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DOE OSTI2025

Distribution Substation Planning Toolkit (dsp-toolkit) v1.0

The Distribution Substation Planning Toolkit (DSP Toolkit) is a software suite designed to streamline the planning and optimization of distribution substations. This toolkit offers a comprehensive set of tools and APIs for data curation, short-term electric load forecasting, and weather-sensitive load adjustment, making it an essential resource for utility companies, engineers, and researchers. Features • Data Preprocessing and Curation: Efficiently manage and preprocess large datasets to ensure high-quality input for analysis. • Short-Term Load Forecasting: Utilize data-driven models to predict short-term electric loads accurately. • Weather-Sensitive Modeling: Automatically adjust load forecasts based on weather data to predict future peak demands more precisely. Uses The DSP Toolkit is ideal for planning and optimizing distribution substations, providing a user-friendly interface and comprehensive documentation. It is suitable for both novice and experienced users, facilitating efficient and accurate planning processes. Advantages • Efficiency: Automates complex planning tasks, reducing manual effort and minimizing errors. • Scalability: Handles large datasets and complex models, making it suitable for large-scale projects. • Community and Support: Open-source with active community contributions, ensuring continuous improvement and support. • Extensibility: Easily extendable with custom modules and plugins, allowing users to tailor the toolkit to their specific needs. The DSP Toolkit stands out by offering a robust, flexible, and user-friendly solution for distribution substation planning. Public Abstract

Li, Han [Lawrence Berkeley National Laboratory (LB↗

DOE OSTI2026

AstraAI v1

AstraAI is an open-source, structure-aware AI coding agent designed for large scientific and DOE-HPC codebases such as AMReX-based applications. Unlike general-purpose coding assistants, AstraAI combines retrieval-augmented generation (RAG) with compiler-level Abstract Syntax Tree (AST) analysis to perform precise, scope-constrained code modifications. It identifies exact function spans, enforces locality of edits, and maintains cross-file invariants, enabling deterministic and build-safe transformations in complex C++/GPU environments. AstraAI is intended for developers working on large, evolving HPC frameworks where correctness, reproducibility, and structural integrity are critical. Typical use cases include modifying physics kernels, updating GPU device lambdas, and performing multi-file refactors without breaking compilation or runtime semantics. Compared to conventional LLM-based coding agents - even those with repository access - AstraAI provides structural guarantees rather than free-form text patches. It minimizes unintended diffs, prevents scope drift, preserves formatting and build stability, and reduces structural hallucinations. By integrating compiler tooling directly into the generation loop, AstraAI transforms AI-assisted coding from probabilistic text editing into deterministic, structure-preserving program transformation suitable for mission-critical scientific software.

Natarajan, Mahesh [Lawrence Berkeley National Labo↗

DOE OSTI2025

Software For Advanced Large-scale Analysis Of Magnetic Confinement For Numerical Design, Engineering & Research (salamander)

As magnetic confinement fusion energy gains traction internationally to enable abundant energy production, designing components for fusion systems is a pressing challenge. During the planned lifetime of a fusion device, components evolve in extreme environments and must withstand large, repeated thermal loads and bombardment by 14 MeV neutrons, plasma ions, and neutral particles (deuterium, tritium, and helium), corrosive conditions, etc. All these physical processes take place simultaneously, interact in intricate ways, and impose important constraints that can affect performance. Experimental data is rare and costly to obtain, making design particularly challenging. Predictive computational frameworks must be an integral part of an accelerated and cost-effective design process by modeling fusion system performance in simulated environments. To better understand component degradation and operational impacts on their performance, the Software for Advanced Large-scale Analysis of MAgnetic confinement for Numerical Design, Engineering & Research (SALAMANDER) is designed as an open-source, fully integrated, multiphysics, multiscale, NQA-1 compliant framework facilitating 3D, high-fidelity fusion system modeling. To that end, SALAMANDER is a MOOSE-based framework, and therefore leverages MOOSE upstream libraries such as PETSc and libMesh to deliver sophisticated finite element, finite volume, and nonlinear solver technology for fusion energy simulations. SALAMANDER couples MOOSE physics module capabilities—such as thermal hydraulics, heat conduction, Navier-Stokes, and thermomechanics—with tritium transport via TMAP8, neutronics via Cardinal, and nascent particle-in-cell capabilities. Direct simulation Monte Carlo methods will be used to address neutral transport near the walls. By coupling all these physics in an integrated application, SALAMANDER will enable high-fidelity modeling of irradiation levels and plasma exposure conditions of plasma facing components and their impact on heat and tritium distributions, as well as the resulting mechanical constraints experienced by the plasma facing components and performance of blanket systems. Furthermore, SALAMANDER will be particularly suited for engineering studies thanks to the stochastic tool module readily available in MOOSE, allowing for extended uncertainty quantification and risk analysis studies. It is also able to use computer-aided design (CAD) meshes to model complex geometries, which is indispensable for fusion systems. SALAMANDER therefore supports design, safety, engineering, and research projects for magnetic confinement fusion systems

