Timothy Scheibe - Academia.edu (original) (raw)

Papers by Timothy Scheibe

Hydrogeologic Models of Sedimentary Aquifers, 1998

Hydrogeologists working on problems related to groundwater contamination, remediation, or water q... more Hydrogeologists working on problems related to groundwater contamination, remediation, or water quality protection face an extraordinary challenge. The fundamental transport and reaction processes that control contaminant fate occur at length scales that are many orders of magnitude smaller than the scales at which predictions of observable phenomena are needed. Spatial variability (heterogeneity) of physical and biogeochemical properties exists across the entire range of relevant scales. We will examine a number of case studies that illustrate both the challenges posed and some exciting ways that advanced computational methods are being brought to bear on these problems. We will examine pore-scale simulations of flow, transport, and reactions in porous media, in which the complex geometry of solid grains and pore spaces is explicitly quantified. Pore-scale models are being used to develop new understanding of fundamental processes that can be incorporated into larger-scale models t...

Humans have entered into and explored a wide range of environments, ranging from the deep ocean t... more Humans have entered into and explored a wide range of environments, ranging from the deep ocean to the upper atmosphere and even outer space. But for the most part, the subsurface environment hidden beneath the surface of our planet remains enigmatic and directly observable only through limited points of access. Nevertheless, physical, chemical and biological processes in Earth’s subsurface are central players in several interrelated energy and environmental issues critical to the world’s security and economy. Leadership-class computing will soon be brought to bear on understanding and predicting these processes across a wide range of time and space scales.

ph: (865) 576-8401 fax: (865) 576-5728 email: reports@adonis.osti.gov Available to the public fro... more ph: (865) 576-8401 fax: (865) 576-5728 email: reports@adonis.osti.gov Available to the public from the National Technical Information Service, U.S. Department of Commerce, 5285 Port Royal Rd., Springfield, VA 22161 ph: (800) 553-6847 fax: (703) 605-6900 email: orders@ntis.fedworld.gov online ordering: http://www.ntis.gov/ordering.htm

It has been widely observed in field experiments that the apparent rate of bacterial attachment, ... more It has been widely observed in field experiments that the apparent rate of bacterial attachment, particularly as parameterized by the collision efficiency in filtration-based models, decreases with transport distance (i.e., exhibits scale-dependency). This effect has previously been attributed to microbial heterogeneity; that is, variability in cell-surface properties within a single monoclonal population. We demonstrate that this effect could also be interpreted as a field-scale manifestation of local-scale correlation between physical heterogeneity (hydraulic conductivity variability) and reaction heterogeneity (attachment rate coefficient variability). A field-scale model of bacterial transport developed for the South Oyster field research site located near Oyster, Virginia, and observations from field experiments performed at that site, are used as the basis for this study. Three-dimensional Monte Carlo simulations of bacterial transport were performed under four alternative scenarios: 1) homogeneous hydraulic conductivity (K) and attachment rate coefficient (Kf), 2) heterogeneous K, homogeneous Kf, 3) heterogeneous K and Kf with local correlation based on empirical and theoretical relationships, and 4) heterogeneous K and Kf without local correlation. The results of the 3D simulations were analyzed using 1D model approximations following conventional methods of field data analysis. An apparent decrease with transport distance of effective collision efficiency was observed only in the case where the local properties were both heterogeneous and correlated. This effect was observed despite the fact that the local collision efficiency was specified as a constant in the 3D model, and can therefore be interpreted as a scale effect associated with the local correlated heterogeneity as manifested at the field scale.

Agu Fall Meeting Abstracts, Dec 1, 2004

Field research on biostimulation for remediation of uranium contamination in groundwater is ongoi... more Field research on biostimulation for remediation of uranium contamination in groundwater is ongoing at a field site near Oak Ridge, TN. Several alternative approaches to numerical simulation of field-scale transport and biogeochemical reactions have been implemented to support design and interpretation of field tracer and biostimulation experiments. One such approach involves simulation of advective-dispersive transport, kinetic mass transfer between advection-dominated and diffusion-dominated subdomains, and microbial utilization of carbon source amendments using a discrete particle-based method in which reactions are formulated in terms of particle transformation probabilities rather than concentration changes. We describe the method, demonstrate its application to pre- and post-modeling of tracer and electron donor injection events, and compare model results to field observations.

