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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Permeate fluxes from desalination of brines and produced waters: A reactive transport modeling study

The increasing interest in the use of membrane systems to desalinate inland brackish water, agricultural drainage, and industrially produced wastewater demands improved means of predicting desalination system performance under variable feedwater compositions. The interaction among water flow, solute transport, and chemical composition in these systems impacts permeate flux evolution. Here, an established multicomponent reactive transport simulator that accounts for these coupled processes is applied to compute osmotic pressure and permeate fluxes in reverse osmosis (RO) systems. The model is first validated by predicting permeate fluxes for a set of benchtop crossflow experiments subject to a range of feed flow rates and compositions, under fouling and non-fouling conditions. Results compare favorably with measured data that show that solutions with similar total dissolved solids concentrations but different compositions result in different permeate fluxes. The model is then applied to predict permeate fluxes from the desalination of produced waters using a commercial spiral wound RO module. For NaCl-dominant brines, at total dissolved salt concentrations (TDS) below about 70 g/L, permeate fluxes are inversely proportional to water mole fraction as the latter is a reasonable approximation of water activity (i.e. ideal mixing). In the case of Ca–Cl-, Na–CO3- and Na–SO4-dominant brines below about 70 g/L TDS, this relationship does not hold as well and tends to overpredict osmotic pressure and thus underpredict permeate fluxes. However, the opposite becomes true at higher TDS values for typical produced waters. The scaling potential of these waters is also computed by allowing the precipitation of minerals above their saturation limit on the RO membrane. This work demonstrates how reactive transport models developed for the analysis of waters from geological systems can be extended to improve process design, optimization, and control in desalination systems from produced waters and beyond.

Molins, Sergi↗
DOE OSTI2021

Reactive Transport Modeling of Aquifer Thermal Energy Storage System at Stockton, NJ

This is the modeling data (input/output files of TOUGHREACT 4.10) used to simulate the reactive transport processes of the Aquifer Thermal Energy Storage (ATES) operations at Stockton University, NJ. Readme.txt lists all the files. TOUGHREACT 4.10 requires to reproduce the modeling output. The modeling data in this submission is related to the Aquifer Injection for Energy Storage purposes outlined in "Reactive Transport Modeling of Aquifer Thermal Energy Storage System at Stockton, NJ During Seasonal Operations".

15 GEOTHERMAL ENERGY↗
DOE OSTI2023

A level-set immersed boundary method for reactive transport in complex topologies with moving interfaces

A simulation framework based on the level-set and the immersed boundary methods (LS-IBM) has been developed for reactive transport problems in porous media involving a moving solid-fluid interface. The interface movement due to surface reactions is tracked by the level-set method, while the immersed boundary method captures the momentum and mass transport at the interface. The proposed method is capable of accurately modeling transport near evolving boundaries in Cartesian grids. The framework formulation guarantees second order accuracy in space. Since the interface velocity is only defined at the moving boundary, an interface velocity propagation method is also proposed. The method can be applied to other moving interface problems of the “Stefan” type. Here, we validate the proposed LS-IBM both for flow and transport close to an immersed object with reactive boundaries as well as for crystal growth. Lastly, the proposed method provides a powerful tool to model more realistic problems involving moving reactive interfaces in complex domains.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

A deep learning upscaling framework: Reactive transport and mineral precipitation in fracture-matrix systems

