Results for “Computer Programming and Softwar” — Page 12

DOE OSTI2025

Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE

Summary Protein property prediction via machine learning with and without labeled data is becoming increasingly powerful, yet methods are disparate and capabilities vary widely over applications. The software presented here, “Artificial Intelligence Driven protein Estimation (AIDE)”, enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods for variants and variable length homologs in a single, reproducible notebook or script by defining a modular, standardized application programming interface (API), i.e. drop-in compatible with scikit-learn transformers and pipelines. Availability and implementation AIDE is an installable, importable python package inheriting from scikit-learn classes and API and is installable on Windows, Mac, and Linux. Many of the wrapped models internal to AIDE will be effectively inaccessible without a GPU, and some assume CUDA. The newest stable, tested version can be found at https://github.com/beckham-lab/aide_predict and a full user guide and API reference can be found at https://beckham-lab.github.io/aide_predict/. Static versions of both at the time of writing can be found on Zenodo.

36 MATERIALS SCIENCE↗

DOE OSTI2025

MontePy: a Python library for reading, editing, and writing MCNP input files.

The Monte Carlo N-Particle (MCNP) radiation transport code is a highly capable and accurate code with a long legacy. MCNP uses the Monte Carlo simulation process to simulate the path of particles (e.g., neutrons, photons, charged particles, etc.), and their interaction with materials. It is widely used in nuclear engineering, high-energy physics, and other fields. Its origins in the mid-twentieth century predate many modern software conventions. MCNP users provide an input file to MCNP, which it then uses to create an internal representation of the simulation problem. These input files originally had to be stored as punchcard decks, and the user manual still uses the terminology of cards and decks, despite moving beyond punchcards. MCNP predates nearly all modern human readable markup or data serialization languages, such as the extensible Markup Language (XML), the Standard Generalized Markup Language (SGML), YAML (YAML Ain’t Markup Language), and Javascript Object Notation (JSON). Due to this, MCNP uses an entirely custom defined syntax language for its input, making off-the-shelf libraries for XML, YAML, and JSON impossible to use for scripting various operations on MCNP input files (Kulesza et al., 2022).

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Validation and Verification of Python based Neutron Spectrum Unfolding Software

To validate and verify the python-based code (PySL), designed to replicate the programs used by STAYSL for Beam Correction Factor (BCF) and Self-Shielding Factor (SHIELD), a series of tests were performed. To test BCF a python script was written to generate a random flux history file and both versions of the code processed the data. The test verified matching values up to at least one decimal place, approximately 10,000 tests where run and each one passed. Isotopes began to fail the tests once neutron saturation was reached. To verify this the total time of exposure was varied the isotopes that failed were compared to a list of their half-lives. The test process for SHIELD was very similar but, in this case, the code began by producing an input file with varying thickness and device type/environment for the SHIELD input. The failure condition for this test was if any of the data points for an isotope had a difference above 3%. Approximately 40 of these tests were run and there were only 3 isotopes that had reoccurring failures but only 2% of their points were above the 3% difference. A visual comparison was conducted by plotting the results from both programs. Although the test failed, the differences between their values were minuscule, and the self-shielding factor’s shape was preserved when plotted. Next steps for this project will be validating and verifying the python-based SigPhi code and then reproducing and testing the least squares unfolding performed by STAYSL.

73 - NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

An Integrated Framework for Risk Assessment of Safety-related Digital Instrumentation and Control Systems in Nuclear Power Plants: Methodology Advancement and Application

This report documents activities performed by Idaho National Laboratory (INL) during fiscal year (FY) 2024 for the U.S. Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program, Risk Informed Systems Analysis (RISA) Pathway, Digital Instrumentation and Control (DI&C) Risk Assessment project. The goal of the RISA Pathway is to optimize safety margins and minimize uncertainties to achieve economic efficiencies while maintaining high levels of safety. This is accomplished by providing scientific basis to better represent safety margins and factors that contribute to cost and safety, and by developing new technologies that reduce operating costs. The research efforts for FY 2024 encompass methodology refinement and exploration. The efforts include: (1) The implementation of a natural language processing tool to expedite key aspects of the reliability analysis methods developed by INL; (2) advances to support intersystem CCF analysis by providing guidance for and identification of coupling mechanisms that may contribute to CCF; (3) the investigation of how generative artificial intelligence tools can aid in hazard analysis and diversity and defense in depth (i.e., D3) assessments; (4) Industry collaboration, allowing the demonstration of and INL's risk assessment tools to support risk assessment of DI&C systems at early and late stages of development; (4) a roadmap for the development of a software for each of INL's risk assessment tools; (5) The development of a theory and methodology manual for a risk quantification methodology; (6) the development of a reliability analysis for machine learning (ML)-integrated control systems.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

