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Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities

Abstract The gut microbiome plays a major role in human health; however, little is known about the structural arrangement of microbes and factors governing their distribution. In this work, we present an in silico agent-based model (ABM) to conceptually simulate the dynamics of gut mucosal bacterial communities. We explored how various types of metabolic interactions, including competition, neutralism, commensalism, and mutualism, affect community structure, through nutrient consumption and metabolite exchange. Results showed that, across scenarios with different initial species abundances, cross-feeding promotes species coexistence. Morphologically, competition and neutralism resulted in segregation, while mutualism and commensalism fostered high intermixing. In addition, cooperative relations resulted in community properties with little sensitivity to the selective uptake of metabolites produced by the host. Moreover, metabolic interactions strongly influenced colonization success following the invasion of newcomer species. These results provide important insights into the utility of ABM in deciphering complex microbiome patterns.

Biotechnology & Applied Microbiology

Conceptual Model Testing Related to SDU 6 Drainwell Observations

From its inception in the early 1950s through the end of the Cold War in the early 1990s, the Savannah River Site (SRS) produced nuclear materials for national defense in five reactors. Additionally, irradiated reactor fuel and target tubes were dissolved in nitric acid to recover plutonium and uranium using the PUREX (Plutonium Uranium Reduction EXtraction) process. Liquid waste from these chemical separations processes was then stored onsite in 51 underground tanks. Eight waste storage tanks have been operationally closed (i.e. cleaned and grouted) and the remaining tanks hold a mixture of liquids, insoluble solids, and precipitated salts (SRMC-LWP-2022-00001), the latter generated by evaporating water from the liquid waste. Waste is currently being retrieved from tanks and separated into 1) high-radioactivity, low-volume, and 2) low-radioactivity, high-volume components, principally through the Salt Waste Processing Facility (SWPF) (SRMC-LWP-2023-00001). The former waste stream is vitrified in the Defense Waste Processing Facility (DWPF), stored onsite, and destined for offsite disposal in a deep geologic repository. The latter stream is mixed with dry cementitious materials in the Saltstone Production Facility (SPF) and the wet slurry placed in onsite Saltstone Disposal Units (SDUs) within the Saltstone Disposal Facility (SDF), where it hardens into a cement waste form termed saltstone. A low-infiltration surface cover system will be placed over the SDF at closure, where SDUs will then be in the subsurface post-closure (SRR-CWDA-2019-00001).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W

Data from: "Towards CONUS-Wide ML-Augmented Conceptually-Interpretable Modeling of Catchment-Scale Precipitation-Storage-Runoff Dynamics"

This data package was generated to support the manuscript “Towards CONUS-Wide Machine Learning-Augmented Conceptually Interpretable Modeling of Catchment-Scale Precipitation-Storage-Runoff Dynamics.” It provides input files, model outputs, plotting data, scripts, notebooks, and documentation used to develop, evaluate, and reproduce Mass-Conserving Perceptron (MCP)-based hydrologic modeling experiments across 513 selected Catchment Attributes and Meteorology for Large-sample Studies in the United States (CAMELS-US) basins. The files are organized by modeling component and analysis purpose, including rainfall–runoff experiments, snow module experiments, coupled hydrologic-snow experiments, Long Short-Term Memory (LSTM) benchmark results, model skill metrics, initialization and epoch records, cell-state normalization files, Akaike Information Criterion (AIC)-based model comparison files, and data used to generate manuscript figures. Tabular files can be opened using standard spreadsheet software or Python/R data-analysis tools. Python scripts, Jupyter notebooks, and selected MATLAB scripts are included for model execution, postprocessing, plotting, and statistical analysis. Quality assurance and quality control were conducted through the source-data selection and modeling workflow. Meteorological forcing, streamflow, and static catchment attributes were derived from the CAMELS-US dataset, and snow water equivalent data were derived from the University of Arizona (UA) Snow Water Equivalent dataset. Selected basins and time periods were screened during the associated research workflow to avoid missing observations or poor-quality cases. Static geospatial features were processed primarily using Quantum Geographic Information System (QGIS) and Geospatial Data Abstraction Library (GDAL) workflows. Additional details are provided in the associated manuscript and documentation.