Pore-scale modeling has limited applicability at large scales due to its high computational cost. One common approach to upscale pore-scale models is the use of effective medium theories, which homogenize small-scale features in a porous structure and characterize the medium by macroscale properties (e.g., permeability) and equations (e.g., Darcy’s law). However, there are classes of physical processes for which effective medium approximations may become inaccurate, e.g., mineral precipitation and clogging during reactive transport. We have developed a deep learning upscaling framework, in which pore-scale modeling is directly employed in macroscale systems, without relying on effective medium approximations. The upscaling framework is first developed for general multiscale systems and then applied to modeling reactive transport with mineral precipitation in the altered layer in fracture-matrix structures. Solute transport from the fractures to the matrix is modeled as a wall boundary condition for the fractures, which, in turn, is predicted by recurrent neural networks using the concentration histories at the fracture-matrix boundary. Specifically, we consider a meter-scale fracture network embedded in sandstones, where the smallest feature is at the micron scale. Here the proposed framework allows us to span five orders of magnitude in length scales by capturing mineral precipitation in the altered layer of the rock matrix at the pore scale across the entire meter-scale fracture network.

42 ENGINEERING↗
DOE OSTI2023

Numerical investigations to identify environmental factors for field-scale reactive transport of pathogens at riverbank filtration sites

While induced bank filtration is a proven method for facilitating sustainable drinking water production, it is at risk from surface water contaminations (e.g., pathogens). Induced bank filtration and pathogen transport in groundwater have been studied extensively. However, long-term studies that consider real-world conditions are missing. These conditions include seasonal changes to environmental conditions and waterworks operations. Therefore, to analyze the effect of seasonal changes on the transport of human pathogenic viruses and their indicators in induced bank filtration, concentrations of adenoviruses and pathogen indicators were monitored over 16 months at an active bank filtration plant at the Rhine River, in Düsseldorf (Germany). Based on this data, a 2D groundwater model was created in PFLOTRAN that simulated flow, heat transport, conservative transport of chloride and the resulting electrical conductivity, reactive transport of oxygen and nitrate, and colloid-based transport of coliforms, somatic coliphages, and adenoviruses. The results show that reduced travel time was the key factor determining periods with a low removal of coliforms and somatic coliphages in the aquifer. Travel time was controlled by river level variations during rainy seasons, and the waterworks extraction rates during dry seasons. Further, for adenovirus transport, travel distance in the subsurface appeared to be the key factor, while travel time had no significant impact. Coliform removal increased when the colmation layer permeability decreased, while coliphage and adenovirus removal was unaffected by the colmation layer permeability. Seasonal changes in temperature and oxygen content did not significantly impact the removal of coliphages and adenoviruses in groundwater. Denitrifying conditions correlated with a lowered coliform removal, but the modelling could not establish a connection between denitrifying conditions and coliform removal. Our study showed that removal of pathogens and pathogen indicators at induced bank filtration plants varies greatly in time and space (e.g., for coliforms from 1 to 4 log-levels at 20m travel distance), and that adenovirus transport differs considerably from transport of coliforms and somatic coliphages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Integration of Omics into a New Comprehensive Rate Law for Competitive Terminal Electron-Accepting Processes in Reactive Transport Models: Application to N, Fe, S, and Contaminant Transformations in Stream and Wetland Sediments

