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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 91 records · Page 5

TX$^2$: Transformer eXplainability and eXploration

The Transformer eXplainability and eXploration (Martindale & Stewart, 2021), or TX 2 software package, is a library designed for artificial intelligence researchers to better understand the performance of transformer models (Vaswani et al., 2017) used for sequence classification. The tool is capable of integrating with a trained transformer model and a dataset split into training and testing populations to produce an ipywidget (Project Jupyter Contributors, 2021) dashboard with a number of visualizations to understand model performance with an emphasis on explainability and interpretability. The TX 2 package is primarily intended to integrate into a workflow centered around Jupyter Notebooks (Kluyver et al., 2016), and currently assumes the use of PyTorch (Paszke et al., 2019) and Hugging Face transformers library (Wolf et al., 2020). The dashboard includes visualization and data exploration features to aid researchers, including an interactive UMAP embedding graph (McInnes et al., 2018) to understand classification clusters, a word salience map that can be updated as researchers alter textual entries in near real time, a set of tools to understand word frequency and importance based on the clusters in the UMAP embedding graph, and a set of traditional confusion matrix analysis tools.

97 MATHEMATICS AND COMPUTING↗

CyanoCyc cyanobacterial web portal

CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the needs of the cyanobacterial research and biotechnology communities. The 277 annotated cyanobacterial genomes currently in CyanoCyc are supplemented with computational inferences including predicted metabolic pathways, operons, protein complexes, and orthologs; and with data imported from external databases, such as protein features and Gene Ontology (GO) terms imported from UniProt. Five of the genome databases have undergone manual curation with input from more than a dozen cyanobacteria experts to correct errors and integrate information from more than 1,765 published articles. CyanoCyc has bioinformatics tools that encompass genome, metabolic pathway and regulatory informatics; omics data analysis; and comparative analyses, including visualizations of multiple genomes aligned at orthologous genes, and comparisons of metabolic networks for multiple organisms. CyanoCyc is a high-quality, reliable knowledgebase that accelerates scientists’ work by enabling users to quickly find accurate information using its powerful set of search tools, to understand gene function through expert mini-reviews with citations, to acquire information quickly using its interactive visualization tools, and to inform better decision-making for fundamental and applied research.

59 BASIC BIOLOGICAL SCIENCES↗

An interactive machine learning platform for analyzing multi-particle coincidence data from cold target recoil ion momentum spectroscopy

We present SCULPT (Supervised Clustering and Uncovering Latent Patterns with Training), a comprehensive software platform for analyzing tabulated high-dimensional multi-particle coincidence data from Cold Target Recoil Ion Momentum Spectroscopy (COLTRIMS) experiments. The software addresses critical challenges in modern momentum spectroscopy by integrating advanced machine learning techniques with physics-informed analysis in an interactive web-based environment. SCULPT implements uniform manifold approximation and projection for non-linear dimensionality reduction to reveal correlations in high-dimensional data. We also discuss potential extensions to deep autoencoders for feature learning and genetic programming for automated discovery of physically meaningful observables. A novel adaptive confidence scoring system provides quantitative reliability assessments by evaluating user-selected clustering quality metrics with predefined weights that reflect each metric’s robustness. The platform features configurable molecular profiles for different experimental systems, interactive visualization with selection tools, and comprehensive data filtering capabilities. Utilizing a subset of SCULPT’s capabilities, we analyze photo-double-ionization data measured using the COLTRIMS method for three-body dissociation of the D 2 O molecule, revealing distinct fragmentation channels and their correlations with physics parameters. The software’s modular architecture and web-based implementation make it accessible to the broader atomic and molecular physics community, significantly reducing the time required for complex multi-dimensional analyses. This opens the door to finding and isolating rare events exhibiting non-linear correlations on the fly during experimental measurements, which can help steer exploration and improve the efficiency of experiments.