A small-scale field tracer test with a long pulse injection (48 hours) was performed in a highly ... more A small-scale field tracer test with a long pulse injection (48 hours) was performed in a highly heterogeneous aquifer. Diffusive/dispersive mass transfer between a highly conductive gravel layer and adjacent saprolitic materials was hypothesized as a significant solute transport process. Some solutes of interest (e.g., uranium) are also strongly impacted by sorption to aquifer solids. In addition to observations of

A field experiment is being conducted at the Oak Ridge Reservation in Tennessee to evaluate biolo... more A field experiment is being conducted at the Oak Ridge Reservation in Tennessee to evaluate biologically- mediated in situ immobilization of uranium in groundwater. Ethanol (as an electron donor) and a bromide tracer are being delivered by daily pulsed injection to a highly heterogeneous surficial aquifer, and the biogeochemical responses are being monitored over a period of several months. Monitoring

A new pore-scale reactive transport model for simulating growth of metal-reducing bacteria in por... more A new pore-scale reactive transport model for simulating growth of metal-reducing bacteria in porous media is presented. The pore-scale model uses the Smoothed Particle Hydrodynamics (SPH) method to simulate saturated water flow, transport of a soluble electron acceptor (acetate), and microbially-mediated reduction of solid-phase iron at grain surfaces coupled to acetate oxidation. A constraint-based metabolic model is used to describe

Agu Fall Meeting Abstracts, Dec 1, 2006

Hydrogeology is among the most data-limited of the earth sciences, so that uncertainty arises in ... more Hydrogeology is among the most data-limited of the earth sciences, so that uncertainty arises in every aspect of subsurface flow and transport modeling, from conceptual model to spatial discretization to parameter values. Thus treatment of uncertainty is unavoidable, and the literature and conference proceedings are replete with approaches, templates, paradigms and such for doing so. However, such tools remain not well used, especially those of the stochastic analytic sort, leading recently to explicit inquiries about why this is the case, in response to which entire journal issues have been dedicated. In an effort to continue this discussion in a constructive way we report on an informal yet extensive survey of hydrogeology practitioners, as the "marketplace" for techniques to deal with uncertainty. We include scientists, engineers, regulators, and others in the survey, that reports on quantitative (or not) methods for uncertainty characterization and analysis, frequency and level of usage, and reasons behind the selection or avoidance of available methods. Results shed light on fruitful directions for future research in uncertainty quantification in hydrogeology.

Several field and laboratory experiments have demonstrated that the growth and activity of iron-r... more 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.

Agu Fall Meeting Abstracts, Dec 1, 2005

Identification of regions of an uncertain parameter space that correspond to predictions that are... more Identification of regions of an uncertain parameter space that correspond to predictions that are consistent with observed system responses is the focus of model calibration / inverse modeling efforts. Many systematic model inversion methods utilize gradient search methods to find an optimal solution based on minimization of differences between predicted and observed responses. Associated uncertainty estimates are commonly based on local model sensitivities at the optimal solution parameter set. We have developed an alternative approach, based on iterative approximation of the complete model response surface, that provides a means of assessing global parameter uncertainty. We apply the methodology to a regional transient groundwater model of the U. S. Department of Energy's Hanford Site and compare our approach with results of parameter estimation and uncertainty assessment obtained by a conventional inverse modeling approach.