Surface waters represent important sources of alternate energy and drinking water in the United States, and characterizing the biogeochemical processes that affect surface water quality is relevant to the DOE-BER mission. Sediment biogeochemical processes regulate the release of carbon (C), nutrients, and contaminants to surface waters and thus influence water quality. Sediment biogeochemical processes are dynamic and affected by the deposition and remobilization of solid material and changes in environmental conditions driven by water discharge variations. Wetlands are important natural filters of surface waters which may either trap, metabolize, or mobilize nutrients and contaminants. Despite their importance, biogeochemical processes regulating nutrient and contaminant release and C transformation in stream and wetland sediments cannot be predicted accurately by current mathematical models. These reactive transport models largely rely on detectable changes in geochemical conditions to activate metabolic processes, do not accurately account for the competition between microbial processes, and poorly constrain effects of hydrological perturbations on biogeochemical processes. In this BER-SBR exploratory project, metagenomic and geochemical signatures were combined to identify microbially-mediated redox processes in anaerobic stream and wetland sediments from the Savannah River Site (SRS, ANL SFA) and East Fork Poplar Creek (EFPC, ORNL SFA) that play important roles in C, uranium (U), and mercury (Hg) transformations. In addition, sediment incubations were conducted to examine the competition between anaerobic respiration processes Finally, new rate laws were developed for reactive transport models that rely on complementary metagenomic and geochemical signatures to identify the underlying anaerobic microbial processes in stream and wetland sediments, describe the competition between the dominant metabolic processes involved in nutrient release and U and Hg mobilization, and more accurately quantify carbon transformation and the response of microbial processes to changes in redox conditions associated with hydrological forcing. These rate laws were optimized in batch reactors with SRS wetland sediments, where iron and sulfate reduction dominate. Anaerobic carbon remineralization processes followed the expected thermodynamic sequence of microbial respiration with depth in both sediments, except that geochemical signals indicated that sulfate reduction was inactive in EFPC sediments and moderate in SRS wetland sediments. Estimates indicated that microbial iron reduction contributed to at least half of the production of reduced iron in these sediments. Incubations demonstrated that nitrate reduction, denitrification, and dissimilatory nitrate reduction to ammonium were active in the natural EFPC sediment and activated upon nitrate amendment in these nitrate-rich sediments. In turn, these processes were outcompeted by the addition of either iron oxides or sulfate as alternative terminal electron acceptors. Although geochemical products of sulfate reduction were not detected in the incubations, the abundance of sulfate reduction genes increased with depth in the sediment and was equally more pronounced in treatments amended with either iron oxides or sulfate. Simultaneously, anaerobic sulfide oxidizing bacteria coupling sulfide oxidation to DNRA (and not conventional denitrification) were apparently enriched over time, regardless of the treatments. These findings indicate that sulfate reduction is important in freshwater stream sediments and probably catalyzed by a cryptic sulfur cycle involving nitrogen species, in which the sulfur products from sulfate reduction are immediately removed by side reactions and not detectable by geochemical measurements alone. Similar experiments in SRS sediments, however, demonstrated little interaction between nitrogen and sulfur cycling microorganisms. Sulfate reduction was impacted by the addition of more thermodynamically favorable electron acceptors, suggesting either that iron-reducing microorganisms outcompeted sulfate-reducing microorganisms for organic substrate, depleting the stock of electron donor available for sulfate reduction, or that the cryptic sulfur cycle was shunted by the precipitation of FeS generated as a result of the abiotic reduction of iron oxides by dissolved sulfide. A diagnostic modeling exercise was conducted to further investigate the competition between terminal electron accepting processes. As conventional kinetic models typically do not account for cryptic cycles and used inaccurate formulations to describe competition between microbial communities, new metabolic rate laws were developed that explicitly express the electron acceptor-specific enzyme of each energetically favorable metabolic process based on gene abundance detected in the incubations. The model was tested with the sediment slurry incubation data to determine whether substrate competition could explain the decrease in sulfate reduction observed in the presence of iron oxide competitor. The model was able to reproduce geochemical concentrations really well in each treatment once the model was calibrated with the unamended control, suggesting that microbial competition was indeed driven by thermodynamic considerations. Overall, carbon remineralization processes and rates will be reproduced much more realistically with the new metabolic rate laws.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

ATS (Advanced Terrestrial Simulator) integrated hydrology and reactive transport model output in Copper Creek, Colorado

This dataset is generated using the ATS (Advanced Terrestrial Simulator) model at Copper Creek, Colorado, the largest catchment in the East River watershed. ATS is an integrated hydrology and reactive transport model to simulate the Concentration-Discharge (C-Q) relationship, and is used to quantify the geochemical export and understand how watersheds respond to climate disturbances. Key hydrogeochemical variables, including discharge, precipitation, evapotranspiration, and geochemical concentrations, were simulated and output at a daily frequency at the Copper Creek outlet. A group of hydrology and geochemical model variables over the spatial domain are output at a bi-monthly frequency. The model used 1-km resolution daily frequency Daymet meteorological forcing, and mineral composition from previous studies. The simulations are performed on NERSC. The datasets include the input files for running the ATS (Advanced Terrestrial Simulator) simulation, including the mesh file, input script and geochemical model files. The output files from the ATS (Advanced Terrestrial Simulator) are the daily time-series discharge and geochemical concentration simulated at the outlet of Copper Creek, and the bi-monthly spatial output over the simulation domain.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Optimization of direct air capture processes using reactive transport models of adsorption-desorption cycles

