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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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All sourcesNASA NTRSDOE OSTI
NASA NTRS2016

Stewardship of NASA's Earth Science Data and Ensuring Long-Term Active Archives

Program, NASA has followed an open data policy, with non-discriminatory access to data with no period of exclusive access. NASA has well-established processes for assigning and or accepting datasets into one of 12 Distributed Active Archive Centers (DAACs) that are parts of EOSDIS. EOSDIS has been evolving through several information technology cycles, adapting to hardware and software changes in the commercial sector. NASA is responsible for maintaining Earth science data as long as users are interested in using them for research and applications, which is well beyond the life of the data gathering missions. For science data to remain useful over long periods of time, steps must be taken to preserve: (1) Data bits with no corruption, (2) Discoverability and access, (3) Readability, (4) Understandability, (5) Usability' and (6). Reproducibility of results. NASAs Earth Science data and Information System (ESDIS) Project, along with the 12 EOSDIS Distributed Active Archive Centers (DAACs), has made significant progress in each of these areas over the last decade, and continues to evolve its active archive capabilities. Particular attention is being paid in recent years to ensure that the datasets are published in an easily accessible and citable manner through a unified metadata model, a common metadata repository (CMR), a coherent view through the earthdata.gov website, and assignment of Digital Object Identifiers (DOI) with well-designed landing product information pages.

Data Management↗
DOE OSTI2023

Surface Complexation/Ion Exchange Hybrid Model for Radionuclide Sorption to Clay Minerals (M4SF-23LL010301062)

This progress report (Level 4 Milestone Number M4SF-23LL010301062) summarizes research conducted at Lawrence Livermore National Laboratory (LLNL) within the Argillite International Collaborations Activity Number SF-23LL01030106. The activity is focused on our long-term commitment to engaging our partners in international nuclear waste repository research. The focus of this milestone is the establishment of international collaborations for surface complexation modeling and the associated impacts of unlocking larger, community-based datasets. More specifically, we are developing a database framework for Spent Fuel and Waste and Science Technology (SFWST) that is aligned with the Helmholtz Zentrum Dresden Rossendorf (HZDR) sorption database development group in support of the database needs of the SFWST program. In our FY22 effort, we described a detailed analysis of U(VI) sorption to quartz through both traditional surface complexation modeling and through a hybrid ML framework. In FY23, effort was placed on publication of these results and expansion of the LLNL surface complexation and ion exchange database (L-SCIE) in order to assess mineral-based radionuclide retardation under a wider variety of geochemical conditions (e.g., ionic strength, varying electrolyte compositions). Efforts were initiated to expand L-SCIE to include radionuclide surface complexation and ion exchange to clays that are relevant to subsurface geochemical processes occurring at nuclear waste repositories. In particular, a large source of sorption data for clays resides at the Paul Scherrer Institute (PSI) (work primarily by Bradbury and Baeyens) and we initiated discussions on how to retrieve those data and apply FAIR principles to those datasets. In addition to L-SCIE development, two hybrid models that incorporate AI/ML were investigated and compared to discern the most promising approaches for accurate and precise estimations of radionuclide retardation. Key considerations for future model development include (1) the ability to reduce computational burden on determining retardation coefficients for PA and (2) the ability to quantify and predict radionuclide-mineral partitioning at a more efficient, rapid pace due to automated workflows. Upon the careful consideration of the most effective modeling approaches, we are identifying ways to implement these approaches into PA. Ultimately, the data science-based workflows will provide a major incentive for other institutions to adopt a FAIR-formatted, interoperable database. LLNL will play a key role in disseminating sorption data and acting as good data stewards by updating the database in a consistent format and assessing the quality of the newly assimilated data in an organized fashion. To this end, all data and workflows are open access and made available on the LLNL Seaborg research website (https://seaborg.llnl.gov/resources/geochemical-databases-modeling-codes).

