitrate is the number one drinking water contaminant in the United States. It is pervasive in surface and groundwater systems, and its principal anthropogenic sources have increased dramatically in the last 50 years. In California alone, one third of the public drinking-water wells has been lost since 1988 and nitrate contamination is the most common reason for abandonment. Effective nitrate management in groundwater is complicated by uncertainties related to multiple point and non-point sources, hydrogeologic complexity, geochemical reactivity, and quantification of dentrification processes. In this paper, we review an integrated experimental and simulation-based framework being developed to study the fate of nitrate in a 25 km-long groundwater subbasin south of San Jose, California, a historically agricultural area now undergoing rapid urbanization with increasing demands for groundwater. The modeling approach is driven by a need to integrate new and archival data that support the hypothesis that nitrate fate and transport at the basin scale is intricately related to hydrostratigraphic complexity, variability of flow paths and groundwater residence times, microbial activity, and multiple geochemical reaction mechanisms. This study synthesizes these disparate and multi-scale data into a three-dimensional and highly resolved reactive transport modeling framework.

  12. Energetic Ion Transport and Concomitant Change of the Fusion Reactivity during Reconnection Events in Spherical Tori

    SciTech Connect

    Ya.I. Kolesnichenko; V.V. Lutsenko; R.B. White; Yu.V. Yakovenko

    2004-07-06

    Effects of MHD reconnection events on the beam-plasma fusion reactivity and transport of the beam ions are studied. Based on the analysis of fusion reactivity changes induced by MHD events, the conclusion is drawn that the strong drops of the neutron yield during sawtooth crashes observed in the National Spherical Torus experiment (NSTX) [M. Ono et al., Nucl. Fusion 40, 557 (2000)] are associated with both a particle redistribution inside the plasma and a loss of the beam ions. Mechanisms of the energetic ion transport during sawtooth crashes are analyzed, in particular, with the use of the resonance adiabatic invariant derived in this paper. A numerical simulation of the particle motion during a sawtooth crash in NSTX is done with the code OFSEF [Ya. I. Kolesnichenko, et al., Nucl. Fusion 40, 1325 (2000)] extended for a better description of the particle precession. It is shown that the motion of toroidally passing particles in NSTX can become stochastic under the influence of a crash. This stochasticity, as well as the motion along the resonance island, leads to the escape of some particles from the plasma.

  13. Reactive Transport Modeling of CO2 Storage in a Saline Aquifer

    NASA Astrophysics Data System (ADS)

    Lu, C.; McNab, W. W.; Carroll, S. A.; Hao, Y.

    2010-12-01

    Since 2004, over 3 million tonnes of CO2, recovered from extracted natural gas, has been injected at the Krechba gas field in central Algeria. The objective of this research was to develop a reactive transport model which addresses the long-term fate of the injected CO2 in the reservoir centuries after the cessation of active injection. Reactive mineral phases and rates of precipitation and dissolution employed by the model were posited based upon the results of laboratory batch experiments involving the exposure of lithologic samples from Krechba to CO2 under reservoir temperature and pressure conditions. These experiments have indicated that an Fe-rich chlorite and Ca-,Fe-, and/or Mg-bearing carbonate phase(s) initially present in the reservoir materials will react most readily with injected CO2. Possible secondary phases which form as a result of reaction of these phases with CO2 include include a smectite phase, amorphous SiO2, gibbsite and/or kaolinite. Multiphase flow and transport modeling indicates buoyancy-driven migration of the separate-phase CO2, both upward in the reservoir relative to the interface with the caprock and laterally in response to elevation differences, will occur after active injection halts. Dissolution of separate-phase CO2 into the brine in the context of the reactive mineral phases and reaction rates identified in the geochemistry experiments results in some mineral trapping of CO2 (approximately 1 - 5 kg/m3 after 500 years), primarily from siderite and magnesite precipitation. Little impact to porosity or permeability in the reservoir is expected over this time scale.

  14. Coupling stress and reactive transport in fractures: Effects on contacting asperities, permeability and stiffness

    NASA Astrophysics Data System (ADS)

    Spokas, K.; Peters, C. A.; Pyrak-Nolte, L. J.; Morris, J.; Fitts, J. P.; Deng, H.

    2015-12-01

    The permeability and geomechanical stability of fractured rock can be altered by reactive flow that induces mineral dissolution and/or precipitation. Understanding the coupling of geochemical and geomechanical processes is critical for predicting and identifying leakage pathways for environmentally-relevant fluids in the subsurface. This study couples a two-dimensional reactive transport model with a mechanical deformation model to simulate reaction, flow and deformation in a fractured carbonate rock under subsurface confining pressures. The fracture is represented as a homogenous calcite material subjected to high-pressure reactive CO2-acidified brine, and the dissolution reaction is modeled to be kinetically-limited by carbonic acid. Initial conditions for the simulations were based on fractured Indiana Limestone geometries obtained from xCT data. Simulation of reactive flow results in the enlargement of apertures and reduction in contact area along preferential flow paths, while apertures outside these channelized flow paths remain relatively unchanged. At high confining pressures, contact area occurred mainly in regions where channelization did not occur, resulting in a two- to three-fold reduction in the fracture specific stiffness. Moreover, at high confining stresses, channelized regions were preserved, enabling permeability to remain relatively unchanged compared to non-channelized regions, which in contrast showed an order of magnitude decrease in permeability when stressed. These simulations suggest that differences in dissolution patterns can lead to significant variations in fracture permeability and stiffness when subject to subsurface confining stresses. This work has important applications for geologic carbon sequestration, natural gas storage, hydraulic fracturing, geothermal energy and deep well injection of hazardous waste.

  15. A novel heterocyclic compound targeting the dopamine transporter improves performance in the radial arm maze and modulates dopamine receptors D1-D3.

    PubMed

    Saroja, Sivaprakasam R; Aher, Yogesh D; Kalaba, Predrag; Aher, Nilima Y; Zehl, Martin; Korz, Volker; Subramaniyan, Saraswathi; Miklosi, Andras G; Zanon, Lisa; Neuhaus, Winfried; Höger, Harald; Langer, Thierry; Urban, Ernst; Leban, Johann; Lubec, Gert

    2016-10-01

    A series of compounds targeting the dopamine transporter (DAT) haS been shown to improve memory performance most probably by re-uptake inhibition. Although specific DAT inhibitors are available, there is limited information about specificity, mechanism and in particular the effect on dopamine receptors. It was therefore the aim of the study to test the DAT inhibitor 4-(diphenyl-methanesulfinylmethyl)-2-methyl-thiazole (code: CE-111), synthetized in our laboratory for the specificity to target DAT, for the effects upon spatial memory and for induced dopamine receptor modulation. Re-uptake inhibition was tested for DAT (IC50=3.2μM), serotonin transporter, SERT (IC50=272291μM) and noradrenaline transporter, NET (IC50=174μM). Spatial memory was studied in the radial arm maze (RAM) in male Sprague-Dawley rats that were intraperitoneally injected with CE-111 (1 or 10mg/kg body weight). Performance in the RAM was improved using 1 and 10mg/kg body weight of CE-111. Training and treatment effects on presynaptic, postsynaptic and extrasynaptic D1 and D2- receptors and dopamine receptor containing complexes as well as on activated DAT were observed. CE-111 was crossing the blood-brain barrier comparable to modafinil and was identified as effective to improve memory performance in the RAM. Dopamine re-uptake inhibition along with modulations in dopamine receptors are proposed as potential underlying mechanisms. PMID:27288589

  16. Physics of a magnetic filter for negative ion sources. I. Collisional transport across the filter in an ideal, 1D filter

    SciTech Connect

    Boeuf, J. P.; Chaudhury, B.; Garrigues, L.

    2012-11-15

    Magnetic filters are used in negative ion sources for neutral beam injection in fusion devices to reduce the electron temperature in the extraction region in order to limit negative ion destruction by fast electrons. The drop in electron temperature through the filter is due to the enhanced residence time and collisional energy losses of electrons trapped in the magnetic field. The mechanisms controlling particle and energy transport through the magnetic filter in negative ion sources of the ITER type are still not clear and the aim of this paper is to clarify and quantify these mechanisms. A particle-in-cell Monte Carlo simulation is used to revisit and analyze the role and operation of the magnetic filter in an 'ideal' one-dimensional configuration and to study the stability of the one-dimensional solution in a two-dimensional configuration with periodic boundary conditions. The roles of collisions and instabilities on electron transport through the filter are discussed. The influence of a more realistic geometry on electron transport through the filter is analyzed in the companion paper [Boeuf et al., Phys. Plasmas 19, 113510 (2012)].

  17. Reactive transport model of growth and methane production by high-temperature methanogens in hydrothermal regions of the subseafloor

    NASA Astrophysics Data System (ADS)

    Stewart, L. C.; Algar, C. K.; Topçuoğlu, B. D.; Fortunato, C. S.; Larson, B. I.; Proskurowski, G. K.; Butterfield, D. A.; Vallino, J. J.; Huber, J. A.; Holden, J. F.

    2014-12-01

    Hydrogenotrophic methanogens are keystone high-temperature autotrophs in deep-sea hydrothermal vents and tracers of habitability and biogeochemical activity in the hydrothermally active subseafloor. At Axial Seamount, nearly all thermophilic methanogens are Methanothermococcus and Methanocaldococcus species, making this site amenable to modeling through pure culture laboratory experiments coupled with field studies. Based on field microcosm incubations with 1.2 mM, 20 μM, or no hydrogen, the growth of methanogens at 55°C and 80°C is limited primarily by temperature and hydrogen availability, with ammonium amendment showing no consistent effect on total methane output. The Arrhenius constants for methane production by Methanocaldococcus jannaschii (optimum 82°C) and Methanothermococcus thermolithotrophicus (optimum 65°C) were determined in pure culture bottle experiments. The Monod constants for hydrogen concentration were measured by growing both organisms in a 2-liter chemostat at two dilution rates; 55°C, 65°C and 82°C; and variable hydrogen concentrations. M. jannaschii showed higher ks and Vmax constants than M. thermolithotrophicus. In the field, hydrogen and methane concentrations in hydrothermal end-member and low-temperature diffuse fluids were measured, and the concentrations of methanogens that grow at 55°C and 80°C in diffuse fluids were determined using most-probable-number estimates. Methane concentration anomalies in diffuse fluids relative to end-member hydrothermal concentrations and methanogen cell concentrations are being used to constrain a 1-D reactive transport model using the laboratory-determined Arrhenius and Monod constants for methane production by these organisms. By varying flow path length and subseafloor cell concentrations in the model, our goal is to determine solutions for the potential depth of the subseafloor biosphere coupled with the amount of methanogenic biomass it contains.

  18. Moffett Field Funnel and Gate TCE Treatment System: Interpretation of Field Performance using Reactive Transport Modeling

    SciTech Connect

    Yabusaki, Steven B.; Cantrell, Kirk J.; Sass, B. M.

    2001-06-30

    A multicomponent reactive transport simulator was used to understand the behavior of chemical components, including TCE and cis-1,2-DCE, in groundwater transported through the pilot-scale funnel and gate chemical treatment system at Moffett Field, California. Field observations indicated that zero-valent iron emplaced in the gate to effect the destruction of chlorinated hydrocarbons also resulted in increases in pH and hydrocarbons, as well as decreases in EH, alkalinity, dissolved O2 and CO2, and major ions (i.e., Ca, Mg, Cl, sulfate, nitrate). Of concern are chemical transformations that may reduce the effectiveness or longevity of the iron cell and/or create secondary contaminants. A coupled model of transport and reaction processes was developed to account for mobile and immobile components undergoing equilibrium and kinetic reactions including TCE degradation, parallel iron dissolution reactions, precipitation of secondary minerals, and complexation reactions. The model reproduced solution chemistry observed in the iron cell using reaction parameters from the literature and laboratory studies. Mineral precipitation in the iron zone, which is critical to correctly predicting the aqueous concentrations, was predicted to account for up to 3 percent additional mineral volume annually. Interplay between rates of transport and rates of reaction in the field was key to understanding system behavior.

  19. Assessment of Controlling Processes for Field-Scale Uranium Reactive Transport under Highly Transient Flow Conditions

    SciTech Connect

    Ma, Rui; Zheng, Chunmiao; Liu, Chongxuan; Greskowiak, Janek; Prommer, Henning; Zachara, John M.

    2014-02-06

    This paper presents the results of a comprehensive model-based analysis of a uranium tracer test conducted at the U.S Department of Energy Hanford 300 Area (300A) IFRC site. A three-dimensional multi-component reactive transport model was employed to assess the key factors and processes that control the field-scale uranium reactive transport. Taking into consideration of relevant physical and chemical processes, the selected conceptual/numerical model replicates the spatial and temporal variations of the observed U(VI) concentrations reasonably well in spite of the highly complex field conditions. A sensitivity analysis was performed to interrogate the relative importance of various processes and factors for reactive transport of U(VI) at the field-scale. The results indicate that multi-rate U(VI) sorption/desorption, U(VI) surface complexation reactions, and initial U(VI) concentrations were the most important processes and factors controlling U(VI) migration. On the other hand, cation exchange reactions, the choice of the surface complexation model, and dual-domain mass transfer processes, which were previously identified to be important in laboratory experiments, played less important roles under the field-scale experimental condition at the 300A site. However, the model simulations also revealed that the groundwater chemistry was relatively stable during the uranium tracer experiment and therefore presumably not dynamic enough to appropriately assess the effects of ion exchange reaction and the choice of surface complexation models on U(VI) sorption and desorption. Furthermore, it also showed that the field experimental duration (16 days) was not sufficiently long to precisely assess the role of a majority of the sorption sites that were accessed by slow kinetic processes within the dual domain model. The sensitivity analysis revealed the crucial role of the intraborehole flow that occurred within the long-screened monitoring wells and thus significantly

  20. Development of a numerical reactive transport modelling framework - Concept & Case Studies

    NASA Astrophysics Data System (ADS)

    Kalbacher, T.; Jang, E.; He, W.; Shao, H.; Zolfaghari, R.; Kolditz, O.

    2014-12-01

    Civilization and in particular agriculture worldwide depends on the availability of clean freshwater resources stored in the underlying soil and aquifer systems. Unfortunately, water quality is often deteriorating, which is e.g. due to the extensive use of fertilizers or pesticides in agriculture or infiltrating waste water from cities and industries. All groundwater bodies commonly discharge into the nearby surface-water bodies like streams, lakes, or springs, and soil water is a direct water source for the biosphere. Therefore, bio-hydro-geochemical reaction systems along flow paths of the unsaturated as well as the saturated zone can have a strong impact on aquatic and terrestrial ecosystems. The simulation of such reactive transport problems in different hydrological compartments can help to understanding the comprehensive processes chain. One way to evaluate the water quality in space and time is to model the mass transport in soil and/or groundwater together with the contemporaneous chemical reactions numerically. Such physical and bio- hydro- geochemical driven forward simulations are usually solved by standard finite differences, finite element or finite volume methods, but simulating these scenarios at catchment scales is a challenging task due to the extreme computational load, numerical stability issues and different scale-dependencies. The main focus of the present study is the numerical simulation of reactive transport processes in heterogeneous porous media at large scales, i.e. from field scale, over hill slopes towards catchment scale. The objective of the study is, to develop a robust modelling framework which allows to identify appropriate levels of heterogeneity as well as the possibly dominating structural features (e.g. S-shaped clay lenses) with respect to specific reaction systems. The presented modelling framework will describe the functional interaction of different numerical methods and high performing computing (HPC) techniques by the use

  1. Suppressor mutations in the Glutamine Dumper1 protein dissociate disturbance in amino acid transport from other characteristics of the Gdu1D phenotype

    PubMed Central

    Yu, Shi; Pratelli, Réjane; Denbow, Cynthia; Pilot, Guillaume

    2015-01-01

    Intracellular amino acid transport across plant membranes is critical for metabolic pathways which are often split between different organelles. In addition, transport of amino acids across the plasma membrane enables the distribution of organic nitrogen through the saps between leaves and developing organs. Amino acid importers have been studied for more than two decades, and their role in this process is well-documented. While equally important, amino acid exporters are not well-characterized. The over-expression of GDU1, encoding a small membrane protein with one transmembrane domain, leads to enhancement of amino acid export by Arabidopsis cells, glutamine secretion at the leaf margin, early senescence and size reduction of the plant, possibly caused by the stimulation of amino acid exporter(s). Previous work reported the identification of suppressor mutations of the GDU1 over-expression phenotype, which affected the GDU1 and LOG2 genes, the latter encoding a membrane-bound ubiquitin ligase interacting with GDU1. The present study focuses on the characterization of three additional suppressor mutations affecting GDU1. Size, phenotype, glutamine transport and amino acid tolerance were recorded for recapitulation plants and over-expressors of mutagenized GDU1 proteins. Unexpectedly, the over-expression of most mutated GDU1 led to plants with enhanced amino acid export, but failing to display secretion of glutamine and size reduction. The results show that the various effects triggered by GDU1 over-expression can be dissociated from one another by mutagenizing specific residues. The fact that these residues are not necessarily conserved suggests that the diverse biochemical properties of the GDU1 protein are not only born by the characterized transmembrane and VIMAG domains. These data provide a better understanding of the structure/function relationships of GDU1 and may enable modifying amino acid export in plants without detrimental effects on plant fitness

  2. A heterocyclic compound CE-103 inhibits dopamine reuptake and modulates dopamine transporter and dopamine D1-D3 containing receptor complexes.

    PubMed

    Sase, Ajinkya; Aher, Yogesh D; Saroja, Sivaprakasam R; Ganesan, Minu Karthika; Sase, Sunetra; Holy, Marion; Höger, Harald; Bakulev, Vasiliy; Ecker, Gerhard F; Langer, Thierry; Sitte, Harald H; Leban, Johann; Lubec, Gert

    2016-03-01

    A series of compounds have been reported to enhance memory via the DA system and herein a heterocyclic compound was tested for working memory (WM) enhancement. 2-((benzhydrylsulfinyl)methyl)thiazole (CE-103) was synthesized in a six-step synthesis. Binding of CE-103 to the dopamine (DAT), serotonin (SERT) and norepinephrine (NET) transporters and dopamine reuptake inhibition was tested as well as blood brain permeation and a screen for GPCR targets. 60 male Sprague Dawley rats were divided into six groups: CE-103 treated 1-10 mg/kg body weight, trained (TDI) and yoked (YDI) and vehicle treated, trained (TVI) and yoked (YVI) rats. Daily single intraperitoneal injections for a period of 10 days were administered and rats were tested in a radial arm maze (RAM). Hippocampi were taken 6 h following the last day of training and complexes containing the unphosphorylated or phosphorylated dopamine transporter (DAT) and complexes containing the D1-3 dopamine receptor subunits were determined. CE-103 was binding to the DAT but insignificantly to SERT or NET and dopamine reuptake was blocked specifically (IC50 = 14.73 μM). From day eight the compound was decreasing WM errors in the RAM significantly at both doses tested as compared to the vehicle controls. In the trained CE-103-treated group levels of the complex containing the phosphorylated dopamine transporter (pDAT) as well as D1R were decreased while levels of complexes containing D2R and D3R were significantly increased. CE-103 was shown to enhance spatial WM and DA reuptake inhibition with subsequent modulation of D1-3 receptors is proposed as a possible mechanism of action. PMID:26407764

  3. Measurement of the differential cross section of the photoinitiated reactive collision of O(1D)+D2 using only one molecular beam: A study by three dimensional velocity mapping

    NASA Astrophysics Data System (ADS)

    Kauczok, S.; Maul, C.; Chichinin, A. I.; Gericke, K.-H.

    2010-06-01

    velocities. Using the benchmark system O(D1)+D2 with N2O as the precursor, we demonstrate that the technique is also applicable in a very general sense (i.e., also with a large spread in reactant velocities, products much faster than reactants) and therefore can be used also if such unfortunate conditions cannot be avoided. Since the resulting distribution of velocities in the laboratory frame is not cylindrically symmetric, three dimensional velocity mapping is the method of choice for the detection of the ionized products. For the reconstruction, the distance between the two laser beams is an important parameter. We have measured this distance using the photodissociation of HBr at 193 nm, detecting the H atoms near 243 nm. The collision energy resulting from the 193 nm photodissociation of N2O is 5.2±1.9 kcal/mol. Our results show a preference for backward scattered D atoms with the OH partner fragment in the high vibrational states (v =4-6), in accord with previously published results claiming the growing importance of a linear abstraction mechanism for collision energies higher than 2.4 kcal/mol.

  4. Combined Estimation of Hydrogeologic Scenario, Model, and Parameter Uncertainty and Sensitivity with Application to Groundwater Reactive Transport Modeling

    NASA Astrophysics Data System (ADS)

    Dai, H.; Ye, M.

    2013-12-01

    Groundwater contamination has been a serious health and environmental problem in many areas over the world nowadays. Groundwater reactive transport modeling is vital to make predictions of future contaminant reactive transport. However, these predictions are inherently uncertain, and uncertainty is one of the greatest obstacles in groundwater reactive transport. We propose a Bayesian network approach for quantifying the uncertainty and implement the network for a groundwater reactive transport model for illustration. In the Bayesian network, different uncertainty sources are described as uncertain nodes. All the nodes are characterized by multiple states, representing their uncertainty, in the form of continuous or discrete probability distributions that are propagated to the model endpoint, which is the spatial distribution of contaminant concentrations. After building the Bayesian network, uncertainty quantification is conducted through Monte Carlo simulations to obtain probability distributions of the variables of interest. In this study, uncertainty sources include scenario uncertainty, model uncertainty, parameter uncertainty, and data uncertainty. Variance decomposition is used to quantify relative contribution from the various sources to predictive uncertainty. Based on the variance decomposition, the Sobol' global sensitivity index is extended from parametric uncertainty to consider model and scenario uncertainty, and individual parameter sensitivity index is estimated with consideration of multiple models and scenarios. While these new developments are illustrated using a relatively simple groundwater reactive transport model, our methods is applicable to a wide range of models. The results of uncertainty quantification and sensitivity analysis are useful for environmental management and decision-makers to formulate policies and strategies.

  5. Reactive transport in porous media: pore-network model approach compared to pore-scale model.

    PubMed

    Varloteaux, Clément; Vu, Minh Tan; Békri, Samir; Adler, Pierre M

    2013-02-01

    Accurate determination of three macroscopic parameters governing reactive transport in porous media, namely, the apparent solute velocity, the dispersion, and the apparent reaction rate, is of key importance for predicting solute migration through reservoir aquifers. Two methods are proposed to calculate these parameters as functions of the Péclet and the Péclet-Dahmköhler numbers. In the first method called the pore-scale model (PSM), the porous medium is discretized by the level set method; the Stokes and convection-diffusion equations with reaction at the wall are solved by a finite-difference scheme. In the second method, called the pore-network model (PNM), the void space of the porous medium is represented by an idealized geometry of pore bodies joined by pore throats; the flow field is computed by solving Kirchhoff's laws and transport calculations are performed in the asymptotic regime where the solute concentration undergoes an exponential evolution with time. Two synthetic geometries of porous media are addressed by using both numerical codes. The first geometry is constructed in order to validate the hypotheses implemented in PNM. PSM is also used for a better understanding of the various reaction patterns observed in the asymptotic regime. Despite the PNM approximations, a very good agreement between the models is obtained, which shows that PNM is an accurate description of reactive transport. PNM, which can address much larger pore volumes than PSM, is used to evaluate the influence of the concentration distribution on macroscopic properties of a large irregular network reconstructed from microtomography images. The role of the dimensionless numbers and of the location and size of the largest pore bodies is highlighted. PMID:23496613

  6. Numerical simulation of fracture permeability evolution due to reactive transport and pressure solution processes

    NASA Astrophysics Data System (ADS)

    Watanabe, N.; Sun, Y.; Taron, J.; Shao, H.; Kolditz, O.

    2013-12-01

    Modeling fracture permeability evolution is of great interest in various geotechnical applications including underground waste repositories, carbon capture and storage, and engineered geothermal systems where fractures dominate transport behaviors. In this study, a numerical model is presented to simulate fracture permeability evolution due to reactive transport and pressure solution processes in single fractures. The model was developed within the international benchmarking project for radioactive waste disposals, DECOVALEX 2015 (Task C1). The model combines bulk behavior in pore spaces with intergranular process at asperity contacts. Hydraulic flow and reactive transport including mineral dissolution and precipitation in fracture pore space are simulated using the Galerkin finite element method. A pressure solution model developed by Taron and Elsworth (2010 JGR) is applied to simulating stress-enhanced dissolution, solute exchange with pore space, and volume removal at grain contacts. Fracture aperture and contact area ratio are updated as a result of the pore-space reaction and intergranular dissolution. In order to increase robustness and time step size, relevant processes are monolithically coupled with the simulations. The model is implemented in a scientific open-source project OpenGeoSys (www.opengeosys.org) for numerical simulation of thermo-hydro-mechanical/chemical processes in porous and fractured media. Numerical results are compared to previous experiment performed by Yasuhara et al. (2006) on flow through fractures in the Arkansas novaculite sample. The novaculite is approximated as pure quartz aggregates. Only with fitted quartz dissolution rate constants and solubility is the current model capable of reproducing observed hydraulic aperture reduction and aqueous silicate concentrations. Future work will examine reaction parameters and further validate the model against experimental results.

  7. Evaluating remedial alternatives for an acid mine drainage stream: Application of a reactive transport model

    USGS Publications Warehouse

    Runkel, R.L.; Kimball, B.A.

    2002-01-01

    A reactive transport model based on one-dimensional transport and equilibrium chemistry is applied to synoptic data from an acid mine drainage stream. Model inputs include streamflow estimates based on tracer dilution, inflow chemistry based on synoptic sampling, and equilibrium constants describing acid/base, complexation, precipitation/dissolution, and sorption reactions. The dominant features of observed spatial profiles in pH and metal concentration are reproduced along the 3.5-km study reach by simulating the precipitation of Fe(III) and Al solid phases and the sorption of Cu, As, and Pb onto freshly precipitated iron-(III) oxides. Given this quantitative description of existing conditions, additional simulations are conducted to estimate the streamwater quality that could result from two hypothetical remediation plans. Both remediation plans involve the addition of CaCO3 to raise the pH of a small, acidic inflow from ???2.4 to ???7.0. This pH increase results in a reduced metal load that is routed downstream by the reactive transport model, thereby providing an estimate of post-remediation water quality. The first remediation plan assumes a closed system wherein inflow Fe(II) is not oxidized by the treatment system; under the second remediation plan, an open system is assumed, and Fe(II) is oxidized within the treatment system. Both plans increase instream pH and substantially reduce total and dissolved concentrations of Al, As, Cu, and Fe(II+III) at the terminus of the study reach. Dissolved Pb concentrations are reduced by ???18% under the first remediation plan due to sorption onto iron-(III) oxides within the treatment system and stream channel. In contrast, iron(III) oxides are limiting under the second remediation plan, and removal of dissolved Pb occurs primarily within the treatment system. This limitation results in an increase in dissolved Pb concentrations over existing conditions as additional downstream sources of Pb are not attenuated by

  8. River networks and ecological corridors: Reactive transport on fractals, migration fronts, hydrochory

    NASA Astrophysics Data System (ADS)

    Bertuzzo, E.; Maritan, A.; Gatto, M.; Rodriguez-Iturbe, I.; Rinaldo, A.

    2007-04-01

    Moving from a recent quantitative model of the US colonization in the 19th century that relies on analytical and numerical results of reactive-diffusive transport on fractal river networks, this paper considers its generalization to include an embedded flow direction which biases transport. We explore the properties of biased reaction-dispersal models, in which the reaction rates are described by a logistic equation. The relevance of the work is related to the prediction of the role of hydrologic controls on invasion processes (of species, populations, propagules, or infective agents, depending on the specifics of reaction and transport) occurring in river basins. Exact solutions are obtained along with general numerical solutions, which are applied to fractal constructs like Peano basins and real rivers. We also explore similarities and departures from different one-dimensional invasion models where a bias is added to both the diffusion and the telegraph equations, considering their respective ecological insight. We find that the geometrical constraints imposed by the fractal networks imply strong corrections on the speed of traveling fronts that can be enhanced or smoothed by the bias. Applications to real river networks show that the chief morphological parameters affecting the front speed are those characterizing the node-to-node distances measured along the network structure. The spatial density and number of reactive sites thus prove to be a vital hydrologic control on invasions. We argue that our solutions, currently tied to the validity of the logistic growth, might be relevant to the general study of species' spreading along ecological corridors defined by the river network structure.

  9. Modeling reactive geochemical transport of concentrated aqueous solutions in variably saturated media

    SciTech Connect

    Zhang, Guoxiang; Zheng, Zuoping; Wan, Jiamin

    2004-01-28

    Concentrated aqueous solutions (CAS) have unique thermodynamic and physical properties. Chemical components in CAS are incompletely dissociated, especially those containing divalent or polyvalent ions. The problem is further complicated by the interaction between CAS flow processes and the naturally heterogeneous sediments. As the CAS migrates through the porous media, the composition may be altered subject to fluid-rock interactions. To effectively model reactive transport of CAS, we must take into account ion-interaction. A combination of the Pitzer ion-interaction and the ion-association model would be an appropriate way to deal with multiple-component systems if the Pitzer' parameters and thermodynamic data of dissolved components and the related minerals are available. To quantify the complicated coupling of CAS flow and transport, as well as the involved chemical reactions in natural and engineered systems, we have substantially extended an existing reactive biogeochemical transport code, BIO-CORE{sup 2D}{copyright}, by incorporating a comprehensive Pitzer ion-interaction model. In the present paper, the model, and two test cases against measured data were briefly introduced. Finally we present an application to simulate a laboratory column experiment studying the leakage of the high alkaline waste fluid stored in Hanford (a site of the U.S. Department of Energy, located in Washington State, USA). With the Pitzer ion-interaction ionic activity model, our simulation captures measured pH evolution. The simulation indicates that all the reactions controlling the pH evolution, including cation exchanges, mineral precipitation and dissolution, are coupled.