PMDT: AI-Enabled Predictive Maintenance Digital Twins for Advanced Nuclear Reactors

Our team made substantial technical progress on various fronts during the course of the program. Multiple milestones were geared towards demonstrating the feasibility of machine learning based predictive maintenance digital twins towards reducing O&M costs, whereas some other milestones actually focused on identifying technical gaps and developing technologies such as humble AI to provide necessary robustness to the ML-based models. We were able to demonstrate in many cases that Machine learning-based methods can be successfully adapted for Nuclear plant environments especially for remote monitoring applications. Detailed analyses were carried out with plant and full scope simulation data along with capabilities of enhanced analytics to assess and set realistic expectations on cost reductions in O&M. These assessments are paving the way for investments towards reactor design improvements as well project planning for SMR projects as they develop and mature in the next few years. Technology developed under this program got direct visibility to GE Hitachi and their utility customers and resulted in positive intents to deploy some of the elements from design phase. The project additionally resulted in several reports, publications, software and data generation that will be useful in deployment and O&M services for BWRX300 fleets.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2026

Requirements Description of DASSH-F

This report reviews the modeling and simulation capabilities of Argonne National Laboratory’s DASSH code that is used in present reactor analysis activities. These capabilities will be used to establish the set of verification tasks necessary to verify DASSH for use on commercial projects. A similar approach was taken for the PERSENT, REBUS and DIF3D software packages. The DASSH program is a thermal analysis code designed to rapidly allow a reactor design engineer to obtain flow rates requirements that satisfy peak temperature constraints in the domain. DASSH is a follow-on development to the SE2-ANL software and SUPERENERGY-2 software that it is based upon. DASSH was designed to account for both neutron and gamma heating and is inherently connected to the GAMSOR part of the ARC suite of fast reactor analysis software. SE2-ANL is a developed piece of software from the 1980s while DASSH is a modern implementation with notable improvements in geometry handling. The most important upgrade of DASSH relative to SE2-ANL is that it can analyze multiple time points in a single run where SE2-ANL can only treat a single time point. This allows the user to understand the impact of and search the flow distribution for the entire operational period of a reactor design considering pressure drop, peak coolant and fuel temperatures, and thermal striping. DASSH has three input paths that have to be verified. The first input path builds the geometry and power distribution based upon the DIF3D model but ignores the gamma heating aspects of the problem. The second input path also builds the geometry from the DIF3D model but it takes the neutron and gamma heating distributions from GAMSOR. The third input path is to take the geometry and power distribution directly from user input (i.e. not coupled to DIF3D or GAMSOR). DASSH also has many built in correlations for material properties along with a user defined specification of the fuel, structure, and coolant properties. There are correlations for flow split, mixing, pressure drop, and heat transfer coefficients (subchannel rather than a direct methodology). In total, verification of DASSH will require an extensive testing to cover all possible user features of the software.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

National User Resource for Biological Accelerator Mass Spectrometry (Final Report)

