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Sample records for 1d reactive transport

  1. Mechanisms of 1D crystal growth in reactive vapor transport: indium nitride nanowires.

    PubMed

    Vaddiraju, Sreeram; Mohite, Aditya; Chin, Alan; Meyyappan, M; Sumanasekera, Gamini; Alphenaar, Bruce W; Sunkara, Mahendra K

    2005-08-01

    Indium nitride (InN) nanowire synthesis using indium (In) vapor transport in a dissociated ammonia environment (reactive vapor transport) is studied in detail to understand the nucleation and growth mechanisms involved with the so-called "self-catalysis" schemes. The results show that the nucleation of InN crystal occurs first on the substrate. Later, In droplets are formed on top of the InN crystals because of selective wetting of In onto InN crystals. Further growth via liquid-phase epitaxy through In droplets leads the growth in one dimension (1D), resulting in the formation of InN nanowires. The details about the nucleation and growth aspects within these self-catalysis schemes are rationalized further by demonstrating the growth of heteroepitaxially oriented nanowire arrays on single-crystal substrates and "tree-like" morphologies on a variety of substrates. However, the direct nitridation of In droplets using dissociated ammonia results in the spontaneous nucleation and basal growth of nanowires directly from the In melt surface, which is quite different from the above-mentioned nucleation mechanism with the reactive vapor transport case. The InN nanowires exhibit a band gap of 0.8 eV, whereas the mixed phase of InN and In(2)O(3) nanowires exhibit a peak at approximately 1.9 eV in addition to that at 0.8 eV.

  2. 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.

  3. 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

  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. DNA charge transport: Moving beyond 1D

    NASA Astrophysics Data System (ADS)

    Zhang, Yuqi; Zhang, William B.; Liu, Chaoren; Zhang, Peng; Balaeff, Alexander; Beratan, David N.

    2016-10-01

    Charge transport across novel DNA junctions has been studied for several decades. From early attempts to move charge across DNA double crossover junctions to recent studies on DNA three-way junctions and G4 motifs, it is becoming clear that efficient cross-junction charge migration requires strong base-to-base electronic coupling at the junction, facilitated by favorable pi-stacking. We review recent progress toward the goal of manipulating and controlling charge transport through DNA junctions.

  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. 1D-transport properties of single superconducting lead nanowires

    NASA Astrophysics Data System (ADS)

    Michotte, S.; Mátéfi-Tempfli, S.; Piraux, L.

    2003-09-01

    We report on the transport properties of single superconducting lead nanowires grown by an electrodeposition technique, embedded in a nanoporous track-etched polymer membrane. The nanowires are granular, have uniform diameter of ∼40 nm and a very large aspect ratio (∼500). The diameter of the nanowire is small enough to ensure a 1D superconducting regime in a wide temperature range below Tc. The non-zero resistance in the superconducting state and its variation caused by fluctuations of the superconducting order parameter were measured versus temperature, magnetic field, and applied DC current (or voltage). The current induced breakdowns in the V- I characteristics may be explained by the formation of phase slip centers. Moreover, DC voltage driven measurements reveal the existence of a new S-shape behavior near the formation of these phase slip centers.

  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. Molecular characterization of zebrafish Oatp1d1 (Slco1d1), a novel organic anion-transporting polypeptide.

    PubMed

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

    2013-11-22

    The organic anion-transporting polypeptide (OATP/Oatp) superfamily includes a group of polyspecific transporters that mediate transport of large amphipathic, mostly anionic molecules across cell membranes of eukaryotes. OATPs/Oatps are involved in the disposition and elimination of numerous physiological and foreign compounds. However, in non-mammalian species, the functional properties of Oatps remain unknown. We aimed to elucidate the role of Oatp1d1 in zebrafish to gain insights into the functional and structural evolution of the OATP1/Oatp1 superfamily. We show that diversification of the OATP1/Oatp1 family occurs after the emergence of jawed fish and that the OATP1A/Oatp1a and OATP1B/Oatp1b subfamilies appeared at the root of tetrapods. The Oatp1d subfamily emerged in teleosts and is absent in tetrapods. The zebrafish Oatp1d1 is similar to mammalian OATP1A/Oatp1a and OATP1B/Oatp1b members, with the main physiological role in transport and balance of steroid hormones. Oatp1d1 activity is dependent upon pH gradient, which could indicate bicarbonate exchange as a mode of transport. Our analysis of evolutionary conservation and structural properties revealed that (i) His-79 in intracellular loop 3 is conserved within OATP1/Oatp1 family and is crucial for the transport activity; (ii) N-glycosylation impacts membrane targeting and is conserved within the OATP1/Oatp1 family with Asn-122, Asn-133, Asn-499, and Asn-512 residues involved; (iii) the evolutionarily conserved cholesterol recognition interaction amino acid consensus motif is important for membrane localization; and (iv) Oatp1d1 is present in dimeric and possibly oligomeric form in the cell membrane. In conclusion, we describe the first detailed characterization of a new Oatp transporter in zebrafish, offering important insights into the functional evolution of the OATP1/Oatp1 family and the physiological role of Oatp1d1.

  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. Roles of TBC1D1 and TBC1D4 in insulin- and exercise-stimulated glucose transport of skeletal muscle

    PubMed Central

    Cartee, Gregory D.

    2014-01-01

    This review focuses on two paralogue Rab GTPase activating proteins known as TBC1D1 Tre-2/BUB2/cdc 1 domain family (TBC1D) 1 and TBC1D4 (also called Akt Substrate of 160 kDa, AS160) and their roles in controlling skeletal muscle glucose transport in response to the independent and combined effects of insulin and exercise. Convincing evidence implicates Akt2-dependent TBC1D4 phosphorylation on T642 as a key part of the mechanism for insulin-stimulated glucose uptake by skeletal muscle. TBC1D1 phosphorylation on several insulin-responsive sites (including T596, a site corresponding to T642 in TBC1D4) does not appear to be essential for in vivo insulin-stimulated glucose uptake by skeletal muscle. In vivo exercise or ex vivo contraction of muscle result in greater TBC1D1 phosphorylation on S237 that is likely to be secondary to increased AMP-activated protein kinase activity and potentially important for contraction-stimulated glucose uptake. Several studies that evaluated both normal and insulin-resistant skeletal muscle stimulated with a physiological insulin concentration after a single exercise session found that greater post-exercise insulin-stimulated glucose uptake was accompanied by greater TBC1D4 phosphorylation on several sites. In contrast, enhanced post-exercise insulin sensitivity was not accompanied by greater insulin-stimulated TBC1D1 phosphorylation. The mechanism for greater TBC1D4 phosphorylation in insulin-stimulated muscles after acute exercise is uncertain, and a causal link between enhanced TBC1D4 phosphorylation and increased post-exercise insulin sensitivity has yet to be established. In summary, TBC1D1 and TBC1D4 have important, but distinct roles in regulating muscle glucose transport in response to insulin and exercise. PMID:25280670

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. Reactivation of cell surface transport in Reticulomyxa.

    PubMed

    Orokos, D D; Bowser, S S; Travis, J L

    1997-01-01

    Granuloreticulosean protists transport particles (e.g., bacteria, algae, and sand grains) along the outer surfaces of their pseudopodia. This cell surface transport plays a vital role in feeding, reproduction, shell construction, and locomotion and can be visualized by the movements of extracellularly adherent polystyrene microspheres (i.e., latex beads). Our videomicroscopic analyses of transport associated with the pseudopodia of Reticulomyxa filosa revealed two distinct types of both intracellular and cell surface transport: (1) saltatory, bidirectional transport of individual or clustered organelles and/or surface-attached particles, and (2) continuous, unidirectional bulk or "resolute" motion of aggregated organelles and/or surface-bound particles. Organelles and surface-attached polystyrene microspheres remained firmly attached to the microtubule cytoskeletons of detergent-extracted pseudopodia. Both saltatory and resolute organelle and surface transport reactivated upon the addition of 0.01-1.0 mM ATP. At 1 mM ATP, the velocities of reactivated saltatory transport were indistinguishable from those observed in vivo. The reactivated transport was microtubule-dependent and was not inhibited by incubation with Ca(2+)-gelsolin under conditions that abolish rhodamine-phalloidin detection of actin filaments. These findings provide further support that both intracellular organelle and membrane surface transport are mediated by a common mechanism, and establish Reticulomyxa as a unique model system to further study the mechanochemistry of cell surface transport in vitro.

  3. 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)

  4. Experimental investigations of heat transport dynamics in a 1D porous medium column

    NASA Astrophysics Data System (ADS)

    Cherubini, Claudia; Pastore, Nicola; Giasi, Concetta I.; Allegretti, Nicoletta M.

    2016-04-01

    A laboratory physical model has been set up to analyse the forced convective flow and the related heat transport dynamics through a 1d porous medium column. In particular, the experiments regard the observation of thermal breakthrough curves obtained through a continuous flow injection in correspondence of eight thermocouple positioned uniformly along a thermally isolated column of porous medium. The experiment has been conducted for different flow rates in order to investigate the critical issues regarding heat transport phenomena such as the influence of non-linear flow regime, the relationship between the thermal dispersion with the flow velocity and the validity of the local thermal equilibrium assumption between the fluid and solid phase. The results emphasize the magnitude of the errors of the commonly used assumptions in the numerical modelling of heat transport.

  5. Long distance transport of ultracold atoms using a 1D optical lattice

    NASA Astrophysics Data System (ADS)

    Schmid, Stefan; Thalhammer, Gregor; Winkler, Klaus; Lang, Florian; Hecker Denschlag, Johannes

    2006-08-01

    We study the horizontal transport of ultracold atoms over macroscopic distances of up to 20 cm with a moving 1D optical lattice. By using an optical Bessel beam to form the optical lattice, we can achieve nearly homogeneous trapping conditions over the full transport length, which is crucial in order to hold the atoms against gravity for such a wide range. Fast transport velocities of up to 6 m s-1 (corresponding to about 1100 photon recoils) and accelerations of up to 2600 m s-2 are reached. Even at high velocities the momentum of the atoms is precisely defined with an uncertainty of less than one photon recoil. This allows for construction of an atom catapult with high kinetic energy resolution, which might have applications in novel collision experiments.

  6. 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.

  7. Fluctuation theory of the coupling between diffusion and reaction in 1D: coalescence with point reactivities

    NASA Astrophysics Data System (ADS)

    Molski, Andrzej

    1996-04-01

    Fluctuation theory of the one-dimensional coalescence of point particles with finite intrinsic reactivity, k0, is presented. For irreversible coalescence, A + A → A, a closed nonclassic rate equation is derived. For reversible coalescence, A + A ⇌ A, the kinetics of relaxation to equilibrium are discussed. For steady states maintained by an external source, S → A, an implicit relation between the input rate and the concentrations is found. An analytic model developed by Ben-Avraham, Burschka and Doering (BBD) [J. Stat. Phys. 60 (1990) 695] is used to test the approximations of the fluctuation theory for the limiting case of infinite intrinsic reactivity, k0 → ∞. Semiquantitative agreement is found between the fluctuation theory and the BBD model except for relaxation to equilibrium. The kinetic relationships between coalescence ( A + A → A) and annihilation ( A + A → 0) predicted by the fluctuation theory coincide with those from the model analytic kinetics.

  8. Transient 1D transport equation simulated by a mixed Green element formulation

    NASA Astrophysics Data System (ADS)

    Taigbenu, Akpofure Efemena; Onyejekwe, Okey Oseloka

    1997-08-01

    New discrete element equations or coefficients are derived for the transient 1D diffusion-advection or transport equation based on the Green element replication of the differential equation using linear elements. The Green element method (GEM), which solves the singular boundary integral theory (a Fredholm integral equation of the second kind) on a typical element, gives rise to a banded global coefficient matrix which is amenable to efficient matrix solvers. It is herein derived for the transient 1D transport equation with uniform and non-uniform ambient flow conditions and in which first-order decay of the containment is allowed to take place. Because the GEM implements the singular boundary integral theory within each element at a time, the integrations are carried out in exact fashion, thereby making the application of the boundary integral theory more utilitarian. This system of discrete equations, presented herein for the first time, using linear interpolating functions in the spatial dimensions shows promising stable characteristics for advection-dominant transport. Three numerical examples are used to demonstrate the capabilities of the method. The second-order-correct Crank-Nicolson scheme and the modified fully implicit scheme with a difference weighting value of two give superior solutions in all simulated examples.

  9. Evaluation of the Transport of Natural Radioactive Materials in Large Lysimeters Using Hydrus-1D

    NASA Astrophysics Data System (ADS)

    Pontedeiro, E.; Cipriani, M.; van Genuchten, M.; Simunek, J.

    2007-12-01

    The mining industry in Brazil often uses raw materials that contain relatively high concentrations of naturally occurring radioactive materials (referred to as NORM). Ores of relatively low grade typically are used to produce refined metals of high purity (e.g., Nb, Ta, Sn, and Au) using pyrometallurgic processes. The final waste is a slag rich in natural radioactive contaminants (the U and Th decay series), which are then usually deposited in industrial landfills. To study the long-term fate and transport of radionuclides leached from the NORM wastes, several large (3 m deep) lysimeters were constructed at the Pocos de Caldas Laboratory of the Brazilian Nuclear Energy Commision (CNEN). The lysimeters were packed with surface soils and slags from one of the mining sites in South East Brazil. Main purpose of our lysimeter experiments was to follow the dissolution and transport of radionuclides from the slags under natural climatic conditions. Leaching rates and radionuclide concentrations of the effluent were observed during a three-year time period. A variety of physical and chemical properties of the soils and slags (including laboratory batch equilibrium sorption values) were also determined. The data were analyzed using several computer software packages, including the STANMOD code for analytical modeling of decay chain transport during steady flow, the HYDRUS-1D code for variably-saturated flow and the transport of multiple solutes, and the HP1 code for a more comprehensive analysis of the geochemistry involved. In this presentation we describe the experimental setup and provide preliminary results of the theoretical analyses, especially those using HYDRUS-1D.

  10. 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.

  11. On a 1D nonlocal transport equation with nonlocal velocity and subcritical or supercritical diffusion

    NASA Astrophysics Data System (ADS)

    Lazar, Omar

    2016-11-01

    We study a 1D transport equation with nonlocal velocity with subcritical or supercritical dissipation. For all data in the weighted Sobolev space Hk (wλ,κ) ∩L∞, where k = max ⁡ (0 , 3 / 2 - α) and wλ,κ is a given family of Muckenhoupt weights, we prove a global existence result in the subcritical case α ∈ (1 , 2). We also prove a local existence theorem for large data in H2 (wλ,κ) ∩L∞ in the supercritical case α ∈ (0 , 1). The proofs are based on the use of the weighted Littlewood-Paley theory, interpolation along with some new commutator estimates.

  12. 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.

  13. Review of existing reactive transport software

    SciTech Connect

    Glassley, W., LLNL

    1998-02-03

    Simulations of thermal and hydrological evolution following the potential emplacement of a subterranean nuclear waste repository at Yucca Mountain, NV provide data that suggest the inevitability of dependent, simultaneous chemical evolution in this system. These chemical changes will modify significantly both the magnitude and structure of local porosity and permeability; hence, they will have a dynamic feedback effect on the evolving thermal and hydrological regime. Yet, despite this intimate interdependence of transport and chemical processes, a rigorous quantitative analysis of the post- emplacement environment that incorporates this critical feedback mechanism has not been completed to date. As an initial step in this direction, the present document outlines the fundamental chemical and transport processes that must be accounted for in such an analysis, and reviews the inventory of existing software that encodes these processed in explicitly coupled form. A companion report describes the prioritization of specific capabilities that are needed for modeling post-emplacement reactive transport at Yucca Mountain.

  14. Mesoscopic Modeling of Reactive Transport Processes

    NASA Astrophysics Data System (ADS)

    Kang, Q.; Chen, L.; Deng, H.

    2012-12-01

    Reactive transport processes involving precipitation and/or dissolution are pervasive in geochemical, biological and engineered systems. Typical examples include self-assembled patterns such as Liesegang rings or bands, cones of stalactites in limestones caves, biofilm growth in aqueous environment, formation of mineral deposits in boilers and heat exchangers, uptake of toxic metal ions from polluted water by calcium carbonate, and mineral trapping of CO2. Compared to experimental studies, a numerical approach enables a systematic study of the reaction kinetics, mass transport, and mechanisms of nucleation and crystal growth, and hence provides a detailed description of reactive transport processes. In this study, we enhance a previously developed lattice Boltzmann pore-scale model by taking into account the nucleation process, and develop a mesoscopic approach to simulate reactive transport processes involving precipitation and/or dissolution of solid phases. The model is then used to simulate the formation of Liesegang precipitation patterns and investigate the effects of gel on the morphology of the precipitates. It is shown that this model can capture the porous structures of the precipitates and can account for the effects of the gel concentration and material. A wide range of precipitation patterns is predicted under different gel concentrations, including regular bands, treelike patterns, and for the first time with numerical models, transition patterns from regular bands to treelike patterns. The model is also applied to study the effect of secondary precipitate on the dissolution of primary mineral. Several types of dissolution and precipitation processes are identified based on the morphology and structures of the precipitates and on the extent to which the precipitates affect the dissolution of the primary mineral. Finally the model is applied to study the formation of pseudomorph. It is demonstrated for the first time by numerical simulation that a

  15. 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.

  16. 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.

  17. 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

  18. Disparate effects of depletion of CD1d-reactive T cells during early versus late stages of disease in a genetically susceptible model of lupus.

    PubMed

    Jacinto, J; Kim, P J; Singh, R R

    2012-04-01

    Some T cells react with lipid antigens bound to antigen-presenting molecule CD1d. Numbers and functions of a subset of such lipid-reactive T cells are reduced in patients with systemic lupus erythematosus (SLE) and their relatives, as well as in genetically susceptible and chemically induced animal models of lupus-like disease. We have reported that the germline deletion of CD1d exacerbates lupus, suggesting a protective role of these cells in the development of lupus. The use of a knockout mouse model in this study, however, did not allow examination of the role of these cells at different stages of disease. Here, we describe an approach to deplete CD1d-dependent T cells, which allowed us to investigate the role of these cells at different stages of disease in genetically lupus-prone NZB/NZW F1 (BWF1) mice. Repeated intravenous injections of large numbers of CD1d-transfected cells resulted in ∼50-75% reduction in these cells, as defined by the expression of CD4, NK1.1 and CD122, and lack of expression of CD62 ligand. TCR γδ (+)NK1.1(+) cells were also reduced in the recipients of CD1d-transfected cells as compared with control recipients. Such depletion of CD1d-reactive T cells in preclinical BWF1 mice resulted in disease acceleration with a significant increase in proteinuria and mortality. In older BWF1 mice having advanced nephritis, however, such depletion of CD1d-reactive T cells resulted in some disease improvement. Taken together, these data as well as our published studies suggest that CD1d-reactive T cells protect against the development of lupus in animal models. However, these cells appear to be unable to suppress established lupus nephritis in these animals, and might even play a disease aggravating role in late stages of disease.

  19. Stability and accuracy of 3D neutron transport simulations using the 2D/1D method in MPACT

    DOE PAGES

    Collins, Benjamin; Stimpson, Shane; Kelley, Blake W.; Young, Mitchell T. H.; Kochunas, Brendan; Graham, Aaron; Larsen, Edward W.; Downar, Thomas; Godfrey, Andrew

    2016-08-25

    We derived a consistent “2D/1D” neutron transport method from the 3D Boltzmann transport equation, to calculate fuel-pin-resolved neutron fluxes for realistic full-core Pressurized Water Reactor (PWR) problems. The 2D/1D method employs the Method of Characteristics to discretize the radial variables and a lower order transport solution to discretize the axial variable. Our paper describes the theory of the 2D/1D method and its implementation in the MPACT code, which has become the whole-core deterministic neutron transport solver for the Consortium for Advanced Simulations of Light Water Reactors (CASL) core simulator VERA-CS. We also performed several applications on both leadership-class and industry-classmore » computing clusters. Results are presented for whole-core solutions of the Watts Bar Nuclear Power Station Unit 1 and compared to both continuous-energy Monte Carlo results and plant data.« less

  20. 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.

  1. 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.

  2. 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...

  3. 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

  4. 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...

  5. 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

  6. 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.

  7. 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.

  8. Reactive and nonreactive quenching of O(1D) by the potent greenhouse gases SO2F2, NF3, and SF5CF3.

    PubMed

    Zhao, Zhijun; Laine, Patrick L; Nicovich, J Michael; Wine, Paul H

    2010-04-13

    A laser flash photolysis-resonance fluorescence technique has been employed to measure rate coefficients and physical vs. reactive quenching branching ratios for O((1)D) deactivation by three potent greenhouse gases, SO(2)F(2)(k(1)), NF(3)(k(2)), and SF(5)CF(3)(k(3)). In excellent agreement with one published study, we find that k(1)(T) = 9.0 x 10(-11) exp(+98/T) cm(3) molecule(-1) s(-1) and that the reactive quenching rate coefficient is k(1b) = (5.8 +/- 2.3) x 10(-11) cm(3) molecule(-1) s(-1) independent of temperature. We find that k(2)(T) = 2.0 x 10(-11) exp(+52/T) cm(3) molecule(-1) s(-1) with reaction proceeding almost entirely (approximately 99%) by reactive quenching. Reactive quenching of O((1)D) by NF(3) is more than a factor of two faster than reported in one published study, a result that will significantly lower the model-derived atmospheric lifetime and global warming potential of NF(3). Deactivation of O((1)D) by SF(5)CF(3) is slow enough (k(3) < 2.0 x 10(-13) cm(3) molecule(-1) s(-1) at 298 K) that reaction with O((1)D) is unimportant as an atmospheric removal mechanism for SF(5)CF(3). The kinetics of O((1)D) reactions with SO(2) (k(4)) and CS(2) (k(5)) have also been investigated at 298 K. We find that k(4) = (2.2 +/- 0.3) x 10(-10) and k(5) = (4.6 +/- 0.6) x 10(-10) cm(3) molecule(-1) s(-1); branching ratios for reactive quenching are 0.76 +/- 0.12 and 0.94 +/- 0.06 for the SO(2) and CS(2) reactions, respectively. All uncertainties reported above are estimates of accuracy (2sigma) and rate coefficients k(i)(T) (i = 1,2) calculated from the above Arrhenius expressions have estimated accuracies of +/- 15% (2sigma).

  9. Quantum transport through disordered 1D wires: Conductance via localized and delocalized electrons

    SciTech Connect

    Gopar, Víctor A.

    2014-01-14

    Coherent electronic transport through disordered systems, like quantum wires, is a topic of fundamental and practical interest. In particular, the exponential localization of electron wave functions-Anderson localization-due to the presence of disorder has been widely studied. In fact, Anderson localization, is not an phenomenon exclusive to electrons but it has been observed in microwave and acoustic experiments, photonic materials, cold atoms, etc. Nowadays, many properties of electronic transport of quantum wires have been successfully described within a scaling approach to Anderson localization. On the other hand, anomalous localization or delocalization is, in relation to the Anderson problem, a less studied phenomenon. Although one can find signatures of anomalous localization in very different systems in nature. In the problem of electronic transport, a source of delocalization may come from symmetries present in the system and particular disorder configurations, like the so-called Lévy-type disorder. We have developed a theoretical model to describe the statistical properties of transport when electron wave functions are delocalized. In particular, we show that only two physical parameters determine the complete conductance distribution.

  10. 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

  11. Impact of water table fluctuations on water flow and solute transport in 1D column systems

    NASA Astrophysics Data System (ADS)

    Rühle, F.; Stumpp, C.

    2012-04-01

    Although hydrological processes and mass fluxes in the unsaturated and saturated zone have been well studied separately, little is known about transition processes between these zones. Since the transition zone is dynamic and varies spatially and temporally with fluctuations of the water table, water flow and solute transport are believed to vary dynamically, too. This may influence the transport and fate of dissolved contaminants and consequently the quality of groundwater. In order to protect and maintain drinking water resources, improved understanding about hydrological processes at the dynamic interface between the unsaturated and saturated zone is needed. The objective of this study was to investigate the impact of water table fluctuations on one-dimensional vertical flow and solute transport in laboratory column systems. Therefore, two flow-through columns were constantly irrigated with groundwater at an infiltration rate of 4.7 cm/d. In one column the water table was kept statically fixed in the middle, in the other column the water table was continually fluctuated by regularly raising and lowering the outflow tube. Several multi-tracer experiments were conducted and compared injecting the tracers bromide, deuterium and 18-oxygen at different water levels. Data modelling was performed with a lumped parameter model to simulate the hydrological fluxes. Our results showed that at static water table and similar water fluxes in both columns, structural heterogeneities due to packing lead to differences in solute transport, e.g. different dispersivity. Tracer breakthrough curves were well simulated with the lumped parameter model indicating that the systems were at steady state. When the water table was fluctuated small differences in solute transport were observed. Even with a fluctuating water table the lumped parameter model yielded high modelling accuracy and indicated that under certain hydrological conditions water table fluctuations lead to slightly

  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. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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)

  1. 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

  2. Analytical Solution for Reactive Solute Transport Considering Incomplete Mixing

    NASA Astrophysics Data System (ADS)

    Bellin, A.; Chiogna, G.