ESS-DIVE CSV File Formatting Guidelines Reporting

Benchmark study of a new simplified DFN model for shearing of intersecting fractures and faults

It is challenging to quantitatively predict shearing of intersecting fractures/faults because of dynamic frictional contacts accompanied by possible nonlinear rock deformation. To address such challenges, a new conceptual model—the simplified DFN model—was proposed and validated by Hu et al. 46 to use major paths (MPs) to represent complicated DFNs for calculation of shearing. In this work, we conducted a benchmark study for three examples that involve different levels of complexity of intersecting fractures, and correspondingly different numbers of MPs. The codes and software that were used in the benchmark cover a range of continuum, discontinuum and hybrid numerical methods: NMM (LBNL), FLAC3D (LBNL), GBDEM (KIGAM), FRACOD (DynaFrax), and CASRock (CAS). The general consistency between DFN and MP cases as predicted by all the codes/software demonstrates that major paths can be used to simplify the geometry of DFNs in a wide range of software. Disagreement in results made by some software and potential future improvements are discussed. We show that (1) shearing of one or multiple major fractures can be reduced if there are multiple smaller intersecting fractures in that area, which is a useful basis for understanding and controlling induced seismicity and merits further analysis, and (2) the agreement achieved in the benchmark examples provide confidence that the simplified DFN model is a promising conceptual model that can be used for different types of numerical approaches and software for simplifying the analysis of the shearing of intersecting fractures and faults.

58 GEOSCIENCES

3D Play Fairway Analysis for Examining of Superhot Reservoir Production Scenarios

The DEEPEN (DE-risking Exploration for geothermal Plays in magmatic ENvironments) project was a multi-laboratory, international effort to reduce uncertainty and improve resource characterization in superhot geothermal systems. Building on this foundation, this work advances open-source tools designed to lower the exploration risk and cost of superhot geothermal projects while promoting transparency, reproducibility, and efficiency in exploration workflows. These tools are being tested at two key sites: (1) the Nesjavellir Geothermal Area in Iceland, where the Icelandic Deep Drilling Project (IDDP) will drill its third well, and (2) Newberry Volcano in Oregon, USA, where Mazama Energy will pilot the first superhot enhanced geothermal system (EGS). A major outcome is the creation of a modular, open-source Python framework for play fairway analysis (PFA) in 2D and 3D, called geoPFA. The PFA workflow has been expanded to produce pseudo conceptual models, and will soon be refined to assess reservoir components through integration with the thermo-hydraulic-mechanical-chemical (THMC) simulator TReactMech, to enable iterative coupling between PFA and THMC models, improving characterization of superhot systems. All three of the Icelandic Deep Drilling Project's production scenarios were analyzed via this framework: (1) a superhot deep injection well paired with conventional production wells at Nesjavellir, (2) a superhot deep production well at Nesjavellir, and (3) superhot enhanced geothermal system at Newberry Volcano. This analysis provides useful insights around conceptual modeling of these production scenarios, helping to inform decisions around which scenario is best suited for which types of environments.

15 GEOTHERMAL ENERGY

3D Play Fairway Analysis for Examining of Superhot Drilling Production Scenarios: Preprint

The DEEPEN (DE-risking Exploration for geothermal Plays in magmatic ENvironments) project was a multi-laboratory, international effort to reduce uncertainty and improve resource characterization in superhot geothermal systems. Building on this foundation, this work advances open-source tools designed to lower the exploration risk and cost of superhot geothermal projects while promoting transparency, reproducibility, and efficiency in exploration workflows. These tools are being tested at two key sites: (1) the Nesjavellir Geothermal Area in Iceland, where the Icelandic Deep Drilling Project (IDDP) will drill its third well, and (2) Newberry Volcano in Oregon, USA, where Mazama Energy will pilot the first superhot enhanced geothermal system (EGS). A major outcome is the creation of a modular, open-source Python framework for play fairway analysis (PFA) in 2D and 3D, called geoPFA. The PFA workflow has been expanded to produce pseudo conceptual models, and will soon be refined to assess reservoir components through integration with the thermo-hydraulic-mechanical-chemical (THMC) simulator TReactMech, to enable iterative coupling between PFA and THMC models, improving characterization of superhot systems. All three of the Icelandic Deep Drilling Project's production scenarios were analyzed via this framework: (1) a superhot deep injection well paired with conventional production wells at Nesjavellir, (2) a superhot deep production well at Nesjavellir, and (3) superhot enhanced geothermal system at Newberry Volcano. This analysis provides useful insights around conceptual modeling of these production scenarios, helping to inform decisions around which scenario is best suited for which types of environments.