  10. Hyperfine-induced spin relaxation of a hopping carrier: implications for spin transport in 1-D vs 3-D organic semiconductors

    NASA Astrophysics Data System (ADS)

    Mkhitaryan, Vagharsh; Dobrovitski, Viatcheslav; 0 Team

    2015-03-01

    The hyperfine coupling of a carrier spin to a nuclear spin bath is a predominant channel for the carrier spin relaxation in organic semiconductors. We investigate the hyperfine-induced spin relaxation of a carrier performing a random walk on a d-dimensional regular lattice theoretically, in a transport regime typical for organic semiconductors. We show that in d = 1 and d = 2 the time dependence of spin polarization, P (t) , is dominated by a superexponential decay, crossing over to an exponential tail at long times. The faster decay is attributed to multiple self-intersections (returns) of the random walk trajectories, which occur more often in lower dimensions. We also show, analytically and numerically, that the returns lead to sensitivity of P (t) to external electric and magnetic fields, and this sensitivity strongly depends on dimensionality of the system (d = 1 vs. d = 3). Furthermore, we consider the coordinate dependence of spin polarization, σ (r) , in a hypothetic lateral or vertical organic spin-valve device. We demonstrate that, while σ (r) is essentially exponential, the effect of multiple self-intersections can be identified in transport measurements from the specific field-dependence of spin relaxation length. This work was supported by the Department of Energy-Basic Energy Sciences under Contract No. DE-AC02-07CH11358.

  11. Reactive Transport Models with Geomechanics to Mitigate Risks of CO2 Utilization and Storage

    SciTech Connect

    Deo, Milind; Huang, Hai; Kweon, Hyukmin; Guo, Luanjing

    2015-12-31

    Reactivity of carbon dioxide (CO2), rocks and brine is important in a number of practical situations in carbon dioxide sequestration. Injectivity of CO2 will be affected by near wellbore dissolution or precipitation. Natural fractures or faults containing specific minerals may reactivate leading to induced seismicity. In this project, we first examined if the reactions between CO2, brine and rocks affect the nature of the porous medium and properties including petrophysical properties in the timeframe of the injection operations. This was done by carrying out experiments at sequestration conditions (2000 psi for corefloods and 2400 psi for batch experiments, and 600C) with three different types of rocks – sandstone, limestone and dolomite. Experiments were performed in batch mode and corefloods were conducted over a two-week period. Batch experiments were performed with samples of differing surface area to understand the impact of surface area on overall reaction rates. Toughreact, a reactive transport model was used to interpret and understand the experimental results. The role of iron in dissolution and precipitation reactions was observed to be significant. Iron containing minerals – siderite and ankerite dissolved resulting in changes in porosity and permeability. Corefloods and batch experiments revealed similar patterns. With the right cationic balance, there is a possibility of precipitation of iron bearing carbonates. The results indicate that during injection operations mineralogical changes may lead to injectivity enhancements near the wellbore and petrophysical changes elsewhere in the system. Limestone and dolomite cores showed consistent dissolution at the entrance of the core. The dissolution led to formation of wormholes and interconnected dissolution zones. Results indicate that near wellbore dissolution in these rock-types may lead to rock failure. Micro-CT images of the cores before and after the experiments revealed that an initial high

  12. A conservative, positivity preserving scheme for reactive solute transport problems in moving domains

    NASA Astrophysics Data System (ADS)

    Mabuza, Sibusiso; Kuzmin, Dmitri; Čanić, Sunčica; Bukač, Martina

    2014-11-01

    We study the mathematical models and numerical schemes for reactive transport of a soluble substance in deformable media. The medium is a channel with compliant adsorbing walls. The solutes are dissolved in the fluid flowing through the channel. The fluid, which carries the solutes, is viscous and incompressible. The reactive process is described as a general physico-chemical process taking place on the compliant channel wall. The problem is modeled by a convection-diffusion adsorption-desorption equation in moving domains. We present a conservative, positivity preserving, high resolution ALE-FCT scheme for this problem in the presence of dominant transport processes and wall reactions on the moving wall. A Patankar type time discretization is presented, which provides conservative treatment of nonlinear reactive terms. We establish CFL-type constraints on the time step, and show the mass conservation of the time discretization scheme. Numerical simulations are performed to show validity of the schemes against effective models under various scenarios including linear adsorption-desorption, irreversible wall reaction, infinite adsorption kinetics, and nonlinear Langmuir kinetics. The grid convergence of the numerical scheme is studied for the case of fixed meshes and moving meshes in fixed domains. Finally, we simulate reactive transport in moving domains under linear and nonlinear chemical reactions at the wall, and show that the motion of the compliant channel wall enhances adsorption of the solute from the fluid to the channel wall. Consequences of this result are significant in the area of, e.g., nano-particle cancer drug delivery. Our result shows that periodic excitation of the cancerous tissue using, e.g., ultrasound, may enhance adsorption of cancer drugs carried by nano-particles via the human vasculature. For Taylor dispersion and for other convection dominated flows, numerical schemes for solute transport may lead to undesirable numerical artefacts. These

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

    SciTech Connect

    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

  14. Experimental investigation of the link between pore scale velocities, transport and reactivity in porous media

    NASA Astrophysics Data System (ADS)

    Meheust, Y.; Turuban, R.; Jimenez-Martinez, J.; De Anna, P.; Tabuteau, H.; Le Borgne, T.

    2014-12-01

    Pore scale characterization of flow velocities and concentration spatial distributions is a key to understanding non-Fickian transport and mixing in porous media. We present a millifluidic setup aimed at investigating those processes in transparent porous media, at the pore scale. The porous media are quasi-2D, consisting of a Hele-Shaw cell containing cylindrical grains. They are made by soft lithography from a numerical model and provide full control on the geometry (medium porosity, permeability and heterogeneity). The setup allows for the study of primary drainage/imbibition, or the joint continuous injection of two fluids (e. g. water and air). A camera records the distributions of fluid phases, the position of solid tracers, and spatially-resolved images of light emissions inside the flow cell. The pore scale velocity field is thus measured from particle tracking, while pore scale concentration fields are measured accurately in passive transport experiments, using fluorescein; both continuous injection and finite volume solute injections can be achieved. Using two chemo-luminescent liquids, the reaction of which produces photons in addition to the reaction product, we are also able to study the local production rate of the reaction product as the reactive liquids flow through the system [1]. Pressure drops across the medium are also measured. This complete characterization (phase distributions, velocity and concentration fields, pressure drops) of the system allows to explain non-Fickian behaviors and test models that upscale transport and mixing properties from pore scale data. As examples, we shall discuss the upscaling of transport from the knowledge of Lagrangian velocities and the relationships between conservative and reactive transport under mixing-limited conditions (very large Damkhöler number). Other applications include the prediction of the mixing rate from the sole knowledge of the flow stretching [2], and the characterization of mixing by

  15. Assessment of Alternative Conceptual Models Using Reactive Transport Modeling with Monitoring Data

    NASA Astrophysics Data System (ADS)

    Dai, Z.; Price, V.; Heffner, D.; Hodges, R.; Temples, T.; Nicholson, T.

    2005-12-01

    Monitoring data proved very useful in evaluating alternative conceptual models, simulating contaminant transport behavior, and reducing uncertainty. A graded approach using three alternative conceptual site models was formulated to simulate a field case of tetrachloroethene (PCE) transport and biodegradation. These models ranged from simple to complex in their representation of subsurface heterogeneities. The simplest model was a single-layer homogeneous aquifer that employed an analytical reactive transport code, BIOCHLOR (Aziz et al., 1999). Due to over-simplification of the aquifer structure, this simulation could not reproduce the monitoring data. The second model consisted of a multi-layer conceptual model, in combination with numerical modules, MODFLOW and RT3D within GMS, to simulate flow and reactive transport. Although the simulation results from the second model were comparatively better than those from the simple model, they still did not adequately reproduce the monitoring well concentrations because the geological structures were still inadequately defined. Finally, a more realistic conceptual model was formulated that incorporated heterogeneities and geologic structures identified from well logs and seismic survey data using the Petra and PetraSeis software. This conceptual model included both a major channel and a younger channel that were detected in the PCE source area. In this model, these channels control the local ground-water flow direction and provide a preferential chemical transport pathway. Simulation results using this conceptual site model proved compatible with the monitoring concentration data. This study demonstrates that the bias and uncertainty from inadequate conceptual models are much larger than those introduced from an inadequate choice of model parameter values (Neuman and Wierenga, 2003; Meyer et al., 2004; Ye et al., 2004). This case study integrated conceptual and numerical models, based on interpreted local hydrogeologic and

  16. Comparing approaches for simulating the reactive transport of U(VI) in ground water

    USGS Publications Warehouse

    Curtis, G.P.; Kohler, M.; Davis, J.A.

    2009-01-01

    The reactive transport of U(VI) in a well-characterized shallow alluvial aquifer at a former U(VI) mill located near Naturita, CO, was predicted for comparative purposes using a surface complexation model (SCM) and a constant K d approach to simulate U(VI) adsorption. The ground water at the site had U(VI) concentrations that ranged from 0.01 to 20 ??M, alkalinities that ranged from 2.5 to 18 meq/L, and a nearly constant pH of 7.1. The SCM used to simulate U(VI) adsorption was previously determined independently using laboratory batch adsorption experiments. Simulations obtained using the SCM approach were compared with simulations that used a constant K d approach to simulate adsorption using previously determined site-specific K d values. In both cases, the ground water flow and transport models used a conceptual model that was previously calibrated to a chloride plume present at the site. Simulations with the SCM approach demonstrated that the retardation factor varied temporally and spatially because of the differential transport of alkalinity and dissolved U(VI) and the nonlinearity of the U(VI) adsorption. The SCM model also simulated a prolonged slow decline in U(VI) concentration, which was not simulated using a constant K d model. Simulations using the SCM approach and the constant K d approach were similar after 20 years of transport but diverged significantly after 60 years. The simulations demonstrate the need for site-specific geochemical information on U(VI) adsorption to produce credible simulations of future transport. ?? 2009 Springer-Verlag.

  17. Modeling the transport of chemical warfare agents and simulants in polymeric substrates for reactive decontamination

    NASA Astrophysics Data System (ADS)

    Pearl, Thomas; Mantooth, Brent; Varady, Mark; Willis, Matthew

    2014-03-01

    Chemical warfare agent simulants are often used for environmental testing in place of highly toxic agents. This work sets the foundation for modeling decontamination of absorbing polymeric materials with the focus on determining relationships between agents and simulants. The correlations of agents to simulants must consider the three way interactions in the chemical-material-decontaminant system where transport and reaction occur in polymer materials. To this end, diffusion modeling of the subsurface transport of simulants and live chemical warfare agents was conducted for various polymer systems (e.g., paint coatings) with and without reaction pathways with applied decontamination. The models utilized 1D and 2D finite difference diffusion and reaction models to simulate absorption and reaction in the polymers, and subsequent flux of the chemicals out of the polymers. Experimental data including vapor flux measurements and dynamic contact angle measurements were used to determine model input parameters. Through modeling, an understanding of the relationship of simulant to live chemical warfare agent was established, focusing on vapor emission of agents and simulants from materials.

  18. Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation.

    PubMed

    Wu, Yuxin; Ajo-Franklin, Jonathan B; Spycher, Nicolas; Hubbard, Susan S; Zhang, Guoxiang; Williams, Kenneth H; Taylor, Joanna; Fujita, Yoshiko; Smith, Robert

    2011-01-01

    Ureolytically-driven calcium carbonate precipitation is the basis for a promising in-situ remediation method for sequestration of divalent radionuclide and trace metal ions. It has also been proposed for use in geotechnical engineering for soil strengthening applications. Monitoring the occurrence, spatial distribution, and temporal evolution of calcium carbonate precipitation in the subsurface is critical for evaluating the performance of this technology and for developing the predictive models needed for engineering application. In this study, we conducted laboratory column experiments using natural sediment and groundwater to evaluate the utility of geophysical (complex resistivity and seismic) sensing methods, dynamic synchrotron x-ray computed tomography (micro-CT), and reactive transport modeling for tracking ureolytically-driven calcium carbonate precipitation processes under site relevant conditions. Reactive transport modeling with TOUGHREACT successfully simulated the changes of the major chemical components during urea hydrolysis. Even at the relatively low level of urea hydrolysis observed in the experiments, the simulations predicted an enhanced calcium carbonate precipitation rate that was 3-4 times greater than the baseline level. Reactive transport modeling results, geophysical monitoring data and micro-CT imaging correlated well with reaction processes validated by geochemical data. In particular, increases in ionic strength of the pore fluid during urea hydrolysis predicted by geochemical modeling were successfully captured by electrical conductivity measurements and confirmed by geochemical data. The low level of urea hydrolysis and calcium carbonate precipitation suggested by the model and geochemical data was corroborated by minor changes in seismic P-wave velocity measurements and micro-CT imaging; the latter provided direct evidence of sparsely distributed calcium carbonate precipitation. Ion exchange processes promoted through NH4

  19. Are reactive transport models reliable tools for reconstructing historical contamination scenarios?

    NASA Astrophysics Data System (ADS)

    Clement, P.

    2009-12-01

    This presentation will be based on a recent project effort that I completed while serving as a member of National Academy of Sciences and Engineering panel. The primary goal of this congressionally-mandated project effort was to review scientific evidence on the association between adverse health effect s and exposure to a contaminated water supply system at the U.S. Marine Corps Base Camp Lejeune (CLJ) in North Carolina. The detailed NRC study report was released in June 2009, and is available at this NRC weblink: http://www.nap.edu/catalog.php?record_id=12618. Multiple water supply systems at this Marine Base were contaminated with harmful chemicals, such as PCE, TCE and other waste products, since the early 50s. In 1982, a routine water quality survey completed at the site indicated the presence of several volatile organic compounds including PCE and TCE. Further investigations revealed that there are several waste disposal facilities located on-site that have discharged TCE and other waste products into groundwater systems. In addition, there was also an off-site dry cleaning facility located close to the Tarawa Terrace in-take well locations that disposed PCE into the subsurface environment. The dry cleaner has been using PCE since 1953 and disposed various forms of PCE-contaminated wastes in a septic tank and in several shallow pits. Therefore, the residents who lived in Tarawa Terrace on-site family housing units had the potential to be exposed to these harmful environmental contaminants through the drinking water source. In late 1980s, the concerns raised by CLJ public lead to an epidemiological study to evaluate the potential associations of utero and infant exposures to the VOCs and childhood cancers and birth defects. The study included births occurring during the period of 1968-1985 to women who were pregnant while they resided at the base. Since there was no monitoring data available for the study period (1968-1982), researchers used reactive transport

  20. Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation

    SciTech Connect

    Wu, Y.; Ajo-Franklin, J.B.; Spycher, N.; Hubbard, S.S.; Zhang, G.; Williams, K.H.; Taylor, J.; Fujita, Y.; Smith, R.

    2011-07-15

    Ureolytically-driven calcium carbonate precipitation is the basis for a promising in-situ remediation method for sequestration of divalent radionuclide and trace metal ions. It has also been proposed for use in geotechnical engineering for soil strengthening applications. Monitoring the occurrence, spatial distribution, and temporal evolution of calcium carbonate precipitation in the subsurface is critical for evaluating the performance of this technology and for developing the predictive models needed for engineering application. In this study, we conducted laboratory column experiments using natural sediment and groundwater to evaluate the utility of geophysical (complex resistivity and seismic) sensing methods, dynamic synchrotron x-ray computed tomography (micro-CT), and reactive transport modeling for tracking ureolytically-driven calcium carbonate precipitation processes under site relevant conditions. Reactive transport modeling with TOUGHREACT successfully simulated the changes of the major chemical components during urea hydrolysis. Even at the relatively low level of urea hydrolysis observed in the experiments, the simulations predicted an enhanced calcium carbonate precipitation rate that was 3-4 times greater than the baseline level. Reactive transport modeling results, geophysical monitoring data and micro-CT imaging correlated well with reaction processes validated by geochemical data. In particular, increases in ionic strength of the pore fluid during urea hydrolysis predicted by geochemical modeling were successfully captured by electrical conductivity measurements and confirmed by geochemical data. The low level of urea hydrolysis and calcium carbonate precipitation suggested by the model and geochemical data was corroborated by minor changes in seismic P-wave velocity measurements and micro-CT imaging; the latter provided direct evidence of sparsely distributed calcium carbonate precipitation. Ion exchange processes promoted through NH{sub 4}{sup

  1. Geophysical Monitoring and Reactive Transport Modeling of Ureolytically-Driven Calcium Carbonate Precipitation

    SciTech Connect

    Yuxin Wu; Jonathan B. Ajo-Franklin; Nicolas Spycher; Susan S. Hubbard; Guoxiang Zhang; Kenneth H. Williams; Joanna Taylor; Yoshiko Fujita; Robert Smith

    2011-09-01

    Ureolytically-driven calcium carbonate precipitation is the basis for a promising in-situ remediation method for sequestration of divalent radionuclide and trace metal ions. It has also been proposed for use in geotechnical engineering for soil strengthening applications. Monitoring the occurrence, spatial distribution, and temporal evolution of calcium carbonate precipitation in the subsurface is critical for evaluating the performance of this technology and for developing the predictive models needed for engineering application. In this study, we conducted laboratory column experiments using natural sediment and groundwater to evaluate the utility of geophysical (complex resistivity and seismic) sensing methods, dynamic synchrotron x-ray computed tomography (micro-CT), and reactive transport modeling for tracking ureolytically-driven calcium carbonate precipitation processes under site relevant conditions. Reactive transport modeling with TOUGHREACT successfully simulated the changes of the major chemical components during urea hydrolysis. Even at the relatively low level of urea hydrolysis observed in the experiments, the simulations predicted an enhanced calcium carbonate precipitation rate that was 3-4 times greater than the baseline level. Reactive transport modeling results, geophysical monitoring data and micro-CT imaging correlated well with reaction processes validated by geochemical data. In particular, increases in ionic strength of the pore fluid during urea hydrolysis predicted by geochemical modeling were successfully captured by electrical conductivity measurements and confirmed by geochemical data. The low level of urea hydrolysis and calcium carbonate precipitation suggested by the model and geochemical data was corroborated by minor changes in seismic P-wave velocity measurements and micro-CT imaging; the latter provided direct evidence of sparsely distributed calcium carbonate precipitation. Ion exchange processes promoted through NH4

  2. Reactive transport modeling of CO2 mineral sequestration in basaltic rocks

    NASA Astrophysics Data System (ADS)

    Aradottir, E. S.; Sonnenthal, E. L.; Bjornsson, G.; Jonsson, H.

    2011-12-01

    CO2 mineral sequestration in basalt may provide a long lasting, thermodynamically stable, and environmentally benign solution to reduce greenhouse gases in the atmosphere. Multi-dimensional, field scale, reactive transport models of this process have been developed with a focus on the CarbFix pilot CO2 injection in Iceland. An extensive natural analog literature review was conducted in order to identify the primary and secondary minerals associated with water-basalt interaction at low and elevated CO2 conditions. Based on these findings, an internally consistent thermodynamic database describing the mineral reactions of interest was developed and validated. Hydrological properties of field scale mass transport models were properly defined by calibration to field data using iTOUGH2. Reactive chemistry was coupled to the models and TOUGHREACT used for running predictive simulations carried out with the objective of optimizing long-term management of injection sites, to quantify the amount of CO2 that can be mineralized, and to identify secondary minerals that compete with carbonates for cations leached from the primary rock. Calibration of field data from the CarbFix reservoir resulted in a horizontal permeability for lava flows of 300 mD and a vertical permeability of 1700 mD. Active matrix porosity was estimated to be 8.5%. The CarbFix numerical models were a valuable engineering tool for designing optimal injection and production schemes aimed at increasing groundwater flow. Reactive transport simulations confirm dissolution of primary basaltic minerals as well as carbonate formation, and thus indicate in situ CO2 mineral sequestration in basalts to be a viable option. Furthermore, the simulations imply that clay minerals are most likely to compete with magnesite-siderite solid solutions for Mg and Fe leached from primary minerals, whereas zeolites compete with calcite for dissolved Ca. In the case of the CarbFix pilot injection, which involves a continuous

  3. Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation

    PubMed Central

    2011-01-01

    Ureolytically-driven calcium carbonate precipitation is the basis for a promising in-situ remediation method for sequestration of divalent radionuclide and trace metal ions. It has also been proposed for use in geotechnical engineering for soil strengthening applications. Monitoring the occurrence, spatial distribution, and temporal evolution of calcium carbonate precipitation in the subsurface is critical for evaluating the performance of this technology and for developing the predictive models needed for engineering application. In this study, we conducted laboratory column experiments using natural sediment and groundwater to evaluate the utility of geophysical (complex resistivity and seismic) sensing methods, dynamic synchrotron x-ray computed tomography (micro-CT), and reactive transport modeling for tracking ureolytically-driven calcium carbonate precipitation processes under site relevant conditions. Reactive transport modeling with TOUGHREACT successfully simulated the changes of the major chemical components during urea hydrolysis. Even at the relatively low level of urea hydrolysis observed in the experiments, the simulations predicted an enhanced calcium carbonate precipitation rate that was 3-4 times greater than the baseline level. Reactive transport modeling results, geophysical monitoring data and micro-CT imaging correlated well with reaction processes validated by geochemical data. In particular, increases in ionic strength of the pore fluid during urea hydrolysis predicted by geochemical modeling were successfully captured by electrical conductivity measurements and confirmed by geochemical data. The low level of urea hydrolysis and calcium carbonate precipitation suggested by the model and geochemical data was corroborated by minor changes in seismic P-wave velocity measurements and micro-CT imaging; the latter provided direct evidence of sparsely distributed calcium carbonate precipitation. Ion exchange processes promoted through NH4

  4. Towards a realistic approach to validation of reactive transport models for performance assessment

    SciTech Connect

    Siegel, M.D.

    1993-12-31

    Performance assessment calculations are based on geochemical models that assume that interactions among radionuclides, rocks and groundwaters under natural conditions, can be estimated or bound by data obtained from laboratory-scale studies. The data include radionuclide distribution coefficients, measured in saturated batch systems of powdered rocks, and retardation factors measured in short-term column experiments. Traditional approaches to model validation cannot be applied in a straightforward manner to the simple reactive transport models that use these data. An approach to model validation in support of performance assessment is described in this paper. It is based on a recognition of different levels of model validity and is compatible with the requirements of current regulations for high-level waste disposal. Activities that are being carried out in support of this approach include (1) laboratory and numerical experiments to test the validity of important assumptions inherent in current performance assessment methodologies,(2) integrated transport experiments, and (3) development of a robust coupled reaction/transport code for sensitivity analyses using massively parallel computers.

  5. Subsurface Multiphase Flow and Multicomponent Reactive Transport Modeling using High-Performance Computing

    SciTech Connect

    Hammond, Glenn E.; Lichtner, Peter C.; Lu, Chuan

    2007-07-16

    Numerical modeling has become a critical tool to the U.S. Department of Energy for evaluating the environmental impact of alternative energy sources and remediation strategies for legacy waste sites. Unfortunately, the physical and chemical complexity of many sites overwhelms the capabilities of even most “state of the art” groundwater models. Of particular concern are the representation of highly-heterogeneous stratified rock/soil layers in the subsurface and the biological and geochemical interactions of chemical species within multiple fluid phases. Clearly, there is a need for higher-resolution modeling (i.e. more spatial, temporal, and chemical degrees of freedom) and increasingly mechanistic descriptions of subsurface physicochemical processes. We present SciDAC-funded research being performed in the development of PFLOTRAN, a parallel multiphase flow and multicomponent reactive transport model. Written in Fortran90, PFLOTRAN is founded upon PETSc data structures and solvers. We are employing PFLOTRAN in the simulation of uranium transport at the Hanford 300 Area, a contaminated site of major concern to the Department of Energy, the State of Washington, and other government agencies. By leveraging the billions of degrees of freedom available through high-performance computation using tens of thousands of processors, we can better characterize the release of uranium into groundwater and its subsequent transport to the Columbia River, and thereby better understand and evaluate the effectiveness of various proposed remediation strategies.

  6. Subsurface multiphase flow and multicomponent reactive transport modeling using high-performance computing

    NASA Astrophysics Data System (ADS)

    Hammond, Glenn; Lichtner, Peter; Lu, Chuan

    2007-07-01

    Numerical modeling is a critical tool to the U.S. Department of Energy for evaluating the environmental impact of remediation strategies for subsurface legacy waste sites. Unfortunately, the physical and chemical complexity of many sites overwhelms the capabilities of even most state of the art groundwater models. Of particular concern is the representation of highly-heterogeneous stratified rock/soil layers in the subsurface and the biological and geochemical interactions of chemical species within multiple fluid phases. There is clearly a need for higher-resolution modeling (i.e. increased spatial and temporal resolution) and increasingly mechanistic descriptions of subsurface physicochemical processes (i.e. increased chemical degrees of freedom). We present SciDAC-funded research being performed in furthering the development of PFLOTRAN, a parallel multiphase flow and multicomponent reactive transport model. Written in Fortran90, PFLOTRAN is founded upon PETSc data structures and solvers. We are employing PFLOTRAN to simulate uranium transport at the Hanford 300 Area, a contaminated site of major concern to the Department of Energy, the State of Washington, and other government agencies. By leveraging the billions of degrees of freedom available through high-performance computation using tens of thousands of processors, we can better characterize the release of uranium into groundwater and its subsequent transport to the Columbia River, and thereby better understand and evaluate the effectiveness of various proposed remediation strategies.

  7. Dissolution-precipitation processes in tank experiments for testing numerical models for reactive transport calculations: Experiments and modelling

    NASA Astrophysics Data System (ADS)

    Poonoosamy, Jenna; Kosakowski, Georg; Van Loon, Luc R.; Mäder, Urs

    2015-06-01

    In the context of testing reactive transport codes and their underlying conceptual models, a simple 2D reactive transport experiment was developed. The aim was to use simple chemistry and design a reproducible and fast to conduct experiment, which is flexible enough to include several process couplings: advective-diffusive transport of solutes, effect of liquid phase density on advective transport, and kinetically controlled dissolution/precipitation reactions causing porosity changes. A small tank was filled with a reactive layer of strontium sulfate (SrSO4) of two different grain sizes, sandwiched between two layers of essentially non-reacting quartz sand (SiO2). A highly concentrated solution of barium chloride was injected to create an asymmetric flow field. Once the barium chloride reached the reactive layer, it forced the transformation of strontium sulfate into barium sulfate (BaSO4). Due to the higher molar volume of barium sulfate, its precipitation caused a decrease of porosity and lowered the permeability. Changes in the flow field were observed with help of dye tracer tests. The experiments were modelled using the reactive transport code OpenGeosys-GEM. Tests with non-reactive tracers performed prior to barium chloride injection, as well as the density-driven flow (due to the high concentration of barium chloride solution), could be well reproduced by the numerical model. To reproduce the mineral bulk transformation with time, two populations of strontium sulfate grains with different kinetic rates of dissolution were applied. However, a default porosity permeability relationship was unable to account for measured pressure changes. Post mortem analysis of the strontium sulfate reactive medium provided useful information on the chemical and structural changes occurring at the pore scale at the interface that were considered in our model to reproduce the pressure evolution with time.

  8. Dissolution-precipitation processes in tank experiments for testing numerical models for reactive transport calculations: Experiments and modelling.

    PubMed

    Poonoosamy, Jenna; Kosakowski, Georg; Van Loon, Luc R; Mäder, Urs

    2015-01-01

    In the context of testing reactive transport codes and their underlying conceptual models, a simple 2D reactive transport experiment was developed. The aim was to use simple chemistry and design a reproducible and fast to conduct experiment, which is flexible enough to include several process couplings: advective-diffusive transport of solutes, effect of liquid phase density on advective transport, and kinetically controlled dissolution/precipitation reactions causing porosity changes. A small tank was filled with a reactive layer of strontium sulfate (SrSO4) of two different grain sizes, sandwiched between two layers of essentially non-reacting quartz sand (SiO2). A highly concentrated solution of barium chloride was injected to create an asymmetric flow field. Once the barium chloride reached the reactive layer, it forced the transformation of strontium sulfate into barium sulfate (BaSO4). Due to the higher molar volume of barium sulfate, its precipitation caused a decrease of porosity and lowered the permeability. Changes in the flow field were observed with help of dye tracer tests. The experiments were modelled using the reactive transport code OpenGeosys-GEM. Tests with non-reactive tracers performed prior to barium chloride injection, as well as the density-driven flow (due to the high concentration of barium chloride solution), could be well reproduced by the numerical model. To reproduce the mineral bulk transformation with time, two populations of strontium sulfate grains with different kinetic rates of dissolution were applied. However, a default porosity permeability relationship was unable to account for measured pressure changes. Post mortem analysis of the strontium sulfate reactive medium provided useful information on the chemical and structural changes occurring at the pore scale at the interface that were considered in our model to reproduce the pressure evolution with time. PMID:25805363

  9. A reactive transport model for mercury fate in soil--application to different anthropogenic pollution sources.

    PubMed

    Leterme, Bertrand; Blanc, Philippe; Jacques, Diederik

    2014-11-01

    Soil systems are a common receptor of anthropogenic mercury (Hg) contamination. Soils play an important role in the containment or dispersion of pollution to surface water, groundwater or the atmosphere. A one-dimensional model for simulating Hg fate and transport for variably saturated and transient flow conditions is presented. The model is developed using the HP1 code, which couples HYDRUS-1D for the water flow and solute transport to PHREEQC for geochemical reactions. The main processes included are Hg aqueous speciation and complexation, sorption to soil organic matter, dissolution of cinnabar and liquid Hg, and Hg reduction and volatilization. Processes such as atmospheric wet and dry deposition, vegetation litter fall and uptake are neglected because they are less relevant in the case of high Hg concentrations resulting from anthropogenic activities. A test case is presented, assuming a hypothetical sandy soil profile and a simulation time frame of 50 years of daily atmospheric inputs. Mercury fate and transport are simulated for three different sources of Hg (cinnabar, residual liquid mercury or aqueous mercuric chloride), as well as for combinations of these sources. Results are presented and discussed with focus on Hg volatilization to the atmosphere, Hg leaching at the bottom of the soil profile and the remaining Hg in or below the initially contaminated soil layer. In the test case, Hg volatilization was negligible because the reduction of Hg(2+) to Hg(0) was inhibited by the low concentration of dissolved Hg. Hg leaching was mainly caused by complexation of Hg(2+) with thiol groups of dissolved organic matter, because in the geochemical model used, this reaction only had a higher equilibrium constant than the sorption reactions. Immobilization of Hg in the initially polluted horizon was enhanced by Hg(2+) sorption onto humic and fulvic acids (which are more abundant than thiols). Potential benefits of the model for risk management and remediation of

  10. [Transporting models of reactive X-3B red dye in water-soil-crop continuums].