    2013-12-01

    The laboratory experiments of Gramling et al. (2002) showed that incomplete mixing at the pore scale exerts a significant impact on transport of reactive solutes and that assuming complete mixing leads to overestimation of product concentration in bimolecular reactions. We consider here the family of equilibrium reactions for which the concentration of the reactants and the product can be expressed as a function of the mixing ratio, the concentration of a fictitious non reactive solute. For this type of reactions we propose, in agreement with previous studies, to model the effect of incomplete mixing at scales smaller than the Darcy scale assuming that the mixing ratio is distributed within an REV according to a Beta distribution. We compute the parameters of the Beta model by imposing that the mean concentration is equal to the value that the concentration assumes at the continuum Darcy scale, while the variance decays with time as a power law. We show that our model reproduces the concentration profiles of the reaction product measured in the Gramling et al. (2002) experiments using the transport parameters obtained from conservative experiments and an instantaneous reaction kinetic. The results are obtained applying analytical solutions both for conservative and for reactive solute transport, thereby providing a method to handle the effect of incomplete mixing on multispecies reactive solute transport, which is simpler than other previously developed methods. Gramling, C. M., C. F. Harvey, and L. C. Meigs (2002), Reactive transport in porous media: A comparison of model prediction with laboratory visualization, Environ. Sci. Technol., 36(11), 2508-2514.

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. Coupling Flow and Thermal and Reactive Geochemical Transport

    NASA Astrophysics Data System (ADS)

    Yeh, G.

    2004-12-01

    The couplings among fluid flows, thermal transport, geochemical reactions, advective and diffusive transport of solutes in fractured media or soils, and changes in hydraulic properties due to precipitation and dissolution along fractures and rock matrix are important for understanding interplays between fluid flows and dynamic transport processes. This paper describes the development and demonstrative applications of a mechanistic-based numerical model of coupled fluid flow and thermal and reactive geochemical transport, including both fast and slow reactions, in variably saturated media. Theoretical bases, numerical implementations, and two numerical experiments using the model will be presented. 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 geochemical 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.

  9. From conservative to reactive transport under diffusion-controlled conditions

    NASA Astrophysics Data System (ADS)

    Babey, Tristan; de Dreuzy, Jean-Raynald; Ginn, Timothy R.

    2016-05-01

    We assess the possibility to use conservative transport information, such as that contained in transit time distributions, breakthrough curves and tracer tests, to predict nonlinear fluid-rock interactions in fracture/matrix or mobile/immobile conditions. Reference simulated data are given by conservative and reactive transport simulations in several diffusive porosity structures differing by their topological organization. Reactions includes nonlinear kinetically controlled dissolution and desorption. Effective Multi-Rate Mass Transfer models (MRMT) are calibrated solely on conservative transport information without pore topology information and provide concentration distributions on which effective reaction rates are estimated. Reference simulated reaction rates and effective reaction rates evaluated by MRMT are compared, as well as characteristic desorption and dissolution times. Although not exactly equal, these indicators remain very close whatever the porous structure, differing at most by 0.6% and 10% for desorption and dissolution. At early times, this close agreement arises from the fine characterization of the diffusive porosity close to the mobile zone that controls fast mobile-diffusive exchanges. At intermediate to late times, concentration gradients are strongly reduced by diffusion, and reactivity can be captured by a very limited number of rates. We conclude that effective models calibrated solely on conservative transport information like MRMT can accurately estimate monocomponent kinetically controlled nonlinear fluid-rock interactions. Their relevance might extend to more advanced biogeochemical reactions because of the good characterization of conservative concentration distributions, even by parsimonious models (e.g., MRMT with 3-5 rates). We propose a methodology to estimate reactive transport from conservative transport in mobile-immobile conditions.

  10. EFFECTS OF INCOMPLETE MIXING ON MULTICOMPONENT REACTIVE TRANSPORT

    SciTech Connect

    Tartakovsky, Alexandre M.; Tartakovsky, Guzel D.; Scheibe, Timothy D.

    2009-09-06

    Darcy scale description of multi-component reactive transport can significantly over-predict the extent of mixing-controlled reactions. In this letter we describe a systematic pore- and Darcy-scale study of multicomponent reactive transport for various Peclet ($Pe$) and Damkohler ($Da$) numbers. We used pore-scale models to parameterize and validate Darcy scale simulations. We found that for small $Pe$, the Darcy scale model of mixing-controlled reactions is accurate, but its accuracy deteriorates with increasing $Pe$. The dilution index was calculated based on the pore-scale simulations as a measure of the degree of true solute mixing (dilution) for different $Pe$. We found that true mixing decreases with increasing $Pe$. A strong correlation was found between the magnitude of the dilution index and the error in the Darcy scale model prediction. The error (over-prediction of the mass of a product of the mixing controlled reaction) increases with decreasing dilution index (reduced dilution).

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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

  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.

  19. Bed-load transport modelling by coupling an empirical routing scheme and a hydrological-1-D-hydrodynamic model - case study application for a large alpine valley

    NASA Astrophysics Data System (ADS)

    Gems, B.; Achleitner, S.; Plörer, M.; Schöberl, F.; Huttenlau, M.; Aufleger, M.

    2012-12-01

    Sediment transport in mountain rivers and torrents is a substantial process within the assessment of flood related hazard potential and vulnerability in alpine catchments. Focusing on fluvial transport processes, river bed erosion and deposition considerably affects the extent of inundation. The present work deals with scenario-specific bed-load transport modelling in a large alpine valley in the Austrian Alps. A routing scheme founding on empirical equations for the calculation of transport capacities, incipient motion conditions and drag forces is set up and applied to the case study area for two historic flood events. The required hydraulic data result from a distributed hydrological-1-D-hydraulic model. Hydraulics and bed-load transport are simulated sequentially providing a technically well-founded and feasible methodology for the estimation of bed-load transport rates during flood events.

  20. 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.

  1. 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.

  2. Transport of secondary electrons and reactive species in ion tracks

    NASA Astrophysics Data System (ADS)

    Surdutovich, Eugene; Solov'yov, Andrey V.

    2015-08-01

    The transport of reactive species brought about by ions traversing tissue-like medium is analysed analytically. Secondary electrons ejected by ions are capable of ionizing other molecules; the transport of these generations of electrons is studied using the random walk approximation until these electrons remain ballistic. Then, the distribution of solvated electrons produced as a result of interaction of low-energy electrons with water molecules is obtained. The radial distribution of energy loss by ions and secondary electrons to the medium yields the initial radial dose distribution, which can be used as initial conditions for the predicted shock waves. The formation, diffusion, and chemical evolution of hydroxyl radicals in liquid water are studied as well. COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy.

  3. 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

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

    DOE PAGES

    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.

  5. Adaptive Mesh Refinement in Reactive Transport Modeling of Subsurface Environments

    NASA Astrophysics Data System (ADS)

    Molins, S.; Day, M.; Trebotich, D.; Graves, D. T.

    2015-12-01

    Adaptive mesh refinement (AMR) is a numerical technique for locally adjusting the resolution of computational grids. AMR makes it possible to superimpose levels of finer grids on the global computational grid in an adaptive manner allowing for more accurate calculations locally. AMR codes rely on the fundamental concept that the solution can be computed in different regions of the domain with different spatial resolutions. AMR codes have been applied to a wide range of problem including (but not limited to): fully compressible hydrodynamics, astrophysical flows, cosmological applications, combustion, blood flow, heat transfer in nuclear reactors, and land ice and atmospheric models for climate. In subsurface applications, in particular, reactive transport modeling, AMR may be particularly useful in accurately capturing concentration gradients (hence, reaction rates) that develop in localized areas of the simulation domain. Accurate evaluation of reaction rates is critical in many subsurface applications. In this contribution, we will discuss recent applications that bring to bear AMR capabilities on reactive transport problems from the pore scale to the flood plain scale.

  6. 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.

  7. 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%).

  8. ESCRIPT-RT: Reactive transport simulation in PYTHON using ESCRIPT

    NASA Astrophysics Data System (ADS)

    Poulet, T.; Gross, L.; Georgiev, D.; Cleverley, J.

    2012-08-01

    We present ESCRIPT-RT, a new reactive transport simulation code for fully saturated porous media which is based on a finite element method (FEM) combined with three other components: (i) a Gibbs minimisation solver for equilibrium modelling of fluid-rock interactions, (ii) an equation of state for pure water to calculate fluid properties and (iii) a thermodynamically consistent material database to determine rocks' material properties. Using decoupling of most of the standard governing equations, this code solves sequentially for temperature, pressure, mass transport and chemical equilibrium. In contrast, pressure and Darcy flow velocities are solved as a coupled system. The reactive transport itself is performed using the masses of chemical elements instead of chemical species. In such way it requires less computing memory and time than the majority of other packages. The code is based on ESCRIPT, a parallelised platform which supports efficient stepwise simulation of realistic geodynamic scenarios at multiple scales. It is particularly suitable to analyse hydrothermal systems involving geometrically complex geological structures with strong permeability contrasts and subject to complex fluid-rock chemical interactions. The modular architecture of the code and its high level Python interface also provide flexibility for modellers who can easily modify or add new feedbacks between the different physical processes. In addition, the implemented abstract user interface allows geologists to run the code without knowledge of the underlying numerical implementation. As an example we show the simulation of hydrothermal gold precipitation in a granite-greenstone geological sequence, which illustrates the important coupling between thermal response and mass transfer to the localisation of gold.

  9. 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...

  10. Nonlocal reactive transport with physical and chemical heterogeneity: Localization errors

    SciTech Connect

    Cushman, J.H.; Hu, B.X.; Deng, F.W.

    1995-09-01

    The origin of nonlocality in {open_quotes}macroscale{close_quotes} models for subsurface chemical transport is illustrated. It is argued that media that are either nonperiodic (e.g., media with evolving heterogeneity) or periodic viewed on a scale wherein a unit cell is discernible must display some nonlocality in the mean. A metaphysical argument suggests that owing to the scarcity of information on natural scales of heterogeneity and on scales of observation associated with an instrument window, constitutive theories for the mean concentration should at the outset of any modeling effort always be considered nonlocal. The intuitive appeal to nonlocality is reinforced with an analytical derivation of the constitutive theory for a conservative tracer without appeal to any mathematical approximations. Comparisons are made between the fully nonlocal (FNL), nonlocal in time (NLT), and fully localized (FL) theories. For conservative transport, there is little difference between the first-order FL and FNL models for spatial moments up to and including the third. However, for conservative transport the first-order NLT model differs significantly from the FNL model in the third spatial moments. For reactive transport, all spatial moments differ between the FNL and FL models. The second transverse-horizontal and third longitudinal-horizontal moments for the NLT model differ from the FNL model. These results suggest that localized first-order transport models for conservative tracers are reasonable if only lower-order moments are desired. However, when the chemical reacts with its environment, the localization approximation can lead to significant error in all moments, and a FNL model will in general be required for accurate simulation. 18 refs., 9 figs., 1 tab.

  11. 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...

  12. Kinetic theory of transport processes in partially ionized reactive plasma, II: Electron transport properties

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

    The previously obtained in (Zhdanov and Stepanenko, 2016) general transport equations for partially ionized reactive plasma are employed for analysis of electron transport properties in molecular and atomic plasmas. We account for both elastic and inelastic interaction channels of electrons with atoms and molecules of plasma and also the processes of electron impact ionization of neutral particles and three-body ion-electron recombination. The system of scalar transport equations for electrons is discussed and the expressions for non-equilibrium corrections to electron ionization and recombination rates and the diagonal part of the electron pressure tensor are derived. Special attention is paid to analysis of electron energy relaxation during collisions with plasma particles having internal degrees of freedom and the expression for the electron coefficient of inelastic energy losses is deduced. We also derive the expressions for electron vector and tensorial transport fluxes and the corresponding transport coefficients for partially ionized reactive plasma, which represent a generalization of the well-known results obtained by Devoto (1967). The results of numerical evaluation of contribution from electron inelastic collisions with neutral particles to electron transport properties are presented for a series of molecular and atomic gases.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. Glucose transporter type I deficiency (G1D) at 25 (1990–2015): Presumptions, facts and the lives of persons with this rare disease

    PubMed Central

    Pascual, Juan M.; Ronen, Gabriel M.

    2015-01-01

    As is often the case for rare diseases, the number of published reviews and case reports of Glucose transporter type I deficiency (G1D) approaches or exceeds that of original research. This can indicate medical interest, but also scientific stagnation. In assessing this state of affairs here, we focus not on what is peculiar or disparate about G1D, but on the assumptions that have reigned thus far undisputed, and critique them as a potential impediment to progress. To summarize the most common G1D phenotype, we trace the 25-year story of G1D in parallel with the natural history of one of two index patients, identified in 1990 by one of us (G.M.R.) and brought up to date by the other (J.M.P.) while later examining widely-repeated but little-scrutinized statements. Among them are those that pertain to assumptions about brain fuels; energy-failure; cerebrospinal glucose concentration; the purpose of ketogenic diet; the role of the defective blood brain barrier; genotype-phenotype correlations; a bewildering array of phenotypes; ictogenesis, seizures and the electroencephalogram; the use of mice to model the disorder; and what treatments may and may not be expected to accomplish. We reach the forgone conclusion that the proper study of mankind - and of one of its ailments (G1D) - is man itself (rather than mice, isolated cells or extrapolated inferences), and propose a framework for rigorous investigation that we hope will lead to a better understanding and to better treatments for this and for rare disorders in general. These considerations, together with experience drawn from other disorders, lead, as a logical consequence, to the nullification of the view that therapeutic development (i.e., trials) for rare diseases could or should be accelerated without the most vigorous scientific scrutiny: Trial and error constitute an inseparable couple, such that, at the present time, hastening the former is bound to precipitate the latter. PMID:26341673

  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. 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.

  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. Saposins modulate human invariant Natural Killer T cells self-reactivity and facilitate lipid exchange with CD1d molecules during antigen presentation

    PubMed Central

    Salio, Mariolina; Ghadbane, Hemza; Dushek, Omer; Shepherd, Dawn; Cypen, Jeremy; Gileadi, Uzi; Aichinger, Michael C.; Napolitani, Giorgio; Qi, Xiaoyang; van der Merwe, P. Anton; Wojno, Justyna; Veerapen, Natacha; Cox, Liam R.; Besra, Gurdyal S.; Yuan, Weiming; Cresswell, Peter; Cerundolo, Vincenzo

    2013-01-01

    Lipid transfer proteins, such as molecules of the saposin family, facilitate extraction of lipids from biological membranes for their loading onto CD1d molecules. Although it has been shown that prosaposin-deficient mice fail to positively select invariant natural killer T (iNKT) cells, it remains unclear whether saposins can facilitate loading of endogenous iNKT cell agonists in the periphery during inflammatory responses. In addition, it is unclear whether saposins, in addition to loading, also promote dissociation of lipids bound to CD1d molecules. To address these questions, we used a combination of cellular assays and demonstrated that saposins influence CD1d-restricted presentation to human iNKT cells not only of exogenous lipids but also of endogenous ligands, such as the self-glycosphingolipid β-glucopyranosylceramide, up-regulated by antigen-presenting cells following bacterial infection. Furthermore, we demonstrated that in human myeloid cells CD1d-loading of endogenous lipids after bacterial infection, but not at steady state, requires trafficking of CD1d molecules through an endo-lysosomal compartment. Finally, using BIAcore assays we demonstrated that lipid-loaded saposin B increases the off-rate of lipids bound to CD1d molecules, providing important insights into the mechanisms by which it acts as a “lipid editor,” capable of fine-tuning loading and unloading of CD1d molecules. These results have important implications in understanding how to optimize lipid-loading onto antigen-presenting cells, to better harness iNKT cells central role at the interface between innate and adaptive immunity. PMID:24248359

  5. 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.

  6. 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...

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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

  12. Reactive Transport Modeling of Vadose Zone Contamination: Feedback between Reactions and Gas-Phase Transport

    NASA Astrophysics Data System (ADS)

    Molins, S.; Mayer, K.

    2007-05-01

    The unsaturated zone acts as a buffer zone for contaminants on their way to the water table but can also attenuate the emission of contaminants leaving the subsurface environment through the gas phase. A reactive transport model that includes multicomponent gas transport has been developed to investigate the processes that contribute to the generation and attenuation of contaminants in the unsaturated zone. In particular, the model is suitable to study the feedback processes between advective-diffusive gas transport and geochemical reactions. The model is also able to estimate diffusive and advective contributions to gas transport in multicomponent systems. Two model applications are presented that investigate gas transport and reactions in mine tailings and at a site with organic contamination. In mine tailings, atmospheric oxygen transported into the sediment column is consumed in the oxidation of sulfide minerals. Gas volume loss caused by the consumption of atmospheric oxygen drives advective fluxes. In the absence of carbonate minerals, the advective component accounts for 16 % of the net oxygen flux into the column, while, in a carbonate-rich system, advection accounts for 10 % of the net oxygen flux. Dissolution of carbonate minerals has a moderating effect on advective gas transport since carbon dioxide can partially compensate for the depletion of oxygen. At an oil spill site, volatilization and degradation of organic contaminants cause advective and diffusive fluxes of organic vapors away from the source zone. At early stages, volatilization dominates and oxidation of these organic vapors attenuates the emission of contaminants to the atmosphere. The contribution of advection to organic vapor fluxes is significant initially but decreases with time. At later stages, the oil source becomes depleted of its most volatile fraction, and anaerobic degradation of aromatic compounds and heavier n-alkanes results in the production of methane. Up to 15 % of methane

  13. Measurement and modeling of engineered nanoparticle transport and aging dynamics in a reactive porous medium

    NASA Astrophysics Data System (ADS)

    Naftaly, Aviv; Dror, Ishai; Berkowitz, Brian

    2016-07-01

    A continuous time random walk particle tracking (CTRW-PT) method was employed to model flow cell experiments that measured transport of engineered nanoparticles (ENPs) in a reactive porous medium. The experiments involved a water-saturated medium containing negatively charged, polyacrylamide beads, resembling many natural soils and aquifer materials, and having the same refraction index as water. Negatively and positively charged ENPs were injected into a uniform flow field in a 3-D horizontal flow cell, and the spatial and temporal concentrations of the evolving ENP plumes were obtained via image analysis. As a benchmark, and to calibrate the model, Congo red tracer was employed in 1-D column and 3-D flow cell experiments, containing the same beads. Negatively charged Au and Ag ENPs demonstrated migration patterns resembling those of the tracer but were slightly more dispersive; the transport was well represented by the CTRW-PT model. In contrast, positively charged AgNPs displayed an unusual behavior: establishment of an initial plume of essentially immobilized ENPs, followed by development of a secondary, freely migrating plume. The mobile plume was found to contain ENPs that, with aging, exhibited aggregation and charge inversion, becoming negatively charged and mobile. In this case, the CTRW-PT model was modified to include a probabilistic law for particle immobilization, to account for the decreasing tendency (over distance and time) of the positively charged AgNPs to attach to the porous medium. The agreement between experimental results and modeling suggests that the CTRW-PT framework can account for the non-Fickian and surface-charge-dependent transport and aging exhibited by ENPs in porous media.

  14. 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

  15. 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.

  16. 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

  17. Quasi steady-states, spin statistics, and interaction-induced transport of ultra-cold atoms in 1D optical lattices

    NASA Astrophysics Data System (ADS)

    Chien, Chih-Chun; Zwolak, Michael; di Ventra, Massimiliano

    2012-02-01

    We consider several non-equilibrium scenarios where ultra-cold atoms are initially loaded into the ground state of a 1D optical lattice. The system is then set out of equilibrium either by inducing a density imbalance or by imposing time-dependent inhomogeneous interactions. To monitor the dynamics, we have implemented the micro-canonical approach to transport [1] which has been previously used to study electron dynamics in nanoscale systems. We have found that by removing particles on the right half of the lattice, fermions form a quasi steady-state current, which can be observed as a plateau in the current as a function of time. In contrast, the bosonic current oscillates and decays to zero in the thermodynamic limit [2]. The difference appears in uniform lattices as well as lattices with a harmonic trap. Further, when light-induced interactions are applied to half of the lattice, we have found, using a Hartree-Fock approximation, a conducting-nonconducting transition in the fermionic case as the interaction increases. Our studies are relevant to recent experiments on transport of ultra-cold atoms and address fundamental issues in nanoscale electronic transport. [4pt] [1] Di Ventra and Todorov,J. Phys. Cond. Matt. 16, 8025 (2004).[0pt] [2] Chien, Zwolak, Di Ventra, arXiv: 1110.1646.

  18. 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...

  19. 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...

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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%.

  5. 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%.

  6. Reactive Transport Modeling of the Yucca Mountain Site, Nevada

    SciTech Connect

    G. Bodvarsson

    2004-04-20

    The Yucca Mountain site has a dry climate and deep water table, with the repository located in the middle of an unsaturated zone approximately 600 m thick. Radionuclide transport processes from the repository to the water table are sensitive to the unsaturated zone flow field, as well as to sorption, matrix diffusion, radioactive decay, and colloid transport mechanisms. The unsaturated zone flow and transport models are calibrated against both physical and chemical data, including pneumatic pressure, liquid saturation, water potential, temperature, chloride, and calcite. The transport model predictions are further compared with testing specific to unsaturated zone transport: at Alcove 1 in the Exploratory Studies Facility (ESF), at Alcove 8 and Niche 3 of the ESF, and at the Busted Butte site. The models are applied to predict the breakthroughs at the water table for nonsorbing and sorbing radionuclides, with faults shown as the important paths for radionuclide transport. Daughter products of some important radionuclides, such as {sup 239}Pu and {sup 241}Am, have faster transport than the parents and must be considered in the unsaturated zone transport model. Colloid transport is significantly affected by colloid size, but only negligibly affected by lunetic declogging (reverse filtering) mechanisms. Unsaturated zone model uncertainties are discussed, including the sensitivity of breakthrough to the active fracture model parameter, as an example of uncertainties related to detailed flow characteristics and fracture-matrix interaction. It is expected that additional benefits from the unsaturated zone barrier for transport can be achieved by full implementation of the shadow zone concept immediately below the radionuclide release points in the waste emplacement drifts.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. Reactive transport modeling in fractured rock: A state-of-the-science review

    NASA Astrophysics Data System (ADS)

    MacQuarrie, Kerry T. B.; Mayer, K. Ulrich

    2005-10-01

    The field of reactive transport modeling has expanded significantly in the past two decades and has assisted in resolving many issues in Earth Sciences. Numerical models allow for detailed examination of coupled transport and reactions, or more general investigation of controlling processes over geologic time scales. Reactive transport models serve to provide guidance in field data collection and, in particular, enable researchers to link modeling and hydrogeochemical studies. In this state-of-science review, the key objectives were to examine the applicability of reactive transport codes for exploring issues of redox stability to depths of several hundreds of meters in sparsely fractured crystalline rock, with a focus on the Canadian Shield setting. A conceptual model of oxygen ingress and redox buffering, within a Shield environment at time and space scales relevant to nuclear waste repository performance, is developed through a review of previous research. This conceptual model describes geochemical and biological processes and mechanisms materially important to understanding redox buffering capacity and radionuclide mobility in the far-field. Consistent with this model, reactive transport codes should ideally be capable of simulating the effects of changing recharge water compositions as a result of long-term climate change, and fracture-matrix interactions that may govern water-rock interaction. Other aspects influencing the suitability of reactive transport codes include the treatment of various reaction and transport time scales, the ability to apply equilibrium or kinetic formulations simultaneously, the need to capture feedback between water-rock interactions and porosity-permeability changes, and the representation of fractured crystalline rock environments as discrete fracture or dual continuum media. A review of modern multicomponent reactive transport codes indicates a relatively high-level of maturity. Within the Yucca Mountain nuclear waste disposal

  15. 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

  16. 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.

  17. Geochemical & Physical Aquifer Property Heterogeneity: A Multiscale Sedimentologic Approach to Reactive Solute Transport

    SciTech Connect

    Murray, Chris; Allen-King, Richelle; Weissmann, Gary

    2006-06-01

    This project is testing the hypothesis that sedimentary lithofacies determine the geochemical and physical hydrologic properties that control reactive solute transport (Figure 1). We are testing that hypothesis for one site, a portion of the saturated zone at the Hanford Site (Ringold Formation), and for a model solute, carbon tetrachloride (CT). The representative geochemical and physical aquifer properties selected for quantification in the proposed project are the properties that control CT transport: hydraulic conductivity (K) and reactivity (sorption distribution coefficient, Kd, and anaerobic transformation rate constant, kn). We are combining observations at outcrop analog sites (to measure lithofacies dimensions and statistical relations) with measurements from archived and fresh core samples (for geochemical experiments and to provide additional constraint to the stratigraphic model) from the Ringold Formation to place local-scale lithofacies successions, and their distinct hydrologic property distributions, into the basinal context, thus allowing us to estimate the spatial distributions of properties that control reactive solute transport in the subsurface.

  18. 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.

  19. Pore scale to flood plain scale modeling of reactive transport processes

    NASA Astrophysics Data System (ADS)

    Steefel, C.; Molins, S.; Andre, B.; Trebotich, D.; Shen, C.; Landrot, G.; Maxwell, R. M.

    2012-12-01

    Reactive transport processes operate at a wide variety of scales in the subsurface, although modeling these across the scales remains a challenge. The need to treat reactive transport processes across scales is necessary because of the hierarchical nature of porous media in the subsurface, with physical, chemical, and potentially microbial heterogeneities present all the way from the pore to flood plain (watershed) or reservoir scale. The need to address the hierarchical nature of subsurface porous media is particularly important for resolving the long-standing "discrepancy" between laboratory and field rates, which are likely due at least in part to the development of gradients in concentration and thus reaction rate at all scales of heterogeneity. The huge range in modeling scales (microns to kilometers) are a computational challenge, but so is the need to consider differing constitutive equations, for example Navier-Stokes versus Darcy flow equations, or explicitly resolved mineral-microbe-fluid interfaces versus volume-averaged reactive surface areas, at the differing scales. Pore scale processes focusing on carbonate dissolution and precipitation are addressed by solving the Navier-Stokes or Stokes equation for flow at the pore scale coupled to reactive transport calculations in which the interfacial area for mineral dissolution and precipitation is taken directly from the pore geometry. Partial or complete diffusion control of reaction rates is accounted for directly by resolving velocity gradients in the vicinity of reactive mineral grains. Hydrologic accessibility of reactive surface area is also accounted for in this approach, although in general this is an additional factor that needs to be factored into simulations of reactive transport in volume-averaged porous media. At a scale above the pore scale, we use volume-averaged micro-continuum models to address reactivity and transport at the centimeter scale using a sample from the Cranfield formation in

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. Reactive Transport in a Pipe in Soluble Rock: a Theoretical and Experimental Study

    NASA Astrophysics Data System (ADS)

    Li, W.; Opolot, M.; Sousa, R.; Einstein, H. H.

