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At least 1,117 records · Page 62

An Open-source Llm Enhanced-tool Specialized In Helping Moose Related Problems And Tasks

MOOSEenger is an open-source, terminal-first chat application for the MOOSE ecosystem that couples specialized parsing of MOOSE documentation and “.i” input files with retrieval-augmented generation to deliver grounded answers about multiphysics modeling and workflows. It includes dedicated readers for MOOSE-style HTML and a pyhit-based parser that uses the MOOSE syntax tree to preserve block structure and attach retrieval metadata. A data-ingestion pipeline performs semantic chunking into atomic facts and stores them hierarchically in a local Chroma vector database that maintains parent–child relationships across documents; the system can ingest directories, individual files, and single-page web content, and it provides CRUD operations (insert, update, delete) to manage the corpus. At query time, relevant chunks are embedded, retrieved, and fused into the model context, with interactive features such as token streaming, persistent chat history, and dynamic RAG (retrieval triggered by user input or intermediate model output). Deployment is flexible: MOOSEenger runs with local Ollama models or remote Hugging Face/OpenAI backends—typically coordinating generation, lightweight tagging/summarization, and embeddings across three models—and it also supports a server mode and integration with the VS Code Continue interface.

Li, Mengnan [Idaho National Laboratory (INL), Idah↗

Polar primary aerosols across the ocean-sea ice-snow-atmosphere interface: From sources to impacts

Primary aerosols play a critical role in polar climate systems, influencing cloud formation, precipitation, radiative balance, and surface energy budgets. This paper provides a comprehensive synthesis of primary aerosol sources, transformation and removal processes, and broader atmospheric impacts in polar regions, emphasizing their links to ocean and sea ice biogeochemistry. These aerosols (including sea salt, primary organic aerosol, and primary biological aerosol particles) originate from marine and cryospheric environments and are emitted through physical processes, such as wave breaking, bubble bursting, and blowing snow. Emission sources include seawater, sea ice, snow, and freshwater from river discharge and glacial runoff. Once airborne, these particles can serve as a chemical reservoir, influencing atmospheric composition and reactivity, and as seeds for cloud droplet and ice crystal formation, influencing cloud microphysics and polar climate. Despite their importance, many of the processes governing primary aerosol emissions and transformations remain poorly constrained. The most pressing knowledge gaps pertain to emission processes, limited spatiotemporal observational coverage, instrumentation constraints, parameterization development, and the integration of interdisciplinary expertise. To improve our understanding of primary aerosol drivers and their response to climate, future research efforts should prioritize strategically coordinated and cross-disciplinary process studies, advancements in measurement technologies and coverage, and close collaboration between modelers and observational scientists to inform and refine model parameterizations. As polar regions continue to undergo profound changes marked by increased precipitation, reduced sea and land ice, freshening oceans, and shifting ecosystem dynamics, characterizing present-day primary aerosol populations is vital. Improved understanding will be essential for anticipating future changes in aerosol-radiation and aerosol-cloud interactions and their implications for polar and global climate systems.

Aerosol-cloud↗

Framework for a Digital Documented Safety Analysis

This framework is developed to progress the digital implementation of digital tools applied to the DOE authorization process, with future applications to NRC SAR development/review, to accelerate the design and review processes of advanced nuclear reactors. The engineering design and licensing process for nuclear reactors is currently burdened by a document-based approach that leads to duplications and errors due to a lack of traceability among numerous static documents. Changes to design information require labor-intensive manual tracing through these documents, creating a high potential for human error. The adoption of a digital ecosystem, utilizing a digital thread to link various aspects of project design and analysis, promises dynamic documentation generation, automatic updates, and error reduction. Model Based Definition (MBD) and Product Lifecycle Management (PLM) tools are central to this digital transformation.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Complete Demonstration of a Prototype Version of FORCE User Interface and Conduct Analyst Survey Collecting Feedback on Interface Features and Usability

