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DOE OSTI2024

Data and Scripts associated with “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling.”

This data package is associated with the publication “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling” submitted to Geoscientific Model Development (Muller et al., 2024). In this manuscript, organic matter chemistry and thermodynamics are directly connected to reactive transport simulators through the newly developed Lambda-PFLOTRAN (Parallel Reactive Flow and Transport model) workflow tool that succinctly incorporates organic matter chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate aerobic respiration of the organic matter and the resulting biogeochemistry. Lambda-PFLOTRAN is a python-based workflow, executed through a Jupyter Notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow, and transport code PFLOTRAN. This data package contains Jupyter Notebook based workflows for two test cases for running biogeochemical simulations of organic matter oxidation identified by FTICR-MS. It contains four primary folders (workflow, data, src, and analysis), a file-level metadata file (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_flmd.csv) that lists all the files contained in this data package with a short description of each, and a data dictionary (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_dd.csv) file that describes the tabular column headers. The ‘workflow’ folder contains the Jupyter Notebook based workflows for running the lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘data’ folder contains the FTICR-MS data, initial conditions, and incubation data for test cases 1 and 2 in folders titled ‘WHONDRS’ and ‘Colloids’, respectively. The data folder also has a ‘Database’ folder containing a reaction network for bulk organic matter (assumed to be CH2O) and a general database for PFLOTRAN (hanford_rxn_network). The CH2O reaction network defines bulk organic matter oxidation. Biogeochemical simulations are completed for both the lambda binned organic matter and bulk organic matter reaction networks. The ‘hanford_rxn_network’ database includes information required for PFLTORAN simulations including ion size, molar mass, and charge of the aqueous species, gases, and minerals phases. The ‘src’ folder contains python source codes for performing lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘analysis’ folder contains outputs from the test cases 1 and 2 including lambda analysis, PFLOTRAN runs and the calibration results.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Modeling supercritical CO 2 flow and mineralization in reactive host rocks with PFLOTRAN v7.0

Understanding the flow and reactivity of CO 2 injected into geological reservoirs is important for many subsurface applications including secure geologic carbon storage (GCS), critical mineral extraction, enhanced geothermal systems (EGS), and enhanced oil recovery (EOR). Traditionally, subsurface CO 2 injection for GCS applications has focused on geologic formations with favorable subsurface configurations for CO 2 migration and trapping through non-reactive mechanisms such as structural, solubility, and petrophysical trapping. Recently, CO 2 -reactive rocks such as mafic and ultramafic basalts have been investigated for their potential to react with injected CO 2 in situ to simultaneously dissolve host rock minerals and mineralize CO 2 as carbonates. Engineering rapid CO 2 mineralization in the subsurface is attractive because of the increased density of stored CO 2 , the additional safety factors associated with solidification, and the potential to extract valuable critical minerals. Here we present recent developments in the parallel flow and reactive transport simulator PFLOTRAN to model coupled CO 2 -brine flow and reactive transport for a wide range of injection and production applications involving reactive CO 2 -brine systems. These developments are based on the well established and trusted CO 2 flow capabilities in the STOMP-CO 2 simulator. New capabilities added to PFLOTRAN include new CO 2 -brine equations of state with optional thermal coupling, several new constitutive relationships like capillary pressure smoothing and scanning path hysteresis, a fully implicit well model, and native linkage with PFLOTRAN's well-established reactive transport libraries. A series of benchmarks between PFLOTRAN and STOMP-CO 2 verify the newly developed CO 2 -brine flow capabilities. Demonstrations of coupled CO 2 -brine flow modeling and reactive transport show how CO 2 mineralization can be engineered in reactive host rocks. Finally, an example use case involving copper leaching by CO 2 and critical mineral extraction is presented to showcase the strengths of this new implementation. Several limitations still remain, including limited availability of field data to parameterize models. Future work should constrain the evolution of mineral surface area during mineralization and the temperature and/or pH dependence of geochemical reactions for specific systems of interest.