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
NASA NTRS2013

Adoption of Test Driven Development and Continuous Integration for the Development of the Trick Simulation Toolkit

This paper describes the adoption of a Test Driven Development approach and a Continuous Integration System in the development of the Trick Simulation Toolkit, a generic simulation development environment for creating high fidelity training and engineering simulations at the NASA/Johnson Space Center and many other NASA facilities. It describes what was learned and the significant benefits seen, such as fast, thorough, and clear test feedback every time code is checked-in to the code repository. It also describes a system that encourages development of code that is much more flexible, maintainable, and reliable. The Trick Simulation Toolkit development environment provides a common architecture for user-defined simulations. Trick builds executable simulations using user-supplied simulation-definition files (S_define) and user supplied "model code". For each Trick-based simulation, Trick automatically provides job scheduling, checkpoint / restore, data-recording, interactive variable manipulation (variable server), and an input-processor. Also included are tools for plotting recorded data and various other supporting tools and libraries. Trick is written in C/C++ and Java and supports both Linux and MacOSX. Prior to adopting this new development approach, Trick testing consisted primarily of running a few large simulations, with the hope that their complexity and scale would exercise most of Trick's code and expose any recently introduced bugs. Unsurprising, this approach yielded inconsistent results. It was obvious that a more systematic, thorough approach was required. After seeing examples of some Java-based projects that used the JUnit test framework, similar test frameworks for C and C++ were sought. Several were found, all clearly inspired by JUnit. Googletest, a freely available Open source testing framework, was selected as the most appropriate and capable. The new approach was implemented while rewriting the Trick memory management component, to eliminate a fundamental design flaw. The benefits became obvious almost immediately, not just in the correctness of the individual functions and classes but also in the correctness and flexibility being added to the overall design. Creating code to be testable, and testing as it was created resulted not only in better working code, but also in better-organized, flexible, and readable (i.e., articulate) code. This was, in essence the Test-driven development (TDD) methodology created by Kent Beck. Seeing the benefits of Test Driven Development, other Trick components were refactored to make them more testable and tests were designed and implemented for them.

Penn, John M.↗
DOE OSTI2023

Management and International Sorption Model Collaboration (M4SF-23LL010302062-NEA-TDB)

This progress report (Level 4 Milestone Number M4SF-23LL010302062) summarizes research conducted at Lawrence Livermore National Laboratory (LLNL) within the Crystalline International Collaborations Activity Number SF-23LL01030206. The activity is focused on our long-term commitment of engaging our partners in international nuclear waste repository research. This includes participation in the Nuclear Energy Agency Thermochemical Database (NEA-TDB) Project and development of methodologies for integrating US and international thermodynamic databases for use in SFWST Generic Disposal System Assessment (GDSA) efforts. A continuing focus for FY23 efforts has been to support the US participation in the NEA-TDB effort (Mavrik Zavarin replaced Cindy Atkins-Duffin on the NEA-TDB Management Board (MB) and Executive Group (EG)) and developing mechanisms for integration of NEA-TDB thermochemical data with LLNL’s SUPCRTNE thermodynamic database that supports the SFWST GDSA activities. This effort is coordinated with the Argillite work package SUPCRTNE database development efforts. The goal is to provide a downloadable database that will be hosted on a LLNL website which integrates NEA-TDB data into the LLNL SUPCRTNE database where appropriate. As part of our international activities, we continue our effort to integrate international sorption databases into L-SCIE (Zavarin et al., 2022b). We presented opportunities to include sorption in the next phase of NEA-TDB efforts at the April 2023 EG meeting in Paris. FY23 efforts focused on ensuring interoperable database development across multiple international database development activities. The overall goal is to produce an open source database that can be shared and integrated with multiple nuclear waste programs internationally and harness modern data science workflows and algorithms to incorporate these new approaches into reactive transport and performance assessment models. In collaboration with our Helmholtz Zentrum Dresden Rossendorf partners, we recently demonstrated the power of FAIR open source databases by fitting iron oxide (hydrous ferric oxide, goethite, hematite, and magnetite) protolysis constants to all available L-SCIE data. The results were submitted as a manuscript to J. Colloid Interface Science. This work will inform future metal sorption studies on a variety of iron oxides in order to discern the most appropriate acidity constants and surface complexation modeling constructs to account for pH-dependent mineral surface charge behavior. This work also explored automated surface complexation model development workflows in order to generate higher throughput model input files for a more facile incorporation into GDSA activities.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
NASA NTRSDate not supplied

