ABSTRACT This study examined the impacts of reservoir properties on carbon dioxide (CO2) migratio... more ABSTRACT This study examined the impacts of reservoir properties on carbon dioxide (CO2) migration after subsurface injection and evaluated the possibility of characterizing reservoir properties using CO2 monitoring data such as spatial–temporal distributions of gas pressure, which can be reasonably monitored in practice. The injection reservoir was assumed to be located 1,400–1,500 m below the ground surface such that CO2 remained in the supercritical state. The reservoir was assumed to contain layers with alternating conductive and resistive properties, which is analogous to actual geological formations such as the Mount Simon Sandstone unit. The CO2 injection simulation used a cylindrical grid setting in which the injection well was situated at the center of the domain, which extended out 8,000 m from the injection well. The CO2 migration was simulated using the latest version of the simulator, subsurface transport over multiple phases (the water–salt–CO2–energy module), developed by Pacific Northwest National Laboratory. A nonlinear parameter estimation and optimization modeling software package, Parameter ESTimation (PEST), is adopted for automated reservoir parameter estimation. The effects of data quality, data worth, and data redundancy were explored regarding the detectability of reservoir parameters using gas pressure monitoring data, by comparing PEST inversion results using data with different levels of noises, various numbers of monitoring wells and locations, and different data collection spacing and temporal sampling intervals. This study yielded insight into the use of CO2 monitoring data for reservoir characterization and how to design the monitoring system to optimize data worth and reduce data redundancy. The feasibility of using CO2 saturation data for improving reservoir characterization was also discussed.
ABSTRACT Reactions that lead to the formation of mineral precipitates, colloids or growth of biof... more ABSTRACT Reactions that lead to the formation of mineral precipitates, colloids or growth of biofilms in porous media often depend on the molecular-level diffusive mixing. For example, for the formation of mineral phases, exceeding the saturation index for a mineral is a minimum requirement for precipitation to proceed. Solute mixing frequently occurs at the interface between two solutions each containing one or more soluble reactants, particularly in engineered systems where contaminant degradation or modification or fluid flow are objectives. Although many of the fundamental component processes involved in the deposition or solubilization of solid phases are reasonably well understood, including precipitation equilibrium and kinetics, fluid flow and solute transport, the deposition of chemical precipitates, biofilms and colloidal particles are all coupled to flow, and the science of such coupled processes is not well developed. How such precipitates (and conversely, dissolution of solids) are distributed in the subsurface along flow paths with chemical gradients is a complex and challenging problem. This is especially true in systems that undergo rapid change where equilibrium conditions cannot be assumed, particularly in subsurface systems where reactants are introduced rapidly, compared to most natural flow conditions, and where mixing fronts are generated. Although the concept of dispersion in porous media is frequently used to approximate mixing at macroscopic scales, dispersion does not necessarily describe pore-level or molecular level mixing that must occur for chemical and biological reactions to be possible. An example of coupling between flow, mixing and mineral precipitation, with practical applications to controlling fluid flow or contaminant remediation in subsurface environments is shown in the mixing zone between parallel flowing solutions. Two- and three-dimensional experiments in packed-sand media were conducted where solutions containing calcium and carbonate ions came into contact along a parallel flow boundary and mixed by dispersion and diffusion. The result is the propagation of calcium carbonate precipitates along the solution-solution boundary in the direction of flow. As carbonate precipitates fill the pore space mixing of the two solutions is restricted and therefore precipitation, flow, and transport are coupled. The distribution of carbonate phases is a complex interaction involving precipitation and dissolution kinetics, which are functions of pore-scale saturation indices and solute ratios, heterogeneous vs. homogeneous nucleation and growth mechanisms and changes in porosity and flow. Experimental and modeling results illustrate challenges in understanding the macroscopic and microscopic phenomena that depend on solute mixing, the relevance of molecular and pore-scale processes to the macroscopic behavior, and potential impact on metal mobility in porous media. Mineral precipitation and changes in porosity are simulated at the pore-scale using the Smooth Particle Hydrodynamics method. Macroscopic simulations were performed using discretized, continuum-scale modeling with parameterization representing macroscopic media properties. One of the modeling goals is to use pore-scale simulations to provide the basis for parameterization of macroscopic (more practical) model predictions.