    2015-12-01

    Reactive transport processes within the dominant underground flow pathways such as fractures can lead to the widening or narrowing of rock fractures, potentially altering the flow and transport processes in the fractures. A flow-through experiment was designed to study the reactive transport process in a pipe in soluble rock to serve as a simplified representation of a fracture in soluble rock. Assumptions were made to formulate the problem as three coupled, one-dimensional partial differential equations: one for the flow, one for the transport and one for the radius change due to dissolution. Analytical and numerical solutions were developed to predict the effluent concentration and the change in pipe radius. The positive feedback of the radius increase is captured by the experiment and the numerical model. A comparison between the experiment and the simulation results demonstrates the validity of the analytical and numerical models.

  6. 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

  7. 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

  8. 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.

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

    PubMed

    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 CO(2) and/or H(2)S in geological formations. Potential applications are geological sequestration of CO(2) 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.

  10. 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.

  11. 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

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

    DOE PAGES

    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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. ParFlow.RT: Development and Verification of a New Reactive Transport Model

    NASA Astrophysics Data System (ADS)

    Beisman, J. J., III

    2015-12-01

    In natural subsurface systems, total elemental fluxes are often heavily influenced by areas of disproportionately high reaction rates. These pockets of high reaction rates tend to occur at interfaces, such as the hyporheic zone, where a hydrologic flowpath converges with either a chemically distinct hydrologic flowpath or a reactive substrate. Understanding the affects that these highly reactive zones have on the behavior of shallow subsurface systems is integral to the accurate quantification of nutrient fluxes and biogeochemical cycling. Numerical simulations of these systems may be able to offer some insight. To that end, we have developed a new reactive transport model, ParFlow.RT, by coupling the parallel flow and transport code ParFlow with the geochemical engines of both PFLOTRAN and CrunchFlow. The coupling was accomplished via the Alquimia biogeochemistry API, which provides a unified interface to several geochemical codes and allows a relatively simple implementation of advanced geochemical functionality in flow and transport codes. This model uses an operator-splitting approach, where the transport and reaction steps are solved separately. Here, we present the details of this new model, and the results of verification simulations and biogeochemical cycling simulations of the DOE's East River field site outside of Gothic, CO.

  1. Mineralogical compositions of aquifer matrix as necessary initial conditions in reactive contaminant transport models.

    PubMed

    Zhu, C; Burden, D S

    2001-10-01

    Mineralogical compositions and their spatial distributions are important initial conditions for reactive transport modeling. However, popular Kd-based "reactive" transport models only require contaminant concentrations in the pore fluids as initial conditions, and minerals implicitly represent infinite sources and sinks in these models. That situation results in a general neglect of mineralogical characterization in site investigations. This study uses a coupled multi-component reactive mass transport model to predict the natural attenuation of a ground water plume at a uranium mill tailings site in western USA. Numerous ground water geochemistry data are available at this site, but mineralogical data are sketchy. Even given the well-defined pore fluid chemistry, variations of secondary mineral species and mineral abundances in the aquifer resulted in significantly different modeling outcomes. Results show that the amount of calcite in the aquifer determines the distances of plume migration. The possible presence of jurbanite, an aluminum sulfate phase, can store acidity temporarily but cause more severe contamination on a later date. The surfaces of iron oxyhydroxides can store significant amounts of sulfate and protons and serve as a second source for prolonged contamination. These simulations under field conditions illustrate that mineralogical compositions are an essential requirement for accurate prediction of contaminant fate and transport. PMID:11588823

  2. 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.

  3. 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.

  4. Reactive Transport Modelling By Using Euleria-Lagrangian Methods Based on Mixing

    NASA Astrophysics Data System (ADS)

    soler Sagarra, J.; Nardi, A.; Saaltink, M.; Carrera, J.

    2014-12-01

    Reactive transport use to be a complicated problem by the difficulty of finding a universal numerical method, which reproduces the natural behaviour. Eulerian methods provide accurate results, since they give second order convergence, but they require meeting stability conditions that restrict their actual applicability. Eulerian - Lagrangian methods overcome these limitations, but often cause additional mixing by numerical dispersion. This is a particularly serious problem when transport is coupled to fast chemical reactions, whose rate is controlled by mixing. This work proposes an Eulerian-Lagrangià method without numerical dispersion for solving reactive transport based on mixing. The method consists on the construction of a streamline oriented grid such that the transit time between sequential cells remains constant (isochronal mesh). We have tested the method performances in two different cases: 1) Instantaneous point injection with analytical solution and 2) considering an isolated fracture. In both we have compared the proposed method against existing Eulerian and Eulerian-Lagrangian methods. The results confirm that the proposed method is superior to the two existing cases where dispersivities are medium and low, although the method needs additional refinements in mediums with great heterogeneous. In addition, a new reactive transport method has been obtained.

  5. 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.

  6. 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.

  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. 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.

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

    USGS Publications Warehouse

    Johnson, Raymond H.; Tutu, Hlanganani; Brown, Adrian; Figueroa, Linda; Wolkersdorfer, Christian

    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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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-}.

  19. 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.

  20. 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.

  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.

    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.

  2. Stable isotope reactive transport modeling in water-rock interactions during CO2 injection

    NASA Astrophysics Data System (ADS)

    Hidalgo, Juan J.; Lagneau, Vincent; Agrinier, Pierre

    2010-05-01

    Stable isotopes can be of great usefulness in the characterization and monitoring of CO2 sequestration sites. Stable isotopes can be used to track the migration of the CO2 plume and identify leakage sources. Moreover, they provide unique information about the chemical reactions that take place on the CO2-water-rock system. However, there is a lack of appropriate tools that help modelers to incorporate stable isotope information into the flow and transport models used in CO2 sequestration problems. In this work, we present a numerical tool for modeling the transport of stable isotopes in groundwater reactive systems. The code is an extension of the groundwater single-phase flow and reactive transport code HYTEC [2]. HYTEC's transport module was modified to include element isotopes as separate species. This way, it is able to track isotope composition of the system by computing the mixing between the background water and the injected solution accounting for the dependency of diffusion on the isotope mass. The chemical module and database have been expanded to included isotopic exchange with minerals and the isotope fractionation associated with chemical reactions and mineral dissolution or precipitation. The performance of the code is illustrated through a series of column synthetic models. The code is also used to model the aqueous phase CO2 injection test carried out at the Lamont-Doherty Earth Observatory site (Palisades, New York, USA) [1]. References [1] N. Assayag, J. Matter, M. Ader, D. Goldberg, and P. Agrinier. Water-rock interactions during a CO2 injection field-test: Implications on host rock dissolution and alteration effects. Chemical Geology, 265(1-2):227-235, July 2009. [2] Jan van der Lee, Laurent De Windt, Vincent Lagneau, and Patrick Goblet. Module-oriented modeling of reactive transport with HYTEC. Computers & Geosciences, 29(3):265-275, April 2003.

  3. 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)

  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. 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

  6. 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

  7. 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.

  8. 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

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

    PubMed

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

    2007-06-16

    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 N(E) equilibrium reactions and a set of reactive transport equations of M-N(E) 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.

  10. Reactive transport modeling of chromium isotope fractionation during Cr(VI) reduction.

    PubMed

    Jamieson-Hanes, Julia H; Amos, Richard T; Blowes, David W

    2012-12-18

    Chromium isotope fractionation is indicative of mass-transfer processes, such as reduction of Cr(VI) to Cr(III) during groundwater remediation. Laboratory experiments comparing batch and column treatment of Cr(VI) using organic carbon suggest that the associated isotope fractionation may be influenced by solute-transport mechanisms. These batch and column experiments were simulated using the reactive transport model MIN3P to further evaluate the effects of Cr reduction and transport on isotope fractionation under saturated flow conditions. Simulation of the batch experiment provided a good fit to the experimental data, where a fractionation factor (α₅₃) of 0.9965 was attributed to a single, dominant Cr(VI) removal mechanism. Calibration of the column simulations to the experimental results suggested the presence of a second, more rapid Cr(VI) removal mechanism with α₅₃ = 0.9992. Results from this study demonstrate that the interpretation of Cr isotope fractionation during reduction can be complex, particularly where multiple removal mechanisms are evident. Reactive transport modeling of Cr isotope fractionation can provide a quantitative assessment of the contaminant removal mechanisms, thus improving the application of Cr isotope measurements as a tool to track Cr(VI) migration and attenuation in groundwater.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

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

    PubMed

    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.

  17. 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.

  18. 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.

  19. A solution for multicomponent reactive transport under equilibrium and kinetic reactions

    NASA Astrophysics Data System (ADS)

    Sanchez-Vila, Xavier; Donado, Leonardo David; Guadagnini, Alberto; Carrera, Jesus

    2010-07-01

    Analysis of the space-time evolution of reactive solutes in porous systems is complex owing to the presence of different types of chemical reactions. The complete description of a reactive transport scenario entails calculating the spatial and temporal distribution of species concentrations and reaction rates. Here we develop an exact explicit expression for the space-time distribution of reaction rates for a scenario where the geochemical system can be described by an arbitrary number of equilibrium (fast) reactions and one kinetic (slow) reaction, in the absence of non-constant-activity immobile species. The key result is that the equilibrium reaction rate is the sum of two terms representing the availability of reactants. One term involves diffusion and dispersion and represents the contribution of mixing. The other term includes the contribution of the kinetic reaction. The approach also yields the local concentrations of all dissolved species. Yet the latter are not needed for the direct computation of equilibrium reaction rates. We illustrate the approach by means of a simple reactive transport scenario, involving a common ion effect in the presence of a kinetic and an equilibrium reaction leading to precipitation and dissolution processes within a one-dimensional fully saturated porous medium. The example highlights the highly nonlinear and nonmonotonic response of the system to the controlling input parameters.

  20. 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.

  1. A parametric transfer function methodology for analyzing reactive transport in nonuniform flow.

    PubMed

    Luo, Jian; Cirpka, Olaf A; Fienen, Michael N; Wu, Wei-min; Mehlhorn, Tonia L; Carley, Jack; Jardine, Philip M; Criddle, Craig S; Kitanidis, Peter K

    2006-02-01

    We analyze reactive transport during in-situ bioremediation in a nonuniform flow field, involving multiple extraction and injection wells, by the method of transfer functions. Gamma distributions are used as parametric models of the transfer functions. Apparent parameters of classical transport models may be estimated from those of the gamma distributions by matching temporal moments. We demonstrate the method by application to measured data taken at a field experiment on bioremediation conducted in a multiple-well system in Oak Ridge, TN. Breakthrough curves (BTCs) of a conservative tracer (bromide) and a reactive compound (ethanol) are measured at multi-level sampling (MLS) wells and in extraction wells. The BTCs of both compounds are jointly analyzed to estimate the first-order degradation rate of ethanol. To quantify the tracer loss, we compare the approaches of using a scaling factor and a first-order decay term. Results show that by including a scaling factor both gamma distributions and inverse-Gaussian distributions (transfer functions according to the advection-dispersion equation) are suitable to approximate the transfer functions and estimate the reactive rate coefficients for both MLS and extraction wells. However, using a first-order decay term for tracer loss fails to describe the BTCs at the extraction well, which is affected by the nonuniform distribution of travel paths.

  2. Modeling reactive transport of organic compounds in groundwater using a partial redox disequilibrium approach

    NASA Astrophysics Data System (ADS)

    McNab, W. W.; Narasimhan, T. N.

    1994-09-01

    The chemical transformation of organic contaminants in natural groundwater systems is clearly dependent upon local geochemistry which determines the thermodynamically favorable degradation reactions and the nature of local microbial populations. Conversely, groundwater geochemistry may be impacted significantly in terms of pH and redox couple speciation by the chemical transformation of sufficient quantities of organic compounds. Therefore an understanding of the coupling between degradation reactions, local geochemistry, and chemical transport is essential in predicting the chemical evolution of contaminated aquifers. Equilibrium-based reactive chemical transport models are usually not utilized for problems involving the transport of degradable organic compounds due to slow reaction kinetics and the persistence of intermediate degradation products. In this study we propose a reactive geochemical transport model which considers these types of degradation reactions. An expert system approach is used to postulate a set of sequential, first-order degradation reactions for the organic compounds based upon thermodynamic considerations and user-defined rules. Redox disequilibrium provides the driving force for the abiotic or microbially mediated transformation of the organic compounds as well as the associated response of groundwater geochemistry. Coupling between local inorganic geochemistry and reacting organic compounds is achieved by assuring conservation of operational valence and mass balance. The composite geochemical model is in turn coupled with an integral finite difference transport algorithm using a two-step sequential solution approach. The transport equation is solved separately for each inorganic aqueous species, complex, and dissolved organic species, allowing a high degree of flexibility in problem definition. We apply the model to an illustrative example problem concerning the introduction of aromatic hydrocarbons and chlorinated ethenes into an

  3. Modeling reactive transport of organic compounds in groundwater using a partial redox disequilibrium approach

    SciTech Connect

    McNab, W.W. Jr.; Narasimhan, T.N. )

    1994-09-01

    The chemical transformation of organic contaminants in natural groundwater systems is clearly dependent upon local geochemistry which determines the thermodynamically favorable degradation reactions and the nature of local microbial populations. Conversely, groundwater geochemistry may be impacted significantly in terms of pH and redox couple speciation by the chemical transformation of sufficient quantities of organic compounds. Therefore an understanding of the coupling between degradation reactions, local geochemistry, and chemical transport is essential in predicting the chemical evolution of contaminated aquifers. Equilibrium-based reactive chemical transport models are usually not utilized for problems involving the transport of degradable organic compounds due to slow reaction kinetics and the persistence of intermediate degradation products. In this study we propose a reactive geochemical transport model which considers these types of degradation reactions. An expert system approach is used to postulate a set of sequential, first-order degradation reactions for the organic compounds based upon thermodynamic considerations and user-defined rules. Redox disequilibrium provides the driving force for the abiotic or microbially mediated transformation of the organic compounds as well as the associated response of groundwater geochemistry. Coupling between local inorganic geochemistry and reacting organic compounds is achieved by assuring conservation of operation valence and mass balance. The composite geochemical model is in turn coupled with an integral finite difference transport algorithm using a two-step sequential solution approach. The transport equation is solved separately for each inorganic aqueous species, complex, and dissolved organic species, allowing degree of flexibility in problem definition. 58 refs., 18 figs., 2 tabs.

  4. 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.

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

    PubMed

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

    2006-11-20

    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. PMID:16844261

  6. Reactive iron transport in an acidic mountain stream in Summit County, Colorado: A hydrologic perspective

    USGS Publications Warehouse

    McKnight, Diane M.; Bencala, K.E.

    1989-01-01

    A pH perturbation experiment was conducted in an acidic, metal-enriched, mountain stream to identify relative rates of chemical and hydrologic processes as they influence iron transport. During the experiment the pH was lowered from 4.2 to 3.2 for three hours by injection of sulfuric acid. Amorphous iron oxides are abundant on the streambed, and dissolution and photoreduction reactions resulted in a rapid increase in the dissolved iron concentration. The increase occurred simultaneously with the decrease in pH. Ferrous iron was the major aqueous iron species. The changes in the iron concentration during the experiment indicate that variation exists in the solubility properties of the hydrous iron oxides on the streambed with dissolution of at least two compartments of hydrous iron oxides contributing to the iron pulse. Spatial variations of the hydrologic properties along the stream were quantified by simulating the transport of a coinjected tracer, lithium. A simulation of iron transport, as a conservative solute, indicated that hydrologie transport had a significant role in determining downstream changes in the iron pulse. The rapidity of the changes in iron concentration indicates that a model based on dynamic equilibrium may be adequate for simulating iron transport in acid streams. A major challenge for predictive solute transport models of geochemical processes may be due to substantial spatial and seasonal variations in chemical properties of the reactive hydrous oxides in such streams, and in the physical and hydrologic properties of the stream. ?? 1989.

  7. Coupled Geochemical and Reactive Transport Modeling of Organic Contaminants in a Pyrite-Rich Aquifer

    NASA Astrophysics Data System (ADS)

    Sarioglu, S. M.; Copty, N. K.

    2004-12-01

    Although pH is recognized as a key factor influencing bacterial activity, existing groundwater transport models generally do not directly account for the effect of pH on the biodegradation of organic compounds. The purpose of this study is to develop a coupled reactive transport and geochemical model that explicitly incorporates the effect of spatial and temporal variations of the pH on the biodegradation of organic contaminants. The model consists of two modules: a transport module and a geochemical module. The transport module uses a Crank-Nicholson finite-difference formulation to solve the groundwater flow and transport equations for the hydrocarbon, dissolved oxygen, microbial mass and all reactive groundwater species influencing the hydrocarbon biodegradation and pH distribution. The geochemical module allows for the simulation of both kinetically defined as well as geochemical equilibrium reactions. The governing non-linear system of equations is solved using an iterative multi-step operator-splitting algorithm. Both modules account for heterogeneity in the definition of the hydrogeological and biochemical parameters. For demonstration, the model is applied to a hypothetical pyrite-rich aquifer contaminated with petroleum hydrocarbons. A commonly used practice for the remediation of aquifers contaminated with petroleum hydrocarbons is the delivery of oxygen for the enhanced aerobic biodegradation of the organic contaminant. However, the presence of pyrite may interfere with the intended purpose of the supplied oxygen, leading to undesirable side effects. Specifically, oxygen readily reacts with the sulfide minerals leading to depletion of oxygen and acidification of the subsurface environment and, subsequently, the inadvertent inhibition of the microbial activity. The developed coupled geochemical and reactive transport model is used to quantify these processes and assess the dominance of the various chemical reactions. Both abiotic and biotic pyrite

  8. A Practical Upscaling of Mixing-Limited Reactive Transport Using the Concept of Lamellae.

    NASA Astrophysics Data System (ADS)

    Ginn, T. R.; Le Borgne, T.; Nassar, M.; Bennethum, L. S.; Dentz, M.

    2014-12-01

    Understanding reactive transport of solutes in porous media underlies problems ranging from in-situ remediation or natural attenuation, to quantifying redox processes and/or precipitation rates in natural biogeochemical cycling, to design of geothermal systems. Despite decades of research, we remain essentially unable to predict multicomponent reactive transport in natural porous media. We report on a new approach to upscaling mixing-limited reactive transport, that combines a Lagrangian focus on transport of the moving interface between the mixing solutions, with kinetics of mixing-limitation governed by scalar dissipation rates. We treat the moving interface between reacting solutions as a chain of individual strips, or lamellae, after Ranz, and Villermaux, and upscale mixing-limited reaction extent using the scalar dissipation of an analogous passive solute after de Simoni. Given the statistical description of how the entire set of lamella behave (achievable in principle for any given rendition of a porous media), the problem reduces to one of predicting the reactions on a given lamella as it evolves kinematically due to stretching and diffusion. This simplification reduces much of the complexity while honoring the mixing on the lamella during its advection along with the moving front. The resulting framework for upscaling reaction extent is: a. characterize the deformation of the individual lamellae, b. determine the reaction extent on each one, and c. sum the reaction extents on each lamella to obtain an expression for global reaction extent. We describe details of the development and demonstrate its utility in several idealized problems by comparison to explicit numerical simulation of the reactive transport processes. The Figure below shows a linear flood with flow left-to-right in a 2D heterogeneous flow field,with solution B displacing solution A. The left panel shows influent solution boundary at initial time to as dashed line on left with an individual

  9. 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.

  10. Highly parameterized inversion of groundwater reactive transport for a complex field site.

    PubMed

    Carniato, Luca; Schoups, Gerrit; van de Giesen, Nick; Seuntjens, Piet; Bastiaens, Leen; Sapion, Hans

    2015-02-01

    In this study a numerical groundwater reactive transport model of a shallow groundwater aquifer contaminated with volatile organic compounds is developed. In addition to advective-dispersive transport, the model includes contaminant release from source areas, natural attenuation, abiotic degradation by a permeable reactive barrier at the site, and dilution by infiltrating rain. Aquifer heterogeneity is parameterized using pilot points for hydraulic conductivity, specific yield and groundwater recharge. A methodology is developed and applied to estimate the large number of parameters from the limited data at the field site (groundwater levels, groundwater concentrations of multiple chemical species, point-scale measurements of soil hydraulic conductivity, and lab-scale derived information on chemical and biochemical reactions). The proposed methodology relies on pilot point parameterization of hydraulic parameters and groundwater recharge, a regularization procedure to reconcile the large number of spatially distributed model parameters with the limited field data, a step-wise approach for integrating the different data sets into the model, and high performance computing. The methodology was proven to be effective in reproducing multiple contaminant plumes and in reducing the prior parameter uncertainty of hydraulic conductivity and groundwater recharge. Our results further indicate that contaminant transport predictions are strongly affected by the choice of the groundwater recharge model and flow parameters should be identified using both head and concentration measurements.

  11. Highly parameterized inversion of groundwater reactive transport for a complex field site

    NASA Astrophysics Data System (ADS)

    Carniato, Luca; Schoups, Gerrit; van de Giesen, Nick; Seuntjens, Piet; Bastiaens, Leen; Sapion, Hans

    2015-02-01

    In this study a numerical groundwater reactive transport model of a shallow groundwater aquifer contaminated with volatile organic compounds is developed. In addition to advective-dispersive transport, the model includes contaminant release from source areas, natural attenuation, abiotic degradation by a permeable reactive barrier at the site, and dilution by infiltrating rain. Aquifer heterogeneity is parameterized using pilot points for hydraulic conductivity, specific yield and groundwater recharge. A methodology is developed and applied to estimate the large number of parameters from the limited data at the field site (groundwater levels, groundwater concentrations of multiple chemical species, point-scale measurements of soil hydraulic conductivity, and lab-scale derived information on chemical and biochemical reactions). The proposed methodology relies on pilot point parameterization of hydraulic parameters and groundwater recharge, a regularization procedure to reconcile the large number of spatially distributed model parameters with the limited field data, a step-wise approach for integrating the different data sets into the model, and high performance computing. The methodology was proven to be effective in reproducing multiple contaminant plumes and in reducing the prior parameter uncertainty of hydraulic conductivity and groundwater recharge. Our results further indicate that contaminant transport predictions are strongly affected by the choice of the groundwater recharge model and flow parameters should be identified using both head and concentration measurements.

  12. 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

  13. Modeling Field-Scale Uranium Reactive Transport in Physically and Chemically Heterogeneous Media (Invited)

    NASA Astrophysics Data System (ADS)

    Zheng, C.; Ma, R.; Prommer, H.; Greskowiak, J.; Liu, C.; Zachara, J. M.; Rockhold, M. L.

    2009-12-01

    Reactive transport modeling in the presence of strong physical and chemical heterogeneities that characterize the subsurface media remains a fundamental challenge in hydrologic science. This study explores field-scale modeling of U(VI) reactive transport through incorporation of laboratory and field data at the U.S. Department of Energy (DOE), Hanford 300A site, Washington. Hanford 300A is one of the three “Integrated Subsurface Research Challenge (IFRC)” sites supported by the DOE’s Office of Science. The primary objective of the Hanford 300A IFRC project is to test the latest theoretical understanding and laboratory-scale models of uranium reactive transport in a series of well-controlled field experiments in an effort to advance our field-scale predictive modeling capabilities that are required for cost-effective remediation of numerous uranium contaminated sites. In this study, a field-scale reactive transport model was developed that accommodates the combined effects of physical and chemical heterogeneities by incorporating laboratory-characterized U(VI) surface complexation reactions (SCR) and dual-domain, multi-rate mass transfer processes, and field-measured hydrogeochemical conditions. The field-scale model was used to assess the importance of multi-rate mass transfer processes on U(VI) reactive transport and to evaluate the effect of variable geochemical conditions caused by dynamic river water-groundwater interactions on U(VI) plume migration. Model simulations revealed complex spatio-temporal relationships between groundwater composition and U(VI) speciation, adsorption, and plume migration. In general, river water intrusion enhances uranium adsorption and lowers aqueous uranium concentration, as river water dilution increases pH and decreases aqueous bicarbonate concentration, leading to overall enhanced U(VI) surface complexation. Strong U(VI) retardation was computed for the field-measured hydrogeochemical conditions, suggesting a slow

  14. 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

  15. 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

  16. Semianalytical solutions of radioactive or reactive solute transport in variably fractured layered media

    NASA Astrophysics Data System (ADS)

    Moridis, George J.

    2002-12-01

    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 nonflowing matrix account for (1) diffusion, (2) surface diffusion, (3) mass transfer between mobile and immobile water fractions, (4) linear kinetic or equilibrium physical, chemical, or combined sorption or colloid filtration, and (5) 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 and numerical solutions for limiting cases of solute and colloid transport through fractured and porous media. The effect of important parameters on the transport of 3H, 99Tc, 237Np, and 239Pu (and its daughters) is investigated in several test problems involving layered geological systems of varying complexity.

  17. 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.

  18. 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.

  19. The reactive transport of trichloroethene is influenced by residence time and microbial numbers

    NASA Astrophysics Data System (ADS)

    Haest, P. J.; Philips, J.; Springael, D.; Smolders, E.