Critical Minerals↗

DOE OSTI2021

Coupling Surface Flow with High-performance Subsurface Reactive Flow and Transport Code PFLOTRAN

Water exchange between the surface and subsurface is important for both water resource management and environmental protection. In this paper, we develop coupled surface and subsurface flow simulation capability in a parallel subsurface flow and reactive transport code PFLOTRAN. We sequentially couple the diffusion wave-based surface flow with the subsurface flow governedby the Richards equation in PFLOTRAN. These two flow domains are linked with a boundary condition switching method that ensures continuity of pressure and flux at the surface-subsurface interface. We verify the coupled code against other existing hydrologic models and observation data using a number of numerical experiments. The coupled hydrological model exhibits good performance in strong parallel scaling tests. The new coupled surface and subsurface simulator significantly advance community simulation capability towards improving integrated hydrologic and biogeochemical understanding of complex systems such as watersheds and river corridors. Keywords: Surface flow, Integrated hydrological modeling, Boundary condition switching, Parallel computing

Wu, Runjian↗

DOE OSTI2020

EBS Task Force: Task 9/FEBEX Modeling Final Report: Thermo-Hydrological Modeling with PFLOTRAN

This report outlines Sandia National Laboratories modeling studies applied to Stage 1 and Stage 2 of the Full-scale Engineered Barriers Experiment in Crystalline Host Rock (FEBEX) in situ test for the SKB EBS Task Force Task 9. The FEBEX test was a full-scale test conducted over ~18 years at the Grimsel, Switzerland Underground Research Laboratory (URL) managed by NAGRA. It involved emplacing simulated waste packages, in the form of welded cylindrical heaters, inside a tunnel in crystalline granitic rock and surrounded by a bentonite barrier and cement plug. Sensors emplaced within the bentonite monitored the wetting-up, heating, and drying out of the bentonite barrier, and the large resulting data set provides an excellent opportunity for validation of multiphysics Thermal-Hydrological (TH), Thermal-Hydrologic-Chemical (THC), and Thermal-Hydrological-Mechanical (THM) modeling approaches for underground nuclear waste storage and the performance of engineered bentonite barriers. The present status of the EBS Task Force is finalizing Task 9, which follows years of modeling studies of the FEBEX test, by many notable modeling teams (Gens et al., 2009; Sanchez et al. 2010; 2012; Samper et al., 2018). These modeling studies generally use two-dimensional axisymmetric meshes, ignoring threedimensional effects, gravity and asymmetric wetting and dry out of the bentonite engineered barrier. This study investigates these effects with use of the PFLOTRAN THC code with massively parallel computational methods in modeling FEBEX Stage 1 and Stage 2 results. The PFLOTRAN numerical code is an open source, state-of-the-art, massively parallel subsurface flow and reactive transport code operating in a high-performance computing environment (Hammond et al., 2014). Section 2 describes the applied partial differential equations describing mass, momentum and energy balance used in this study, considerations derived by assuming phase equilibrium between gas and liquid phases, constitutive equations for granite, cement plug, and bentonite domains, and specific approaches for use inthe PFLOTRAN code. Section 3 describes the geometry, meshing, and model set-up. Section 4 describes modeling results, Section 5 compares modeling results to field testing data, and Section 6 gives conclusions. The Appendix provides detailed information required by the EBSTask Force for final reporting.

42 ENGINEERING↗

DOE OSTI2025

Modeling commercial-scale CO 2 storage in the gas hydrate stability zone with PFLOTRAN v6.0

Abstract. Safe and secure carbon dioxide (CO2) storage is likely to be critical for mitigating some of the most dangerous effects of climate change. In the last decade, there has been a significant increase in activity associated with reservoir characterization and site selection for large-scale CO2 storage projects across the globe. These prospective storage sites tend to be selected for their optimal structural, petrophysical, and geochemical trapping potential. However, it has also been suggested that storing CO2 in reservoirs within the CO2 hydrate stability zone (GHSZ), characterized by high pressures and low temperatures (e.g., Arctic or marine environments), could provide a natural thermodynamic barrier to gas leakage. Evaluating the prospect of commercial-scale, long-term storage of CO2 in the GHSZ requires reservoir-scale modeling capabilities designed to account for the unique physics and thermodynamics associated with these systems. We have developed the HYDRATE flow mode and the accompanying fully implicit parallel well model in the massively parallel subsurface flow and reactive transport simulator PFLOTRAN to model CO2 injection into the marine GHSZ. We have applied these capabilities to a set of CO2 injection scenarios designed to reveal the challenges and opportunities for commercial-scale CO2 storage in the GHSZ.