There are two different ways to model reactive transport: ad hoc and innovative reaction-based ap... more There are two different ways to model reactive transport: ad hoc and innovative reaction-based approaches. The former, such as the Kd simplification of adsorption, has been widely employed by practitioners, while the latter has been mainly used in scientific communities for elucidating mechanisms of biogeochemical transport processes. It is believed that innovative mechanistic-based models could serve as protocols for environmental remediation as well. This paper reviews the development of a mechanistically coupled fluid flow, thermal transport, hydrologic transport, and reactive biogeochemical model and example-applications to environmental remediation problems. Theoretical bases are sufficiently described. Four example problems previously carried out are used to demonstrate how numerical experimentation can be used to evaluate the feasibility of different remediation approaches. The first one involved the application of a 56-species uranium tailing problem to the Melton Branch Subwatershed at Oak Ridge National Laboratory (ORNL) using the parallel version of the model. Simulations were made to demonstrate the potential mobilization of uranium and other chelating agents in the proposed waste disposal site. The second problem simulated laboratory-scale system to investigate the role of natural attenuation in potential off-site migration of uranium from uranium mill tailings after restoration. It showed inadequacy of using a single Kd even for a homogeneous medium. The third example simulated laboratory experiments involving extremely high concentrations of uranium, technetium, aluminum, nitrate, and toxic metals (e.g., Ni, Cr, Co). The fourth example modeled microbially-mediated immobilization of uranium in an unconfined aquifer using acetate amendment in a field-scale experiment. The purposes of these modeling studies were to simulate various mechanisms of mobilization and immobilization of radioactive wastes and to illustrate how to apply reactive transport models for environmental remediation.► The transformation of biogeochemical processes into reaction networks is a challenge. ► A reaction network is needed for truly reactive transport modeling. ► The distribution coefficient ranges from three to 13 orders of magnitude. ► The use of Kd approach to modeling reactive transport must be exercised with care. ► Calibrated reactive models can be exported to different environmental settings.
Three-dimensional, coupled variably saturated flow and biogeochemical reactive transport modeling... more 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 in higher concentrations of TEAP reaction products when terminal electron donors and acceptors were not limiting. Finally, facies-based porosity and reactive surface area variations were shown to affect aqueous uranium concentration distributions with localized effects of the fine lithofacies having the largest impact on U(VI) surface complexation.The ability to model the comprehensive biogeochemical reaction network, and spatially and temporally variable processes, properties, and conditions controlling uranium behavior during engineered bioremediation in the naturally complex Rifle IFRC subsurface system required a subsurface simulator that could use the large memory and computational performance of a massively parallel computer. In this case, the eSTOMP simulator, operating on 128 processor cores for 12 h, was used to simulate the 110-day field experiment and 50 days of post-biostimulation behavior.► 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. The simulations targeted 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. ► Products of biologically-mediated terminal electron acceptor process reactions significantly alter geochemical controls on uranium mobility through increases in pH, alkalinity, exchangeable cations, and highly reactive reduction products. ► New knowledge on simultaneously active metal- and sulfate-reducing bacteria has been incorporated into the modeling, where an initially small population of slow growing sulfate-reducing bacteria is active from the initiation of biostimulation. ► Three-dimensional, variably saturated flow modeling was used to address impacts of a falling water table during acetate injection. These impacts included a significant reduction in aquifer saturated thickness and isolation of residual 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. ► Large computer memory and high computational performance were required to simulate the detailed coupled process models for multiple biogeochemical components in highly resolved heterogeneous materials for the 110-day field experiment and 50 days of post-biostimulation behavior. In this case, a highly-scalable subsurface simulator operating on 128 processor cores for 12 h was used to simulate each realization. An equivalent simulation without parallel processing would have taken 60 days, assuming sufficient memory was available.