In this study, we develop and implement a reactive transport model in COMSOL Multiphysics® to address the challenges of direct air carbon capture. The model is validated against experimental data and used to simulate the cyclic steady state of the adsorption-desorption process. The optimization of this model is achieved through advanced trust-region methods integrated with Gaussian Processes. Key decision variables, including adsorption and desorption times, desorption temperature and pressure, input velocity, bed porosity, column length, and radius were optimized to minimize the capture cost. After optimization, a sensitivity analysis revealed the complex interplay between the decision variables and their effect on the specific energy and cost of removing the CO 2 . We optimized the capture cost while taking into account the trade-off between energy consumption and productivity. The resulting minimum capture cost was determined to be 265.2 $/t-CO 2 , which aligns with expected values reported in the literature. Numerical results suggest the effectiveness of the optimization strategies applied, and underscore the importance of simultaneous decision variable selection in improving the performance in direct air capture processes. We also extend the modeling approach to a 2D axisymmetric model to better visualize CO₂ uptake and temperature profiles, revealing significant radial gradients during the regeneration step. As a main drawback, this enhanced model comes with a computational cost approximately 40 times higher than that of the 1D model.

Adsorption-desorption process↗
DOE OSTI2022

Supercritical, liquid, and gas CO 2 reactive transport and carbonate formation in portland cement mortar

In this paper, we investigate carbonate formation and reactive transport rate in variably saturated portland cement mortars when high concentrations of gas, liquid, or supercritical CO 2 flow through their pore network. Xray computed tomography completed during CO 2 flow is used to quantify the microstructural evolution as the mortar carbonates. After in situ tests, higher resolution scans, thermogravimetric analysis, and desorption isotherm analysis are performed to further quantify microstructural changes. We found that at dry conditions supercritical CO 2 moves more rapidly through the pore space and precipitates more carbonates than liquid or gas CO 2 . However, at 50% degree of saturation (DOS) the CO 2 state did not affect the rate of transport in that each specimen exposed to a different CO 2 state carbonated within the first hour of CO 2 exposure. When the pore space is at 50 or 100% DOS, supercritical CO 2 did not react with hydration products more rapidly nor did it result in more carbonate formation during exposure compared to gas or liquid CO 2 . The amount of Ca(OH) 2 that contributes to CaCO 3 formation is correlated to the DOS. For the mortar composition analyzed, Ca(OH) 2 contributes to approximately 40% of the carbonates formed in the 50% DOS specimens and 15% in the 100% DOS specimens. In other words, as the amount of moisture in the pore space increases, phases other than Ca(OH) 2 contribute to more than 50% of the total CaCO 3 formed.

42 ENGINEERING↗
DOE OSTI2022

Geochemical Modeling of Celestite (SrSO 4 ) Precipitation and Reactive Transport in Shales