NASA GeneLab: Open Science for Life in Space

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 350 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab Sequencing Lab. The GLDS contains rich metadata about each experiment and has integrated radiation dosimetry data from experiments flown on the Space Shuttle, International Space Station, and Free Flying spacecrafts. With the increasing amount and complexity of omics data being generated, GeneLab utilizes community-defined, common models for metadata and terminology so that omics data and results are discoverable and reliably reproducible. GeneLab uses the ISA-Tab specification and semantic model for organizing and representing omics metadata. In addition to metadata standards, data files must be open-source file or common exchange formats to ensure accessibility and usability by all users. To ease data ingestion and transfer, the web-based submission tool allows PIs a user-friendly user interface to curate, organize, and publish their space relevant omics data. In the more recent years, data curation and submission portal has incorporated the FAIR principles making data findable, accessible, interoperable, and reusable. To increase reusability of data, GeneLab has implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 200 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. To train the next generation of scientists, NASA offers training programs such as GeneLab 4 High School (GL4HS) and GeneLab 4 Universities. NLM Curation at a Scale Workshop 2022 | NASA GeneLab (GL4U) to teach students bioinformatics and computational biology methods to analyze omics data. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

GeneLab↗
DOE OSTI2020

SciPy 1.0: fundamental algorithms for scientific computing in Python

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗
NASA NTRS1993

The Advanced Technology Operations System: ATOS

Mission control systems supporting new space missions face ever-increasing requirements in terms of functionality, performance, reliability and efficiency. Modern data processing technology is providing the means to meet these requirements in new systems under development. During the past few years the European Space Operations Centre (ESOC) of the European Space Agency (ESA) has carried out a number of projects to demonstrate the feasibility of using advanced software technology, in particular, knowledge based systems, to support mission operations. A number of advances must be achieved before these techniques can be moved towards operational use in future missions, namely, integration of the applications into a single system framework and generalization of the applications so that they are mission independent. In order to achieve this goal, ESA initiated the Advanced Technology Operations System (ATOS) program, which will develop the infrastructure to support advanced software technology in mission operations, and provide applications modules to initially support: Mission Preparation, Mission Planning, Computer Assisted Operations, and Advanced Training. The first phase of the ATOS program is tasked with the goal of designing and prototyping the necessary system infrastructure to support the rest of the program. The major components of the ATOS architecture is presented. This architecture relies on the concept of a Mission Information Base (MIB) as the repository for all information and knowledge which will be used by the advanced application modules in future mission control systems. The MIB is being designed to exploit the latest in database and knowledge representation technology in an open and distributed system. In conclusion the technological and implementation challenges expected to be encountered, as well as the future plans and time scale of the project, are presented.

Kaufeler, J.-F.↗
DOE OSTI2026

Xanthos-Lake Model Source Code

This repository contains the source code for Xanthos-Lake, a lake-modeling extension of the Xanthos framework that introduces a coupled lake component comprising the Xanthos-Lake Snow and Ice Model (xLSIM) and the Xanthos-Lake Water Balance Model (xLWBM). xLSIM is a basin-aware machine-learning model for lake snow, ice, and thermal conditions. It predicts monthly lake ice thickness, snow depth, snow-cover fraction, mixing-layer temperature, and lake ice fraction from meteorological forcing and lake surface-area information. It uses sequence-based deep-learning architectures, including Transformer and hybrid Long Short-Term Memory–Transformer (LSTM–Transformer) models, together with seasonal encoding, multi-lake learning, physical masking, and basin-level cryospheric and non-cryospheric classification. The training workflow uses Ray for scalable execution and includes optional Ray Tune hyperparameter optimization. Model predictions, observations, diagnostics, and feature-importance outputs are written in NetCDF. xLWBM is the water-balance component of the new lake framework. It simulates monthly lake storage, surface area, evaporation, inflow, outflow, and lake–groundwater exchange. It combines physical water-balance equations with calibrated bathymetric relationships, weir-based outlet flow, modified Penman open-water evaporation, groundwater head relaxation, Penman–Monteith snow and ice sublimation, and snow, ice, and thermal conditions supplied by xLSIM. The model calibrates lake parameters against satellite-derived surface-area data, using evaporation-based calibration where surface-area data are unavailable, and supports small, medium, and large lake classes. For large lakes, xLWBM is integrated with the managed-routing workflow so that lake storage and outflow interact directly with downstream river routing and reservoir operations. Together, xLSIM and xLWBM provide Xanthos with a coupled lake-modeling capability. xLSIM supplies the snow, ice, and thermal conditions that affect lake evaporation and snow- and ice-related water exchanges, while xLWBM translates those conditions into dynamic lake storage, surface area, evaporation, and discharge. In return, xLWBM supplies evolving lake surface area to xLSIM. This coupling enables Xanthos to represent lakes as active hydrologic components within basin-scale water-availability and routing simulations.