Artificial neural networks↗

ElasTool v3.0: Efficient computational and visualization toolkit for elastic and mechanical properties of materials

Efficient computation and visualization of elastic and mechanical properties are crucial in the selection of materials and the design of new materials. Here, the ElasTool v3.0 toolkit marks a significant advancement in the computational analysis and visualization of elastic and mechanical properties of materials, essential in material selection and design. This enhanced version extends beyond standard calculations like elastic tensor, Young's modulus, bulk modulus, and Poisson's ratio. It introduces capabilities for computing minimum thermal conductivity, linear compressibility, rendering the Christoffel equation, and elastic energy density. Notably, it integrates advanced visualization tools, including compatibility with Plotly and Elate web platforms for interactive web-based property exploration. A key feature of ElasTool v3.0 is the implementation of second-order elastic constants (SOECs) for tubular 2D-based nanostructures and nanotubes. Leveraging high-efficiency strain-matrix sets (OHESS), the toolkit now facilitates efficient computation of elastic constants and mechanical properties at both zero and finite temperatures for 1D, 2D, and 3D dimensions. ElasTool is openly accessible on GitHub: https://github.com/gmp007/elastool.

1D, 2D, 3D, and tubular 2D nanostructure and nanot↗

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES↗

Selection Algorithm for electron neutrino charged current interactions in SBND

The Short Baseline Neutrino (SBN) program at Fermilab is a joint proposal by three experimental collaborations primarily for the investigation of the cause behind the low-energy electron-like event excess observed by the MiniBoone experiment. This dissertation focuses on the near detector of the project, named the Short Baseline Near Detector (SBND), a Liquid Argon Time Projection Chamber apparatus which will conduct searches for sterile neutrinos in the mass range of 1 ${eV}^2/{c}^4$, as well as provide cross-section measurements for neutrino interactions in argon and perform other beyond the standard model studies.\\ \indent As is the case for all detectors in the program, the SBND will use the Booster Neutrino Beam as its source, which will provide it with both muon and electron neutrinos. Given that the ability to discern between the neutrino flavors will be crucial to the fulfillment of the detector's physics goals, the objective of this work is to provide the collaboration with a tool capable of doing so. As such, we here present the development process for an inclusive selection algorithm for the identification of electron neutrino charged current (CC) events regardless of their interaction channel. This is done through a combination of traditional techniques, such as the implementation of cuts on the reconstructed interaction properties, with the use of the Convolutional Visual Network, a machine learning algorithm capable of classifying particle interactions through the analysis of the topology of their final states. With this approach, we have developed a selection process that is capable of identifying $\nu_e$ CC interactions across a wide range of topologies with 34.4\% efficiency, as well as a purity of 91.2\%, making it especially promising for use in cross section studies.

Freire, Hector Moya [ABC Federal U.] (ORCID:000900↗

Nested Tracking Graphs

Tracking graphs are a well established tool in topological analysis to visualize the evolution of components and their properties over time, i.e., when components appear, disappear, merge, and split. However, tracking graphs are limited to a single level threshold and the graphs may vary substantially even under small changes to the threshold. To examine the evolution of features for varying levels, users have to compare multiple tracking graphs without a direct visual link between them. We propose a novel, interactive, nested graph visualization based on the fact that the tracked superlevel set components for different levels are related to each other through their nesting hierarchy. This approach allows us to set multiple tracking graphs in context to each other and enables users to effectively follow the evolution of components for different levels simultaneously. We show the effectiveness of our approach on datasets from finite pointset methods, computational fluid dynamics, and cosmology simulations.

97 MATHEMATICS AND COMPUTING↗

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↗

Web-based Preprocessing and Visualization of 3D FIB Tomography Data for Nuclear Fuel Characterization

Three-dimensional (3D) focused ion beam (FIB) tomography enables reconstruction of internal nuclear fuel features that can't be fully evaluated through surface imaging alone. This capability supports characterization of fuel constituents and defects under thermal and irradiation conditions relevant to microreactor development. However, large tomography datasets can create data-handling, loading, and visualization challenges, especially when image-stack preparation and file conversion must be completed with separate tools. The Computational Ultraspatial Tomography Toolkit for High-Resolution Object Analysis Tools (CUTTRHOAT) is an open-source web application being developed to display FIB tomography datasets available through the Nuclear Research Data System (NRDS). The current alpha version requires prepared HDF5 datasets and has limited integrated data-preparation capabilities. This project improves CUTTHROAT by adding dataset-folder selection, automatic input detection, dataset scanning, missing-slice identification, blank-slice insertion, and image-stack-to-HDF5 conversion. Two applications will be compared: the baseline CUTTHROAT alpha workflow and the updated application containing the integrated data-handling and preprocessing functions. Evaluation will consider dataset detection accuracy, conversion success, loading time, rendering responsiveness, application stability, and user interaction. Preliminary results demonstrate successful loading of existing HDF5 files and converted image stacks, while testing also identified performance reductions caused by excessive blank-slice generation. The updated workflow reduces reliance on external preparation tools and supports more direct movement from image stacks to color-code 3D visualization. Future work includes refining missing-slice handling, integrating additional preprocessing functions, like a denoising feature, parsing TIFF metadata for automatic voxel scaling, and adding manual X, Y, and Z voxel-spacing inputs for PNG and JPEG.

