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DOE OSTI2025

Leveraging public AI tools to explore systems biology resources in mathematical modeling

Predictive mathematical modeling is an essential part of systems biology and is interconnected with information management. Systems biology information is often stored in specialized formats to facilitate data storage and analysis. These formats are not designed for easy human readability and thus require specialized software to visualize and interpret results. Therefore, comprehending modeling and underlying networks and pathways is contingent on mastering systems biology tools, which is particularly challenging for users with no or little background in data science or system biology. To address this challenge, we investigated the usage of public Artificial Intelligence (AI) tools in exploring systems biology resources in mathematical modeling. We tested public AI’s understanding of mathematics in models, related systems biology data, and the complexity of model structures. Our approach can enhance the accessibility of systems biology for non-system biologists and help them understand systems biology without a deep learning curve.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗

DOE OSTI2021

2D-to-3D image translation of complex nanoporous volumes using generative networks

Image-based characterization offers a powerful approach to studying geological porous media at the nanoscale and images are critical to understanding reactive transport mechanisms in reservoirs relevant to energy and sustainability technologies such as carbon sequestration, subsurface hydrogen storage, and natural gas recovery. Nanoimaging presents a trade off, however, between higher-contrast sample-destructive and lower-contrast sample-preserving imaging modalities. Furthermore, high-contrast imaging modalities often acquire only 2D images, while 3D volumes are needed to characterize fully a source rock sample. In this work, we present deep learning image translation models to predict high-contrast focused ion beam-scanning electron microscopy (FIB-SEM) image volumes from transmission X-ray microscopy (TXM) images when only 2D paired training data is available. We introduce a regularization method for improving 3D volume generation from 2D-to-2D deep learning image models and apply this approach to translate 3D TXM volumes to FIB-SEM fidelity. We then segment a predicted FIB-SEM volume into a flow simulation domain and calculate the sample apparent permeability using a lattice Boltzmann method (LBM) technique. Results show that our image translation approach produces simulation domains suitable for flow visualization and allows for accurate characterization of petrophysical properties from non-destructive imaging data.

58 GEOSCIENCES↗

DOE OSTI2025

LatticeAnalytics: Strut-Level Visualization and Inspection of Additively Manufactured Lattice Structures

Additive manufacturing (AM) is revolutionizing the production of custom components with complex internal geometries, essential for high-performance applications in diverse fields such as medicine and defense. These AM parts optimize strength while minimizing weight by utilizing internal lattice structures consisting of large quantities of small interconnected struts. However, the complexity of these structures, combined with the challenges of using X-ray Computed Tomography (XCT) data, makes validation of part reliability difficult. This ultimately inhibits the development of novel parts for our collaborating material scientists. Here, we introduce LatticeAnalytics, a novel framework specifically designed for visual inspection of defects in these lattice structures. Our framework offers an end-to-end solution that includes the data management of XCT scans, enables remote access for geographically dispersed teams through a web-based dashboard, and incorporates novel visualizations. Our analysis is facilitated by a coarse alignment between the lattice’s nominal model, a spatial graph, and the XCT data. We employ a simple VR-based approach for fast and rough alignment, followed by an offline registration and identification of the struts. With the nodes and struts aligned and identified in the volume, our framework allows querying of subvolumes containing a single strut at multiple resolutions. This avoids computation over the entire lattice and also allow for easy parallelization of down-stream computations, such as strut-specific metrics. To depict a fast overview of the strut quality, we introduce two innovative visual encodings, crucial for our collaborators’ research in creating novel AM parts: the Contour View and the Roughness Map, which depict critical geometrical and surface features of individual struts in standardized two 2D views. We evaluated the integrated system through expert interviews. The feedback confirms the framework’s practicality and its effectiveness in enhancing current inspection workflows. It solves major bottlenecks for our collaborators, ultimately helping them create novel parts with advanced properties.

