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DOE OSTI2025

Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications

Lack of standardization in biofoundries limits the scalability and efficiency of synthetic biology research. Here, we propose an abstraction hierarchy that organizes biofoundry activities into four interoperable levels: Project, Service/Capability, Workflow, and Unit Operation, effectively streamlining the Design‑Build‑Test‑Learn (DBTL) cycle. This framework enables more modular, flexible, and automated experimental workflows. It improves communication between researchers and systems, supports reproducibility, and facilitates better integration of software tools and artificial intelligence. Our approach lays the foundation for a globally interoperable biofoundry network, advancing collaborative synthetic biology and accelerating innovation in response to scientific and societal challenges.

Kim, Haseong↗

DOE OSTI2026

Report of the 2026 Workshop on Next-Generation Ecosystems for Scientific Computing: Harnessing Community, Software, and AI for Cross-Disciplinary Team Science

Scientific computing is undergoing rapid transformation as advances in artificial intelligence, heterogeneous computing, automation, and data-intensive research reshape not only computational tools but also the institutions, workforce models, and collaborative practices that support scientific discovery. This report synthesizes insights from the 2026 Workshop on Next-Generation Ecosystems for Scientific Computing, the second in a three-year series focused on strengthening scientific computing ecosystems through socio-technical co-design. Workshop discussions identified four interdependent strategic themes: software ecosystems for AI-enabled scientific discovery; trust, validation, and traceability; human-AI teaming and paradigm shifts; and workforce, pedagogy, and governance. The report translates these themes into eight priorities for community action spanning shared research infrastructure, trust and traceability, user experience, human-AI teaming, workforce development, cross-sector coordination, stewardship and sustainability, and evaluation of scientific value. Together, these priorities outline directions for building scientific computing ecosystems that remain trustworthy, sustainable, innovative, and resilient as AI assumes a growing role in scientific work.

AI↗

DOE OSTI2024

Enhancing Discoverability and Management of Atmospheric Data at Scale: Solutions from the ARM Data Center

The Atmospheric Radiation Measurement (ARM) is a multi-laboratory and multi-institutional U.S. Department of Energy (DOE) Office of Science National User Facility. The ARM Data Center (ADC), located at Oak Ridge National Laboratory, collects, archives, and shares vast atmospheric data crucial for climate research. The ADC manages over 7 PB of data from 460 instruments worldwide, processing it into more than 11,000 diverse data products using the Network Common Data Form (NetCDF) for machine-independent accessibility. The primary challenge addressed in this paper is the efficient management and distribution of vast and diverse datasets essential for the climate research community, enhancing accessibility through advanced tools like Data Discovery. The ADC has developed advanced infrastructure and software architecture to handle the continuous influx of heterogeneous data to enhance data discoverability, resulting in increased scientific collaboration. In 2023, users from over 34 countries downloaded and utilized ARM data, resulting in 1,455 publications. The ADC’s efforts have significantly improved the discoverability and usability of atmospheric data, fostering extensive scientific research and collaboration. This paper details the solutions implemented by the ADC team for efficient data discovery and distribution, and it demonstrates ARM’s capability of staging processed data for scientific analysis.

Shah, Chirag [ORNL] (ORCID:0000000203145737)↗

DOE OSTI2025

Towards An Updated Simulation of the Booster Neutrino Beam

Precise, accurate neutrino flux predictions for neutrino beam experiments are crucial for physics results. Flux predictions for the Booster Neutrino Beam at Fermilab were first published in 2009 by the MiniBooNE collaboration. It is no longer possible to run the simulation used to create these predictions due to outdated software versions. In this exciting period for the Short-Baseline Neutrino Program at Fermilab, with both the far detector (ICARUS) and the near detector (SBND) operating, an updated flux model for the BNB is necessary. For the purpose of using a dynamic, up-to-date beam model, the SBN program has created a new simulation named G4BNB. This framework contains new features, such as a full neutrino ancestry to handle hadron production systematics with more precision, and the inclusion of neutral mesons from the proton-beryllium scatter to allow the study of exotic BSM scenarios.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2026