The activity of microorganisms often plays an important role in dynamic natural attenuation or en... more 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 modeling system is designed in such a way that constraint-based models targeting different microorganisms or competing organism communities can be easily plugged into the system. Constraint-based modeling is very costly given the size of a genome-scale reaction network. To save computation time, a binary tree is traversed to examine the concentration and solution pool generated during the simulation in order to decide whether the constraint-based model should be called. We also show preliminary results from the integrated model including a comparison of the direct and indirect coupling approaches and evaluated the ability of the approach to simulate field experiment.► We directly a reactive transport model with in silico models using BABEL. ► Dynamic functionality of microorganisms can be simulated by the model. ► Different microorganisms communities can be easily plugged into the model system. ► Computation time is saved by examining the solution pool generated by in silico model. ► Model can be applied to contaminant bioremediation without empirical calibration.
This paper presents a generic biogeochemical simulator, BIOGEOCHEM. The simulator can read a ther... more This paper presents a generic biogeochemical simulator, BIOGEOCHEM. The simulator can read a thermodynamic database based on the EQ3/EQ6 database. It can also read user-specified equilibrium and kinetic reactions (reactions not defined in the format of that in EQ3/EQ6 database) symbolically. BIOGEOCHEM is developed with a general paradigm. It overcomes the requirement in most available reaction-based models that reactions and rate laws be specified in a limited number of canonical forms. The simulator interprets the reactions and rate laws of virtually any type for input to the MAPLE symbolic mathematical software package. MAPLE then generates Fortran code for the analytical Jacobian matrix used in the Newton-Raphson technique, which is copiled and linked into the BIOGEOCHEM executable. With this feature, the users are exempted from recoding the simulator to accept new equilibrium expressions or kinetic rate laws. Two examples are used to demonstrate the new features of the simulator.
Efficient multicast routing metric is critical for one-to-many communications in wireless mesh ne... more Efficient multicast routing metric is critical for one-to-many communications in wireless mesh networks. The existing unicast routing metrics do not perform well in multicast due to the distinctive differences between unicast and multicast routing in frame exchange manners in the link layer. It is thus necessary to propose specialized routing metrics for multicast. The focus of this paper is to investigate multicast routing metrics in multi-radio multi-channel wireless mesh networks. We first solve multicast throughput optimization problem in concurrent multicast flows and show that the throughput can be improved by seeking the multicast route with lower channel congestion degree. Then, the multicast routing metrics and protocol are designed by considering this aspect. The main contribution of our work is to propose two load-aware multicast routing metrics named FLMM and FLMMR. Both metrics account for channel diversity, interference and wireless broadcast advantage. FLMM aids in finding multicast route that are better in terms of reduced intra-flow and inter-flow interference and exploits channel diversity to improve bandwidth usage and network throughput. Compared with FLMM, FLMMR further considers the unreliability of MAC multicast. The effectiveness of the two metrics is empirically examined through simulations. Finally, we present the further work from two aspects: the joint multicast routing and channel assignment problem for optimal multicast and the practicality of proposed metrics.