    2011-01-01

    The dechlorination rate in a flow-through porous matrix can be described by the species specific dechlorination rate observed in a liquid batch unless mass transport limitations prevail. This hypothesis was examined by comparing dechlorination rates in liquid batch with that in column experiments at various flow rates (3-9-12 cm day - 1 ). Columns were loaded with an inoculated sand and eluted with a medium containing 1 mM trichloroethene (TCE) for 247 days. Dechlorination in the column treatments increased with decreasing flow rate, illustrating the effect of the longer residence time. Zeroth order TCE or cis-DCE degradation rates were 4-7 folds larger in columns than in corresponding batch systems which could be explained by the higher measured Geobacter and Dehalococcoides numbers per unit pore volume in the columns. The microbial numbers also explained the variability in dechlorination rate among flow rate treatments marked by a large elution of the dechlorinating species' yield as flow increased. Stop flow events did not reveal mass transport limitations for dechlorination. We conclude that flow rate effects on reactive transport of TCE in this coarse sand are explained by residence time and by microbial transport and that mass transport limitations in this porous matrix are limited.

  20. 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

  1. 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)].

  2. Intercomparison of reactive transport models applied to UO2 oxidative dissolution and uranium migration.

    PubMed

    De Windt, L; Burnol, A; Montarnal, P; van der Lee, J

    2003-03-01

    Oxidative dissolution of uranium dioxide (UO(2)) and the subsequent migration of uranium in a subsurface environment and an underground waste disposal have been simulated with reactive transport models. In these systems, hydrogeological and chemical processes are closely entangled and their interdependency has been analyzed in detail, notably with respect to redox reactions, kinetics of mineralogical evolution and hydrodynamic migration of species of interest. Different codes, where among CASTEM, CHEMTRAP and HYTEC, have been used as an intercomparison and verification exercise. Although the agreement between codes is satisfactory, it is shown that the discretization method of the transport equation (i.e. finite elements (FE) versus mixed-hybrid FE and finite differences) and the sequential coupling scheme may lead to systematic discrepancies.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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

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

    PubMed

    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

  9. 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

  10. MODFLOW/MT3DMS-based reactive multicomponent transport modeling.

    PubMed

    Prommer, H; Barry, D A; Zheng, C

    2003-01-01

    This paper presents a three-dimensional, MODFLOW/MT3DMS-based reactive multicomponent transport model for saturated porous media. Based on a split-operator technique, the model, referred to as PHT3D, couples the transport simulator MT3DMS and the geochemical modeling code PHREEQC-2. Through the flexible, generic nature of PHREEQC-2, PHT3D can handle a broad range of equilibrium and kinetically controlled reactive processes, including aqueous complexation, mineral precipitation/dissolution, and ion exchange. The diversity of potential applications is demonstrated through simulation of five existing literature benchmarks and a new three-dimensional sample problem. The model might be applied to simulate the geochemical evolution of pristine and contaminated aquifers as well as their cleanup. The latter problem class includes the natural and enhanced attenuation/remediation schemes of a wide range of organic and inorganic contaminants. Processes/reactions not included in the standard PHREEQC-2 database but typical for this type of application (e.g., NAPL dissolution, microbial growth/decay) can be defined and included via the extensible PHREEQC-2 database file.

  11. 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.

  12. 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.

  13. A sensibility analysis of model selection in modeling the reactive transport of cesium in crushed granite.

    PubMed

    Cheng, Hwai-Ping; Li, Ming-Hsu; Li, Samuel

    2003-03-01

    We performed a sensibility analysis of model selection in modeling the reactive transport of cesium in crushed granite through model calibration and validation. Based on some solid phase analysis data and kinetic batch experimental results, we hypothesized three two-site sorption models in the LEHGC reactive transport model to fit the breakthrough curves (BTCs) from the corresponding column experiments. The analysis of breakthrough curves shows that both the empirical two-site kinetic linear sorption model and the semi-mechanistic/semi-empirical two-site kinetic surface complexation model, regardless of their complexity, can match our experimental data fairly well under given test conditions. A numerical experiment to further compare the two models shows that they behave differently when the pore velocity is not of the same order of magnitude as our test velocities. This result indicates that further investigations to help determine a better model are needed. We suggest that a multistage column experiment, which tests over the whole range of practical flow velocities, should be conducted to help alleviate inadequate hypothesized models.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Reactive transport modeling of uranium 238 and radium 226 in groundwater of the Königstein uranium mine, Germany

    NASA Astrophysics Data System (ADS)

    Nitzsche, O.; Merkel, B.

    Knowledge of the transport behavior of radionuclides in groundwater is needed for both groundwater protection and remediation of abandoned uranium mines and milling sites. Dispersion, diffusion, mixing, recharge to the aquifer, and chemical interactions, as well as radioactive decay, should be taken into account to obtain reliable predictions on transport of primordial nuclides in groundwater. This paper demonstrates the need for carrying out rehabilitation strategies before closure of the Königstein in-situ leaching uranium mine near Dresden, Germany. Column experiments on drilling cores with uranium-enriched tap water provided data about the exchange behavior of uranium. Uranium breakthrough was observed after more than 20 pore volumes. This strong retardation is due to the exchange of positively charged uranium ions. The code TReAC is a 1-D, 2-D, and 3-D reactive transport code that was modified to take into account the radioactive decay of uranium and the most important daughter nuclides, and to include double-porosity flow. TReAC satisfactorily simulated the breakthrough curves of the column experiments and provided a first approximation of exchange parameters. Groundwater flow in the region of the Königstein mine was simulated using the FLOWPATH code. Reactive transport behavior was simulated with TReAC in one dimension along a 6000-m path line. Results show that uranium migration is relatively slow, but that due to decay of uranium, the concentration of radium along the flow path increases. Results are highly sensitive to the influence of double-porosity flow. Résumé La protection des eaux souterraines et la restauration des sites miniers et de prétraitement d'uranium abandonnés nécessitent de connaître le comportement des radionucléides au cours de leur transport dans les eaux souterraines. La dispersion, la diffusion, le mélange, la recharge de l'aquifère et les interactions chimiques, de même que la décroissance radioactive, doivent être

  4. Macropore system characteristics controls on non-reactive solute transport at different flow rates

    NASA Astrophysics Data System (ADS)

    Larsbo, Mats; Koestel, John

    2014-05-01

    Preferential flow and transport in macroporous soils are important pathways for the leaching of agrochemicals through soils. Preferential solute transport in soil is to a large extent determined by the macropore system characteristics and the water flow conditions. The importance of different characteristics of the macropore system is likely to vary with the flow conditions. The objective of this study was to determine which properties of the macropore system that control the shape of non-reactive tracer solute breakthrough curves at different steady-state flow rates. We sampled five undisturbed columns (20 cm high, 20 cm diameter) from the soil surface of four soils with clay contents between 21 and 50 %. Solute transport experiments were carried out under unsaturated conditions at 2, 4, 6, 8 and 12 mm h-1 flow rates. For each flow rate a pulse of potassium bromide solution was applied at the soil surface and the electrical conductivity was measured with high temporal resolution in the column effluent. We used the 5 % arrival time and the holdback factor to estimate the degree of preferential transport from the resulting breakthrough curves. Unsaturated hydraulic conductivities were measured at the soil surface of the columns using a tension disc infiltrometer. The macropore system was imaged by industrial X-ray computed tomography at a resolution of 125 μm in all directions. Measures of the macropore system characteristics including measures of pore continuity were calculated from these images using the ImageJ software. Results show that the degree of preferential transport is generally increasing with flow rate when larger pores become active in the transport. The degree of preferential flow was correlated to measures of macropore topology. This study show that conclusions drawn from experiments carried out at one flow rate should generally not be extrapolated to other flow rates.

  5. 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

  6. 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

  7. Measurement of the differential cross section of the photoinitiated reactive collision of O((1)D)+D(2) using only one molecular beam: A study by three dimensional velocity mapping.

    PubMed

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

    2010-06-28

    velocities. Using the benchmark system O((1)D)+D(2) with N(2)O 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 N(2)O 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.

  8. 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.

  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. 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.

  11. 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

  12. Kinetic parameter estimation in N. europaea biofilms using a 2-D reactive transport model.

    PubMed

    Lauchnor, Ellen G; Semprini, Lewis; Wood, Brian D

    2015-06-01

    Biofilms of the ammonia oxidizing bacterium Nitrosomonas europaea were cultivated to study microbial processes associated with ammonia oxidation in pure culture. We explored the hypothesis that the kinetic parameters of ammonia oxidation in N. europaea biofilms were in the range of those determined with batch suspended cells. Oxygen and pH microelectrodes were used to measure dissolved oxygen (DO) concentrations and pH above and inside biofilms and reactive transport modeling was performed to simulate the measured DO and pH profiles. A two dimensional (2-D) model was used to simulate advection parallel to the biofilm surface and diffusion through the overlying fluid while reaction and diffusion were simulated in the biofilm. Three experimental studies of microsensor measurements were performed with biofilms: i) NH3 concentrations near the Ksn value of 40 μM determined in suspended cell tests ii) Limited buffering capacity which resulted in a pH gradient within the biofilms and iii) NH3 concentrations well below the Ksn value. Very good fits to the DO concentration profiles both in the fluid above and in the biofilms were achieved using the 2-D model. The modeling study revealed that the half-saturation coefficient for NH3 in N. europaea biofilms was close to the value measured in suspended cells. However, the third study of biofilms with low availability of NH3 deviated from the model prediction. The model also predicted shifts in the DO profiles and the gradient in pH that resulted for the case of limited buffering capacity. The results illustrate the importance of incorporating both key transport and chemical processes in a biofilm reactive transport model.

  13. Accelerating flow propagator measurements for the investigation of reactive transport in porous media

    NASA Astrophysics Data System (ADS)

    Colbourne, A. A.; Sederman, A. J.; Mantle, M. D.; Gladden, L. F.

    2016-11-01

    NMR propagator measurements are widely used for identifying the distribution of molecular displacements over a given observation time, characterising a flowing system. However, where high q-space resolution is required, the experiments are time consuming and therefore unsuited to the study of dynamic systems. Here, it is shown that with an appropriately sampled subset of the q-space points in a high-resolution flow propagator measurement, one can quickly and robustly reconstruct the fully sampled propagator through interpolation of the acquired raw data. It was found that exponentially sampling ∼4% of the original data-points allowed a reconstruction with the deviation from the fully sampled propagator below the noise level, in this case reducing the required experimental time from ∼2.8 h to <7 min. As a demonstration, this approach is applied to observe the temporal evolution of the reactive flow of acid through an Estaillades rock core plug. It is shown that 'wormhole' formation in the rock core plug provides a channel for liquid flow such that the remaining pore space is by-passed, thereby causing the flow velocity of the liquid in the remaining part of the plug to become stagnant. The propagator measurements are supported by both 1D profiles and 2D imaging data. Such insights are of importance in understanding well acidisation and CO2 sequestration processes.

  14. 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

  15. Transient Modeling of Reactive Solute Transport in a Submarine Groundwater Discharge Zone

    NASA Astrophysics Data System (ADS)

    Colman, J. A.; Bratton, J. F.; Crusius, J.; Kroeger, K. D.; Baldwin, S.; Lee, K.

    2009-12-01

    Submarine groundwater discharge (SGD) is the dominant means of freshwater delivery to many coastal embayments on the glaciated coast of Cape Cod (Mass.). This discharge is the focus of considerable research, in part because the common disposal of sewage via septic systems has led to elevated concentrations of nutrients in groundwater. Subsurface mixing and chemical reactivity prior to discharge can affect the amounts of nutrients entering the embayments. Water-quality problems including eutrophication and harmful algal blooms appear to be controlled by the timing and intensity of SGD at our field site, Salt Pond, a weakly stratified estuary 8.2 ha in area with a maximum depth of 9 m and tidal amplitude of 2 m. The site is located at the northern (inland) end of Nauset Marsh on outer Cape Cod. We estimated mixing and reaction rates in the discharge area by fitting a 2-D reactive-solute-transport model (PHAST) to chemical observations in the intertidal subsurface using hydrologic forcing from aquifer recharge and tides. Chemical measurements in the subsurface, taken at 5 intervals spanning the seasons from a multilevel-sampler (MLS) array, 20 m long by 6 m deep, indicate a change in the position of the groundwater salt front on both tidal and seasonal time scales, with a maximum horizontal movement of approximately 4 m. Observed movement of the salt front corresponded with simulated movement modeled by changing seasonal recharge to the aquifer. Kinetics of oxygen consumption in the subsurface were modeled using end-member concentrations of oxygen in upgradient fresh groundwater and in water-column saltwater, assumed biological oxygen demand in saltwater, and model-determined residence time in the subsurface. High measured concentrations of nitrate (up to 7 mg/L as N) in intertidal groundwater were unaffected by denitrification prior to discharge based on both chemical analysis of denitrification indicators in MLS samples, and model results. This work demonstrates

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. High resolution direct upscaling of flow and reactive transport: bridging the continuum gap

    NASA Astrophysics Data System (ADS)

    Engdahl, N. B.; Fogg, G. E.

    2010-12-01

    Upscaling of flow and transport systems at any scale has been a significant challenge to modern hydrogeology. There is still great uncertainty in the validity of assumptions made during the upscaling process, particularly for reactive transport where locally unresolved concentration distributions can strongly control contaminant fate. Pore-scale modeling may provide a means of investigating the problem, but conventional pore scale models fail to represent the broad range (clay to sand/gravel) of pore sizes in typical geologic media. We present a modeling framework capable of explicitly modelling nearly all of the pore-scale heterogeneities that are believed to influence flow and transport. This framework has pore-scale resolution but the final simulation domain will be the size of a small laboratory column experiment (20cm length) enabling us to compare the detailed pore-scale parameter fields directly to their upscaled equivalents. Knowledge of the complete parameter field allows explicit volume averaging to be done which will permit us to investigate the validity of many of the assumptions commonly invoked when upscaling. The simulations will balance model size, resolution, and a realistic representation of the media using a triple continuum domain which includes: (1) open pore space flows through granular material, (2) Darcy flow through finer material (silt and clay), and (3) immobile diffusion regions within grains. The domains will be directly coupled and solved simultaneously using the Lattice-Boltzmann method which we are optimizing to run on graphical processing unit enabled computers. In addition to flow and passive transport, we will add the ability to simulate any number of reactions in any of the domains for which the mechanics of the reaction are defined. We will also be able to selectively volume average the different domains to determine the mobile and immobile portions of the complete parameter distributions. These models will help us to determine

  1. Modeling of Reactive Transport of Nitrate in a Heterogeneous Alluvial Fan Aquifer, San Joaquin Valley, California

    NASA Astrophysics Data System (ADS)

    Green, C. T.; Phillips, S. P.

    2005-12-01

    Fate of nitrate in an alluvial fan aquifer in the San Joaquin Valley, California, was investigated with combined laboratory analyses, field measurements, geostatistics, and flow and reactive transport modeling. In the summer of 2003, groundwater wells and lysimeters were installed along a 1-km transect extending upgradient from the Merced River through an unfarmed riparian zone, a corn field, and an orchard. Groundwater levels have been monitored continuously. Saturated and unsaturated pore waters were analyzed quarterly for nutrients, anions, and cations. Sediment core samples from above and below the water table were analyzed for organic matter, nutrients, inorganic chemistry, and potential denitrification using denitrification enzyme assays (DEA's) based on the acetylene block technique. Curve fitting of DEA's provided core-scale estimates of microbial populations and growth coefficients. DEA biomass was similar to values obtained with the most probable number technique. Growth coefficients were found to be relatively uniform across the site, while biomass varied by several orders of magnitude. Age dates estimated from Chlorofluorocarbon (CFC) and Sulfur Hexafluoride (SF6), together with analyses of nitrogen species and excess nitrogen gas, provided approximate aquifer-scale, zero-order denitrification rates. The field and laboratory measurements served as input for geostatistical realizations of sediment properties and simulations of reactive transport of nitrate in the saturated zone. Analyses of cores, drillers' logs, and previous interpretations of the local geology were used to generate transition probability models of hydrofacies distributions within Holocene alluvium and pre-Holocene fans, and maps of the boundaries between these stratigraphic sequences. Multiple 3-D realizations were created and ranked based on lateral and vertical bulk-flow properties. For realizations representing a range of geological conditions, 3-D flow was computed with boundary

  2. 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

    2011-09-23

    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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Modeling reactive transport of reclaimed water through large soil columns with different low-permeability layers

    NASA Astrophysics Data System (ADS)

    Hu, Haizhu; Mao, Xiaomin; Barry, D. A.; Liu, Chengcheng; Li, Pengxiang

    2015-03-01

    The efficacy of different proportions of silt-loam/bentonite mixtures overlying a vadose zone in controlling solute leaching to groundwater was quantified. Laboratory experiments were carried out using three large soil columns, each packed with 200-cm-thick riverbed soil covered by a 2-cm-thick bentonite/silt-loam mixture as the low-permeability layer (with bentonite mass accounting for 12, 16 and 19 % of the total mass of the mixture). Reclaimed water containing ammonium (NH4 +), nitrate (NO3 -), organic matter (OM), various types of phosphorus and other inorganic salts was applied as inflow. A one-dimensional mobile-immobile multi-species reactive transport model was used to predict the preferential flow and transport of typical pollutants through the soil columns. The simulated results show that the model is able to predict the solute transport in such conditions. Increasing the amount of bentonite in the low-permeability layer improves the removal of NH4 + and total phosphorous (TP) because of the longer contact time and increased adsorption capacity. The removal of NH4 + and OM is mainly attributed to adsorption and biodegradation. The increase of TP and NO3 - concentration mainly results from discharge and nitrification in riverbed soils, respectively. This study underscores the role of low-permeability layers as barriers in groundwater protection. Neglect of fingers or preferential flow may cause underestimation of pollution risk.

  9. Modeling hydrology and reactive transport in roads: the effect of cracks, the edge, and contaminant properties.

    PubMed

    Apul, Defne S; Gardner, Kevin H; Eighmy, T Taylor

    2007-01-01

    The goal of this research was to provide a tool for regulators to evaluate the groundwater contamination from the use of virgin and secondary materials in road construction. A finite element model, HYDRUS2D, was used to evaluate generic scenarios for secondary material use in base layers. Use of generic model results for particular applications was demonstrated through a steel slag example. The hydrology and reactive transport of contaminants were modeled in a two-dimensional cross section of a road. Model simulations showed that in an intact pavement, lateral velocities from the edge towards the centerline may transport contaminants in the base layer. The dominant transport mechanisms are advection closer to the edge and diffusion closer to the centerline. A shoulder joint in the pavement allows 0.03 to 0.45 m(3)/day of infiltration per meter of joint length as a function of the base and subgrade hydrology and the rain intensity. Scenario simulations showed that salts in the base layer of pavements are depleted by 99% in the first 20 years, whereas the metals may not reach the groundwater in 20 years at any significant concentrations if the pavement is built on adsorbing soils. PMID:17521900

  10. Isotopic fractionation by transverse dispersion: flow-through microcosms and reactive transport modeling study.

    PubMed

    Rolle, Massimo; Chiogna, Gabriele; Bauer, Robert; Griebler, Christian; Grathwohl, Peter

    2010-08-15

    Flow-through experiments were carried out to investigate the role of transverse dispersion on the isotopic behavior of an organic compound during conservative and bioreactive transport in a homogeneous porous medium. Ethylbenzene was selected as model contaminant and a mixture of labeled (perdeuterated) and light isotopologues was continuously injected in a quasi two-dimensional flow-through system. We observed a significant fractionation of ethylbenzene isotopologues during conservative transport at steady state. This effect was particularly pronounced at the plume fringe and contrasted with the common assumption that physical processes only provide a negligible contribution to isotope fractionation. Under the experimental steady state conditions, transverse hydrodynamic dispersion was the only process that could have caused the observed fractionation. Therefore, the measured isotope ratios at the outlet ports were interpreted with different parameterizations of the transverse dispersion coefficient. A nonlinear compound-specific parameterization showed the best agreement with the experimental data. Successively, bioreactive experiments were performed in two subsequent stages: a first oxic phase, involving a single strain of ethylbenzene degraders and a second phase with aerobic and anaerobic (i.e., ethylbenzene oxidation coupled to nitrate reduction) degradation. Significant fractionation through biodegradation occurred exclusively due to the metabolic activity of the anaerobic degraders. We performed analytical and numerical reactive transport simulations of the different experimental phases which confirmed that both the effects of physical processes (diffusion and dispersion) and microbially mediated reactions have to be considered to match the observed isotopic fractionation behavior.

  11. Modeling hydrology and reactive transport in roads: the effect of cracks, the edge, and contaminant properties.

    PubMed

    Apul, Defne S; Gardner, Kevin H; Eighmy, T Taylor

    2007-01-01

    The goal of this research was to provide a tool for regulators to evaluate the groundwater contamination from the use of virgin and secondary materials in road construction. A finite element model, HYDRUS2D, was used to evaluate generic scenarios for secondary material use in base layers. Use of generic model results for particular applications was demonstrated through a steel slag example. The hydrology and reactive transport of contaminants were modeled in a two-dimensional cross section of a road. Model simulations showed that in an intact pavement, lateral velocities from the edge towards the centerline may transport contaminants in the base layer. The dominant transport mechanisms are advection closer to the edge and diffusion closer to the centerline. A shoulder joint in the pavement allows 0.03 to 0.45 m(3)/day of infiltration per meter of joint length as a function of the base and subgrade hydrology and the rain intensity. Scenario simulations showed that salts in the base layer of pavements are depleted by 99% in the first 20 years, whereas the metals may not reach the groundwater in 20 years at any significant concentrations if the pavement is built on adsorbing soils.

  12. Modeling hydrology and reactive transport in roads: The effect of cracks, the edge, and contaminant properties

    SciTech Connect

    Apul, Defne S. Gardner, Kevin H. Eighmy, T. Taylor

    2007-07-01

    The goal of this research was to provide a tool for regulators to evaluate the groundwater contamination from the use of virgin and secondary materials in road construction. A finite element model, HYDRUS2D, was used to evaluate generic scenarios for secondary material use in base layers. Use of generic model results for particular applications was demonstrated through a steel slag example. The hydrology and reactive transport of contaminants were modeled in a two-dimensional cross section of a road. Model simulations showed that in an intact pavement, lateral velocities from the edge towards the centerline may transport contaminants in the base layer. The dominant transport mechanisms are advection closer to the edge and diffusion closer to the centerline. A shoulder joint in the pavement allows 0.03 to 0.45 m{sup 3}/day of infiltration per meter of joint length as a function of the base and subgrade hydrology and the rain intensity. Scenario simulations showed that salts in the base layer of pavements are depleted by 99% in the first 20 years, whereas the metals may not reach the groundwater in 20 years at any significant concentrations if the pavement is built on adsorbing soils.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. [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

  18. 34S/32S fractionation during sulfate reduction in groundwater treatment systems: reactive transport modeling.

    PubMed

    Gibson, Blair D; Amos, Richard T; Blowes, David W

    2011-04-01

    Isotope ratio measurements provide a tool for indicating the relative significance of biogeochemical reactions and for constraining estimates of the extent and rate of reactions in passive treatment systems. In this paper, the reactive transport model MIN3P is used to evaluate sulfur isotope fractionation in column experiments designed to simulate treatment of contaminated water by microbially mediated sulfate reduction occurring within organic carbon-based and iron and carbon-based permeable reactive barriers. A mass dependent fractionation model was used to determine reaction rates for 32S and 34S compounds during reduction, precipitation, and dissolution reactions and to track isotope-dependent mass transfer during SO4 removal. The δ34S values obtained from the MIN3P model were similar to those obtained from the Rayleigh equation, indicating that there was not a significant difference between the conceptual models. Differences between the MIN3P derived α value and the Rayleigh equation derived value were attributed to minor changes in the dissolution and precipitation rate of gypsum and mathematical differences in the fitting models. The results indicated that the prediction of δ34S was fairly insensitive to differences in the fractionation factor at the concentration ranges measured in the current study. However, more significant differences would be expected at low sulfate conditions.

  19. Can nuclear magnetic resonance provide useful microscale data for quantitative testing of reactive transport models? (Invited)

    NASA Astrophysics Data System (ADS)

    Seymour, J. D.; Codd, S. L.

    2010-12-01

    In posing the query in our title we are inherently answering the query posed by the conveners, ‘Is microscale information needed in reactive transport models?’, in the affirmative. Our perspective on this is derived in large part from the NMR measurements of displacement time and length scale dependent molecular dynamics through a range of porous media with very different microscale structures which will be presented. The measured dynamics of hydrodynamic dispersion in model monodisperse beadpacks subjected to bioreactions which form biofilms [1] and precipitate [2] and colloidal deposition, as well as an open cell solid polymer foam [3], show strong dependence on microscale structure. As an example of what is required for direct quantitative comparison of experimental data, analytical theory [4] and simulation the foam structure provides a system with an ill defined microscale length scale and a mean velocity field that is highly heterogeneous[3,5]. The NMR data directly provides a dynamic length scale [6]. The agreement found between the non equilibrium statistical mechanics model of preasymptotic hydrodynamic dispersion [4], which inputs the microstructure into the form of the velocity autocorrelation function, and the data [3] argues for the role of microscale structure in transport. Recently developed 2D magnetic relaxation time and diffusion correlation and exchange experiments are shown to provide unique new data on the pore structure and surface properties in model and rock porous systems subjected to bioreaction and supercritical fluid challenges. Coupling of these measurements and hydrodynamic dispersion measurements can provide the relation between microscale structure and transport dynamics. The direct comparison of theory and experiment is required to test and advance predictive reactive transport models and the difficulties and needs to enhance direct quantitative comparisons with NMR data will be addressed, along with the significant limitations

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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

  6. Pore-scale modeling of multiphase reactive transport with phase transitions and dissolution-precipitation processes in closed systems.