Machine Learning↗
NASA NTRS2012

From EXOSAT to the High Energy Astrophysics Science Archive (HEASARC): X-ray Astronomy Comes of Age

In May 1983 the European Space Agency launched EXOSAT, its first X-ray astronomy observatory. Even though it lasted only 3 short years, this mission brought not only new capabilities that resulted in unexpected discoveries, but also a pioneering approach to operations and archiving that changed X-ray astronomy from observations led by small instrument teams, to an observatory approach open to the entire community through a guest observer program. The community use of the observatory was supported by a small dedicated team of scientists, the precursor to the data center activities created to support e.g. Chandra and XMM-Newton. The new science capabilities of EX OS AT included a 90 hr highly eccentric high earth orbit that allow unprecedented continuous coverage of sources as well as direct communication with the satellite that allowed real time decisions to respond to unexpected events through targets of opportunity. The advantages of this orbit demonstrated by EXOSAT resulted in Chandra and XMM-Newton selecting similar orbits. The three instruments on board the EXOSAT observatory were complementary, designed to give complete coverage over a wide energy band pass of 0.05-50 keY. An onboard processor could be programmed to give multiple data modes that could be optimized in response to science discoveries: These new capabilities resulted in many new discoveries including the first comprehensive study of AGN variability, new orbital periods in X-ray binaries and cataclysmic variables, new black holes, quasi-periodic oscillations from neutron stars and black holes and broad band X-ray spectroscopy. The EXOSAT team generated a well-organized database accessible worldwide over the nascent internet, allowing remote selection of data products, making samples and undertaking surveys from the data. The HEASARC was established by NASA at Goddard Space Flight Center in 1990 as the repository of NASA X-ray and Gamma-ray data. The proven EXOSAT database system became the core of the HEASARC infrastructure. The HEASARC pioneered many concepts now taken for granted including standardized formats using FITS files, restoring data from earlier missions, multi-mission analysis tools and a searchable archive over the world wide web.

White, Nicholas E.↗
NASA NTRSDate not supplied

FAIR-ness Assessment of NASA’s Earth Observation System Data and Information System (EOSDIS)

This presentation addresses the challenge of evaluating a multi-disciplinary institutional network of data repositories in operation since 1994 against the relatively recent criteria that constitute FAIR (Findable, Accessible, Interoperable, Reusable) data. NASA’s Earth Observation System Data and Information System (EOSDIS), with its 12 discipline-based Distributed Active Archive Centers (DAACs), preceded the definition and popularization of FAIR by over two decades. An assessment is very useful to describe how well the FAIR principles are met and to identify any improvements needed. In 2020, A “self-assessment” of EOSDIS and DAACs was performed by the ESDIS Project staff and the DAACs from the points of view of human actionability and machine actionability. More recently, a draft of a Science Mission Directorate (SMP) Program Directive (SPD-41a) has been released by NASA Headquarters for comment, where it is recommended that all SMD-funded data should follow the FAIR principles. This presentation is timely to initiate community discussion within the Information Quality Cluster (IQC) of the Earth Science Information Partners (ESIP) and help strategize and develop implementation guidelines for EOSDIS and DAACs to conform to FAIR principles.