As more complex biogeochemical situations are being investigated (e.g., evolving reactivity, pass... more As more complex biogeochemical situations are being investigated (e.g., evolving reactivity, passivation of reactive surfaces, dissolution of sorbates), there is a growing need for biogeochemical simulators to flexibly and facilely address new reaction forms and rate laws. This paper presents an approach that accommodates this need to efficiently simulate general biogeochemical processes, while insulating the user from additional code development.The approach allows for the automatic extraction of fundamental reaction stoichiometry and thermodynamics from a standard chemistry database, and the symbolic entry of arbitrarily complex user-specified reaction forms, rate laws, and equilibria. The user-specified equilibria and kinetic rates (i.e., they are not defined in the format of the standardized database) are interpreted by the Maple V (Waterloo Maple) symbolic mathematical software package. FORTRAN 90 code is then generated by Maple for (1) the analytical Jacobian matrix (if preferred over the numerical Jacobian matrix) used in the Newton–Raphson solution procedure, and (2) the residual functions for governing equations, user-specified equilibrium expressions and rate laws. Matrix diagonalization eliminates the need to conceptualize the system of reactions as a tableau, which comprises a list of components, species, the stoichiometric matrix, and the formation equilibrium constant vector that forms the species from components (Morel and Hering, 1993), while identifying a minimum rank set of basis species with enhanced numerical convergence properties. The newly generated code, which is designed to operate in the BIOGEOCHEM biogeochemical simulator, is then compiled and linked into the BIOGEOCHEM executable. With these features, users can avoid recoding the simulator to accept new equilibrium expressions or kinetic rate laws, while still taking full advantage of the stoichiometry and thermodynamics provided by an existing chemical database. Thus, the approach introduces efficiencies in the specification of biogeochemical reaction networks and eliminates opportunities for mistakes in preparing input files and coding errors. Test problems are used to demonstrate the features of the procedure.
A reaction network integrating abiotic and microbially mediated reactions has been developed to s... more A reaction network integrating abiotic and microbially mediated reactions has been developed to simulate biostimulation field experiments at a former Uranium Mill Tailings Remedial Action (UMTRA) site in Rifle, Colorado. The reaction network was calibrated using data from the 2002 field experiment, after which it was applied without additional calibration to field experiments performed in 2003 and 2007. 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 terminal electron-accepting processes (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 UMTRA site that demonstrated that the bulk (∼90%) of initial Fe(III) bioreduction is associated with phyllosilicate rather than oxide forms of iron. The uranium reaction network includes a U(VI) surface complexation model based on laboratory studies with Rifle site sediments and aqueous complexation reactions that include ternary complexes (e.g., calcium–uranyl–carbonate). The bioreduced U(IV), Fe(II), and sulfide components produced during the experiments are strongly associated with the solid phases and may play an important role in long-term uranium immobilization.
ABSTRACT This study examined the impacts of reservoir properties on carbon dioxide (CO2) migratio... more ABSTRACT This study examined the impacts of reservoir properties on carbon dioxide (CO2) migration after subsurface injection and evaluated the possibility of characterizing reservoir properties using CO2 monitoring data such as spatial–temporal distributions of gas pressure, which can be reasonably monitored in practice. The injection reservoir was assumed to be located 1,400–1,500 m below the ground surface such that CO2 remained in the supercritical state. The reservoir was assumed to contain layers with alternating conductive and resistive properties, which is analogous to actual geological formations such as the Mount Simon Sandstone unit. The CO2 injection simulation used a cylindrical grid setting in which the injection well was situated at the center of the domain, which extended out 8,000 m from the injection well. The CO2 migration was simulated using the latest version of the simulator, subsurface transport over multiple phases (the water–salt–CO2–energy module), developed by Pacific Northwest National Laboratory. A nonlinear parameter estimation and optimization modeling software package, Parameter ESTimation (PEST), is adopted for automated reservoir parameter estimation. The effects of data quality, data worth, and data redundancy were explored regarding the detectability of reservoir parameters using gas pressure monitoring data, by comparing PEST inversion results using data with different levels of noises, various numbers of monitoring wells and locations, and different data collection spacing and temporal sampling intervals. This study yielded insight into the use of CO2 monitoring data for reservoir characterization and how to design the monitoring system to optimize data worth and reduce data redundancy. The feasibility of using CO2 saturation data for improving reservoir characterization was also discussed.