In 2024 the US Department of Energy (DOE) Office of Nuclear Energy (NE) Integrated Energy System (IES) program continued to develop the Framework for Optimization of Resources and Economics (FORCE) analysis ecosystem into a more traditional toolset with simplified software installation, automated workflows, and interactive results visualization. The DOE-NE Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench continued to be leveraged for user input, application workflow and runtime environment, and interactive results visualization capabilities. This report documents the demonstration of a FORCE User Interface (UI) prototype and the results of a survey of analysts’ using the Holistic Energy Resource Optimization Network (HERON) tool in FORCE with the prototype UI.

97 MATHEMATICS AND COMPUTING↗

Response Of Salt Intrusion In A Tidal Estuary To Regional Climatic Forcing (FVCOM Output for the baseline scenario)

Salinity distribution in a large tidal estuary is subject to estuarine adjustment under the influences of multiple physical drivers such as freshwater pulses and sea level rise, and is crucial to upstream water quality, aquaculture, and ecosystem functions of the estuary. To better understand the estuarine salinity response to climate change, the unstructured-grid Finite Volume Community Ocean Model was implemented to simulate the salt intrusion in the Delaware Bay Estuary. The model was first validated by multiple observational data sets and subsequently applied in an idealized setting to examine the response of salt front to freshwater pulses in high flow conditions, followed by a long-term drought condition supported by a multi-decadal streamflow drought analysis in the estuary. The model results showed that after the freshwater pulses the salt front location moved further upstream with sea level rise. Under the simulated long-term drought condition, the adjustment timescale of salt intrusion varies nonlinearly with sea level rise. With a significant increase in sea level rise, the adjustment timescale starts to decrease. This shift suggests a transition into a different regime where the estuary becomes more stratified, as indicated by an increasing bulk Simpson number with rising sea levels. These findings have been summarized into a journal manuscript. The data included in this information release request are FVCOM model output associated with the numerical simulations described in the journal manuscript.

Liu, Jinliang↗

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen

Abstract Soil organic nitrogen (N) is a critical resource for plants and microbes, but the processes that govern its cycle are not well-described. To promote a holistic understanding of soil N dynamics, we need an integrated model that links soil organic matter (SOM) cycling to bioavailable N in both unmanaged and managed landscapes, including agroecosystems. We present a framework that unifies recent conceptual advances in our understanding of three critical steps in bioavailable N cycling: organic N (ON) depolymerization and solubilization; bioavailable N sorption and desorption on mineral surfaces; and microbial ON turnover including assimilation, mineralization, and the recycling of microbial products. Consideration of the balance between these processes provides insight into the sources, sinks, and flux rates of bioavailable N. By accounting for interactions among the biological, physical, and chemical controls over ON and its availability to plants and microbes, our conceptual model unifies complex mechanisms of ON transformation in a concrete conceptual framework that is amenable to experimental testing and translates into ideas for new management practices. This framework will allow researchers and practitioners to use common measurements of particulate organic matter (POM) and mineral-associated organic matter (MAOM) to design strategic organic N-cycle interventions that optimize ecosystem productivity and minimize environmental N loss.

Environmental Sciences & Ecology↗

Deployment and Evaluation of SciStream on OLCF's Advanced Computing Ecosystem (ACE)

The growing demand for real-time analysis, experimental steering, and decision-making in scientific workflows has created a need for tightly coupled integrations between experimental facilities and high-performance computing (HPC) systems. The Department of Energy’s Integrated Research Infrastructure (IRI) initiative highlights data streaming as a key capability for enabling memory-to-memory data transfers, bypassing the limitations of traditional store-and-forward models. SciStream is a toolkit developed by researchers at Argonne National Laboratory (ANL) to support such streaming by addressing cross-domain security, delegated authentication, and application transparency. We deployed and evaluated SciStream on the Oak Ridge Leadership Computing Facility’s (OLCF) Advanced Computing Ecosystem (ACE) infrastructure, leveraging the Olivine OpenShift cluster and its high-bandwidth Data Streaming Nodes (DSNs) as gateway nodes. Our evaluation included synthetic streaming workloads derived from IRI science workflows, a streaming simulator, and integration with RabbitMQ to handle low-level messaging. This report documents the deployment process, performance evaluation, and challenges encountered, along with opportunities for future improvements.