Simon, Pierre-Clement [Idaho National Laboratory (↗

DOE OSTI2025

A Comprehensive Machine Learning Model for Metal–Ligand Binding Prediction: Applications in Chemistry and Biology

A machine-learning (ML) model that predicts metal–ligand binding constants was developed using the open-source Chemprop software. The model was trained on over 30,000 experimental log K 1 values, which include both protonation and metal–ligand stability constants, comprising over 3500 ligands and 10 2 metal ions from 73 total elements, thus generalizing beyond existing limited approaches, which focus only on specific metals or ligand families. The best-performing model included a combination of SMILES-based molecular representations along with descriptors for the metal ion and experimental conditions. It had an external test R 2 value of 0.942, and MAE value of 0.834. A “SMILES-only” simpler version also produced accurate predictions and preserved the binding trends, serving as a quick and easily accessible alternative for users without computational expertise. The SMILES-only model performed comparably to density functional theory (DFT) calculations but utilized a fraction of the computational resources. The model was successfully applied across diverse domains, including bioinorganic chemistry, heavy metal remediation, and sensor development and demonstrated its effectiveness as a rapid and reliable screening tool for both academic and industrial uses.

Ligands↗

DOE OSTI2025

Subject-specific modeling framework for particle deposition using computational fluid dynamics

Quantifying particle deposition and dose in the respiratory tract requires a physiologically realistic representation and reproducible computational workflows. However, existing modeling frameworks, such as the International Commission on Radiological Protection (ICRP) compartmental models and the Multiple Path Particle Dosimetry (MPPD) tool, lack detailed deposition profiles and subject-specific capabilities. The combination of advances in computer vision algorithms applied to the respiratory tract and Computational Fluid and Particle Dynamics (CFPD) allows high-fidelity simulations of particle behavior in anatomically accurate geometries derived from individual CT scans. The segmentation, preprocessing, and file preparation task for a CFPD simulation was often time-consuming, and no prior studies to-date have yet presented a fully automated framework. This work presents a fully automated workflow to obtain individualized particle deposition profiles in the human respiratory tract. The pipeline starts with segmenting upper and lower airway geometries using morphological and deep learning-based methods, generating three-dimensional (3D) models from CT imaging data. Next, a series of algorithms are presented to quality check and prepare the 3D geometry for a CFD or CFPD simulation. The preprocessing step includes correcting geometric artifacts, enforcing a physically consistent mesh, and automatically identifying and capping multiple outlets, which is required for CFD/CFPD simulations. These processed models are then input into open-source (OpenFOAM) or commercial (StarCCM+) CFD solvers, where flow and transient particle transport equations — including turbulence and particle–wall interactions are solved under realistic breathing conditions. Finally, the resulting particle deposition profiles can be integrated with Monte Carlo radiation transport codes and state-of-the-art computational phantoms to assess organ-specific absorbed doses in scenarios of radioactive aerosol inhalation. The presented work streamlines respiratory tract segmentation, preprocessing for CFD/CFPD simulations, and integration with dose assessment workflows, reducing manual intervention and improving access to high-fidelity, subject-specific modeling. The high precision in predicted particle deposition and dose distributions can improve personalized treatment strategies in respiratory medicine and refine dose estimates for radiation protection.

