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Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package

Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system’s bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Considerations regarding the Use of Computer Vision Machine Learning in Safety-Related or Risk-Significant Applications in Nuclear Power Plants

With the advancements made to date in the field of artificial intelligence (AI), significant potential exists to utilize AI capabilities for nuclear power plant (NPP) applications. AI can replicate human decision making and it is usually faster and more accurate than humans. For implementations that impact critical NPP applications (e.g., safety-related or non-safety systems that potentially affect overall plant risk), a deeper safety analysis of the AI methods is necessary. AI applied to NPP operations could resemble the use of digital I&C (DI&C) because such applications involve digital computer hardware and custom-designed software that input plant data, execute complex software algorithms, and output the results to a system or licensed human operator to potentially provoke an action. For AI methods to be compliant with current safety requirements for DI&C, AI compatibility must be evaluated, and AI-related gaps may exist that prevent the prompt deployment of AI in NPPs. This effort aims to evaluate how example AI technologies align with the DI&C safety framework, and discusses how they could be analyzed, modeled, tested, and validated in a manner similar to typical DI&C technologies. Because AI is a broad field that encompasses areas such as machine learning (ML), natural language processing, and computer vision, this research focused on a subset of methods categorized as the computer vision ML (CVML) methods. This report explores two CVML use cases, gauge reading and fire watch, considered relevant to the DI&C standards, as they could play a safety-critical role. For the gauge reading use case, a CVML-enabled technology that can read gauges at oblique angles is utilized. For the fire watch use case, a CVML-enabled technology is utilized that migrates fire watch from a manual (human) approach to automated fire detection. These use cases are mainly intended to give context to the CVML system discussion. This effort assumes the worst-case scenario, with the CVML system being used to replace a safety-related or risk-significant system, thus requiring evaluation. Evaluating CVML against most of the relevant safety requirements for DI&C yielded several CVML-specific considerations due to the uniqueness of its characteristics in comparison with typical DI&C systems. For example, CVML models often employ commonly used (open-source) datasets, and it is not always possible to determine the level of overlap among open-source datasets. Therefore, the independence of the developed CVML models when demonstrating diversity is questionable, therefore creating vulnerability to common cause failure (CCF). The design verification process is also impacted since the data overlap could result in overestimation of the software validation and verification (V&V) performance results. Section 2 of this report evaluates a list of the identified CVML-specific characteristics and discusses the resulting considerations and potential solutions in the context of each referenced requirement. A summation is provided in Section 3. This report is not to be used as a guideline. It was developed to identify and consider issues in the implementation of ML technologies used to augment activities that may have a bearing on plant operation. The report draws parallels to the use of DI&C technologies, for which many standards are available to guide their use in nuclear plant operation. It considers the technologies and some of the potential implications of their use in safety-related applications but is not intended to address regulatory or licensing related issues.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

pvplr-python: Python package implementation of PVplr for Performance Loss Rate (PLR) analysis

Due to software fragmentation, PV system modeling teams can be limited to language specific packages, preventing cross-sectional analysis of different modeling techniques and workflows. To this end, PVplr, a popular PV performance modeling R software package, has been ported to the Python programming language. To verify and test the robustness of the port, NSRDB data has been used to simulated PV installations at native resolution (~2 million Sites), with a variety of degradation rates, degradation patterns, and modules. Performance Ratios were calculated using the ported functions from pvplr-python and compared against Rdtools YoY values. Due to the complicated nature of degradation, a new metric has been proposed to quantify the performance loss of a system. The cumulative production loss, is the total amount of energy lost due to the degrading performance of the system. Cumulative production loss alleviates the problems with fitting linear functions to non-linear degradation. Cumulative Production loss was shown to better estimate the total lost revenue for non-linear degradation patterns. $XbX + UTC$ was found to most accurately predict the total lost revenue in simulated systems.

Kumar, Suraj↗

Accelerated Data Analytics for Power-System Time-Series (ADAPT) [Final Project Report]

Over the past decade, electric utilities have made significant progress in deploying networks of phasor measurement units (PMUs). The high-speed measurements provided by PMUs are valuable for offline analysis, but the sheer volume of data presents a challenge for utilities. The Accelerated Data Analytics for Power-System Time-Series (ADAPT) project was created to address this challenge by developing SciSync, an open-source software tool that enables utilities to rapidly read, process, analyze, and review grid measurements. SciSync was designed to provide the capabilities of Archive Walker, a research tool developed by PNNL, along with the reliability and performance of commercial-grade software.