Miao, Haichao [Lawrence Livermore National Laborat↗

DOE OSTI2021

Surface distribution of heterogenous clathrin assemblies in resorbing osteoclasts

Highlights: • Platinum replica microscopy has revealed new structural data on the clathrins on the ventralmembrane of osteoclasts. • Various clathrins were visualized, suggesting that they followed variations in the surface topography of the apatite. • Most of the flat clathrins may participate in the adhesive and mechnosensory functions in co-operation with podosomes. • The present findings in osteoclast biology reveal potential novel drug targets or treatment regimens. Osteoclasts seeded on either glass coverslips or apatite pellets have at least two morphologically distinct substrate adhesion sites: actin-based adhesion structures including podosome belts and sealing zones, and adjacent clathrin sheets. Clathrin-coated structures are exclusively localized at the podosome belts and sealing zone, in both of which the plasma membrane forms a tight attachment to the substrate surface. When cultured on apatite osteoclasts can degrade the apatite leading to the formation of resorption lacunae. The sealing zone divides the ventral membrane into different domains, outside and inside of the sealing zones. The former facing the smooth-surfaced intact apatite contains relatively solitary or networks of larger flat clathrin structures; and the latter, facing the rough-surfaced degraded apatite in the resorption lacunae contain clathrin in various shapes and sizes. Clathrin assemblies on the membrane domain facing not only a resorption lacuna, or trails but also intact apatite indeed were observed to be heterogeneous in size and intensity, suggesting that they appeared to follow variations in the surface topography of the apatite surface. These results provide a detailed insight into the flat clathrin sheets that have been suggested to be the sites of adhesion and mechanosensing in co-operation with podosomes.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Imaging Bragg Edge Analysis TooLs for Engineering Structures (iBeatles)

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) provides pulsed neutrons with energies varying from epithermal to cold. In preparation for VENUS, the neutron imaging beamline to be located at beam port 10, we have performed a series of experiments focused on wavelength-dependent radiography and computed tomography for a broad range of applications, from materials science to biological tissues.One of the time-of-flight (TOF) techniques that is of interest to the scientific community is the 2-dimensional mapping of phases and average crystalline plane orientation in samples both ex-situ and during applied stresses such as tensile loading and heating. This technique is known as Bragg edgeimaging and relies on the identification of changes of transmission values, fitting of the edge to measure its displacement, and thus identify the shift in lattice parameter due to stresses. One of the challenges of TOF imaging measurements is the amount of data and the inability to observe Bragg edge shifts in real time during an experiment. Thus, we have been focusing on creating a Python-based interface that allows fast data processing and instantaneous mapping and fitting of the Bragg edges, and their evolution through time. Python libraries and Jupyter notebooks have been implemented to facilitate decision making during an experiment. The advantage of the notebooks is the possibility to guide an experiment as they can quickly process and display Bragg edge data. These notebooks can be used independently, or can be combined in a Python Graphical User Interface (GUI) tool called iBeatles. This interface permits visualization and fitting of the Bragg edges, and ultimately back-projects the fitting results onto the radiographs to display a strain map. Assuming data collection has sufficient statistics, the strain mapping analysis can be performed on a pixel-by-pixel basis. This development is a step forward toward a better user experience at the future VENUS beamline in terms of live feedback and productivity. Analysis that used to take days of switching between different applications can now be done in minutes within the

Bilheux, JeanChristophe [Oak Ridge National Labora↗

DOE OSTI2021

Intelligent Monitoring Systems and Advanced Well Integrity and Mitigation

Long-term seismic monitoring of carbon capture and storage projects is needed to verify that the injected gas is safely stored in the subsurface until permanence can be assured. Conventional surface seismic monitoring techniques are usually expensive, require highly invasive surface operations, and need significant time investments on the part of personnel for both the field effort and processing the acquired data. For these reasons, permanent reservoir monitoring technologies are preferred, as they can offer a cost-effective solution for long-term monitoring. As part of the monitoring program of the Archer Daniels Midland’s large-scale injection of CO 2 in Decatur, Illinois, USA, a continuous seismic monitoring array was installed using a combination of surface orbital vibrator (SOV) sources and fiber-optic cables for distributed acoustic sensing (DAS) acquisition with the objective to build a continuous monitoring array. The aim of the presented project was to build a monitoring array and platform that integrates real-time seismic data with conventional data streams and provides continuous data analysis using dynamic computational models to deliver a comprehensive real-time assessment of subsurface conditions. It is in this context that the Intelligent Monitoring Systems and Advanced Well Integrity and Mitigation project was proposed with the objective to develop an integrated architecture that utilizes a permanent seismic monitoring network, combines the real-time geophysical and process data with reservoir flow and geomechanical models to create a comprehensive monitoring, visualization, and control system that delivers critical information for process surveillance and optimization.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

A New Way to Discover Strong Gravitational Lenses: Pairwise Spectroscopic Search from DESI DR1