AI↗

DOE OSTI2025

Catalight─An Open-Source Automated Photocatalytic Reactor Package Illustrated through Plasmonic Acetylene Hydrogenation

An open-source and modular Python package, Catalight, is developed and demonstrated to automate (photo)catalysis measurements. (Photo)catalysis experiments require studying several parameters to evaluate performance, including the temperature, gas flow rate and composition, illumination power, and spectral profile. Catalight orchestrates measurements over this complicated parameter space and systematically stores, analyzes, and visualizes the results. To showcase the capabilities of Catalight, we perform an automated apparent activation barrier measurement of acetylene hydrogenation over a plasmonic AuPd catalyst on an Al 2 O 3 support, simultaneously varying laser power, wavelength, and temperature in a multiday experiment controlled by a simple Python script. Our chemical results unexpectedly show an increased activation barrier upon light excitation, contrary to previous findings for other plasmonic reactions and catalysts. We show that the reaction rate order with respect to both acetylene and hydrogen remains unchanged upon illumination, suggesting that molecular surface coverage is not changed by light. By analyzing the inhomogeneity of the laser-induced heating, we attribute these results to a partial photothermal effect combined with a photochemical/hot electron-driven mechanism. In conclusion, our findings highlight the capabilities of a new experiment automation tool; explore the photocatalytic mechanism for an industrially relevant reaction; and identify systematic sources of error in canonical photocatalysis experimental procedures.

Catalysts↗

DOE OSTI2026

PVDeg: Enhancing Usability and AI-Driven Multi-Mechanism Degradation Modeling

PVDeg version 0.7.0, released in December 2025, introduced major enhancements to improve usability and performance. This update reorganized tutorials and tool notebooks to create a more intuitive experience, enabling users to easily follow and adapt workflows for their specific analyses. In addition to structural improvements, both the notebooks and core logic underwent significant optimization for efficiency, robustness, and style. These refinements were supported by new testing frameworks built on nbval and pytest, adherence to PEP8 standards, and extensive code refactoring, which collectively simplify onboarding for new developers. Looking ahead, version 0.8.0 will deliver advanced AI-driven capabilities. The primary focus is to further develop and automate the degradation workflow, designed to analyze PV module degradation across diverse locations and system configurations. By integrating large language models (LLMs) to scan literature and compile a comprehensive database of materials and degradation rates, this feature will enable modeling of multiple materials and mechanisms within a single, streamlined workflow. Users will be able to evaluate degradation impacts on different system architectures under varying environmental conditions, facilitating informed decisions on bill-of-materials optimization for specific deployment scenarios. These advancements position PVDeg as a powerful, user-friendly tool for accelerating PV reliability research and system design.

14 SOLAR ENERGY↗

DOE OSTI2025

Enhancing 2D hydrodynamic flood models through machine learning and urban drainage integration