carbon storage↗

DOE OSTI2022

Geologic Disposal Safety Assessment (GDSA) Biosphere Model Development

The Spent Fuel and Waste Science and Technology Campaign of the U.S. Department of Energy Office of Nuclear Energy, Office of Spent Fuel and Waste Disposition is conducting research and development on geologic disposal of spent nuclear fuel and high-level nuclear waste. This work includes the Geologic Disposal Safety Assessment (GDSA) program which is charged with development of generic deep geologic repository concepts and system performance assessment models. One part of the GDSA framework is the development of a biosphere model capable of assessing doses to potential receptors exposed to radionuclides released from geologic disposal sites. As part of the GDSA framework, a biosphere model compatible with the PFLOTRAN massively parallel subsurface flow and reactive transport code is under development. The PFLOTRAN model provides the radionuclide source term for the biosphere model. The GDSA Biosphere model then assesses the potential movement of radionuclides through the surface biosphere and the subsequent exposure to a human receptor living in the biosphere. The biosphere model includes pathways originating from the groundwater as well as pathways originating from surface water bodies that have a water exchange with a contaminated groundwater body. The pathways for human exposure include consumption of drinking water, irrigated crops, meat animals, aquatic vegetation, and animals, etc.; external exposure from irrigated ground surfaces, surface water bodies, recreational activities, etc.; and inadvertent exposures such as ingestion of contaminated soils or shower water, etc. The GDSA Biosphere model was designed to be flexible and generic in order to accommodate a variety of different sites and climate states. This presentation will present the on the purpose, design, and development progress of the GDSA Biosphere Model.

GDSA, biosphere, repository↗

DOE OSTI2020

Development of PFLOTRAN Transport Capability for Use in the Waste Isolation Pilot Plant Performance Assessment - 20545

Waste Isolation Pilot Plant (WIPP) performance assessment (PA) calculations estimate the probability of radionuclide release from the repository to the land surface and across the land withdrawal boundary for a regulatory period of 10,000 years after facility closure. Simulations of flow and transport in the repository and the surrounding Salado Formation are foundational to the PA. Because proposed additional waste emplacement panels would result in an asymmetric repository layout, the US Department of Energy (DOE) is preparing to transition to use of a three-dimensional (3-D) model domain for simulation of flow and transport instead of the two-dimensional (2-D) flared grid domain currently used. DOE has charged Sandia National Laboratories with developing the capability necessary to simulate processes affecting flow and transport in the WIPP in PFLOTRAN, an open-source massively parallel multi-phase flow and reactive transport code. The new flow and transport capabilities developed in PFLOTRAN incorporate WIPP-specific process models and will replace the 2-D simulators (BRAGFLO and NUTS) that are currently utilized for Salado flow and transport calculations in WIPP PA. The focus of this paper is on the development of a new Nuclear Waste Transport (NWT) mode in PFLOTRAN that has all of the capabilities necessary for Salado transport simulations, including the ability to handle complete dry-out (100% gas saturation) of arbitrary cells in the model domain, radionuclide mass conservation at step changes in porosity associated with borehole intrusion, and the ability to calculate fluxes on a flared grid. The new PFLOTRAN transport capability and a suite of verification tests were designed around a list of functional requirements for WIPP PA calculations. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

TReactMech v4.217

TReactMech couples geomechanical processes (poroelasticity, failure, and inelastic strain) with multiphase nonisothermal flow (derived from TOUGH2) and reactive geochemical transport. At its core is the reactive-transport code TOUGHREACT v4.13. TReactMech is an efficient hybrid parallel simulator, solving the geomechanics using finite elements and MPI/PetSc, the multiphase flow using integrated finite difference and MPI/PETSc, and the reactive chemistry using OpenMP. The advantages of TReactMech are in its multiphase flow capabilities (e.g., supercritical CO2, supercritical water, air) and parallel geomechanics including full 3-D stress tensor, shear and tensile failure, coupled to porosity and permeability changes. It is backwardly compatible with TOUGH2 and TOUGHREACT v4.13, allowing for easier transitions between the codes. TReactMech can be used to simulate many natural and engineered subsurface systems, including geothermal reservoirs, borehole heat exchangers, geologic carbon sequestration, geologic storage of nuclear waste, groundwater resources, weathering, sediment diagenesis, seafloor hydrothermal circulation, hydrofracturing in unconventional reservoirs, and injection/production-induced surface deformation.