Agu Fall Meeting Abstracts, Dec 1, 2002

A numerical simulation model of bacterial U(VI) reduction in fractured subsurface sediments was d... more A numerical simulation model of bacterial U(VI) reduction in fractured subsurface sediments was developed and used to test the potential feasibility of biomineralization at the fracture/matrix interface as a mechanism for immobilization of uranium in structured subsurface media. The simulations depict flow of anaerobic groundwater, with and without acetate as an electron donor for stimulation of U(VI) reduction by dissimilatory metal-reducing bacteria (DMRB), within mobile macropores along a 1-dimensional flow path. As the groundwater moves along the flow path, U(VI) trapped in the immobile mesopore and micropore domains (the sediment matrix) becomes desorbed and transferred to the mobile macropores (fractures) via a first-order exchange mechanism. By allowing bacterial U(VI) reduction to occur in the mesopore domain (assumed to account for 12 % of total sediment pore volume) according to experimentally-determined biomass-dependent kinetic parameters and an assumed DMRB abundance of 107 cells per cm3 bulk sediment, the concentration of U(VI) in the macropore domain was reduced ca. 10-fold compared that predicted in the absence of mesopore DMRB activity after a 6-month simulation period. Our results suggest that input of soluble electron donors over a period of years could lead to a major redistribution of subsurface uranium contamination in fractured subsurface sediments, converting potentially mobile sorbed U(VI) to an insoluble reduced phase (i.e. uraninite, UO2(s)) in the mesopore domain that is be expected to be permanently immobile under sustained anaerobic conditions.

Random-walk particle tracking methods have been used extensively to simulate transport of conserv... more Random-walk particle tracking methods have been used extensively to simulate transport of conservative solutes in groundwater systems, and are particularly advantageous in cases of heterogeneous flow and advection- dominated transport. However, such models have not been broadly applied to reactive transport simulations, mostly because reactions are formulated in terms of concentrations and conversion back and forth between particle density and

Biogeochemical processes, such as mineral precipitation, microbial growth, or filtration of biolo... more Biogeochemical processes, such as mineral precipitation, microbial growth, or filtration of biological or mineral colloids, can lead to localized solid deposition and changes in flow and permeability in porous media. The coupling between these processes and flow depends on instantaneous flow paths, dispersive or diffusional mixing, localized flow velocities and the kinetics of the biogeochemical reactions themselves. We have conducted

Field research on biostimulation for remediation of uranium contamination in groundwater is ongoi... more Field research on biostimulation for remediation of uranium contamination in groundwater is ongoing at a field site near Oak Ridge, TN. As part of the site characterization program, a low-stress pumping test was conducted within a relatively low-permeability fractured saprolite aquifer underlying the site. Despite the low pumping rate used (~25 ml/min), clearly discernable water-level responses were observed as far

Hydrogeologic Models of Sedimentary Aquifers, 1998

Hydrogeologists working on problems related to groundwater contamination, remediation, or water q... more Hydrogeologists working on problems related to groundwater contamination, remediation, or water quality protection face an extraordinary challenge. The fundamental transport and reaction processes that control contaminant fate occur at length scales that are many orders of magnitude smaller than the scales at which predictions of observable phenomena are needed. Spatial variability (heterogeneity) of physical and biogeochemical properties exists across the entire range of relevant scales. We will examine a number of case studies that illustrate both the challenges posed and some exciting ways that advanced computational methods are being brought to bear on these problems. We will examine pore-scale simulations of flow, transport, and reactions in porous media, in which the complex geometry of solid grains and pore spaces is explicitly quantified. Pore-scale models are being used to develop new understanding of fundamental processes that can be incorporated into larger-scale models t...

Humans have entered into and explored a wide range of environments, ranging from the deep ocean t... more Humans have entered into and explored a wide range of environments, ranging from the deep ocean to the upper atmosphere and even outer space. But for the most part, the subsurface environment hidden beneath the surface of our planet remains enigmatic and directly observable only through limited points of access. Nevertheless, physical, chemical and biological processes in Earth’s subsurface are central players in several interrelated energy and environmental issues critical to the world’s security and economy. Leadership-class computing will soon be brought to bear on understanding and predicting these processes across a wide range of time and space scales.

ph: (865) 576-8401 fax: (865) 576-5728 email: reports@adonis.osti.gov Available to the public fro... more ph: (865) 576-8401 fax: (865) 576-5728 email: reports@adonis.osti.gov Available to the public from the National Technical Information Service, U.S. Department of Commerce, 5285 Port Royal Rd., Springfield, VA 22161 ph: (800) 553-6847 fax: (703) 605-6900 email: orders@ntis.fedworld.gov online ordering: http://www.ntis.gov/ordering.htm