    PubMed

    Zhou, Qixing

    2002-02-01

    Reactive X-3B red dye entering into environment is a typical persistent organic pollutant(POPs). Transport of the dye from water to soil and from soil to crop compartment is a continuous ecological process. According to the cognitionm, the quantitative depiction of the process using mathematical models was theoretically discussed. Some of the mathematical models were also verified using burozem-soybean, cinnamon soil-wheat, krasnozem-radish, aquorizem-rice systems. In particular, transference of the dye from water compartment to soil compartment by way of adsorbent mechanisms was accorded with the Langmuir model, and movement of the dye from soil compartment to crop compartment on the basis of root-absorbing mechanisms could be expressed using logarithmic crop-soil accumulation factor(CSAF) models. PMID:11993110

  11. Microbial respiration and dissolution precipitation reactions of minerals: thermo-kinetics and reactive transport modelling

    NASA Astrophysics Data System (ADS)

    Azaroual, M. M.; Parmentier, M.; Andre, L.; Croiset, N.; Pettenati, M.; Kremer, S.

    2010-12-01

    Microbial processes interact closely with abiotic geochemical reactions and mineralogical transformations in several hydrogeochemical systems. Reactive transport models are aimed to analyze these complex mechanisms integrating as well as the degradation of organic matter as the redox reactions involving successive terminal electron acceptors (TEAPs) mediated by microbes through the continuum of unsaturated zone (soil) - saturated zone (aquifer). The involvement of microbial processes in reactive transport in soil and subsurface geologic greatly complicates the mastery of the major mechanisms and the numerical modelling of these systems. The introduction of kinetic constraints of redox reactions in aqueous phase requires the decoupling of equilibrium reactions and the redefinition of mass balance of chemical elements including the concept of basis species and secondary species of thermodynamic databases used in geochemical modelling tools. An integrated methodology for modelling the reactive transport has been developed and implemented to simulate the transfer of arsenic, denitrification processes and the role of metastable aqueous sulfur species with pyrite and organic matter as electron donors entities. A mechanistic rate law of microbial respiration in various geochemical environments was used to simulate reactive transport of arsenic, nitrate and organic matter combined to the generalized rate law of mineral dissolution - precipitation reactions derived from the transition state theory was used for dissolution - precipitation of silica, aluminosilicate, carbonate, oxyhydroxide, and sulphide minerals. The kinetic parameters are compiled from the literature measurements based on laboratory constrained experiments and field observations. Numerical simulations, using the geochemical software PHREEQC, were performed aiming to identify the key reactions mediated by microbes in the framework of in the first hand the concept of the unsaturated - saturated zones of an

  12. Multicomponent reactive transport simulation of the Elder problem: Effects of chemical reactions on salt plume development

    NASA Astrophysics Data System (ADS)

    Post, V. E. A.; Prommer, H.

    2007-10-01

    A numerical modeling approach was used to investigate the relevancy of the feedback mechanisms between geochemical reactions and variable density flow during free convection. The problem was studied by reformulating the classic Elder problem as a reactive multicomponent transport problem. It was found that for the studied system, the importance of this feedback decreased with increasing density contrast between intruding salinized water and the ambient fresh water body. For the smaller density contrasts, the flow patterns that develop during intrusion in the reactive simulations are characterized by different convection cells, higher rates of plume descent, and an increase in the total mass of solutes by up to 22% at the end of the simulation compared to the nonreactive simulations. For field situations, the results suggest that it may be necessary to consider the feedback between reactions and variable density flow where subtle density variations drive flow such as in contaminant plumes. For seawater intrusion problems, however, the feedback mechanism appears to be negligible for most cases.

  13. Three-dimensional model for multi-component reactive transport with variable density groundwater flow

    USGS Publications Warehouse

    Mao, X.; Prommer, H.; Barry, D.A.; Langevin, C.D.; Panteleit, B.; Li, L.

    2006-01-01

    PHWAT is a new model that couples a geochemical reaction model (PHREEQC-2) with a density-dependent groundwater flow and solute transport model (SEAWAT) using the split-operator approach. PHWAT was developed to simulate multi-component reactive transport in variable density groundwater flow. Fluid density in PHWAT depends not on only the concentration of a single species as in SEAWAT, but also the concentrations of other dissolved chemicals that can be subject to reactive processes. Simulation results of PHWAT and PHREEQC-2 were compared in their predictions of effluent concentration from a column experiment. Both models produced identical results, showing that PHWAT has correctly coupled the sub-packages. PHWAT was then applied to the simulation of a tank experiment in which seawater intrusion was accompanied by cation exchange. The density dependence of the intrusion and the snow-plough effect in the breakthrough curves were reflected in the model simulations, which were in good agreement with the measured breakthrough data. Comparison simulations that, in turn, excluded density effects and reactions allowed us to quantify the marked effect of ignoring these processes. Next, we explored numerical issues involved in the practical application of PHWAT using the example of a dense plume flowing into a tank containing fresh water. It was shown that PHWAT could model physically unstable flow and that numerical instabilities were suppressed. Physical instability developed in the model in accordance with the increase of the modified Rayleigh number for density-dependent flow, in agreement with previous research. ?? 2004 Elsevier Ltd. All rights reserved.

  14. Reactive transport modeling of subsurface arsenic removal systems in rural Bangladesh.

    PubMed

    Rahman, M M; Bakker, M; Patty, C H L; Hassan, Z; Röling, W F M; Ahmed, K M; van Breukelen, B M

    2015-12-15

    Subsurface Arsenic Removal (SAR) is a technique for in-situ removal of arsenic from groundwater. Extracted groundwater is aerated and re-injected into an anoxic aquifer, where the oxygen in the injected water reacts with ferrous iron in the aquifer to form hydrous ferric oxide (HFO). Subsequent extraction of groundwater contains temporarily lower As concentrations, because As sorbs onto the HFO. Injection, storage, and extraction together is called a cycle. A reactive transport model (RTM) was developed in PHREEQC to determine the hydrogeochemical processes responsible for As (im)mobilization during experimental SAR operation performed in Bangladesh. Oxidation of Fe(II) and As(III) were modeled using kinetic-rate expressions. Cation exchange, precipitation of HFO, and surface complexation, were modeled as equilibrium processes. A best set of surface complexation reactions and corresponding equilibrium constants was adopted from previous studies to simulate all 20 cycles of a SAR experiment. The model gives a reasonable match with observed concentrations of different elements in the extracted water (e.g., the r(2) value of As was 0.59 or higher). As concentrations in the extracted water are governed by four major processes. First, As concentration decreases in response to the elevated pH of injection water and likewise increases when native neutral pH groundwater flows in. Second, the sorption capacity for As increases due to the gradual buildup of HFO. Third, As sorption is enhanced by preferential removal of As(V). Fourth, competitive sorption of Si limits the capacity of freshly precipitated HFO for As sorption. Transferability of the developed reactive transport model was demonstrated through successful application of the model, without further calibration, to two additional SAR sites in Bangladesh. This gives confidence that the model could be useful to assess potential SAR performance at locations in Bangladesh based on local hydrogeochemical conditions. PMID

  15. Verifying accelerated physical modeling of reactive solute transport: the long term development of pore water solute profiles in a thick clay till.

    NASA Astrophysics Data System (ADS)

    Timms, W.; Hendry, J.

    2003-04-01

    Accelerated physical modeling, using a geotechnical centrifuge, is yet to be verified for reactive solute transport in very low permeability geologic materials. Whilst scaling relationships between the centrifuge model and corresponding prototype are established for physical parameters, scaling of chemical reactions requires special consideration. Centrifuge modeling was carried out on duplicate core samples of unoxidised clay rich till obtained from a research site in southern Saskatchewan, Canada. At this site, naturally occurring solutes, principally comprised of Na and SO4, concentrated at ˜70,000 mg/L TDS in the oxidized zone, have diffused downwards over the past 2-10 k years to background concentrations of 3,200 mg/L TDS. Data from new (N=9) and existing piezometers (N>7) were used to identify solute fronts between 12-22 m depth, revealing the K, Sr, Mg and Na were slightly retarded relative to Cl, δ2H and δ18O. Despite the very low hydraulic conductivity of the samples (1.2 ×10-11 m/s), approximately ˜20 k years of solute transport were simulated within 3 months of centrifuge modeling at ˜330×g. Stresses at the base of the samples were less than in situ preconsolidation pressure (550 kPa), yet centrifuge speed was sufficiently high that the Peclet number, based on measured flow rate and porosity, indicated advective and diffusive transport components. Over 4 pore volumes of NaCl, with a concentration equivalent to that at the top of the unoxidised zone (I=0.5) permeated the cores. Breakthrough of Na was significantly retarded and characterized by a lengthy tail below C0. The loss of Na from solution was accounted for by an increase of Ca and Mg due to cation exchange. The scaled prototype indicated retardation of Na by ion exchange over a period of thousands of years, similar to that observed at the field site. To account for minor scale differences, additional centrifuge models and PHREEQC geochemical models of 1D reactive solute transport are in

  16. Technical Basis for Peak Reactivity Burnup Credit for BWR Spent Nuclear Fuel in Storage and Transportation Systems

    SciTech Connect

    Marshall, William BJ J; Ade, Brian J; Bowman, Stephen M; Gauld, Ian C; Ilas, Germina; Mertyurek, Ugur; Radulescu, Georgeta

    2015-01-01

    Oak Ridge National Laboratory and the United States Nuclear Regulatory Commission have initiated a multiyear project to investigate application of burnup credit for boiling-water reactor (BWR) fuel in storage and transportation casks. This project includes two phases. The first phase (1) investigates applicability of peak reactivity methods currently used in spent fuel pools (SFPs) to storage and transportation systems and (2) evaluates validation of both reactivity (keff) calculations and burnup credit nuclide concentrations within these methods. The second phase will focus on extending burnup credit beyond peak reactivity. This paper documents the first phase, including an analysis of lattice design parameters and depletion effects, as well as both validation components. Initial efforts related to extended burnup credit are discussed in a companion paper. Peak reactivity analyses have been used in criticality analyses for licensing of BWR fuel in SFPs over the last 20 years. These analyses typically combine credit for the gadolinium burnable absorber present in the fuel with a modest amount of burnup credit. Gadolinium burnable absorbers are used in BWR assemblies to control core reactivity. The burnable absorber significantly reduces assembly reactivity at beginning of life, potentially leading to significant increases in assembly reactivity for burnups less than 15–20 GWd/MTU. The reactivity of each fuel lattice is dependent on gadolinium loading. The number of gadolinium-bearing fuel pins lowers initial lattice reactivity, but it has a small impact on the burnup and reactivity of the peak. The gadolinium concentration in each pin has a small impact on initial lattice reactivity but a significant effect on the reactivity of the peak and the burnup at which the peak occurs. The importance of the lattice parameters and depletion conditions are primarily determined by their impact on the gadolinium depletion. Criticality code validation for BWR burnup

  17. Basin scale reactive-transport simulations of CO2 leakage and resulting metal transport in a shallow drinking water aquifer

    NASA Astrophysics Data System (ADS)

    Navarre-Sitchler, A.; Maxwell, R. M.; Hammond, G. E.; Lichtner, P. C.

    2011-12-01

    Leakage of CO2 from underground storage formations into overlying aquifers will decrease groundwater pH resulting in a geochemical response of the aquifer. If metal containing aquifer minerals dissolve as a part of this response, there is a risk of exceeding regulatory limits set by the EPA. Risk assessment methods require a realistic prediction of the maximum metal concentration at wells or other points of exposure. Currently, these predictions are based on numerical reactive transport simulations of CO2 leaks. While previous studies have simulated galena dissolution as a source of lead to explore the potential for contamination of drinking water aquifers, it may be more realistic to simulate lead release from more common minerals that are known to contain trace amounts of metals, e.g. calcite. Model domains for these previous studies are often sub-km in scale or have very coarse grid resolution, due to computation limitations. In this study we simulate CO2 leakage into a drinking water aquifer using the massively parallel subsurface flow and reactive transport code PFLOTRAN. The regional model domain is 4km x 1km x 0.1 km. Even with fairly coarse grid spacing (~ 9 m x 9 m x 0.9 m), the simulations have > 49 million degrees of freedom, requiring the use of High-Performance Computing (HPC). Our simulations are run on Jaguar at Oak Ridge National Laboratory. Lead concentrations in extraction wells 3 km down gradient from a CO2 leak increase above background concentrations due to kinetic mineral dissolution along the flow path. Increases in aqueous concentrations are less when lead is allowed to sorb onto mineral surfaces. Surprisingly, lead concentration increases are greater in simulations where lead is present as a trace constituent in calcite (5% by volume) relative to simulations with galena (0.001% by volume) as the lead source. It appears that galena becomes oversaturated and begins to precipitate, a result observed in previous modeling studies, and its low

  18. Measurement and modelling of reactive transport in geological barriers for nuclear waste containment.

    PubMed

    Xiong, Qingrong; Joseph, Claudia; Schmeide, Katja; Jivkov, Andrey P

    2015-11-11

    Compacted clays are considered as excellent candidates for barriers to radionuclide transport in future repositories for nuclear waste due to their very low hydraulic permeability. Diffusion is the dominant transport mechanism, controlled by a nano-scale pore system. Assessment of the clays' long-term containment function requires adequate modelling of such pore systems and their evolution. Existing characterisation techniques do not provide complete pore space information for effective modelling, such as pore and throat size distributions and connectivity. Special network models for reactive transport are proposed here using the complimentary character of the pore space and the solid phase. This balances the insufficient characterisation information and provides the means for future mechanical-physical-chemical coupling. The anisotropy and heterogeneity of clays is represented using different length parameters and percentage of pores in different directions. Resulting networks are described as mathematical graphs with efficient discrete calculus formulation of transport. Opalinus Clay (OPA) is chosen as an example. Experimental data for the tritiated water (HTO) and U(vi) diffusion through OPA are presented. Calculated diffusion coefficients of HTO and uranium species are within the ranges of the experimentally determined data in different clay directions. This verifies the proposed pore network model and validates that uranium complexes are diffusing as neutral species in OPA. In the case of U(vi) diffusion the method is extended to account for sorption and convection. Rather than changing pore radii by coarse grained mathematical formula, physical sorption is simulated in each pore, which is more accurate and realistic. PMID:26524292

  19. Exposure-time based modeling of nonlinear reactive transport in porous media subject to physical and geochemical heterogeneity.

    PubMed

    Sanz-Prat, Alicia; Lu, Chuanhe; Amos, Richard T; Finkel, Michael; Blowes, David W; Cirpka, Olaf A

    2016-09-01

    Transport of reactive solutes in groundwater is affected by physical and chemical heterogeneity of the porous medium, leading to complex spatio-temporal patterns of concentrations and reaction rates. For certain cases of bioreactive transport, it could be shown that the concentrations of reactive constituents in multi-dimensional domains are approximately aligned with isochrones, that is, lines of identical travel time, provided that the chemical properties of the matrix are uniform. We extend this concept to combined physical and chemical heterogeneity by additionally considering the time that a water parcel has been exposed to reactive materials, the so-called exposure time. We simulate bioreactive transport in a one-dimensional domain as function of time and exposure time, rather than space. Subsequently, we map the concentrations to multi-dimensional heterogeneous domains by means of the mean exposure time at each location in the multi-dimensional domain. Differences in travel and exposure time at a given location are accounted for as time difference. This approximation simplifies reactive-transport simulations significantly under conditions of steady-state flow when reactions are restricted to specific locations. It is not expected to be exact in realistic applications because the underlying assumption, such as neglecting transverse mixing altogether, may not hold. We quantify the error introduced by the approximation for the hypothetical case of a two-dimensional, binary aquifer made of highly-permeable, non-reactive and low-permeable, reactive materials releasing dissolved organic matter acting as electron donor for aerobic respiration and denitrification. The kinetically controlled reactions are catalyzed by two non-competitive bacteria populations, enabling microbial growth. Even though the initial biomass concentrations were uniform, the interplay between transport, non-uniform electron-donor supply, and bio-reactions led to distinct spatial patterns of

  20. Exposure-time based modeling of nonlinear reactive transport in porous media subject to physical and geochemical heterogeneity

    NASA Astrophysics Data System (ADS)

    Sanz-Prat, Alicia; Lu, Chuanhe; Amos, Richard T.; Finkel, Michael; Blowes, David W.; Cirpka, Olaf A.

    2016-09-01

    Transport of reactive solutes in groundwater is affected by physical and chemical heterogeneity of the porous medium, leading to complex spatio-temporal patterns of concentrations and reaction rates. For certain cases of bioreactive transport, it could be shown that the concentrations of reactive constituents in multi-dimensional domains are approximately aligned with isochrones, that is, lines of identical travel time, provided that the chemical properties of the matrix are uniform. We extend this concept to combined physical and chemical heterogeneity by additionally considering the time that a water parcel has been exposed to reactive materials, the so-called exposure time. We simulate bioreactive transport in a one-dimensional domain as function of time and exposure time, rather than space. Subsequently, we map the concentrations to multi-dimensional heterogeneous domains by means of the mean exposure time at each location in the multi-dimensional domain. Differences in travel and exposure time at a given location are accounted for as time difference. This approximation simplifies reactive-transport simulations significantly under conditions of steady-state flow when reactions are restricted to specific locations. It is not expected to be exact in realistic applications because the underlying assumption, such as neglecting transverse mixing altogether, may not hold. We quantify the error introduced by the approximation for the hypothetical case of a two-dimensional, binary aquifer made of highly-permeable, non-reactive and low-permeable, reactive materials releasing dissolved organic matter acting as electron donor for aerobic respiration and denitrification. The kinetically controlled reactions are catalyzed by two non-competitive bacteria populations, enabling microbial growth. Even though the initial biomass concentrations were uniform, the interplay between transport, non-uniform electron-donor supply, and bio-reactions led to distinct spatial patterns of

  1. Simulating the reactive transport of nitrogen species in a regional irrigated agricultural groundwater system

    NASA Astrophysics Data System (ADS)

    Bailey, R. T.; Gates, T. K.

    2011-12-01

    The fate and transport of nitrogen (N) species in irrigated agricultural groundwater systems is governed by irrigation patterns, cultivation practices, aquifer-surface water exchanges, and chemical reactions such as oxidation-reduction, volatilization, and sorption, as well as the presence of dissolved oxygen (O2). We present results of applying the newly-developed numerical model RT3D-AG to a 50,400-ha regional study site within the Lower Arkansas River Valley in southeastern Colorado, where elevated concentrations of NO3 have been observed in both groundwater and surface water during the recent decade. Furthermore, NO3 has a strong influence on the fate and transport of other contaminants in the aquifer system such as selenium (Se) through inhibition of reduction of dissolved Se as well as oxidation of precipitate Se from outcropped and bedrock shale. RT3D-AG, developed by appending the multi-species reactive transport finite-difference model RT3D with modular packages that account for variably-saturated transport, the cycling of carbon (C) and N, and the fate and transport of O2 within the soil and aquifer system, simulates organic C and organic N decomposition and mineralization, oxidation-reduction reactions, and sorption. System sources/sinks consist of applied fertilizer and manure; crop uptake of ammonium (NH4) and NO3 during the growing season; mass of O2, NO3, and NH4 associated with irrigation water and canal seepage; mass of O2, NO3, and NH4 transferred to canals and the Arkansas River from the aquifer; and dead root mass and after-harvest stover mass incorporated into the soil organic matter at the end of the growing season. Chemical reactions are simulated using first-order Monod kinetics, wherein the rate of reaction is dependent on the concentration of the reactants as well as temperature and water content of the soil. Fertilizer and manure application timing and loading, mass of seasonal crop uptake, and end-of-season root mass and stover mass are

  2. Reactive transport of gentisic acid in a hematite-coated sand column: Experimental study and modeling

    NASA Astrophysics Data System (ADS)

    Hanna, K.; Rusch, B.; Lassabatere, L.; Hofmann, A.; Humbert, B.

    2010-06-01

    The adsorption of gentisic acid (GA) by hematite nano-particles was examined under static and dynamic conditions by conducting batch and column tests. To simulate natural sediments, the iron oxide was deposited on 10 μm quartz particles. The GA adsorption was described by a surface complexation model fitted to pH-adsorption curves with GA concentrations of 0.1-1 mM in a pH range of 3-10. The surface was described with one type of site ( tbnd FeOH°), while gentisic acid at the surface was described by two surface complexes ( tbnd FeLH 2°, log Kint = 8.9 and tbnd FeLH -, log Kint = -8.2). Modeling was conducted with PHREEQC-2 using the MINTEQ database. From a kinetic point of view, the intrinsic chemical reactions were likely to be the rate-limiting step of sorption (˜10 -3 s -1) while external and internal mass transfer rates (˜10 2 s -1) were much faster. Under flow through conditions (column), adsorption of GA to hematite-coated sand was about 7-times lower than under turbulent mixing (batch). This difference could not be explained by chemical adsorption kinetics as shown by test calculations run with HYDRUS-1D software. Surface complexation model simulations however successfully described the data when the surface area was adjusted, suggesting that under flow conditions the accessibility to the reactive surface sites was reduced. The exact mechanism responsible for the increased mobility of GA could not be determined but some parameters suggested that decreased external mass transfer between solution and surface may play a significant role under flow through conditions.

  3. Impact of immobile porosity architecture on reactive transport in mobile/immobile models

    NASA Astrophysics Data System (ADS)

    Babey, T.; De Dreuzy, J.; Rapaport, A.; Casenave, C.

    2011-12-01

    Diffusive porosity structures in aquifers can display a large diversity of topologies, from intergranular porosity to the ';dead-ends' of fracture networks. Here we study numerically the influence of this topology on solute transport parameters, such as dispersion coefficient, and on a simple equilibrium reaction. We build a model where diffusive structures of variable topology (with junctions, loops...) exchange with a fast, advective zone. We show that the internal organization of volumes of the diffusive structure has a strong and non-trivial influence on transport and reactivity. We also show, through Multi-Rate Mass Transfer framework, that the signature of this topology on residence times is often sufficient to reproduce the initial reaction rates. We thus propose new ways to determine the appropriate MRMT models for a wide range of porosity types. However, more complex chemical / physical processes (kinetic-limited reactions, gravity effects...) may diminish this relevance of MRMT models to reproduce reaction rates, and additional parameters linked to the topology of diffusive structures may be required.

  4. Impact of immobile porosity architecture on reactive transport in mobile/immobile models

    NASA Astrophysics Data System (ADS)

    Babey, T.; De Dreuzy, J.; Rapaport, A.; Casenave, C.

    2013-12-01

    Diffusive porosity structures in aquifers can display a large diversity of topologies, from intergranular porosity to the ';dead-ends' of fracture networks. Here we study numerically the influence of this topology on solute transport parameters, such as dispersion coefficient, and on a simple equilibrium reaction. We build a model where diffusive structures of variable topology (with junctions, loops...) exchange with a fast, advective zone. We show that the internal organization of volumes of the diffusive structure has a strong and non-trivial influence on transport and reactivity. We also show, through Multi-Rate Mass Transfer framework, that the signature of this topology on residence times is often sufficient to reproduce the initial reaction rates. We thus propose new ways to determine the appropriate MRMT models for a wide range of porosity types. However, more complex chemical / physical processes (kinetic-limited reactions, gravity effects...) may diminish this relevance of MRMT models to reproduce reaction rates, and additional parameters linked to the topology of diffusive structures may be required.

  5. Visualization and analysis of nanoparticle transport and ageing in reactive porous media.

    PubMed

    Naftaly, Aviv; Edery, Yaniv; Dror, Ishai; Berkowitz, Brian

    2015-12-15

    We present quasi-3D visualization and analysis of engineered nanoparticle (ENP) transport behavior in an experimental setup that uses a transmitted light imaging technique. A flow cell was packed with specially adapted, water-transparent, spherical polyacrylamide beads, which carry a negative surface charge representative of many natural environments. Ubiquitous, oppositely-charged ENPs - Au and Ag NPs - were synthesized and introduced into a flow cell subjected to a macroscopically uniform flow field via point source pulse injection, at three different flow rates. The negatively-charged ENPs behaved like a conservative tracer, in terms of spatio-temporal plume evolution. The positive AgNPs, however, displayed a decrease in their initially strong tendency to attach to the oppositely-charged porous medium. As a result, immobilization of the positive AgNPs was spatially and temporally limited to the vicinity of the point of injection; beyond this region, the AgNPs were mobile and effluent contained AgNPs with hydrodynamic diameters significantly larger than those of the injected AgNPs. This behavior is understood by dynamic light scattering and ζ potential measurements, which showed aggregation processes and inversion in particle surface charge to occur during transport of the positive ENPs. These findings have broad implications for ENP mobility and reactivity in the environment. PMID:26252995

  6. Reactive chemical transport in ground-water hydrology: Challenges to mathematical modeling

    SciTech Connect

    Narasimhan, T.N.; Apps, J.A.

    1990-07-01

    For a long time, earth scientists have qualitatively recognized that mineral assemblages in soils and rocks conform to established principles of chemistry. In the early 1960's geochemists began systematizing this knowledge by developing quantitative thermodynamic models based on equilibrium considerations. These models have since been coupled with advective-dispersive-diffusive transport models, already developed by ground-water hydrologists. Spurred by a need for handling difficult environmental issues related to ground-water contamination, these models are being improved, refined and applied to realistic problems of interest. There is little doubt that these models will play an important role in solving important problems of engineering as well as science over the coming years. Even as these models are being used practically, there is scope for their improvement and many challenges lie ahead. In addition to improving the conceptual basis of the governing equations, much remains to be done to incorporate kinetic processes and biological mediation into extant chemical equilibrium models. Much also remains to be learned about the limits to which model predictability can be reasonably taken. The purpose of this paper is to broadly assess the current status of knowledge in modeling reactive chemical transport and to identify the challenges that lie ahead.

  7. PFLOTRAN: Reactive Flow & Transport Code for Use on Laptops to Leadership-Class Supercomputers

    SciTech Connect

    Hammond, Glenn E.; Lichtner, Peter C.; Lu, Chuan; Mills, Richard T.

    2012-04-18

    PFLOTRAN, a next-generation reactive flow and transport code for modeling subsurface processes, has been designed from the ground up to run efficiently on machines ranging from leadership-class supercomputers to laptops. Based on an object-oriented design, the code is easily extensible to incorporate additional processes. It can interface seamlessly with Fortran 9X, C and C++ codes. Domain decomposition parallelism is employed, with the PETSc parallel framework used to manage parallel solvers, data structures and communication. Features of the code include a modular input file, implementation of high-performance I/O using parallel HDF5, ability to perform multiple realization simulations with multiple processors per realization in a seamless manner, and multiple modes for multiphase flow and multicomponent geochemical transport. Chemical reactions currently implemented in the code include homogeneous aqueous complexing reactions and heterogeneous mineral precipitation/dissolution, ion exchange, surface complexation and a multirate kinetic sorption model. PFLOTRAN has demonstrated petascale performance using 2{sup 17} processor cores with over 2 billion degrees of freedom. Accomplishments achieved to date include applications to the Hanford 300 Area and modeling CO{sub 2} sequestration in deep geologic formations.

  8. Release of aged contaminants from weathered sediments: Effects of sorbate speciation on scaling of reactive transport

    SciTech Connect

    Chorover, Jon; Perdrial, Nico; Mueller, Karl; Strepka, Caleb; O’Day, Peggy; Rivera, Nelson; Um, Wooyong; Chang, Hyun-Shik; Steefel, Carl; Thompson, Aaron

    2012-11-05

    Hanford sediments impacted by hyperalkaline high level radioactive waste have undergone incongruent silicate mineral weathering concurrent with contaminant uptake. In this project, we studied the impact of background pore water (BPW) on strontium, cesium and iodine desorption and transport in Hanford sediments that were experimentally weathered by contact with simulated hyperalkaline tank waste leachate (STWL) solutions. Using those lab-weathered Hanford sediments (HS) and model precipitates formed during nucleation from homogeneous STWL solutions (HN), we (i) provided thorough characterization of reaction products over a matrix of field-relevant gradients in contaminant concentration, partial pressure of carbon dioxide, and reaction time; (ii) improved molecular-scale understanding of how sorbate speciation controls contaminant desorption from weathered sediments upon removal of caustic sources; and (iii) developed a mechanistic, predictive model of meso- to field-scale contaminant reactive transport under these conditions. In this final report, we provide detailed descriptions of our results from this three-year study, completed in 2012 following a one-year no cost extension.

