Sergi Molins

Reactive transport codes for subsurface environmental simulation

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 high-level list of capabilities for each of the codes, along with a selective list of applications that highlight their capabilities and historical development.

An investigation of the effect of pore scale flow on average geochemical reaction rates using direct numerical simulation

An Investigation of the Effect of Pore Scale Flow on Average Geochemical Reaction Rates Using Direct Numerical Simulation Sergi Molins 1 David Trebotich 2 Carl I. Steefel 1 Chaopeng Shen 2 Earth Sciences Division Lawrence Berkeley National Laboratory One Cyclotron Road, Mail Stop 90R1116, Berkeley, California 94720, USA Computational Research Division Lawrence Berkeley National Laboratory One Cyclotron Road, Mail Stop 50A-1148, Berkeley, California 94720, USA

Pore-scale controls on calcite dissolution rates from flow-through laboratory and numerical experiments.

A combination of experimental, imaging, and modeling techniques were applied to investigate the pore-scale transport and surface reaction controls on calcite dissolution under elevated pCO2 conditions. The laboratory experiment consisted of the injection of a solution at 4 bar pCO2 into a capillary tube packed with crushed calcite. A high resolution pore-scale numerical model was used to simulate the experiment based on a computational domain consisting of reactive calcite, pore space, and the capillary wall constructed from volumetric X-ray microtomography images. Simulated pore-scale effluent concentrations were higher than those measured by a factor of 1.8, with the largest component of the discrepancy related to uncertainties in the reaction rate model and its parameters. However, part of the discrepancy was apparently due to mass transport limitations to reactive surfaces, which were most pronounced near the inlet where larger diffusive boundary layers formed around grains and in slow-flowing pore spaces that exchanged mass by diffusion with fast flow paths. Although minor, the difference between pore- and continuum-scale results due to transport controls was discernible with the highly accurate methods employed and is expected to be more significant where heterogeneity is greater, as in natural subsurface materials.

Timing the Onset of Sulfate Reduction over Multiple Subsurface Acetate Amendments by Measurement and Modeling of Sulfur Isotope Fractionation

Stable isotope fractionations of sulfur are reported for three consecutive years of acetate-enabled uranium bioremediation at the US Department of Energys Rifle Integrated Field Research Challenge (IFRC) site. The data show a previously undocumented decrease in the time between acetate addition and the onset of sulfate reducing conditions over subsequent amendments, from 20 days in the 2007 experiment to 4 days in the 2009 experiment. Increased sulfide concentrations were observed at the same time as δ(34)S of sulfate enrichment in the first year, but in subsequent years elevated sulfide was detected up to 15 days after increased δ(34)S of sulfate. A biogeochemical reactive transport model is developed which explicitly incorporates the stable isotopes of sulfur to simulate fractionation during the 2007 and 2008 amendments. A model based on an initially low, uniformly distributed population of sulfate reducing bacteria that grow and become spatially variable with time reproduces measured trends in solute concentration and δ(34)S, capturing the change in onset of sulfate reduction in subsequent years. Our results demonstrate a previously unrecognized hysteretic effect in the spatial distribution of biomass growth during stimulated subsurface bioremediation.

High-Resolution Simulation of Pore-Scale Reactive Transport Processes Associated with Carbon Sequestration

New investigative tools, combined with experiments and computational methods, are being developed to build a next-generation understanding of molecular-to-pore-scale processes in fluid-rock systems and to demonstrate the ability to control critical aspects of flow and transport in porous rock media, in particular, as applied to geologic sequestration of CO2. Of scientific interest is to establish the rules governing emergent behavior at the porous-continuum macroscale under far from equilibrium conditions by carefully understanding the behavior at the underlying pore microscale. To this end, the authors present a direct numerical simulation modeling capability that can resolve flow and transport processes in geometric features obtained from the image data of realistic pore space at unprecedented scale and resolution. Here, they focus on scaling a new algorithmic approach based on embedded boundary, finite-volume methods and algebraic multigrid. They demonstrate the scalability of this new capability, known as Chombo-Crunch, to more than 100,000 processor cores and show results from pore-scale flow and transport in the realistic pore space obtained from image data.