We present a new method to search for strong gravitational-lensing systems by pairing spectra that are close together on the sky in a spectroscopic survey. We visually inspect 26,621 spectra in the Dark Energy Spectroscopic Instrument (DESI) Data Release 1 that are selected in this way. We further inspect the 11,848 images corresponding to these spectra in the DESI Legacy Imaging Surveys Data Release 10, and obtain 2046 conventional strong gravitational lens candidates, of which 1906 are new. This constitutes the largest sample of lens candidates identified to date in spectroscopic data. Besides the conventional candidates, we identify a new class of systems that we term “dimple lenses.” These systems have a low-mass foreground galaxy as a lens, typically smaller in angular extent and fainter compared with the lensed background source galaxy, producing subtle surface brightness indentations in the latter. We report the discovery of 318 of these “dimple lens” candidates. We suspect that these represent dwarf galaxy lensing. With follow-up observations, they could offer a new avenue to test the cold dark matter model by probing their mass profiles, stellar mass–halo mass relation, and halo mass function for M Halo ≲ 10 13 M ⊙ . Thus, in total, we report 2164 new lens candidates. Our method demonstrates the power of pairwise spectroscopic analysis and provides a pathway complementary to imaging-based and single-spectrum lens searches.

Hsu, Yuan-Ming 許淵明 [National Taiwan University, Ta↗

DOE OSTI2025

Landscaper v1

Understanding the inner workings of machine learning models through their loss landscapes offers crucial insights into model properties, optimization dynamics, and generalizability. However, accessing these insights has traditionally required specialized mathematical expertise, limiting broader adoption. Landscaper is an open-source Python package designed to bridge this gap. Landscaper seamlessly integrates a suite of multi-dimensional loss landscape analyses with cutting-edge topological data analysis (TDA) methods. This powerful combination makes both fundamental loss landscape analysis and advanced TDA techniques accessible to the broader scientific ML community, without requiring deep pre-existing mathematical knowledge. Landscaper offers three key functionalities: * Construction: Builds detailed loss landscape representations through versatile low and high-dimensional sampling techniques. * Quantification: Applies advanced metrics, including a novel topological data analysis (TDA) based smoothness metric, enabling new perspectives on model behavior. * Visualization: Offers intuitive tools to visualize and interpret loss landscapes, providing actionable insights beyond traditional performance metrics.

Weber, Gunther [Lawrence Berkeley National Laborat↗

DOE OSTI2022

Exploring MDSplus data-acquisition software and custom devices

MDSplus is a software tool designed for data acquisition, storage, and analysis of complex scientific experiments. Over the years, MDSplus has primarily been used for data management for fusion experiments. This paper demonstrates that MDSplus can be used for a much wider variety of systems and experiments. We present a step-by-step tutorial describing how to create a simple experiment, manage the data, and analyze it using MDSplus and Python. To this end, a custom example device was developed to be used as the data source. This device was built on an opensource electronic hardware platform, and it consists of a microcontroller and two sensors. We read data from these sensors, store it in MDSplus, and use JupyterLab to visualize and process it. This project and code demo are available on the GitHub site at this URL: https://github.com/santorofer/MDSplusAndCustomeDevices

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Microbial sensor system for monitoring the environment and surfaces

A microbial sensor, system and method that can be used to determine the biochemical conditions of waters, saturated sediments, unsaturated soils, rhizosphere and other environments is disclosed. The flexibility of the microbial sensor design allows for the monitoring of surfaces (skin, ventilation conduits, etc.). An electrochemical microbial sensor system is composed of an indicator electrode(s) and a reference electrode. The reference electrode employs a hydrogen permeable membrane. The electrochemical system is interfaced into a signal/communication module allowing the manual or automated collection of data from field deployments and laboratory investigations. The data is transmitted using various communication technologies including Bluetooth™, cellular, satellite and radio telemetry to cloud-based data management systems. The stored data may be downloaded by users using open-source dashboard and visualization software to image the various environments and/or surfaces investigated.