  9. Reactive transport in porous media: a comparison of model prediction with laboratory visualization.

    PubMed

    Gramling, Carolyn M; Harvey, Charles F; Meigs, Lucy C

    2002-06-01

    Groundwater transport models that accurately describe spreading of nonreactive solutes in an aquifer can poorly predict concentrations of reactive solutes. The dispersive term in the advection-dispersion equation can overpredict pore-scale mixing, and thereby overpredict homogeneous chemical reaction. We quantified this experimentally by imaging instantaneous colorimetric reactions between solutions of aqueous CuSO4 and EDTA4- within a 30-cm long translucent chamber packed with cryolite sand that closely matched the optical index of refraction of water. A charge-coupled device camera was used to quantify concentrations of blue CuEDTA2- within the chamber as it was produced by mixing of the two reactants at different flow rates. We compared these experimental results with a new analytic solution for instantaneous bimolecular reaction coupled with advection and dispersion of the product and reactants. For all flow rates, the concentrations of CuEDTA2- recorded in the experiments were about 20% less than predicted by the analytic solution, thereby demonstrating that models assuming complete mixing at the pore scale can overpredict reaction during transport. PMID:12075812

  10. Reactive Transport of Nitrate in Northern California Groundwater basins: An Integrated Characterization and Modeling Approach

    NASA Astrophysics Data System (ADS)

    Esser, B. K.; Moran, J. E.; Hudson, G. B.; Carle, S. F.; McNab, W.; Tompson, A. F.; Moore, K.; Beller, H.; Kane, S.; Eaton, G.

    2003-12-01

    More than 1/3 of active public drinking water supply wells in California produce water with nitrate-N levels indicative of anthropogenic inputs (> 4 mg/L). Understanding how the distribution of nitrate in California groundwater basins will evolve is vital to water supply and infrastructure planning. To address this need, we are studying the basin-scale reactive transport of nitrate in the Livermore and Llagas basins of Northern California. Both basins have increasingly urban populations heavily reliant on groundwater. A distinct nitrate "plume" exists in the Livermore Basin (Alameda County) whereas pervasive nitrate contamination exists in shallow groundwaters of the Llagas Basin (Santa Clara County). The sources and timing of nitrate contamination in these basins are not definitively known; septic systems, irrigated agriculture and livestock operations exist or have existed in both areas. The role of denitrification in controlling nitrate distribution is also unknown; dissolved oxygen levels are sufficiently low in portions of each basin as to indicate the potential for denitrification. We have collected water from 60 wells, and are determining both groundwater age (by the 3H/3He method) and the extent of denitrification (by the excess N2 method). Excess nitrogen is being determined by both membrane-inlet and noble gas mass spectrometry, using Ar and Ne content to account for atmospheric N2. We are also analyzing for stable istotopes of nitrate and water, nitrate co-contaminants, and general water quality parameters. Preliminary analysis of archival water district data from both basins suggests positive correlations of nitrate with Ca+2, Mg+2 and bicarbonate and negative correlation with pH. In the Llagas Basin, a negative correlation also exists between nitrate and temperature. Flow path-oriented reactive transport modeling is being explored as a tool to aid in the identification of both the sources of nitrate and evidence for denitrification in both basins

  11. Evaluating remedial alternatives for an acid mine drainage stream: application of a reactive transport model.

    PubMed

    Runkel, Robert L; Kimball, Briant A

    2002-03-01

    A reactive transport model based on one-dimensional transport and equilibrium chemistry is applied to synoptic data from an acid mine drainage stream. Model inputs include streamflow estimates based on tracer dilution, inflow chemistry based on synoptic sampling, and equilibrium constants describing acid/base, complexation, precipitation/dissolution, and sorption reactions. The dominant features of observed spatial profiles in pH and metal concentration are reproduced along the 3.5-km study reach by simulating the precipitation of Fe(III) and Al solid phases and the sorption of Cu, As, and Pb onto freshly precipitated iron(III) oxides. Given this quantitative description of existing conditions, additional simulations are conducted to estimate the streamwater quality that could result from two hypothetical remediation plans. Both remediation plans involve the addition of CaCO3 to raise the pH of a small, acidic inflow from approximately 2.4 to approximately 7.0. This pH increase results in a reduced metal load that is routed downstream by the reactive transport model, thereby providing an estimate of post-remediation water quality. The first remediation plan assumes a closed system wherein inflow Fe(II) is not oxidized by the treatment system; under the second remediation plan, an open system is assumed, and Fe(II) is oxidized within the treatment system. Both plans increase instream pH and substantially reduce total and dissolved concentrations of Al, As, Cu, and Fe(II+III) at the terminus of the study reach. Dissolved Pb concentrations are reduced by approximately 18% under the first remediation plan due to sorption onto iron(III) oxides within the treatment system and stream channel. In contrast, iron(III) oxides are limiting under the second remediation plan, and removal of dissolved Pb occurs primarily within the treatment system. This limitation results in an increase in dissolved Pb concentrations over existing conditions as additional downstream sources of

  12. Reactive transport modeling in the subsurface environment with OGS-IPhreeqc

    NASA Astrophysics Data System (ADS)

    He, Wenkui; Beyer, Christof; Fleckenstein, Jan; Jang, Eunseon; Kalbacher, Thomas; Naumov, Dimitri; Shao, Haibing; Wang, Wenqing; Kolditz, Olaf

    2015-04-01

    Worldwide, sustainable water resource management becomes an increasingly challenging task due to the growth of population and extensive applications of fertilizer in agriculture. Moreover, climate change causes further stresses to both water quantity and quality. Reactive transport modeling in the coupled soil-aquifer system is a viable approach to assess the impacts of different land use and groundwater exploitation scenarios on the water resources. However, the application of this approach is usually limited in spatial scale and to simplified geochemical systems due to the huge computational expense involved. Such computational expense is not only caused by solving the high non-linearity of the initial boundary value problems of water flow in the unsaturated zone numerically with rather fine spatial and temporal discretization for the correct mass balance and numerical stability, but also by the intensive computational task of quantifying geochemical reactions. In the present study, a flexible and efficient tool for large scale reactive transport modeling in variably saturated porous media and its applications are presented. The open source scientific software OpenGeoSys (OGS) is coupled with the IPhreeqc module of the geochemical solver PHREEQC. The new coupling approach makes full use of advantages from both codes: OGS provides a flexible choice of different numerical approaches for simulation of water flow in the vadose zone such as the pressure-based or mixed forms of Richards equation; whereas the IPhreeqc module leads to a simplification of data storage and its communication with OGS, which greatly facilitates the coupling and code updating. Moreover, a parallelization scheme with MPI (Message Passing Interface) is applied, in which the computational task of water flow and mass transport is partitioned through domain decomposition, whereas the efficient parallelization of geochemical reactions is achieved by smart allocation of computational workload over

  13. Reactive transport modeling in variably saturated porous media with OGS-IPhreeqc

    NASA Astrophysics Data System (ADS)

    He, W.; Beyer, C.; Fleckenstein, J. H.; Jang, E.; Kalbacher, T.; Shao, H.; Wang, W.; Kolditz, O.

    2014-12-01

    Worldwide, sustainable water resource management becomes an increasingly challenging task due to the growth of population and extensive applications of fertilizer in agriculture. Moreover, climate change causes further stresses to both water quantity and quality. Reactive transport modeling in the coupled soil-aquifer system is a viable approach to assess the impacts of different land use and groundwater exploitation scenarios on the water resources. However, the application of this approach is usually limited in spatial scale and to simplified geochemical systems due to the huge computational expense involved. Such computational expense is not only caused by solving the high non-linearity of the initial boundary value problems of water flow in the unsaturated zone numerically with rather fine spatial and temporal discretization for the correct mass balance and numerical stability, but also by the intensive computational task of quantifying geochemical reactions. In the present study, a flexible and efficient tool for large scale reactive transport modeling in variably saturated porous media and its applications are presented. The open source scientific software OpenGeoSys (OGS) is coupled with the IPhreeqc module of the geochemical solver PHREEQC. The new coupling approach makes full use of advantages from both codes: OGS provides a flexible choice of different numerical approaches for simulation of water flow in the vadose zone such as the pressure-based or mixed forms of Richards equation; whereas the IPhreeqc module leads to a simplification of data storage and its communication with OGS, which greatly facilitates the coupling and code updating. Moreover, a parallelization scheme with MPI (Message Passing Interface) is applied, in which the computational task of water flow and mass transport is partitioned through domain decomposition, whereas the efficient parallelization of geochemical reactions is achieved by smart allocation of computational workload over

  14. Uncertainty in the reactive transport model response to analkaline perturbation in a clay formation

    SciTech Connect

    Burnol, A.; Blanc, P.; Xu, T.; Spycher, N.; Gaucher, E.C.

    2006-03-15

    The mineral alteration in the concrete barrier and in the clay formation around long-lived intermediate-level radioactive waste in the French deep geological disposal concept is evaluated using numerical modeling. There are concerns that the mineralogical composition of the surrounded clay will not be stable under the high alkaline pore fluid conditions caused by concrete (pH {approx} 12). Conversely, the infiltration of CO{sub 2}-rich groundwater from the clay formation into initially unsaturated concrete, at the high temperature (T {approx} 70 C) produced from the decay of radionuclides, could cause carbonation, thereby potentially affecting critical performance functions of this barrier. This could also lead to significant changes in porosity, which would affect aqueous diffusive transport of long-lived radionuclides. All these processes are therefore intimately coupled and advanced reactive transport models are required for long-term performance assessment. The uncertainty in predictions of these models is one major question that must be answered. A mass-transfer model response to an alkaline perturbation in clay with standard model values is first simulated using the two-phase non-isothermal reactive transport code TOUGHREACT. The selection of input parameters is thereafter designed to sample uncertainties in a wide range of physico-chemical processes without making a priori assumptions about the relative importance of different feedbacks. This 'base-case' simulation is perturbed by setting a parameter to a minimum, intermediate or maximum value or by switching on/off a process. This sensitivity analysis is conducted using grid computing facilities of BRGM (http://iggi.imag.fr). Our evaluation of the preliminary results suggests that the resaturation and the heating of the near-field will be of long enough duration to cause a limited carbonation through all the width of the concrete barrier. Another prediction is the possibility of self-sealing at the concrete

  15. Validating Mechanistic Sorption Model Parameters and Processes for Reactive Transport in Alluvium

    SciTech Connect

    Zavarin, M; Roberts, S K; Rose, T P; Phinney, D L

    2002-05-02

    The laboratory batch and flow-through experiments presented in this report provide a basis for validating the mechanistic surface complexation and ion exchange model we use in our hydrologic source term (HST) simulations. Batch sorption experiments were used to examine the effect of solution composition on sorption. Flow-through experiments provided for an analysis of the transport behavior of sorbing elements and tracers which includes dispersion and fluid accessibility effects. Analysis of downstream flow-through column fluids allowed for evaluation of weakly-sorbing element transport. Secondary Ion Mass Spectrometry (SIMS) analysis of the core after completion of the flow-through experiments permitted the evaluation of transport of strongly sorbing elements. A comparison between these data and model predictions provides additional constraints to our model and improves our confidence in near-field HST model parameters. In general, cesium, strontium, samarium, europium, neptunium, and uranium behavior could be accurately predicted using our mechanistic approach but only after some adjustment was made to the model parameters. The required adjustments included a reduction in strontium affinity for smectite, an increase in cesium affinity for smectite and illite, a reduction in iron oxide and calcite reactive surface area, and a change in clinoptilolite reaction constants to reflect a more recently published set of data. In general, these adjustments are justifiable because they fall within a range consistent with our understanding of the parameter uncertainties. These modeling results suggest that the uncertainty in the sorption model parameters must be accounted for to validate the mechanistic approach. The uncertainties in predicting the sorptive behavior of U-1a and UE-5n alluvium also suggest that these uncertainties must be propagated to nearfield HST and large-scale corrective action unit (CAU) models.

  16. Subsurface Multiphase Flow and Multicomponent Reactive Transport Modeling using High-Performance Computing

    SciTech Connect

    Hammond, Glenn E.; Lichtner, Peter C.; Lu, Chuan

    2007-08-01

    Numerical modeling has become a critical tool to the Department of Energy for evaluating the environmental impact of alternative energy sources and remediation strategies for legacy waste sites. Unfortunately, the physical and chemical complexity of many sites overwhelms the capabilities of even most “state of the art” groundwater models. Of particular concern are the representation of highly-heterogeneous stratified rock/soil layers in the subsurface and the biological and geochemical interactions of chemical species within multiple fluid phases. Clearly, there is a need for higher-resolution modeling (i.e. more spatial, temporal, and chemical degrees of freedom) and increasingly mechanistic descriptions of subsurface physicochemical processes. We present research being performed in the development of PFLOTRAN, a parallel multiphase flow and multicomponent reactive transport model. Written in Fortran90, PFLOTRAN is founded upon PETSc data structures and solvers and has exhibited impressive strong scalability on up to 4000 processors on the ORNL Cray XT3. We are employing PFLOTRAN in the simulation of uranium transport at the Hanford 300 Area, a contaminated site of major concern to the Department of Energy, the State of Washington, and other government agencies where overly-simplistic historical modeling erroneously predicted decade removal times for uranium by ambient groundwater flow. By leveraging the billions of degrees of freedom available through high-performance computation using tens of thousands of processors, we can better characterize the release of uranium into groundwater and its subsequent transport to the Columbia River, and thereby better understand and evaluate the effectiveness of various proposed remediation strategies.

  17. REACTIVE TRANSPORT MODELING USING A PARALLEL FULLY-COUPLED SIMULATOR BASED ON PRECONDITIONED JACOBIAN-FREE NEWTON-KRYLOV

    SciTech Connect

    Luanjing Guo; Chuan Lu; Hai Huang; Derek R. Gaston

    2012-06-01

    Systems of multicomponent reactive transport in porous media that are large, highly nonlinear, and tightly coupled due to complex nonlinear reactions and strong solution-media interactions are often described by a system of coupled nonlinear partial differential algebraic equations (PDAEs). A preconditioned Jacobian-Free Newton-Krylov (JFNK) solution approach is applied to solve the PDAEs in a fully coupled, fully implicit manner. The advantage of the JFNK method is that it avoids explicitly computing and storing the Jacobian matrix during Newton nonlinear iterations for computational efficiency considerations. This solution approach is also enhanced by physics-based blocking preconditioning and multigrid algorithm for efficient inversion of preconditioners. Based on the solution approach, we have developed a reactive transport simulator named RAT. Numerical results are presented to demonstrate the efficiency and massive scalability of the simulator for reactive transport problems involving strong solution-mineral interactions and fast kinetics. It has been applied to study the highly nonlinearly coupled reactive transport system of a promising in situ environmental remediation that involves urea hydrolysis and calcium carbonate precipitation.

  18. Use of Bioluminescence to Study Reactive Solute Transport and Biofilm Growth and Activity in Porous Media

    NASA Astrophysics Data System (ADS)

    Sharp, R. R.; Gerlach, R.; Al, C. B.

    2004-12-01

    Using a meso-scale porous media flat plate reactor we utilized a naturally bioluminescent biofilm (V. fischeri) and tracer studies to obtain information on the interactions between biofilms and reactive flow in porous media. The growth and development of the V. fischeri biofilm in a porous media geometry was studied using digital time lapse images of the bioluminescent signal given off by the developing biofilm. The effect of biofilm development on porous media hydrodynamics was examined using dye tracer studies and image analysis. The natural bioluminescence of the V. fischeri allowed real-time, in-situ study of biofilm development in porous media, without destruction of the biofilm. Dye studies and image analysis enabled the study of effects of biofilm accumulation on porous media hydraulics, with comparisons to plug flow and completely mixed systems with varying degrees of biofilm accumulation. The hydraulic conductivity of the porous media/biofilm system was continuously monitored showing a 1 to 4 order of magnitude decrease in hydraulic conductivity as a function of biofilm thickness and accumulation. The real-time nature of the study permitted us to visualize dynamic flow channel formation within the biofilm/porous media system. In addition, the sensitivity of the V. fischeri biofilm to dissolved oxygen allowed us to capture real-time images of reactive transport within the system. Using bioluminescent imaging, the location of active biomass, as well as the relative degree of biological activity, could be visualized and monitored over time. This work is the first meso-scale visualization of the interactions between biofilm and flow in porous media.

  19. Reactive Transport Modeling and Geophysical Monitoring of Bioclogging at Reservoir Scale

    NASA Astrophysics Data System (ADS)

    Surasani, V.; Commer, M.; Ajo Franklin, J. B.; Li, L.; Hubbard, S. S.

    2012-12-01

    In Microbial-Enhanced-Hydrocarbon-Recovery (MEHR), preferential bioclogging targets the growth of the biofilms (def. immobilized biopolymers with active cells embodied in it) in highly permeable thief zones to enhance sweep efficiency in oil reservoirs. During MEHR, understanding and controlling bioclogging is hindered by the lack of advanced modeling and monitoring tools; these deficiencies contribute to suboptimal performance. Our focus in this study was on developing a systematic approach to understand and monitor bioclogging at the reservoir scale using a combination of reactive transport modeling and geophysical imaging tools (EM & seismic). In this study, we created a realistic reservoir model from a heterogeneous gas reservoir in the Southern Sacramento basin, California; the model well (Citizen Green #1) was characterized using sonic, electrical, nuclear, and NMR logs for hydrologic and geophysical properties. From the simplified 2D log data model, a strip of size 150m x75m with several high permeability streaks is identified for bioclogging simulation experiments. From the NMR log data it is observed that a good linear correlation exist between logarithmic permeability (0.55- 3.34 log (mD)) versus porosity (0.041-0.28). L. mesenteroides was chosen as the model bacteria. In the presence of sucrose, it enzymatically catalyzes the production of dextran, a useful bioclogging agent. Using microbial kinetics from our laboratory experiment and reservoir heterogeneity, a reactive transport model (RTM) is established for two kinds of bioclogging treatments based on whether microbes are present in situ or are supplied externally. In both cases, sucrose media (1.5 M) is injected at the rate of 1 liter/s for 20 days into the center of high permeable strip to stimulate microbes. Simulations show that the high dextran production was deep into the formation from the injection well. This phenomenon can be explained precisely with bacterial kinetics and injection rate. In

  20. Interplay between subsurface structural heterogeneity and multi-species reactive transport in human health risk predictions

    NASA Astrophysics Data System (ADS)

    Henri, C.; Fernandez-Garcia, D.; de Barros, F.

    2013-12-01

    The increasing presence of toxic chemicals released in the subsurface has led to a rapid growth of social concerns and to the need to develop and employ models that can predict the impact of groundwater contamination in human health under uncertainty. Monitored natural attenuation is a common remediation action in many contamination cases and represents an attractive decontamination method. However, natural attenuation can lead to the production of subspecies of distinct toxicity that may pose challenges in pollution management strategies. The actual threat that these contaminants pose to human health and ecosystems greatly depends on the interplay between the complexity of the geological system and the toxicity of the pollutants and their byproducts. In this work, we examine the interplay between multispecies reactive transport and the heterogeneous structure of the contaminated aquifer on human health risk predictions. The structure and organization of hydraulic properties of the aquifer can lead to preferential flow channels and fast contamination pathways. Early travel times, associated to channeling effects, are intuitively perceived as an indicator for high risk. However, in the case of multi-species systems, early travel times may also lead a limited production of daughter species that may contain higher toxicity as in the case of chlorinated compounds. In this work, we model a Perchloroethylene (PCE) contamination problem followed by the sequential first-order production/biodegradation of its daughter species Trichloroethylene (TCE), Dichloroethylene (DCE) and Vinyl Chlorine (VC). For this specific case, VC is known to be a highly toxic contaminant. By performing numerical experiments, we evaluate transport for two distinct three-dimensional aquifer structures. First, a multi-Gaussian hydraulic conductivity field and secondly, a geostatistically equivalent connected field. These two heterogeneity structures will provide two distinct ranges of mean travel

  1. Preliminary Reactive Geochemical Transport Modeling Study on Changes in Water Chemistry Induced by CO2 Injection at Frio Pilot Test Site

    NASA Astrophysics Data System (ADS)

    Xu, T.; Kharaka, Y.; Benson, S.

    2006-12-01

    A total of 1600 tons of CO2 were injected into the Frio ~{!0~}C~{!1~} sandstone layer at a depth of 1500 m over a period of 10 days. The pilot, located near Dayton, Texas, employed one injection well and one observation well, separated laterally by about 30 m. Each well was perforated over 6 m in the upper portion of the 23-m thick sandstone. Fluid samples were taken from both wells before, during, and after the injection. Following CO2 breakthrough, observations indicate drops in pH (6.5 to 5.7), pronounced increases in concentrations of HCO3- (100 to 3000 mg/L), in Fe (30 to 1100), and dissolved organic carbon. Numerical modeling was used in this study to understand changes of aqueous HCO3- and Fe caused by CO2 injection. The general multiphase reactive geochemical transport simulator TOUGHREACT was used, which includes new fluid property module ECO2N with an accurate description of the thermophysical properties of mixtures of water, brine, and CO2 at conditions of interest for CO2 storage. A calibrated 1-D radial well flow model was employed for the present reactive geochemical transport simulations. Mineral composition used was taken from literatures relevant to Frio sandstone. Increases in HCO3- concentration were well reproduced by an initial simulation. Several scenarios were used to capture increases in Fe concentration including (1) dissolution of carbonate minerals, (2) dissolution of iron oxyhydroxides, (3) de-sorption of previously coated Fe. Future modeling, laboratory and field investigations are proposed to better understand the CO2-brine-mineral interactions at the Frio site. Results from this study could have broad implication for subsurface storage of CO2 and potential water quality impacts.

  2. Implementing fluid dynamics obtained from GeoPET in reactive transport models

    NASA Astrophysics Data System (ADS)

    Lippmann-Pipke, Johanna; Eichelbaum, Sebastian; Kulenkampff, Johannes

    2016-04-01

    Flow and transport simulations in geomaterials are commonly conducted on high-resolution tomograms (μCT) of the pore structure or stochastic models that are calibrated with measured integral quantities, like break through curves (BTC). Yet, there existed virtually no method for experimental verification of the simulated velocity distribution results. Positron emission tomography (PET) has unrivaled sensitivity and robustness for non-destructive, quantitative, spatio-temporal measurement of tracer concentrations in body tissue. In the past decade, we empowered PET for its applicability in opaque/geological media - GeoPET (Kulenkampff et al.; Kulenkampff et al., 2008; Zakhnini et al., 2013) and have developed detailed correction schemes to bring the images into sharp focus. Thereby it is the appropriate method for experimental verification and calibration of computer simulations of pore-scale transport by means of the observed propagation of a tracer pulse, c_PET(x,y,z,t). In parallel, we aimed at deriving velocity and porosity distributions directly from our concentration time series of fluid flow processes in geomaterials. This would allow us to directly benefit from lab scale observations and to parameterize respective numerical transport models. For this we have developed a robust spatiotemporal (3D+t) parameter extraction algorithm. Here, we will present its functionality, and demonstrate the use of obtained velocity distributions in finite element simulations of reactive transport processes on drill core scale. Kulenkampff, J., Gruendig, M., Zakhnini, A., Gerasch, R., and Lippmann-Pipke, J.: Process tomography of diffusion with PET for evaluating anisotropy and heterogeneity, Clay Minerals, in press. Kulenkampff, J., Gründig, M., Richter, M., and Enzmann, F.: Evaluation of positron emission tomography for visualisation of migration processes in geomaterials, Physics and Chemistry of the Earth, 33, 937-942, 2008. Zakhnini, A., Kulenkampff, J., Sauerzapf, S

  3. The Development and Application of Reactive Transport Modeling Techniques to Study Radionuclide Migration at Yucca Mountain, NV

    SciTech Connect

    Viswanathan, Hari Selvi

    1999-09-01

    Yucca Mountain, Nevada has been chosen as a possible site for the first high level radioactive waste repository in the United States. As part of the site investigation studies, we need to make scientifically rigorous estimations of radionuclide migration in the event of a repository breach. Performance assessment models used to make these estimations are computationally intensive. We have developed two reactive transport modeling techniques to simulate radionuclide transport at Yucca Mountain: (1) the selective coupling approach applied to the convection-dispersion-reaction (CDR) model and (2) a reactive stream tube approach (RST). These models were designed to capture the important processes that influence radionuclide migration while being computationally efficient. The conventional method of modeling reactive transport models is to solve a coupled set of multi-dimensional partial differential equations for the relevant chemical components in the system. We have developed an iterative solution technique, denoted the selective coupling method, that represents a versatile alternative to traditional uncoupled iterative techniques and the filly coupled global implicit method. We show that selective coupling results in computational and memory savings relative to these approaches. We develop RST as an alternative to the CDR method for solving large two- or three-dimensional reactive transport simulations for cases in which one is interested in predicting the flux across a specific control plane. In the RST method, the multidimensional problem is reduced to a series of one-dimensional transport simulations along streamlines. The key assumption with RST is that mixing at the control plane approximates the transverse dispersion between streamlines. We compare the CDR and RST approaches for several scenarios that are relevant to the Yucca Mountain Project. For example, we apply the CDR and RST approaches to model an ongoing field experiment called the Unsaturated Zone

  4. Feedbacks between deformation and reactive melt transport in the mantle lithosphere during rifting

    NASA Astrophysics Data System (ADS)

    Tommasi, A.; Baptiste, V.; Vauchez, A. R.; Fort, A.

    2014-12-01

    The East-African rift associates lithospheric thinning with extensive volcanism. Melts, even at low fractions, reduce the mantle viscosity. They also carry and exchange heat, mainly via reactions (latent heat), modifying the temperature and the rheology, which in turn controls their transport through the lithospheric mantle. Analysis of microstructures and crystal preferred orientations of mantle xenoliths from different localities along the East-African rift system highlights strong feedbacks between deformation, melt transport, and thermal evolution in the lithospheric mantle. Microstructures change markedly from south (young) to north (mature rift). In Tanzania, mylonitic to porphyroclastic peridotites predominate in on-axis localities, while off-axis ones are coarse-granular to porphyroclastic, pointing to heterogeneous deformation and variable annealing due to local interaction with fluids or to different time lags between deformation and extraction. Mylonites point to strain localization but there is no evidence for dominant grain boundary sliding: ubiquituous intracrystalline deformation in olivine and orthopyroxene and strong CPO record dislocation creep with dominant [100] glide in olivine. Synkinematic replacement of opx by olivine in both mylonitic and porphyroclastic peridotites suggests that deformation continued in the presence of melt under near-solidus conditions. This heating was transient: exsolutions in opx record cooling before extraction. Mega peridotites, which sample the southern border of the Ethiopian plateau, are coarse-porphyroclastic and show widespread metasomatism by basalts or by evolved volatile-rich low melt fractions. The former predated or was coeval to deformation, since olivine and pyroxene CPO are coherent. Exsolutions in opx imply that the high primary equilibration temperatures, which are consistent with the coarse-grained microstructures, are linked to transient heating. Finally, the fine-grained polygonal microstructures

  5. Reactive Transport from Path3D: A Stream Tube Approach for Heterogeneous Aquifers

    NASA Astrophysics Data System (ADS)

    LI, L.

    2001-05-01

    Path3D (Zheng, 1991) is a popular computer program run in series with MODFLOW. Remediation engineers and hydrogeologist use it to track contaminant paths and to estimate solute travel time at heterogeneous sites. In order to predict fate and transport of multiple species at heterogeneous sites, numerical modeling packages, such as MT3D (Zheng,1990) or RT3D (Clement 1997) are often employed. These packages also are based on pre-processing with MODFLOW. However, for complex cases with aquifer heterogeneity, MT3D and RT3D often require very long computer run times. This paper addresses a new, stream-tube, approach that is both highly efficient and accurate to predict multi-species reactive transport at heterogeneous sites with steady flow. Our application of the stream tube approach is different from other stream tube approaches that apply the advection-dispersion-reaction equation in each stream tube (such as Ginn, 2000, Yabusaki, 1998, Charbeneau, 2000). In this work, the authors make use of properties of a linear system,working with decoupled reaction and sorption processes and mixing processes described by residence time distributions (RTDs). RTDs are abstracted from Path3D particle-tracking results and additional temporal and spatial dispersion (not caused by aquifer heterogeneity) is ignored. Reactions, including first order reactions and linear, reversible sorption, are applied through analytical transfer functions (called kinetic response functions). Convolution can then be applied to determine contaminant concentrations at monitoring points, using the RTDs determined from Path3D, kinetic transfer functions (expressed analytically), and expected trends of the source concentration. We are currently testing the approach and noting significant computational advantages for problems in three-dimensions, with first order reaction pathways and different retardation factors. We will demonstrate the method with several examples and compare the performance with MT3D and

  6. Permeability evolution due to dissolution and precipitation of carbonates using reactive transport modeling in pore networks

    NASA Astrophysics Data System (ADS)

    Nogues, Juan P.; Fitts, Jeffrey P.; Celia, Michael A.; Peters, Catherine A.

    2013-09-01

    A reactive transport model was developed to simulate reaction of carbonates within a pore network for the high-pressure CO2-acidified conditions relevant to geological carbon sequestration. The pore network was based on a synthetic oolithic dolostone. Simulation results produced insights that can inform continuum-scale models regarding reaction-induced changes in permeability and porosity. As expected, permeability increased extensively with dissolution caused by high concentrations of carbonic acid, but neither pH nor calcite saturation state alone was a good predictor of the effects, as may sometimes be the case. Complex temporal evolutions of interstitial brine chemistry and network structure led to the counterintuitive finding that a far-from-equilibrium solution produced less permeability change than a nearer-to-equilibrium solution at the same pH. This was explained by the pH buffering that increased carbonate ion concentration and inhibited further reaction. Simulations of different flow conditions produced a nonunique set of permeability-porosity relationships. Diffusive-dominated systems caused dissolution to be localized near the inlet, leading to substantial porosity change but relatively small permeability change. For the same extent of porosity change caused from advective transport, the domain changed uniformly, leading to a large permeability change. Regarding precipitation, permeability changes happen much slower compared to dissolution-induced changes and small amounts of precipitation, even if located only near the inlet, can lead to large changes in permeability. Exponent values for a power law that relates changes in permeability and porosity ranged from 2 to 10, but a value of 6 held constant when conditions led to uniform changes throughout the domain.