24 POWER TRANSMISSION AND DISTRIBUTION↗

ARCADE (Advanced Reactor Cyber Analysis and Development Environment)

SAND2025-11780O ARCADE (Advanced Reactor Cyber Analysis and Development Environment) software performs cybersecurity experiments on Defensive Cyber Security Architectures (DCSA) for Distributed Control Systems (DCSs). The application is integrated into a cohesive environment that performs cyber risk analyses and reduces costs. ARCADE can investigate the entire cyber-attack surface of a DCS from the physics of control, down to the firmware of individual components with automated efficiency. ARCADE has five major functional components: the Data Broker system, the virtualization environment, the cyber-attack simulator, the cyber-physical analysis system, and the physics simulator. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Valme, Romuald↗

A Data Processing Pipeline To Extract A Knowledge Graph From Heterogeneous Data For Socio-technical Analysis Of Critical Infrastructure Influence

The code is written in Python and consists of the following pipeline that is implemented in Apache Airflow. This pipeline intends to understand the companies that are directly or indirectly involved with a type of critical infrastructure system at some point in that system's lifecycle. The pipeline takes a configuration file that specifies a list of initial companies to consider, a geographic region of interest, and a set of SEC form types as well as other data sources (e.g. CrunchBase) from which to extract entities and relations. There are four main components to this pipeline as currently implemented: Entity Extraction, Network Construction, Analysis, and Visualization. First, Entity Extraction, is implemented as the `topear-extract_organizations` Apache Airflow workflow. Given an initial query that specifies a geographic region of interest and a time interval, the software will extract CI facilities of interest and organizations that have a direct influence relationship to those facilities (e.g. ownership). During the course of the LDRD, we focused on Electric Vehicle charging stations and this information is available via the Department of Energy (DOE) database on fueling stations maintained by NREL. Within the context of the DOE CESER project, we have focused on Battery Energy Storage Systems (BESS). Second, the Network Extraction component will iteratively construct a social network graph given the set of organizations and people extracted in the previous step. Organizations (and eventually People if desired) are then fed as a query to the `topgear-construct_social_network` Apache Airflow workflow which given a set of initial companies and data sets (e.g. SEC EDGAR form types, OpenCorporates, Crunchbase). This Airflow workflow will iteratively query such data sources to discover relationships with new organizations and people. For example, this module can iteratively query SEC EDGAR for metadata that documents the number of each type of form for the given set of companies and their location. This forms metadata represents a catalog of data sources from SEC EDGAR for the extracted social network knowledge graph. The pipeline then downloads these forms from the website and saves them in a build directory for further processing. These documents are then parsed for entities and relations. Again, we note that in additional to SEC data sources, this step can also pull in information on organizations via API services such as CrunchBase and OpenCorporates or bulk data sources. At the end of this step, the resultant social network, the Critical Infrastructure network, and the edges that encode relationships between organizations and CI facilities, form the Adversarial Socio-Technical Network (ASTN) that informs the analysis. Third, the Analysis component processes these generated ASTN. Previously, that has included the ability to compare prevalence of different vendors for a given infrastructure component type across different regions as well as identify common public and private investors across those vendors. This was demonstrated for EV Charging Stations across several different metropolitan areas within an IEEE PES GridEdge publication. More recently, we have looked at ways to identify infrastructure owners and operators of BESS with the most nameplate capacity across different states as well as other indictors of risk resulting from changes in ownership over time. Finally, the Visualization component consists of an HTML/CSS/JS framework by which users can interact geospatial, operational, and organizational relationships across a given portfolio of Critical Infrastructure facilities. The objective is to provide a library of UI/UX modules that can be repurposed for stakeholder-specific dashboards. All of the modules are related via a common event model that enables UI actions in one view to percolate across the other views.