Burge, Scott R.↗

DOE OSTI2023

2023 Real-time Optimization Workflow Status Update

Nuclear integrated energy systems are composed of a diverse set of energy generation sources and exist in dynamic and competitive electricity markets. With the inclusion of thermal energy storage, nuclear power systems can store heat for future use through various processes, such as water desalination or hydrogen generation. This heat storage can be managed in such a way as to economically optimize its usage. By combining real-time price data from the day-ahead and real-time markets with predictive and intelligent models, the charging and discharging of the thermal energy storage may be determined and optimized. This research details an approach through models and systems for the real-time optimization (RTO) of capacity allocation. Virtual models of the energy system and its physics phenomenon and component interactions provide intelligence to verification and prediction of operations. An optimization framework can use data generated from both a set of physical assets as well as the virtual models to predict future performance and create optimization and control workflows. Data warehouse technologies can be used to combine data across models, optimization workflows, market price data, and sensor data to intuitively store various types of data and provide integrations to physical control systems as well as user visualizations. Put together, these components can create a system for the RTO of nuclear integrated energy systems. Various virtual models and bench-scale physical demonstrations have been successfully performed and verified using this system. Larger scale testbeds that include thermal energy storage systems have been identified as future opportunities. A gap analysis that details the steps necessary to reach a physical demonstration at this scale is provided, along with conclusions on the current effort and future work.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Automated Waterbox Inspection for Nuclear Power Plants Using Computer Vision - Based Change Detection

Nuclear power plant waterboxes require regular inspection for leaks, missing components, and structural damage during maintenance outages. Traditional manual inspection is time-consuming and poses safety risks from confined space entry. We developed an automated computer vision system for drone-based waterbox inspection in partnership with Florida Light and Power. Our approach uses feature detection and matching to identify critical changes between baseline and current inspection images, automatically flagging additions (leaks/debris), removals (missing plugs), and translations (displaced components) while compensating for drone movement and environmental variations. We systematically evaluated six feature matching methods, from classical approaches (SIFT+BF) to state-of-the-art neural networks (SuperPoint+SuperGlue), using both standard benchmarks (HPatches) and waterbox-specific validation with real-world augmentations. SuperPoint+SuperGlue achieved superior performance with 7.82 pixels RMSE and 100% success rate—2.8x better accuracy than our baseline. While the pre-trained model has commercial licensing restrictions for nuclear deployment, our findings validate this architecture for custom training. We implemented a real-time GUI demonstrating the SIFT+BF approach for immediate deployment, processing drone feeds at 30 FPS with color-coded change visualization. Future work includes training a custom SuperPoint+SuperGlue model on waterbox data and integrating Vision-Language Models for automated reporting and maintenance guidance.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗

DOE OSTI2025

Development of a Digital Twin for Hydrogen Dispersion and Safety Assessment in an Electrolyzer Based Hydrogen Production Facility

Digital twin models are virtual representations of physical systems that use real-time data to simulate and optimize performance. This study presents the development and initial implementation of a digital twin (DT) for the electrolyzer-based hydrogen production facility at NREL's Advanced Research on Integrated Energy Systems (ARIES), focused on enhancing safety and optimizing sensor placement through physics-based simulations and metadata integration. The DT incorporates detailed facility-specific information, including component layout, leak locations, and controlled release parameters, to model hydrogen dispersion under varying environmental conditions. Using steady-state computational fluid dynamics (CFD) simulations informed by real meteorological data, such as wind speed, direction, and vertical wind profiles, the DT enables visualization of hydrogen plume behavior and spatial concentration distributions. Comparative analysis between high and low wind speed scenarios illustrates the significant influence of wind dynamics on plume shape and extent, with horizontal momentum dominating dispersion at higher speeds, while buoyancy effects become more prominent under low wind conditions. These simulations generate a rich dataset embedded within the DT, allowing users to assess potential leak outcomes and identify optimal sensor locations based on concentration thresholds. The model supports scenario-based analysis to guide safety strategies and equipment deployment for open-area hydrogen infrastructure. The digital twin thus serves as a dynamic platform for virtual prototyping, providing predictive insight into hydrogen behavior and enhancing risk-informed decision-making. This initial phase establishes a validated foundation for future integration of transient, uncontrolled leak scenarios and real-time sensor feedback, positioning the DT as a critical tool for safety design, operational planning, and adaptive monitoring in hydrogen systems. Overall, the approach demonstrates the value of combining environmental data with digital simulations to inform safer and more efficient deployment of hydrogen technologies.