97 MATHEMATICS AND COMPUTING↗

Coupled primary production and respiration in a large river contrasts with smaller rivers and streams

Abstract Although time series in ecosystem metabolism are well characterized in small and medium rivers, patterns in the world's largest rivers are almost unknown. Large rivers present technical difficulties, including depth measurements, gas exchange (, ) estimates, and the presence of large dams, which can supersaturate gases. We estimated reach‐scale metabolism for the Hanford Reach of the Columbia River (Washington state, USA), a free‐flowing stretch with an average discharge of 3173 . We calculated from semi‐empirical models and directly estimated it from tracer measurements. We fixed at the median value from these calculations (0.5 ), and used maximum likelihood to estimate reach‐scale, open‐channel metabolism. Both gross primary production (GPP) and ecosystem respiration (ER) were high (GPP range: 0.3–30.8 g , ER range: 0.8–30.6 g ), with peak GPP and ER occurring in the late summer or early fall. GPP increased exponentially with temperature, consistent with metabolic theory, while light was seasonally saturating. Annual average GPP, estimated at 1500 g carbon , was in the top 2% of estimates for other rivers. GPP and ER were tightly coupled and 90% of GPP was immediately respired, resulting in net ecosystem production near 0. Patterns in the Hanford Reach contrast with those in small‐medium rivers, suggesting that metabolism magnitudes and patterns in large rivers may not be simply scaled from knowledge of smaller rivers.

54 ENVIRONMENTAL SCIENCES↗

Model code and data: biomass allocation adjustments induced by elevated CO2 and warming in a C3 brackish marsh, 2017-2022, Maryland

This dataset and R script accompany the published paper Bruns et al. (2024) in Geophysical Research Letters. The data are from the first six years of a field manipulation of whole-ecosystem warming and elevated CO2 experiment (Salt Marsh Accretion Response to Temperature eXperiment, or SMARTX) in the Smithsonian's Global Change Research Wetland (GCReW), a brackish, microtidal wetland site on a subestuary of the Chesapeake Bay. These data were generated to understand how warming and elevated CO2 interact to structure ecosystem-level responses to global change, particularly in terms of carbon sequestration. The dataset covers 2017-2022 and includes peak annual above ground biomass, annual belowground fine root productivity, and porewater NH4 for each experimental plot. The overall experiment is replicated in two locations on the marsh, a lower elevation zone dominated the C3 sedge S. Americanus and a higher elevation plot dominated by the C4 species. This paper and its data release is only for the C3 plot. Variable descriptions for data file is available in variable_descriptions.pdf. The R script Bruns_et_al_2024_GRL_make_figures.Rmd contains model code and other scripts used to generate all paper figures.

54 ENVIRONMENTAL SCIENCES↗

Causality guided machine learning model on wetland CH 4 emissions across global wetlands

Wetland CH 4 emissions are among the most uncertain components of the global CH 4 budget. The complex nature of wetland CH 4 processes makes it challenging to identify causal relationships for improving our understanding and predictability of CH 4 emissions. In this study, we used the flux measurements of CH 4 from eddy covariance towers (30 sites from 4 wetlands types: bog, fen, marsh, and wet tundra) to construct a causality-constrained machine learning (ML) framework to explain the regulative factors and to capture CH 4 emissions at sub-seasonal scale. We found that soil temperature is the dominant factor for CH 4 emissions in all studied wetland types. Ecosystem respiration (CO 2 ) and gross primary productivity exert controls at bog, fen, and marsh sites with lagged responses of days to weeks. Integrating these asynchronous environmental and biological causal relationships in predictive models significantly improved model performance. More importantly, modeled CH 4 emissions differed by up to a factor of 4 under a +1°C warming scenario when causality constraints were considered. These results highlight the significant role of causality in modeling wetland CH 4 emissions especially under future warming conditions, while traditional data-driven ML models may reproduce observations for the wrong reasons. Our proposed causality-guided model could benefit predictive modeling, large-scale upscaling, data gap-filling, and surrogate modeling of wetland CH 4 emissions within earth system land models.