Remote sensing↗
DOE OSTI2021

Model America: Data and Models for every U.S. Building

The 5-year goal of the “Model America” concept was to generate a model of every building in the United States. This data repository delivers on that goal with "Model America v1". Oak Ridge National Laboratory (ORNL) has developed the Automatic Building Energy Modeling (AutoBEM) software suite to process multiple types of data, extract building-specific descriptors, generate building energy models, and simulate them on High Performance Computing (HPC) resources. For more information, see AutoBEM-related publications (bit.ly/AutoBEM). There were 125,715,609 buildings detected in the United States. Of this number, 122,146,671 (97.2%) buildings resulted in a successful generation and simulation of a building energy model. This dataset includes the full 125 million buildings. Future updates may include additional buildings, data improvements, or other algorithmic model enhancements in "Model America v2". This dataset contains OSM and IDF zip files for every U.S. county. Each zip file contains the generated buildings from that county. The .csv input data contains the following data fields: 1. ID - the Unique Building Identifier (UBID), generated using the Pacific Northwest National Laboratory (PNNL) BuildingID framework 2. Centroid - building center location in latitude/longitude (from Footprint2D) 3. Footprint2D - building polygon of 2D footprint (lat1/lon1_lat2/lon2_...) 4. State_abbr - state name 5. Area - estimate of total conditioned floor area (ft2) 6. Area2D - footprint area (ft2) 7. Height - building height (ft) 8. NumFloors - number of floors (above-grade) 9. WWR_surfaces - percent of each facade (pair of points from Footprint2D) covered by fenestration/windows (average 14.5% for residential, 40% for commercial buildings) 10. CZ - ASHRAE Climate Zone designation 11. BuildingType - DOE prototype building designation (IECC=residential) as implemented by OpenStudio-standards 12. Standard - building vintage This data is made free and openly available in hopes of stimulating any simulation-informed use case. Data is provided as-is with no warranties, express or implied, regarding fitness for a particular purpose. We wish to thank our sponsors which include Oak Ridge National Laboratory (ORNL) Laboratory Directed Research and Development (LDRD), U.S. Dept. of Energy’s (DOE) Building Technologies Office (BTO), Office of Electricity (OE), Biological and Environmental Research (BER), and National Nuclear Security Administration (NNSA). Update (September 23, 2025): We corrected the ID field in all state-level.csv input files to ensure one-to-one consistency with the corresponding .osm and .idf output files. The schema and file structure are unchanged; only the values in the ID column were modified. No files were added or removed, and the .zip bundles (containing .osm / .idf) are unchanged. The corrected .csv inputs were re-extracted in March 2025 from the original data generated ~ 2021 (Theta supercomputer runs), and published here to align input IDs with model outputs. Update (September 6, 2026): The Model America dataset was updated to replace the previous building ID field with the Unique Building Identifier (UBID), using the Pacific Northwest National Laboratory (PNNL) BuildingID framework. UBIDs provide standardized, location-based identifiers for individual building footprints and improve interoperability with other building and geospatial datasets. The data files containing the previous building identifiers were updated to include UBIDs. This update standardizes building identification; the underlying Model America building characteristics and energy simulation results were not recomputed as part of this update.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Precursor Analysis Report: Industroyer2 and Wiper Malware Targeting Ukrainian Energy Provider 2022

The Industroyer2 and Wiper Malware Targeting Ukrainian Energy Provider 2022 Precursor Analysis Report leverages publicly available information about the Industroyer2 cyber attack and catalogs anomalous observables for each technique employed in the attack. This analysis is based upon the methodology of the Cybersecurity for the Operational Technology Environment (CyOTE) program. An adversary attempted to cause a blackout in Ukraine in April 2022 by using the Industroyer2 malware against a regional Ukrainian energy provider. The adversary targeted eight high-voltage electrical substations and utilized the malware in tandem with disk wipers for Windows, Linux, and Solaris operating systems in an attempt to make response and recovery efforts more difficult. The adversary reused a piece of the original Industroyer malware designed to open circuit breakers and de-energize target substations. The adversary gained initial access to the victim’s enterprise network through unknown means in February 2022 and was able to perform reconnaissance, pivot to the operations network, and reside in the system for at least 51 days. This gave the adversary a detailed understanding of the environment and allowed them to customize the Industroyer2 malware to the victim’s operations network. However, defenders detected and stopped the attack before the adversary could achieve their intended impact. Had the Industroyer2 attack been successful, it could have caused a blackout for more than two million people during the early stages of Russia’s invasion of Ukraine. Researchers and analysts identified 22 unique techniques (used in a sequence of 31 steps) utilized during the attack with a total of 297 observables using MITRE ATT&CK® for Industrial Control Systems. The CyOTE program assesses observables accompanying techniques used prior to the triggering event to identify opportunities to detect malicious activity. If observables accompanying the attack techniques are perceived and investigated prior to the triggering event, earlier comprehension of malicious activity can take place. Twenty-three of the identified techniques used during the Industroyer2 cyber attack were precursors to the triggering event. Analysis identified 224 observables associated with these precursor techniques, 122 of which were assessed to have an increased likelihood of being perceived in the 51 days preceding the triggering event. The response and comprehension time could have been reduced if the observables had been identified earlier. The information gathered in this report contributes to a library of observables tied to a repository of artifacts, data sources, and technique detection references for practitioners and developers to support the comprehension of indicators of attack. Asset owners and operators can use these products if they experience similar observables or to prepare for comparable scenarios.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2026