Two-dimensional hydrodynamic flood models are commonly employed for simulating flood extent and inundation depth. However, the influence of urban drainage network (UDN) is frequently overlooked in these models, potentially compromising their accuracy. Furthermore, the expensive computational costs and longer processing times make them challenging for large-scale hydrodynamic simulation. To address these challenges, this paper develops a machine learning (ML)-driven emulator for an open-source flood model, the Two-dimensional Runoff Inundation Toolkit for Operational Needs (TRITON). A TRITON-ML Emulator (TR-Emulator) that utilizes Convolutional Long Short-Term Memory is developed to capture the spatiotemporal features of flood events based on the outputs from TRITON. We further enhance the emulator by integrating UDN parameters (TR-UDN), such as the flow capacity of drainage pipes, pipe size, and pipe length, via an ML stacking technique to improve the water surface elevation (WSE) simulation. Hurricane Harvey 2017 in Houston, TX is used as the case study. We compare WSE results from TRITON, TR-Emulator, TR-UDN, and the United States Geological Survey (USGS) observations to evaluate the performance of these models. The results indicate that the TR-Emulator effectively replicates the WSE simulated by TRITON. Additionally, TR-UDN performs well in capturing WSE patterns and peak flows, aligning more closely with USGS observations, except in areas with milder slopes where conveyance discrepancies are observed. We further test the generalizability of our ML-based models using another smaller event. This paper shows that the TR-Emulator is effective for users and engineers to emulate a 2D hydrodynamic model, and the enhanced version of the TR-Emulator, TR-UDN, can be an efficient tool for predicting WSEs during urban flooding.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Parallelizing autotuning for HPC applications: Unveiling the potential of the speculation strategy in Bayesian optimization

In the exascale computing era, tuning High-Performance Computing (HPC) applications has become a significant computational challenge. Although Bayesian optimization (BO) has emerged as a promising tool for HPC performance tuning, the BO workflow is inherently sequential (i.e., one function evaluation at a time) and cannot leverage the huge amount of parallel resources present in modern supercomputers, resulting in a considerable underutilization of their computational capabilities. This paper explores the trade-off between search quality and parallelism in BO, investigating a diverse set of methods. Building upon both previous approaches from the literature and novel methodologies introduced in this work, our study provides a deep analysis to accelerate BO performance tuning. By examining a set of synthetic functions and practical HPC applications, our exploration analyzes the interaction among various BO methods for parallelization, the quantity of parallel resources, the runtime distribution of target HPC applications, and the costs associated with different search orchestration mechanisms that have been overlooked in previous studies. Compared to sequential BO, our novel methodology achieves comparable quality while demonstrating robust scalability in search time as the amount of parallel resources increases; it also outperforms a state-of-the-art tuner, which supports parallelization, achieving up to 3.67x faster search time. We provide high-value insights for practitioners seeking to leverage the power of parallel computing for efficient HPC application tuning. Additionally, to further assist researchers in accelerating the performance tuning of their HPC applications, we provide an extension of an existing open-source tuning framework that incorporates our methods.

Bayesian optimization↗

DOE OSTI2025

Feedforward equilibrium trajectory optimization with GSPulse

One of the common tasks required for designing new plasma scenarios or evaluating capabilities of a tokamak is to design the desired equilibria using a Grad-Shafranov (GS) equilibrium solver. However, most standard equilibrium solvers are time-independent and do not include dynamic effects such as plasma current flux consumption, induced vessel currents, or voltage constraints. Another class of tools, plasma equilibrium evolution simulators, do include time-dependent effects. These are generally structured to solve the forward problem of evolving the plasma equilibrium given feedback-controlled voltages. In this work, we introduce GSPulse, a novel algorithm for equilibrium trajectory optimization, that is more akin to a pulse planner than a pulse simulator. GSPulse includes time-dependent effects and solves the inverse problem: given a user-specified set of target equilibrium shapes, as well as limits on the coil currents and voltages, the optimizer returns trajectories of the voltages, currents, and achievable equilibria. This task is useful for scoping performance of a tokamak and exploring the space of achievable pulses. The computed equilibria satisfy both Grad-Shafranov force balance and axisymmetric circuit dynamics. The optimization is performed by restructuring the free-boundary equilibrium evolution equations into a form where it is computationally efficient to optimize the entire dynamic sequence. GSPulse can solve for hundreds of equilibria simultaneously within a few minutes. GSPulse has been validated against NSTX-U and MAST-U experiments and against SPARC feedback control simulations, and is being used to perform scenario design for SPARC. The computed trajectories can be used as feedforward inputs that are connected to the feedback controller to inform and improve feedback performance. The code for GSPulse is available open-source at github.com/jwai-cfs/GSPulse_public.