54 ENVIRONMENTAL SCIENCES↗

X-ray chemical imaging for assessing redox microsites within soils and sediments

Redox reactions underlie several biogeochemical processes and are typically spatiotemporally heterogeneous in soils and sediments. However, redox heterogeneity has yet to be incorporated into mainstream conceptualizations and modeling of soil biogeochemistry. Anoxic microsites, a defining feature of soil redox heterogeneity, are non-majority oxygen depleted zones in otherwise oxic environments. Neglecting to account for anoxic microsites can generate major uncertainties in quantitative assessments of greenhouse gas emissions, C sequestration, as well as nutrient and contaminant cycling at the ecosystem to global scales. However, only a few studies have observed/characterized anoxic microsites in undisturbed soils, primarily, because soil is opaque and microsites require µm-cm scale resolution over cm-m scales. Consequently, our current understanding of microsite characteristics does not support model parameterization. To resolve this knowledge gap, we demonstrate through this proof-of-concept study that X-ray fluorescence (XRF) 2D mapping can reliably detect, quantify, and provide basic redox characterization of anoxic microsites using solid phase “forensic” evidence. First, we tested and developed a systematic data processing approach to eliminate false positive redox microsites, i.e., artefacts, detected from synchrotron-based multiple-energy XRF 2D mapping of Fe (as a proxy of redox-sensitive elements) in Fe-“rich” sediment cores with artificially injected microsites. Then, spatial distribution of Fe II and Fe III species from full, natural soil core slices (over cm-m lengths/widths) were mapped at 1–100 µm resolution. These investigations revealed direct evidence of anoxic microsites in predominantly oxic soils such as from an oak savanna and toeslope soil of a mountainous watershed, where anaerobicity would typically not be expected. We also revealed preferential spatial distribution of redox microsites inside aggregates from oak savanna soils. We anticipate that this approach will advance our understanding of soil biogeochemistry and help resolve “anomalous” occurrences of reduced products in nominally oxic soils.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assessing Shifts in Regional Hydroclimatic Conditions of U.S. River Basins in Response to Climate Change over the 21st Century

Characterization of shifts in regional hydroclimatic conditions helps reduce negative consequences on agriculture, environment, economy, society, and ecosystem. This study assesses shifts in regional hydroclimatic conditions across the conterminous United States in response to climate change over the 21 st Century. The hydrological responses of five downscaled climate models from the Multivariate Adaptive Constructed Analogs (MACA) dataset ranging from the driest to wettest and least warm to hottest were simulated using the Variable Infiltration Capacity (VIC) model. Shifts in regional hydroclimatic conditions at 8-digit hydrologic unit scale (HUC8) were evaluated by the magnitude and direction of movements in the Budyko space. HUC8 river basins were then clustered into seven unique hydroclimatic behavior groups using the K-means method. A tree classification method was proposed to illustrate the relationships between hydroclimatic behavior groups and regional characteristics. The results indicate that hydroclimatic responses may vary from a river basin to another, but basins in the same neighborhood follow a similar movement in the Budyko space. The systematic hydroclimatic behavior of river basins is highly associated with their regional landform, climate, and ecosystem characteristics. Most HUC8s with Mountain, Plateau and Basin landform types will likely experience less arid conditions. However, most HUC8s with Plain landform type behave differently according to the regional ecosystem and climate. This study provides a potential roadmap of shifts in regional hydroclimatic conditions of U.S. river basins, which can be used to improve regional preparedness and ability of various sectors to mitigate or adapt to the impacts of future hydroclimate change.