ABSTRACT Reactions that lead to the formation of mineral precipitates, colloids or growth of biof... more ABSTRACT Reactions that lead to the formation of mineral precipitates, colloids or growth of biofilms in porous media often depend on the molecular-level diffusive mixing. For example, for the formation of mineral phases, exceeding the saturation index for a mineral is a minimum requirement for precipitation to proceed. Solute mixing frequently occurs at the interface between two solutions each containing one or more soluble reactants, particularly in engineered systems where contaminant degradation or modification or fluid flow are objectives. Although many of the fundamental component processes involved in the deposition or solubilization of solid phases are reasonably well understood, including precipitation equilibrium and kinetics, fluid flow and solute transport, the deposition of chemical precipitates, biofilms and colloidal particles are all coupled to flow, and the science of such coupled processes is not well developed. How such precipitates (and conversely, dissolution of solids) are distributed in the subsurface along flow paths with chemical gradients is a complex and challenging problem. This is especially true in systems that undergo rapid change where equilibrium conditions cannot be assumed, particularly in subsurface systems where reactants are introduced rapidly, compared to most natural flow conditions, and where mixing fronts are generated. Although the concept of dispersion in porous media is frequently used to approximate mixing at macroscopic scales, dispersion does not necessarily describe pore-level or molecular level mixing that must occur for chemical and biological reactions to be possible. An example of coupling between flow, mixing and mineral precipitation, with practical applications to controlling fluid flow or contaminant remediation in subsurface environments is shown in the mixing zone between parallel flowing solutions. Two- and three-dimensional experiments in packed-sand media were conducted where solutions containing calcium and carbonate ions came into contact along a parallel flow boundary and mixed by dispersion and diffusion. The result is the propagation of calcium carbonate precipitates along the solution-solution boundary in the direction of flow. As carbonate precipitates fill the pore space mixing of the two solutions is restricted and therefore precipitation, flow, and transport are coupled. The distribution of carbonate phases is a complex interaction involving precipitation and dissolution kinetics, which are functions of pore-scale saturation indices and solute ratios, heterogeneous vs. homogeneous nucleation and growth mechanisms and changes in porosity and flow. Experimental and modeling results illustrate challenges in understanding the macroscopic and microscopic phenomena that depend on solute mixing, the relevance of molecular and pore-scale processes to the macroscopic behavior, and potential impact on metal mobility in porous media. Mineral precipitation and changes in porosity are simulated at the pore-scale using the Smooth Particle Hydrodynamics method. Macroscopic simulations were performed using discretized, continuum-scale modeling with parameterization representing macroscopic media properties. One of the modeling goals is to use pore-scale simulations to provide the basis for parameterization of macroscopic (more practical) model predictions.
There are two different ways to model reactive transport: ad hoc and innovative reaction-based ap... more There are two different ways to model reactive transport: ad hoc and innovative reaction-based approaches. The former, such as the Kd simplification of adsorption, has been widely employed by practitioners, while the latter has been mainly used in scientific communities for elucidating mechanisms of biogeochemical transport processes. It is believed that innovative mechanistic-based models could serve as protocols for environmental remediation as well. This paper reviews the development of a mechanistically coupled fluid flow, thermal transport, hydrologic transport, and reactive biogeochemical model and example-applications to environmental remediation problems. Theoretical bases are sufficiently described. Four example problems previously carried out are used to demonstrate how numerical experimentation can be used to evaluate the feasibility of different remediation approaches. The first one involved the application of a 56-species uranium tailing problem to the Melton Branch Subwatershed at Oak Ridge National Laboratory (ORNL) using the parallel version of the model. Simulations were made to demonstrate the potential mobilization of uranium and other chelating agents in the proposed waste disposal site. The second problem simulated laboratory-scale system to investigate the role of natural attenuation in potential off-site migration of uranium from uranium mill tailings after restoration. It showed inadequacy of using a single Kd even for a homogeneous medium. The third example simulated laboratory experiments involving extremely high concentrations of uranium, technetium, aluminum, nitrate, and toxic metals (e.g., Ni, Cr, Co). The fourth example modeled microbially-mediated immobilization of uranium in an unconfined aquifer using acetate amendment in a field-scale experiment. The purposes of these modeling studies were to simulate various mechanisms of mobilization and immobilization of radioactive wastes and to illustrate how to apply reactive transport models for environmental remediation.► The transformation of biogeochemical processes into reaction networks is a challenge. ► A reaction network is needed for truly reactive transport modeling. ► The distribution coefficient ranges from three to 13 orders of magnitude. ► The use of Kd approach to modeling reactive transport must be exercised with care. ► Calibrated reactive models can be exported to different environmental settings.