Weaver, Gabriel [Idaho National Laboratory (INL), ↗

UrbanScaping: Community Spatial Data Visualization & Analytics

Evaluating the electrification potential of buildings through retrofitting is crucial for reducing carbon emissions and the carbon footprint of built environments. This study leverages the Automatic Building Energy Modeling (AutoBEM) software, integrating the Model America database to create an urban context-based spatial analysis platform for community engagement and development. We selected Camp Hill Borough, PA, as a case study to analyze building-specific energy performance and evaluate the electrification potential of each building by switching to different Heating, Ventilation, and Air Conditioning (HVAC) systems and measurement components. The simulation results generated by the workflow provide retrofitting suggestions to help mitigate the carbon footprint as well as energy saving statistics of buildings. Additionally, the developed web-based interface serves as a community engagement platform, allowing residents to provide feedback and further develop interactive communication protocols. The outcomes of this project offer a baseline for community electrification planning and contribute to the design of low-carbon communities.

Chowdhury, Shovan [ORNL]↗

Analysis and Grading of the Test Performance of PS Modules for the CMS Phase-2 Outer Tracker Upgrade

The Outer Tracker of the CMS experiment provides information about the trajectory of charged particles produced in proton-proton collisions at the LHC. During the High Luminosity LHC upgrade, scheduled for the late 2020s, the Outer Tracker will be replaced with new modules capable of transmitting data to the L1 Trigger. These modules are being assembled at several facilities around the world, including Fermilab, necessitating coordinated standards of module quality. Here I discuss the development of POTATO (Phase-2 Outer Tracker Analyzer of Test Outputs), a C++ software which provides a standardized procedure for analyzing and grading test results of the Outer Tracker modules. The particular focus of this poster is on the analysis and grading of the PS (pixel-strip) modules in POTATO.

Riggall, Caroline↗

Spectrum and extension of the inverse-Compton emission of the Crab Nebula from a combined Fermi -LAT and H.E.S.S. analysis

The Crab Nebula is a unique laboratory for studying the acceleration of electrons and positrons through their non-thermal radiation. Observations of very-high-energy γ rays from the Crab Nebula have provided important constraints for modelling its broadband emission. We present the first fully self-consistent analysis of the Crab Nebula’s γ-ray emission between 1 GeV and ∼100 TeV, that is, over five orders of magnitude in energy. Using the open-source software package GAMMAPY, we combined 11.4 yr of data from the Fermi Large Area Telescope and 80 h of High Energy Stereoscopic System (H.E.S.S.) data at the event level and provide a measurement of the spatial extension of the nebula and its energy spectrum. We find evidence for a shrinking of the nebula with increasing γ-ray energy. Furthermore, we fitted several phenomenological models to the measured data, finding that none of them can fully describe the spatial extension and the spectral energy distribution at the same time. Especially the extension measured at TeV energies appears too large when compared to the X-ray emission. Our measurements probe the structure of the magnetic field between the pulsar wind termination shock and the dust torus, and we conclude that the magnetic field strength decreases with increasing distance from the pulsar. We complement our study with a careful assessment of systematic uncertainties.

79 ASTRONOMY AND ASTROPHYSICS↗

Model-based data center cooling controls comparative co-design

This article presents a comparative simulation-based control logic design process. It uses the Control Description Language (CDL) and the ASHRAE Guideline 36 high-performing building control sequences with the Modelica Buildings Library (MBL) to demonstrate a comparative analysis of two control designs for a data center chilled water plant. Details include a description of the closed-loop plant and control design methodology, including sizing and parameterization, base and alternative (Guideline 36) control logic with software implementation structure, and outline of the simulation experimentation process. The selected control designs are paired with comparable chilled water plant configurations. The models include a chiller, a water-side economizer, and an evaporative cooling tower. The plant provides cooling at 27ºC zone supply air temperature to a data center in Sacramento, CA. The comparative simulation results examined the impacts of a selected control logic detail, and present an example model-based design application. Overall, the simulation results showed a 25% annual and a 18% summer energy use reduction for alternative controls. This shows that simulation-based control logic design performance evaluation can improve energy efficiency and resilience aspects of system controls at large.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Cyber State Awareness For Resilience

Characterization of cyber-physical attacks requires a holistic understanding of cyber and physical behavior in a system. Machine Learning Anomaly Detection provides a compelling solution for continuously identifying suspicious behavior within these complex systems. In our software, we present an approach for holistic characterization of cyber-physical systems based on cyber and physical anomaly correlation. The approach consists of three main components: 1) an architecture for real-time data acquisition, management, and analysis of both cyber and physical data; 2) cyber and physical data driven anomaly detection systems (ADSs), 3) a metric that combines cyber and physical ADSs to provide a holistic characterization of the system..