54 ENVIRONMENTAL SCIENCES↗

A research agenda for nonvascular photoautotrophs under climate change

Nonvascular photoautotrophs (NVP), including bryophytes, lichens, terrestrial algae, and cyanobacteria, are increasingly recognized as being essential to ecosystem functioning in many regions of the world. Current research suggests that climate change may pose a substantial threat to NVP, but the extent to which this will affect the associated ecosystem functions and services is highly uncertain. Here, we propose a research agenda to address this urgent question, focusing on physiological and ecological processes that link NVP to ecosystem functions while also taking into account the substantial taxonomic diversity across multiple ecosystem types. Accordingly, we developed a new categorization scheme, based on microclimatic gradients, which simplifies the high physiological and morphological diversity of NVP and world-wide distribution with respect to several broad habitat types. We found that habitat-specific ecosystem functions of NVP will likely be substantially affected by climate change, and more quantitative process understanding is required on (1) potential for acclimation, (2) response to elevated CO 2 , (3) role of the microbiome, and (4) feedback to (micro)climate. We suggest an integrative approach of innovative, multimethod laboratory and field experiments and ecophysiological modelling, for which sustained scientific collaboration on NVP research will be essential.

54 ENVIRONMENTAL SCIENCES↗

Biodiversity and Stoichiometric Plasticity Increase Pico‐Phytoplankton Contributions to Marine Net Primary Productivity and the Biological Pump

Earth System Models generally predict increasing upper ocean stratification from 21st century warming, which will cause a decrease in the vertical nutrient flux forcing declines in marine net primary productivity (NPP) and carbon export. Recent advances in quantifying marine ecosystem carbon to nutrient stoichiometry have identified large latitudinal and biome variability, with low-latitude oligotrophic systems harboring pico-sized phytoplankton exhibiting large phosphorus to carbon cellular plasticity. The climate forced changes in nutrient flux stoichiometry and phytoplankton community composition are thus likely to alter the ocean's biogeochemical response and feedback with the carbon-climate system. We have added three pico-phytoplankton functional types within the Biogeochemical Elemental Cycling component of the Community Earth System Model while incorporating variable cellular phosphorus to carbon stoichiometry for all represented phytoplankton types. The model simulates Prochlorococcus and Synechococcus populations that dominate the productivity and sinking carbon export of the tropical and subtropical ocean, and pico-eukaryote populations that contribute significantly to productivity and export within the subtropical to mid-latitude transition zone, with the western subtropical regions of each basin supporting the most P-poor stoichiometries. Subtropical gyre recirculation regions along the poleward flanks of surface western boundary currents are identified as regional hotspots of enhanced carbon export exhibiting C-rich/P-poor stoichiometry, preferentially inhabited by pico-eukaryotes and diatoms. Collectively, pico-phytoplankton contribute ∼58% of global NPP and ∼46% of global particulate organic carbon export below 100 m through direct and ecosystem processing pathways. Biodiversity and cellular nutrient plasticity in marine pico-phytoplankton combine to increase their contributions to ocean productivity and the biological carbon pump.

Environmental Sciences & Ecology↗

Characterization of Surface Heterogeneity-Induced Convection Using Cluster Analysis