It has been widely observed in field experiments that the apparent rate of bacterial attachment, ... more It has been widely observed in field experiments that the apparent rate of bacterial attachment, particularly as parameterized by the collision efficiency in filtration-based models, decreases with transport distance (i.e., exhibits scale-dependency). This effect has previously been attributed to microbial heterogeneity; that is, variability in cell-surface properties within a single monoclonal population. We demonstrate that this effect could also be interpreted as a field-scale manifestation of local-scale correlation between physical heterogeneity (hydraulic conductivity variability) and reaction heterogeneity (attachment rate coefficient variability). A field-scale model of bacterial transport developed for the South Oyster field research site located near Oyster, Virginia, and observations from field experiments performed at that site, are used as the basis for this study. Three-dimensional Monte Carlo simulations of bacterial transport were performed under four alternative scenarios: 1) homogeneous hydraulic conductivity (K) and attachment rate coefficient (Kf), 2) heterogeneous K, homogeneous Kf, 3) heterogeneous K and Kf with local correlation based on empirical and theoretical relationships, and 4) heterogeneous K and Kf without local correlation. The results of the 3D simulations were analyzed using 1D model approximations following conventional methods of field data analysis. An apparent decrease with transport distance of effective collision efficiency was observed only in the case where the local properties were both heterogeneous and correlated. This effect was observed despite the fact that the local collision efficiency was specified as a constant in the 3D model, and can therefore be interpreted as a scale effect associated with the local correlated heterogeneity as manifested at the field scale.

Agu Fall Meeting Abstracts, Dec 1, 2004

Field research on biostimulation for remediation of uranium contamination in groundwater is ongoi... more Field research on biostimulation for remediation of uranium contamination in groundwater is ongoing at a field site near Oak Ridge, TN. Several alternative approaches to numerical simulation of field-scale transport and biogeochemical reactions have been implemented to support design and interpretation of field tracer and biostimulation experiments. One such approach involves simulation of advective-dispersive transport, kinetic mass transfer between advection-dominated and diffusion-dominated subdomains, and microbial utilization of carbon source amendments using a discrete particle-based method in which reactions are formulated in terms of particle transformation probabilities rather than concentration changes. We describe the method, demonstrate its application to pre- and post-modeling of tracer and electron donor injection events, and compare model results to field observations.

A small-scale field tracer test with a long pulse injection (48 hours) was performed in a highly ... more A small-scale field tracer test with a long pulse injection (48 hours) was performed in a highly heterogeneous aquifer. Diffusive/dispersive mass transfer between a highly conductive gravel layer and adjacent saprolitic materials was hypothesized as a significant solute transport process. Some solutes of interest (e.g., uranium) are also strongly impacted by sorption to aquifer solids. In addition to observations of

A field experiment is being conducted at the Oak Ridge Reservation in Tennessee to evaluate biolo... more A field experiment is being conducted at the Oak Ridge Reservation in Tennessee to evaluate biologically- mediated in situ immobilization of uranium in groundwater. Ethanol (as an electron donor) and a bromide tracer are being delivered by daily pulsed injection to a highly heterogeneous surficial aquifer, and the biogeochemical responses are being monitored over a period of several months. Monitoring

A new pore-scale reactive transport model for simulating growth of metal-reducing bacteria in por... more A new pore-scale reactive transport model for simulating growth of metal-reducing bacteria in porous media is presented. The pore-scale model uses the Smoothed Particle Hydrodynamics (SPH) method to simulate saturated water flow, transport of a soluble electron acceptor (acetate), and microbially-mediated reduction of solid-phase iron at grain surfaces coupled to acetate oxidation. A constraint-based metabolic model is used to describe

Agu Fall Meeting Abstracts, Dec 1, 2006

Hydrogeology is among the most data-limited of the earth sciences, so that uncertainty arises in ... more Hydrogeology is among the most data-limited of the earth sciences, so that uncertainty arises in every aspect of subsurface flow and transport modeling, from conceptual model to spatial discretization to parameter values. Thus treatment of uncertainty is unavoidable, and the literature and conference proceedings are replete with approaches, templates, paradigms and such for doing so. However, such tools remain not well used, especially those of the stochastic analytic sort, leading recently to explicit inquiries about why this is the case, in response to which entire journal issues have been dedicated. In an effort to continue this discussion in a constructive way we report on an informal yet extensive survey of hydrogeology practitioners, as the "marketplace" for techniques to deal with uncertainty. We include scientists, engineers, regulators, and others in the survey, that reports on quantitative (or not) methods for uncertainty characterization and analysis, frequency and level of usage, and reasons behind the selection or avoidance of available methods. Results shed light on fruitful directions for future research in uncertainty quantification in hydrogeology.