equilibrium↗

DOE OSTI2026

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↗

DOE OSTI2026

Predicting Li-Ion Battery Capacity Fade Using Early-Life Data and a Hybrid Data-Driven Gaussian Process-Bayesian Regression Approach

Accurately predicting Li-ion battery capacity trajectories using early-life data can dramatically improve battery-life understandings and be used to rapidly evaluate design/cost/performance trade-offs when developing new battery materials. Accurate early-life predictions enable researchers to quickly iterate over cell designs and material precursor properties without consistently cycling cells to failure. To this end, we present a toolbox that uses a combined Gaussian Process and Bayesian regression approach that capitalizes on signals other than just capacity (e.g., dQ/dV, voltage drops) to rapidly predict capacity-fade trajectories. The prediction tool uses Bayesian regression to fit functional forms, e.g., power law, sigmoids, etc., to predict capacity-fade dynamics. By fitting functional forms, the capacity fade can be interrogated at any point in the future, allowing for early cell-failure prediction. Additionally, Bayesian regression allows for accurate uncertainty estimates that account for cell-to-cell variability (aleatoric uncertainty) and the lack of observation data (epistemic uncertainty). By only using early cycle data to predict the capacity fade trajectory, uncertainty bounds at end-of-life can be extremely large. The large uncertainty bounds are further exacerbated because there is no systematic way to define the prior distribution of the functional forms' parameters. We improve our the predicted trajectory confidence interval of our predicted trajectory using two methods. First, we shows that a small amount of held-out cycling data is sufficientuse some train cells, that have been cycled to failure to derive information regarding the appropriate prior distributions for the functional forms' parameters of the functional form, effectively leading to data-driven priors.. We propose constructing the data-driven priors by first running a Bayesian regression starting with uninformed priors to generate intermediate cell-specific posterior parameter distributions. These posterior distributions are combined using a Ggaussian mixture model for each parameter to create the data-driven priors. These mixture models serve as the data-driven prior distributions for the parameters for. Second, we derive multiple features, e.g., C_dchg 0.5 DoD 0.5, log (|mean(dQ/dV_(w_3-w_0 ) (V)|), etc., from the train cellsheld-out cycling data, identify which the features are that best predicting capacity at early/mid-life cycles, and then create Ggaussian process regression models that are used for predicting capacity at early/mid-life cycles for the test cells (see blue dots with error bars in Fig 1b). Finally, these predicted data-points are used in addition to the actual early cycle data capacity fade to construct the Bayesian regression trajectory for the test cell s. Notably. We note that these two methods are complementary and can be combined with each other. We evaluate the performance of our proposed method on an testing open-source dataset from Iowa State University and Iowa Lakes Community College (ISU-ILCC). This dataset comprises of 251 nickel-manganese-cobalt/graphite Lithium-ion cells that are cycled under 63 different conditions. We compute the mean average percentage error (MAPE) and negative log predictive density (NLPD) to quantify the efficacy of our method. Our initial findings suggest that, when only few observations are available, for test cells, when using only Bayesian regression with uninformed priors, a power law functional provides the most accurate predictions. with very few data points. However, asHowever, a the number of data points increases, a twin sigmoidal function becomes more accurate as the number of observations further increases. We also find that using as little as 10% of the data set towards generating data-driven priors can lead to significant improvement in prediction accuracy when using early cycle data. Lastly, we found that augmenting early-cycle data with Gaussian process-predicted capacity data for Bayesian regression greatly improves the prediction accuracy. We will present a comprehensive comparison of our methods to other methods available in the literature and apply this method to additional battery datasets.

42 ENGINEERING↗

DOE OSTI2025

PSCF+: An Extended and Improved Open-Source Software Package for Polymer Self-Consistent Field Calculations

This work introduces PSCF+, a freely available open‑source software tool for modeling how block copolymers self‑assemble into ordered nanoscale structures. The software allows researchers to study a wide range of polymer models and interaction types, making it possible to directly compare theoretical predictions with molecular and simulation‑based studies in a consistent way. PSCF+ incorporates several recently developed numerical methods that significantly reduce computer memory requirements and speed up calculations, enabling efficient use of modern GPU hardware. Here, it also provides automated tools to calculate free‑energy landscapes and phase boundaries, which are essential for understanding and predicting material behavior. Together, these advances make PSCF+ a powerful and flexible platform for studying polymer self‑assembly and support the design of new polymeric materials for scientific and technological applications.