Sonnenthal, Eric↗

DOE OSTI2023

Coupled Lattice Boltzmann Modeling Framework for Pore-Scale Fluid Flow and Reactive Transport

In this paper, we propose a modeling framework for pore-scale fluid flow and reactive transport based on a coupled lattice Boltzmann model (LBM). We develop a modeling interface to integrate the LBM modeling code parallel lattice Boltzmann solver and the PHREEQC reaction solver using multiple flow and reaction cell mapping schemes. The major advantage of the proposed workflow is the high modeling flexibility obtained by coupling the geochemical model with the LBM fluid flow model. Consequently, the model is capable of executing one or more complex reactions within desired cells while preserving the high data communication efficiency between the two codes. Meanwhile, the developed mapping mechanism enables the flow, diffusion, and reactions in complex pore-scale geometries. We validate the coupled code in a series of benchmark numerical experiments, including 2D single-phase Poiseuille flow and diffusion, 2D reactive transport with calcite dissolution, as well as surface complexation reactions. The simulation results show good agreement with analytical solutions, experimental data, and multiple other simulation codes. In addition, we design an AI-based optimization workflow and implement it on the surface complexation model to enable increased capacity of the coupled modeling framework. Compared to the manual tuning results proposed in the literature, our workflow demonstrates fast and reliable model optimization results without incorporating pre-existing domain knowledge.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

PFLOTRAN 5

PFLOTRAN leverages massively parallel, high performance computing to simulate large-scale non-isothermal multiphase flow, multicomponent reactive transport and electrical resistivity tomography (ERT) problems in the subsurface environment. Researchers have employed PFLOTRAN to simulate these Earth system processes on leadership class supercomputers for over two decades. The code is designed to predict the future estate of environmental systems and better inform stakeholders in the regulatory decision making process (e.g., fate of contaminants, long-term stewardship for nuclear waste, impact of climate change, etc.). A diverse team of scientists oversees PFLOTRAN development and maintenance under an open-source licensing agreement and manages contributions from an international community of researchers.

Hammond, Glenn↗

DOE OSTI2025

2D reactive transport model of shale chemical weathering and biogeochemical fluxes along a mountainous hillslope, East River Watershed, Colorado: Input files and simulation results

This data package contains input files and simulation results for a two-dimensional (2D) reactive transport model used to quantitatively analyze the coupled hydrological and biogeochemical processes governing shale weathering and associated biogeochemical fluxes under realistic environmental conditions in the high-elevation East River Watershed. These data support the conclusions presented in Stolze et al. (Water Resources Research, under review), "Model-based interpretation of solute exports and carbon partitioning during shale weathering in a mountainous hillslope". The model simulates atmospheric-subsurface gas exchange, subsurface water flow, and shale weathering processes under dynamic, year-scale conditions along a shale-underlain hillslope located in the East River watershed. The simulations were performed using the PFLOTRAN flow and reactive transport code and executed on the Perlmutter supercomputer to leverage its large-scale parallel computing capabilities. The data package contains two zipped folders, "model_input_files" and "simulation_results", and one readme.txt file. "model_input_files" contains the necessary input files to run the calibrated base-base model presented in Stolze et al. (Water Resources Research, under review). "simulation_results" contains a single hdf5 file ("Output_2D_hillslope_model.h5") which includes the results of simulation performed using the base-case model. This file can be opened with HDFView 3.1.4, Python, or MATLAB. "readme.txt" contains relevant information about the base-case model and provides guidelines on how to run the associated input files provided in the folder "model_input_files". Furthermore, readme.txt provides information regarding the model results provided in "Output_2D_hillslope_model.h5" such as matrix dimensionality and output units. Field datasets used to evaluate model performance were collected at three monitoring wells located along a hillslope transect (PLM1, PLM2, and PLM3). Dissolved ion concentration data were collected from November 2016 to October 2021 for Ca, Mg, DIC, Na, K, SO4 (Dong et al., 2025 - dic_npoc_data_2014_2024.zip - DOI:10.15485/1660459; Williams et al., 2025 - anion_data_2014_2024.zip - DOI:10.15485/1668054; Dong et al., 2025 - cation_data_2014_2024.zip - DOI:10.15485/1668055). Note that we used the files named er_PLM1_xx_yy, er_PLM2_xx_yy, and er_PLM3_xx_yy where xx stands for the name of the aqueous species and yy stands for the depth where the measurements were performed. Soil water content ([0 - 1] m) and water table depth were collected from November 2016 to October 2021 (Wan et al., 2024 - Dynamic_water_table__depthsFig2b.csv and Soil_water_content_Fig4e.csv - DOI:10.15485/2322567). Gaseous CO2 concentration were collected from October 2020 to December 2021(Wan et al., 2024 - Soil_CO2_concentrations_Fig4h.csv - DOI:10.15485/2322567) Gaseous CO2 flux from the subsurface to the atmosphere were collected in the vicinity of PLM2 from October 2019 to May 2022 (Wu et al., 2025). Soil microbial biomass concentration was measured from August 2016 to June 2017 (Sorensen et al., 2019 - 2017_East_River_Pumphouse_Microbial_Biomass__1_.csv - DOI:10.15485/1577267) All field data are published as CSV files compatible with Microsoft Excel, MATLAB, and Python, or as text files. The coordinates of the monitoring wells and the CO2(g) flux sensor in the coordinate system WGS84 are: -PLM1: [38.9197710 ; -106.9492750] -PLM2: [38.9201580 ; -106.9487170] -PLM3: [38.9207843 ; -106.9483668] -PLM4: 38.9210060 ; -106.9479528] -CO2(g) flux sensor: [38.9199180 ; -106.9489906] ------------------------------------------------------------------------------------------- This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility using NERSC award BER-ERCAP 23980, BER-ERCAP 28550, and BER-ERCAP 33789.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