15 GEOTHERMAL ENERGY

Impacts of photovoltaic solar energy on soil carbon: A global systematic review and framework

Globally, solar energy is anticipated to be the primary source of electricity as early as 2050, and the greatest additions in capacity are currently in the form of large, ground-mounted photovoltaic solar energy facilities (GPVs). Growing interest lies in understanding and anticipating opportunities to increase soil carbon sequestration across the footprint and perimeter of both conventional and multi-use GPVs (e.g., ecovoltaics, agrivoltaics, and rangevolatics), especially as operators increasingly deputize as land managers. To date, studies on the relationship between soils and PV solar energy are limited to unique, localized sites. This study employed a systematic review to (i) identify a global corpus of 18 studies on interactions between GPVs and soils, (ii) collect and characterize 113 soil and soil-related experimental variables interacting with GPVs from this corpus, and (iii) synthesize trends among these experimental variables. Next, this study combined data from the systematic review with an iterative, knowledge co-production approach to produce a conceptual model for the study of soil and GPV interactions that applies to multiple installation types, scales, and contexts where GPVs are deployed, and identified research opportunities, threats, and priorities. This study's baseline understanding, conceptual model, and co-produced knowledge confer unique insight into the feasibility of combining soil carbon sequestration with the climate change mitigation potential of PV solar energy.

agrivoltaics

Collaborative Proposal: Improving understanding of the internal structure and dynamics of deep convection using ARM observations and large eddy simulations

Recent observational and large eddy simulation (LES) modeling studies have nearly unanimously supported the view of deep cumulus convection being composed of a series of quasi-spherical bubbles of buoyant air, known as moist thermals. Despite the prevalence of moist thermals in deep convection, a comprehensive theory for the dynamics of these structures is lacking. Most current conceptual models for cumulus convection are based on canonical scaling theories for dry thermals or plumes; however, there is considerable evidence that the behavior of moist thermals differs markedly from these theories. Furthermore, the theoretical basis for most cumulus parameterizations originates from the plume conceptual model, and therefore these parameterizations are inconsistent with the real structure of moist convection. Motivated by the aforementioned knowledge gaps, this “end-to-end” research effort use theory, observations, numerical simulations, and direct improvements to the Zhang-McFarlane (ZM) convection scheme in the global climate Community Atmosphere Model (CAM) to address the following research questions: What key environmental parameters determine whether or not shallow convection will transition into deep convection, in the context of thermal-like updrafts? What factors regulate the size of thermals within cumulus updrafts? How does vertical wind shear influence thermal behavior, and as a consequence, vertical velocity and mass flux profiles and the shallow-to-deep convective transition? What are the critical processes that determine updraft vertical velocities and their connection to the vertical mass flux profile for thermal-like updrafts? Idealized LES modeling will be used in conjunction with theoretical models for the core properties of thermal-like updrafts to better understand key processes that regulate thermal ascent rates and entrainment properties. Thermal-tracking procedures will be used to characterize the behavior of thermals within the LES, and recently developed direct measures of entrainment and detrainment will be used to quantify entrainment/detrainment rates. Building from these results, we will analyze the structure of moist thermals from hemispheric range-height indicator scans taken during the Atmospheric Radiation Measurement Cloud, Aerosol, and Complex Terrain Interactions (CACTI) field campaign, and from “real case” LES of CACTI events. This combined modeling and observational analysis will provide essential validation for the existing body of research on moist thermal dynamics, which is based primarily on modeling studies. With the insight gained from the aforementioned activities, we will modify the Zhang-McFarlane convection scheme to improve its representation of updraft vertical velocity and entrainment rate profiles. These process-level changes will be tested in the Community Atmosphere Model to assess the impact on global climate simulations.