Several field and laboratory experiments have demonstrated that the growth and activity of iron-r... more 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.

Agu Fall Meeting Abstracts, Dec 1, 2005

Identification of regions of an uncertain parameter space that correspond to predictions that are... more Identification of regions of an uncertain parameter space that correspond to predictions that are consistent with observed system responses is the focus of model calibration / inverse modeling efforts. Many systematic model inversion methods utilize gradient search methods to find an optimal solution based on minimization of differences between predicted and observed responses. Associated uncertainty estimates are commonly based on local model sensitivities at the optimal solution parameter set. We have developed an alternative approach, based on iterative approximation of the complete model response surface, that provides a means of assessing global parameter uncertainty. We apply the methodology to a regional transient groundwater model of the U. S. Department of Energy's Hanford Site and compare our approach with results of parameter estimation and uncertainty assessment obtained by a conventional inverse modeling approach.

Agu Fall Meeting Abstracts, Dec 1, 2002

A numerical simulation model of bacterial U(VI) reduction in fractured subsurface sediments was d... more A numerical simulation model of bacterial U(VI) reduction in fractured subsurface sediments was developed and used to test the potential feasibility of biomineralization at the fracture/matrix interface as a mechanism for immobilization of uranium in structured subsurface media. The simulations depict flow of anaerobic groundwater, with and without acetate as an electron donor for stimulation of U(VI) reduction by dissimilatory metal-reducing bacteria (DMRB), within mobile macropores along a 1-dimensional flow path. As the groundwater moves along the flow path, U(VI) trapped in the immobile mesopore and micropore domains (the sediment matrix) becomes desorbed and transferred to the mobile macropores (fractures) via a first-order exchange mechanism. By allowing bacterial U(VI) reduction to occur in the mesopore domain (assumed to account for 12 % of total sediment pore volume) according to experimentally-determined biomass-dependent kinetic parameters and an assumed DMRB abundance of 107 cells per cm3 bulk sediment, the concentration of U(VI) in the macropore domain was reduced ca. 10-fold compared that predicted in the absence of mesopore DMRB activity after a 6-month simulation period. Our results suggest that input of soluble electron donors over a period of years could lead to a major redistribution of subsurface uranium contamination in fractured subsurface sediments, converting potentially mobile sorbed U(VI) to an insoluble reduced phase (i.e. uraninite, UO2(s)) in the mesopore domain that is be expected to be permanently immobile under sustained anaerobic conditions.

Random-walk particle tracking methods have been used extensively to simulate transport of conserv... more Random-walk particle tracking methods have been used extensively to simulate transport of conservative solutes in groundwater systems, and are particularly advantageous in cases of heterogeneous flow and advection- dominated transport. However, such models have not been broadly applied to reactive transport simulations, mostly because reactions are formulated in terms of concentrations and conversion back and forth between particle density and

Biogeochemical processes, such as mineral precipitation, microbial growth, or filtration of biolo... more Biogeochemical processes, such as mineral precipitation, microbial growth, or filtration of biological or mineral colloids, can lead to localized solid deposition and changes in flow and permeability in porous media. The coupling between these processes and flow depends on instantaneous flow paths, dispersive or diffusional mixing, localized flow velocities and the kinetics of the biogeochemical reactions themselves. We have conducted

Field research on biostimulation for remediation of uranium contamination in groundwater is ongoi... more Field research on biostimulation for remediation of uranium contamination in groundwater is ongoing at a field site near Oak Ridge, TN. As part of the site characterization program, a low-stress pumping test was conducted within a relatively low-permeability fractured saprolite aquifer underlying the site. Despite the low pumping rate used (~25 ml/min), clearly discernable water-level responses were observed as far