  7. Reactive transport modeling of secondary water quality impacts due to anaerobic bioremediation

    NASA Astrophysics Data System (ADS)

    Ng, G. H. C.; Bekins, B. A.; Kent, D. B.; Borden, R. C.; Tillotson, J.

    2014-12-01

    Bioremediation using electron donor addition produces reducing conditions in an aquifer that promote the anaerobic biodegradation of contaminants such as chlorinated solvents. There is growing concern about secondary water quality impacts (SWQIs) triggered by the injection of electron donors, due to redox reactions with electron acceptors other than the target contaminant. Secondary plumes, including those with elevated concentrations of Mn(II), Fe(II), and CH4, may create long-lasting impairment of water quality. Understanding conditions that control the production and attenuation of SWQIs is needed for guiding responsible bioremediation strategies that limit unintended consequences. Using a reactive transport model developed with data from long-term anaerobic biodegradation monitoring sites, we simulate diverse geochemical scenarios to examine the sensitivity of secondary plume extent and persistence to a range of aquifer properties and treatment implementations. Data compiled from anaerobic bioremediation sites, which include variable physical and geochemical relationships, provide the basis for the conditions evaluated. Our simulations show that reduced metal and CH4 plumes may be significantly attenuated due to immobilization (through sorption and/or precipitation) and outgassing, respectively, and that recovery time to background conditions depends strongly on the chemical forms of reduced metals on sediments. Unsurprisingly, scenarios that do not easily allow outgassing (e.g. deeper injections) led to higher CH4 concentrations, and scenarios with higher hydraulic conductivity produced more dilute concentrations of secondary species. Results are sensitive to the assumed capacity for Fe(II) sorption and reductive dissolution rates of Fe(III) oxides, which control Fe(II) concentrations. Simulations also demonstrated the potential importance of chemical reactions between different secondary components. For example, limited CH4 loss from outgassing and Fe

  8. Reactive transport simulation in a tropical horizontal subsurface flow constructed wetland treating domestic wastewater.

    PubMed

    Mburu, N; Rousseau, D P L; van Bruggen, J J A; Thumbi, G; Llorens, E; García, J; Lens, P N L

    2013-04-01

    A promising approach to the simulation of flow and conversions in the complex environment of horizontal subsurface flow constructed wetlands (HSSF-CWs) is the use of reactive transport models, in which the transport equation is solved together with microbial growth and mass-balance equations for substrate transformation and degradation. In this study, a tropical pilot scale HSSF-CW is simulated in the recently developed CWM1-RETRASO mechanistic model. The model predicts organic matter, nitrogen and sulfur effluent concentrations and their reaction rates within the HSSF-CW. Simulations demonstrated that these reactions took place simultaneously in the same (fermentation, methanogenesis and sulfate reduction) or at different (aerobic, anoxic and anaerobic) locations. Anaerobic reactions occurred over large areas of the simulated HSSF-CW and contributed (on average) to the majority (68%) of the COD removal, compared to aerobic (38%) and anoxic (1%) reactions. To understand the effort and compare computing resources needed for the application of a mechanistic model, the CWM1-RETRASO simulation is compared to a process-based, semi-mechanistic model, run with the same data. CWM1-RETRASO demonstrated the interaction of components within the wetland in a better way, i.e. concentrations of microbial functional groups, their competition for substrates and the formation of intermediary products within the wetland. The CWM1-RETRASO model is thus suitable for simulations aimed at a better understanding of the CW system transformation and degradation processes. However, the model does not support biofilm-based modeling, and it is expensive in computing and time resources required to perform the simulations. PMID:23434579

  9. On the effect of serum on the transport of reactive oxygen species across phospholipid membranes.

    PubMed

    Szili, Endre J; Hong, Sung-Ha; Short, Robert D

    2015-01-01

    The transport of plasma generated reactive oxygen species (ROS) across a simple phospholipid membrane mimic of a (real) cell was investigated. Experiments were performed in cell culture media (Dulbecco's modified Eagle's medium, DMEM), with and without 10% serum. A (broad spectrum) ROS reporter dye, 2,7-dichlorodihydrofluorescein (DCFH), was used to detect the generation of ROS by a helium (He) plasma jet in DMEM using free DCFH and with DCFH encapsulated inside phospholipid membrane vesicles dispersed in DMEM. The authors focus on the concentration and on the relative rates (arbitrary units) for oxidation of DCFH [or the appearance of the oxidized product 2,7-dichlorofluorescein (DCF)] both in solution and within vesicles. In the first 1 h following plasma exposure, the concentration of free DCF in DMEM was ~15× greater in the presence of serum (cf. to the serum-free DMEM control). The DCF in vesicles was ~2× greater in DMEM containing serum compared to the serum-free DMEM control. These data show that serum enhances plasma ROS generation in DMEM. As expected, the role of the phospholipid membrane was to reduce the rate of oxidation of the encapsulated DCFH (with and without serum). And the efficiency of ROS transport into vesicles was lower in DMEM containing serum (at 4% efficiency) when compared to serum-free DMEM (at 32% efficiency). After 1 h, the rate of DCFH oxidation was found to have significantly reduced. Based upon a synthesis of these data with results from the open literature, the authors speculate on how the components of biological fluid and cellular membranes might affect the kinetics of consumption of plasma generated ROS. PMID:25910641

  10. Reactive Transport Modeling of the CO2 Core Flooding Experiments for the Weyburn CO2 Storage Project

    NASA Astrophysics Data System (ADS)

    Hao, Y.; Sholokhova, Y.; Smith, M. M.; Carroll, S.

    2011-12-01

    Geologic CO2 sequestration and storage in hydrocarbon reservoirs such as Weyburn oil field has a large potential to reduce net CO2 released into atmosphere and, therefore, mitigate man-made global warming. One key research area for CO2 sequestration/EOR (enhanced oil recovery) operations, requiring both numerical and experimental investigations, is to develop a good understanding of the chemical rock-fluid interactions induced by CO2 injection that influence rock porosity and permeability evolution, and may potentially alter reservoir performance. In this study we apply a Darcy scale continuum model to simulate reactive transport and mineral-dissolution processes for the core flooding experiments in which the CO2-equilibrated brine is injected into carbonate rock samples of both the Midale Vuggy and Marly units from the Weyburn oil field. The three-dimensional reactive-transport model is developed and constrained based on physical characterization of the Vuggy and Marly flow units (e.g. mineral distribution and pore-space identification) and solution chemistry data, which are obtained from X-ray computed microtomography (XCMT) analysis, and experimental measurements. It is observed experimentally that the mineral dissolution fronts become more unstable in highly heterogeneous Vuggy limestone, ultimately leading to the formation of highly porous flow channels, often referred to as "wormholes". In order to effectively account for strong coupling between flow, reactive transport and mineral dissolution processes, in particular within the wormholes, we employ empirical correlations to quantify the relationships between mineral dissolution and the resulting increases in porosity and permeability. The reactive transport simulations are performed by the Nonisothermal Unsaturated Flow and Transport (NUFT) code, and their results are compared with experimental data. Our simulation results indicate that Darcy-scale based flow and reactive transport models are able to

  11. Integrated Microbial Trait Based-Reactive Transport Modeling Approach Towards Understanding Microbial Reservoir Souring and Desouring

    NASA Astrophysics Data System (ADS)

    Li, L.; Cheng, Y.; Bouskill, N.; Hubbard, C. G.; Engelbrektson, A. L.; Coates, J. D.; Ajo Franklin, J. B.

    2014-12-01

    Microbially mediated sulfate reduction is the major metabolic process that leads to the production of hydrogen sulfide (H2S) in oil reservoirs. Biogenesis of H2S (souring) has detrimental impacts on oil production operations and can cause significant environmental and health problems. Understanding the processes that control the rates and patterns of sulfate reduction is a crucial step in developing a predictive understanding of reservoir souring and associated mitigation processes. In this study, we describe the development of a microbial trait-based model that is coupled to a reactive transport model. The model represents several anaerobic microbial functional guilds with different resource acquisition (e.g., electron donor, sulfate) traits. The integrated model was used to simulate the temporal and spatial evolution of the primary chemical species (e.g. sulfate, sulfide, nitrate, chlorate and perchlorate) and the microbial community dynamics involved in the souring and desouring processes as revealed in a recent laboratory column experiment comparing the effectiveness of nitrate, chlorate and perchlorate treatments as souring control strategies. Simulation of the laboratory experimental results shows that the model captured the spatio-temporal trend of the chemical species and microbial guilds during both souring and desouring. Model parameters derived through modeling of the column data are utilized in subsequent field-scale model simulations across a set of reservoir relevant environmental conditions. This integrated model demonstrates that interactions between SRBs and other heterotrophs can significantly impact the occurrence and extent of H2S production.

  12. A reactive transport model for mercury fate in contaminated soil--sensitivity analysis.

    PubMed

    Leterme, Bertrand; Jacques, Diederik

    2015-11-01

    We present a sensitivity analysis of a reactive transport model of mercury (Hg) fate in contaminated soil systems. The one-dimensional model, presented in Leterme et al. (2014), couples water flow in variably saturated conditions with Hg physico-chemical reactions. The sensitivity of Hg leaching and volatilisation to parameter uncertainty is examined using the elementary effect method. A test case is built using a hypothetical 1-m depth sandy soil and a 50-year time series of daily precipitation and evapotranspiration. Hg anthropogenic contamination is simulated in the topsoil by separately considering three different sources: cinnabar, non-aqueous phase liquid and aqueous mercuric chloride. The model sensitivity to a set of 13 input parameters is assessed, using three different model outputs (volatilized Hg, leached Hg, Hg still present in the contaminated soil horizon). Results show that dissolved organic matter (DOM) concentration in soil solution and the binding constant to DOM thiol groups are critical parameters, as well as parameters related to Hg sorption to humic and fulvic acids in solid organic matter. Initial Hg concentration is also identified as a sensitive parameter. The sensitivity analysis also brings out non-monotonic model behaviour for certain parameters. PMID:26099598

  13. Reactive transport modeling of column experiments on the evolution of saline alkaline waste solutions

    NASA Astrophysics Data System (ADS)

    Zheng, Zuoping; Zhang, Guoxiang; Wan, Jiamin

    2008-04-01

    Leakage of saline-alkaline tank waste solutions often creates a serious environmental contamination problem. To better understand the mechanisms controlling the fate of such waste solutions in the Hanford vadose zone, we simulated reactive transport in columns designed to represent local site conditions. The Pitzer ion interaction module was used, with principal geochemical processes considered in the simulation including quartz dissolution, precipitation of brucite, calcite, and portlandite, multi-component cation exchange, and aqueous complexation reactions. Good matches were observed between the simulated and measured column data at ambient temperature (˜ 21 °C). Relatively good agreement was also obtained at high temperature (˜ 70 °C). The decrease of pH at the plume front is examined through formation of secondary mineral phases and/or quartz dissolution. Substantial formation of secondary mineral phases resulting from multi-component cation exchange suggests that these phases are responsible for a decrease in pH within the plume front. In addition, a sensitivity analysis was conducted with respect to cation exchange capacity, selectivity coefficient, mineral assemblage, temperature, and ionic strength. This study could serve as a useful guide to subsequent experimental work, to thermodynamic models developed for the concentrated solutions at high ionic strength and to other types of waste plume studies.

  14. Reactive transport modeling of column experiments on the evolution of saline-alkaline waste solutions.

    PubMed

    Zheng, Zuoping; Zhang, Guoxiang; Wan, Jiamin

    2008-04-01

    Leakage of saline-alkaline tank waste solutions often creates a serious environmental contamination problem. To better understand the mechanisms controlling the fate of such waste solutions in the Hanford vadose zone, we simulated reactive transport in columns designed to represent local site conditions. The Pitzer ion interaction module was used, with principal geochemical processes considered in the simulation including quartz dissolution, precipitation of brucite, calcite, and portlandite, multi-component cation exchange, and aqueous complexation reactions. Good matches were observed between the simulated and measured column data at ambient temperature ( approximately 21 degrees C). Relatively good agreement was also obtained at high temperature ( approximately 70 degrees C). The decrease of pH at the plume front is examined through formation of secondary mineral phases and/or quartz dissolution. Substantial formation of secondary mineral phases resulting from multi-component cation exchange suggests that these phases are responsible for a decrease in pH within the plume front. In addition, a sensitivity analysis was conducted with respect to cation exchange capacity, selectivity coefficient, mineral assemblage, temperature, and ionic strength. This study could serve as a useful guide to subsequent experimental work, to thermodynamic models developed for the concentrated solutions at high ionic strength and to other types of waste plume studies. PMID:18313795

  15. Reactive transport modelling of the interaction of fission product ground contamination with alkaline and cementitious leachates

    SciTech Connect

    Kwong, S.; Small, J.

    2007-07-01

    The fission products Cs-137 and Sr-90 are amongst the most common radionuclides occurring in ground contamination at the UK civil nuclear sites. Such contamination is often associated with alkaline liquids and the mobility of these fission products may be affected by these chemical conditions. Similar geochemical effects may also result from cementitious leachate associated with building foundations and the use of grouts to remediate ground contamination. The behaviour of fission products in these scenarios is a complex interaction of hydrogeological and geochemical processes. A suite of modelling tools have been developed to investigate the behaviour of a radioactive plume containing Cs and Sr. Firstly the effects of sorption due to cementitious groundwater is modelled using PHREEQC. This chemical model is then incorporated into PHAST for the 3-D reactive solute transport modeling. Results are presented for a generic scenario including features and processes that are likely to be relevant to a number of civil UK nuclear sites. Initial results show that modelling can be a very cost-effective means to study the complex hydrogeological and geochemical processes involved. Modelling can help predict the mobility of contaminants in a range of site end point scenarios, and in assessing the consequences of decommissioning activities. (authors)

  16. Mineralogical heterogeneity in fractured, porous media and itsrepresentation in reactive transport models

    SciTech Connect

    Glassley, W.E.; Simmons, A.M.; Kerchner, J.

    2000-08-08

    Reactive transport models that simulate processes in porous media have, generally, required abstracted representation of porosity, permeability, and mineralogy. This study compares abstracted, homogeneous representations of porosity and permeability, mineral surface areas and distributions, to discrete distribution representation of these same properties. Discretization was accomplished by high-resolution (ca. 1mu-m2) characterization of fractured tuffaceous rock from Yucca Mountain,Nevada, using optical microscopy and X-ray fluorescence spectroscopy. A sample area of 106 mu-m2 was mapped in detail, and the resulting element and porosity maps were digitized. The domain was decomposed into 12,208 cells that were 8.77 x 10-6 m on a side. Simulations were conducted in which a dilute fluid enters the discretized porous medium at modest flowrates. Simulation results using a discrete mineral distribution point to the conclusion that slow flow rates, in which fluid residence times are on the order of days, provide fluid composition results that are very similar to those obtained from the homogeneous mineral distribution representation. At higher flow rates, where fluid residence times are on the order of hours, contrasts in fluid composition persist throughout the flow domain. The results demonstrate that the fluid composition characteristics in the homogeneous and discrete mineral representations will be similar only when the bulk average contact times for the individual mineral phases along the flow paths are approximately equivalent (within a few percent) for the two cases.

  17. Chemical reactivity and long-range transport potential of polycyclic aromatic hydrocarbons--a review.

    PubMed

    Keyte, Ian J; Harrison, Roy M; Lammel, Gerhard

    2013-12-21

    Polycyclic aromatic hydrocarbons (PAHs) are of considerable concern due to their well-recognised toxicity and especially due to the carcinogenic hazard which they present. PAHs are semi-volatile and therefore partition between vapour and condensed phases in the atmosphere and both the vapour and particulate forms undergo chemical reactions. This article briefly reviews the current understanding of vapour-particle partitioning of PAHs and the PAH deposition processes, and in greater detail, their chemical reactions. PAHs are reactive towards a number of atmospheric oxidants, most notably the hydroxyl radical, ozone, the nitrate radical (NO3) and nitrogen dioxide. Rate coefficient data are reviewed for reactions of lower molecular weight PAH vapour with these species as well as for heterogeneous reactions of higher molecular weight compounds. Whereas the data for reactions of the 2-3-ring PAH vapour are quite extensive and generally consistent, such data are mostly lacking for the 4-ring PAHs and the heterogeneous rate data (5 and more rings), which are dependent on the substrate type and reaction conditions, are less comprehensive. The atmospheric reactions of PAH lead to the formation of oxy and nitro derivatives, reviewed here, too. Finally, the capacity of PAHs for long range transport and the results of numerical model studies are described. Research needs are identified. PMID:24077263

  18. Reactive transport modelling of a remediation measure at a former gasworks site in Southern Germany

    NASA Astrophysics Data System (ADS)

    Ptak, T.; Herold, M.; Greskowiak, J.; Prommer, H.

    2009-12-01

    The aquifer beneath a former manufactured gas plant site is contaminated with polycyclic and heterocyclic aromatic hydrocarbons that form large plumes and are only slowly degraded under natural conditions. This leaves active remediation as the only viable option to eliminate the risks of toxic substances to reach potential receptors. The aims of the study presented here were to verify the proposed conceptual model of interacting physical and biogeochemical processes and to assess the effectiveness of a proposed in-situ remediation approach with the help of multi-component reactive transport modelling, focusing on the situations (i) prior to the implementation of the in-situ remediation scheme and (ii) following the operation of a circulation well with O2 and H2O2 injection to aid aerobic microbial degradation of the contaminants in the otherwise anoxic surroundings. The model incorporates microbially mediated redox reactions, mineral precipitation/dissolution reactions as well as subsequent changes in the chemical composition of the aquifer. The degradation pathways proposed in the conceptual model could be verified. The model was then used (i) to explore two possible remediation scenarios where the results highlighted the importance of source remediation and (ii) to study the uncertainty regarding the presence of another electron donor in the form of pyrite.

  19. A field, laboratory and modeling study of reactive transport of groundwater arsenic in a coastal aquifer

    PubMed Central

    Jung, Hun Bok; Charette, Matthew A.; Zheng, Yan

    2009-01-01

    A field, laboratory, and modeling study of As in groundwater discharging to Waquoit Bay, MA, shed light on coupled control of chemistry and hydrology on reactive transport of As in a coastal aquifer. Dissolved Fe(II) and As(III) in a reducing groundwater plume bracketed by an upper and a lower redox interface are oxidized as water flows towards the bay. This results in precipitation of Fe(III) oxides, along with oxidation and adsorption of As to sediment at the redox interfaces where concentrations of sedimentary HCl-leachable Fe (80~90% Fe(III)) are 734±232 mg kg-1, sedimentary phosphate extractable As (90~100% As(V)) are 316±111 μg kg-1, and are linearly correlated. Batch adsorption of As(III) onto orange, brown and gray sediments follows Langmuir isotherms, and can be fitted by a surface complexation model (SCM) assuming a diffuse layer for ferrihydrite. The sorption capacity and distribution coefficient for As increase with decreasing sediment Fe(II)/Fe. To allow accumulation of the amount of sediment As, similar hydrogeochemical conditions would have been operating for thousands of years at Waquoit Bay. The SCM simulated the observed dissolved As concentration better than a parametric approach based on Kd. Site specific isotherms should be established for Kd or SCM based models. PMID:19708362

  20. Reaction-Based Reactive Transport Modeling of Fe(III) and U(V) Reduction

    SciTech Connect

    Burgos, William D.; Roden, Eric E.; Yeh, Gour-Tsyh

    2005-06-01

    Our new research project (started Fall 2004) was funded by a grant to The Pennsylvania State University, University of Central Florida, and The University of Alabama in the Integrative Studies Element of the NABIR Program (DE-FG04-ER63914/63915/63196). Our previous NABIR project (DE-FG02-01ER63180/63181/63182, funded within the Biotransformation Element) focused on (1) microbial reduction of Fe(III) and U(VI) individually, and concomitantly in natural sediments, (2) Fe(III) oxide surface chemistry, specifically with respect to reactions with Fe(II) and U(VI), (3) the influence of humic substances on Fe(III) and U(VI) bioreduction, and on U(VI) complexation, and (4) the development of reaction-based reactive transport biogeochemical models to numerically simulate our experimental results. The new project focuses on the development of a mechanistic understanding and quantitative models of coupled Fe(III)/U(VI) reduction in FRC Area 2 sediments. This work builds on our previous studies of microbial Fe(III) and U(VI) reduction, and is directly aligned with the Scheibe et al. NABIR FRC Field Project at Area 2.

  1. Influence of permeability anisotropy on mixing controlled reactive transport simulations in porous media

    NASA Astrophysics Data System (ADS)

    Chiogna, Gabriele; Herrera, Paulo

    2015-04-01

    Several studies have demonstrated how plume deformation induced by flow heterogeneity in porous media can enhance mixing of reactants. This enhancement can have important impact on mixing controlled reactions such a biodegradation of plumes of organic compounds. On the other hand, recent studies have indicated the possibility of observing complex flow topology on groundwater flow that occurs in anisotropic yet homogenous porous media. Moreover, it has been demonstrated that those complex flow topologies can also enhance solute mixing. We study the effect of medium anisotropy on reactive solute transport for the case of a chemical reactor composed of two homogeneous anisotropic layers. We simulate different injection strategies for different chemical reactions that involve two reactants. We demonstrate the effect of the medium anisotropy by analyzing the results of the simulations and identify best strategies for the operation and design of the system to maximize reaction rates. These findings could have potential application in the design of new remediation systems for contaminated groundwater, chemical reactors and other engineering problems that involve flow through porous media.

  2. Incorporating Non-Linear Sorption into High Fidelity Subsurface Reactive Transport Models

    NASA Astrophysics Data System (ADS)

    Matott, L. S.; Rabideau, A. J.; Allen-King, R. M.

    2014-12-01

    A variety of studies, including multiple NRC (National Research Council) reports, have stressed the need for simulation models that can provide realistic predictions of contaminant behavior during the groundwater remediation process, most recently highlighting the specific technical challenges of "back diffusion and desorption in plume models". For a typically-sized remediation site, a minimum of about 70 million grid cells are required to achieve desired cm-level thickness among low-permeability lenses responsible for driving the back-diffusion phenomena. Such discretization is nearly three orders of magnitude more than is typically seen in modeling practice using public domain codes like RT3D (Reactive Transport in Three Dimensions). Consequently, various extensions have been made to the RT3D code to support efficient modeling of recently proposed dual-mode non-linear sorption processes (e.g. Polanyi with linear partitioning) at high-fidelity scales of grid resolution. These extensions have facilitated development of exploratory models in which contaminants are introduced into an aquifer via an extended multi-decade "release period" and allowed to migrate under natural conditions for centuries. These realistic simulations of contaminant loading and migration provide high fidelity representation of the underlying diffusion and sorption processes that control remediation. Coupling such models with decision support processes is expected to facilitate improved long-term management of complex remediation sites that have proven intractable to conventional remediation strategies.

  3. Glutamate Transporter EAAT2 Expression is Up-Regulated in Reactive Astrocytes in Human Periventricular Leukomalacia

    PubMed Central

    DESILVA, TARA M.; BILLIARDS, SARAID S.; BORENSTEIN, NATALIA S.; TRACHTENBERG, FELICIA L.; VOLPE, JOSEPH J.; KINNEY, HANNAH C.; ROSENBERG, PAUL A.

    2010-01-01

    The major neuropathological correlate of cerebral palsy in premature infants is periventricular leukomalacia (PVL), a disorder of the immature cerebral white matter. Cerebral ischemia leading to excitotoxicity is thought to be important in the pathogenesis of this disorder, implying a critical role for glutamate transporters, the major determinants of extracellular glutamate concentration. Previously, we found that EAAT2 expression is limited primarily to premyelinating oligodendrocytes early in development and is rarely observed in astrocytes until >40 weeks. In this study, we analyzed the expression of EAAT2 in cerebral white matter from PVL and control cases. Western blot analysis suggested an up-regulation of EAAT2 in PVL compared with control cases. Single- and double-label immunocytochemistry showed a significantly higher percentage of EAAT2-immunopositive astrocytes in PVL (51.8% ± 5.6%) compared with control white matter (21.4% ± 5.6%; P = 0.004). Macrophages in the necrotic foci in PVL also expressed EAAT2. Premyelinating oligodendrocytes in both PVL and control cases expressed EAAT2, without qualitative difference in expression. The previously unrecognized up-regulation of EAAT2 in reactive astrocytes and its presence in macrophages in PVL reported here may reflect a response to either hypoxic-ischemic injury or inflammation. PMID:18314905

  4. Reactive transport modelling of groundwater chemistry in a chalk aquifer at the watershed scale

    NASA Astrophysics Data System (ADS)

    Mangeret, A.; De Windt, L.; Crançon, P.

    2012-09-01

    This study investigates thermodynamics and kinetics of water-rock interactions in a carbonate aquifer at the watershed scale. A reactive transport model is applied to the unconfined chalk aquifer of the Champagne Mounts (France), by considering both the chalk matrix and the interconnected fracture network. Major element concentrations and main chemical parameters calculated in groundwater and their evolution along flow lines are in fair agreement with field data. A relative homogeneity of the aquifer baseline chemistry is rapidly reached in terms of pH, alkalinity and Ca concentration since calcite equilibrium is achieved over the first metres of the vadose zone. However, incongruent chalk dissolution slowly releases Ba, Mg and Sr in groundwater. Introducing dilution effect by rainwater infiltration and a local occurrence of dolomite improves the agreement between modelling and field data. The dissolution of illite and opal-CT, controlling K and SiO2 concentrations in the model, can be approximately tackled by classical kinetic rate laws, but not the incongruent chalk dissolution. An apparent kinetic rate has therefore been fitted on field data by inverse modelling: 1.5 × 10- 5 molchalk L - 1water year - 1. Sensitivity analysis indicates that the CO2 partial pressure of the unsaturated zone is a critical parameter for modelling the baseline chemistry over the whole chalk aquifer.

  5. Reactive Transport Model of Sulfur Cycling as Impacted by Perchlorate and Nitrate Treatments.

    PubMed

    Cheng, Yiwei; Hubbard, Christopher G; Li, Li; Bouskill, Nicholas; Molins, Sergi; Zheng, Liange; Sonnenthal, Eric; Conrad, Mark E; Engelbrektson, Anna; Coates, John D; Ajo-Franklin, Jonathan B

    2016-07-01

    Microbial souring in oil reservoirs produces toxic, corrosive hydrogen sulfide through microbial sulfate reduction, often accompanying (sea)water flooding during secondary oil recovery. With data from column experiments as constraints, we developed the first reactive-transport model of a new candidate inhibitor, perchlorate, and compared it with the commonly used inhibitor, nitrate. Our model provided a good fit to the data, which suggest that perchlorate is more effective than nitrate on a per mole of inhibitor basis. Critically, we used our model to gain insight into the underlying competing mechanisms controlling the action of each inhibitor. This analysis suggested that competition by heterotrophic perchlorate reducers and direct inhibition by nitrite produced from heterotrophic nitrate reduction were the most important mechanisms for the perchlorate and nitrate treatments, respectively, in the modeled column experiments. This work demonstrates modeling to be a powerful tool for increasing and testing our understanding of reservoir-souring generation, prevention, and remediation processes, allowing us to incorporate insights derived from laboratory experiments into a framework that can potentially be used to assess risk and design optimal treatment schemes. PMID:27267666

  6. Reactive transport modelling of groundwater chemistry in a chalk aquifer at the watershed scale.

    PubMed

    Mangeret, A; De Windt, L; Crançon, P

    2012-09-01

    This study investigates thermodynamics and kinetics of water-rock interactions in a carbonate aquifer at the watershed scale. A reactive transport model is applied to the unconfined chalk aquifer of the Champagne Mounts (France), by considering both the chalk matrix and the interconnected fracture network. Major element concentrations and main chemical parameters calculated in groundwater and their evolution along flow lines are in fair agreement with field data. A relative homogeneity of the aquifer baseline chemistry is rapidly reached in terms of pH, alkalinity and Ca concentration since calcite equilibrium is achieved over the first metres of the vadose zone. However, incongruent chalk dissolution slowly releases Ba, Mg and Sr in groundwater. Introducing dilution effect by rainwater infiltration and a local occurrence of dolomite improves the agreement between modelling and field data. The dissolution of illite and opal-CT, controlling K and SiO(2) concentrations in the model, can be approximately tackled by classical kinetic rate laws, but not the incongruent chalk dissolution. An apparent kinetic rate has therefore been fitted on field data by inverse modelling: 1.5×10(-5) mol(chalk)L (-1) water year (-1). Sensitivity analysis indicates that the CO(2) partial pressure of the unsaturated zone is a critical parameter for modelling the baseline chemistry over the whole chalk aquifer. PMID:22797192

  7. Generic reactive transport codes as flexible tools to integrate soil organic matter degradation models with water, transport and geochemistry in soils

    NASA Astrophysics Data System (ADS)

    Jacques, Diederik; Gérard, Fréderic; Mayer, Uli; Simunek, Jirka; Leterme, Bertrand

    2016-04-01

    A large number of organic matter degradation, CO2 transport and dissolved organic matter models have been developed during the last decades. However, organic matter degradation models are in many cases strictly hard-coded in terms of organic pools, degradation kinetics and dependency on environmental variables. The scientific input of the model user is typically limited to the adjustment of input parameters. In addition, the coupling with geochemical soil processes including aqueous speciation, pH-dependent sorption and colloid-facilitated transport are not incorporated in many of these models, strongly limiting the scope of their application. Furthermore, the most comprehensive organic matter degradation models are combined with simplified representations of flow and transport processes in the soil system. We illustrate the capability of generic reactive transport codes to overcome these shortcomings. The formulations of reactive transport codes include a physics-based continuum representation of flow and transport processes, while biogeochemical reactions can be described as equilibrium processes constrained by thermodynamic principles and/or kinetic reaction networks. The flexibility of these type of codes allows for straight-forward extension of reaction networks, permits the inclusion of new model components (e.g.: organic matter pools, rate equations, parameter dependency on environmental conditions) and in such a way facilitates an application-tailored implementation of organic matter degradation models and related processes. A numerical benchmark involving two reactive transport codes (HPx and MIN3P) demonstrates how the process-based simulation of transient variably saturated water flow (Richards equation), solute transport (advection-dispersion equation), heat transfer and diffusion in the gas phase can be combined with a flexible implementation of a soil organic matter degradation model. The benchmark includes the production of leachable organic matter

  8. Reactive transport of uranium in fractured crystalline rock: Upscaling in time and distance.

    PubMed

    Dittrich, Timothy M; Reimus, Paul W

    2016-01-01

    Batch adsorption and breakthrough column experiments were conducted to evaluate uranium transport through altered material that fills fractures in a granite rock system at the Grimsel Test Site in Switzerland at pH 6.9 and 7.9. The role of adsorption and desorption kinetics was evaluated with reactive transport modeling by comparing one-, two-, and three-site models. Emphasis was placed on describing long desorption tails that are important for upscaling in time and distance. The effect of increasing pH in injection solutions was also evaluated. For pH 6.9, a three-site model with forward rate constants between 0.07 and 0.8 ml g(-1) h(-1), reverse rate constants between 0.001 and 0.06 h(-1), and site densities of 1.3, 0.104, and 0.026 μmol g(-1) for 'weak/fast', 'strong/slow', and 'very strong/very slow' sites provided the best fits. For pH 7.9, a three-site model with forward rate constants between 0.05 and 0.8 mL g(-1) h(-1), reverse rate constants between 0.001 and 0.6 h(-1), and site densities of 1.3, 0.039, and 0.013 μmol g(-1) for a 'weak/fast', 'strong/slow', and 'very strong/very slow' sites provided the best fits. Column retardation coefficients (Rd) were 80 for pH 6.9 and 10.3 for pH 7.9. Model parameters determined from the batch and column experiments were used in 50 year large-scale simulations for continuous and pulse injections and indicated that a three-site model is necessary at pH 6.9, although a Kd-type equilibrium partition model with one-site was adequate for large scale predictions at pH 7.9. Batch experiments were useful for predicting early breakthrough times in the columns while column experiments helped differentiate the relative importance of sorption sites and desorption rate constants on transport. PMID:26431639

  9. Reactive transport of uranium in fractured crystalline rock: Upscaling in time and distance

    SciTech Connect

    Dittrich, Timothy M.; Reimus, Paul W.