Land-atmosphere interactions and boundary layer processes often control the formation of shallow clouds and subsequently deep convective precipitation over the Southern Great Plains. In this study, we examine the impacts of large-scale advection on the cloud populations and land-atmospheric coupling observed during the Holistic Interactions of Shallow Clouds, Aerosols, and Land-Ecosystems (HI-SCALE) field campaign in 2016. In this work, we performed two Large Eddy Simulations (LES) using the Weather Research and Forecasting Model for a day in which the transition from clear-sky to shallow precipitating clouds and isolated deep convection was observed. The control simulation reproduced the overall distribution of cloud populations by using realistic soil conditions with an interactive land model. In the sensitivity simulation where large-scale advection is removed, a strong relationship between the land and boundary layer is found. To study the timing, location, and intensity of convective initiation and the relationship of clouds with land surface properties, a cluster analysis of equivalent potential temperature is performed for the simulation without large-scale advection. That analysis shows that convective clouds first form over regions with higher surface sensible heat flux. Precipitation from those convective clouds likely triggers new updrafts nearby about two hours later through the lifting associated with cold pools. Furthermore, the cluster analysis also shows that in addition to the spatial pattern of soil moisture, land use and soil texture in western Oklahoma also influence the location of convective initiation.

54 ENVIRONMENTAL SCIENCES↗

Sequential Abiotic-Biotic Processes Drive Organic Carbon Transformation in Peat Bogs

Peatlands, which store one-third of the terrestrial carbon (C), are subject to large disturbances under a changing climate. It is crucial to understand how microbial and physiochemical factors affect the vulnerability of these large C stores to predict climate induced greenhouse gas fluxes. Here, we used a combination of mass spectrometry and spectroscopy techniques, to understand sequential biotic and abiotic degradation pathways of Sphagnum fallax leachate in an anaerobic incubation experiment, in the presence and absence of microorganisms. Removal of microorganisms was carried out by passing aqueous samples through 0.2 µm filters. In this work, our results revealed that Sphagnum fallax leachate degradation by abiotic reactions is a significant contributor to CO 2 production. Further, abiotic factors, such as low pH, are responsible for partial dissolved organic carbon (DOC) degradation that produces bioavailable compounds that shift microbial metabolic pathways and stimulate respiration in peat bogs. Acid-catalyzed hydrolysis of Sphagnum-produced glycosides can provide the microbial communities with glucose and stimulate microbial respiration of DOC to CO 2 . These results, while unique to peatlands, demonstrate the importance and underscore the complexity of sequential abiotic and biotic processes on C cycling in peat bogs. It is therefore crucial to incorporate abiotic degradation and sequential below-ground biotic and abiotic interactions into climate models for a better prediction of the influence of climate change on DOC stability in peatlands. These findings might not be representative of other ecosystems with different environmental conditions including mineral-rich peatlands and plant matter in surface peat horizons that comprise discrete microbial populations, and DOC composition.

54 ENVIRONMENTAL SCIENCES↗

Are Remote Sensing Evapotranspiration Models Reliable Across South American Ecoregions?

Many remote sensing-based evapotranspiration (RSBET) algorithms have been proposed in the past decades and evaluated using flux tower data, mainly over North America and Europe. Model evaluation across South America has been done locally or using only a single algorithm at a time. Here, in this work, we provide the first evaluation of multiple RSBET models, at a daily scale, across a wide variety of biomes, climate zones, and land uses in South America. We used meteorological data from 25 flux towers to force four RSBET models: Priestley–Taylor Jet Propulsion Laboratory (PT-JPL), Global Land Evaporation Amsterdam Model (GLEAM), Penman–Monteith Mu model (PM-MOD), and Penman–Monteith Nagler model (PM-VI). ET was predicted satisfactorily by all four models, with correlations consistently higher (R 2 > 6) for GLEAM and PT-JPL, and PM-MOD and PM-VI presenting overall better responses in terms of percent bias (-10 < PBIAS < 10%). As for PM-VI, this outcome is expected, given that the model requires calibration with local data. Model skill seems to be unrelated to land-use but instead presented some dependency on biome and climate, with the models producing the best results for wet to moderately wet environments. Our findings show the suitability of individual models for a number of combinations of land cover types, biomes, and climates. At the same time, no model outperformed the others for all conditions, which emphasizes the need for adapting individual algorithms to take into account intrinsic characteristics of climates and ecosystems in South America.

54 ENVIRONMENTAL SCIENCES↗