54 ENVIRONMENTAL SCIENCES

The impact of capillary heterogeneity on CO 2 flow and trapping across scales

Capillary heterogeneity has been identified over the last decade as a key control on subsurface CO 2 flow behavior during geological CO 2 sequestration. These heterogeneities can be formed in all sedimentary rocks, ranging from slight variations in the sand grain sizes to extensive sequences of interbedded sands, shales, and limestones. Capillary heterogeneity has been largely, although not entirely, overlooked in subsurface flow modeling because it is assumed to only directly influence fluid redistribution over scales of centimeters to meters. However, even small-scale fluid movements can result in dramatic impacts on the mobility and trapping of the CO 2 over kilometers. Therefore, neglecting capillary heterogeneity at multiple scales could potentially lead to errors in modeling and predicting field-scale plume migration. In this review paper, we aim to provide a consistent overview to (1) establish that capillary heterogeneity can have a major impact on CO 2 plume migration, (2) establish the respective length scales at which capillary heterogeneity matters, and (3) provide guidance for numerical modeling. This review covers pertinent literature and extracts key observations from the core to the field scales. Experimental studies have shown that millimeter-decimeter scale capillary heterogeneity can cause the so-called capillary heterogeneity trapping in addition to pore-scale residual trapping. Even at such a small scale, capillary heterogeneity can already lead to complex upscaled constitutive relationships, such as flow-rate dependent and anisotropic relative permeability, which affects field-scale CO 2 migration even when field-scale heterogeneities are present. Under gravity-dominated flow regimes, centimeter-meter scale capillary heterogeneity can entrap a significant amount of CO 2 at field scale, not just after imbibition but also during drainage. In certain cases, the presence of capillary heterogeneity can even completely stop the vertical movement of the CO 2 plume, hence greatly reducing leakage risks. At meter-kilometer scale, the influence of capillary heterogeneity is more pronounced and can hinder or redirect CO 2 migration in both lateral and vertical directions. The impact of capillary heterogeneity across multiple spatial scales poses a great challenge in modeling CO 2 migration at field scale, because it is practically impossible to build a field-scale earth model with grid blocks at millimeter scale. We recommend a hierarchical modeling approach to address this challenge. At field scale, earth models are built to capture geological features and heterogeneities in high but still practical grid resolutions. For each facies or rock type of the field-scale model, high- resolution meter-scale “conceptual” models are built with millimeter-scale grid blocks to capture representative fine-scale bedding geometries and heterogeneities in various environments of deposition, bridging the gap from subcore scale to the size of a field-scale simulation grid block. Upscaling is then used to preserve the smaller-scale flow dynamics of various rock types in field-scale simulations. Here, future work is needed to (1) refine, improve, and validate the hierarchical modeling approach; (2) build libraries of fine-scale bedding models for facies in various environments of deposition; (3) quantify multiscale capillary heterogeneity effects under subsurface uncertainties; (4) gain learning from different storage formations; and (5) establish best practices that balance accuracy and computational speed.

Capillary heterogeneity

Identifying synoptic controls on boundary layer thermodynamic and cloud properties in a regional forecast model

Although most of our understanding of boundary layer cloudiness is based on idealized, subtropical, barotropic marine environments, boundary layer clouds exist across a range of conditions. In this study, we use the Naval Research Laboratory's Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS) and an automated cold-front-relative analysis framework to explore the boundary layer structure associated with low clouds across a transect through the cold front of a midlatitude synoptic cyclone. The model credibly captures boundary layer structure in line with conceptual models of midlatitude cyclones and ground-based observations at Graciosa Island in the Azores. The warm sector is conditionally unstable, with clouds that are too shallow and with too little liquid water, compared to cloud property retrievals from satellite and surface-based instruments. The cold-frontal region exhibits convection associated with weak stability and ascent. Northwest of the cold front, the boundary layer is well mixed, deeper, and capped by a strong inversion maintained by large-scale subsidence. Simulated clouds in frontal and post-frontal regions are mostly too thick, with too much liquid water and too little cloud base drizzle. The post-frontal clouds are associated with grid-scale updrafts, which appear to be the model's attempt to represent mesoscale organization of cellular convection typically observed in the cold sector of midlatitude cyclones. The deep, well-mixed post-frontal boundary layers and cloudiness are maintained by strong surface fluxes, as in cold air outbreaks. Our analysis framework serves as a unique approach to model verification, and our results offer insights into differences in boundary layer cloud behavior between subtropical and synoptic cold-sector regimes.