36 - MATERIALS SCIENCE↗

Event-modeled Risk Assessment Using Linked Diagrams

Event Modeling Risk Assessment using Linked Diagrams (EMRALD) is a software tool developed at INL for researching the capabilities of dynamic PRA (Probabilistic Risk Assessment). In order to promote the effective use of dynamic PRA by the general community, EMRALD focuses on the following key aspects: Simplifying the modeling process by providing a structure that corresponds to traditional PRA modeling methods Providing a user interface (UI) that makes it easy for the user to model and visualize complex interactions Allowing the user to couple with other analysis applications such as physics based simulations. This includes one-way communication for most applications and two-way loose coupling for customizable applications Providing the sequence and timing of events that lead to the specified outcomes when calculating results Traditional aspects of components with basic events, fault trees, and event trees are all captured in a dynamic framework of state diagrams, which are displayed.

Prescott, SteveR↗

New tool for kinematic regime estimation in semi-inclusive deep-inelastic scattering

We introduce a new phenomenological tool based on momentum region indicators to guide the analysis and interpretation of semi-inclusive deep-inelastic scattering measurements. The new tool, referred to as “affinity”, is devised to help visualize and quantify the proximity of any experimental kinematic bin to a particular hadron production region, such as that associated with transverse momentum dependent factorization. We apply the affinity estimator to existing HERMES and COMPASS data and expected data from Jefferson Lab and the future Electron-Ion Collider. We also provide an interactive notebook based on Machine Learning for fast evaluation of affinity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

New Models and Methods for the Electroweak Scale

This is the Final Technical Report to the US Department of Energy for grant DE-SC0013529, New Models and Methods for the Electroweak Scale, covering the time period April 1, 2015 to March 31, 2017. The goal of this project was to maximize the understanding of fundamental weak scale physics in light of current experiments, mainly the ongoing run of the Large Hadron Collider and the space based satellite experiements searching for signals Dark Matter annihilation or decay. This research program focused on the phenomenology of supersymmetry, Higgs physics, and Dark Matter. The properties of the Higgs boson are currently being measured by the Large Hadron collider, and could be a sensitive window into new physics at the weak scale. Supersymmetry is the leading theoretical candidate to explain the natural nessof the electroweak theory, however new model space must be explored as the Large Hadron collider has disfavored much minimal model parameter space. In addition the nature of Dark Matter, the mysterious particle that makes up 25% of the mass of the universe is still unknown. This project sought to address measurements of the Higgs boson couplings to the Standard Model particles, new LHC discovery scenarios for supersymmetric particles, and new measurements of Dark Matter interactions with the Standard Model both in collider production and annihilation in space. Accomplishments include new creating tools for analyses of Dark Matter models in Dark Matter which annihilates into multiple Standard Model particles, including new visualizations of bounds for models with various Dark Matter branching ratios; benchmark studies for new discovery scenarios of Dark Matter at the Large Hardon Collider for Higgs-Dark Matter and gauge boson-Dark Matter interactions; New target analyses to detect direct decays of the Higgs boson into challenging final states like pairs of light jets, and new phenomenological analysis of non-minimal supersymmetric models, namely the set of Dirac Gaugino Models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Blue Keanu: A Scientific Visualization Tool For Network Data

This software allows the user to visualize complex PCAP-ng files captured from network capture software such as Wireshark. The visualization runs in a GUI window that can be zoomed or moved to areas of interest in a waterfall type display. The user then can see an area of interest that looks different than the typical traffic visually, such as a human interaction or non-repetitive area of data. The program will tell the user the packet number and byte offset of interest for fast analysis of discrete atomic or non-random events. This is particularly useful for visualization of unknown binary format data, such as in PLC or SCADA protocols that may have human or other non-repetitive activity for further analysis, reverse engineering, or fast forensic analysis.