Cooperative Education

Los Alamos National Laboratory (LANL) is a multidisciplinary national laboratory that conducts research and development in national security, engineering, materials science, computational modeling, and advanced manufacturing. The laboratory develops innovative technologies to address complex scientific and engineering challenges. This project focuses on the development and evaluation of high-performance absorbing structures through computational design, simulation, and engineering analysis. Absorbing structures are used in applications where damage mitigation, structural protection, and material efficiency are critical performance requirements. The increasing demand for lightweight, high-strength, and highly efficient structural systems has created a need for improved design methodologies capable of maximizing absorption while minimizing weight and material usage. The project utilizes advanced engineering software, including 3D CAD software and FEA, to generate and optimize structural concepts. Computational simulations are performed to evaluate structural behavior under loading conditions, while mathematical analyses are conducted using Python-based tools as well as established analytical equations from material and structural mechanics. The project benefits LANL by supporting the development of advanced design methodologies and improving the understanding of material and structural performance. During the internship term, a significant portion of the design development, simulation, and data analysis activities will be completed. Success of the project depends on collaboration among engineering mentors and technical staff members. Work will be conducted at Los Alamos National Laboratory using laboratory computing resources and engineering software.

42 ENGINEERING↗

DOE OSTI2025

MPACT Safeguards Modeling: FY25 Update

Sandia National Laboratories develops and maintains several open-source software packages to support material accountancy analyses. This includes the Material Accountancy Performance Indicator Toolkit (MAPIT), the Fissile Facility Flow Modeler (F3M) and the Separation and Safeguards Performance Model Library (SSPM-L). MAPIT is responsible for performing statistical safeguards analyses on bulk and itemized data from nuclear fuel cycle facilities and can operate on real or synthetic data. MAPIT is the only open-source software for such analyses. F3M is a library of modules, built in MATLAB Simulink, that contain pre made blocks to represent different generic fuel cycle processes. These blocks can be used together in a modular fashion to represent and simulate nuclear fuel cycle processes with the goal of improving facility-level accountancy during the design phase. F3M is also an open-source library. Finally, the SSPM-L library is a series of completed models built from F3M. The library includes facility models such as a generic PUREX facility and a fuel fabrication facility. The SSPM-L library is not open source, but is available to collaborators with a relevant use case. These tools include modeling and simulation pipelines to simulate nuclear fuel cycle facilities and the underlying software needed to simulate measurement uncertainty and perform statistical analyses. Together, these tools can perform end-to-end nuclear material accountancy analyses. This report documents the various improvements made to these tools in FY25. Specifically, we added new statistical test, new statistical modeling capabilities, new fuel cycle facility models, and launched a new open-source model component library.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Creating Apptainer Workflows with Docker-Compose-like Utilities

Creating Apptainer Workflows with Docker-Compose-like Utilities In this presentation, I will explore the utilization of a tool called process-compose, inspired by docker-compose, to create Apptainer-based services. This approach allows for easy deployment and management of fully containerized applications on High Performance Computing (HPC) systems without requiring elevated privileges. Benefits to the Ecosystem: By incorporating process-compose and Apptainer, I aim to address several key challenges in the HPC ecosystem: Simplified Workflow Management: Process-compose provides a user-friendly interface for defining and managing complex containerized application services, reducing the setup time and lowering the barrier to entry for new users. Enhanced Portability: Apptainer ensures that containerized applications can run consistently across different HPC environments, promoting greater portability and reducing compatibility issues. Process-compose is also a single binary that does not need to be installed by admin level users. Community Driven Solutions: This approach aligns with the goals of the High Performance Software Foundation (HPSF) to advance community-driven solutions. By sharing our experiences and insights, I hope to foster collaboration and innovation within the HPC community. Increased Productivity: The combination of process-compose and Apptainer streamlines the serve deployment process, allowing researchers and developers to focus more on their scientific work rather than the intricacies of system or service administration. Through this presentation, attendees will gain valuable insights into the practical implementation of containerized workflows on HPC systems, learn about the benefits of using process-compose and Apptainer, and understand how these tools can contribute to a more efficient HPC ecosystem.