    PubMed

    Chen, Li; Kang, Qinjun; Robinson, Bruce A; He, Ya-Ling; Tao, Wen-Quan

    2013-04-01

    A pore-scale model based on the lattice Boltzmann (LB) method is developed for multiphase reactive transport with phase transitions and dissolution-precipitation processes. The model combines the single-component multiphase Shan-Chen LB model [X. Shan and H. Chen, Phys. Rev. E 47, 1815 (1993)], the mass transport LB model [S. P. Sullivan et al., Chem. Eng. Sci. 60, 3405 (2005)], and the dissolution-precipitation model [Q. Kang et al., J. Geophys. Res. 111, B05203 (2006)]. Care is taken to handle information on computational nodes undergoing solid-liquid or liquid-vapor phase changes to guarantee mass and momentum conservation. A general LB concentration boundary condition is proposed that can handle various concentration boundaries including reactive and moving boundaries with complex geometries. The pore-scale model can capture coupled nonlinear multiple physicochemical processes including multiphase flow with phase separations, mass transport, chemical reactions, dissolution-precipitation processes, and dynamic evolution of the pore geometries. The model is validated using several multiphase flow and reactive transport problems and then used to study the thermal migration of a brine inclusion in a salt crystal. Multiphase reactive transport phenomena with phase transitions between liquid-vapor phases and dissolution-precipitation processes of the salt in the closed inclusion are simulated and the effects of the initial inclusion size and temperature gradient on the thermal migration are investigated.

  7. 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

  8. 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

  9. 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

  10. Modelling of sulfide oxidation with reactive transport at a mine drainage site

    NASA Astrophysics Data System (ADS)

    Bain, J. G.; Blowes, D. W.; Robertson, W. D.; Frind, E. O.

    2000-01-01

    A plume of groundwater affected by sulfide oxidation extends 160 m downgradient from the Nickel Rim Mine tailings impoundment and discharges to a small lake. The plume water has near neutral pH, but contains high concentrations of Fe and SO 4. Field observations indicate that the release of SO 4, H +, Fe 2+ and other metals and their distribution in the aquifer is controlled by the rate of sulfide oxidation in the vadose zone of the tailings and by subsequent dissolution and precipitation of carbonate and oxyhydroxide mineral phases in the tailings and aquifer. Using field-determined aqueous and solid geochemistry, a conceptual geochemical model for the site was developed. This model accounts for trends in pH and in the concentrations of Fe and SO 4. The numerical model MINTOX was used in conjunction with this conceptual model to simulate sulfide oxidation and two-dimensional reactive transport of dissolved sulfide oxidation products. Simulated sulfide oxidation and transport are compared to trends observed in the field after 35 years of oxidation. Similarity between observed and simulated concentrations demonstrates that, when used with a well-developed conceptual geochemical model, MINTOX is capable of simulating sulfide oxidation and plume evolution at mine drainage sites.

  11. Phast4Windows: a 3D graphical user interface for the reactive-transport simulator PHAST.

    PubMed

    Charlton, Scott R; Parkhurst, David L

    2013-01-01

    Phast4Windows is a Windows® program for developing and running groundwater-flow and reactive-transport models with the PHAST simulator. This graphical user interface allows definition of grid-independent spatial distributions of model properties-the porous media properties, the initial head and chemistry conditions, boundary conditions, and locations of wells, rivers, drains, and accounting zones-and other parameters necessary for a simulation. Spatial data can be defined without reference to a grid by drawing, by point-by-point definitions, or by importing files, including ArcInfo® shape and raster files. All definitions can be inspected, edited, deleted, moved, copied, and switched from hidden to visible through the data tree of the interface. Model features are visualized in the main panel of the interface, so that it is possible to zoom, pan, and rotate features in three dimensions (3D). PHAST simulates single phase, constant density, saturated groundwater flow under confined or unconfined conditions. Reactions among multiple solutes include mineral equilibria, cation exchange, surface complexation, solid solutions, and general kinetic reactions. The interface can be used to develop and run simple or complex models, and is ideal for use in the classroom, for analysis of laboratory column experiments, and for development of field-scale simulations of geochemical processes and contaminant transport.

  12. 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.

  13. 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.

  14. 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.

  15. Effects of autoregulation and CO2 reactivity on cerebral oxygen transport.

    PubMed

    Payne, S J; Selb, J; Boas, D A

    2009-11-01

    Both autoregulation and CO(2) reactivity are known to have significant effects on cerebral blood flow and thus on the transport of oxygen through the vasculature. In this paper, a previous model of the autoregulation of blood flow in the cerebral vasculature is expanded to include the dynamic behavior of oxygen transport through binding with hemoglobin. The model is used to predict the transfer functions for both oxyhemoglobin and deoxyhemoglobin in response to fluctuations in arterial blood pressure and arterial CO(2) concentration. It is shown that only six additional nondimensional groups are required in addition to the five that were previously found to characterize the cerebral blood flow response. A resonant frequency in the pressure-oxyhemoglobin transfer function is found to occur in the region of 0.1 Hz, which is a frequency of considerable physiological interest. The model predictions are compared with results from the published literature of phase angle at this frequency, showing that the effects of changes in breathing rate can significantly alter the inferred phase dynamics between blood pressure and hemoglobin. The question of whether dynamic cerebral autoregulation is affected under conditions of stenosis or stroke is then examined.

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. A reactive transport model of neptunium migration from the potential repository at Yucca Mountain

    NASA Astrophysics Data System (ADS)

    Viswanathan, Hari S.; Robinson, Bruce A.; Valocchi, Albert J.; Triay, Ines R.

    1998-08-01

    Characterization and performance assessment studies for the potential high-level nuclear waste repository at Yucca Mountain have identified 237Np as a radionuclide of concern for the proposed repository. To predict the migration of neptunium after a repository breach, an understanding of the relevant hydrologic and geochemical processes is required. The hydrologic flow in the unsaturated zone at Yucca Mountain is dependent on the infiltration rate, the stratigraphy of the vadose zone, and the heat generated by the decaying radioactive waste. The geochemical processes that strongly affect 237Np migration include: solubility-limited release of 237Np from the near-field environment, aqueous speciation of neptunium into non-sorbing carbonate/hydroxy complexes and the sorbing NpO 2+ cation, sorption of neptunium onto the zeolitic tuffs via an ion exchange mechanism, and radioactive decay. The finite element heat and mass transfer (FEHM) code was used to investigate the coupled effects of chemical interactions and heat on neptunium transport from the potential repository to the water table. The selective coupling method is introduced to solve these reactive transport problems. The simulations indicate that in the absence of irreversible changes in the hydrologic and transport properties, the heat pulse does not significantly affect the migration of neptunium, as the time scale of heat pulse propagation is shorter than the time scales associated with neptunium release and migration. Water chemistry, particularly pH, calcium, and sodium concentration significantly affect the retardation of neptunium by the zeolitic rocks between the repository and the water table.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. Large-scale modeling of reactive solute transport in fracture zones of granitic bedrocks.

    PubMed

    Molinero, Jorge; Samper, Javier

    2006-01-10

    Final disposal of high-level radioactive waste in deep repositories located in fractured granite formations is being considered by several countries. The assessment of the safety of such repositories requires using numerical models of groundwater flow, solute transport and chemical processes. These models are being developed from data and knowledge gained from in situ experiments such as the Redox Zone Experiment carried out at the underground laboratory of Aspö in Sweden. This experiment aimed at evaluating the effects of the construction of the access tunnel on the hydrogeological and hydrochemical conditions of a fracture zone intersected by the tunnel. Most chemical species showed dilution trends except for bicarbonate and sulphate which unexpectedly increased with time. Molinero and Samper [Molinero, J. and Samper, J. Groundwater flow and solute transport in fracture zones: an improved model for a large-scale field experiment at Aspö (Sweden). J. Hydraul. Res., 42, Extra Issue, 157-172] presented a two-dimensional water flow and solute transport finite element model which reproduced measured drawdowns and dilution curves of conservative species. Here we extend their model by using a reactive transport which accounts for aqueous complexation, acid-base, redox processes, dissolution-precipitation of calcite, quartz, hematite and pyrite, and cation exchange between Na+ and Ca2+. The model provides field-scale estimates of cation exchange capacity of the fracture zone and redox potential of groundwater recharge. It serves also to identify the mineral phases controlling the solubility of iron. In addition, the model is useful to test the relevance of several geochemical processes. Model results rule out calcite dissolution as the process causing the increase in bicarbonate concentration and reject the following possible sources of sulphate: (1) pyrite dissolution, (2) leaching of alkaline sulphate-rich waters from a nearby rock landfill and (3) dissolution of

  7. Observations of Chemical Transport and Reaction in Porous Media in 3D with Applications to Understanding the Role of Heterogeneity in Reactive Transport

    NASA Astrophysics Data System (ADS)

    Boon, M.; Niu, B.; Krevor, S. C.

    2014-12-01

    Processes involving feedbacks between chemical reaction and fluid flow through porous media are poorly understood. Non-reactive and reactive core flooding experiments have been carried out in sandstone and two carbonate cores with varying degrees of heterogeneity. The dispersion, mixing and reaction of chemical components in an aqueous solution injected into rock cores were visualised in 3D with the use of chemical dopants and a medical x-ray CT scanner. With regards to solid-fluid reactions, the impact of rock dissolution on subsequent chemical transport was observed by injecting a carefully selected acidic solution. Simultaneous observations of the permeability evolution were made along with analysis of the effluent chemistry using an ICP-MS. This has resulted in a high quality 3D data set of the space and time evolution of the concentration of aqueous chemical components in non-reactive and reactive core-flooding experiments in rocks with different degrees of heterogeneity in combination with precise data of the effluent composition and rock permeability. This will allow us to assess the effect of flow and transport heterogeneity on upscaled effective reaction rates. Furthermore, these observations can be used as a future benchmark test for numerical models for chemical transport and fluid-solid reactions and in the development of upscaling techniques for accurate and efficient modelling of chemical processes during flow in porous media.

  8. Inference of reactive transport model parameters using a Bayesian multivariate approach

    NASA Astrophysics Data System (ADS)

    Carniato, Luca; Schoups, Gerrit; van de Giesen, Nick

    2014-08-01

    Parameter estimation of subsurface transport models from multispecies data requires the definition of an objective function that includes different types of measurements. Common approaches are weighted least squares (WLS), where weights are specified a priori for each measurement, and weighted least squares with weight estimation (WLS(we)) where weights are estimated from the data together with the parameters. In this study, we formulate the parameter estimation task as a multivariate Bayesian inference problem. The WLS and WLS(we) methods are special cases in this framework, corresponding to specific prior assumptions about the residual covariance matrix. The Bayesian perspective allows for generalizations to cases where residual correlation is important and for efficient inference by analytically integrating out the variances (weights) and selected covariances from the joint posterior. Specifically, the WLS and WLS(we) methods are compared to a multivariate (MV) approach that accounts for specific residual correlations without the need for explicit estimation of the error parameters. When applied to inference of reactive transport model parameters from column-scale data on dissolved species concentrations, the following results were obtained: (1) accounting for residual correlation between species provides more accurate parameter estimation for high residual correlation levels whereas its influence for predictive uncertainty is negligible, (2) integrating out the (co)variances leads to an efficient estimation of the full joint posterior with a reduced computational effort compared to the WLS(we) method, and (3) in the presence of model structural errors, none of the methods is able to identify the correct parameter values.

  9. Multiphase Fluid Flow and Multicomponent Reactive Transport at the Hanford SX Tank Farm

    SciTech Connect

    Yabusaki, Steven B.

    2002-03-01

    In the next five years, critical decisions on the future disposition of wastes on the Hanford Site will be made: * barriers to control recharge at the ground surface,* procedures for retrieval and stabilization of tank waste, and* remediation of contaminated sediments.These decisions will be based, in part, on model predictions of contaminant transport in the vadose zone. Our investigation focuses on high-level radioactive waste tanks in the SX Tank Farm in the 200 West Area of the Hanford Site. The historical SX tank wastes were the hottest, highest pH, highest ionic strength, highest aluminum wastes in Hanford single-shell tanks (SST); 10 of these tanks are confirmed or suspected leakers. Over the last two years, an integrated program of scientific and engineering study has been directed at the SX tank farm, including (1) laboratory experiments on waste-sediment interactions, (2) field experiments on the migration of dense, hypersaline solutions, (3) estimates of historical tank leak source-terms, (4) characterization of hydrostratigraphic units, and (5) physical and chemical analyses of soil samples from the SX tank farm. In this presentation, we describe how these disparate data sets have been used to identify detailed process models and parameterizations that are incorporated into simulators of nonisothermal multiphase fluid flow and multicomponent reactive transport. This modeling framework provides a testbed to systematically assess the appropriateness of the identified process representations in the context of site-specific, field-scale properties, and more importantly, observed historical and contemporary behaviors (e.g., hydrology, chemistry). The ultimate goal is to provide a technically defensible basis for the prediction of long-term contaminant behavior. An important technological issue in the comprehensively detailed modeling approach is addressing the computationally intensive calculations that are required.

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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

  15. A 2.5D Reactive Transport Model for Fracture Alteration Simulation.

    PubMed

    Deng, Hang; Molins, Sergi; Steefel, Carl; DePaolo, Donald; Voltolini, Marco; Yang, Li; Ajo-Franklin, Jonathan

    2016-07-19

    Understanding fracture alteration resulting from geochemical reactions is critical in predicting fluid migration in the subsurface and is relevant to multiple environmental challenges. Here, we present a novel 2.5D continuum reactive transport model that captures and predicts the spatial pattern of fracture aperture change and the development of an altered layer in the near-fracture region. The model considers permeability heterogeneity in the fracture plane and updates fracture apertures and flow fields based on local reactions. It tracks the reaction front of each mineral phase and calculates the thickness of the altered layer. Given this treatment, the model is able to account for the diffusion limitation on reaction rates associated with the altered layer. The model results are in good agreement with an experimental study in which a CO2-acidified brine was injected into a fracture in the Duperow Dolomite, causing dissolution of calcite and dolomite that result in the formation of a preferential flow channel and an altered layer. With an effective diffusion coefficient consistent with the experimentally observed porosity of the altered layer, the model captures the progressive decrease in the dissolution rate of the fast-reacting mineral in the altered layer. PMID:27357572

  16. 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

  17. 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.

  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. 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.

  1. Interaction Between Hyperalkaline Fluids and Rocks Hosting Repositories for Radioactive Waste: Reactive Transport Simulations

    SciTech Connect

    Soler, Josep M.; Maeder, Urs K.

    2005-09-15

    Reactive transport calculations simulating the interaction between hyperalkaline solutions derived from the degradation of cement and potential host rocks for repositories for low- and intermediate-level radioactive waste have been performed. Two different cases are shown: (a) The example of the planned repository at Wellenberg and (b) the modeling of the GTS-HPF experiment at the Grimsel Test Site. The GIMRT code has been used for the simulations. Mineral reactions are described by kinetic rate laws. The reaction rates for the primary minerals are based on experimentally determined rates published in the literature and geometric considerations combined with measurements regarding mineral surface areas. Relatively fast rates for the secondary minerals have been used, so the results resemble the local equilibrium solution for these minerals. In both cases, the alteration of the rock and the precipitation of secondary phases cause a reduction in the permeability of the system, which would actually be beneficial for the performance of a repository. Mineral surface area controls, to a large extent, the amount of mineral alteration and the change in permeability.

  2. Electron transport chain inhibitors induce microglia activation through enhancing mitochondrial reactive oxygen species production.

    PubMed

    Ye, Junli; Jiang, Zhongxin; Chen, Xuehong; Liu, Mengyang; Li, Jing; Liu, Na

    2016-01-15

    Reactive oxygen species (ROS) are believed to be mediators of excessive microglial activation, yet the resources and mechanism are not fully understood. Here we stimulated murine microglial BV-2 cells and primary microglial cells with different inhibitors of electron transport chain (ETC), rotenone, thenoyltrifluoroacetone (TTFA), antimycin A, and NaN3 to induce mitochondrial ROS production and we observed the role of mitochondrial ROS in microglial activation. Our results showed that ETC inhibitors resulted in significant changes in cell viability, microglial morphology, cell cycle arrest and mitochondrial ROS production in a dose-dependent manner in both primary cultural microglia and BV-2 cell lines. Moreover, ETC inhibitors, especially rotenone and antimycin A stimulated secretion of interleukin 1β (IL-1β), interleukin 6 (IL-6), interleukin 12 (IL-12) and tumor necrosis factor α (TNF-α) by microglia with marked activation of mitogen-activated proteinkinases (MAPKs) and nuclear factor κB (NF-κB), which could be blocked by specific inhibitors of MAPK and NF-κB and mitochondrial antioxidants, Mito-TEMPO. Taken together, our results demonstrated that inhibition of mitochondrial respiratory chain in microglia led to production of mitochondrial ROS and therefore may activate MAPK/NF-кB dependent inflammatory cytokines release in microglia, which indicated that mitochondrial-derived ROS were contributed to microglial activation.

  3. Reactive transport of metal contaminants in alluvium - Model comparison and column simulation

    USGS Publications Warehouse

    Brown, J.G.; Bassett, R.L.; Glynn, P.D.

    2000-01-01

    A comparative assessment of two reactive-transport models, PHREEQC and HYDROGEOCHEM (HGC), was done to determine the suitability of each for simulating the movement of acidic contamination in alluvium. For simulations that accounted for aqueous complexation, precipitation and dissolution, the breakthrough and rinseout curves generated by each model were similar. The differences in simulated equilibrium concentrations between models were minor and were related to (1) different units in model output, (2) different activity coefficients, and (3) ionic-strength calculations. When adsorption processes were added to the models, the rinseout pH simulated by PHREEQC using the diffuse double-layer adsorption model rose to a pH of 6 after pore volume 15, about 1 pore volume later than the pH simulated by HGC using the constant-capacitance model. In PHREEQC simulation of a laboratory column experiment, the inability of the model to match measured outflow concentrations of selected constituents was related to the evident lack of local geochemical equilibrium in the column. The difference in timing and size of measured and simulated breakthrough of selected constituents indicated that the redox and adsorption reactions in the column occurred slowly when compared with the modeled reactions. MINTEQA2 and PHREEQC simulations of the column experiment indicated that the number of surface sites that took part in adsorption reactions was less than that estimated from the measured concentration of Fe hydroxide in the alluvium.

  4. 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

  5. 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

  6. Reactive transport of uranium in fractured crystalline rock: Upscaling in time and distance

    DOE PAGES

    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

  7. 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.

  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.

  9. 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.

  10. Reactive Transport Analysis of Fault 'Self-sealing' Associated with CO2 Storage

    NASA Astrophysics Data System (ADS)

    Patil, V.; McPherson, B. J. O. L.; Priewisch, A.; Franz, R. J.

    2014-12-01

    We present an extensive hydrologic and reactive transport analysis of the Little Grand Wash fault zone (LGWF), a natural analog of fault-associated leakage from an engineered CO2 repository. Injecting anthropogenic CO2 into the subsurface is suggested for climate change mitigation. However, leakage of CO2 from its target storage formation into unintended areas is considered as a major risk involved in CO2 sequestration. In the event of leakage, permeability in leakage pathways like faults may get sealed (reduced) due to precipitation or enhanced (increased) due to dissolution reactions induced by CO2-enriched water, thus influencing migration and fate of the CO2. We hypothesize that faults which act as leakage pathways can seal over time in presence of CO2-enriched waters. An example of such a fault 'self-sealing' is found in the LGWF near Green River, Utah in the Paradox basin, where fault outcrop shows surface and sub-surface fractures filled with calcium carbonate (CaCO3). The LGWF cuts through multiple reservoirs and seal layers piercing a reservoir of naturally occurring CO2, allowing it to leak into overlying aquifers. As the CO2-charged water from shallower aquifers migrates towards atmosphere, a decrease in pCO2 leads to supersaturation of water with respect to CaCO3, which precipitates in the fractures of the fault damage zone. In order to test the nature, extent and time-frame of the fault sealing, we developed reactive flow simulations of the LGWF. Model parameters were chosen based on hydrologic measurements from literature. Model geochemistry was constrained by water analysis of the adjacent Crystal Geyser and observations from a scientific drilling test conducted at the site. Precipitation of calcite in the top portion of the fault model led to a decrease in the porosity value of the damage zone, while clay precipitation led to a decrease in the porosity value of the fault core. We found that the results were sensitive to the fault architecture

  11. 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.

  12. 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.

  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. Investigating the role of gas bubble formation and entrapment in contaminated aquifers: Reactive transport modelling.

    PubMed

    Amos, Richard T; Ulrich Mayer, K

    2006-09-10

    In many natural and contaminated aquifers, geochemical processes result in the production or consumption of dissolved gases. In cases where methanogenesis or denitrification occurs, the production of gases may result in the formation and growth of gas bubbles below the water table. Near the water table, entrapment of atmospheric gases during water table rise may provide a significant source of O(2) to waters otherwise depleted in O(2). Furthermore, the presence of bubbles will affect the hydraulic conductivity of an aquifer, resulting in changes to the groundwater flow regime. The interactions between physical transport, biogeochemical processes, and gas bubble formation, entrapment and release is complex and requires suitable analysis tools. The objective of the present work is the development of a numerical model capable of quantitatively assessing these processes. The multicomponent reactive transport code MIN3P has been enhanced to simulate bubble growth and contraction due to in-situ gas production or consumption, bubble entrapment due to water table rise and subsequent re-equilibration of the bubble with ambient groundwater, and permeability changes due to trapped gas phase saturation. The resulting formulation allows for the investigation of complex geochemical systems where microbially mediated redox reactions both produce and consume gases as well as affect solution chemistry, alkalinity, and pH. The enhanced model has been used to simulate processes in a petroleum hydrocarbon contaminated aquifer where methanogenesis is an important redox process. The simulations are constrained by data from a crude oil spill site near Bemidji, MN. Our results suggest that permeability reduction in the methanogenic zone due to in-situ formation of gas bubbles, and dissolution of entrapped atmospheric bubbles near the water table, both work to attenuate the dissolved gas plume emanating from the source zone. Furthermore, the simulations demonstrate that under the given

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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).

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. The importance of conceptual models in the reactive transport simulation of oxygen ingress in sparsely fractured crystalline rock.

    PubMed

    Macquarrie, K T B; Mayer, K U; Jin, B; Spiessl, S M

    2010-03-01

    Redox evolution in sparsely fractured crystalline rocks is a key, and largely unresolved, issue when assessing the geochemical suitability of deep geological repositories for nuclear waste. Redox zonation created by the influx of oxygenated waters has previously been simulated using reactive transport models that have incorporated a variety of processes, resulting in predictions for the depth of oxygen penetration that may vary greatly. An assessment and direct comparison of the various underlying conceptual models are therefore needed. In this work a reactive transport model that considers multiple processes in an integrated manner is used to investigate the ingress of oxygen for both single fracture and fracture zone scenarios. It is shown that the depth of dissolved oxygen migration is greatly influenced by the a priori assumptions that are made in the conceptual models. For example, the ability of oxygen to access and react with minerals in the rock matrix may be of paramount importance for single fracture conceptual models. For fracture zone systems, the abundance and reactivity of minerals within the fractures and thin matrix slabs between the fractures appear to provide key controls on O(2) attenuation. The findings point to the need for improved understanding of the coupling between the key transport-reaction feedbacks to determine which conceptual models are most suitable and to provide guidance for which parameters should be targeted in field and laboratory investigations.

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Three-dimensional density-dependent flow and multicomponent reactive transport modeling of chlorinated solvent oxidation by potassium permanganate.

    PubMed

    Henderson, Thomas H; Mayer, K Ulrich; Parker, Beth L; Al, Tom A

    2009-05-12

    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.

  12. 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

  13. 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

  14. 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

  15. Regional CO2 flux estimates from estuarine environments: a reactive-transport modeling approach

    NASA Astrophysics Data System (ADS)

    Goossens, Nicolas; Laruelle, Goulven G.; Arndt, Sandra; Regnier, Pierre

    2013-04-01

    Estuaries are key components of the land-ocean continuum and play an important role in the global carbon cycle. Large amounts of terrestrial carbon are channelled through estuaries before reaching the ocean. During estuarine transit, numerous biogeochemical processes transform the carbon flux, resulting in a significant CO2 evasion flux to the atmosphere. The global estuarine CO2 outgassing is evaluated at 0.25±0.25 PgC yr-1. Yet, these estimates rely on the extrapolation of local measurements and the scarcity of such measurements conducts to large uncertainties. Furthermore, the global quantification is biased towards anthropogenically impacted estuarine systems located in industrialized countries. Here we provide a first assessment of the estuarine carbon budget and, in particular, CO2 evasion fluxes using a generic and effective reactive-transport model (RTM) approach that is applicable at the regional scale. The new approach is based on the mutual dependency between estuarine geometry and hydrodynamics and uses idealized estuarine geometries. Global river databases (GLORICH) and watershed model outputs (GlobalNEWS) are used to quantify input fluxes for the generic estuarine model. The new modeling approach provides not only a quantification of the estuarine carbon budget, but also allows disentangling the relative contributions of biogeochemical and physical processes to estuarine CO2 emissions. Preliminary results are presented for the North Eastern coast of the US. Model results are consistent with observations and indicate that the net heterotrophy of these systems is the major contributor to estuarine CO2 fluxes (>50%), followed by outgassing of supersaturated riverine waters and nitrification. Results also highlight the strong seasonality in the biogeochemical dynamics. In addition, significant heterogeneity is observed across different estuaries due to spatial heterogeneities in climate forcing, estuarine geometry or riverine input fluxes. The proposed

  16. 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

  17. 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

  18. 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

  19. 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.