08 HYDROGEN↗

DOE OSTI2026

Development of a Digital Twin for Hydrogen Dispersion and Safety Assessment in an Electrolyzer-Based Hydrogen Production Facility: Preprint

Digital twin models are virtual representations of physical systems that use real-time data to simulate and optimize performance. This study presents the development and initial implementation of a digital twin (DT) for the electrolyzer-based hydrogen production facility at the National Renewable Energy Laboratory (NREL)'s Advanced Research on Integrated Energy Systems (ARIES), focused on enhancing safety and optimizing sensor placement through physics-based simulations and metadata integration. The DT incorporates detailed facility-specific information, including component layout, leak locations, and controlled release parameters, to model hydrogen dispersion under varying environmental conditions. Using steady-state computational fluid dynamics (CFD) simulations informed by real meteorological data, such as wind speed, direction, and vertical wind profiles, the DT enables visualization of hydrogen plume behavior and spatial concentration distributions. Comparative analysis between high and low wind speed scenarios illustrates the significant influence of wind dynamics on plume shape and extent, with horizontal momentum dominating dispersion at higher speeds, while buoyancy effects become more prominent under low wind conditions. These simulations generate a rich dataset embedded within the DT, allowing users to assess potential leak outcomes and identify optimal sensor locations based on concentration thresholds. The model supports scenario-based analysis to guide safety strategies and equipment deployment for open-area hydrogen infrastructure. The digital twin thus serves as a dynamic platform for virtual prototyping, providing predictive insight into hydrogen behavior and enhancing risk-informed decision-making. This initial phase establishes a validated foundation for future integration of transient, uncontrolled leak scenarios and real-time sensor feedback, positioning the DT as a critical tool for safety design, operational planning, and adaptive monitoring in hydrogen systems. Overall, the approach demonstrates the value of combining environmental data with digital simulations to inform safer and more efficient deployment of hydrogen technologies.

08 HYDROGEN↗

DOE OSTI2022

BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data

Bacterial microcompartments (BMCs) are protein-based organelles found across the bacterial tree of life. They consist of a shell, made of proteins that oligomerize into hexagonally and pentagonally shaped building blocks, that surrounds enzymes constituting a segment of a metabolic pathway. The proteins of the shell are unique to BMCs. They also provide selective permeability; this selectivity is dictated by the requirements of their cargo enzymes. We have recently surveyed the wealth of different BMC types and their occurrence in all available genome sequence data by analyzing and categorizing their components found in chromosomal loci using HMM (Hidden Markov Model) protein profiles. To make this a “do-it yourself” analysis for the public we have devised a webserver, BMC Caller (https://bmc-caller.prl.msu.edu), that compares user input sequences to our HMM profiles, creates a BMC locus visualization, and defines the functional type of BMC, if known. Shell proteins in the input sequence data are also classified according to our function-agnostic naming system and there are links to similar proteins in our database as well as an external link to a structure prediction website to easily generate structural models of the shell proteins, which facilitates understanding permeability properties of the shell. Additionally, the BMC Caller website contains a wealth of information on previously analyzed BMC loci with links to detailed data for each BMC protein and phylogenetic information on the BMC shell proteins. Our tools greatly facilitate BMC type identification to provide the user information about the associated organism’s metabolism and enable discovery of new BMC types by providing a reference database of all currently known examples.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

2018 Renewable Energy Grid Integration Data Book

The 2018 Renewable Energy Grid Integration Data Book identifies the status, key trends, challenges, and solutions of renewable energy grid integration in a highly visual format. It provides an overview of selected key grid integration metrics that represent complex interactions among generation characteristics, market rules, and environmental and safety factors, which may vary by geography, season, and time of day; and the data book presents metrics that either indicate how much variable renewable energy (VRE) is currently being integrated onto the grid or measure factors that may increase or decrease the challenges associated with integrating VRE generation onto the grid.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2021

Explorative Visualization for Traffic Safety using Adaptive Study Areas

The pressing need to improve traffic safety has become a societal concern in many cities around the world. Many traffic accidents are not occurring as stand-alone events but as consequences of other road incidents and hazards. To capture the traffic safety indications from a holistic aspect, this paper presents a suite of visualization techniques to explore large traffic safety datasets collected from different sources using adaptive study areas which include the whole region (Hamilton County, Ohio, U.S.) as well as smaller sub-areas. In the present study, these data source include (1) Hamilton County’s 911 emergency response data, which includes traffic incidents as well as other types of incidents throughout the county, and (2) Tennessee crash data, which contains only vehicle crashes with more detail on the circumstances of each crash. We find that both abstract and spatial visualization techniques are used to derive a better understanding of traffic safety patterns for different traffic participants in various urban environments. In addition to the entire region of Hamilton County, safety is examined on the highways, in the downtown area, and in a shopping district east of the city center. It is possible to characterize incidents in the different areas, gain a better understanding of common incident patterns, and identify outliers in the data. Finally, a textured tile calendar is presented to compare spatiotemporal patterns.

99 GENERAL AND MISCELLANEOUS↗