Chemical calculations↗

DOE OSTI2026

Development of MOSCATO: A CFD-Level Electrochemistry and Corrosion Simulator for Molten Salt Systems

For both coolant and fueled variants of molten salt reactors (MSRs), the corrosion of structural materials is a significant challenge. The corrosion stems from chemical and electrochemical reactions initiated by fissile material, fission products, and impurities in the salt. Lower-fidelity models rely on empirical correlations for mass transfer, simplified lumped temperature profiles, and similar assumptions. They do not capture detailed spatial variations in complex geometries, creating the need for high-fidelity modeling to bridge this gap.As we approach the demonstration and possible deployment of MSRs in this decade, the development of a high-fidelity, high-performance simulator becomes imperative. To simulate the complex electrochemical environment and corrosion within molten salt systems, we have developed the Molten Salt Chemistry And TranspOrt (MOSCATO) code. This endeavor is comprised of three essential components. First, mass transfer equations are coupled with the Navier-Stokes equations in order to account for the transport of species in the salt. Second, the diffusion of alloy constituents, such as Cr, Fe, Ni, etc. is simulated within the structural metals. Third, the alloy and salt domains are coupled to account for the heterogeneous chemical and electrochemical reactions that occur at the salt-alloy interface.MOSCATO manages all three components within the framework of the highly scalable, open-source spectral element method computational fluid dynamics code Nek5000/NekRS. This integration enables MOSCATO to harness the immense computational power of modern high-performance computing resources, ensuring both high fidelity and computational speed.In addition to code development, we have initiated a comprehensive verification and validation campaign, utilizing data from diverse sources. First, MOSCATO's electrochemical solver was verified with reference numerical data. Then validation occurred against experiments: one of a thermal galvanic cell and the other for corrosion in flowing molten salt of FLiNaK (LiF-NaF-KF). This campaign verified and validated MOSCATO as a reliable tool for simulating electrochemical environments and corrosion in molten salt systems.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

BOSC 2025, the 26th Bioinformatics Open Source Conference

The 26th annual Bioinformatics Open Source Conference (BOSC 2025, open-bio.org/events/bosc-2025) brought its community-driven focus on open-source bioinformatics and open science to the 2025 conference on Intelligent Systems for Molecular Biology and the European Conference on Computational Biology (ISMB/ECCB 2025). Since its launch in 2000, BOSC has been the premier annual meeting covering open-source bioinformatics and open science. Framed by two keynote addresses and a thought-provoking panel discussion, the two-day conference included sessions dedicated to open data, analytic tools and pipelines, workflow platforms, knowledge representation, and the application of AI/ML. The first keynote talk was delivered by Christine Orengo: “Working together to develop, promote and protect our data resources: Lessons learnt developing CATH and TED.” A joint session with the Bio-Ontologies and Knowledge Representation (BOKR) track the second day of BOSC started with a keynote talk by Chris Mungall entitled “Open Knowledge Bases in the Age of Generative AI”. A closing panel on Data Sustainability, moderated by Mónica Muñoz Torres, featured panelists Scott Edmunds, Varsha Khodiyar, Tony Burdett, Nicky Mulder, and Chris Mungall. This year, the CollaborationFest collaborative work event that typically precedes or follows ISMB was incorporated as part of the main conference and organized by BOSC with help from the Function and 3D-SIG tracks.

bioinformatics↗

DOE OSTI2025

Open-source simulation program for extreme ultraviolet and soft x-ray sources based on high-harmonic generation

Light sources based on high-harmonic generation (HHG) underpin ultrafast spectroscopy experiments across a large range of photon energies, spanning from the extreme ultraviolet to the soft x-ray. To this day, their design, implementation, and improvement presens unique challenges, but can be aided by numerical tools. Here we present a new simulation program designed for this purpose, which takes both macroscopic and microscopic aspects of high-harmonic generation into account and is therefore applicable across the broad range of parameters which HHG based light sources are today utilized. The program is validated by comparison with published experimental results and by calculating harmonic emission in four common experimental configurations.