    2015-09-29

    In this study, batch adsorption and breakthrough column experiments were conducted to evaluate uranium transport through altered material that fills fractures in a granite rock system at the Grimsel Test Site in Switzerland at pH 6.9 and 7.9. The role of adsorption and desorption kinetics was evaluated with reactive transport modeling by comparing one-, two-, and three-site models. Emphasis was placed on describing long desorption tails that are important for upscaling in time and distance. The effect of increasing pH in injection solutions was also evaluated. For pH 6.9, a three-site model with forward rate constants between 0.07 and 0.8 ml g–1 h–1, reverse rate constants between 0.001 and 0.06 h–1, and site densities of 1.3, 0.104, and 0.026 μmol g–1 for ‘weak/fast’, ‘strong/slow’, and ‘very strong/very slow’ sites provided the best fits. For pH 7.9, a three-site model with forward rate constants between 0.05 and 0.8 mL g–1 h–1, reverse rate constants between 0.001 and 0.6 h–1, and site densities of 1.3, 0.039, and 0.013 μmol g–1 for a ‘weak/fast’, ‘strong/slow’, and ‘very strong/very slow’ sites provided the best fits. Column retardation coefficients (Rd) were 80 for pH 6.9 and 10.3 for pH 7.9. Model parameters determined from the batch and column experiments were used in 50 year large-scale simulations for continuous and pulse injections and indicated that a three-site model is necessary at pH 6.9, although a Kd-type equilibrium partition model with one-site was adequate for large scale predictions at pH 7.9. Batch experiments were useful for predicting early breakthrough times in the columns while column experiments helped differentiate the relative importance of sorption sites and desorption rate constants on transport.

  10. Reactive transport of uranium in fractured crystalline rock: Upscaling in time and distance

    DOE PAGESBeta

    Dittrich, Timothy M.; Reimus, Paul W.

    2015-09-29

    In this study, batch adsorption and breakthrough column experiments were conducted to evaluate uranium transport through altered material that fills fractures in a granite rock system at the Grimsel Test Site in Switzerland at pH 6.9 and 7.9. The role of adsorption and desorption kinetics was evaluated with reactive transport modeling by comparing one-, two-, and three-site models. Emphasis was placed on describing long desorption tails that are important for upscaling in time and distance. The effect of increasing pH in injection solutions was also evaluated. For pH 6.9, a three-site model with forward rate constants between 0.07 and 0.8more » ml g–1 h–1, reverse rate constants between 0.001 and 0.06 h–1, and site densities of 1.3, 0.104, and 0.026 μmol g–1 for ‘weak/fast’, ‘strong/slow’, and ‘very strong/very slow’ sites provided the best fits. For pH 7.9, a three-site model with forward rate constants between 0.05 and 0.8 mL g–1 h–1, reverse rate constants between 0.001 and 0.6 h–1, and site densities of 1.3, 0.039, and 0.013 μmol g–1 for a ‘weak/fast’, ‘strong/slow’, and ‘very strong/very slow’ sites provided the best fits. Column retardation coefficients (Rd) were 80 for pH 6.9 and 10.3 for pH 7.9. Model parameters determined from the batch and column experiments were used in 50 year large-scale simulations for continuous and pulse injections and indicated that a three-site model is necessary at pH 6.9, although a Kd-type equilibrium partition model with one-site was adequate for large scale predictions at pH 7.9. Batch experiments were useful for predicting early breakthrough times in the columns while column experiments helped differentiate the relative importance of sorption sites and desorption rate constants on transport.« less

  11. Coupling a Genome-Scale Metabolic Model with a Reactive Transport Model to Describe In Situ Uranium Bioremediation

    SciTech Connect

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

    2009-03-01

    Quantitative numerical simulation codes known as reactive transport models are widely used for simulating the hydrologic transport and geochemical speciation of dissolved constituents in the subsurface (Steefel et al., 2005). Because the activity of microorganisms strongly influences the fate of many constituents, both organic and inorganic, such models often include microbially-mediated reactions in their reaction networks (Hunter et al., 1998; Burgos et al., 2002; Fang et al., 2006; Scheibe et al., 2006; Yabusaki et al., 2007). However, the canonical form and stoichiometry of microbial reactions, reaction rate formulations and parameters, and biomass growth yield coefficients are prescribed a priori and applied over the entire range of simulated conditions. This approach does not account for the fact that fundamental microbial functions vary in response to local variations in environmental conditions(Stewart and Franklin, 2008). Multiple alternative reaction pathways are encoded in microbial genomes; specific pathways become active or inactive in response to, for example, nutrient limitation. Recent advances in genomic analysis allow us to define cellular metabolic networks, and accurate predictions of active pathways and reaction fluxes have been made using constraint-based metabolic models (Mahadevan et al., 2002; Price et al., 2003; Reed and Palsson, 2003; Mahadevan et al., 2006). Here, we demonstrate for the first time a methodology of coupling constraint-based metabolic models with reactive transport models. Our approach integrates advanced microbiological characterization, hydrology, and geochemistry in a powerful manner that will significantly improve subsurface reactive transport models.

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

    NASA Astrophysics Data System (ADS)

    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.

  13. Reactive transport modeling of CO2 injection in the Farnsworth, Texas hydrocarbon field

    NASA Astrophysics Data System (ADS)

    Ahmmed, B.; Appold, M. S.; McPherson, B. J. O. L.; Grigg, R.; White, M. D.

    2014-12-01

    The Farnsworth hydrocarbon field in northern Texas has been an experimental site for CO2 sequestration and enhanced oil recovery for the U.S. Department of Energy-sponsored Southwest Partnership (SWP) since April, 2013. CO2 is to be injected into the Pennsylvanian Morrow Sandstone at a rate of 200,000 tonnes per year for at least five years. The Morrow is a quartz-rich sandstone that lies at a depth of about 2400 m. Pore water in the Morrow has a total dissolved solids content of about 3600 mg/L dominated by Na, Cl, bicarbonate, and Ca. A reactive solute transport model was constructed for a 1700 × 1700 × 95 m volume using the TOUGHREACT software and the ECO2N equation of state for aqueous brine and CO2. Simulations were carried out to 100 years. The results showed immiscible CO2 gas to be concentrated in a lateral plume extending radially from the well screen, its ascent impeded by vigorous lateral groundwater flow in the more permeable upper Morrow. CO2 was much more widespread in aqueous solution, lowering pH throughout much of the model volume after 100 years, to a minimum of about 4.7. The low reactivity of the Morrow Sandstone due to its quartz-rich matrix and dilute pore fluid resulted in little mineral precipitation or dissolution, with net volume changes for any mineral no higher than order 10-4. The simulations predicted net dissolution of albite, calcite, and chlorite, and net precipitation of dawsonite, illite, and magnesite. The Morrow matrix was predicted to undergo slight net dissolution overall, resulting in porosity increases of up to 0.01%, suggesting that the Morrow would be resistant to significant changes in hydraulic properties as a result of the proposed amount of CO2 injection. For the 100 year simulation times calculated thus far, only a small fraction of the injected CO2 would be sequestered as carbonate minerals, with most of the injected CO2 dissolved in the aqueous phase.

  14. Electrodermal reactivity during the Trier Social Stress Test for children: interaction between the serotonin transporter polymorphism and children's attachment representation.

    PubMed

    Gilissen, Renske; Bakermans-Kranenburg, Marian J; van Ijzendoorn, Marinus H; Linting, Mariëlle

    2008-09-01

    This study explores the relation between variations in the serotonin transporter gene (5-HTTLPR; long vs. short allele), the child's attachment representation (assessed with the Attachment Story Completion Task, reflecting the security of the parent-child relationship), and electrodermal reactivity during a public speaking task, the Trier Social Stress Test for Children (TSST-C) in a sample of 92 7-year-old. Electrodermal reactivity during the TSST-C was not directly associated with variations in 5-HTT. However, there was a significant gene-environment interaction effect of 5-HTT and attachment security on electrodermal reactivity. Results are interpreted in terms of cumulative protection: Children with a secure attachment representation as well as long 5-HTT alleles appeared to be less stressed during the TSST-C. PMID:18683185

  15. Strong Coupling between Nanofluidic Transport and Interfacial Chemistry: How Defect Reactivity Controls Liquid-Solid Friction through Hydrogen Bonding.

    PubMed

    Joly, Laurent; Tocci, Gabriele; Merabia, Samy; Michaelides, Angelos

    2016-04-01

    Defects are inevitably present in nanofluidic systems, yet the role they play in nanofluidic transport remains poorly understood. Here, we report ab initio molecular dynamics (AIMD) simulations of the friction of liquid water on defective graphene and boron nitride sheets. We show that water dissociates at certain defects and that these "reactive" defects lead to much larger friction than the "nonreactive" defects at which water molecules remain intact. Furthermore, we find that friction is extremely sensitive to the chemical structure of reactive defects and to the number of hydrogen bonds they can partake in with the liquid. Finally, we discuss how the insight obtained from AIMD can be used to quantify the influence of defects on friction in nanofluidic devices for water treatment and sustainable energy harvesting. Overall, we provide new insight into the role of interfacial chemistry on nanofluidic transport in real, defective systems. PMID:27012818

  16. A comparison of results obtained with two subsurface non-isothermal multiphase reactive transport simulators, FADES-CORE and TOUGHREACT

    SciTech Connect

    Juncosa Rivera, Ricardo; Xu, Tianfu; Pruess, Karsten

    2001-01-01

    FADES-CORE and TOUGHREACT are codes used to model the non-isothermal multiphase flow with multicomponent reactive transport in porous media. Different flow and reactive transport problems were used to compare the FADES-CORE and TOUGHREACT codes. These problems take into account the different cases of multiphase flow with and without heat transport, conservative transport, and reactive transport. Consistent results were obtained from both codes, which use different numerical methods to solve the differential equations resulting from the various physicochemical processes. Here we present the results obtained from both codes for various cases. Some results are slightly different with minor discrepancies, which have been remedied, so that both codes would be able to reproduce the same processes using the same parameters. One of the discrepancies found is related to the different calculation for thermal conductivity in heat transport, which affects the calculation of the temperatures, as well as the pH of the reaction of calcite dissolution problem modeled. Therefore it is possible to affirm that the pH is highly sensitive to temperature. Generally speaking, the comparison was concluded to be highly satisfactory, leading to the complete verification of the FADES-CORE code. However, we must keep in mind that, as there are no analytical solutions available with which to verify the codes, the TOUGHREACT code has been thoroughly corroborated, given that the only possible way to prove that the code simulation is correct, is by comparing the results obtained with both codes for the identical problems, or to validate the simulation results with actual measured data.

  17. Reactive sputter deposition of pyrite structure transition metal disulfide thin films: Microstructure, transport, and magnetism

    SciTech Connect

    Baruth, A.; Manno, M.; Narasimhan, D.; Shankar, A.; Zhang, X.; Johnson, M.; Aydil, E. S.; Leighton, C.

    2012-09-01

    Transition metal disulfides crystallizing in the pyrite structure (e.g., TMS{sub 2}, with TM = Fe, Co, Ni, and Cu) are a class of materials that display a remarkably diverse array of functional properties. These properties include highly spin-polarized ferromagnetism (in Co{sub 1-x}Fe{sub x}S{sub 2}), superconductivity (in CuS{sub 2}), an antiferromagnetic Mott insulating ground state (in NiS{sub 2}), and semiconduction with close to optimal parameters for solar absorber applications (in FeS{sub 2}). Exploitation of these properties in heterostructured devices requires the development of reliable and reproducible methods for the deposition of high quality pyrite structure thin films. In this manuscript, we report on the suitability of reactive sputter deposition from metallic targets in an Ar/H{sub 2}S environment as a method to achieve exactly this. Optimization of deposition temperature, Ar/H{sub 2}S pressure ratio, and total working gas pressure, assisted by plasma optical emission spectroscopy, reveals significant windows over which deposition of single-phase, polycrystalline, low roughness pyrite films can be achieved. This is illustrated for the test cases of the ferromagnetic metal CoS{sub 2} and the diamagnetic semiconductor FeS{sub 2}, for which detailed magnetic and transport characterization are provided. The results indicate significant improvements over alternative deposition techniques such as ex situ sulfidation of metal films, opening up exciting possibilities for all-sulfide heterostructured devices. In particular, in the FeS{sub 2} case it is suggested that fine-tuning of the sputtering conditions provides a potential means to manipulate doping levels and conduction mechanisms, critical issues in solar cell applications. Parenthetically, we note that conditions for synthesis of phase-pure monosulfides and thiospinels are also identified.

  18. Using Reactive Transport Modeling to Evaluate the Source Term at Yucca Mountain

    SciTech Connect

    Y. Chen

    2001-12-19

    The conventional approach of source-term evaluation for performance assessment of nuclear waste repositories uses speciation-solubility modeling tools and assumes pure phases of radioelements control their solubility. This assumption may not reflect reality, as most radioelements (except for U) may not form their own pure phases. As a result, solubility limits predicted using the conventional approach are several orders of magnitude higher then the concentrations of radioelements measured in spent fuel dissolution experiments. This paper presents the author's attempt of using a non-conventional approach to evaluate source term of radionuclide release for Yucca Mountain. Based on the general reactive-transport code AREST-CT, a model for spent fuel dissolution and secondary phase precipitation has been constructed. The model accounts for both equilibrium and kinetic reactions. Its predictions have been compared against laboratory experiments and natural analogues. It is found that without calibrations, the simulated results match laboratory and field observations very well in many aspects. More important is the fact that no contradictions between them have been found. This provides confidence in the predictive power of the model. Based on the concept of Np incorporated into uranyl minerals, the model not only predicts a lower Np source-term than that given by conventional Np solubility models, but also produces results which are consistent with laboratory measurements and observations. Moreover, two hypotheses, whether Np enters tertiary uranyl minerals or not, have been tested by comparing model predictions against laboratory observations, the results favor the former. It is concluded that this non-conventional approach of source term evaluation not only eliminates over-conservatism in conventional solubility approach to some extent, but also gives a realistic representation of the system of interest, which is a prerequisite for truly understanding the long

  19. The reactivity of chlorite surfaces: Microscopic alteration processes and the transport behaviour of uranium(VI)

    NASA Astrophysics Data System (ADS)

    Bosbach, D.; Brandt, F.; Arnold, T.; Krawczyk-Baersch, E.; Bernhard, G.

    2003-04-01

    The transport of U(VI) in phyllite rocks or on granitic fractures is significantly affected by the dissolution of chlorite and the re-precipitation of various secondary phases. However, in order to be able to predict the behaviour of radionuclides in these systems a sound understanding of the reaction kinetics of chlorite alteration/dissolution processes as well as the precipitation of secondary phases is required. We have studied the dissolution of chlorite with mixed-flow reactor experiments and in-situ AFM observations far from equilibrium over a broad pH range. Key parameters such as the reactive surface area as well as the stoichiometry and pH dependency of the dissolution reaction were determined. Speciation calculations indicate that no secondary phases have formed (except under neutral pH conditions). Under acidic conditions the brucite-like layer of the chlorite structure dissolves faster than the 2:1 TOT layer whereas above pH 8 a reverse dissolution behaviour was observed. Under acidic conditions (pH < 5) chlorite transforms to a vermiculite-like clay mineral, which has also been identified in field studies. In addition, static batch dissolution experiments with chlorite were performed in order to mimic more closely natural systems. In these experiments various secondary phases including hydrous ferrous oxides (HFO) were formed as coatings on chlorite surfaces and as colloids in solution. Batch adsorption experiments indicate that U(VI) has a strong affinity to HFO and that retardation of U(VI) occurs via adsorption to immobile HFO coatings on chlorite surfaces. Heterogeneous HFO formation seems to be favoured on {hk0} edge surfaces in the near neutral pH range. The formation mechanism of HFO coatings was studied systematically with titration experiments, in order to be able to quantify the homogeneous and heterogeneous formation of these secondary phases as a function of the geochemical conditions.

  20. Evolution of carbon isotope signatures during reactive transport of hydrocarbons in heterogeneous aquifers

    NASA Astrophysics Data System (ADS)

    Höyng, Dominik; Prommer, Henning; Blum, Philipp; Grathwohl, Peter; Mazo D'Affonseca, Fernando

    2015-03-01

    Compound-specific isotope analysis (CSIA) of organic pollutants has become a well-established tool for assessing the occurrence and extent of biodegradation processes in contaminated aquifers. However, the precision of CSIA is influenced by the degree to which assumptions underlying CSIA data interpretation hold under realistic field-scale conditions. For the first time this study demonstrates how aquifer analogs combined with reactive transport models offer an underexplored way to develop generic process understanding, evaluate monitoring and quantification strategies in highly heterogeneous subsurface settings. Data from high-resolution aquifer analogs were used in numerical experiments to track the propagation of a representative oxidizable organic compound (toluene) within a variety of realistic heterogeneous aquifers and to investigate its detailed fate. The simulations were used to analyze (1) the effects of physical aquifer heterogeneities on spatiotemporal patterns of contaminant concentrations and isotope signatures, (2) the performance of the commonly applied Rayleigh equation and (3) the applicability of an extension of the Rayleigh equation for complex hydrogeological conditions. The results indicate that if field-derived enrichment factors are applied without corrections for dilution, the conventional Rayleigh equation is inaccurate and estimates for biodegradation are typically overestimated and unreliable in heterogeneous aquifers. Underestimations can occur due to the partial source zone depletion. In contrast, if dilution can be accurately accounted for, field-derived enrichment factors comprise a suitable alternative to laboratory-derived and redox-specific enrichment factors. The study also examines to what extent variations in monitoring/sampling strategies influence the obtained results. Especially measurements from long-screened wells (> 1 m) reveal to be inappropriate for the application of the Rayleigh equation in the investigated aquifer

  1. Analysis of acidity production during enhanced reductive dechlorination using a simplified reactive transport model

    NASA Astrophysics Data System (ADS)

    Brovelli, A.; Barry, D. A.; Robinson, C.; Gerhard, J. I.

    2012-07-01

    Build-up of fermentation products and hydrochloric acid at a contaminated site undergoing enhanced reductive dechlorination can result in groundwater acidification. Sub-optimal pH conditions can inhibit microbial activity and lead to reduced dechlorination rates. The extent of acidification likely to occur is site-specific and depends primarily on the extent of fermentation and dechlorination, the geochemical composition of soil and groundwater, and the pH-sensitivity of the active microbial populations. Here, the key chemical and physical mechanisms that control the extent of groundwater acidification in a contaminated site were examined, and the extent to which the remediation efficiency was affected by variations in groundwater pH was evaluated using a simplified process-based reactive-transport model. This model was applied successfully to a well-documented field site and was then employed in a sensitivity analysis to identify the processes likely to significantly influence acidity production and subsequent microbial inhibition. The accumulation of organic acids produced from the fermentation of the injected substrate was the main cause of the pH change. The concentration of dissolved sulphates controlled substrate utilisation efficiency because sulphate-reducing biomass competed with halo-respiring biomass for the fermentation products. It was shown further that increased groundwater velocity increases dilution and reduces the accumulation of acidic products. As a consequence, the flow rate corresponding to the highest remediation efficiency depends on the fermentation and dechlorination rates. The model enables investigation and forecasting of the extent and areal distribution of pH change, providing a means to optimise the application of reductive dechlorination for site remediation.

  2. Reactive transport modeling of the clogging process at Maqarin natural analogue site

    NASA Astrophysics Data System (ADS)

    Shao, Haibing; Kosakowski, Georg; Berner, Urs; Kulik, Dmitrii A.; Mäder, Urs; Kolditz, Olaf

    The Maqarin site in Jordan has been investigated for three decades as a natural analogue for the long term changes of materials in contact with hyper-alkaline solutions. Similar processes are expected in radioactive waste disposal sites, where cement based materials are in contact with natural rocks or other e.g. clay based materials. In this context, a numerical reactive transport model was used to study local geochemical alterations and induced porosity changes for the Maqarin marl rock in contact with the hyper-alkaline solution. The geochemical setup for the rock mineralogy and the pore water was calibrated to match measurements from the Maqarin site. The setup includes several clay and zeolite minerals, considers cation exchange processes, and a state-of-the-art model for cement phases. Similar to earlier calculations by Steefel and Lichtner (1998) who used a much simpler geochemical model, the pore clogging occurred after several hundred years at a distance of 5-10 mm from the contact to the hyper-alkaline solution. In our calculations, this was caused by a massive precipitation of ettringite and C-S-H minerals. We performed a sensitivity study by varying the intrinsic diffusion coefficient, the Archie's law exponential factor, and the mineral surface area available for dissolution and precipitation. We found that the dissolution of clay minerals controls the availability of Al, which is needed for ettringite and C-S-H phase precipitation. Thus, the amount and kinetically controlled dissolution of clay minerals controls the spatial and temporal evolution of porosity changes. The simulations reveal that neither cation exchange processes nor the formation of zeolite minerals strongly influence the geochemical evolution of the system.

  3. Hierarchical Testing with Automated Document Generation for Amanzi, ASCEM's Subsurface Flow and Reactive Transport Simulator

    NASA Astrophysics Data System (ADS)

    Moulton, J. D.; Steefel, C. I.; Yabusaki, S.; Castleton, K.; Scheibe, T. D.; Keating, E. H.; Freedman, V. L.

    2013-12-01

    The Advanced Simulation Capabililty for Environmental Management (ASCEM) program is developing an approach and open-source tool suite for standardized risk and performance assessments at legacy nuclear waste sites. These assessments use a graded and iterative approach, beginning with simplified highly abstracted models, and adding geometric and geologic complexity as understanding is gained. To build confidence in this assessment capability, extensive testing of the underlying tools is needed. Since the tools themselves, such as the subsurface flow and reactive-transport simulator, Amanzi, are under active development, testing must be both hierarchical and highly automated. In this presentation we show how we have met these requirements, by leveraging the python-based open-source documentation system called Sphinx with several other open-source tools. Sphinx builds on the reStructured text tool docutils, with important extensions that include high-quality formatting of equations, and integrated plotting through matplotlib. This allows the documentation, as well as the input files for tests, benchmark and tutorial problems, to be maintained with the source code under a version control system. In addition, it enables developers to build documentation in several different formats (e.g., html and pdf) from a single source. We will highlight these features, and discuss important benefits of this approach for Amanzi. In addition, we'll show that some of ASCEM's other tools, such as the sampling provided by the Uncertainty Quantification toolset, are naturally leveraged to enable more comprehensive testing. Finally, we will highlight the integration of this hiearchical testing and documentation framework with our build system and tools (CMake, CTest, and CDash).

  4. Influence of biofilm accumulation on flow and reactive transport through porous media

    NASA Astrophysics Data System (ADS)

    Sharp, R.; Adgie, M.; Cunningham, A.

    2003-04-01

    A series of continuous flow, porous media reactor studies were performed to characterize the development of thick biofilms in porous media and the subsequent effects on flow and reactive transport. The bioluminescent organism Vibrio fischeri was used to produce various degrees of biofilm growth within the porous media system. V. fischeri biofilm growth, distribution, and activity in the porous media reactors was evaluated using bioluminescent imaging. Bulk fluid flow and flow channel dynamics in the porous media were monitored by imaging pulses of nigrosine bulk fluid dye. Hydrodynamics of the porous media/biofilm systems were analyzed using fluorescein break through curves and head loss across the system. Bioluminescent and bulk-fluid dye imaging, along with fluoroscein break through curve analysis, provided quantitative information on the transient distribution of biofilm within the reactor and the dynamic relationship between biofilm development and porous media hydraulics. Bioluminescent and bulk-fluid dye images showed continuous creation and closure of flow channels in the biofilm/porous media matrix. Flow channel size and distribution changed with increasing degrees of biofilm growth. Bioluminescence showed not only the density and distribution of biofilm growth in the porous media, but also the rate of oxygen uptake across the flow field. Results from the breakthrough curves suggest that thin biofilms transform the well-defined plug flow regime of clean porous media to a flow with severe axial and longitudinal dispersion. As the biofilm thickens, the flow regime is transformed to dispersed plug flow with an accelerated residence time. These studies provide a better quantitative understanding of the fundamental relationship between biofilm development and bulk fluid hydrodynamics in porous media. Results demonstrate the simultaneous visualization of biofilm growth and bulk fluid flow in porous media at the meso-scale. The studies also establish a novel

  5. Reactive Transport Modeling of Subsurface Arsenic Removal Systems in Rural Bangladesh

    NASA Astrophysics Data System (ADS)

    Bakker, M.; Rahman, M. M.; van Breukelen, B. M.; Ahmed, K. M.

    2014-12-01

    Elevated concentrations of arsenic (As) in the groundwater of the shallow aquifers of Bangladesh are a major public health concern. Subsurface Arsenic Removal (SAR) is a relatively new treatment option that can potentially be a cost effective method for arsenic removal for community-based drinking water supplies. The basic idea of SAR is to extract water, aerate it, and re-inject it, after which groundwater with reduced arsenic concentrations may be extracted. The main process for As reduction is sorption to Hydrous Ferric Oxides (HFO) that forms after injection of the aerated water. The purpose of this poster is to investigate the major geochemical processes responsible for the (im)mobilization of As during SAR operation. SAR was applied at a test site in Muradnagar upazila in Comilla district about 100 km southeast of Dhaka in Bangladesh. Multiple extraction/aeration/re-injection cycles were performed and water samples were analyzed. A PHREEQC reactive transport model (RTM) was used in a radial flow setting to try to reproduce the measurements. Kinetic oxidation/dissolution reactions, cation exchange, and surface complexation were simulated. The simulation of different reactions enables the possibility to discern the reaction parameters involved in the im(mobilization) of As. The model fit has reasonable agreement with the observed data for major ions and trace elements. The model suggests an increasing sorption capacity due to the gradual development of HFO precipitates resulting from the injection phases. Modeled breakthrough curves of As, Fe(II), and Mn, match the measured increase of As, Fe(II), and Mn removal with successive cycles. The model illustrates that the pH of groundwater during SAR operation has a great impact on As sorption in the subsurface. The surface complexation modeling suggests that competitive displacement of As by H4SiO4 is an important factor limiting As removal during SAR operation.

  6. Hybrid finite-volume/transported PDF method for the simulation of turbulent reactive flows

    NASA Astrophysics Data System (ADS)

    Raman, Venkatramanan

    A novel computational scheme is formulated for simulating turbulent reactive flows in complex geometries with detailed chemical kinetics. A Probability Density Function (PDF) based method that handles the scalar transport equation is coupled with an existing Finite Volume (FV) Reynolds-Averaged Navier-Stokes (RANS) flow solver. The PDF formulation leads to closed chemical source terms and facilitates the use of detailed chemical mechanisms without approximations. The particle-based PDF scheme is modified to handle complex geometries and grid structures. Grid-independent particle evolution schemes that scale linearly with the problem size are implemented in the Monte-Carlo PDF solver. A novel algorithm, in situ adaptive tabulation (ISAT) is employed to ensure tractability of complex chemistry involving a multitude of species. Several non-reacting test cases are performed to ascertain the efficiency and accuracy of the method. Simulation results from a turbulent jet-diffusion flame case are compared against experimental data. The effect of micromixing model, turbulence model and reaction scheme on flame predictions are discussed extensively. Finally, the method is used to analyze the Dow Chlorination Reactor. Detailed kinetics involving 37 species and 158 reactions as well as a reduced form with 16 species and 21 reactions are used. The effect of inlet configuration on reactor behavior and product distribution is analyzed. Plant-scale reactors exhibit quenching phenomena that cannot be reproduced by conventional simulation methods. The FV-PDF method predicts quenching accurately and provides insight into the dynamics of the reactor near extinction. The accuracy of the fractional time-stepping technique in discussed in the context of apparent multiple-steady states observed in a non-premixed feed configuration of the chlorination reactor.