  20. Reactive transport modeling of stable carbon isotope fractionation in a multi-phase multi-component system during carbon sequestration

    DOE PAGES

    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

  1. 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.

  2. 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.

  3. Quinone-reactive proteins devoid of haem b form widespread membrane-bound electron transport modules in bacterial respiration.

    PubMed

    Simon, Jörg; Kern, Melanie

    2008-10-01

    Many quinone-reactive enzyme complexes that are part of membrane-integral eukaryotic or prokaryotic respiratory electron transport chains contain one or more haem b molecules embedded in the membrane. In recent years, various novel proteins have emerged that are devoid of haem b but are thought to fulfil a similar function in bacterial anaerobic respiratory systems. These proteins are encoded by genes organized in various genomic arrangements and are thought to form widespread membrane-bound quinone-reactive electron transport modules that exchange electrons with redox partner proteins located at the outer side of the cytoplasmic membrane. Prototypic representatives are the multihaem c-type cytochromes NapC, NrfH and TorC (NapC/NrfH family), the putative iron-sulfur protein NapH and representatives of the NrfD/PsrC family. Members of these protein families vary in the number of their predicted transmembrane segments and, consequently, diverse quinone-binding sites are expected. Only a few of these enzymes have been isolated and characterized biochemically and high-resolution structures are limited. This mini-review briefly summarizes predicted and experimentally demonstrated properties of the proteins in question and discusses their role in electron transport and bioenergetics of anaerobic respiration.

  4. 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

  5. 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.

  6. 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.

  7. Human health risk assessment of CO2 leakage into overlying aquifers using a stochastic, geochemical reactive transport approach.

    PubMed

    Atchley, Adam L; Maxwell, Reed M; Navarre-Sitchler, Alexis K

    2013-06-01

    Increased human health risk associated with groundwater contamination from potential carbon dioxide (CO2) leakage into a potable aquifer is predicted by conducting a joint uncertainty and variability (JUV) risk assessment. The approach presented here explicitly incorporates heterogeneous flow and geochemical reactive transport in an efficient manner and is used to evaluate how differences in representation of subsurface physical heterogeneity and geochemical reactions change the calculated risk for the same hypothetical aquifer scenario where a CO2 leak induces increased lead (Pb(2+)) concentrations through dissolution of galena (PbS). A nested Monte Carlo approach was used to take Pb(2+) concentrations at a well from an ensemble of numerical reactive transport simulations (uncertainty) and sample within a population of potentially exposed individuals (variability) to calculate risk as a function of both uncertainty and variability. Pb(2+) concentrations at the well were determined with numerical reactive transport simulation ensembles using a streamline technique in a heterogeneous 3D aquifer. Three ensembles with variances of log hydraulic conductivity (σ(2)lnK) of 1, 3.61, and 16 were simulated. Under the conditions simulated, calculated risk is shown to be a function of the strength of subsurface heterogeneity, σ(2)lnK and the choice between calculating Pb(2+) concentrations in groundwater using equilibrium with galena and kinetic mineral reaction rates. Calculated risk increased with an increase in σ(2)lnK of 1 to 3.61, but decreased when σ(2)lnK was increased from 3.61 to 16 for all but the highest percentiles of uncertainty. Using a Pb(2+) concentration in equilibrium with galena under CO2 leakage conditions (PCO2 = 30 bar) resulted in lower estimated risk than the simulations where Pb(2+) concentrations were calculated using kinetic mass transfer reaction rates for galena dissolution and precipitation. This study highlights the importance of

  8. Human health risk assessment of CO2 leakage into overlying aquifers using a stochastic, geochemical reactive transport approach.

    PubMed

    Atchley, Adam L; Maxwell, Reed M; Navarre-Sitchler, Alexis K

    2013-06-01

    Increased human health risk associated with groundwater contamination from potential carbon dioxide (CO2) leakage into a potable aquifer is predicted by conducting a joint uncertainty and variability (JUV) risk assessment. The approach presented here explicitly incorporates heterogeneous flow and geochemical reactive transport in an efficient manner and is used to evaluate how differences in representation of subsurface physical heterogeneity and geochemical reactions change the calculated risk for the same hypothetical aquifer scenario where a CO2 leak induces increased lead (Pb(2+)) concentrations through dissolution of galena (PbS). A nested Monte Carlo approach was used to take Pb(2+) concentrations at a well from an ensemble of numerical reactive transport simulations (uncertainty) and sample within a population of potentially exposed individuals (variability) to calculate risk as a function of both uncertainty and variability. Pb(2+) concentrations at the well were determined with numerical reactive transport simulation ensembles using a streamline technique in a heterogeneous 3D aquifer. Three ensembles with variances of log hydraulic conductivity (σ(2)lnK) of 1, 3.61, and 16 were simulated. Under the conditions simulated, calculated risk is shown to be a function of the strength of subsurface heterogeneity, σ(2)lnK and the choice between calculating Pb(2+) concentrations in groundwater using equilibrium with galena and kinetic mineral reaction rates. Calculated risk increased with an increase in σ(2)lnK of 1 to 3.61, but decreased when σ(2)lnK was increased from 3.61 to 16 for all but the highest percentiles of uncertainty. Using a Pb(2+) concentration in equilibrium with galena under CO2 leakage conditions (PCO2 = 30 bar) resulted in lower estimated risk than the simulations where Pb(2+) concentrations were calculated using kinetic mass transfer reaction rates for galena dissolution and precipitation. This study highlights the importance of

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. PoreFlow: A complex pore-network model for simulation of reactive transport in variably saturated porous media

    NASA Astrophysics Data System (ADS)

    Raoof, A.; Nick, H. M.; Hassanizadeh, S. M.; Spiers, C. J.

    2013-12-01

    This study introduces PoreFlow, a pore-network modeling tool capable of simulating fluid flow and multi-component reactive and adsorptive transport under saturated and variably saturated conditions. PoreFlow includes a variety of modules, such as: pore network generator, drainage simulator, calculation of pressure and velocity distributions, and modeling of reactive solute transport accounting for advection and diffusion. The pore space is represented using a multi-directional pore-network capable of capturing the random structure of a given porous media with user-defined directional connectivities for anisotropic pore structures. The chemical reactions can occur within the liquid phase, as well as between the liquid and solid phases which may result in an evolution of porosity and permeability. Under variably saturated conditions the area of interfaces changes with degree of the fluid saturation. PoreFlow uses complex formulations for more accurate modeling of transport problems in presence of the nonwetting phase. This is done by refining the discretization within drained pores. An implicit numerical scheme is used to solve the governing equations, and an efficient substitution method is applied to considerably minimize computational times. Several examples are provided, under saturated and variably saturated conditions, to demonstrate the model applicability in hydrogeology problems and petroleum fields. We show that PoreFlow is a powerful tool for upscaling of flow and transport in porous media, utilizing different pore scale information such as various interfaces, phase distributions and local fluxes and concentrations to determine macro scale properties such as average saturation, relative permeability, solute dispersivity, adsorption coefficients, effective diffusion and tortuosity. Such information can be used as constitutive relations within continuum scale governing equations to model physical and chemical processes more accurately at the larger scales.

  14. The effect of the serotonin transporter (5-HTTLPR) polymorphism on empathic and self-conscious emotional reactivity

    PubMed Central

    Gyurak, Anett; Haase, Claudia M.; Sze, Jocelyn; Goodkind, Madeleine S.; Coppola, Giovanni; Lane, Jessica; Miller, Bruce L.; Levenson, Robert W.

    2012-01-01

    We examined the relationship between a functional polymorphism of the serotonin transporter (5-HTTLPR) gene 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

  15. Interaction of reactive fronts during transport in a homogeneous porous medium with initial small non-uniformity.

    PubMed

    Chen, Jui-Sheng; Liu, Chen-Wuing

    2004-08-01

    A reactive fluid circulating within a porous medium can dissolve minerals with which it is out of equilibrium and modify the porosity and permeability. The positive feedback between fluid transport and mineral dissolution causes complex reaction front morphologies such as fingers or wormholes. This study presents a numerical model to investigate reaction front instability, temporal aquifer porosity, and species concentration evolution during reactive transport in a homogeneous porous medium with two small, initially local non-uniformities. Simulation results indicate that a stable planar front develops for a small upstream pressure gradient while the growth of two non-uniformities becomes unstable for a large upstream pressure gradient. Moreover, the unstable reaction front may be either double- or single-finger in shape. Reaction front shape selection depends on the spacing of the two local non-uniformities and the upstream pressure gradients. A behavior diagram is constructed to identify a planar, single- or double-front morphology. The critical non-uniformities spacing at which a reaction front begins to merge into a single-finger decreases with increasing upstream pressure gradient.

  16. Biogeochemical Reactive Transport Model of the Redox Zone Experiment of the Aespoe Hard Rock Laboratory in Sweden

    SciTech Connect

    Molinero-Huguet, Jorge; Samper-Calvete, F. Javier; Zhang Guoxiang; Yang Changbing

    2004-11-15

    Underground facilities are being operated by several countries around the world for performing research and demonstration of the safety of deep radioactive waste repositories. The Aespoe Hard Rock Laboratory is one such facility launched and operated by the Swedish Nuclear Fuel and Waste Management Company where various in situ experiments have been performed in fractured granites. One such experiment is the redox zone experiment, which aimed at evaluating the effects of the construction of an access tunnel on the hydrochemical conditions of a fracture zone. Dilution of the initially saline groundwater by fresh recharge water is the dominant process controlling the hydrochemical evolution of most chemical species, except for bicarbonate and sulfate, which unexpectedly increase with time. We present a numerical model of water flow, reactive transport, and microbial processes for the redox zone experiment. This model provides a plausible quantitatively based explanation for the unexpected evolution of bicarbonate and sulfate, reproduces the breakthrough curves of other reactive species, and is consistent with previous hydrogeological and solute transport models.

  17. 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.

  18. A coupled non-isothermal reactive transport model for long-term geochemical evolution of a HLW repository in clay

    NASA Astrophysics Data System (ADS)

    Yang, Changbing; Samper, Javier; Montenegro, Luis

    2008-02-01

    A numerical model of coupled saturated/unsaturated water flow, heat transfer and multi-component reactive solute transport is presented to evaluate the long-term geochemical evolution in bentonite, concrete and clay formation for a potential geological radioactive waste repository. Changes in formation porosity caused by mineral dissolution/precipitation reactions are taken into account. Simulations were carried out with a general-purpose multicomponent reactive transport code, CORE2D V4. Numerical results show that pH in the bentonite porewater can vary from neutral to up to 13 over a time scale of 1 Ma although dissolution of silica minerals and precipitation of secondary calcium silicate hydrate (CSH) minerals in bentonite buffer the effect of the hyperalkaline plume. Mineral precipitation reduces the volume of pore space in bentonite close to the bentonite concrete interface due to the precipitation of CSH minerals. Model results indicate that bentonite porosity decreases less than 25%. The hyperalkaline plume from the concrete only extends to a distance of 0.7 m in the clay formation over the time range of 1 Ma.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  20. Reactive transport modeling to study changes in water chemistry induced by CO2 injection at the Frio-I Brine Pilot

    USGS Publications Warehouse

    Xu, T.; Kharaka, Y.K.; Doughty, C.; Freifeld, B.M.; Daley, T.M.

    2010-01-01

    To demonstrate the potential for geologic storage of CO2 in saline aquifers, the Frio-I Brine Pilot was conducted, during which 1600 tons of CO2 were injected into a high-permeability sandstone and the resulting subsurface plume of CO2 was monitored using a variety of hydrogeological, geophysical, and geochemical techniques. Fluid samples were obtained before CO2 injection for baseline geochemical characterization, during the CO2 injection to track its breakthrough at a nearby observation well, and after injection to investigate changes in fluid composition and potential leakage into an overlying zone. Following CO2 breakthrough at the observation well, brine samples showed sharp drops in pH, pronounced increases in HCO3- and aqueous Fe, and significant shifts in the isotopic compositions of H2O and dissolved inorganic carbon. Based on a calibrated 1-D radial flow model, reactive transport modeling was performed for the Frio-I Brine Pilot. A simple kinetic model of Fe release from the solid to aqueous phase was developed, which can reproduce the observed increases in aqueous Fe concentration. Brine samples collected after half a year had lower Fe concentrations due to carbonate precipitation, and this trend can be also captured by our modeling. The paper provides a method for estimating potential mobile Fe inventory, and its bounding concentration in the storage formation from limited observation data. Long-term simulations show that the CO2 plume gradually spreads outward due to capillary forces, and the gas saturation gradually decreases due to its dissolution and precipitation of carbonates. The gas phase is predicted to disappear after 500 years. Elevated aqueous CO2 concentrations remain for a longer time, but eventually decrease due to carbonate precipitation. For the Frio-I Brine Pilot, all injected CO2 could ultimately be sequestered as carbonate minerals. ?? 2010 Elsevier B.V.

  1. Reactive transport modeling to study changes in water chemistry induced by CO2 injection at the Frio-I brine pilot

    SciTech Connect

    Kharaka, Y.K; Doughty, C.; Freifeld, B.M.; Daley, T.M.; Xu, T.

    2009-11-01

    To demonstrate the potential for geologic storage of CO{sub 2} in saline aquifers, the Frio-I Brine Pilot was conducted, during which 1600 tons of CO{sub 2} were injected into a high-permeability sandstone and the resulting subsurface plume of CO{sub 2} was monitored using a variety of hydrogeological, geophysical, and geochemical techniques. Fluid samples were obtained before CO{sub 2} injection for baseline geochemical characterization, during the CO{sub 2} injection to track its breakthrough at a nearby observation well, and after injection to investigate changes in fluid composition and potential leakage into an overlying zone. Following CO{sub 2} breakthrough at the observation well, brine samples showed sharp drops in pH, pronounced increases in HCO{sub 3}{sup -} and aqueous Fe, and significant shifts in the isotopic compositions of H{sub 2}O and dissolved inorganic carbon. Based on a calibrated 1-D radial flow model, reactive transport modeling was performed for the Frio-I Brine Pilot. A simple kinetic model of Fe release from the solid to aqueous phase was developed, which can reproduce the observed increases in aqueous Fe concentration. Brine samples collected after half a year had lower Fe concentrations due to carbonate precipitation, and this trend can be also captured by our modeling. The paper provides a method for estimating potential mobile Fe inventory, and its bounding concentration in the storage formation from limited observation data. Long-term simulations show that the CO{sub 2} plume gradually spreads outward due to capillary forces, and the gas saturation gradually decreases due to its dissolution and precipitation of carbonates. The gas phase is predicted to disappear after 500 years. Elevated aqueous CO{sub 2} concentrations remain for a longer time, but eventually decrease due to carbonate precipitation. For the Frio-I Brine Pilot, all injected CO{sub 2} could ultimately be sequestered as carbonate minerals.

  2. 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–environment interaction research on 5-HTTLPR as they possibly capture the net effects of environmental influences relevant for stress-related phenotypes under serotonergic control. PMID:25226552

  3. Sulfide mineral oxidation and subsequent reactive transport of oxidation products in mine tailings impoundments: A numerical model

    NASA Astrophysics Data System (ADS)

    Wunderly, M. D.; Blowes, D. W.; Frind, E. O.; Ptacek, C. J.

    1996-10-01

    A versatile numerical model that couples oxygen diffusion and sulfide-mineral oxidation (PYROX) has been developed to simulate the oxidation of pyrite in the vadose zone of mine tailings. A shrinking-core oxidation model and a finite element numerical scheme are used to simulate the transport of oxygen and oxidation of pyrite grains. The rate of pyrite oxidation is assumed to be limited by the transport of oxygen to the reaction site. The model determines the spatially variable bulk diffusion coefficient for oxygen on the basis of moisture content, porosity, and temperature, all of which are variable input parameters. The model PYROX has been coupled to an existing reactive transport model (MINTRAN), which uses a finite element scheme for transport of contaminants and MINTEQA2 to solve for the equilibrium geochemistry. The reactions described by MINTRAN are subject to the local equilibrium assumption. The resulting model, MINTOX, is capable of simulating tailings impoundments where the oxidation of pyrite or pyrrhotite is causing acidic drainage and where acid neutralization and attenuation of dissolved metals can be attributed to equilibrium reactions. Because MINTOX uses realistic boundary conditions and hydrogeological properties, the potential benefits of various remediation schemes, such as moisture-retaining covers, can be quantitatively evaluated.

  4. Comparative assessment of continuum-scale models of bimolecular reactive transport in porous media under pre-asymptotic conditions

    NASA Astrophysics Data System (ADS)

    Porta, G. M.; Ceriotti, G.; Thovert, J.-F.

    2016-02-01

    We compare the ability of various continuum-scale models to reproduce the key features of a transport setting associated with a bimolecular reaction taking place in the fluid phase and numerically simulated at the pore-scale level in a disordered porous medium. We start by considering a continuum-scale formulation which results from formal upscaling of this reactive transport process by means of volume averaging. The resulting (upscaled) continuum-scale system of equations includes nonlocal integro-differential terms and the effective parameters embedded in the model are quantified directly through computed pore-scale fluid velocity and pore space geometry attributes. The results obtained through this predictive model formulation are then compared against those provided by available effective continuum models which require calibration through parameter estimation. Our analysis considers two models recently proposed in the literature which are designed to embed incomplete mixing arising from the presence of fast reactions under advection-dominated transport conditions. We show that best estimates of the parameters of these two models heavily depend on the type of data employed for model calibration. Our upscaled nonlocal formulation enables us to reproduce most of the critical features observed through pore-scale simulation without any model calibration. As such, our results clearly show that embedding into a continuum-scale model the information content associated with pore-scale geometrical features and fluid velocity yields improved interpretation of typically available continuum-scale transport observations.

  5. TOUGHREACT User's Guide: A Simulation Program for Non-isothermal Multiphase Reactive geochemical Transport in Variable Saturated Geologic Media

    SciTech Connect

    Xu, Tianfu; Sonnenthal, Eric; Spycher, Nicolas; Pruess, Karsten

    2004-05-24

    Coupled modeling of subsurface multiphase fluid and heat flow, solute transport and chemical reactions can be used for the assessment of mineral alteration in hydrothermal systems, waste disposal sites, acid mine drainage remediation, contaminant transport, and groundwater quality. A comprehensive non-isothermal multi-component reactive fluid flow and geochemical transport simulator, TOUGHREACT, has been developed. A wide range of subsurface thermo-physical-chemical processes is considered under various thermohydrological and geochemical conditions of pressure, temperature, water saturation, and ionic strength. The program can be applied to one-, two- or three-dimensional porous and fractured media with physical and chemical heterogeneity. The model can accommodate any number of chemical species present in liquid, gas and solid phases. A variety of equilibrium chemical reactions are considered, such as aqueous complexation, gas dissolution/exsolution, and cation exchange. Mineral dissolution/precipitation can proceed either subject to local equilibrium or kinetic conditions. Changes in porosity and permeability due to mineral dissolution and precipitation can be considered. Linear adsorption and decay can be included. For the purpose of future extensions, surface complexation by double layer model is coded in the program. Xu and Pruess (1998) developed a first version of a non-isothermal reactive geochemical transport model, TOUGHREACT, by introducing reactive geochemistry into the framework of the existing multi-phase fluid and heat flow code TOUGH2 (Pruess, 1991). Xu, Pruess, and their colleagues have applied the program to a variety of problems such as: (1) supergene copper enrichment (Xu et al, 2001), (2) caprock mineral alteration in a hydrothermal system (Xu and Pruess, 2001a), and (3) mineral trapping for CO{sub 2} disposal in deep saline aquifers (Xu et al, 2003b and 2004a). For modeling the coupled thermal, hydrological, and chemical processes during

  6. The serotonin transporter gene-linked polymorphic region (5-HTTLPR) and cortisol stress reactivity: a meta-analysis.

    PubMed

    Miller, R; Wankerl, M; Stalder, T; Kirschbaum, C; Alexander, N

    2013-09-01

    Recent meta-analyses have stimulated an active debate on whether the serotonin transporter gene-linked polymorphic region (5-HTTLPR) is associated with an elevated vulnerability to psychiatric diseases upon exposure to environmental adversity. As a potential mechanism explaining genotype-dependent differences in stress sensitivity, altered stress-induced activation of the hypothalamus-pituitary-adrenal (HPA) axis has been investigated in several experimental studies, with most of these studies comprising small samples. We evaluated the association of 5-HTTLPR genotype and cortisol reactivity to acute psychosocial stress by applying a meta-analytical technique based on eleven relevant data sets (total N=1686), which were identified through a systematic literature search up to October 2011. This meta-analysis indicates a small (d=0.27), but significant association between 5-HTTLPR genotype and HPA-axis reactivity to acute psychosocial stress with homozygous carriers of the S allele displaying increased cortisol reactivity compared with individuals with the S/L and L/L genotype. The latter association was not further moderated by participants' age, sex or the type of stressor. Formal testing revealed no evidence for a substantial selection or publication bias. Our meta-analytical results are consistent with a wide variety of experimental studies indicating a significant association between 5-HTTLPR genotype and intermediate phenotypes related to stress sensitivity. Future studies are needed to clarify the consistency of this effect and to further explore whether altered HPA-axis stress reactivity reflects a potential biological mechanism conveying an elevated risk for the development of stress-related disorders in S allele carriers. PMID:22945032

  7. RESEARCH ACTIVITIES AT U.S. GOVERNMENT AGENCIES IN SUBSURFACE REACTIVE TRANSPORT MODELING

    EPA Science Inventory

    The fate of contaminants in the environment is controlled by both chemical reactions and transport phenomena in the subsurface. Our ability to understand the significance of these processes over time requires an accurate conceptual model that incorporates the various mechanisms ...

  8. Reactive solute transport in streams. 1. Development of an equilibrium- based model

    USGS Publications Warehouse

    Runkel, R.L.; Bencala, K.E.; Broshears, R.E.; Chapra, S.C.

    1996-01-01

    An equilibrium-based solute transport model is developed for the simulation of trace metal fate and transport in streams. The model is formed by coupling a solute transport model with a chemical equilibrium submodel based on MINTEQ. The solute transport model considers the physical processes of advection, dispersion, lateral inflow, and transient storage, while the equilibrium submodel considers the speciation and complexation of aqueous species, precipitation/dissolution and sorption. Within the model, 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 (water-borne) 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.

  9. Heterogeneous reactive transport under unsaturated transient conditions characterized by 3D electrical resistivity tomography and advanced lysimeter methods

    NASA Astrophysics Data System (ADS)

    Wehrer, Markus; Slater, Lee

    2015-04-01

    Our ability to predict flow and transport processes in the unsaturated critical zone is considerably limited by two characteristics: heterogeneity of flow and transience of boundary conditions. The causes of heterogeneous flow and transport are fairly well understood, yet the characterization and quantification of such processes in natural profiles remains challenging. This is due to current methods of observation, such as staining and isotope tracers, being unable to observe multiple events on the same profile and offering limited spatial information. In our study we demonstrate an approach to characterize preferential flow and transport processes applying a combination of geoelectrical methods and advanced lysimeter techniques. On an agricultural soil profile, which was transferred undisturbed into a lysimeter container, we systematically applied a variety of input flow boundary conditions, resembling natural precipitation events. We measured breakthroughs of a conservative tracer and of nitrate, originating from the application of a slow release fertilizer and serving as a reactive tracer. Flow and transport in the soil column were observed using electrical resistivity tomography (ERT), tensiometers, water content probes and a multicompartment suction plate (MSP). These techniques allowed a direct validation of water content dynamics and tracer breakthrough under transient boundary conditions characterized noninvasively by ERT. We were able to image the advancing infiltration front and the advancing front of tracer and nitrate using time lapse ERT. Water content changes associated with the advancing infiltration front dominated over pore fluid conductivity changes during short term precipitation events. Conversely, long-term displacement of the solute fronts was monitored during periods of constant water content in between infiltration events. We observed preferential flow phenomena through ERT and through the MSP, which agreed in general terms. The preferential

  10. Reactive-transport simulation of phosphorus in the sewage plume at the Massachusetts Military Reservation, Cape Cod, Massachusetts

    USGS Publications Warehouse

    Parkhurst, David L.; Stollenwerk, Kenneth G.; Colman, John A.