Femtosecond lasers↗

DOE OSTI2025

Data-driven Community-centered Resilient Assessment and Planning Toolkit for Nexus of Energy and Water (DCRAPT-NEW)

Urban areas, including Detroit and Pittsburgh, have suffered significant dual outages of the electrical and water infrastructure in the past decade due, in part, to the increasing number of extreme weather events. With increasing temperatures and rainfall intensity, these regions need to prepare for increasing extreme events through community-based energy and water resilience analysis, planning, and enhancement. This project developed a suite of open-source, open-access, community-centered, data-driven assessment and distributed energy resource (DER) and planning tools for energy and water resilience enhancement in urban areas. Through establishing a multi-level community awareness and engagement mechanism and a comprehensive collection of power outage and flooding data, an innovative group of community energy and water resilience assessment and planning tools have been developed for a wide range of users with differing and variable sets of data available to them. The developed tools include (1) DOE EAGLE-I data-driven, deep-learning assisted resilience assessment and DER planning tools at the county level with socioeconomic factors incorporated; (2) Utility annual power outage data-driven tools for long term resilience assessment and DER planning and 15-min power outage data-driven tools for short term resilience assessment and planning; (3) Detailed engineering tools for energy and water systems resilience assessment and planning when the system topology and component fragility curves are available; (4) Alternative Resiliency Metric Calculation that extracts and separates outage and restoration processes; and (5) Co-optimization tools that evaluate the resilience of the power and sewage system and allow users to conduct joint planning with energy and wastewater systems. The developed tools provide planners, decision-makers, and stakeholders with powerful capabilities to systematically evaluate system/community resilience and optimal and actionable guidance for enhancing resilience while prioritizing DER investments. The tools have been used and validated in Detroit and Pittsburgh and can be used in other areas of the nation. In addition, this project will (1) advance the knowledge and applications of machine-learning methods in analyzing and fusing different layers of information and generating meaningful data points such as generating rare weather events; (2) significantly improve the energy and water resilience of the identified communities in Detroit and Pittsburgh and prepare for more frequent and severe weather conditions; (3) help communities assess extreme weather event impacts and address short-term and long-term resilience-related issues The developed tools have been made public via GitHub and demonstrated to community stakeholders and utility companies via the two annual workshops and numerous community engagement meetings. The project outcomes are also disseminated through publications in various journals and conference proceedings, and presentations at top conferences.

13 HYDRO ENERGY↗

DOE OSTI2025

Evidence-based Graph Adversary Mapping (EGRAM) [Poster]

Cybersecurity companies such as CrowdStrike, Dragos, Microsoft and Unit 42 categorize Advanced Persistent Threats (APTs) using their own naming schemes. As a result, these APTs are mapped to different malware sources and campaigns, all from differing sources, leading to inconsistent mapping. Inconsistent mapping causes confusion and adds further obscurity around these groups, making it difficult to track and mitigate APT cyberattacks. The Evidence-based Graph Adversary Mapping (EGRAM) tool remediates the mapping challenge by collecting, updating and converting adversary data and their sources into a valid, codified STIX v2.1 bundle which is then stored in a Neo4j graph database. It utilizes graph traversal methods and centrality analysis to generate actionable information as a Structured Threat Intelligence Graph (STIG), based on user queries. EGRAM exists as Python code and a Jupyter Notebook that acts as a searchable, evidence-based, source of intelligence for APT groups’ artifacts and cyber campaigns.

24 - POWER TRANSMISSION AND DISTRIBUTION↗