The National User Resource for Biological Accelerator Mass Spectrometry (User Resource) will provide isotopic analysis (primarily radiocarbon or 14C) by accelerator mass spectrometry (AMS) for NIH- funded researchers across the United States and will be the only User Resource of its type in the United States. The User Resource will provide measurement capability and expertise to a research community that requires highly sensitive, quantitative isotope analyses. Since commissioning a new accelerator mass spectrometer in June 2014, we have measured over 4000 samples a year for collaborators and service users. The User Resource will enable us to continue to meet these research needs, as well as provide for new users whose research programs would benefit from AMS as a measurement tool. The User Resource’s forte will be ultra-high sensitivity quantitation of radiocarbon and selected other radioisotopes for research studies where isotopes are required. Radioisotope labeling studies have been and will continue to be an important tool for addressing many complex biomedical science problems. AMS is a specialized and unique type of mass spectrometry that provides absolute quantitation of radiocarbon and other relevant radioisotopes with extreme sensitivity, having limits of detection in real samples on the order of a few attomol/mg of sample at measurement precisions of ~3%. It is the only instrumental method capable of quantifying radioisotope-labeled agents routinely in real-world samples with such precision and sensitivity. The sensitivity of AMS allows for the quantification of radiolabeled metabolites in extremely complex matrices of cells and organisms at very low concentrations and in small samples. AMS allows studies to be conducted without perturbing metabolism leading to more relevant quantification of metabolic rates and pathways. In addition, it enables quantification of pharmacokinetic and metabolic properties of toxicants at environmentally relevant concentrations in model systems as well as the ability to quantify pharmacokinetics and other molecular endpoints directly in humans. Such quantitative assessments can 1) improve risk assessment for toxicants, 2) address safety and efficacy considerations for therapeutic entities, 3) deepen understanding of xenobiotic and intermediary metabolism, 4) help understand the interactions between critical molecular pathways, and 5) improve efforts to model and predict various metabolic and biological states. These capabilities have been applied in a number of areas including research in carcinogenesis, toxicology, nutrition, pharmacology/drug development and basic biological science. As a NIGMS National Resource the National User Resource for Biological Accelerator Mass Spectrometry will help NIH funded scientists achieve a deeper understanding of the etiology of human health concerns by (1) enabling the quantification of pharmacokinetics and other molecular endpoints directly in humans; (2) offering the ability to conduct quantitative studies using biologics such as proteins or lipids, and thereby reducing the amount of radioisotope usage in biomedical labs; and (3) enabling more relevant studies of metabolic pathways in health and disease through the use of much lower, more biologically-relevant, concentrations of metabolic substrates in cells and intact organisms. Such studies support NIGMS’s basic biomedical research areas that contribute to the understanding of fundamental cellular and physiological principles and enable research supported by the Biophysics, Biomedical Technology, and Computational Biosciences (BBCB); Genetics and Molecular, Cellular, and Developmental Biology (GMCDB); Pharmacology, Physiology, Biological Chemistry (PPBC) and Training, Workforce Development, and Diversity (TWD) Divisions. Over the next five years, our goals are to: 1. Improve the efficiency of operation for AMS measurements through installation of new interfaces to our AMS systems, technical modifications to improve gas accepting ion source efficiency and upgrading our data analysis software for improved ease of use and data reporting. 2. Increase the accessibility and visibility of ultra-sensitive 14C measurements for the biomedical research community by training of new investigators and expanding our national user base. 3. Provide high throughput, ultra-sensitive 14C analysis for the NIGMS and NIH user community.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Calibrating a finite-strain phase-field model of fracture for bonded granular materials with uncertainty quantification

To study the mechanical behavior of mock high explosives, an experimental and simulation program was developed to calibrate, with quantified uncertainty, a material model of the bonded granular material Idoxuridine and nitroplasticized Estane-5703. This paper reports on the efficacy of such a framework as a generalizable methodology for calibrating material models against experimental data with uncertainty quantification. Additionally, this paper studies the effect of two manufacturing temperatures and three initial granular configurations on the unconfined compressive behavior of the resulting bonded granular materials. In each of these cases, the same calibration framework was used; in that, hundreds of high-fidelity direct numerical simulations using a new, graphics processing unit-enabled, high-performance finite element method software, Ratel, were run to calibrate a finite-strain phase-field fracture model against experimental data. It was found that manufacturing temperature influenced the elastic response of the mock high explosives, with higher temperatures yielding a stiffer response. By contrast, it was found that the initial configuration of the grains had a negligible impact on the overall behavior of the mock high explosives though it remains possible that local damage accumulation within the specimens could be altered by the initial configurations. Overall, the calibration framework was successful at creating well-calibrated models, showing its usefulness as an engineering and scientific tool.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Fiscal Year 2025 Software Quality Assurance Activities for the ARC Software