Celestite (SrSO 4 ) precipitation is a prevalent example of secondary sulfate mineral scaling issues in hydraulic fracturing systems, particularly in basins where large concentrations of naturally occurring strontium are present. Herein, we present a validated and flexible geochemical model capable of predicting celestite formation under such unconventional environments. Simulations were built using CrunchFlow and guided by experimental data derived from batch reactors. These data allowed the constraint of key kinetic and thermodynamic parameters for celestite precipitation under relevant synthetic hydraulic fracturing fluid conditions. Effects of ionic strength, saturation index, and the presence of additives were considered in the combined experimental and modeling construction. This geochemical model was then expanded into a more complex system where interactions between hydraulic fracturing fluids and shale rocks were allowed to occur subject to diffusive transport. We find that the carbonate content of a given shale and the presence of persulfate breaker in the system strongly impact the location and extent of celestite formation. The results of this study provide a novel multicomponent reactive transport model that may be used to guide future experimental design in the pursuit of celestite and other sulfate mineral scale mitigation under extreme conditions typical of hydraulic fracturing in shale formations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A radioisotope - enabled reactive transport model for deep vadose zone carbon

In mountainous regions, which constitute the principle source of recharge to major rivers and regional aquifers, infiltration occurs through fractured, partially saturated, weathered bedrock that acts as a boundary layer between saturated aquifers and surface soil. Commonly this deep vadose zone (DVZ) is many meters thick, and yet its role in regulating the generation, retention and mobility of reactive solutes, including nutrients, contaminants and weathering products, is largely unknown. In particular, many of the key reactions that drive the formation of the weathered DVZ and the quality of water moving through it are redox processes, regulated by the availability of organic carbon and oxygen below the soil layer. The role of the DVZ is thus also poorly constrained in the context of carbon stocks and mobility, particularly in lithologies that are naturally high in organic carbon, such as shales. The overarching hypothesis of this study is that upland regions developed in geologic settings with abundant petrogenic carbon store and actively cycle carbon in the weathered DVZ below the soil and above the water table at rates that are significant and currently unconstrained. In order to quantify this cycling, the current study combines novel instrumentation techniques allowing new direct sampling of DVZ systems with advanced numerical reactive transport simulations of carbon transport and transformation. Critically, these simulations will explicitly treat the three isotopes of carbon (the abundant 12C, the stable rare 13C and the radioactive 14C) in a unified framework, thus clearly parsing between the contributions of modern surface derived carbon and lithologic carbon sources in integrated measurements of fluid and gas phase fluxes. This novel model capability will be applied to test the role of DVZ carbon cycling as a regulator of water quality and geological weathering in two complementary field sites both located in organic carbon rich shale lithologies. The first is the Eel River Critical Zone Observatory (ERCZO) in Mendocino County, California, and the second is the Lawrence Berkeley National Laboratory Watershed Function Scientific Focus Area (SFA) in the East River watershed, near Crested Butte, Colorado. At the ERCZO, a novel vadose zone monitoring system has been installed in a 20 m thick, partially saturated, weathered shale hillslope, and preliminary data already indicate substantial CO2 flux generated many meters below the soil surface. At the SFA field site, an instrumented hillslope transect indicates a more complex multi-dimensional fluid and solute transport regime, which will serve as a key test of the calibrated models. Collectively, this project will advance understanding of the cycling of carbon belowground and in relation to transport pathways across the poorly constrained DVZ characteristic of primary water recharge areas. The key product of this work will be enhanced isotope simulation capabilities that are robust and publicly available for application across a broad diversity of systems.

58 GEOSCIENCES↗
DOE OSTI2023

Resolving dynamic mineral-organic interactions in the rhizosphere by combining in-situ microsensors with plant-soil reactive transport modeling

