Numerical modeling of coupled fluid flow and thermal and reactive biogeochemical transport in porous and fractured media

Yeh, Gour Tsyh; Fang, Yilin; Zhang, Fan; Sun, Jiangtao; Li, Yuan; Li, Ming Hsu; Siegel, Morris

doi:10.1007/s10596-009-9140-3

Cited by 27 publications

(13 citation statements)

References 38 publications

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“…This effectively decouples the transport of components and kinetic variables from those for the rates of equilibrium reactions. As a result, it facilitates the iterative approach between a much-reduced number of partial differential equations of component and kinetic-variable transport and nonlinear algebraic equations that implicitly define the rates of equilibrium reactions [168,170,171]. In the geomechanics module, the media are treated as consisting of nonlinear viscous-elastic materials.…”

Section: Hydrogeochemmentioning

confidence: 99%

“…Starting with a reaction network of N reactions involving M species, each reaction can involve any number of species, one can write M species transport equations based on the principle of chemical kinetics [172]. Performing GaussJordan reduction of the reaction network [173][174][175], one obtains a system of M transport equations for M reaction extents, each of which is a linear combination of the M species concentrations [170,171]. A reaction extent is called a component when there is no reaction term appearing in its transport equation.…”

Section: Hydrogeochemmentioning

confidence: 99%

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Reactive transport codes for subsurface environmental simulation

et al. 2014

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A general description of the mathematical and numerical formulations used in modern numerical reactive transport codes relevant for subsurface environmental simulations is presented. The formulations are followed by short descriptions of commonly used and available subsurface simulators that consider continuum representations of flow, transport, and reactions in porous media. These formulations are applicable to most of the subsurface environmental benchmark problems included in this special issue. The list of codes described briefly here includes PHREEQC, HPx, PHT3D, OpenGeoSys (OGS), HYTEC, ORCHESTRA, TOUGHREACT, eSTOMP, HYDROGEOCHEM, CrunchFlow, MIN3P, and PFLOTRAN. The descriptions include a C. I. Steefel ( ) · B. Arora · S. Molins · N. Spycher

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Section: Hydrogeochemmentioning

confidence: 99%

Section: Hydrogeochemmentioning

confidence: 99%

Reactive transport codes for subsurface environmental simulation

et al. 2014

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“…(17), depending on computation power and how dynamic the system is. Direct coupling with the reactive transport simulator HYDROGEOCHEM (66) was used in here. In this model, only the TEAP reaction of iron reduction was replaced with the in silico model of G. metallireducens.…”

Section: Methodsmentioning

confidence: 99%

Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens by Using Proteomic Data from a Field Biostimulation Experiment

Fang

Wilkins

Yabusaki

et al. 2012

Appl Environ Microbiol

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bAccurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within an in silico model using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model of Geobacter metallireducens-specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzymecoding genes. Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment. Microbial environments have been engineered for enhanced oil recovery (7,23,29,33,42) and remediation of soil and groundwater contaminated by chlorinated hydrocarbons, metals, and radionuclides (4,24,30,40,47,51,63) in the past 30 years and have recently been studied to manage carbon dioxide (46). Mathematical models of microbial processes have been used for experimental interpretation, design, and prediction in recent decades (3,10,20,22,39,48,49,53,56). These processes were very complex to model because there was no way to measure the detailed metabolisms inside the system. They were usually represented by specific terminal electron acceptor process (TEAP) reactions with fixed stoichiometry throughout the simulation and were traditionally modeled by Monod kinetics. These models are sufficient under nonlimiting conditions of nutrients. However, the kinetic parameters of these models, which were calibrated but not directly measurable, cannot reflect the sophisticated mechanisms developed by microorganisms to adapt to the changing environment through the regulation of metabolic pathways, such as their ability to respond to nutrient gradients and environmental stress (5, 6).With the ad...

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“…The chemical system is a complex reaction network involving dissolution of the sorbing sites to form aqueous species, surface ionization of a solid and changes in sorption equilibria due to thermal transport (Example 16). In addition to the sample problems in the manuals, two recent review papers (Yeh et al 2009(Yeh et al , 2011 provide examples of applications of HYDROGEOCHEM to chemical scenarios relevant to the waste IPSC.…”

Section: Demonstrated Applicationsmentioning

confidence: 99%

“…Descriptions of such simulations are summarized in Yeh et al (2009Yeh et al ( , 2011 and described in more detail in Scheibe et al (2006) and Fang et al (2009).…”

Section: Demonstrated Applicationsmentioning

confidence: 99%

Nuclear Energy Advanced Modeling and Simulation (NEAMS) waste Integrated Performance and Safety Codes (IPSC) : gap analysis for high fidelity and performance assessment code development.

Lee¹,

Siegel²,

Argüello³

et al. 2011

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This report describes a gap analysis performed in the process of developing the Waste Integrated Performance and Safety Codes (IPSC) in support of the U.S. Department of Energy (DOE) Office of Nuclear Energy Advanced Modeling and Simulation (NEAMS) Campaign. The goal of the Waste IPSC is to develop an integrated suite of computational modeling and simulation capabilities to quantitatively assess the long-term performance of waste forms in the engineered and geologic environments of a radioactive waste storage or disposal system. The Waste IPSC will provide this simulation capability (1) for a range of disposal concepts, waste form types, engineered repository designs, and geologic settings, (2) for a range of time scales and distances, (3) with appropriate consideration of the inherent uncertainties, and (4) in accordance with rigorous verification, validation, and software quality requirements.The gap analyses documented in this report were are performed during an initial gap analysis to identify candidate codes and tools to support the development and integration of the Waste IPSC, and during follow-on activities that delved into more detailed assessments of the various codes that were acquired, studied, and tested. The current Waste IPSC strategy is to acquire and integrate the necessary Waste IPSC capabilities wherever feasible, and develop only those capabilities that cannot be acquired or suitably integrated, verified, or validated.The gap analysis indicates that significant capabilities may already exist in the existing THC codes although there is no single code able to fully account for all physical and chemical iv processes involved in a waste disposal system. Large gaps exist in modeling chemical processes and their couplings with other processes. The coupling of chemical processes with flow transport and mechanical deformation remains challenging. The data for extreme environments (e.g., for elevated temperature and high ionic strength media) that are needed for repository modeling are severely lacking. In addition, most of existing reactive transport codes were developed for nonradioactive contaminants, and they need to be adapted to account for radionuclide decay and ingrowth. The accessibility to the source codes is generally limited. Because the problems of interest for the Waste IPSC are likely to result in relatively large computational models, a compact memory-usage footprint and a fast/robust solution procedure will be needed. A robust massively parallel processing (MPP) capability will also be required to provide reasonable turnaround times on the analyses that will be performed with the code.A performance assessment (PA) calculation for a waste disposal system generally requires a large number (hundreds to thousands) of model simulations to quantify the effect of model parameter uncertainties on the predicted repository performance. A set of codes for a PA calculation must be sufficiently robust and fast in terms of code execution. A PA system as a whole must be able to provide multi...

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Numerical modeling of coupled fluid flow and thermal and reactive biogeochemical transport in porous and fractured media

Cited by 27 publications

References 38 publications

Reactive transport codes for subsurface environmental simulation

Reactive transport codes for subsurface environmental simulation

Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens by Using Proteomic Data from a Field Biostimulation Experiment

Nuclear Energy Advanced Modeling and Simulation (NEAMS) waste Integrated Performance and Safety Codes (IPSC) : gap analysis for high fidelity and performance assessment code development.

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