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2025

IBPSA Project 2 BOPTEST: An update on the test cases available in the framework for testing advanced control strategies in buildings

Project 2 develops software infrastructure, test cases, and extensions for the Building Optimization Testing Framework (BOPTEST) to address the expanding needs of building and urban energy system controls through open international collaboration. This paper provides an overview of the new test cases available as of BOPTEST version 0.7.1. Each test case is developed using open-source Modelica libraries and Spawn of EnergyPlus, enabling the creation of high-fidelity building models that incorporate envelope dynamics, Heating Ventilation and Air Conditioning (HVAC) systems, and explicit control representations. Currently, eight test cases are available, with five additional cases under development. These test cases cover a wide range of climates, building types, and HVAC systems. This paper compiles and summarizes test case descriptions, cites original manuscripts that developed them for a more detailed description, and reports baseline control performance metrics. Furthermore, two example applications are presented: one illustrating different levels of control, from supervisory to low-level, and another demonstrating how Model Predictive Control (MPC) solutions must be adapted from continuous to integer to control some building actuators.

Zanetti, Ettore↗

DOE OSTI2024

msdlive-cli-distro

MSD-LIVE, the MultiSector Dynamics – Living, Intuitive, Value-adding, Environment, is a flexible and scalable data and code management system combined with a distributed computational platform that will enable MSD researchers to document and archive their data, run their models and analysis tools, and share their data, software, and multi-model workflows within a robust Community of Practice. MSD-LIVE will facilitate a new open, collaborative, resource-rich, technology-facilitated, community-driven way of doing MSD research.

Lansing, Carina↗

DOE OSTI2025

The Persistent Challenge of Data Locality in the Post-Exascale Era

The era of exascale computing, exemplified by systems like Frontier achieving exaflop-level performance, marks a milestone. However, the quest for sheer compute power leads to strong imbalance in system design. Hence, scaling advancements in memory, network bandwidth, and storage are also necessary and pose challenges, with a crucial need to address data locality issues. This article underscores the fundamental importance of data locality as a key abstraction for optimizing application performance. Despite notable software solutions, the growing complexity of parallelism and memory hierarchy demands performance-portable data locality solutions across diverse computing platforms. Additionally, the article revisits data locality aspects, covering hardware considerations, application perspectives, software stack abstractions, and tool support. It concludes with insights into data locality challenges and opportunities, emphasizing the ongoing significance of collaborative research for progress in this critical issue.

Unat, Didem [Koc University, Istanbul (Turkey)] (O↗

DOE OSTI2025

Open-Source and FAIR Research Software for Proteomics

Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Privacy-Preserving Federated Learning for Science: Challenges and Research Directions

This paper discusses the key challenges and future research directions for privacy-preserving federated learning (PPFL), with a focus on its application to large-scale scientific AI models, in particular, foundation models~(FMs). PPFL enables collaborative model training across distributed datasets while preserving privacy-- an important collaborative approach for science. We discuss the need for efficient and scalable algorithms to address the increasing complexity of FMs, particularly when dealing with heterogeneous clients. In addition, we underscore the need for developing advance privacy-preserving techniques, such as differential privacy, to balance privacy and utility in large FMs emphasizing fairness and incentive mechanisms to ensure equitable participation among heterogeneous clients. Finally, we emphasize the need for a robust software stack supporting scalable and secure PPFL deployments across multiple high-performance computing facilities. We envision that PPFL would play a crucial role to advance scientific discovery and enable large-scale, privacy-aware collaborations across science domains.