Rieger, CraigG.↗

Kinetics Modeling for Design of Continuous Enzymatic Hydrolysis

Enzymatic hydrolysis of cellulose to monomeric sugars continues to be a limiting step in cost-effectively producing sugar and fermentation-based biofuels from biomass. In particular, the high cost of enzymes coupled with the long time-scale of reaction pose challenges to economic viability. Performing enzymatic hydrolysis in a continuous mode with enzyme recycle may provide a path towards substantially reduced costs for sugar production, but design and analysis are complicated by a lack of suitable kinetics models. Computationally attainable models, such as fractal-based models, require knowledge of the reaction-history of the biomass, and are thus only suitable for describing the batch reactions from which they are derived. Fundamental models, while potentially more generalizable, are often too computationally intensive to use in process or reactor modeling. In this work, a phenomenological rate model is proposed based on a two-phase substrate representation. Good agreement is seen between batch and continuous enzymatic hydrolysis (CEH) experiment data, which validates the model and enables us to solve for reactor design parameters, such as CEH reactor size and stream flow rates, based on process variables like yield. This model is integrated with techno-economic analysis software to explore economic sensitivities. Important design optimizations and tradeoffs are identified and quantified, including the relative cost imposed by rate slowdown from sugar inhibition versus the cost to remove and concentrate sugars at a lower concentration. It also identifies, high-leverage avenues for further exploration, such as increasing the maximum feasible solids concentration, and sustaining high membrane flux and reliability.

09 BIOMASS FUELS↗

GIS-Based Graphical User Interface Tools for Analyzing Solar Thermal Desalination Systems & High-Potential Implementation

This project developed a user-friendly, open-source, software that enables a comparative evaluation of solar thermal desalination technology options and employs geospatial data layers to identify regions of high-potential for solar thermal desalination. This was accomplished by integrating solar models with desalination models and enhancing their utility by providing GIS-based data inputs. The developed Solar Energy Desalination Analysis Tool (SEDAT) enables techno-economical evaluation of desalination technologies and selection of regions with the highest potential for using solar energy to power desalination plants. It simplifies the planning, design, and valuation of solar thermal and solar hybrid desalination systems in the U.S. and worldwide. SEDAT uses Dash for integrating various layers of large volumes of GIS data with Python-based models of solar energy generation and desalination technologies. It derives time-series of energy generation and water production, with details of plant performance and suggestions for improving the solar-desalination coupling. It is a one of-a-kind tool of analysis representing a definitive advancement in the state-of-the-art. Of solar desalination modeling This report summarizes the various phases of the tool’s development, and presents examples of the results.