CAHS: Context-Aware Homology Search

Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.

Bhattaram, Swethasree [Georgia Institute of Techno↗
DOE OSTI2024

A digital twin solution for floating offshore wind turbines validated using a full-scale prototype

Abstract. In this work, we implement, verify, and validate a physics-based digital twin solution applied to a floating offshore wind turbine. The digital twin is validated using measurement data from the full-scale TetraSpar prototype. We focus on the estimation of the aerodynamic loads, wind speed, and section loads along the tower, with the aim of estimating the fatigue lifetime of the tower. Our digital twin solution integrates (1) a Kalman filter to estimate the structural states based on a linear model of the structure and measurements from the turbine, (2) an aerodynamic estimator, and (3) a physics-based virtual sensing procedure to obtain the loads along the tower. The digital twin relies on a set of measurements that are expected to be available on any existing wind turbine (power, pitch, rotor speed, and tower acceleration) and motion sensors that are likely to be standard measurements for a floating platform (inclinometers and GPS sensors). We explore two different pathways to obtain physics-based models: a suite of dedicated Python tools implemented as part of this work and the OpenFAST linearization feature. In our final version of the digital twin, we use components from both approaches. We perform different numerical experiments to verify the individual models of the digital twin. In this simulation realm, we obtain estimated damage equivalent loads of the tower fore–aft bending moment with an accuracy of approximately 5 % to 10 %. When comparing the digital twin estimations with the measurements from the TetraSpar prototype, the errors increased to 10 %–15 % on average. Overall, the accuracy of the results is promising and demonstrates the possibility of using digital twin solutions to estimate fatigue loads on floating offshore wind turbines. A natural continuation of this work would be to implement the monitoring and diagnostics aspect of the digital twin to inform operation and maintenance decisions. The digital twin solution is provided with examples as part of an open-source repository.

17 WIND ENERGY↗
NASA NTRS2013

Evolution of International Space Station Program Safety Review Processes and Tools

The International Space Station Program at NASA is constantly seeking to improve the processes and systems that support safe space operations. To that end, the ISS Program decided to upgrade their Safety and Hazard data systems with 3 goals: make safety and hazard data more accessible; better support the interconnection of different types of safety data; and increase the efficiency (and compliance) of safety-related processes. These goals are accomplished by moving data into a web-based structured data system that includes strong process support and supports integration with other information systems. Along with the data systems, ISS is evolving its submission requirements and safety process requirements to support the improved model. In contrast to existing operations (where paper processes and electronic file repositories are used for safety data management) the web-based solution provides the program with dramatically faster access to records, the ability to search for and reference specific data within records, reduced workload for hazard updates and approval, and process support including digital signatures and controlled record workflow. In addition, integration with other key data systems provides assistance with assessments of flight readiness, more efficient review and approval of operational controls and better tracking of international safety certifications. This approach will also provide new opportunities to streamline the sharing of data with ISS international partners while maintaining compliance with applicable laws and respecting restrictions on proprietary data. One goal of this paper is to outline the approach taken by the ISS Progrm to determine requirements for the new system and to devise a practical and efficient implementation strategy. From conception through implementation, ISS and NASA partners utilized a user-centered software development approach focused on user research and iterative design methods. The user-centered approach used on the new ISS hazard system utilized focused user research and iterative design methods employed by the Human Computer Interaction Group at NASA Ames Research Center. Particularly, the approach emphasized the reduction of workload associated with document and data management activities so more resources can be allocated to the operational use of data in problem solving, safety analysis, and recurrence control. The methods and techniques used to understand existing processes and systems, to recognize opportunities for improvement, and to design and review improvements are described with the intent that similar techniques can be employed elsewhere in safety operations. A second goal of this paper is to provide and overview of the web-based data system implemented by ISS. The software selected for the ISS hazard systemMission Assurance System (MAS)is a NASA-customized vairant of the open source software project Bugzilla. The origin and history of MAS as a NASA software project and the rationale for (and advantages of) using open-source software are documented elsewhere (Green, et al., 2009).