  7. Reactive Transport Modeling of Supercritical Carbon Dioxide Injection Into Mafic Rock Reservoirs

    NASA Astrophysics Data System (ADS)

    Podgorney, R.; Hull, L.; Huang, H.; McLing, T.

    2007-12-01

    Technologies to reduce emissions of greenhouse gases and increase the sequestration of CO2 have received increasing attention since the development of the Kyoto protocol. One promising technology is the sequestration of CO2 in geologic formations. The suitability of a fractured basalt reservoir for CO2 sequestration is constrained by three broad categories of issues, which we refer to as physical, technical, and economic constraints. Physical constraints are beyond human control; thus, it is a requirement that a systematic method be developed by which a particular target reservoir may be evaluated to determine if it lies within the bounds required for safe and effective disposal. Technical constraints, on the other hand, are challenges to the ability to design, construct, and/or monitor a sequestration project as a result of limitations on our ability to determine the distribution of properties in the subsurface, our knowledge of the behavior of CO2 in the deep subsurface, and the current state of computational science and subsurface monitoring. Equally important are the heterogeneity of economic costs associated with sequestering CO2 at different sites and within different formations. The work presented here focuses on the technical aspects of CO2 injection, specifically examining reactive transport of CO2 in the subsurface in the vicinity of the injection well using the simulation code TOUGHREACT. Pressure distribution and propagation, kinetics of the geochemical reactions, and resultant changes in permeability/porosity are examined in order to evaluate injection scenarios that maximize the longevity of the injection well and sustainability of the reservoir.

  8. Evolution of carbon isotope signatures during reactive transport of hydrocarbons in heterogeneous aquifers.

    PubMed

    Höyng, Dominik; Prommer, Henning; Blum, Philipp; Grathwohl, Peter; D'Affonseca, Fernando Mazo

    2015-03-01

    Compound-specific isotope analysis (CSIA) of organic pollutants has become a well-established tool for assessing the occurrence and extent of biodegradation processes in contaminated aquifers. However, the precision of CSIA is influenced by the degree to which assumptions underlying CSIA data interpretation hold under realistic field-scale conditions. For the first time this study demonstrates how aquifer analogs combined with reactive transport models offer an underexplored way to develop generic process understanding, evaluate monitoring and quantification strategies in highly heterogeneous subsurface settings. Data from high-resolution aquifer analogs were used in numerical experiments to track the propagation of a representative oxidizable organic compound (toluene) within a variety of realistic heterogeneous aquifers and to investigate its detailed fate. The simulations were used to analyze (1) the effects of physical aquifer heterogeneities on spatiotemporal patterns of contaminant concentrations and isotope signatures, (2) the performance of the commonly applied Rayleigh equation and (3) the applicability of an extension of the Rayleigh equation for complex hydrogeological conditions. The results indicate that if field-derived enrichment factors are applied without corrections for dilution, the conventional Rayleigh equation is inaccurate and estimates for biodegradation are typically overestimated and unreliable in heterogeneous aquifers. Underestimations can occur due to the partial source zone depletion. In contrast, if dilution can be accurately accounted for, field-derived enrichment factors comprise a suitable alternative to laboratory-derived and redox-specific enrichment factors. The study also examines to what extent variations in monitoring/sampling strategies influence the obtained results. Especially measurements from long-screened wells (>1 m) reveal to be inappropriate for the application of the Rayleigh equation in the investigated aquifer

  9. A reactive transport model to simulate uranium immobilization through pH manipulation

    SciTech Connect

    Zhang, Fan; Luo, Wensui; Watson, David B; Peterson, Mark J; Gu, Baohua; Spalding, Brian Patrick; Jardine, Philip M

    2008-07-01

    Saprolite cores collected from around the former S-3 Ponds waste disposal site on the Oak Ridge Reservation in east Tennessee, USA, exhibit low pH and high concentrations of Al, Ca, Mg, Mn, various trace metals such as Ni and Co, and radionuclides such as U and Tc. Because uranium is one of the major contaminants of concern at the site, its behavior was of particular interest. The mobility of uranium depends highly on pH. Groundwater titration experiments showed that when pH was increased from 3.87 to 5.45 with addition of dissolved sodium hydroxide, concentration of aqueous uranium decreased from 50 ppm to less than 5 ppm. However, base additions to the sediments to increase pH are strongly buffered by various precipitation and sorption reactions. This study was undertaken to investigate the geochemical processes that control contaminant mobility and to develop a practical model to predict uranium immobilization under conditions where pH is manipulated for remediation of geochemically complex sites. The method of Spalding and Spalding was utilized to model soil buffer capacity by treating aquifer solids as a polyprotic acid. Aluminum precipitation and dissolution kinetics was included in HydroGeoChem v5.0 in addition to an equilibrium reaction model that considers aqueous complexation, precipitation, sorption and soil buffering with pH-dependent ion exchange capacity. The HydroGeoChem model was successfully utilized to simulate batch titration experiments and comparison of reactive transport model results with pH manipulation column experiments were in close agreement. The model was also calibrated to simulate acidic groundwater percolating through carbonate gravel at the site.

  10. Application of block-scale effective dispersion to reactive transport simulations in groundwater

    NASA Astrophysics Data System (ADS)

    Herrera, Paulo; Cortinez, Joaquin; Valocchi, Albert

    2015-04-01

    In the groundwater literature, macrodispersion has traditionally been derived and applied to account for plume spreading -i.e. deformation of the water volume that contains solute mass- due to the overall heterogeneity of aquifers. Several experimental and numerical studies have verified that the use of a macrodispersion coefficient within an advection-dispersion equation can reproduce plume spreading in mildly heterogeneous aquifers. More recently, there have been new extensions to the macrodispersion theory to separately account for block-scale filtering effects due to the use of finite-size numerical grids, and for deriving effective macrodispersion coefficients to account for solute mixing and dilution. We combine the concepts of block-scale dependent and effective dispersion to account for the effect of unresolved subgrid-scale heterogeneity on synthetic numerical simulations of a mixing controlled bimolecular reaction. We demonstrate that by using a time-dependent effective block-scale dispersion coefficient we are able to reproduce overall reaction rates for different scenarios defined according to parameters such as: grid size, Peclet number, aquifer heterogeneity, etc. Moreover, we verify that for long-times the block-scale effective dispersion coefficient that reproduces mixing is equal to the previously derived block-scale dispersion coefficient that reproduces spreading. Given that the block-scale dispersion coefficient is similar to the traditional macrodispersion coefficient in the limit of infinitely large block-sizes, we conclude that the block-scale time-dependent dispersion coefficient constitutes a natural extension of the macrodispersion theory that provides a unified framework for numerical simulations of reactive transport in heterogeneous aquifers.

  11. CRITIQUE OF DUAL CONTINUUM FORMULATIONS OF MULTICOMPONENT REACTIVE TRANSPORT IN FRACTURED POROUS MEDIA

    SciTech Connect

    Lichtner, P.C.

    2000-02-01

    Subsurface flow processes may take place at many different scales. The different scales refer to rock pore structure, micro-fractures, distinct fracture networks ranging from small to large fracture spacing, and even faults. Presently, there is no satisfactory methodology for describing quantitatively flow and reactive transport in multi-scale media. Approaches commonly applied to model fractured systems include single continuum models (SCM), equivalent continuum models (ECM), discrete fracture models (DFM), and various forms of dual continuum models (DCM). The SCM describes flow in the fracture network only and is valid in the absence of fracture-matrix interaction. The ECM, on the other hand, requires pervasive interaction between fracture and matrix and is based on averaging their properties. The ECM is characterized by equal fracture and matrix solute concentrations, but generally different mineral concentrations. The DFM is perhaps the most rigorous, but would require inordinate computational resources for a highly fractured rock mass. The DCM represents a fractured porous medium as two interacting continua with one continuum corresponding to the fracture network and the other the matrix. A coupling term provides mass transfer between the two continua. Vidues for mineral and solute concentrations and other properties such as liquid saturation state maybe assigned individually to fracture and matrix. Two forms of the DCM are considered characterized by connected and disconnected matrix blocks. The former is referred to as the DCCM (dual continuum connected matrix) model and the latter as the DCDM (dual continuum disconnected matrix) model. In contrast to the DCCM model in which concentration gradients in the matrix are allowed only parallel to the fracture, the DFM provides for matrix concentration gradients perpendicular to the fracture. The DFM and DCCM models can agree with each other only in the case where both reduce to the ECM. The DCCM model exhibits the

  12. Open-Source Development of the Petascale Reactive Flow and Transport Code PFLOTRAN

    NASA Astrophysics Data System (ADS)

    Hammond, G. E.; Andre, B.; Bisht, G.; Johnson, T.; Karra, S.; Lichtner, P. C.; Mills, R. T.

    2013-12-01

    Open-source software development has become increasingly popular in recent years. Open-source encourages collaborative and transparent software development and promotes unlimited free redistribution of source code to the public. Open-source development is good for science as it reveals implementation details that are critical to scientific reproducibility, but generally excluded from journal publications. In addition, research funds that would have been spent on licensing fees can be redirected to code development that benefits more scientists. In 2006, the developers of PFLOTRAN open-sourced their code under the U.S. Department of Energy SciDAC-II program. Since that time, the code has gained popularity among code developers and users from around the world seeking to employ PFLOTRAN to simulate thermal, hydraulic, mechanical and biogeochemical processes in the Earth's surface/subsurface environment. PFLOTRAN is a massively-parallel subsurface reactive multiphase flow and transport simulator designed from the ground up to run efficiently on computing platforms ranging from the laptop to leadership-class supercomputers, all from a single code base. The code employs domain decomposition for parallelism and is founded upon the well-established and open-source parallel PETSc and HDF5 frameworks. PFLOTRAN leverages modern Fortran (i.e. Fortran 2003-2008) in its extensible object-oriented design. The use of this progressive, yet domain-friendly programming language has greatly facilitated collaboration in the code's software development. Over the past year, PFLOTRAN's top-level data structures were refactored as Fortran classes (i.e. extendible derived types) to improve the flexibility of the code, ease the addition of new process models, and enable coupling to external simulators. For instance, PFLOTRAN has been coupled to the parallel electrical resistivity tomography code E4D to enable hydrogeophysical inversion while the same code base can be used as a third

  13. Pareto optimal calibration of highly nonlinear reactive transport groundwater models using particle swarm optimization

    NASA Astrophysics Data System (ADS)

    Siade, A. J.; Prommer, H.; Welter, D.

    2014-12-01

    Groundwater management and remediation requires the implementation of numerical models in order to evaluate the potential anthropogenic impacts on aquifer systems. In many situations, the numerical model must, not only be able to simulate groundwater flow and transport, but also geochemical and biological processes. Each process being simulated carries with it a set of parameters that must be identified, along with differing potential sources of model-structure error. Various data types are often collected in the field and then used to calibrate the numerical model; however, these data types can represent very different processes and can subsequently be sensitive to the model parameters in extremely complex ways. Therefore, developing an appropriate weighting strategy to address the contributions of each data type to the overall least-squares objective function is not straightforward. This is further compounded by the presence of potential sources of model-structure errors that manifest themselves differently for each observation data type. Finally, reactive transport models are highly nonlinear, which can lead to convergence failure for algorithms operating on the assumption of local linearity. In this study, we propose a variation of the popular, particle swarm optimization algorithm to address trade-offs associated with the calibration of one data type over another. This method removes the need to specify weights between observation groups and instead, produces a multi-dimensional Pareto front that illustrates the trade-offs between data types. We use the PEST++ run manager, along with the standard PEST input/output structure, to implement parallel programming across multiple desktop computers using TCP/IP communications. This allows for very large swarms of particles without the need of a supercomputing facility. The method was applied to a case study in which modeling was used to gain insight into the mobilization of arsenic at a deepwell injection site

  14. Assessment of Parametric Uncertainty in Groundwater Reactive Transport Modeling Using Markov Chain Monte Carlo Techniques

    NASA Astrophysics Data System (ADS)

    Shi, X.; Ye, M.; Curtis, G. P.; Lu, D.; Meyer, P. D.; Yabusaki, S.; Wu, J.

    2011-12-01

    Assessment of parametric uncertainty for groundwater reactive transport models is challenging, because the models are highly nonlinear with respect to their parameters due to nonlinear reaction equations and process coupling. The nonlinearity may yield parameter distributions that are non-Gaussian and have multiple modes. For such parameter distributions, the widely used nonlinear regression methods may not be able to accurately quantify predictive uncertainty. One solution to this problem is to use Markov Chain Monte Carlo (MCMC) techniques. Both the nonlinear regression and MCMC methods are used in this study for quantification of parametric uncertainty of a surface complexation model (SCM), developed to simulate hexavalent uranium [U(VI)] transport in column experiments. Firstly, a brute force Monte Carlo (MC) simulation with hundreds of thousands of model executions is conducted to understand the surface of objective function and predictive uncertainty of uranium concentration. Subsequently, the Gauss-Marquardt-Levenberg method is applied to calibrate the model. It shows that, even with multiple initial guesses, the local optimization method has difficulty of finding the global optimum because of the rough surface of the objective function and local optima/minima due to model nonlinearity. Another problem of the nonlinear regression is the underestimation of predictive uncertainty, as both the linear and nonlinear confidence intervals are narrower than that obtained from the native MC simulation. Since the naïve MC simulation is computationally expensive, the above challenges for parameter estimation and predictive uncertainty analysis are addressed using a computationally efficient MCMC technique, the DiffeRential Evolution Adaptive Metropolis algorithm (DREAM) algorithm. The results obtained from running DREAM compared with those from brute force Monte Carlo simulations shown that MCMC not only successfully infers the multi-modals posterior probability

  15. Performance Assessment of Low-Level Waste Disposal Facilities Using Coupled Unsaturated Flow and Reactive Transport Simulators

    SciTech Connect

    Bacon, Diana H.; McGrail, Pete P.; Freedman, Vicky L.; Ventura, Giancarlo; Risoluti, Piero N.; Krupka, Kenneth M.; McGrail, B. P.; Cragnolino, G. A.

    2002-01-01

    Recent advances in development of reactive chemical transport simulators have made it possible to use these tools in performance assessments (PAs) for nuclear waste disposal. Reactive transport codes were used to evaluate the impacts of design modifications on the performance of two shallow subsurface disposal systems for low-level radioactive waste. The first disposal system, located at the Hanford site in Richland, Washington, is for disposal of low-level waste glass. Glass waste blocks will be disposed in subsurface trenches, surrounded by backfill material. The effect of different waste package sizes and layering on technetium release to the vadose zone had a small impact on release rates. The second disposal system involves a hypothetical repository for low-activity waste in Italy. A model of uranium release from a grout waste form was developed using the STORM reactive transport code. Uranium is predicted to be relatively insoluble for several hundred years under the high-pH environment of the cement pore water. The effect of using different filler materials between the waste packages on uranium flux to the vadose zone proved to have a negligible impact on release rates.

  16. Summary of Radionuclide Reactive Transport Experiments in Fractured Tuff and Carbonate Rocks from Yucca Flat, Nevada Test Site

    SciTech Connect

    Zavarin, M; Roberts, S; Reimus, P; Johnson, M

    2006-10-11

    In the Yucca Flat basin of the Nevada Test Site (NTS), 747 shaft and tunnel nuclear detonations were conducted primarily within the tuff confining unit (TCU) or the overlying alluvium. The TCU in the Yucca Flat basin is hypothesized to inhibit radionuclide migration to the highly transmissive and regionally extensive lower carbonate aquifer (LCA) due to its wide-spread aerial extent, low permeability, and chemical reactivity. However, fast transport pathways through the TCU by way of fractures may provide a migration path for radionuclides to the LCA. Radionuclide transport in both TCU and the LCA fractures is likely to determine the location of the contaminant boundary for the Yucca Flat/Climax Mine Corrective Action Unit (CAU). Radionuclide transport through the TCU may involve both matrix and fracture flow. However, radionuclide migration over significant distances is likely to be dominated by fracture transport. Transport through the LCA will almost certainly be dominated by fracture flow, as the LCA has a very dense, low porosity matrix with very low permeability. Because of the complex nature of reactive transport in fractures, a stepwise approach to identifying mechanisms controlling radionuclide transport was used. The simplest LLNL experiments included radionuclide transport through synthetic parallel-plate fractured tuff and carbonate cores. These simplified fracture transport experiments isolated matrix diffusion and sorption effects from all other fracture transport processes (fracture lining mineral sorption, heterogeneous flow, etc.). Additional fracture transport complexity was added by performing induced fractured LCA flowthrough experiments (effect of aperture heterogeneity) or iron oxide coated parallel plate TCU flowthrough experiments (effect of fracture lining minerals). Finally naturally fractured tuff and carbonate cores were examined at LLNL and LANL. All tuff and carbonate core used in the experiments was obtained from the USGS Core Library

  17. Investigating Uranium Mobility Using Stable Isotope Partitioning of 238U/235U and a Reactive Transport Model

    NASA Astrophysics Data System (ADS)

    Bizjack, M.; Johnson, T. M.; Druhan, J. L.; Shiel, A. E.

    2015-12-01

    We report a numerical reactive transport model which explicitly incorporates the effectively stable isotopes of uranium (U) and the factors that influence their partitioning in bioactive systems. The model reproduces trends observed in U isotope ratios and concentration measurements from a field experiment, thereby improving interpretations of U isotope ratios as a tracer for U reactive transport. A major factor contributing to U storage and transport is its redox state, which is commonly influenced by the availability of organic carbon to support metal-reducing microbial communities. Both laboratory and field experiments have demonstrated that biogenic reduction of U(VI) fractionates the stable isotope ratio 238U/235U, producing an isotopically heavy solid U(IV) product. It has also been shown that other common reactive transport processes involving U do not fractionate isotopes to a consistently measurable level, which suggests the capacity to quantify the extent of bioreduction occurring in groundwater containing U using 238U/235U ratios. A recent study of a U bioremediation experiment at the Rifle IFRC site (Colorado, USA) applied Rayleigh distillation models to quantify U stable isotope fractionation observed during acetate amendment. The application of these simplified models were fit to the observations only by invoking a "memory-effect," or a constant source of low-concentration, unfractionated U(VI). In order to more accurately interpret the measured U isotope ratios, we present a multi-component reactive transport model using the CrunchTope software. This approach is capable of quantifying the cycling and partitioning of individual U isotopes through a realistic network of transport and reaction pathways including reduction, oxidation, and microbial growth. The model incorporates physical heterogeneity of the aquifer sediments through zones of decreased permeability, which replicate the observed bromide tracer, major ion chemistry, U concentration, and U

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

    SciTech Connect

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

    2011-02-28

    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

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

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

    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

  1. Three-dimensional density-dependent flow and multicomponent reactive transport modeling of chlorinated solvent oxidation by potassium permanganate

    NASA Astrophysics Data System (ADS)

    Henderson, Thomas H.; Mayer, K. Ulrich; Parker, Beth L.; Al, Tom A.

    2009-05-01

    A popular method for the treatment of aquifers contaminated with chlorinated solvents is chemical oxidation based on the injection of potassium permanganate (KMnO 4). Both the high density (1025 gL - 1 ) and reactivity of the treatment solution influence the fate of permanganate (MnO 4) in the subsurface and affect the degree of contaminant treatment. The MIN3P multicomponent reactive transport code was enhanced to simulate permanganate-based remediation, to evaluate the pathways of MnO 4 utilization, and to assess the role of density contrasts for the delivery of the treatment solution. The modified code (MIN3P-D) provides a direct coupling between density-dependent fluid flow, solute transport, contaminant treatment, and geochemical reactions. The model is used to simulate a field trial of TCE oxidation in a sandy aquifer that is underlain by an aquitard. Three-dimensional simulations are conducted for a coupled reactive system comprised of ten aqueous components, two mineral phases, TCE (dissolved, adsorbed, and NAPL), reactive organic matter, and including ion exchange reactions. Model parameters are constrained by literature data and a detailed data set from the field site under investigation. The general spatial and transient evolution in observed concentrations of the oxidant, dissolved TCE, and reaction products are adequately reproduced by the simulations. The model elucidates the important role of density-induced flow and transport on the distribution of the treatment solution into NAPL containing regions located at the aquifer-aquitard interface. Model results further suggest that reactions that do not directly affect the stability of MnO 4 have a negligible effect on solution density and MnO 4 delivery.

  2. Numerical Modeling of Coupled Variably-Saturated Fluid Flow and Reactive Transport with Fast and Slow Chemical Reactions

    SciTech Connect

    LI, MING-HSU; SIEGEL, MALCOLM D.; YEH, GOUR-TSYH

    1999-09-20

    The couplings among chemical reaction rates, advective and diffusive transport in fractured media or soils, and changes in hydraulic properties due to precipitation and dissolution within fractures and in rock matrix are important for both nuclear waste disposal and remediation of contaminated sites. This paper describes the development and application of LEHGC2.0, a mechanistically-based numerical model for simulation of coupled fluid flow and reactive chemical transport including both fast and slow reactions invariably saturated media. Theoretical bases and numerical implementations are summarized, and two example problems are demonstrated. The first example deals with the effect of precipitation-dissolution on fluid flow and matrix diffusion in a two-dimensional fractured media. Because of the precipitation and decreased diffusion of solute from the fracture into the matrix, retardation in the fractured medium is not as large as the case wherein interactions between chemical reactions and transport are not considered. The second example focuses on a complicated but realistic advective-dispersive-reactive transport problem. This example exemplifies the need for innovative numerical algorithms to solve problems involving stiff geochemical reactions.

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

    NASA Astrophysics Data System (ADS)

    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

  4. Reactive Transport Modeling of Cap Rock Integrity During Natural and Engineered CO2 Storage

    SciTech Connect

    Johnson, J W; Nitao, J J; Morris, J P

    2004-05-26

    Long-term cap rock integrity represents the single most important constraint on the long-term isolation performance of natural and engineered CO{sub 2} storage sites. CO{sub 2} influx that forms natural accumulations and CO{sub 2} injection for EOR/sequestration or saline-aquifer disposal both lead to concomitant geochemical alteration and geomechanical deformation of the cap rock, enhancing or degrading its seal integrity depending on the relative effectiveness of these interdependent processes. Using our reactive transport simulator (NUFT), supporting geochemical databases and software (GEMBOCHS, SUPCRT92), and distinct-element geomechanical model (LDEC), we have shown that influx-triggered mineral dissolution/precipitation reactions within typical shale cap rocks continuously reduce microfracture apertures, while pressure and effective-stress evolution first rapidly increase then slowly constrict them. For a given shale composition, the extent of geochemical enhancement is nearly independent of key reservoir properties (permeability and lateral continuity) that distinguish EOR/sequestration and saline-aquifer settings and CO{sub 2} influx parameters (rate, focality, and duration) that distinguish engineered disposal sites and natural accumulations, because these characteristics and parameters have negligible (indirect) impact on mineral dissolution/precipitation rates. In contrast, the extent of geomechanical degradation is highly dependent on these reservoir properties and influx parameters because they effectively dictate magnitude of the pressure perturbation; specifically, initial geomechanical degradation has been shown inversely proportional to reservoir permeability and lateral continuity and proportional to influx rate. Hence, while the extent of geochemical alteration is nearly independent of filling mode, that of geomechanical deformation is significantly more pronounced during engineered injection. This distinction limits the extent to which naturally

  5. Using a Mechanistic Reactive Transport Model to Represent Soil Organic Matter Dynamics and Climate Sensitivity

    NASA Astrophysics Data System (ADS)

    Guerry, N.; Riley, W. J.; Maggi, F.; Torn, M. S.; Kleber, M.

    2011-12-01

    The nature of long term Soil Organic Matter (SOM) dynamics is uncertain and the mechanisms involved are crudely represented in site, regional, and global models. Recent work challenging the paradigm that SOM is stabilized because of its sequential transformations to more intrinsically recalcitrant compounds motivated us to develop a mechanistic modeling framework that can be used to test hypotheses of SOM dynamics. We developed our C cycling model in TOUGHREACT, an established 3-dimensional reactive transport solver that accounts for multiple phases (aqueous, gaseous, sorbed), multiple species, advection and diffusion, and multiple microbial populations. Energy and mass exchange through the soil boundaries are accounted for via ground heat flux, rainfall, C sources (e.g., exudation, woody, leaf, root litter) and C losses (e.g., CO2 emissions and DOC deep percolation). SOM is categorized according to the various types of compounds commonly found in the above mentioned C sources and microbial byproducts, including poly- and monosaccharides, lignin, amino compounds, organic acids, nucleic acids, lipids, and phenols. Each of these compounds is accounted for by one or more representative species in the model. A reaction network was developed to describe the microbially-mediated processes and chemical interactions of these species, including depolymerization, microbial assimilation, respiration and deposition of byproducts, and incorporation of dead biomass into SOM stocks. Enzymatic reactions are characterized by Michaelis-Menten kinetics, with maximum reaction rates determined by the species' O/C ratio. Microbial activity is further regulated by soil moisture content, O2 availability, pH, and temperature. For the initial set of simulations, literature values were used to constrain microbial Monod parameters, Michaelis-Menten parameters, sorption parameters, physical protection, partitioning of microbial byproducts, and partitioning of litter inputs, although there is

  6. COUPLED REACTIVE TRANSPORT MODELING BASED ON THE NEW BIOGEOCHEMICAL CODE HP1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The migration of many naturally occurring elements and contaminants in the subsurface is affected by a multitude of complex, interactive physical, chemical, mineralogical, geological, and biological processes. Recently, a new comprehensive simulation tool HP1 (HYDRUS1D-PHREEQC) was developed by cou...

  7. Fires in Operating or Abandoned Coal Mines or Heaps of Reactive Materials and the Governing Transport and Reaction Processes

    NASA Astrophysics Data System (ADS)

    Wuttke, M. W.; Kessels, W.; Wessling, S.; Han, J.

    2007-05-01

    Spontaneous combustion is a world wide problem for technical operations in mining, waste disposal and power plant facilities. The principle driving the combustion is every where the same independent of the different reactive materials: Fresh air with the common oxygen content is getting in contact with the reactive material by human operations. The following reaction process produces heat at a usually low but constant rate. The reactive material in operating or abandoned coal mines, heaps of coal, waste or reactive minerals is most times strongly broken or fractured, such that the atmospheric oxygen can deeply penetrate into the porous or fractured media. Because the strongly broken or fractured medium with air filled pores and fractures is often combined with a low thermal conductivity of the bulk material the produced heat accumulates and the temperature increases with time. If the reactivity strongly increases with temperature, the temperature rise accelerates up to the "combustion temperature". Once the temperature is high enough the combustion process is determined by the oxygen transport to the combustion center rather than the chemical reactivity. Spontaneous combustion is thus a self- amplifying process where an initial small variation in the parameters and the starting conditions can create exploding combustion hot spots in an apparently homogenous material. The phenomenon will be discussed by various examples in the context of the German - Sino coal fire project. A temperature monitoring in hot fracture systems documents the strong influence of the weather conditions on the combustion process. Numerical calculations show the sensitivity of the combustion to the model geometries, the boundary conditions and mainly the permeability. The most used fire fighting operations like covering and water injection are discussed. A new method of using saltwater for fire fighting is presented and discussed. References: Kessels, W., Wessling, S., Li, X., and Wuttke, M

  8. Reactive transport modeling of stable carbon isotope fractionation in a multi-phase multi-component system during carbon sequestration

    DOE PAGESBeta

    Zhang, Shuo; DePaolo, Donald J.; Zheng, Liange; Mayer, Bernhard

    2014-12-31

    Carbon stable isotopes can be used in characterization and monitoring of CO2 sequestration sites to track the migration of the CO2 plume and identify leakage sources, and to evaluate the chemical reactions that take place in the CO2-water-rock system. However, there are few tools available to incorporate stable isotope information into flow and transport codes used for CO2 sequestration problems. We present a numerical tool for modeling the transport of stable carbon isotopes in multiphase reactive systems relevant to geologic carbon sequestration. The code is an extension of the reactive transport code TOUGHREACT. The transport module of TOUGHREACT was modifiedmore » to include separate isotopic species of CO2 gas and dissolved inorganic carbon (CO2, CO32-, HCO3-,…). Any process of transport or reaction influencing a given carbon species also influences its isotopic ratio. Isotopic fractionation is thus fully integrated within the dynamic system. The chemical module and database have been expanded to include isotopic exchange and fractionation between the carbon species in both gas and aqueous phases. The performance of the code is verified by modeling ideal systems and comparing with theoretical results. Efforts are also made to fit field data from the Pembina CO2 injection project in Canada. We show that the exchange of carbon isotopes between dissolved and gaseous carbon species combined with fluid flow and transport, produce isotopic effects that are significantly different from simple two-component mixing. These effects are important for understanding the isotopic variations observed in field demonstrations.« less

  9. Reactive transport modeling of stable carbon isotope fractionation in a multi-phase multi-component system during carbon sequestration

    SciTech Connect

    Zhang, Shuo; DePaolo, Donald J.; Zheng, Liange; Mayer, Bernhard

    2014-12-31

    Carbon stable isotopes can be used in characterization and monitoring of CO2 sequestration sites to track the migration of the CO2 plume and identify leakage sources, and to evaluate the chemical reactions that take place in the CO2-water-rock system. However, there are few tools available to incorporate stable isotope information into flow and transport codes used for CO2 sequestration problems. We present a numerical tool for modeling the transport of stable carbon isotopes in multiphase reactive systems relevant to geologic carbon sequestration. The code is an extension of the reactive transport code TOUGHREACT. The transport module of TOUGHREACT was modified to include separate isotopic species of CO2 gas and dissolved inorganic carbon (CO2, CO32-, HCO3-,…). Any process of transport or reaction influencing a given carbon species also influences its isotopic ratio. Isotopic fractionation is thus fully integrated within the dynamic system. The chemical module and database have been expanded to include isotopic exchange and fractionation between the carbon species in both gas and aqueous phases. The performance of the code is verified by modeling ideal systems and comparing with theoretical results. Efforts are also made to fit field data from the Pembina CO2 injection project in Canada. We show that the exchange of carbon isotopes between dissolved and gaseous carbon species combined with fluid flow and transport, produce isotopic effects that are significantly different from simple two-component mixing. These effects are important for understanding the isotopic variations observed in field demonstrations.