The continued goal of the ARC SQA project in the Advanced Reactor Technologies program of DOE is to resolve the QA gaps for the ARC software that limit, or prevent, commercialization of the software for industry users. This project started in earnest in fiscal year 2023 which saw the entire code system moved from a SVN repository to a GitLab repository and an associated software quality assurance plan (SQAP) developed and ratified. Most of the QA gaps in the ARC software were identified in collaboration with industry partners and work begin in fiscal year 2023 and continued through 2024 and 2025. The continuous integration testing was extended to RCT, DASSH, and SE2ANL. Minor changes were required to the original continuous integration methodology to make this happen. When full confidence in the methodology is complete, a report will be created to detail the automated regression testing methodology and minor reports will be created to detail the tolerance settings that have been applied to the output for each ARC code. The primary documentation that is missing includes user manuals, user guides, software verification reports, and code coverage assessments. The DASSH, SE2ANL, and SE2RCT manuals were completed this fiscal year. A review of the SE2ANL software identified that it is unrealistic to include updated correlations or different geometry models and it was scheduled for deprecation in favor of DASSH. The SE2ANL manual is essential for SE2RCT as they are similar but quite different in purpose. The only piece of software missing a manual consistent with the source code is NUBOW-3D which is a focus of the coming year. The code coverage report for DIF3D was updated and code coverage reports were created for REBUS, RCT, PERSENT, GAMSRC, and DASSH. Minor coverage issues were identified for all of these pieces of software which did not prevent the work done to transition them to the OneAPI compiler. Because SE2ANL was scheduled for deprecation, it was not transitioned, but it was successfully tested with the OneAPI compiler. This leaves SE2RCT and NUBOW-3D as the only pieces of software not transitioned to OneAPI and further work is required to get SE2RCT to work properly. The SE2RCT software transition will begin early next year while the NUBOW-3D software requires a manual before it can begin. Software verification work has been completed for DIF3D, REBUS, GAMSOR, GAMSRC, VARPOW, EvaluateFlux, and SUMMAR. The PERSENT software verification work was completed this year which was somewhat delayed because of unexpected bugs in the software. The PERSENT manual was updated to detail some of the issues and discuss the bowing reactivity worth feature added in the previous fiscal year. The RCT, DASSH, SE2RCT, and NUBOW-3D software are the only maintained pieces of software without verification reports. The software verification work for DASSH will be a focus in the upcoming fiscal year and it is hoped that some of the test cases created can serve as verification tests for SE2RCT. The NUBOW-3D work will begin when the manual and requirements report are completed. Only minor industry partner software development funds were provided this year. The DASSH software was updated to handle general axial geometry for each assembly and the NUBOW-3D software was updated to incorporate a new input format and better output. Overall progress on resolving the QA gaps has been good this year.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Fiscal Year 2025 Software Quality Assurance Activities for the ARC Software

The continued goal of the ARC SQA project in the Advanced Reactor Technologies program of DOE is to resolve the QA gaps for the ARC software that limit, or prevent, commercialization of the software for industry users. This project started in earnest in fiscal year 2023 which saw the entire code system moved from a SVN repository to a GitLab repository and an associated software quality assurance plan (SQAP) developed and ratified. Most of the QA gaps in the ARC software were identified in collaboration with industry partners and work begin in fiscal year 2023 and continued through 2024 and 2025. The continuous integration testing was extended to RCT, DASSH, and SE2ANL. Minor changes were required to the original continuous integration methodology to make this happen. When full confidence in the methodology is complete, a report will be created to detail the automated regression testing methodology and minor reports will be created to detail the tolerance settings that have been applied to the output for each ARC code. The primary documentation that is missing includes user manuals, user guides, software verification reports, and code coverage assessments. The DASSH, SE2ANL, and SE2RCT manuals were completed this fiscal year. A review of the SE2ANL software identified that it is unrealistic to include updated correlations or different geometry models and it was scheduled for deprecation in favor of DASSH. The SE2ANL manual is essential for SE2RCT as they are similar but quite different in purpose. The only piece of software missing a manual consistent with the source code is NUBOW-3D which is a focus of the coming year. The code coverage report for DIF3D was updated and code coverage reports were created for REBUS, RCT, PERSENT, GAMSRC, and DASSH. Minor coverage issues were identified for all of these pieces of software which did not prevent the work done to transition them to the OneAPI compiler. Because SE2ANL was scheduled for deprecation, it was not transitioned, but it was successfully tested with the OneAPI compiler. This leaves SE2RCT and NUBOW-3D as the only pieces of software not transitioned to OneAPI and further work is required to get SE2RCT to work properly. The SE2RCT software transition will begin early next year while the NUBOW-3D software requires a manual before it can begin. Software verification work has been completed for DIF3D, REBUS, GAMSOR, GAMSRC, VARPOW, EvaluateFlux, and SUMMAR. The PERSENT software verification work was completed this year which was somewhat delayed because of unexpected bugs in the software. The PERSENT manual was updated to detail some of the issues and discuss the bowing reactivity worth feature added in the previous fiscal year. The RCT, DASSH, SE2RCT, and NUBOW-3D software are the only maintained pieces of software without verification reports. The software verification work for DASSH will be a focus in the upcoming fiscal year and it is hoped that some of the test cases created can serve as verification tests for SE2RCT. The NUBOW-3D work will begin when the manual and requirements report are completed. Only minor industry partner software development funds were provided this year. The DASSH software was updated to handle general axial geometry for each assembly and the NUBOW-3D software was updated to incorporate a new input format and better output. Overall progress on resolving the QA gaps has been good this year.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