A Review of Lattice-Boltzmann Models Coupled with Geochemical Modeling Applied for Simulation of Advanced Waterflooding and Enhanced Oil Recovery Processes

To maintain economic profit and improve the oil production efficiency after the primary and secondary production phase, advanced waterflooding techniques such as low salinity waterflooding in carbonate reservoirs have been investigated in numerical simulations, laboratory experiments, and field pilot tests. Multiple underlying mechanisms have been proposed based on these studies, and they are still under debate. Various numerical modeling approaches are introduced, but there exists a lack of a pore-scale comprehensive modeling scheme to fully understand the processes. Lattice-Boltzmann method (LBM) is a type of numerical fluid flow modeling technique that shows capabilities and flexibilities in modeling pore-scale fluid flow to integrate physical–chemical processes within complex structures. The intrinsic feature of LBM makes it a promising framework for simulating advanced waterflooding due to its flexibility, accuracy, and parallel efficiency. LBM works either by itself for solving reactive transport problems or by coupling with a third-party reaction solver. This review mainly introduces the LBM fluid flow and reactive transport capabilities and the concept and modeling approaches to simulate advanced waterflooding techniques. Meanwhile, an evaluation of the coupled LBM models for enhanced oil recovery (EOR) simulations is discussed with future research challenges and directions concluded.

02 PETROLEUM↗

DOE OSTI2020

Flexible and Modular Simultaneous Modeling of Flow and Reactive Transport in Rivers and Hyporheic Zones

Investigations of coupled multiphysics processes in rivers and hyporheic zones have extensively used numerical models. Most existing models use a sequential, one-way coupling between the surface and subsurface domains. Such one-way coupling potentially introduces error. To overcome this, a fully coupled model, hyporheicFoam, was developed using the open-source computational platform OpenFOAM. It captures the coupled flow and multicomponent reactive transport processes within both surface and subsurface domains and across their interface. The coupling between two domains is implemented by mapping conservative flux boundary conditions at the interface through an iterative algorithm. Reactive transport is enabled by specifying a reaction network. To start, we have implemented reaction kinetics following the double Monod-type model with inhibition. The model capability is illustrated through modeling of both conservative and reactive hyporheic flow and transport through dune bedforms. With the novel coupled model, it is now possible to quantify reactions wherein the reactants and products are constantly exchanging between domains and have feedbacks. hyporheicFoam can simulate large, three-dimensional cases owing to the computational flexibility and power offered by the code structure and parallel design of OpenFOAM.

58 GEOSCIENCES↗

DOE OSTI2022

Less can be more: Insights on the role of electrode microstructure in redox flow batteries from two-dimensional direct numerical simulations

Understanding how to structure a porous electrode to facilitate fluid, mass, and charge transport is key to enhancing the performance of electrochemical devices, such as fuel cells, electrolyzers, and redox flow batteries (RFBs). Here, using a parallel computational framework, direct numerical simulations are carried out on idealized porous electrode microstructures for RFBs. Strategies to improve an electrode design starting from a regular lattice are explored. By introducing vacancies in the ordered arrangement, it is possible to achieve higher voltage efficiency at a given current density, thanks to improved mixing of reactive species, despite reducing the total reactive surface. Careful engineering of the location of vacancies, resulting in a density gradient, outperforms disordered configurations. Our simulation framework is a new tool to explore transport phenomena in RFBs, and our findings suggest new ways to design performant electrodes.