Associations between minerals and organic matter represent one of the most important carbon storage mechanisms in soils. Plant roots are major sources of soil carbon, and resolving the dynamics and dominance of microbial consumption versus mineral sorption of root-derived carbon is critical to understanding soil carbon storage. Here we integrate in-situ rhizosphere microsensor and plant physiological measurements with a 3-D plant-soil reactive transport model to explore the fate of dissolved organic carbon (DOC) in the rhizosphere, particularly its microbial consumption and interaction with Fe oxide minerals. Over several days, a microdialysis probe sampling pore water at the root-soil interface of growing Vicia faba roots in live soil, revealed clear diel patterns of DOC concentration. Daytime DOC spikes coincided with peaks in leaf-level photosynthesis rates and were accompanied by declining redox potential and dissolved oxygen as well as increasing pH in the rhizosphere. Incorporating microsensor data into our modeling framework showed that the measured rapid loss of DOC after each mid-day spike could not be explained by consumption via aerobic respiration, nor via anaerobic respiration dominated by Fe oxide reduction. Rather, in the model, a large fraction of rhizosphere DOC was rapidly immobilized each day by adsorption to Fe oxides. Further, modeled microbial Fe reduction (fueled by DOC) did not mobilize significant organic carbon from Fe oxides during the day. Instead, the model predicted equilibrium desorption of organic carbon from Fe oxides at night. This new mechanistic modeling framework, which couples aboveground plant physiological measurements with non-destructive high-resolution monitoring of rhizosphere processes, has great potential for exploring the dynamics and balance of the various microbial reactions and mineral interactions controlling carbon transformations and storage in soils.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Upscaling Reactive Transport and Clogging in Shale Microcracks by Deep Learning

Fracture networks in shales exhibit multiscale features. A rock system may contain a few main fractures and thousands of microcracks, whose length and aperture are orders of magnitude smaller than the former. It is computationally prohibitive to resolve all the fractures explicitly for such multiscale fracture networks. One traditional approach is to model the small-scale features (e.g., microcracks in shales) as an effective medium. Although this fracture-matrix conceptualization significantly reduces the problem complexity, there are classes of physical processes that cannot be accurately upscaled by effective medium approximations, e.g., microcrack clogging during mineral reactions. Here, we employ deep learning in place of effective medium theory to upscale physical processes in small-scale features. Specifically, we consider reactive transport in a fracture-microcrack network where microcracks can be clogged by precipitation. A deep learning multiscale algorithm is developed, in which the microcracks are upscaled as a wall boundary condition of the main fractures. The wall boundary condition is constructed by recurrent neural networks, which take concentration histories as input and predict the solute transport from main fractures to microcracks. The deep learning multiscale algorithm is firstly employed in specific scenarios, then a general model is developed which can work under various conditions. The new approach is validated against fully resolved simulations and an analytical solution, providing a reliable and efficient solution for problems that cannot be upscaled by effective medium models.

58 GEOSCIENCES↗
DOE OSTI2025

Coupling flux balance analysis with reactive transport modeling through machine learning for rapid and stable simulation of microbial metabolic switching

Integrating genome-scale metabolic networks with reactive transport models (RTMs) provides a detailed description of the dynamic changes in microbial growth and metabolism. Despite promising demonstrations in the past, computational inefficiency has been pointed out as a critical issue to overcome because it requires repeated application of linear programming (LP) to obtain flux balance analysis (FBA) solutions in every time step and spatial grid. To address this challenge, we propose a new simulation method where we train and validate artificial neural networks (ANNs) using randomly sampled FBA solutions and incorporate the resulting surrogate FBA model (represented as algebraic equations) into RTMs as source/sink terms. We demonstrate the efficiency of our method via a case study of Shewanella oneidensis MR-1. During aerobic growth on lactate, S. oneidensis produces metabolic byproducts (such as pyruvate and acetate), which are subsequently consumed as alternative carbon sources when the preferred nutrients are depleted. To effectively simulate these complex dynamics, we used a cybernetic approach that models metabolic switches as the outcome of dynamic competition among multiple growth options. In both zero-dimensional batch and one-dimensional column configurations, the ANN-based surrogate models achieved substantial reduction of computational time by several orders of magnitude compared to the original LP-based FBA models. Moreover, the ANN models produced robust solutions without any special measures to prevent numerical instability. These developments significantly promote our ability to utilize genome-scale networks in complex, multi-physics, and multi-dimensional ecosystem modeling.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2018

Reactive Transport and Mass Balance Modeling of the Stimson Sedimentary Formation and Altered Fracture Zones Constrain Diagenetic Conditions at Gale Crater, Mars