Ratterman, Christian D.↗
DOE OSTI2025

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0

Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable comparative analysis, predictive modeling, and data integration across bioinformatics platforms. While professional biocuration is resource-intensive and usually limited to institutional settings, community-driven approaches can mobilize large-scale annotation of specialized datasets and are more resilient to disruptions in scientific funding. Here, we present a model for community-powered curation applied to the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Through a framework of workflows for metadata capture, annotation validation, and contributor coordination, the MIBiG 4.0 initiative recruited 267 scientists across 178 institutions from 33 countries, volunteering an estimated 4000 h of work. These efforts expanded the MIBiG repository by 22% and enhanced its usability in downstream molecular data analyses in comparative genomic analyses, natural product discovery, and machine learning applications. We provide strategies and actionable lessons for adopting this model, supporting the sustainability of curated bioinformatics resources central to nucleic acid research and related fields.

biocuration↗
DOE OSTI2023

Representing the Future Role of Hydropower and Pumped Storage Hydropower (PSH) in Electricity Planning Tools

Existing tools for long-term electric sector planning struggle to represent hydropower's nuanced site-specific technical and operating characteristics, which depend on technical specifications as well as water management practices and regulations. As a result, long-term planning models and tools insufficiently characterize hydropower value and incentives, and they cannot fully represent the role hydropower can play in a future electricity system that could include a high penetration of variable wind and solar generation, battery storage, and other low-carbon technologies. This presentation demonstrates the culmination of a multi-year effort to enhance hydropower representations in electricity planning models at the National Renewable Energy Laboratory (NREL), as part of the U.S. Department of Energy (USDOE) HydroWIRES Initiative. New modeling techniques are demonstrated using the NREL Regional Energy Deployment System (ReEDS), an open-access electric sector capacity expansion model used extensively in a wide range of technology deployment and integration analysis, including the 2016 USDOE Hydropower Vision. ReEDS uses a least-cost optimization approach to understand investment and operation of electricity generation, storage, and transmission technologies under future scenarios of electricity technology innovation, demand, policy, and other sectoral drivers. ReEDS was modified to better represent value and opportunities for both pumped storage hydropower (PSH) and hydropower systems without pumping. We incorporated a new national closed-loop PSH resource and cost assessment to explore new PSH deployment opportunities and added plant-level data to better represent the existing PSH fleet. New upgrade pathways enable opportunities for enhanced hydropower flexibility by adding pumps, upgrading dispatchability, increasing capacity, or increasing energy availability. The model was also modified to better represent the value of long-duration energy storage beyond diurnal time scales, allowing both hydropower and PSH to better balance energy supply and demand variations in high-renewable systems. These new features are demonstrated under reference and high-renewable futures and a range of sensitivity scenarios to understand which hydropower and PSH deployment and upgrade opportunities are the most attractive. These scenarios indicate potential for new closed-loop PSH deployment and for hydropower flexibility improvements to have important impacts on long-term electricity system emissions and economic outcomes. Increasing flexibility of the existing hydropower fleet can reduce the need to invest in new flexible grid technologies and help achieve decarbonization goals. Systems with sufficient energy storage could also be valuable for balancing seasonal differences in renewable energy availability, particularly from solar energy. The methods developed for ReEDS and subsequent scenario results reveal important considerations for future hydropower and grid system planning, and all data and code is freely available in a public code repository for use throughout the hydropower industry.

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