Eissner, Jordan M. [Univ. of Kansas, Lawrence, KS

Mineral-associated organic matter is heterogeneous and structured by hydrophobic, charged, and polar interactions

The formation of mineral-associated organic matter (MAOM) is a key phenomenon that may explain the slow turnover rates of carbon in soil organic matter (SOM). Despite this, important details pertaining to the structure and dynamics of MAOM remain unknown. In the present study, we use replica-exchange molecular dynamics simulations to gain insight into the structure of MAOM on the surface of prototypical phyllosilicate clay and Fe-oxide minerals, montmorillonite and goethite, fine-grained minerals that strongly impact soil carbon dynamics in temperate and tropical regions, respectively. We examine the impact of aqueous chemistry through the presence of either Na + or Ca 2 + charge balancing counterions. Our results are consistent with the hypothesized multilayer sorption (“onion-skin”) model of MAOM and help to explain previous observations regarding the patchy distribution of SOM on mineral surfaces. In particular, the SOM coatings are partial and laterally heterogeneous, and water retains extensive access to mineral surfaces even when significant SOM sorption occurs. Low molecular weight neutral SOM molecules ( < 200 Da) infrequently interact with the mineral surfaces nor their sorbed organic matter coatings and are increasingly labile with decreasing molecular weight. This observation is inconsistent with a central feature of the predominant soil continuum model of SOM and suggests that further iterations of the conceptual model may be required.

54 ENVIRONMENTAL SCIENCES

Comparing modelling approaches for a generic nuclear waste repository in salt

This paper contains a comparison of five modelling approaches for a simplified nuclear waste repository in a domal salt formation. It is the result of a four-year collaboration between five international teams on Task F of the DECOVALEX-2023 project on performance assessment modelling. The primary objectives of Task F are to build confidence in the models, methods, and software used for performance assessment (PA) of deep geologic nuclear waste repositories, and/or to bring to the fore additional research and development needed to improve PA methodologies. This work demonstrates how these objectives are accomplished through staged development and comparison of the models and methods used by participating teams in their PA frameworks. Participating teams made a wide range of model assumptions, ranging from compartmentalized networks to full 3D models of the salt formation and repository. Despite differences in the modelling strategies, all models indicate that salt compaction and diffusion of radionuclides in brine are key processes in the repository. For the isothermal spent nuclear fuel and vitrified waste scenario with multiple early failures considered, all models indicate little of the disposed radionuclides will migrate beyond the repository seal over the 100,000-year simulations. In general, the model output quantities have the largest differences over the short term and near the waste. Disparities between the models are believed to be due to differing simplifications from the conceptual model.

DECOVALEX

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning

The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.

Artificial intelligence

Hyporheic‐Zone Processes and Stream Oxygen Dynamics: Insights From a Multiscale Reactive Transport Model

Aquatic ecosystem metabolism encapsulates the daily fixation (gross primary production, GPP d ) and mineralization (ecosystem respiration, ER d ) of organic carbon. In fluvial systems, these are commonly estimated by inverse solutions to field observations using a model that describes oxygen concentrations varying in the water column in response to metabolic fluxes and air‐water gas exchange controlled by a rate coefficient (K 600 ). The most common conceptual model is the single‐station metabolism (SSM) model. The simplicity and flexibility of this conceptualization make it attractive; however, it implicitly assumes that all the processes that consume oxygen in fluvial systems can be lumped into a bulk estimate of respiration with poorly understood consequences for estimates of GPP d , ER d , and K 600 . Here, we focus on the implications of using SSM conceptualization when estimating metabolic fluxes from oxygen dynamics in channels where hyporheic exchange occurs. We use a new multiscale numerical model for reactive transport in streams that represents hyporheic exchange and streambed heterotrophic respiration. Nondimensionalization of this model reveals dimensionless groups that collectively control oxygen dynamics. Numerical experiments offer a mechanistic understanding of the impacts of hyporheic exchange on diel oxygen dynamics revealing that potential biases arise from neglecting mass transfer limitations. Specifically, we found that hyporheic exchange significantly affects diel oxygen dynamics, even for nonreactive streambed sediments. Moreover, while the SSM performs well in many situations, we find conditions where significant bias is produced by hyporheic exchange, even when oxygen data are well‐fitted. These situations pose a major challenge in the interpretation of metabolism assessment estimates.

