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

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 Energy’s 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 δ³⁴S of sulfate enrichment in the first year, but in subsequent years elevated sulfide was detected up to 15 days after increased δ³⁴S 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 δ³⁴S, 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

Productivity and Sustainability in a Community-Driven Software Ecosystem for Watershed Science

Through its Science Focus Area (SFA) projects the Subsurface and Biogeochemical Research program within the U.S. Department of Energy is tightly integrating observations, experiments, and modeling to advance a systems-level understanding of how watersheds function, and to translate that understanding into advanced science-based models of watershed systems. To broaden the impact of the existing SFAs, the IDEAS-Watersheds project builds on the success of a synergistic family of IDEAS projects initated in 2014. Specifically, it strives to improve wathershed modeling capacity by increasing software development productivity through an agile approach to creating a sustainable, reliable, parallel, software ecosystem with interoperable components.In this talk we highlight the unique structure of the IDEAS-Watersheds project and describe how it addresses many challenges of software development with interdisciplinary teams. Specifically, it is organized around six Research Activities that develop concrete use cases to drive advances in our software ecosystem. These use cases are designed to balance advancing software design and development practices for parallel architectures with the model and algorithmic development needed to address scientific challenges. In addition, we use a co-funding model to create a team of early career researchers that will be trained in modern software engineering, while acting as liaisons that contribute to shared deliverables.Presented at SIAM PP20 Minisymposium: Improving Productivity and Sustainability for Parallel Computing Software.</div

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

IDEAS: Software Productivity and Sustainability Improvement Plans

Poster presented at SIAM CSE17 PP108 Minisymposterium: Software Productivity and Sustainability for CSE and Data Science<div><br></div><div><div>Scientific software is playing an increasingly important role in both accelerating scientific discovery, and developing a predictive understanding of complex systems needed to inform policy decisions.  To support this role amidst the increasing complexity of the system models, and the disruptive changes in hardware and software, improvements in software development productivity and sustainability are needed. To address this critical need, the Office of Biological and Environmental Research (BER) has have begun exploring the development and use of Software Productivity and Sustainability Improvement Plans (PSIPs) within its Subsurface Biogeochemical Research Program and the Interoperable Development of Extreme-scale Software Applications (IDEAS) project.</div></div

Divergent Aquifer Biogeochemical Systems Converge on Similar and Unexpected Cr(VI) Reduction Products

In this study of reductive chromium immobilization, we found that flow-through columns constructed with homogenized aquifer sediment and continuously infused with lactate, chromate, and various native electron acceptors diverged to have very different Cr­(VI)-reducing biogeochemical regimes characterized by either denitrifying or fermentative conditions (as indicated by effluent chemical data, 16S rRNA pyrotag data, and metatranscriptome data). Despite the two dramatically different biogeochemical environments that evolved in the columns, these regimes created similar Cr­(III)–Fe­(III) hydroxide precipitates as the predominant Cr­(VI) reduction product, as characterized by micro-X-ray fluorescence and micro-X-ray absorption near-edge structure analysis. We discuss two conflicting scenarios of microbially mediated formation of Cr­(III)–Fe­(III) precipitates, each of which is both supported and contradicted by different lines of evidence: (1) enzymatic reduction of Cr­(VI) to Cr­(III) followed by coprecipitation of Cr­(III) and Fe­(III) and (2) both regimes generated at least small amounts of Fe­(II), which abiotically reduced Cr­(VI) to form a Cr–Fe precipitate. Evidence of zones with different levels of Cr­(VI) reduction suggest that local heterogeneity may have confounded interpretation of processes based on bulk measurements. This study indicates that the bulk redox status and biogeochemical regime, as categorized by the dominant electron-accepting process, do not necessarily control the final product of Cr­(VI) reduction

xSDK: Working toward a Community CSE Software Ecosystem

Poster presented at SIAM CSE17 PP108 Minisymposterium: Software Productivity and Sustainability for CSE and Data Science<div><br></div><div><b>Abstract:</b> As CSE increasingly incorporates multiscale and multiphysics modeling, simulation, and analysis, the combined use of software developed by independent groups has become imperative. However, sharing software is difficult due to inconsistencies in configuration, installation, and third-party packages, as well as deeper challenges when interoperability requires control inversion and controlling data across packages.<div><br></div><div>This poster explains how the Extreme-scale Scientific Software Development Kit (xSDK, https://xsdk.info) addresses these difficulties and provides the foundation of a CSE software ecosystem, as we work toward a collection of complementary software elements developed by diverse, independent teams. We demonstrate how the xSDK facilitates investigating climate impacts on the Upper Colorado River System through coupled models for surface-subsurface hydrology and reactive transport. Alquimia, an application-specific xSDK package, provides a common interface library for codes like Amanzi/ATS and ParFlow to access biogeochemistry capabilities from codes such as PFLOTRAN and CrunchFlow. In turn, these applications require the combined use of xSDK numerical libraries, including hypre, PETSc, SuperLU, and Trilinos.</div><div><br></div><div>A key aspect of work is a set of draft xSDK community policies, which improve code quality, sustainability, usability, and interoperability. We invite the CSE community to provide feedback on community policies and contribute to the xSDK.</div></div