  10. Modeling Np and Pu transport with a surface complexation model and spatially variant sorption capacities: implications for reactive transport modeling and performance assessments of nuclear waste disposal sites

    NASA Astrophysics Data System (ADS)

    Glynn, Pierre D.

    2003-04-01

    One-dimensional (1D) geochemical transport modeling is used to demonstrate the effects of speciation and sorption reactions on the ground-water transport of Np and Pu, two redox-sensitive elements. Earlier 1D simulations (Reardon, 1981) considered the kinetically limited dissolution of calcite and its effect on ion-exchange reactions (involving 90Sr, Ca, Na, Mg and K), and documented the spatial variation of a 90Sr partition coefficient under both transient and steady-state chemical conditions. In contrast, the simulations presented here assume local equilibrium for all reactions, and consider sorption on constant potential, rather than constant charge, surfaces. Reardon's (1981) seminal findings on the spatial and temporal variability of partitioning (of 90Sr) are reexamined and found partially caused by his assumption of a kinetically limited reaction. In the present work, sorption is assumed the predominant retardation process controlling Pu and Np transport, and is simulated using a diffuse-double-layer-surface-complexation (DDLSC) model. Transport simulations consider the infiltration of Np- and Pu-contaminated waters into an initially uncontaminated environment, followed by the cleanup of the resultant contamination with uncontaminated water. Simulations are conducted using different spatial distributions of sorption capacities (with the same total potential sorption capacity, but with different variances and spatial correlation structures). Results obtained differ markedly from those that would be obtained in transport simulations using constant Kd, Langmuir or Freundlich sorption models. When possible, simulation results (breakthrough curves) are fitted to a constant Kd advection-dispersion transport model and compared. Functional differences often are great enough that they prevent a meaningful fit of the simulation results with a constant Kd (or even a Langmuir or Freundlich) model, even in the case of Np, a weakly sorbed radionuclide under the simulation

  11. Modeling Np and Pu Transport with a Surface Complexation Model and Spatially Variant Sorption Capacities: Implications for Reactive Transport Modeling and Performance Assessments of Nuclear Waste Disposal Sites

    NASA Astrophysics Data System (ADS)

    Glynn, P. D.

    2002-12-01

    One-dimensional (1D) geochemical transport modeling is used to demonstrate the effects of speciation and sorption reactions on the ground-water transport of Np and Pu, two redox-sensitive elements. Earlier 1D simulations (Reardon, 1981) considered the kinetically-limited dissolution of calcite and its effect on ion-exchange reactions (involving 90Sr, Ca, Na, Mg and K), and documented the spatial variation of a 90Sr partition coefficient under both transient and steady-state chemical conditions. In contrast, the simulations presented here assume local equilibrium for all reactions, and consider sorption on constant potential, rather than constant charge, surfaces. Reardon's (1981) findings documenting the spatial and temporal variability of 90Sr partitioning are reexamined and found partially caused by his assumption of a kinetically-limited reaction. In the present simulations, sorption is assumed the only retardation process controlling Pu and Np transport, and is modeled using a diffuse-double-layer-surface-complexation model. Transport simulations consider the inflow of Np- and Pu-contaminated waters into an initially uncontaminated environment, followed by the cleanup of the resultant contamination with uncontaminated water. Simulations are conducted using different spatial distributions of sorption capacities (with the same total potential sorption capacity, i.e. the same total number of sorption sites, but with different variances and spatial correlation structures). A case with a spatially uniform distribution of sorption capacities was also simulated. Results obtained differ markedly from those that would be obtained in transport simulations using constant Kd, Langmuir, or Freundlich sorption models. When possible, simulation results (breakthrough curves) are fitted to a constant Kd advection-dispersion transport model and compared to each other. Functional differences are often great enough that they prevent a meaningful fit of the simulation results with

  12. Modeling Np and Pu transport with a surface complexation model and spatially variant sorption capacities: Implications for reactive transport modeling and performance assessments of nuclear waste disposal sites

    USGS Publications Warehouse

    Glynn, P.D.

    2003-01-01

    One-dimensional (1D) geochemical transport modeling is used to demonstrate the effects of speciation and sorption reactions on the ground-water transport of Np and Pu, two redox-sensitive elements. Earlier 1D simulations (Reardon, 1981) considered the kinetically limited dissolution of calcite and its effect on ion-exchange reactions (involving 90Sr, Ca, Na, Mg and K), and documented the spatial variation of a 90Sr partition coefficient under both transient and steady-state chemical conditions. In contrast, the simulations presented here assume local equilibrium for all reactions, and consider sorption on constant potential, rather than constant charge, surfaces. Reardon's (1981) seminal findings on the spatial and temporal variability of partitioning (of 90Sr) are reexamined and found partially caused by his assumption of a kinetically limited reaction. In the present work, sorption is assumed the predominant retardation process controlling Pu and Np transport, and is simulated using a diffuse-double-layer-surface-complexation (DDLSC) model. Transport simulations consider the infiltration of Np- and Pu-contaminated waters into an initially uncontaminated environment, followed by the cleanup of the resultant contamination with uncontaminated water. Simulations are conducted using different spatial distributions of sorption capacities (with the same total potential sorption capacity, but with different variances and spatial correlation structures). Results obtained differ markedly from those that would be obtained in transport simulations using constant Kd, Langmuir or Freundlich sorption models. When possible, simulation results (breakthrough curves) are fitted to a constant K d advection-dispersion transport model and compared. Functional differences often are great enough that they prevent a meaningful fit of the simulation results with a constant K d (or even a Langmuir or Freundlich) model, even in the case of Np, a weakly sorbed radionuclide under the

  13. Developing Sediment Transport and Dredging Prediction Model of Ohio River at Olmsted Locks and Dams Area using HEC-RAS (1D/2D)By Ganesh Raj Ghimire1 and Bruce A. Devantier 2

    NASA Astrophysics Data System (ADS)

    Ghimire, G. R.

    2015-12-01

    Sediment deposition is a serious issue in the construction and operation of large reservoir and inland navigation projects in the United States and around the world. Olmsted Locks and Dams in the Ohio River navigation system is facing similar challenges of huge sediment deposition during the ongoing in-wet construction methodology since 1993. HEC-RAS 5.0 integrated with ArcGIS, will be used to yield unsteady 2D hydrodynamic model of Ohio River at Olmsted area. Velocity, suspended sediment, bed sediment and hydrographic survey data acquired from public archives of USGS and USACE Louisville District will be input into the model. Calibration and validation of model will be performed against the measured stage, flow and velocity data. It will be subjected to completely unsteady 1D sediment transport modeling new to HEC-RAS 5.0 which incorporates sediment load and bed gradation via a DSS file, commercial dredging and BSTEM model. Sediment model will be calibrated to replicate the historical bed volume changes. Excavated cross-sections at Olmsted area will also be used to predict the sediment volume trapped inside the ditch over the period between excavations and placement of dam shells at site. Model will attempt to replicate historical dredging volume data and compare with the deposition volume from simulation model to formulate the dredging prediction model. Hence, the results of this research will generate a model that can form a basis for scheduling the dredging event prior to the placement of off-shore cast shells replacing the current as and when required approach of dredging plan. 1 Graduate Student, Department of Civil Engineering, Southern Illinois University Carbondale Carbondale, Illinois, 62901-6603 2 Professor, Department of Civil Engineering, Southern Illinois University Carbondale Carbondale, Illinois, 62901-6603

  14. Reactive transport modeling of hydrothermal circulation in oceanic crust: effect of anhydrite precipitation on the dynamics of submarine hydrothermal systems

    NASA Astrophysics Data System (ADS)

    Yang, J.

    2009-12-01

    Hydrothermal fluid circulation represents an extremely efficient mechanism for the exchange of heat and matter between seawater and oceanic crust. Precipitation and dissolution of minerals associated with hydrothermal flow at ridge axes can alter the crustal porosity and permeability and hence influence the dynamics of hydrothermal systems. In this study, a fully coupled fluid flow, heat transfer and reactive mass transport model was developed using TOUGHREACT to evaluate the role of mineral precipitation and dissolution on the evolution of hydrothermal flow systems, with a particular attention focused on anhydrite precipitation upon heating of seawater in recharge zones and the resultant change in the crustal porosity and permeability. A series of numerical case studies were carried out to assess the effect of temperature and aqueous phase inflow concentrations on the reactive geochemical system. The impact of chemically induced porosity and permeability changes on the dynamics of hydrothermal systems was also addressed.

  15. Development of Modeling Methods and Tools for Predicting Coupled Reactive Transport Processes in Porous Media at Multiple Scales

    SciTech Connect

    Clement, T Prabhakar; Barnett, Mark O; Zheng, Chunmiao; Jones, Norman L

    2010-05-05

    DE-FG02-06ER64213: Development of Modeling Methods and Tools for Predicting Coupled Reactive Transport Processes in Porous Media at Multiple Scales Investigators: T. Prabhakar Clement (PD/PI) and Mark O. Barnett (Auburn), Chunmiao Zheng (Univ. of Alabama), and Norman L. Jones (BYU). The objective of this project was to develop scalable modeling approaches for predicting the reactive transport of metal contaminants. We studied two contaminants, a radioactive cation [U(VI)] and a metal(loid) oxyanion system [As(III/V)], and investigated their interactions with two types of subsurface materials, iron and manganese oxyhydroxides. We also developed modeling methods for describing the experimental results. Overall, the project supported 25 researchers at three universities. Produced 15 journal articles, 3 book chapters, 6 PhD dissertations and 6 MS theses. Three key journal articles are: 1) Jeppu et al., A scalable surface complexation modeling framework for predicting arsenate adsorption on goethite-coated sands, Environ. Eng. Sci., 27(2): 147-158, 2010. 2) Loganathan et al., Scaling of adsorption reactions: U(VI) experiments and modeling, Applied Geochemistry, 24 (11), 2051-2060, 2009. 3) Phillippi, et al., Theoretical solid/solution ratio effects on adsorption and transport: uranium (VI) and carbonate, Soil Sci. Soci. of America, 71:329-335, 2007

  16. Fringe-controlled biodegradation under dynamic conditions: Quasi 2-D flow-through experiments and reactive-transport modeling

    NASA Astrophysics Data System (ADS)

    Eckert, Dominik; Kürzinger, Petra; Bauer, Robert; Griebler, Christian; Cirpka, Olaf A.

    2015-01-01

    Biodegradation in contaminated aquifers has been shown to be most pronounced at the fringe of contaminant plumes, where mixing of contaminated water and ambient groundwater, containing dissolved electron acceptors, stimulates microbial activity. While physical mixing of contaminant and electron acceptor by transverse dispersion has been shown to be the major bottleneck for biodegradation in steady-state plumes, so far little is known on the effect of flow and transport dynamics (caused, e.g., by a seasonally fluctuating groundwater table) on biodegradation in these systems. Towards this end we performed experiments in quasi-two-dimensional flow-through microcosms on aerobic toluene degradation by Pseudomonas putida F1. Plume dynamics were simulated by vertical alteration of the toluene plume position and experimental results were analyzed by reactive-transport modeling. We found that, even after disappearance of the toluene plume for two weeks, the majority of microorganisms stayed attached to the sediment and regained their full biodegradation potential within two days after reappearance of the toluene plume. Our results underline that besides microbial growth, also maintenance and dormancy are important processes that affect biodegradation performance under transient environmental conditions and therefore deserve increased consideration in future reactive-transport modeling.

  17. Characterization of the specific solid-water interfacial area-water saturation relationship and its import to reactive transport

    SciTech Connect

    Saripalli, Kanaka P.; Freedman, Vicky L.; McGrail, B. Peter; Meyer, Philip D.

    2006-05-01

    A modified rate equation for the dissolution of minerals in the unsaturated zone was proposed using a solid-water interfacial area (asw) varying as a function of water saturation (Sw). Vadose zone phenomena, such as infiltration, were discussed as example scenarios where such re-formulation may be useful. A constitutive relationship for the asw - Sw was derived, and used to formulate an approximate model of the proposed rate equation. Implementation of this new model in the reactive transport code CRUNCH was used to evaluate the influence of a changing asw on reactive transport behavior of silica in the vadose zone. These simulations clearly demonstrate that a changing asw can have a significant impact on the silica distribution profiles in the vadose zone. This is to be expected because changes in asw are substantial in the dry Sw range, whereas they are only moderate in the relatively wet region. These findings have significant implications for contaminant transport in the vadose zone, especially in arid regions. Ignoring the effect of a changing asw is likely to result in an overestimation of the net contaminant fluxes in these cases, which leads to highly conservative risk assessments. In case of nutrient flux calculations coupled with dissolution phenomena, it may lead to an overestimation of nutrient availability. Additional theoretical and experimental verification of the proposed models would be valuable.

  18. Large-Eddy Simulation of Chemically Reactive Pollutant Transport from a Point Source in Urban Area

    NASA Astrophysics Data System (ADS)

    Du, Tangzheng; Liu, Chun-Ho

    2013-04-01

    Most air pollutants are chemically reactive so using inert scalar as the tracer in pollutant dispersion modelling would often overlook their impact on urban inhabitants. In this study, large-eddy simulation (LES) is used to examine the plume dispersion of chemically reactive pollutants in a hypothetical atmospheric boundary layer (ABL) in neutral stratification. The irreversible chemistry mechanism of ozone (O3) titration is integrated into the LES model. Nitric oxide (NO) is emitted from an elevated point source in a rectangular spatial domain doped with O3. The LES results are compared well with the wind tunnel results available in literature. Afterwards, the LES model is applied to idealized two-dimensional (2D) street canyons of unity aspect ratio to study the behaviours of chemically reactive plume over idealized urban roughness. The relation among various time scales of reaction/turbulence and dimensionless number are analysed.

  19. Transport of a reactive tracer in saturated alluvium described using a three-component cation-exchange model.

    PubMed

    Sullivan, Enid J; Reimus, Paul W; Counce, Dale A

    2003-01-01

    A weakly sorbing cation, lithium, will be used as a reactive tracer in upcoming field tracer tests in the saturated alluvium south of Yucca Mountain, Nevada. One objective of the field tests is to determine how well field-scale reactive transport can be predicted using transport parameters derived from laboratory experiments. This paper describes several laboratory lithium batch sorption and column transport experiments that were conducted using ground water and alluvium obtained from the site of the planned field tests. In the batch experiments, isotherms were determined over 2.5 orders of magnitude of lithium concentrations, corresponding to the range expected in the field tests. In addition to measuring equilibrium lithium concentrations, concentrations of other cations, namely Na(+), K(+), and Ca(2+), were measured in the batch tests to determine Li(+)-exchangeable equilibria. This information was used in conjunction with alluvium cation exchange capacity measurements to parameterize a three-component cation-exchange model (EQUIL) that describes lithium sorption in the alluvium system. This model was then applied to interpret the transport behavior of lithium ion in saturated alluvium column tests conducted at three different lithium bromide injection concentrations. The concentrations were selected such that lithium ion either dominated, accounted for a little over half, or accounted for only a small fraction of the total cation equivalents in the injection solution. Although tracer breakthrough curves differed significantly under each of these conditions, with highly asymmetric responses occurring at the highest injection concentrations, the three-component cation-exchange model reproduced the observed transport behavior of lithium and the other cations in each case with a similar set of model parameters. In contrast, a linear K(d)-type sorption model could only match the lithium responses at the lowest injection concentration. The three-component model will

  20. Analyzing the impact of reactive transport on the repository performance of TRISO fuel

    NASA Astrophysics Data System (ADS)

    Schmidt, Gregory

    graphite surrounding the spent HTGR fuel will impact the release of aqueous uranium from the TRISO fuel. In order to answer this question, the sorption and partitioning behavior of uranium to graphite under a variety of conditions was investigated. Key systematic variables that were analyzed include solution pH, dissolved carbonate concentration, uranium metal concentration and ionic strength. The kinetics and desorption characteristics of uranium/graphite partitioning were studied as well. The graphite used in these experiments was also characterized by a variety of techniques and conclusions are drawn about the relevant surface chemistry of graphite. This data was then used to generate a model for the reactive transport of uranium in a graphite matrix. This model was implemented with the software code CXTFIT and validated through the use of column studies mirroring the predicted system.

  1. Dynamic Pore-Scale Imaging of Reactive Transport in Heterogeneous Carbonates at Reservior Conditions

    NASA Astrophysics Data System (ADS)

    Menke, Hannah; Bijeljic, Branko; Andrew, Matthew; Blunt, Martin

    2014-05-01

    minor dissolution rate differences between the pores and pore throats. This was not true for the heterogeneous carbonates, Estalliades and Portland Basebed, which formed wormholes. Pore-scale modelling of flow directly on the voxels showed the differences in the evolution of complex flow fields with changes in dissolution regime. The PDFs of normalized velocity for uniform dissolution showed that the maximum pore velocity within the system decreased as dissolution occurred. This is due to dissolution enlarging pores and pore throats. However, in the wormholing regime, there was a large increase in maximum velocity once the wormhole broke through the length of the core and a preferential flow path was created. Additionally, this study serves as a unique benchmark for pore-scale reactive transport modelling directly on the binarized Micro-CT images. This dynamic pore-scale imaging method offers advantages in helping fully explain the dominant physical and chemical processes at the pore scale so that they may be up-scaled to the reservoir scale for increased accuracy in model prediction.

  2. Preparation of a hole transport layer tethered to ITO surface via a self-assembled monolayer with reactive terminal group

    NASA Astrophysics Data System (ADS)

    Hagihara, Yuya; Kim, Seong-Ho; Tanaka, Kuniaki; Advincula, Rigoberto C.; Usui, Hiroaki

    2014-01-01

    Characteristics of a junction between a polymer thin film and an indium-tin oxide (ITO) substrate was controlled by forming covalent chemical bonds at the interface through self-assembled monolayers (SAMs) with reactive terminal groups. For this purpose, SAMs with vinyl, epoxide, and benzophenone terminal groups were formed on ITO substrates, on which a vinyl derivative of a hole transport molecule was vapor-deposited, and then annealed in vacuum. This procedure produced a polymer layer strongly attached to the substrate surface. It was also found that the charge injection from the ITO electrode to the polymer layer can be improved by chemically tethering the interface via the SAMs.

  3. Resonant charge-exchange involving excited helium atoms and reactive transport of local thermodynamic equilibrium helium plasma

    NASA Astrophysics Data System (ADS)

    Kosarim, A. V.; Smirnov, B. M.; Laricchiuta, A.; Capitelli, M.

    2012-06-01

    The cross sections for charge-exchange and charge-transfer processes are evaluated for collisions of helium ions with parent-atoms in ground and excited states, with the principal quantum number n = 1-5, in the collision energy range from thermal up to 10 eV. Corresponding diffusion-type collision integrals are derived, and the role of "abnormal" transport of electronically excited states on the reactive thermal conductivity of equilibrium helium plasma, at atmospheric pressure, estimated in the frame of a simplified approach.

  4. Study of Uranium Transport Utilizing Reactive Numerical Modeling and Experimental Data from Heterogeneous Intermediate-Scale Tanks

    NASA Astrophysics Data System (ADS)

    Rodriguez, D.; Miller, A.; Honeyman, B.

    2007-12-01

    The study of the transport of contaminants in groundwater is critical in order to mitigate risks to downstream receptors from sites where past releases of these contaminants has resulted in the degradation of the water quality of the underlying aquifer. In most cases, the fate and transport of these contaminants occurs in a chemically and physically heterogeneous environment; thereby making the prediction of the ultimate fate of these contaminants difficult. In order to better understand the fundamental processes that have the greatest effect on the transport of these contaminants, careful laboratory study must be completed in a controlled environment. Once the experimental data has been generated, the validation of numerical models may then be achieved. Questions on the management of contaminated sites may center on the long-term release (e.g., desorption, dissolution) behavior of contaminated geomedia. Data on the release of contaminants is often derived from bench-scale experiments or, in rare cases, through field-scale experiments. A central question, however, is how molecular-scale processes (e.g., bond breaking) are expressed at the macroscale. This presentation describes part of a collaborative study between the Colorado School of Mines, the USGS and Lawrence Berkeley National Lab on upscaling pore-scale processes to understanding field-scale observations. In the work described here, two experiments were conducted in two intermediate-scale tanks (2.44 m x 1.22 m x 7.6 cm and 2.44 m x 0.61 m x 7.6 cm) to generate data to quantify the processes of uranium dissolution and transport in fully saturated conditions, and to evaluate the ability of two reactive transport models to capture the relevant processes and predict U behavior at the intermediate scale. Each tank was designed so that spatial samples could be collected from the side of the tank, as well as samples from the effluent end of the tank. The larger tank was packed with a less than 2mm fraction of a

  5. Numerical methods for improving sensitivity analysis and parameter estimation of virus transport simulated using sorptive-reactive processes

    USGS Publications Warehouse

    Barth, G.; Hill, M.C.

    2005-01-01

    Using one- and two-dimensional homogeneous simulations, this paper addresses challenges associated with sensitivity analysis and parameter estimation for virus transport simulated using sorptive-reactive processes. Head, flow, and conservative- and virus-transport observations are considered. The paper examines the use of (1) observed-value weighting, (2) breakthrough-curve temporal moment observations, and (3) the significance of changes in the transport time-step size. The results suggest that (1) sensitivities using observed-value weighting are more susceptible to numerical solution variability, (2) temporal moments of the breakthrough curve are a more robust measure of sensitivity than individual conservative-transport observations, and (3) the transport-simulation time step size is more important than the inactivation rate in solution and about as important as at least two other parameters, reflecting the ease with which results can be influenced by numerical issues. The approach presented allows more accurate evaluation of the information provided by observations for estimation of parameters and generally improves the potential for reasonable parameter-estimation results. ?? 2004 Elsevier B.V. All rights reserved.

  6. 1-D EQUILIBRIUM DISCRETE DIFFUSION MONTE CARLO

    SciTech Connect

    T. EVANS; ET AL

    2000-08-01

    We present a new hybrid Monte Carlo method for 1-D equilibrium diffusion problems in which the radiation field coexists with matter in local thermodynamic equilibrium. This method, the Equilibrium Discrete Diffusion Monte Carlo (EqDDMC) method, combines Monte Carlo particles with spatially discrete diffusion solutions. We verify the EqDDMC method with computational results from three slab problems. The EqDDMC method represents an incremental step toward applying this hybrid methodology to non-equilibrium diffusion, where it could be simultaneously coupled to Monte Carlo transport.

  7. Coupling Sorption to Soil Weathering During Reactive Transport: Impacts of Mineral Transformation and Sorbate Aging on Contaminant Speciation and Mobility

    SciTech Connect

    Chorover, Jon; Mueller, Karl T.; O'Day, Peggy; Serne, R. Jeff; Um, Wooyong; Steefel, Carl

    2006-06-01

    Our work is aimed at developing a predictive-mechanistic understanding of the coupling between mineral weathering from caustic waste release and contaminant (Cs, Sr, I) fate and transport in waste-impacted sediments across space, time and geochemical gradients that encompass the process-level heterogeneity observed at the Hanford DOE site. Our specific objectives are: (1) to assess the molecular-scale mechanisms responsible for time-dependent sequestration of contaminants (Cs, Sr and I) during penetration of waste-induced weathering fronts through sedimentary media; (2) to determine the rate and extent of contaminant release from the sorbed state; (3) to develop a reactive transport model based on molecular mechanisms and macroscopic flow experiments (from (1) and (2)) that accurately simulates adsorption, aging, and desorption at the bench-scale, and that can be applied to--and validated at--field sites such as Hanford.

  8. Final Project Report: Release of aged contaminants from weathered sediments: Effects of sorbate speciation on scaling of reactive transport

    SciTech Connect

    Jon Chorover, University of Arizona; Peggy O'€™Day, University of California, Merced; Karl Mueller, Penn State University; Wooyong Um, Pacific Northwest National Laboratory; Carl Steefel, Lawrence Berkeley National Laboratory

    2012-10-01

    Hanford sediments impacted by hyperalkaline high level radioactive waste have undergone incongruent silicate mineral weathering concurrent with contaminant uptake. In this project, we studied the impact of background pore water (BPW) on strontium, cesium and iodine desorption and transport in Hanford sediments that were experimentally weathered by contact with simulated hyperalkaline tank waste leachate (STWL) solutions. Using those lab-weathered Hanford sediments (HS) and model precipitates formed during nucleation from homogeneous STWL solutions (HN), we (i) provided detailed characterization of reaction products over a matrix of field-relevant gradients in contaminant concentration, PCO2, and reaction time; (ii) improved molecular-scale understanding of how sorbate speciation controls contaminant desorption from weathered sediments upon removal of caustic sources; and (iii) developed a mechanistic, predictive model of meso- to field-scale contaminant reactive transport under these conditions.

  9. The effect of the serotonin transporter polymorphism (5-HTTLPR) on empathic and self-conscious emotional reactivity.

    PubMed

    Gyurak, Anett; Haase, Claudia M; Sze, Jocelyn; Goodkind, Madeleine S; Coppola, Giovanni; Lane, Jessica; Miller, Bruce L; Levenson, Robert W

    2013-02-01

    We examined the relationship between a functional polymorphism of the serotonin transporter gene (5-HTTLPR) and individual differences in emotional reactivity in two laboratory studies. In Study 1, empathic responding and physiological reactivity to viewing films of others in distress were assessed in healthy adults in three age groups. In Study 2, emotional responding to watching oneself in an embarrassing situation was assessed in healthy adults and in patients with neurodegenerative diseases. In Study 1, participants with two short alleles of 5-HTTLPR reported more personal distress and showed higher levels of physiological responses in response to the films than participants with long alleles. In Study 2, participants with two short alleles reported more anger and amusement and displayed more emotional expressive behaviors in response to the embarrassing situation than participants with long alleles. These two findings from diverse samples of participants converge to indicate that individuals who are homozygous for the short allele variant of 5-HTTLPR have greater levels of emotional reactivity in two quite different socially embedded contexts. PMID:22906085

  10. A Reactive-Transport Model Describing Methanogen Growth and Methane Production in Diffuse Flow Vents at Axial Seamount

    NASA Astrophysics Data System (ADS)

    Algar, C. K.

    2015-12-01

    Hydrogenotrophic methanogenesis is an important mode of metabolism in deep-sea hydrothermal vents. Diffuse vent fluids often show a depletion in hydrogen with a corresponding increase in methane relative to pure-mixing of end member fluid and seawater, and genomic surveys show an enrichment in genetic sequences associated with known methanogens. However, because we cannot directly sample the subseafloor habitat where these organisms are living, constraining the size and activity of these populations remains a challenge and limits our ability to quantify the role they play in vent biogeochemistry. Reactive-transport modeling may provide a useful tool for approaching this problem. Here we present a reactive-transport model describing methane production along the flow-path of hydrothermal fluid from its high temperature end-member to diffuse venting at the seafloor. The model is set up to reflect conditions at several diffuse vents in the Axial Seamount. The model describes the growth of the two dominant thermophilic methanogens, Methanothermococcus and Methanocaldococcus, observed at Axial seamount. Monod and Arrhenius constants for Methanothermococcus thermolithotrophicus and Methanocaldococcus jannaschii were obtained for the model using chemostat and bottle experiments at varying temperatures. The model is used to investigate the influence of different mixing regimes on the subseafloor populations of these methanogens. By varying the model flow path length and subseafloor cell concentrations, and fitting to observed hydrogen and methane concentrations in the venting fluid, the subseafloor biomass, fluid residence time, and methane production rate can be constrained.

  11. DNA methylation profiles within the serotonin transporter gene moderate the association of 5-HTTLPR and cortisol stress reactivity

    PubMed Central

    Alexander, N; Wankerl, M; Hennig, J; Miller, R; Zänkert, S; Steudte-Schmiedgen, S; Stalder, T; Kirschbaum, C

    2014-01-01

    The serotonin transporter gene-linked polymorphic region (5-HTTLPR) has been implicated in moderating vulnerability to stress-related psychopathology upon exposure to environmental adversity. A recent meta-analysis suggests a potential biological pathway conveying genotype-dependent stress sensitivity by demonstrating a small, but significant association of 5-HTTLPR and cortisol stress reactivity. An arguably more potent approach to detect larger effects when investigating the 5-HTTLPR stress sensitivity hypothesis is to account for both genetic and epigenetic variation in the serotonin transporter gene (SLC6A4). Here, we applied this approach in an experimental setting. Two hundred healthy adults were exposed to a laboratory stressor (Trier Social Stress Test) and cortisol response patterns were assessed as a function of 5-HTTLPR and DNA methylation profiles in SLC6A4. Specifically, we analyzed 83 CpG sites within a 799-bp promoter-associated CpG island of SLC6A4 using a highly sensitive bisulfite pyrosequencing method. Our results suggest that SLC6A4 methylation levels significantly moderate the association of 5-HTTLPR and cortisol stress reactivity. For individuals displaying low levels of SLC6A4 methylation, the S allele relates to increased cortisol stress reactivity in a dose-dependent fashion accounting for 7–9% of the variance in the endocrine stress response. By contrast, no such effect occurred under conditions of high SLC6A4 methylation, indicating that epigenetic changes may compensate for genotype-dependent differences in stress sensitivity. Studying epigenetic markers may advance gene–en