Three-dimensional, coupled variably saturated flow and biogeochemical reactive transport modeling... more 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 in higher concentrations of TEAP reaction products when terminal electron donors and acceptors were not limiting. Finally, facies-based porosity and reactive surface area variations were shown to affect aqueous uranium concentration distributions with localized effects of the fine lithofacies having the largest impact on U(VI) surface complexation.The ability to model the comprehensive biogeochemical reaction network, and spatially and temporally variable processes, properties, and conditions controlling uranium behavior during engineered bioremediation in the naturally complex Rifle IFRC subsurface system required a subsurface simulator that could use the large memory and computational performance of a massively parallel computer. In this case, the eSTOMP simulator, operating on 128 processor cores for 12 h, was used to simulate the 110-day field experiment and 50 days of post-biostimulation behavior.► 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. The simulations targeted 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. ► Products of biologically-mediated terminal electron acceptor process reactions significantly alter geochemical controls on uranium mobility through increases in pH, alkalinity, exchangeable cations, and highly reactive reduction products. ► New knowledge on simultaneously active metal- and sulfate-reducing bacteria has been incorporated into the modeling, where an initially small population of slow growing sulfate-reducing bacteria is active from the initiation of biostimulation. ► Three-dimensional, variably saturated flow modeling was used to address impacts of a falling water table during acetate injection. These impacts included a significant reduction in aquifer saturated thickness and isolation of residual 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. ► Large computer memory and high computational performance were required to simulate the detailed coupled process models for multiple biogeochemical components in highly resolved heterogeneous materials for the 110-day field experiment and 50 days of post-biostimulation behavior. In this case, a highly-scalable subsurface simulator operating on 128 processor cores for 12 h was used to simulate each realization. An equivalent simulation without parallel processing would have taken 60 days, assuming sufficient memory was available.
The activity of microorganisms often plays an important role in dynamic natural attenuation or en... more 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 modeling system is designed in such a way that constraint-based models targeting different microorganisms or competing organism communities can be easily plugged into the system. Constraint-based modeling is very costly given the size of a genome-scale reaction network. To save computation time, a binary tree is traversed to examine the concentration and solution pool generated during the simulation in order to decide whether the constraint-based model should be called. We also show preliminary results from the integrated model including a comparison of the direct and indirect coupling approaches and evaluated the ability of the approach to simulate field experiment.► We directly a reactive transport model with in silico models using BABEL. ► Dynamic functionality of microorganisms can be simulated by the model. ► Different microorganisms communities can be easily plugged into the model system. ► Computation time is saved by examining the solution pool generated by in silico model. ► Model can be applied to contaminant bioremediation without empirical calibration.
This paper presents a generic biogeochemical simulator, BIOGEOCHEM. The simulator can read a ther... more This paper presents a generic biogeochemical simulator, BIOGEOCHEM. The simulator can read a thermodynamic database based on the EQ3/EQ6 database. It can also read user-specified equilibrium and kinetic reactions (reactions not defined in the format of that in EQ3/EQ6 database) symbolically. BIOGEOCHEM is developed with a general paradigm. It overcomes the requirement in most available reaction-based models that reactions and rate laws be specified in a limited number of canonical forms. The simulator interprets the reactions and rate laws of virtually any type for input to the MAPLE symbolic mathematical software package. MAPLE then generates Fortran code for the analytical Jacobian matrix used in the Newton-Raphson technique, which is copiled and linked into the BIOGEOCHEM executable. With this feature, the users are exempted from recoding the simulator to accept new equilibrium expressions or kinetic rate laws. Two examples are used to demonstrate the new features of the simulator.