25 ENERGY STORAGE↗

DOE OSTI2025

Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators

Alquimia v1.0 is a generic interface to geochemical solvers that facilitates development of multiphysics simulators by enabling code coupling, prototyping and benchmarking. The interface enforces the function arguments and their types for setting up, solving, serving up output data and carrying out other common auxiliary tasks while providing a set of structures for data transfer between the multiphysics code driving the simulation and the geochemical solver. Alquimia relies on a single-cell approach that permits operator splitting coupling and parallel computation. We describe the implementation in Alquimia of two widely used open-source codes that perform geochemical calculations: PFLOTRAN and CrunchFlow. We then exemplify its use for the implementation and simulation of reactive transport in porous media by two open-source flow and transport simulators: Amanzi and ParFlow. We also demonstrate its use for the simulation of coupled processes in novel multiphysics applications including the effect of multiphase flow on reaction rates at the pore scale with OpenFOAM, the role of complex biogeochemical processes in land surface models such as the E3SM Land Model (ELM) and the impact of surface–subsurface hydrological interactions on hydrogeochemical export from watersheds with the Advanced Terrestrial Simulator (ATS). These applications make it apparent that the availability of a well-defined yet flexible interface has the potential to improve the software development workflow, freeing up resources to focus on advances in process models and mechanistic understanding of coupled problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics

Abstract. Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes and that can integrate genome-scale microbial metabolic information into a dynamically changing, spatially explicit representation of environmental conditions. The model couples a lattice Boltzmann implementation of Navier–Stokes (flow) and advection–diffusion-reaction (mass conservation) equations. Reaction formulations can include both kinetic rate expressions and flux balance analysis, thereby integrating reactive transport modeling and systems biology. We also show that the use of surrogate models such as neural network representations of in silico cell models can speed up computations significantly, facilitating applications to complex environmental systems. Parallelization enables simulations that resolve heterogeneity at multiple scales, and a cellular automaton module provides additional capabilities to simulate biofilm dynamics. The code thus constitutes a platform suitable for a range of environmental, engineering and – potentially – medical applications, in particular ones that involve the simulation of microbial dynamics.

58 GEOSCIENCES↗

DOE OSTI2023

Near-continuum, hypersonic oxygen flow over a double cone simulated by direct simulation Monte Carlo informed from quantum chemistry

A large-scale, fully resolved direct simulation Monte Carlo (DSMC) computation of a non-equilibrium, reactive flow of pure oxygen over a double cone is presented. Under the simulated near-continuum conditions, the computational demands are shown to be significant because of the wide range of length scales that must be resolved. Therefore, robust grid adaption capabilities and efficient parallelization of the Stochastic PArallel Rarefied-gas Time-accurate Analyzer (SPARTA) code that is utilized in this work are essential. The thermochemical and transport collision models were selected for efficiency and simplicity. First-principles data, obtained from the highly accurate direct molecular simulation method, were used to inform the collision models’ parameters. Importantly, because SPARTA implements molecular collision models using collision-specific energies, the resulting macroscopic relaxation rates were evaluated a posteriori via zero-dimensional heat bath simulations. The comparisons of surface properties, namely heat flux and pressure, show very close agreement with previous computational fluid dynamics (CFD) results. Differences with the measurements were found to be similar to the CFD simulations. The unresolved discrepancy with the measurements could be due to inconsistent free stream conditions with the actual experimental data or missing physical phenomena altogether, for example atomic and molecular oxygen electronically excited states, three-dimensional effects, or more complex gas–surface interactions. As shown in this work, the advantages of obtaining a DSMC particle solution for these flows reside in the method's ability to be directly informed from first principles and to seamlessly describe internal energy non-equilibrium for all modes. With the advent of exascale computing and beyond, particle methods will be an increasingly important tool to verify the validity of physical assumptions in reduced-order models via fully resolved, experimental-scale simulations, down to the level of molecular-level distributions.

Mechanics↗

NASA NTRS1991

Field-aligned dynamics of chemically induced perturbations to the ionosphere

Ionospheric modification using photochemically reactive vapors is studied with a one-dimensional, multiion, fluid model of plasma flow along magnetic field lines. The magnitudes of ion and electron density changes are determined by considering both chemical processes (i.e., photoionization, ion-molecule reactions, dissociative recombination, electron attachment) and transport processes (i.e., multispecies diffusion, electric currents, ambipolar electric fields). The numerical treatment in the model is not specific to any type of release or any interaction chemistry. It has been used to simulate releases of Ba, CO2, and CF3Br in the ionosphere, but generalization to other species may be easily accomplished. The results of the calculations are found to be in good agreement with experimental observations. The feasibility of modifying the parallel current paths in the auroral F region is examined.

Bernhardt, P. A.↗