Kim, Kibaek [Argonne National Laboratory (ANL)]↗

DOE OSTI2024

Learning Operators for Structure-Informed Surrogate Models

This report summarizes the work performed under the author's two-year John von Neumann LDRD project, which involves the non-intrusive surrogate modeling of dynamical systems with remarkable structural properties. After a brief introduction to the topic, technical accomplishments and project metrics are reviewed including peer-reviewed publications, software releases, external presentations and colloquia, as well as organized conference sessions and minisymposia. The report concludes with a summary of ongoing projects and collaborations which utilize the results of this work.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

ML based control systems for nuclear physics experiments

The Experimental Physics Software and Computing Infrastructure (EPSCI) group at Jefferson Lab is leading the use of machine learning (ML) to enhance control systems in nuclear physics experiments. Collaborating closely with domain experts and data scientists, we have developed an ML-based control system that uses a Gaussian process to dynamically adjust the high voltage of the GlueX Central Drift Chamber. This results in stable detector performance by adapting to environmental changes, thereby reducing the offline calibration effort. Furthermore, we are developing ML-driven systems for optimizing the polarization of photon beams and polarized cryotargets. These systems will maintain the optimal microwave frequency in cryogenic targets and make real-time adjustments to diamond radiators for polarized photon sources, tasks traditionally handled by human operators. By automating these functions, we aim to optimize the polarization, reduce downtime, and minimize human error. This talk will highlight the development of reliable ML-based control systems and the policies to ensure they are both effective and trustworthy.

Jeske, Torri↗

DOE OSTI2025

NFPA Distributed Energy Resources Safety Training (DERST) For Emergency Responders

The National Fire Protection Association, with support from the Department of Energy, executed a multi-year initiative to develop, enhance, and disseminate Distributed Energy Resources Safety Training (DERST) tools for U.S. emergency responders. As Distributed Energy Resources (DER)—such as solar photovoltaics, battery energy storage systems (ESS), electric vehicles (EVs), and associated infrastructure—become increasingly prevalent, the NFPA identified a critical need for up-to-date standardized, accessible, and effective safety training tailored for the fire service and related public safety professionals. The project delivered a comprehensive suite of educational resources to improve responders’ abilities to safely manage DER-related incidents. This included: • Revised Modular Training Courses: Updated classroom-based DER safety courses, now modular and accessible nationwide through fire academies and the North American Fire Training Directors (NAFTD) network. • Live Burn Testing & Research: A full-scale controlled burn of a DER-equipped residential structure provided real-world data and insights, forming the basis for updated best practices. • A Gamified Simulation Tool – Firefighters Incident Response Simulation Tool (FIRST): A first-of-its-kind, multiplayer, scenario-based simulation using the Unreal Engine 5.0 to train responders in a realistic virtual, multi-DER incident environment. • Field Familiarization Software Tools & Prop Guide: Digital DER field familiarization evolutions software guide and a prop development manual to support field-based DER training exercises, enhancing responders' hands-on familiarity with DER infrastructure and collaboration on virtual incident responses. • National Dissemination Strategy: Strategic partnerships with NAFTD, Vector Solutions, and others enabled wide-scale distribution, with over 5,000 departments accessing resources and 1,100+ departments adopting the simulator in the first seven months. Also provided a web portal for easy access to all training and simulation programs developed under this grant for the U.S. responder community. Key findings from the project—particularly from the burn test—led to paradigm shifts in fire response tactics. For example, traditional approaches to garage fires may be hazardous if DERs are present, due to explosive off gassing and thermal runaway risks. The new training emphasizes scene assessment, stand-off approaches, thermal imaging verification, and careful post-incident cooling of DER components to prevent reignition. This initiative has had a significant national impact, raising awareness, enhancing preparedness, and supporting safer DER incident response practices. Significant engagement from the media, public safety organizations, and PBS coverage has further amplified the reach and adoption of NFPA’s DER safety training, tools, and simulations.

14 SOLAR ENERGY↗

DOE OSTI2024

Democratizing uncertainty quantification

Uncertainty Quantification (UQ) is vital to safety-critical model-based analyses, but the widespread adoption of sophisticated UQ methods is limited by technical complexity. In this paper, we introduce UM-Bridge (the UQ and Modeling Bridge), a high-level abstraction and software protocol that facilitates universal interoperability of UQ software with simulation codes. It breaks down the technical complexity of advanced UQ applications and enables separation of concerns between experts. UM-Bridge democratizes UQ by allowing effective interdisciplinary collaboration, accelerating the development of advanced UQ methods, and making it easy to perform UQ analyses from prototype to High Performance Computing (HPC) scale. In addition, we present a library of ready-to-run UQ benchmark problems, all easily accessible through UM-Bridge. These benchmarks support UQ methodology research, enabling reproducible performance comparisons. We demonstrate UM-Bridge with several scientific applications, harnessing HPC resources even using UQ codes not designed with HPC support.