Efficient multicast routing metric is critical for one-to-many communications in wireless mesh ne... more Efficient multicast routing metric is critical for one-to-many communications in wireless mesh networks. The existing unicast routing metrics do not perform well in multicast due to the distinctive differences between unicast and multicast routing in frame exchange manners in the link layer. It is thus necessary to propose specialized routing metrics for multicast. The focus of this paper is to investigate multicast routing metrics in multi-radio multi-channel wireless mesh networks. We first solve multicast throughput optimization problem in concurrent multicast flows and show that the throughput can be improved by seeking the multicast route with lower channel congestion degree. Then, the multicast routing metrics and protocol are designed by considering this aspect. The main contribution of our work is to propose two load-aware multicast routing metrics named FLMM and FLMMR. Both metrics account for channel diversity, interference and wireless broadcast advantage. FLMM aids in finding multicast route that are better in terms of reduced intra-flow and inter-flow interference and exploits channel diversity to improve bandwidth usage and network throughput. Compared with FLMM, FLMMR further considers the unreliability of MAC multicast. The effectiveness of the two metrics is empirically examined through simulations. Finally, we present the further work from two aspects: the joint multicast routing and channel assignment problem for optimal multicast and the practicality of proposed metrics.
As more complex biogeochemical situations are being investigated (e.g., evolving reactivity, pass... more As more complex biogeochemical situations are being investigated (e.g., evolving reactivity, passivation of reactive surfaces, dissolution of sorbates), there is a growing need for biogeochemical simulators to flexibly and facilely address new reaction forms and rate laws. This paper presents an approach that accommodates this need to efficiently simulate general biogeochemical processes, while insulating the user from additional code development.The approach allows for the automatic extraction of fundamental reaction stoichiometry and thermodynamics from a standard chemistry database, and the symbolic entry of arbitrarily complex user-specified reaction forms, rate laws, and equilibria. The user-specified equilibria and kinetic rates (i.e., they are not defined in the format of the standardized database) are interpreted by the Maple V (Waterloo Maple) symbolic mathematical software package. FORTRAN 90 code is then generated by Maple for (1) the analytical Jacobian matrix (if preferred over the numerical Jacobian matrix) used in the Newton–Raphson solution procedure, and (2) the residual functions for governing equations, user-specified equilibrium expressions and rate laws. Matrix diagonalization eliminates the need to conceptualize the system of reactions as a tableau, which comprises a list of components, species, the stoichiometric matrix, and the formation equilibrium constant vector that forms the species from components (Morel and Hering, 1993), while identifying a minimum rank set of basis species with enhanced numerical convergence properties. The newly generated code, which is designed to operate in the BIOGEOCHEM biogeochemical simulator, is then compiled and linked into the BIOGEOCHEM executable. With these features, users can avoid recoding the simulator to accept new equilibrium expressions or kinetic rate laws, while still taking full advantage of the stoichiometry and thermodynamics provided by an existing chemical database. Thus, the approach introduces efficiencies in the specification of biogeochemical reaction networks and eliminates opportunities for mistakes in preparing input files and coding errors. Test problems are used to demonstrate the features of the procedure.
A reaction network integrating abiotic and microbially mediated reactions has been developed to s... more A reaction network integrating abiotic and microbially mediated reactions has been developed to simulate biostimulation field experiments at a former Uranium Mill Tailings Remedial Action (UMTRA) site in Rifle, Colorado. The reaction network was calibrated using data from the 2002 field experiment, after which it was applied without additional calibration to field experiments performed in 2003 and 2007. 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 terminal electron-accepting processes (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 UMTRA site that demonstrated that the bulk (∼90%) of initial Fe(III) bioreduction is associated with phyllosilicate rather than oxide forms of iron. The uranium reaction network includes a U(VI) surface complexation model based on laboratory studies with Rifle site sediments and aqueous complexation reactions that include ternary complexes (e.g., calcium–uranyl–carbonate). The bioreduced U(IV), Fe(II), and sulfide components produced during the experiments are strongly associated with the solid phases and may play an important role in long-term uranium immobilization.
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Papers by Yilin Fang