On a planet as cold and dry as present-day Mars, evidence of multiple aqueous episodes offers an intriguing view into very different past environments. Fluvial, lacustrine, and eolian depositional environments are being investigated by the Mars Science Laboratory Curiosityin Gale crater, Mars. Geochemical and mineralogical observations of these sedimentary rocks suggest diagenetic processes affected the sediments. Here, we analyze diagenesis of the Stimson formation eolian parent material, which caused loss of olivine and formation of magnetite. Additional, later alteration in fracture zones resulted in preferential dissolution of pyroxene and precipitation of secondary amorphous silica and Ca sulfate. The ability to compare the unaltered parent material with the reacted material allows constraints to be placed on the characteristics of the altering solutions. In this work we use a combination of a mass balance approach calculating the fraction of a mobile element lost or gained, τ, with fundamental geochemical kinetics and thermodynamics in the reactive transport code CrunchFlow to examine the characteristics of multiple stages of aqueous alteration at Gale crater, Mars. Our model results indicate that early diagenesis of the Stimson sedimentary formation is consistent with leaching of an eolian deposit by a near-neutral solution, and that formation of the altered fracture zones is consistent with a very acidic, high sulfate solution containing Ca, P and Si. These results indicate a range of past aqueous conditions occurring at Gale crater, Mars, with important implications for past Martian climate and environments.

Gale crater↗
DOE OSTI2026

Reactive Transport Modeling with Physics-Informed Machine Learning for Critical Minerals Applications

This study presents a physics-informed neural network (PINN) framework for reactive transport modeling for simulating fast bimolecular reactions in porous media. Accurate characterization of cAhemical interactions and product formation in surface and subsurface environments is essential for advancing critical mineral extraction and related geoscience applications. The proposed methodology sequentially addresses the flow and diffusion–reaction subproblems. The flow field is computed using a mixed formulation, while the diffusion–reaction system is modeled via two uncoupled tensorial diffusion equations reformulated in terms of chemical invariants. PINNs are employed to solve the governing equations, enabling data-efficient, mesh-free prediction of chemical concentration fields. The framework is validated through a series of benchmark problems involving flow in heterogeneous porous media. Initial verification is conducted using patch tests for the flow field, followed by validation of the transport problem with emphasis on preserving non-negativity of concentrations. The complete fast bimolecular reaction scenario is then solved, yielding spatial distributions of reactants and product species. Results demonstrate that the PINNs-based approach effectively captures sharp, mixing-limited reaction fronts and dispersive mixing behavior, offering reliable predictions of reactive plume evolution. These capabilities are crucial for evaluating long-term subsurface behavior in applications such as fluid storage, energy extraction, and efficient extraction of critical minerals.

42 ENGINEERING↗
DOE OSTI2025

Motion Dynamics of Motile Microbes in Pore-Networks and its Implications for Reactive Transport Processes

This report outlines new methods to improve simulations of microbial transport and microbially mediated reactions in porous media. A range of experimental, modeling, and machine learning tools are introduced to make these simulations faster, more reliable, and useful for real-world applications. At the microscopic level, the study investigates how different types of bacteria move through confined spaces. A new artificial intelligence tool called DeepTrackStat, is introduced to track motions dynamics as observed in videos of particles migrating through pore networks. This tool is especially helpful for studying fast-moving microbes and requires less computing power than traditional tracking methods. At larger scales, the research looks at how microbes and chemicals interact in zones where surface water and groundwater meet. To connect the small- and large-scale findings, the study presents a neural network model called STAMNet. This tool helps scale up detailed small-scale microbial motion behaviors to predict large-scale environmental changes more efficiently. By combining lab experiments, computer models, and artificial intelligence, the research presented supports smarter environmental decision-making, especially in bioremediation of contaminated groundwater and protection of water quality.

54 ENVIRONMENTAL SCIENCES↗