DOE Repository Metadata Profile (DRMP): A Metadata Framework for Advancing Interoperability and AI Readiness Across Scientific Repositories

The Department of Energy (DOE) funds a diverse and distributed ecosystem of repositories that steward scientific data, publications, and software across its research programs, user facilities, and national laboratories. While significant progress has been made in standardizing dataset-level metadata, the metadata describing repositories themselves (their identity, governance, access interfaces, policies, and technical capabilities) remains inconsistent and fragmented across DOE-funded systems. This variability limits discoverability, interoperability, automated validation, and AI-driven analysis, all of which are increasingly essential for modern scientific workflows. To address this gap, the DOE Data Curation Working Group (DCWG) developed the DOE Repository Metadata Profile (DRMP). The DRMP is a practical, community-driven framework that defines how repositories can describe themselves in a consistent, machine-actionable, and scalable manner. The DRMP is not a new metadata schema. Instead, it is a mapping profile and structured element set capturing the essential characteristics of DOE repositories. It harmonizes repository-level metadata across six widely adopted community schemas: RE3Data; DCAT-US v3; Schema.org; Dublin Core; DataCite 4.6; and PREMIS 3.0. This harmonization eliminates reinvention and enables interoperability within DOE and across the broader scientific ecosystem. A core objective of the DRMP is to reduce burden on repositories by allowing them to reuse their existing metadata through a Rosetta-style crosswalk rather than redesigning local implementations. The profile introduces a three-level conformance model that supports incremental adoption: • Level 1 – Minimum Viable Record (MVR): foundational identification elements required for workflows, project registration, and basic repository presence. • Level 2 – Interoperable: structured metadata enabling alignment with national and international discovery systems. • Level 3 – AI-Ready: enhanced provenance, policy transparency, fixity, semantic context, and capabilities that support automated reasoning, model training governance, and machine-assisted curation. To support implementation, the DRMP includes JSON Schema definitions, OpenAPI patterns, and MCP templates that allow repositories to publish machine-readable metadata directly within existing platforms. These resources are modular and lightweight, enabling adoption without major architectural change. Adopting the DRMP enables repositories to: • Enhance discoverability and interoperability by aligning identifiers, classifications, and descriptive elements across widely used schema standards. • Support federated discovery and cross-registration across DOE systems, Data.gov, and international catalogs. • Enable AI agents and workflow orchestration systems to interpret repository-level metadata within the American Science Cloud (AmSC) through Model Context Protocol (MCP)-based context publication. • Demonstrate alignment with DOE’s open science, stewardship, and FAIR data priorities. This guidance represents a community-driven step forward. Through voluntary adoption and continued feedback, the DRMP advances a cohesive, machine-actionable description of DOE repositories that supports FAIR data practices, preparing the infrastructure for AI-enabled research, and strengthening the discoverability and reuse of DOE’s scientific outputs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