Gomez‐Velez, Jesus D. [Oak Ridge National Laborato

High-resolution lidar observations of sedimentation-induced size sorting of droplets near a laboratory cloud top

Cloud optical properties and precipitation, which are crucial to weather and climate, are strongly influenced by cloud microphysical properties that are still poorly understood. Here, we develop a high-resolution time-correlated single-photon-counting lidar and apply it to observe cloud microphysical properties at one-centimeter range resolution in a convection chamber under well-controlled conditions. Together with concurrent in-situ measurements and theoretical analysis, our lidar observations indicate that although turbulent mixing tends to homogenize the cloud in the bulk region, entrainment and sedimentation cause inhomogeneities in droplet concentrations near the cloud top. Specifically, the topmost region is directly affected by entrainment, and lidar profiles show clear evidence of entrained air and detrained cloud filament. The transition region below exhibits vertical size sorting of cloud droplets caused by sedimentation. Our results suggest that using a single sedimentation velocity for all cloud droplets, as is done in many atmospheric models, overlooks key physics relevant to the microphysical structure near the cloud top. In conclusion, our conceptual model used to describe these measurements can serve as a step toward improving the current modeling of processes in the cloud top region.

54 ENVIRONMENTAL SCIENCES

Data for Zheng et al. (2025), "AquaMEND: Reconciling multiple impacts of salinization on soil carbon biogeochemistry"

Soil salinization, exacerbated by climate change, poses a global threat to coastal ecosystems and soil function. Salinity affects soil carbon cycling by directly impacting microbial activity and indirectly altering soil physicochemical properties, but current models inadequately represent these complexities. This dataset contains the observational and modeling data from Zheng et al. (2025), which described a process-based modeling framework that couples soil solution chemistry with microbial carbon cycling reactions to study the impacts of soil salinization. This conceptual model is implemented numerically into the open-source geochemical program PHREEQC 3.0 (Parkhurst and Appelo, 2013). This dataset consists of: - Figure2_AquaMEND_salinity_buffer: Contains model simulation outputs to assess the impact of three different cation exchange and surface complexation processes on salinity buffering (Fig. 2 from Zheng et al. 2025). - Figure3_Salinity_function: Contains salinity function fitting for literature data (Fig. 3 from Zheng et al. 2025). - Figure4_AquaMEND_microbial_mechanisms: Contains model simulation outputs for testing various microbial process-based hypotheses related to soil salinization, including microbial mortality, carbon use efficiency (CUE), extracellular enzyme activity, and other microbial mechanisms (Fig. 4 from Zheng et al. 2025). - Figure5_AquaMEND_Redox: Contains on model simulation outputs to evaluate shifts among key redox processes, such as aerobic respiration, sulfate reduction, and methanogenesis (Fig.5 from Zheng et al. 2025). - Figure6_AquaMEND_sorption: Contains on model simulation outputs for investigating the effects of salinity on dissolved organic matter (DOM) sorption and desorption processes (Fig. 6 from Zheng et al. 2025). - Figure7_AquaMEND_process_couple: Contains on model simulation outputs for exploring coupled biotic-abiotic processes and their interactions (Fig. 7 from Zheng et al. 2025). - data: Includes datasets used to develop salinity response functions and evaluate salinity buffering capacity. Datasets for MEND model calibration. - database: Contains the `.dat` file required by PHREEQC for model execution. - README.md: A Markdown plain text file describing the computational tools and directories. Files are a mixture of plain text CSV (comma-separated value) and plain text *.dat files written by the model; no special software is required to read them.