Benchmarks↗

DOE OSTI2025

Employing MACS/ViBRANT as a Surrogate MARVEL Reactor for Startup Reactivity Tuning and Supervisory Control Processes

Advanced nuclear reactors are a key part of the future of nuclear energy both in the United States and globally. They offer unique benefits for various energy-demanding applications, including use in remote locations, compact size, modular manufacturing, remote monitoring, low and/or variable power rating operation, and reliance on novel technologies to enhance operational safety. To achieve economic feasibility, advanced reactors must significantly reduce their workforces in comparison with the current fleet. Achieving this reduction will occur through reducing staff workloads using technology to achieve autonomous or semi-autonomous operations, demonstrated by comprehensive testing and validation activities. These operations will require both software and hardware platforms during the design and testing phases. While simulations are useful during the design phase, their performance can significantly deviate during actual deployment on hardware. This report presents the outcomes of a collaborative technical initiative between the U.S. Department of Energy (DOE) Microreactor Program (MRP) and Advanced Sensors and Instrumentation (ASI) Program. The collaboration utilized the Microreactor Automated Control System (MACS) hardware platform to bridge the gap between theoretical reactor design and actual startup and control operations. Two key use cases were investigated: facilitating the startup testing period and demonstrating supervisory control. The first use case details the key Microreactor Applications Research Validation and Evaluation (MARVEL) reactor startup physics testing activities conducted using the MACS platform. These activities included drum worth measurements, shutdown margin assessment, temperature feedback analysis, and scram time evaluation, as well as unique testing that would apply to the MARVEL reactor to demonstrate the testing methodologies in a low-risk environment. The MACS platform, serving as a surrogate representation of the MARVEL reactor, proved instrumental in performing these tests. The exercise revealed aspects that led to optimized processes, refined hardware design, and enhanced base software capabilities. By maturing methods and technologies in this manner, the initiative promises to reduce wasted time in the actual on-site reactor deployment effort, thereby saving significant time and resources. The second use case focuses on the development and implementation of supervisory control methods aimed at managing core tilt, which can result from asymmetrical operations or manufacturing imperfections in fuel rods or reactivity control devices. A key objective was to assess and compare the use of artificial intelligence (AI) for supervisory control. The effort aimed to define the role of supervisory control to enhance performance without risking control instability. This effort explored three distinct approaches: rules-based (RB) methods, optimization techniques, and reinforcement learning (RL) algorithms. Each approach was evaluated for its ease of implementation, its usability, and its effectiveness in responding to asymmetries in neutron flux. Comparative analysis of these approaches provided valuable insights into their applicability and effectiveness, offering a robust framework for advanced reactor operations. Together, these two use cases highlight the potential of hardware test beds to help streamline the design, operation, and control of advanced nuclear reactors. This collaborative effort underscores the importance of continued innovation and experimentation in achieving the next generation of safe, reliable, and economically viable nuclear energy solutions.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

PIPES (Pipeline for Integrated Projects in Energy Systems) [SWR-24-89]

The Pipeline for Integrated Projects in Energy Systems (PIPES) is a comprehensive project, data, and workflow management tool designed for integrated modeling teams. PIPES facilitates the management of data requirements, tasks, and progress tracking, serving as a higher-level integration layer that works across various data and modeling software. This tool integrates models, data, and tools to perform large-scale, integrated analysis work at scale. PIPES is designed to streamline integrated modeling projects, enhance collaboration, and ensure the quality and efficiency of data management and workflow processes. https://github.com/nrel-pipes/pipes-api https://github.com/nrel-pipes/pipes-web https://github.com/nrel-pipes/nrel-pipes

Gu, Jianli↗