    2003-01-01

    The subsurface transport of phosphorus introduced by the disposal of treated sewage effluent to ground-infiltration disposal beds at the Massachusetts Military Reservation on western Cape Cod was simulated with a three-dimensional reactive-transport model. The simulations were used to estimate the load of phosphorus transported to Ashumet Pond during operation of the sewage-treatment plant?from 1936 to 1995?and for 60 years following cessation of sewage disposal. The model accounted for spatial and temporal changes in water discharge from the sewage-treatment plant, ground-water flow, transport of associated chemical constituents, and a set of chemical reactions, including phosphorus sorption on aquifer materials, dissolution and precipitation of iron- and manganese-oxyhydroxide and iron phosphate minerals, organic carbon sorption and decomposition, cation sorption, and irreversible denitrification. The flow and transport in the aquifer were simulated by using parameters consistent with those used in previous flow models of this area of Cape Cod, except that numerical dispersion was much larger than the physical dispersion estimated in previous studies. Sorption parameters were fit to data derived from phosphorus sorption and desorption laboratory column experiments. Rates of organic carbon decomposition were adjusted to match the location of iron concentrations in an anoxic iron zone within the sewage plume. The sensitivity of the simulated load of phosphorus transported to Ashumet Pond was calculated for a variety of processes and input parameters. Model limitations included large uncertainties associated with the loading of the sewage beds, the flow system, and the chemistry and sorption characteristics in the aquifer. The results of current model simulations indicate a small load of phosphorus transported to Ashumet Pond during 1965?85, but this small load was particularly sensitive to model parameters that specify flow conditions and the chemical process by

  11. Inverse Reactive Transport Simulator (Inverts): An Inverse Model for Contaminant Transport with Nonlinear Adsorption and Source Terms

    SciTech Connect

    McGrail, B. Peter

    2001-10-31

    A numerically based simulator was developed to assist in the interpretation of complex laboratory experiments examining transport processes of chemical and biological contaminants subject to nonlinear adsorption and/or source terms. The inversion is performed with any of three nonlinear regression methods, Marquardt-Levenberg, conjugate gradient, or quasi-Newton. The governing equations for the problem are solved by the method of finite-differences including any combination of three boundary conditions: (1) Dirichlet, (2) Neumann, and (3) Cauchy. The dispersive terms in the transport equations were solved using the second-order accurate in time and space Crank-Nicolson scheme, while the advective terms were handled using a third-order in time and space, total variation diminishing (TVD) scheme that damps spurious oscillations around sharp concentration fronts. The numerical algorithms were implemented in the computer code INVERTS, which runs on any standard personal computer. Apart from a comprehensive set of test problems, INVERTS was also used to model the elution of a nonradioactive tracer, {sup 185}Re, in a pressurized unsaturated flow (PUF) experiment with a simulated waste glass for low-activity waste immobilization. Interpretation of the elution profile was best described with a nonlinear kinetic model for adsorption.

  12. Kinetic dissolution of carbonates and Mn oxides in acidic water: Measurement of in situ field rates and reactive transport modeling

    USGS Publications Warehouse

    Brown, J.G.; Glynn, P.D.

    2003-01-01

    The kinetics of carbonate and Mn oxide dissolution under acidic conditions were examined through the in situ exposure of pure phase samples to acidic ground water in Pinal Creek Basin, Arizona. The average long-term calculated in situ dissolution rates for calcite and dolomite were 1.65??10-7 and 3.64??10-10 mmol/(cm2 s), respectively, which were about 3 orders of magnitude slower than rates derived in laboratory experiments by other investigators. Application of both in situ and lab-derived calcite and dolomite dissolution rates to equilibrium reactive transport simulations of a column experiment did not improve the fit to measured outflow chemistry: at the spatial and temporal scales of the column experiment, the use of an equilibrium model adequately simulated carbonate dissolution in the column. Pyrolusite (MnO2) exposed to acidic ground water for 595 days increased slightly in weight despite thermodynamic conditions that favored dissolution. This result might be related to a recent finding by another investigator that the reductive dissolution of pyrolusite is accompanied by the precipitation of a mixed Mn-Fe oxide species. In PHREEQC reactive transport simulations, the incorporation of Mn kinetics improved the fit between observed and simulated behavior at the column and field scales, although the column-fitted rate for Mn-oxide dissolution was about 4 orders of magnitude greater than the field-fitted rate. Remaining differences between observed and simulated contaminant transport trends at the Pinal Creek site were likely related to factors other than the Mn oxide dissolution rate, such as the concentration of Fe oxide surface sites available for adsorption, the effects of competition among dissolved species for available surface sites, or reactions not included in the model.

  13. Integration of Genome-Scale Metabolic Nodels of Iron-Reducing Bacteria With Subsurface Flow and Geochemical Reactive Transport Models

    NASA Astrophysics Data System (ADS)

    Scheibe, T. D.; Mahadevan, R.; Fang, Y.; Garg, S.; Long, P. E.; Lovley, D. M.

    2008-12-01

    Several field and laboratory experiments have demonstrated that the growth and activity of iron-reducing bacteria can be stimulated in many subsurface environments by amendment of groundwater with a soluble electron donor. Under strong iron-reducing conditions, these organisms mediate reactions that can impact a wide range of subsurface contaminants including chlorinated hydrocarbons, metals, and radionuclides. Therefore there is strong interest in in-situ bioremediation as a potential technology for cleanup of contaminated aquifers. To evaluate and design bioremediation systems, as well as to evaluate the viability of monitored natural attenuation as an alternative, quantitative models of biogeochemically reactive transport are needed. To date, most such models represent microbial activity in terms of kinetic rate (e.g., Monod- type) formulations. Such models do not account for fundamental changes in microbial functionality (such as utilization of alternative respiratory pathways) that occur as the result of spatial and temporal variations in the geochemical environment experienced by microorganisms. Constraint-based genome-scale in silico models of microbial metabolism present an alternative to simplified rate formulations that provide flexibility to account for changes in microbial function in response to local geochemical conditions. We have developed and applied a methodology for coupling a constraint-based in silico model of Geobacter sulfurreducens with a conventional model of groundwater flow, transport, and geochemical reaction. Two uses of the in silico model are tested: 1) incorporation of modified microbial growth yield coefficients based on the in silico model, and 2) variation of reaction rates in a reactive transport model based on in silico modeling of a range of local geochemical conditions. Preliminary results from this integrated model will be presented.

  14. HYDROGEOCHEM: A coupled model of HYDROlogic transport and GEOCHEMical equilibria in reactive multicomponent systems

    SciTech Connect

    Yeh, G.T.; Tripathi, V.S.

    1990-11-01

    This report presents the development of a hydrogeochemical transport model for multicomponent systems. The model is designed for applications to proper hydrological setting, accommodation of complete suite of geochemical equilibrium processes, easy extension to deal with chemical kinetics, and least constraints of computer resources. The hydrological environment to which the model can be applied is the heterogeneous, anisotropic, saturated-unsaturated subsurface media under either transient or steady state flow conditions. The geochemical equilibrium processes included in the model are aqueous complexation, adsorption-desorption, ion exchange, precipitation-dissolution, redox, and acid-base reactions. To achieve the inclusion of the full complement of these geochemical processes, total analytical concentrations of all chemical components are chosen as the primary dependent variables in the hydrological transport equations. Attendant benefits of this choice are to make the extension of the model to deal with kinetics of adsorption-desorption, ion exchange, precipitation-dissolution, and redox relatively easy. To make the negative concentrations during the iteration between the hydrological transport and geochemical equilibrium least likely, an implicit form of transport equations are proposed. To alleviate severe constraints of computer resources in terms of central processing unit (CPU) time and CPU memory, various optional numerical schemes are incorporated in the model. The model consists of a hydrological transport module and geochemical equilibrium module. Both modules were thoroughly tested in code consistency and were found to yield plausible results. The model is verified with ten examples. 79 refs., 21 figs., 17 tabs.

  15. Preliminary characterization of materials for a reactive transport model validation experiment

    SciTech Connect

    Siegel, M.D.; Ward, D.B.; Cheng, W.C.; Bryant, C.; Chocas, C.S.; Reynolds, C.G.

    1993-03-01

    The geochemical properties of a porous sand and several tracers (Ni, Br, and Li) have been characterized for use in a caisson experiment designed to validate sorption models used in models of inactive transport. The surfaces of the sand grains have been examined by a combination of techniques including potentiometric titration, acid leaching, optical microscopy, and scanning electron microscopy with energy-dispersive spectroscopy. The surface studies indicate the presence of small amounts of carbonate, kaolinite and iron-oxyhydroxides. Adsorption of nickel, lithium and bromide by the sand was measured using batch techniques. Bromide was not sorbed by the sand. A linear (K{sub d}) or an isotherm sorption model may adequately describe transport of Li; however, a model describing the changes of pH and the concentrations of other solution species as a function of time and position within the caisson and the concomitant effects on Ni sorption may be required for accurate predictions of nickel transport.

  16. The effects of gas-fluid-rock interactions on CO2 injection and storage: Insights from reactive transport modeling

    SciTech Connect

    Xiao, Y.; Xu, T.; Pruess, K.

    2008-10-15

    Possible means of reducing atmospheric CO{sub 2} emissions include injecting CO{sub 2} in petroleum reservoirs for Enhanced Oil Recovery or storing CO{sub 2} in deep saline aquifers. Large-scale injection of CO{sub 2} into subsurface reservoirs would induce a complex interplay of multiphase flow, capillary trapping, dissolution, diffusion, convection, and chemical reactions that may have significant impacts on both short-term injection performance and long-term fate of CO{sub 2} storage. Reactive Transport Modeling is a promising approach that can be used to predict the spatial and temporal evolution of injected CO{sub 2} and associated gas-fluid-rock interactions. This presentation will summarize recent advances in reactive transport modeling of CO{sub 2} storage and review key technical issues on (1) the short- and long-term behavior of injected CO{sub 2} in geological formations; (2) the role of reservoir mineral heterogeneity on injection performance and storage security; (3) the effect of gas mixtures (e.g., H{sub 2}S and SO{sub 2}) on CO{sub 2} storage; and (4) the physical and chemical processes during potential leakage of CO{sub 2} from the primary storage reservoir. Simulation results suggest that CO{sub 2} trapping capacity, rate, and impact on reservoir rocks depend on primary mineral composition and injecting gas mixtures. For example, models predict that the injection of CO{sub 2} alone or co-injection with H{sub 2}S in both sandstone and carbonate reservoirs lead to acidified zones and mineral dissolution adjacent to the injection well, and carbonate precipitation and mineral trapping away from the well. Co-injection of CO{sub 2} with H{sub 2}S and in particular with SO{sub 2} causes greater formation alteration and complex sulfur mineral (alunite, anhydrite, and pyrite) trapping, sometimes at a much faster rate than previously thought. The results from Reactive Transport Modeling provide valuable insights for analyzing and assessing the dynamic

  17. Solute Transport in Eroded and Rehabilitated Prairie Landforms. 2. Reactive Solute

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Information regarding the impact of varying soil, landscape, and climate conditions on the off-site transport of pesticides is critical to the development of improved pesticide management practices. We quantified the rate of S-metolachlor dissipation after fall and spring application in eroded and r...

  18. Transport and Reactivity of Engineered Nanoparticles in Partially Saturated Porous Media

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Engineered nanoparticles (ENPs) are being produced in increasing amounts and have numerous applications in a variety of products and industrial processes. The same properties that make these substances so appealing may also cause them to act as persistent and toxic pollutants. The post-use release of ENPs to the environment is inevitable and soil appears to be one of the largest sinks of these potential contaminants. To date, despite the significant attention that ENP behavior in the environment has received, only a few studies have considered the fate and transport of ENPs in partially saturated systems. Here, we report measurements on the transport and fate of three commonly used ENPs - silver (Ag), gold (Au) and zinc oxide (ZnO) - in partially saturated porous media. The results show that ENP interactions with the solid matrix and solution components affect the fate of the ENPs and their transport. The negatively charged ENPs (AgNPs and AuNPs) are shown to be mobile in sand (which is also negatively charged) under various conditions, including water saturation levels and inlet concentration, with transport behavior resembling conservative tracer movement. Various aging scenarios were considered and the interaction of AgNPs with sulfides, chlorides, and calcium ions, all of which are known to interact and change AgNP properties, are shown to affect AgNP fate; however, in some cases, the changed particles remained suspended in solution and mobile. The positively charged ZnO showed very low mobility, but when humic acid was present in the inlet solution, interactions leading to enhanced mobility were observed. The presence of humic acid also changes ENP size and surface charge, transforming them to negatively charged larger aggregates that can be transported through the sand. Finally, remobilization of particles that were retained in the porous media was also demonstrated for ZnO ENPs, indicating possible release of entrapped ENPs upon changes in solution chemistry.

  19. Reactive solute transport in streams: A surface complexation approach for trace metal sorption

    USGS Publications Warehouse

    Runkel, R.L.; Kimball, B.A.; McKnight, Diane M.; Bencala, K.E.

    1999-01-01

    A model for trace metals that considers in-stream transport, metal oxide precipitation-dissolution, and pH-dependent sorption is presented. Linkage between a surface complexation submodel and the stream transport equations provides a framework for modeling sorption onto static and/or dynamic surfaces. A static surface (e.g., an iron-oxide-coated streambed) is defined as a surface with a temporally constant solid concentration. Limited contact between solutes in the water column and the static surface is considered using a pseudokinetic approach. A dynamic surface (e.g., freshly precipitated metal oxides) has a temporally variable solid concentration and is in equilibrium with the water column. Transport and deposition of solute mass sorbed to the dynamic surface is represented in the stream transport equations that include precipitate settling. The model is applied to a pH-modification experiment in an acid mine drainage stream. Dissolved copper concentrations were depressed for a 3 hour period in response to the experimentally elevated pH. After passage of the pH front, copper was desorbed, and dissolved concentrations returned to ambient levels. Copper sorption is modeled by considering sorption to aged hydrous ferric oxide (HFO) on the streambed (static surface) and freshly precipitated HFO in the water column (dynamic surface). Comparison of parameter estimates with reported values suggests that naturally formed iron oxides may be more effective in removing trace metals than synthetic oxides used in laboratory studies. The model's ability to simulate pH, metal oxide precipitation-dissolution, and pH-dependent sorption provides a means of evaluating the complex interactions between trace metal chemistry and hydrologic transport at the field scale.

  20. Modeling of Calcite Precipitation Driven by Bacteria-facilitated Urea Hydrolysis in A Flow Column Using A Fully Coupled, Fully Implicit Parallel Reactive Transport Simulator

    NASA Astrophysics Data System (ADS)

    Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.

    2009-12-01

    One approach for immobilizing subsurface metal contaminants involves stimulating the in situ production of mineral phases that sequester or isolate contaminants. One example is using calcium carbonate to immobilize strontium. The success of such approaches depends on understanding how various processes of flow, transport, reaction and resulting porosity-permeability change couple in subsurface systems. Reactive transport models are often used for such purpose. Current subsurface reactive transport simulators typically involve a de-coupled solution approach, such as operator-splitting, that solves the transport equations for components and batch chemistry sequentially, which has limited applicability for many biogeochemical processes with fast kinetics and strong medium property-reaction interactions. A massively parallel, fully coupled, fully implicit reactive transport simulator has been developed based on a parallel multi-physics object oriented software environment computing framework (MOOSE) developed at the Idaho National Laboratory. Within this simulator, the system of transport and reaction equations is solved simultaneously in a fully coupled manner using the Jacobian Free Newton-Krylov (JFNK) method with preconditioning. The simulator was applied to model reactive transport in a one-dimensional column where conditions that favor calcium carbonate precipitation are generated by urea hydrolysis that is catalyzed by urease enzyme. Simulation results are compared to both laboratory column experiments and those obtained using the reactive transport simulator STOMP in terms of: the spatial and temporal distributions of precipitates and reaction rates and other major species in the reaction system; the changes in porosity and permeability; and the computing efficiency based on wall clock simulation time.

  1. Electron transport and defect structure in highly conducting reactively sputtered ultrathin tin oxide films

    SciTech Connect

    Bansal, Shikha; Pandya, Dinesh K. Kashyap, Subhash C.

    2014-02-24

    Electrical conduction behavior of ultrathin (5–110 nm) SnO{sub 2} films reactively sputtered at 150–400 °C substrate temperatures is presented. The surface roughness studies revealed that the films with lower thickness were smoother (≤0.6 nm). Stoichiometry/defect structure of the films obtained from X-ray photoelectron spectroscopy data and electron mobility are found to be dependent on film thickness and substrate temperature. The observed increase in conductivity of semi-metallic films with decrease in film thickness is attributed to changes in defect structure and surface roughness. Highest value of conductivity of about 715 Ω{sup −1} cm{sup −1} is obtained for 5 nm thick films deposited at 300 °C.

  2. Understanding arsenic mobilization using reactive transport modeling of groundwater hydrochemistry in the Datong basin study plot, China.

    PubMed

    Mapoma, Harold Wilson Tumwitike; Xie, Xianjun; Pi, Kunfu; Liu, Yaqing; Zhu, Yapeng

    2016-03-01

    This paper discusses the reactive transport and evolution of arsenic along a selected flow path in a study plot within the central part of Datong basin. The simulation used the TOUGHREACT code. The spatial and temporal trends in hydrochemistry and mineral volume fraction along a flow path were observed. Furthermore, initial simulation of major ions and pH fits closely to the measured data. The study shows that equilibrium conditions may be attained at different stress periods for each parameter simulated. It is noted that the variations in ionic chemistry have a greater impact on arsenic distribution while reducing conditions drive the mobilization of arsenic. The study concluded that the reduction of Fe(iii) and As(v) and probably SO4/HS cycling are significant factors affecting localized mobilization of arsenic. Besides cation exchange and water-rock interaction, incongruent dissolution of silicates is also a significant control mechanism of general chemistry of the Datong basin aquifer.

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

    SciTech Connect

    Lovley, Derek R.

    2012-10-31

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

  4. A fully coupled model for water-gas-heat reactive transport with methane oxidation in landfill covers.

    PubMed

    Ng, C W W; Feng, S; Liu, H W

    2015-03-01

    Methane oxidation in landfill covers is a complex process involving water, gas and heat transfer as well as microbial oxidation. The coupled phenomena of microbial oxidation, water, gas, and heat transfer are not fully understood. In this study, a new model is developed that incorporates water-gas-heat coupled reactive transport in unsaturated soil with methane oxidation. Effects of microbial oxidation-generated water and heat are included. The model is calibrated using published data from a laboratory soil column test. Moreover, a series of parametric studies are carried out to investigate the influence of microbial oxidation-generated water and heat, initial water content on methane oxidation efficiency. Computed and measured results of gas concentration and methane oxidation rate are consistent. It is found that the coupling effects between water-gas-heat transfer and methane oxidation are significant. Ignoring microbial oxidation-generated water and heat can result in a significant difference in methane oxidation efficiency by 100%.

  5. A fully coupled model for water-gas-heat reactive transport with methane oxidation in landfill covers.

    PubMed

    Ng, C W W; Feng, S; Liu, H W

    2015-03-01

    Methane oxidation in landfill covers is a complex process involving water, gas and heat transfer as well as microbial oxidation. The coupled phenomena of microbial oxidation, water, gas, and heat transfer are not fully understood. In this study, a new model is developed that incorporates water-gas-heat coupled reactive transport in unsaturated soil with methane oxidation. Effects of microbial oxidation-generated water and heat are included. The model is calibrated using published data from a laboratory soil column test. Moreover, a series of parametric studies are carried out to investigate the influence of microbial oxidation-generated water and heat, initial water content on methane oxidation efficiency. Computed and measured results of gas concentration and methane oxidation rate are consistent. It is found that the coupling effects between water-gas-heat transfer and methane oxidation are significant. Ignoring microbial oxidation-generated water and heat can result in a significant difference in methane oxidation efficiency by 100%. PMID:25489976

  6. Understanding arsenic mobilization using reactive transport modeling of groundwater hydrochemistry in the Datong basin study plot, China.

    PubMed

    Mapoma, Harold Wilson Tumwitike; Xie, Xianjun; Pi, Kunfu; Liu, Yaqing; Zhu, Yapeng

    2016-03-01

    This paper discusses the reactive transport and evolution of arsenic along a selected flow path in a study plot within the central part of Datong basin. The simulation used the TOUGHREACT code. The spatial and temporal trends in hydrochemistry and mineral volume fraction along a flow path were observed. Furthermore, initial simulation of major ions and pH fits closely to the measured data. The study shows that equilibrium conditions may be attained at different stress periods for each parameter simulated. It is noted that the variations in ionic chemistry have a greater impact on arsenic distribution while reducing conditions drive the mobilization of arsenic. The study concluded that the reduction of Fe(iii) and As(v) and probably SO4/HS cycling are significant factors affecting localized mobilization of arsenic. Besides cation exchange and water-rock interaction, incongruent dissolution of silicates is also a significant control mechanism of general chemistry of the Datong basin aquifer. PMID:26857449

  7. Regional-scale hydrologic modeling of flow and reactive salt transport in the San Joaquin Valley, CA

    NASA Astrophysics Data System (ADS)

    Hopmans, J. W.; Schoups, G.

    2005-12-01

    A hydro-salinity model was developed to integrate subsurface hydrology with reactive salt transport for a 1,400 km2 study area in the San Joaquin Valley, CA. For the first time, such a modeling framework was used to reconstruct historical changes in salt storage by irrigated agriculture over the past 60 years. We show that patterns in soil and groundwater salinity were caused by spatial variations in soil hydrology, the switching from local groundwater to snowmelt water as the main irrigation water supply, and by occasional droughts. Gypsum dissolution was a critical component of the regional salt balance. Although results show that the total salt input and output were about equal for the past 20 years, the model also predicts salinization of the deeper aquifers, thereby questioning the sustainability of irrigated agriculture.

  8. Transport Properties of Amine/Carbon Dioxide Reactive Mixtures and Implications to Carbon Capture Technologies.

    PubMed

    Turgman-Cohen, Salomon; Giannelis, Emmanuel P; Escobedo, Fernando A

    2015-08-19

    The structure and transport properties of physisorbed and chemisorbed CO2 in model polyamine liquids (hexamethylenediamine and diethylenetriamine) are studied via molecular dynamics simulations. Such systems are relevant to CO2 absorption processes where nonaqueous amines are used as absorbents (e.g., when impregnated or grafted onto mesoporous media or misted in the gas phase). It is shown that accounting for the ionic speciation resulting from CO2 chemisorption enabled us to capture the qualitative changes in extent of absorption and fluidity with time that are observed in thermogravimetric experiments. Simulations reveal that high enough concentration of reacted CO2 leads to strong intermolecular ionic interactions and the arrest of molecular translations. The transport properties obtained from the simulations of the ionic speciated mixtures are also used to construct an approximate continuum-level model for the CO2 absorption process that mimics thermogravimetric experiments.

  9. Transport Properties of Amine/Carbon Dioxide Reactive Mixtures and Implications to Carbon Capture Technologies.

    PubMed

    Turgman-Cohen, Salomon; Giannelis, Emmanuel P; Escobedo, Fernando A

    2015-08-19

    The structure and transport properties of physisorbed and chemisorbed CO2 in model polyamine liquids (hexamethylenediamine and diethylenetriamine) are studied via molecular dynamics simulations. Such systems are relevant to CO2 absorption processes where nonaqueous amines are used as absorbents (e.g., when impregnated or grafted onto mesoporous media or misted in the gas phase). It is shown that accounting for the ionic speciation resulting from CO2 chemisorption enabled us to capture the qualitative changes in extent of absorption and fluidity with time that are observed in thermogravimetric experiments. Simulations reveal that high enough concentration of reacted CO2 leads to strong intermolecular ionic interactions and the arrest of molecular translations. The transport properties obtained from the simulations of the ionic speciated mixtures are also used to construct an approximate continuum-level model for the CO2 absorption process that mimics thermogravimetric experiments. PMID:26200117

  10. Exact PDF equations and closure approximations for advective-reactive transport

    SciTech Connect

    Venturi, D.; Tartakovsky, Daniel M.; Tartakovsky, Alexandre M.; Karniadakis, George E.

    2013-06-01

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

  11. An Assessment of Thermodynamic Database Effects on Reactive Transport Models' Predictions of Permeability Fields: Insights from CO2/Brine Experiments

    NASA Astrophysics Data System (ADS)

    Tutolo, B. M.; Seyfried, W. E.; Saar, M. O.

    2011-12-01

    Numerical modeling software such as TOUGHREACT, ECLIPSE, and Geochemist's Workbench provide modules that couple mineral reactive chemistry with porosity and permeability modifications to predict the behavior of energy byproducts, such as carbon dioxide, in the subsurface. Modern coders have already included increasingly complex equations that describe natural systems (i.e. mineral dissolution/precipitation kinetic parameters and porosity/permeability functions) into these and other software applications. Generally, these computer models use the bulk volumetric changes predicted by geochemical calculations to infer porosity changes, and subsequently use highly simplified porosity/permeability correlation functions, such as the Carman-Kozeny equation, to modify permeability fields. In spite of the computational complexity provided in these models, they require, as a foundation, fundamental information on the thermodynamic stability of minerals and aqueous species at a wide range of temperatures and pressures to produce accurate predictions of the geochemistry of long-term energy byproduct storage in the subsurface, even in the simplest cases. With improvements in geochemical thermodynamic databases, researchers may begin to produce more realistic simulations of the complex interactions between fluid and heat flow and geological systems. Unfortunately, the requisite thermodynamic data is often lacking, or inaccurate. In this study, therefore, we provide a discussion of geochemical thermodynamic databases, discuss the synthesis and reconciliation of the databases used in this study, and compare predictions from reactive transport software with single phase CO2/brine experiments performed at temperatures and pressures applicable to geologic storage conditions.

  12. TOURGHREACT: A Simulation Program for Non-isothermal MultiphaseReactive Geochemical Transport in Variably Saturated GeologicMedia

    SciTech Connect

    Xu, Tianfu; Sonnenthal, Eric; Spycher, Nicolas; Pruess, Karsten

    2004-12-07

    TOUGHREACT is a numerical simulation program for chemically reactive non-isothermal flows of multiphase fluids in porous and fractured media. The program was written in Fortran 77 and developed by introducing reactive geochemistry into the multiphase fluid and heat flow simulator TOUGH2. A variety of subsurface thermo-physical-chemical processes are considered under a wide range of conditions of pressure, temperature, water saturation, ionic strength, and pH and Eh. Interactions between mineral assemblages and fluids can occur under local equilibrium or kinetic rates. The gas phase can be chemically active. Precipitation and dissolution reactions can change formation porosity and permeability. The program can be applied to many geologic systems and environmental problems, including geothermal systems, diagenetic and weathering processes, subsurface waste disposal, acid mine drainage remediation, contaminant transport, and groundwater quality. Here we present two examples to illustrate applicability of the program: (1) injectivity effects of mineral scaling in a fractured geothermal reservoir and (2) CO2 disposal in a deep saline aquifer.