Durller, MichaelGeorge↗

HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies

Changing the course of the human immunodeficiency virus type I (HIV-1) pandemic is a high public health priority with approximately 39 million people currently living with HIV-1 (PLWH) and about 1.5 million new infections annually worldwide. Broadly neutralizing antibodies (bnAbs) typically target highly conserved sites on the HIV-1 envelope glycoproteins (Envs), which mediate viral entry, and block the infection of diverse HIV-1 strains. But different mechanisms of HIV-1 resistance to bnAbs prevent robust application of bnAbs for therapeutic and preventive interventions. Here we report the development of a new database that provides data and computational tools to aid the discovery of resistant features and may assist in analysis of HIV-1 resistance to bnAbs. Bioinformatic tools allow identification of specific patterns in Env sequences of resistant strains and development of strategies to elucidate the mechanisms of HIV-1 escape; comparison of resistant and sensitive HIV-1 strains for each bnAb; identification of resistance and sensitivity signatures associated with specific bnAbs or groups of bnAbs; and visualization of antibody pairs on cross-sensitivity plots. The database has been designed with a particular focus on user-friendly and interactive interface. Our database is a valuable resource for the scientific community and provides opportunities to investigate patterns of HIV-1 resistance and to develop new approaches aimed to overcome HIV-1 resistance to bnAbs.

60 APPLIED LIFE SCIENCES↗

A Methodology to Evaluate the Grid Reliability Impact of Oscillations Induced by Large Loads

The rapid growth of hyperscale AI data centers is bringing renewed attention to the reliability risk that sustained forced oscillations pose to bulk power systems, with cyclic computational workloads emerging as a new forcing source. Unlike the broadband, stochastic disturbances from traditional industrial loads such as arc furnaces, AI training and inference facilities can inject large active power swings concentrated at specific frequencies over extended durations - characteristics that existing grid planning practices do not account for. While the North American Electric Reliability Corporation (NERC) has recognized this gap and called for system-level studies of large load interconnections, no standardized methodology exists to screen, simulate, and quantify these risks at the planning stage. This report presents the Risk Assessment Tool for Large Load-induced Events (RATLLE), a Python-based, publicly available script suite developed at the Pacific Northwest National Laboratory to evaluate bulk power system reliability risks from data center-induced oscillations. RATLLE implements a three-module workflow: a screening module that identifies vulnerable interconnection locations and excitable system modes; a simulation module that models cyclic data center load behavior using a commercial positive sequence simulation platform; and an analysis module that computes risk metrics and generates interactive visualization dashboards. The risk metrics, formulated around simulation observables, map oscillation impacts to a three-stage severity scale spanning latent equipment fatigue through imminent cascading failure. The methodology is demonstrated on two Western Electricity Coordinating Council (WECC) system models: a publicly available 240-bus reduced representation and a detailed 2031 Heavy Winter planning case. Case studies illustrate that even modest 50 MW forced oscillations at resonant frequencies can produce wide-area power swings, N-1 security constraint violations, and cascading generator trips through protection actions - outcomes that would not occur under normal operating conditions without oscillations present. The results underscore the need for standardized oscillation impact assessment in large load interconnection studies and provide a reproducible, extensible framework for utilities to adopt or customize within their existing planning workflows.

Biswas, Shuchismita↗

Structural analyses of macromolecules by solution scattering (CRADA Final Report)

New innovative Small Angle X-ray Scattering (SAXS) methods to visualized macromolecules in solution at low resolution has led the SIBYLS group at Lawrence Berkeley Lab in being a world leader in biological SAXS. This research is particularly important now as LBNL establishes high-priority research topics including molecular to mesoscale analysis. This new expanding area of research relies on and ties in with our efforts towards developing a solution structure modeling tool for RNA structure prediction. Due to the pandemic our efforts focused on the SARS-CoV-2 proteins and RNA interactions. Specifically, we characterized SARS-CoC-2 proteins interaction with RNA (Wilanowski et al. 2021 -Hammel group) and Nucleoprotein interaction with RNA (Schneidman group).