EARTH SCIENCE > AGRICULTURE > SOILS > SOIL SALINIT

DECOVALEX-2023: Task C Final Report

The Full-scale Emplacement (FE) heater experiment at the Mont Terri Underground Rock Laboratory (URL) was designed and conducted by Nagra to replicate an emplacement tunnel of Nagra’s reference repository design at 1:1 scale. Alongside testing the technical feasibility of constructing disposal tunnels, emplacing waste containers in the tunnels and then backfilling them, the main goals of the FE experiment are (1) to obtain a better understanding of the coupled effects of induced thermo-hydro-mechanical (THM) processes that may occur and (2) to validate existing coupled THM models (Müller et al., 2017). A key aspect of ensuring safety for repositories located in low-permeability rock involves minimizing any damage to the rock itself, thereby preserving its integrity and promoting a stable environment Amongst a number of processes that could damage the rock is the increase in pore pressure due to thermal loading caused by heat emitted from the waste. To reduce the potential damage of the rock, it is important to analyse the evolution of heat over time due to the heat load of the containers and assess possible consequences by coupled THM models. The aim of Task C of DECOVALEX-2023 was to build 3D numerical models of the FE experiment, focussing in particular on the heating induced pore pressure change in the Opalinus Clay. Data from a large number of sensors were available from the FE experiment for model comparison. These sensors measured temperature and relative humidity in the bentonite around the heaters, and temperature, pressure and displacement/strain in the surrounding Opalinus clay. Data were available from the start of excavation (April 2012) up to August 2020 for most sensors (more than 5 years from the start of heating in December 2014). To fulfil the overall aim of the task, the work was broken down into a number of steps, starting with simpler models to build confidence in each team’s approach and then moving to more complex models that better represent the FE experiment. Step 0 consisted of 2D benchmark models, gradually increasing the number of processes that are represented from thermal (T) only models in Step 0a, to coupled thermal hydraulic (TH) models in Step 0b with a representation of changing porosity, to coupled thermo-hydro-mechanical (THM) models in Step 0c, where porosity changes are calculated by the mechanical model. A detailed specification of processes, parameters, initial and boundary conditions was provided for this step, with the ambition that all teams would work towards close agreement in their model results, thus building confidence in the model implementations. vi It was not straightforward to achieve agreement between the teams, so additional steps (Step 0b2, 0b3, 0c2, 0c3) were added along with derivation of some analytical solutions against which the models could be compared. The reasons for the differences between teams were investigated and found to be caused primarily by different conceptual model assumptions (including temperature dependence of the thermal expansion of water), different model formulations (including porosity evolution) and differences in modelled domain sizes, boundary conditions and grid discretisation. This demonstrates that comparisons between multiple modelling teams and/or comparison with analytical results and experimental data are highly beneficial in providing an indication of uncertainty in model predictions. At the conclusion of Step 0, almost all teams had achieved a close agreement in model results and those that had not achieved an agreement knew the reason for this. Step 1 moved from 2D models to 3D models of the FE experiment without adding technical features like shotcrete or EDZ, and only considering the heating phase. Initially the 3D model was tightly specified to continue to build confidence in the model implementations (Step 1a). The results of Step 1a were compared to the data from the FE-experiment without the teams seeing the data. The teams were then provided with a sub-set of the data from the FE-experiment and invited to consider how best to use the large dataset for model comparison (Step 1b). Teams were then asked to use the data provided to calibrate their models, only changing material property values rather than adding features or processes to their models (Step 1c). In Step 1, teams were asked to only model the heating phase of the experiment, so pressure in the Opalinus Clay was reported as change in pressure since the initial conditions were specified rather than modelled. The change from 2D to 3D models was accompanied by an increase in the dispersion of results between the teams. Some of this was resolved during the task, but some remained and is potentially due to model discretisation. Calibration of parameters was useful in improving the fit of the models to the data but the remaining differences indicated that the models were missing features or processes. In Step 2, the teams were asked to update their models with additional features and processes as well as calibrating parameters to try and improve the fit of the models to the data. Teams were encouraged to represent ventilation of the open FE tunnel prior to backfilling with heaters and bentonite and in Step 2, the absolute pressure in the Opalinus Clay was compared between the teams. Teams took different approaches, but there was consideration of adding shotcrete and an EDZ into the model, representing stress change during excavation and different approaches to modelling ventilation of the FE tunnel. Overall, the documented results showed a very good agreement for temperature. The results for porewater pressure evolution showed a significant improvement for most teams compared to Step 1c with a good agreement to the measurements for several teams whereas some teams overpredicted the pressure increase and others overpredicted the drainage effect especially for the sensors close to the heater. Step 3 was an opportunity for teams to use the models developed in Step 1 and Step 2 to make predictions about the temperature and pressure changes that will be expected at the FE experiment over the next few years in light of the planned changes in thermal output of the heaters.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W