  13. A simple reactive-transport model of calcite precipitation in soils and other porous media

    NASA Astrophysics Data System (ADS)

    Kirk, G. J. D.; Versteegen, A.; Ritz, K.; Milodowski, A. E.

    2015-09-01

    Calcite formation in soils and other porous media generally occurs around a localised source of reactants, such as a plant root or soil macro-pore, and the rate depends on the transport of reactants to and from the precipitation zone as well as the kinetics of the precipitation reaction itself. However most studies are made in well mixed systems, in which such transport limitations are largely removed. We developed a mathematical model of calcite precipitation near a source of base in soil, allowing for transport limitations and precipitation kinetics. We tested the model against experimentally-determined rates of calcite precipitation and reactant concentration-distance profiles in columns of soil in contact with a layer of HCO3--saturated exchange resin. The model parameter values were determined independently. The agreement between observed and predicted results was satisfactory given experimental limitations, indicating that the model correctly describes the important processes. A sensitivity analysis showed that all model parameters are important, indicating a simpler treatment would be inadequate. The sensitivity analysis showed that the amount of calcite precipitated and the spread of the precipitation zone were sensitive to parameters controlling rates of reactant transport (soil moisture content, salt content, pH, pH buffer power and CO2 pressure), as well as to the precipitation rate constant. We illustrate practical applications of the model with two examples: pH changes and CaCO3 precipitation in the soil around a plant root, and around a soil macro-pore containing a source of base such as urea.

  14. Reactive solute transport in streams. 2. Simulation of a pH modification experiment

    USGS Publications Warehouse

    Runkel, R.L.; McKnight, Diane M.; Bencala, K.E.; Chapra, S.C.

    1996-01-01

    We present an application of an equilibrium-based solute transport model to a pH-modification experiment conducted on the Snake River, an acidic, metal-rich stream located in the Rocky Mountains of Colorado. During the experiment, instream pH decreased from 4.2 to 3.2, causing a marked increase in dissolved iron concentrations. Model application requires specification of several parameters that are estimated using tracer techniques, mass balance calculations, and geochemical data. Two basic questions are addressed through model application: (1) What are the processes responsible for the observed increase in dissolved iron concentrations? (2) Can the identified processes be represented within the equilibrium-based transport model? Simulation results indicate that the increase in iron was due to the dissolution of hydrous iron oxides and the photoreduction of ferric iron. Dissolution from the streambed is represented by considering a trace compartment consisting of freshly precipitated hydrous iron oxide and an abundant compartment consisting of aged precipitates that are less soluble. Spatial variability in the solubility of hydrous iron oxide is attributed to heterogeneity in the streambed sediments, temperature effects, and/or variability in the effects of photoreduction. Solubility products estimated via simulation fall within a narrow range (pK(sp) from 40.2 to 40.8) relative to the 6 order of magnitude variation reported for laboratory experiments (pK(sp) from 37.3 to 43.3). Results also support the use of an equilibrium-based transport model as the predominate features of the iron and p H profiles are reproduced. The model provides a valuable tool for quantifying the nature and extent of pH- dependent processes within the context of hydrologic transport.

  15. Toward efficiency in heterogeneous multispecies reactive transport modeling: A particle-tracking solution for first-order network reactions

    NASA Astrophysics Data System (ADS)

    Henri, Christopher V.; Fernández-Garcia, Daniel

    2014-09-01

    Modeling multispecies reactive transport in natural systems with strong heterogeneities and complex biochemical reactions is a major challenge for assessing groundwater polluted sites with organic and inorganic contaminants. A large variety of these contaminants react according to serial-parallel reaction networks commonly simplified by a combination of first-order kinetic reactions. In this context, a random-walk particle tracking method is presented. This method is capable of efficiently simulating the motion of particles affected by first-order network reactions in three-dimensional systems, which are represented by spatially variable physical and biochemical coefficients described at high resolution. The approach is based on the development of transition probabilities that describe the likelihood that particles belonging to a given species and location at a given time will be transformed into and moved to another species and location afterward. These probabilities are derived from the solution matrix of the spatial moments governing equations. The method is fully coupled with reactions, free of numerical dispersion and overcomes the inherent numerical problems stemming from the incorporation of heterogeneities to reactive transport codes. In doing this, we demonstrate that the motion of particles follows a standard random walk with time-dependent effective retardation and dispersion parameters that depend on the initial and final chemical state of the particle. The behavior of effective parameters develops as a result of differential retardation effects among species. Moreover, explicit analytic solutions of the transition probability matrix and related particle motions are provided for serial reactions. An example of the effect of heterogeneity on the dechlorination of organic solvents in a three-dimensional random porous media shows that the power-law behavior typically observed in conservative tracers breakthrough curves can be largely compromised by the

  16. Toward efficiency in heterogeneous multispecies reactive transport modeling: A particle-tracking solution for first-order network reactions

    NASA Astrophysics Data System (ADS)

    Henri, Christopher; Fernàndez-Garcia, Daniel

    2015-04-01

    Modeling multi-species reactive transport in natural systems with strong heterogeneities and complex biochemical reactions is a major challenge for assessing groundwater polluted sites with organic and inorganic contaminants. A large variety of these contaminants react according to serial-parallel reaction networks commonly simplified by a combination of first-order kinetic reactions. In this context, a random-walk particle tracking method is presented. This method is capable of efficiently simulating the motion of particles affected by first-order network reactions in three-dimensional systems, which are represented by spatially variable physical and biochemical coefficients described at high resolution. The approach is based on the development of transition probabilities that describe the likelihood that particles belonging to a given species and location at a given time will be transformed into and moved to another species and location afterwards. These probabilities are derived from the solution matrix of the spatial moments governing equations. The method is fully coupled with reactions, free of numerical dispersion and overcomes the inherent numerical problems stemming from the incorporation of heterogeneities to reactive transport codes. In doing this, we demonstrate that the motion of particles follows a standard random walk with time-dependent effective retardation and dispersion parameters that depend on the initial and final chemical state of the particle. The behavior of effective parameters develops as a result of differential retardation effects among species. Moreover, explicit analytic solutions of the transition probability matrix and related particle motions are provided for serial reactions. An example of the effect of heterogeneity on the dechlorination of organic solvents in a three-dimensional random porous media shows that the power-law behavior typically observed in conservative tracers breakthrough curves can be largely compromised by the

  17. Vertical Distribution of Denitrification in an Estuarine Sediment: Integrating Sediment Flowthrough Reactor Experiments and Microprofiling via Reactive Transport Modeling▿

    PubMed Central

    Laverman, Anniet M.; Meile, Christof; Van Cappellen, Philippe; Wieringa, Elze B. A.

    2007-01-01

    Denitrifying activity in a sediment from the freshwater part of a polluted estuary in northwest Europe was quantified using two independent approaches. High-resolution N2O microprofiles were recorded in sediment cores to which acetylene was added to the overlying water and injected laterally into the sediment. The vertical distribution of the rate of denitrification supported by nitrate uptake from the overlying water was then derived from the time series N2O concentration profiles. The rates obtained for the core incubations were compared to the rates predicted by a forward reactive transport model, which included rate expression for denitrification calibrated with potential rate measurements obtained in flowthrough reactors containing undisturbed, 1-cm-thick sediment slices. The two approaches yielded comparable rate profiles, with a near-surface, 2- to 3-mm narrow zone of denitrification and maximum in situ rates on the order of 200 to 300 nmol cm−3 h−1. The maximum in situ rates were about twofold lower than the maximum potential rate for the 0- to 1-cm depth interval of the sediment, indicating that in situ denitrification was nitrate limited. The experimentally and model-derived rates of denitrification implied that there was nitrate uptake by the sediment at a rate that was on the order of 50 (± 10) nmol cm−2 h−1, which agreed well with direct nitrate flux measurements for core incubations. Reactive transport model calculations showed that benthic uptake of nitrate at the site is particularly sensitive to the nitrate concentration in the overlying water and the maximum potential rate of denitrification in the sediment. PMID:17071796

  18. Metabolism-Induced CaCO3 Biomineralization During Reactive Transport in a Micromodel: Implications for Porosity Alteration.

    PubMed

    Singh, Rajveer; Yoon, Hongkyu; Sanford, Robert A; Katz, Lynn; Fouke, Bruce W; Werth, Charles J

    2015-10-20

    The ability of Pseudomonas stutzeri strain DCP-Ps1 to drive CaCO3 biomineralization has been investigated in a microfluidic flowcell (i.e., micromodel) that simulates subsurface porous media. Results indicate that CaCO3 precipitation occurs during NO3(-) reduction with a maximum saturation index (SIcalcite) of ∼1.56, but not when NO3(-) was removed, inactive biomass remained, and pH and alkalinity were adjusted to SIcalcite ∼ 1.56. CaCO3 precipitation was promoted by metabolically active cultures of strain DCP-Ps1, which at similar values of SIcalcite, have a more negative surface charge than inactive strain DCP-Ps1. A two-stage NO3(-) reduction (NO3(-) → NO2(-) → N2) pore-scale reactive transport model was used to evaluate denitrification kinetics, which was observed in the micromodel as upper (NO3(-) reduction) and lower (NO2(-) reduction) horizontal zones of biomass growth with CaCO3 precipitation exclusively in the lower zone. Model results are consistent with two biomass growth regions and indicate that precipitation occurred in the lower zone because the largest increase in pH and alkalinity is associated with NO2(-) reduction. CaCO3 precipitates typically occupied the entire vertical depth of pores and impacted porosity, permeability, and flow. This study provides a framework for incorporating microbial activity in biogeochemistry models, which often base biomineralization only on SI (caused by biotic or abiotic reactions) and, thereby, underpredict the extent of this complex process. These results have wide-ranging implications for understanding reactive transport in relevance to groundwater remediation, CO2 sequestration, and enhanced oil recovery.

  19. Simulating Effects of Non-Isothermal Flow on Reactive Transport of Radionuclides Originating from an Underground Nuclear Test

    SciTech Connect

    Carle, S F; Zavarin, M; Shumaker, D E; Tompson, A B; Maxwell, R M; Pawloski, G A

    2006-03-06

    Temperature can significantly affect radionuclide transport behavior. In simulation of radionuclide transport originating from an underground nuclear test, temperature effects from residual test heat include non-isothermal groundwater flow behavior (e.g. convection cells), increased dissolution rates of melt glass containing refractory radionuclides, changes in water chemistry, and, in turn, changes in radionuclide sorption behavior. The low-yield (0.75 kiloton) Cambric underground nuclear test situated in alluvium below the water table offers unique perspectives on radionuclide transport in groundwater. The Cambric test was followed by extensive post-test characterization of the radionuclide source term and a 16-year pumping-induced radionuclide migration experiment that captured more mobile radionuclides in groundwater. Discharge of pumped groundwater caused inadvertent recirculation of radionuclides through a 220-m thick vadose zone to the water table and below, including partial re-capture in the pumping well. Non-isothermal flow simulations indicate test-related heat persists at Cambric for about 10 years and induces limited thermal convection of groundwater. The test heat has relatively little impact on mobilizing radionuclides compared to subsequent pumping effects. However, our reactive transport models indicate test-related heat can raise melt glass dissolution rates up to 10{sup 4} faster than at ambient temperatures depending on pH and species activities. Non-isothermal flow simulations indicate that these elevated glass dissolution rates largely decrease within 1 year. Thermally-induced increases in fluid velocity may also significantly increase rates of melt glass dissolution by changing the fluid chemistry in contact with the dissolving glass.

  20. Modeling of non-reactive solute transport in fractured clayey till during variable flow rate and time.

    PubMed

    Jørgensen, Peter R; Helstrup, Tina; Urup, Johanne; Seifert, Dorte

    2004-02-01

    Fractures and biopores can act as preferential flow paths in clay aquitards and may rapidly transmit contaminants into underlying aquifers. Reliable numerical models for assessment of groundwater contamination from such aquitards are needed for planning, regulatory and remediation purposes. In this investigation, high resolution preferential water-saturated flow and bromide transport data were used to evaluate the suitability of equivalent porous medium (EPM), dual porosity (DP) and discrete fracture/matrix diffusion (DFMD) numerical modeling approaches for assessment of flow and non-reactive solute transport in clayey till. The experimental data were obtained from four large undisturbed soil columns (taken from 1.5 to 3.5 m depth) in which biopores and channels along fractures controlled 96-99% of water-saturated flow. Simulating the transport data with the EPM effective porosity model (FRACTRAN in EPM mode) was not successful because calibrated effective porosity for the same column had to be varied up to 1 order of magnitude in order to simulate solute breakthrough for the applied flow rates between 11 and 49 mm/day. Attempts to simulate the same data with the DP models CXTFIT and MODFLOW/MT3D were also unsuccessful because fitted values for dispersion, mobile zone porosity, and mass transfer coefficient between mobile and immobile zones varied several orders of magnitude for the different flow rates, and because dispersion values were furthermore not physically realistic. Only the DFMD modeling approach (FRACTRAN in DFMD mode) was capable to simulate the observed changes in solute transport behavior during alternating flow rate without changing values of calibrated fracture spacing and fracture aperture to represent the macropores.

  1. Preliminary reactive geochemical transport simulation study on CO2 geological sequestration at the Changhua Coastal Industrial Park Site, Taiwan

    NASA Astrophysics Data System (ADS)

    Sung, R.; Li, M.

    2013-12-01

    assumed throughout the simulation domain. Comparisons among simulated results with different mesh systems of nested meshes and non-nested meshes and considerations of multiphase reactive transport and physical transport were demonstrated in this study. Preliminary results of injection CO2 for 50 years are: (1) about 7 wt.% of injected CO2 was trapped as carbonate minerals mainly as ankerite; (2) porosities were decreased by 0.014 % and increased by 0.102 % at the injection point and beneath the cap rock, respectively, and were subsequently decreased with time due to minerals precipitation mostly as illite and ankerite; (3) differences of simulated aquifer responses between reactive transport and physical transport were insignificant; and (4) projected CO2 plumes with the nested meshes was smaller than those by the non-nested meshes after cease of CO2 injection. Keywords: CO2-Saline-Mineral Interaction, Reactive Geochemical Transport, TOUGHREACT, Mineral Trapping Assessment, Changhua Costal Industrial Park Site, Taiwan Reference: Marini, L., 2006, Geological Sequestration of Carbon Dioxide, Volume 11: Thermodynamics, Kinetics, and Reaction Path Modeling, Elsevier Science, pp.470. Xu, T., J. A. Apps and K. Pruess, 2004, Numerical simulation of CO2 disposal by mineral trapping in deep aquifers, Applied Geochemistry, Vol. 19:917-936.

  2. Reactive transport modelling of As- and P-species in the rhizosphere

    NASA Astrophysics Data System (ADS)

    Szegedi, K.; Vetterlein, D.; Jahn, R.

    2009-04-01

    The toxic arsenate competes with the nutrient phosphate for binding sites in soil, i.e. at goethite or ferrihydrite surfaces and for binding sites at root membranes. P in soil can be mobilised by plants through exudation of organic anions like citrate or by release of protons. These mechanisms may alter the competition between As(V) and P for binding sites and thus enhance arsenate transfer into the food chain. In a compartment system experiment with corn plants the temporal and spatial dynamics of different parameters (soil solution P, As(V), citrate and proton concentration) were measured with different initial application rates of goethite (Vetterlein et al, 2007). For the integration of the different parameters the experiment was modelled using the RhizoMath code (Szegedi et al, 2008), that is based on coupling the mathematical package MATLAB with the geochemical code PHREEQC. The initialization module of RhizoMath was used to determine the number of surface binding sites of goethite and values of the equilibrium constants of corresponding stoichiometric equations describing the surface complexation of As(V) on goethite as given in Szegedi et al. (2008). The transport module of RhizoMath was used to model transport and speciation in the compartment system. Although the model was able to qualitatively represent experimental observations, a quantitative agreement between modelled and measured data could not be achieved. Thus, in a second step, the transport module was extended with a root compartment factor that expresses the relative coverage of the root compartment by the roots and the active root surface behind the unit area of the compartment cross section. This allowed modelling a growing plant in the compartment system. As temporal changes in water flux and nutrient demand are not necessarily identical, temporal changes in water flux and nutrient demand were scaled independently from each other, using constant, linear or measured water consumption and leaf

  3. Effects of water content on reactive transport of 85Sr in Chernobyl sand columns.

    PubMed

    Szenknect, Stéphanie; Ardois, Christophe; Dewière, Lionel; Gaudet, Jean-Paul

    2008-08-20

    It is known that under unsaturated conditions, the transport of solutes can deviate from ideal advective-dispersive behaviour even for macroscopically homogeneous porous materials. Causes may include physical non-equilibrium, sorption kinetics, non-linear sorption, and the irregular distribution of sorption sites. We have performed laboratory experiments designed to identify the processes responsible for the non-ideality of radioactive Sr transport observed under unsaturated flow conditions in an Aeolian sandy deposit from the Chernobyl exclusion zone. Miscible displacement experiments were carried out at various water contents and corresponding flow rates in a laboratory model system. Results of our experiments have shown that breakthrough curves of a conservative tracer exhibit a higher degree of asymmetry when the water content decreases than at saturated water content and same Darcy velocity. It is possible that velocity variations caused by heterogeneities at the macroscopic scale are responsible for this situation. Another explanation is that molecular diffusion drives the solute mass transfer between mobile and immobile water regions, but the surface of contact between these water regions is small. At very low concentrations, representative of a radioactive Sr contamination of the pore water, sorption and physical disequilibrium dominate the radioactive Sr transport under unsaturated flow conditions. A sorption reaction is described by a cation exchange mechanism calibrated under fully saturated conditions. The sorption capacity, as well as the exchange coefficients are not affected by desaturation. The number of accessible exchange sites was calculated on the basis that the solid remained in contact with water and that the fraction of solid phase in contact with mobile water is numerically equal to the proportion of mobile water to total water content. That means that for this type of sandy soil, the nature of mineral phases is the same in advective and non

  4. Reductive dissolution and reactive solute transport in a sewage-contaminated glacial outwash aquifer

    USGS Publications Warehouse

    Lee, R.W.; Bennett, P.C.

    1998-01-01

    Contamination of shallow ground water by sewage effluent typically contains reduced chemical species that consume dissolved oxygen, developing either a low oxygen geochemical environment or an anaerobic geochemical environment. Based on the load of reduced chemical species discharged to shallow ground water and the amounts of reactants in the aquifer matrix, it should be possible to determine chemical processes in the aquifer and compare observed results to predicted ones. At the Otis Air Base research site (Cape Cod, Massachusetts) where sewage effluent has infiltrated the shallow aquifer since 1936, bacterially mediated processes such as nitrification, denitrification, manganese reduction, and iron reduction have been observed in the contaminant plume. In specific areas of the plume, dissolved manganese and iron have increased significantly where local geochemical conditions are favorable for reduction and transport of these constituents from the aquifer matrix. Dissolved manganese and iron concentrations ranged from 0.02 to 7.3 mg/L, and 0.001 to 13.0 mg/L, respectively, for 21 samples collected from 1988 to 1989. Reduction of manganese and iron is linked to microbial oxidation of sewage carbon, producing bicarbonate and the dissolved metal ions as by-products. Calculated production and flux of CO2 through the unsaturated zone from manganese reduction in the aquifer was 0.035 g/m2/d (12% of measured CO2 flux during winter). Manganese is limited in the aquifer, however. A one-dimensional, reaction-coupled transport model developed for the mildly reducing conditions in the sewage plume nearest the source beds showed that reduction, transport, and removal of manganese from the aquifer sediments should result in iron reduction where manganese has been depleted.

  5. Scaling of Reactive Transport in Fracture Networks with Incomplete Mixing: A Metapopulation Network Approach

    NASA Astrophysics Data System (ADS)

    Nicolaides, C.; Cueto-Felgueroso, L.; Juanes, R.

    2011-12-01

    The study of networks as complex systems has revolutionized many disciplines in physics and the social and natural sciences. Recently, the focus of network science has shifted from the analysis of the network topology to the study of the dynamics of processes that take place on them. Here, we adopt a bosonic (metapopulation) network approach to characterize transport and reaction on fracture networks. In a bosonic network, nodes contain populations of particles, which may undertake contact processes within them. This coarse-grained conceptualization permits modeling of nonequilibrium phenomena such as incomplete mixing and kinetic reactions. Particles then move between connected nodes along links, with a rate that reflects the traffic patterns through the network. We generate fracture networks from realistic statistical properties of fracture density, orientation and aperture, and solve potential flow on the network for simple flow configurations. It is well known that the transport of passive particles with complete mixing at the nodes on a fracture network or a scale-free network is anomalous [1,2]. Here, we extend this analysis to account for incomplete mixing at the nodes by considering two types of particles, A and B, which come in contact at the nodes at a rate α (the mixing rate) to produce type-C particles: A+B-> 2C. In the limit of α -> ∞ we recover the instantaneous mixing case. Further, type-C particles decay into stable type-D particles at a rate λ : C→ D. As a result, we capture the interplay among the transport, mixing and reaction time scales on a fracture network. Our analysis demonstrates the strong dependence of global mixing and spreading on incomplete local mixing, and allows us to obtain robust scalings for the spatio-temporal distributions of particles.

  6. Simulation of reactive transport of injected CO2 on the Colorado Plateau, Utah, USA

    USGS Publications Warehouse

    White, S.P.; Allis, R.G.; Moore, J.; Chidsey, T.; Morgan, C.; Gwynn, W.; Adams, M.

    2005-01-01

    This paper investigates injection of CO2 into non-dome-shaped geological structures that do not provide the traps traditionally deemed necessary for the development of artificial CO2 reservoirs. We have developed a conceptual and two numerical models of the geology and groundwater along a cross-section lying approximately NW-SE and in the vicinity of the Hunter power station on the Colorado Plateau, Central Utah and identified a number of potential sequestration sites on this cross-section. Preliminary modeling identified the White Rim Sandstone as appearing to offer the properties required of a successful sequestration site. Detailed modeling of injection of CO2 into the White Rim Sandstone using the reactive chemical simulator ChemTOUGH found that 1000 years after the 30 year injection period began approximately 21% of the injected CO2 was permanently sequestered as a mineral, 52% was beneath the ground surface as a gas or dissolved in the groundwater and 17% had leaked to the surface and leakage to the surface was continuing. ?? 2005 Elsevier B.V. All rights reserved.

  7. Optical and electron transport properties of reactively sputtered Cu/sub x/S

    SciTech Connect

    Leong, J.Y.C.

    1980-06-30

    Thin films of Cu/sub x/S were deposited on glass slides by sputtering Cu in a reactive H/sub 2/S/Ar environment. Optical transmittance and reflectance measurements were used to explore the infrared absorption spectra of the material. Analysis of the absorption edge characteristics resulted in the identification of an indirect bandgap at 1.15 (+-.05) eV, a direct bandgap at 1.30 (+-.05) eV, and an electron effective mass of 1.0 (+-0.2) m/sub 0/. Electrical data consisting of resistivity and Hall effect measurements from liquid nitrogen to room temperature were analyzed to determine the dominant scattering mechanisms limiting the hole mobility in the material. Ionized impurity scattering was the dominant mechanism at low temperatures (T < 100/sup 0/K) and polar optical phonon scattering was most effective at high temperatures (T > 150/sup 0/K). All films were p-type. Effects of sputtering gas pressure, heat treatments, and temperature on the properties were studied.

  8. Aging process of Saharan dust during transport over the Atlantic Ocean: Calcite reactivity and sulfate coating

    NASA Astrophysics Data System (ADS)

    Desboeufs, K. V.; Cautenet, G.; Minvielle, F.; Lasserre, F.

    2003-04-01

    Several field measurements emphasized that dust particles are mixed with sulfate during their transport. This state of mixing could be important on the climatic effect of these particles, since the optical properties of particles are not conservative in the case of internal mixing, and the addition of soluble species on the dust can modify their capacity to act as CCN. The aging process of dust particles in Tropical Africa and Atlantic Ocean is investigated using the three dimensional transport RAMS and chemistry model coupled on line. To describe the mixing process of dust, we considered the chemical reaction occurring between the calcite (calcium carbonate) in the Saharan dust and the various sulfur species to yield sulfate coating. The results by the model predictions are consistent with field and observations studies. We will discuss about the potential consequences of this coating on the direct and indirect effect of mineral dust in the Earth radiative budget. An analysis of cloud occurrence observed by satellites and mixed dust content will be presented.

  9. Review of pore network modelling of porous media: Experimental characterisations, network constructions and applications to reactive transport

    NASA Astrophysics Data System (ADS)

    Xiong, Qingrong; Baychev, Todor G.; Jivkov, Andrey P.

    2016-09-01

    Pore network models have been applied widely for simulating a variety of different physical and chemical processes, including phase exchange, non-Newtonian displacement, non-Darcy flow, reactive transport and thermodynamically consistent oil layers. The realism of such modelling, i.e. the credibility of their predictions, depends to a large extent on the quality of the correspondence between the pore space of a given medium and the pore network constructed as its representation. The main experimental techniques for pore space characterisation, including direct imaging, mercury intrusion porosimetry and gas adsorption, are firstly summarised. A review of the main pore network construction techniques is then presented. Particular focus is given on how such constructions are adapted to the data from experimentally characterised pore systems. Current applications of pore network models are considered, with special emphasis on the effects of adsorption, dissolution and precipitation, as well as biomass growth, on transport coefficients. Pore network models are found to be a valuable tool for understanding and predicting meso-scale phenomena, linking single pore processes, where other techniques are more accurate, and the homogenised continuum porous media, used by engineering community.

  10. Coupling Sorption to Soil Weathering During Reactive Transport: Impacts of Mineral Transformation and Sorbent Aging