A 2.5D Reactive Transport Model for Fracture Alteration Simulation.

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.

ParCrunchFlow: an efficient, parallel reactive transport simulation tool for physically and chemically heterogeneous saturated subsurface environments

Understanding the interactions between physical, geochemical, and biological processes in the shallow subsurface is integral to the development of effective contamination remediation techniques, or the accurate quantification of nutrient fluxes and biogeochemical cycling. Hydrology is a primary control on the behavior of shallow subsurface environments and must be realistically represented if we hope to accurately model these systems. ParCrunchFlow is a new parallel reactive transport model that was created by coupling a multicomponent geochemical code (CrunchFlow) with a parallel hydrologic model (ParFlow). These models are coupled in an explicit operator-splitting manner. ParCrunchFlow can simulate three-dimensional multicomponent reactive transport in highly resolved, field-scale systems by taking advantage of ParFlow’s efficient parallelism and robust hydrologic abilities, and CrunchFlow’s extensive geochemical abilities. Here, the development of ParCrunchFlow is described and two simple verification simulations are presented. The parallel performance is evaluated and shows that ParCrunchFlow has the ability to simulate very large problems. A series of simulations involving the biologically mediated reduction of nitrate in a floodplain aquifer were conducted. These floodplain simulations show that this code enables us to represent more realistically the variability in chemical concentrations observed in many field-scale systems. The numerical formulation implemented in ParCrunchFlow minimizes numerical dispersion and allows the use of higher-order explicit advection schemes. The effects that numerical dispersion can have on finely resolved, field-scale reactive transport simulations have been evaluated. The smooth gradients produced by a first-order advection scheme create an artificial mixing effect, which decreases the spatial variance in solute concentrations and leads to an increase in overall reaction rates. The work presented here is the first step in a larger effort to couple these models in a transient, variably saturated surface-subsurface framework, with additional geochemical abilities.

Reactive Transport Model of Sulfur Cycling as Impacted by Perchlorate and Nitrate Treatments

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.

A benchmark for microbially mediated chromium reduction under denitrifying conditions in a biostimulation column experiment

Bioremediation efforts in aquifers contaminated with redox-sensitive contaminants often rely on in situ reductive immobilization. The bioremediation treatment usually involves injection of organic carbon into the subsurface (e.g., acetate) to stimulate the growth of indigenous bacteria that mediate the relevant redox processes that immobilize the target contaminant. Batch and flow-through column experimental studies are conducted to elucidate reaction networks associated with specific electron acceptor pathways and/or specific bacterial isolates. The proposed benchmark involves the simulation of microbially mediated chromium reduction under denitrifying conditions in biostimulated batch and flow-through column experiments. Simulated reactive processes include multicomponent aqueous complexation, kinetically controlled mineral precipitation and dissolution, biologically mediated reactions, and biomass growth and decay. The focus of the benchmark problem set is on the simulation of microbially mediated redox reactions with the explicit inclusion of the microbial community dynamics and the impacts on reaction rates. Rate expressions for microbially mediated redox reactions include kinetic limitations (Monod and inhibition terms) as well as thermodynamic limitations. Both catabolic (energy) and anabolic pathways (biomass growth) are considered in the microbially mediated reactions. Microbial biomass is assumed to be bound to the sediment (non-planktonic). Any reactive transport model used to reproduce results of this benchmark problem must be capable of simulating multicomponent aqueous complexation, kinetically controlled mineral precipitation and dissolution and kinetically controlled aqueous reactions. Though convenient, it is not necessary to allow for specific stoichiometric relationships for catabolic and anabolic pathways; only the overall reaction stoichiometry is used. Rate expressions for microbially mediated reaction must include a rate constant, the biomass concentration, and a number of Monod and inhibition terms. To ensure that the results presented in this paper were the correct solutions to the problems posed, the general-purpose reactive transport codes CrunchFlow, PHT3D, ToughReact, and MIN3P were used to perform the simulations. In general, results obtained with all codes show excellent agreement.