14 SOLAR ENERGY↗

Energy Intensity Baselining and Tracking Guidance

Each company joining the U.S. Department of Energy’s (DOE’s) Better Buildings, Better Plants Program (Better Plants) commits to establishing an energy consumption and energy intensity (EI) baseline and to tracking its energy performance over a 10-year period against that baseline. The baseline must reflect a company’s energy consumption over a 12-month period, covering all its U.S.-based operations. Energy consumption is calculated by fuel type in terms of primary energy (also known as source energy). EI is broadly defined as the amount of energy consumed per unit of output produced. For this guidance document and for the program, the term energy performance represents an evaluation of a facility’s capacity to use energy efficiently. Metrics used to assess a facility’s energy performance can include EI, energy consumption, improvements in EI, etc. Establishing an energy baseline and tracking system is a critical first step in effectively managing energy use. Developing a baseline can help a company understand energy use within the corporation and give it a point of comparison to evaluate future efforts to improve energy performance. It can also support efforts to validate a company’s energy management activities, improve comparative analyses when using benchmarks, and help in predicting future energy needs. In addition, a company that normalizes its performance data can determine highly defensible measures of energy savings generated through implemented energy efficiency projects. Establishing a baseline and tracking energy performance is also a requirement for ISO 50001 certification. Although basic energy data can be collected through utility bills, most manufacturers will have to perform additional analyses to develop accurate and robust energy baselines and tracking systems. Energy is consumed in many ways within the manufacturing sector and can come from multiple sources. Energy is sometimes generated and sold to other parties or captured and reused on-site. External events can exert a significant impact on a facility or company’s energy use independent of any purposeful efforts to improve energy efficiency. Operational changes, such as production shifts—which may be inevitable for some companies over the 10-year period covered by the program—can also make a big difference in energy use. Since Better Plants asks companies to account for all their U.S.-based operations, mergers, acquisitions, and divestitures can also have significant implications for a company’s energy metrics. This document aims to demystify the sometimes complex baselining process. It devotes special attention to the task of normalizing and adjusting energy consumption to account for external factors, such as weather and production changes. A key recommendation is that companies use regression analysis to normalize their energy consumption data whenever possible. Regression analysis is a statistical technique that estimates the dependence of a variable (i.e., energy use in the context of Better Plants) on one or more independent variables such as ambient temperature, while controlling for the influence of other variables at the same time. A properly developed regression analysis can provide a reliable estimate of energy savings resulting from energy improvement strategies and projects by accounting for the effects of variables such as annual production levels and weather. DOE has developed a companion Energy Performance Indicator software tool (EnPI) to simplify the baselining process. This tool can run regression models, calculate changes in EI at the facility level, and automatically compile facility-level data into a corporate-wide metric. Note that although the relevant equations used to calculate EI are provided in this document, the EnPI tool will automatically perform most calculations for the user. Additionally, Better Plants Partners (Partners) can call on their Technical Account Manager (TAM) to help them establish a baseline and assist with the necessary calculations to track progress.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

SBbadger: biochemical reaction networks with definable degree distributions

Abstract Motivation An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis. Results In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software. Availability and implementation SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into ‘iVirus’ on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus’s functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy’s Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as “live” protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems.

Bolduc, Benjamin (ORCID:0000000324200755)↗

2024 Workshop - Remote Sensing and Fluxes Upscaling for Real-world Impact - Tutorial v1

The software-tutorial was developed within the 2024 Remote Sensing and Fluxes Upscaling for Real-world Impact workshop as part of the hands-on session. The workshop was supported by AmeriFlux, National Ecological Observatory Network (NEON) and CarbonDew. The software provides basic tools to perform the following tasks: - gather remote sensing images using Google Earth Engine API; - gather flux data; - perform basic functions, such as plotting time-series, perform QA of the data, compute vegetation indices; - perform correlation analysis between flux data and remote sensing data; - perform flux predictions based on remote sensing data integrated in different modalities.

Falco, Nicola [Lawrence Berkeley National Laborato↗

VA EDH Advanced Software Pipeline Framework Report: Enhancing Automation and Scalability

The VA Environmental Determinants of Health (EDH) Advanced Software Pipeline Framework is designed to enhance the efficiency, scalability, and security of geospatial data processing workflows. This framework integrates modern data orchestration and containerization technologies, including Prefect for workflow automation, Docker for containerization, and PostgreSQL/PostGIS for geospatial data storage and analysis. It ensures standardized, reproducible, and automated data processing, supporting VA objectives related to substance use risk assessment and recovery research. The pipeline addresses key scalability and performance challenges through horizontal and vertical scaling, high-performance computing (HPC) integration, parallel processing, task caching, and dynamic resource allocation. These optimizations improve throughput and reduce latency, allowing the system to efficiently manage large and complex datasets. Additionally, security and compliance measures—such as data encryption (SSL), Role-Based Access Control (RBAC), and adherence to GDPR and HIPAA standards—safeguard sensitive information throughout data transmission and storage. A key implementation of this framework includes the automation of shelter list geolocation workflows, ensuring that up-to-date data is readily available for VA decision-making. Lessons learned from this project include the transition from in-memory processing to incremental storage writes, improving resource management and reliability. Future enhancements aim to expand automation, integrate AI-driven anomaly detection, and incorporate high-performance computing resources. This framework provides a scalable, secure, and adaptable solution for managing geospatial datasets, reinforcing the VA’s ability to support clinical and strategic initiatives through data-driven decision-making.

97 MATHEMATICS AND COMPUTING↗