59 BASIC BIOLOGICAL SCIENCES↗

Toward Human-Centric Transportation and Energy Metrics: Influence of Mode, Vehicle Occupancy, Trip Distance, and Fuel Economy

Traditional metrics measuring transportation and energy outcomes can be augmented to better represent impacts on people's lives and systems-level performance. In this context, this study introduces two novel metrics: road capacity (as number of people traveling and accessing services) and energy intensity (as energy use for people traveling and accessing services). Current national-level distributions of available data in the United States for factors contributing to the two new integrated metrics are used as context to evaluate potential outcomes. These factors include vehicle occupancy, mode share, fuel economy, and trip distance. Variations in input values provide insights on how these factors shape efficiencies in road capacity and energy intensity. Parametric sensitivity analysis indicates that the impact of each input depends upon the metric being evaluated. For the human-centered road capacity mobility metric, increasing vehicle occupancy has the largest effect – twice that of increasing mode share for bike, walk, and transit. For the energy intensity mobility metric, the effect of improving fuel economy is the largest. However, when the focus is on accessibility (instead of mobility), for both metrics the effect of lowering average trip distance is the largest. Additionally, a novel interactive tool to visualize the results for various parameter combinations makes the metrics practitioner ready. The findings suggest that the diffusion of new human-centric metrics that benchmark outcomes associated with road capacity and energy may be significant in motivating new sustainable transportation investments and efficient utilization of infrastructure, mobility assets, and services.

ADVANCED PROPULSION SYSTEMS↗

Web-Based Tools for Data-Informed Remedy Optimization: Software Theory and User Guide

This report documents the development and application of two web-based decision-support tools for pump-and-treat (P&T) groundwater remediation systems: PTOLEMY (Pump-and-Treat Optimized Location Evaluation to Maximize Yields) and OPTIMA (Optimization for Pump-and-Treat Implementation, Management, & Assessment). These tools enhance remedy design and management by leveraging advanced computational methods – specifically deep learning and multi-objective optimization – within a user-friendly platform. By integrating data-driven models with established hydrogeological knowledge, PTOLEMY and OPTIMA enable more efficient evaluation of well placement and operational strategies, helping site managers balance multiple remediation objectives under complex conditions. Both tools are implemented as modules within the SOCRATES (Suite Of Comprehensive Rapid Analysis Tools for Environmental Sites) web platform, which provides data access, visualization, and analytics to support remedy optimization across sites in the U.S. Department of Energy Office of Environmental Management complex. PTOLEMY is a rapid screening module designed to identify promising locations for new extraction wells. It employs a multi-channel three-dimensional convolutional neural network (MC3D-CNN) trained on high-fidelity simulation data to predict the relative performance (in terms of contaminant mass recovery) of potential well sites. Through an interactive web interface, PTOLEMY visualizes the probability of high performance across a site, highlighting areas where an extraction well is likely to yield above-threshold contaminant removal over a multi-year period. PTOLEMY’s map-based displays and exportable results support transparent communication of screening analyses. By focusing attention on the most favorable candidate locations, the tool augments traditional engineering judgment and physics-based modeling, providing a data informed basis for subsequent detailed evaluations. OPTIMA is a multi objective optimization module designed to find wellfield layouts and operating schedules that meet various cleanup goals. It quickly evaluates thousands of candidate setups – combinations of well locations, timing, and rates – and returns a small set of best trade-off options for comparison. At its core, OPTIMA uses a U-Net-based surrogate model – a deep-learning emulator of a groundwater flow and transport simulator – to dramatically accelerate scenario evaluations. Coupling this fast surrogate with the NSGA-II (Non-dominated Sorting Genetic Algorithm II) evolutionary algorithm, OPTIMA explores a wide decision space of well locations and schedules to identify Pareto-optimal solutions that trade off key objectives (e.g., minimizing cleanup time, maximizing contaminant mass removal, and minimizing plume extent). The tool outputs a family of optimal configurations and visualizes their trade-offs (Pareto frontiers of cleanup metrics and maps of optimized well placements). Site managers can use these results to understand the range of viable strategies and to select candidate designs for more detailed verification. OPTIMA is currently under active development and not yet fully released; this guide provides early documentation to support planning and gather user feedback.

54 ENVIRONMENTAL SCIENCES↗