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DOE OSTI2024

Laminography as a tool for imaging large-size samples with high resolution

Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high-resolution scanning of very thick and absorbing samples, such as a whole mouse brain stained with heavy elements, and, extending further, brains of primates. Samples are typically cut into smaller parts, to ensure a sufficient X-ray transmission, and scanned separately. Compared with the standard tomography setup where the sample would be cut into many pillars, the laminographic geometry operates with slab-shaped sections significantly reducing the number of sample parts to be prepared, the cutting damage and data stitching problems. In this work, a laminography pipeline for imaging large samples (>1 cm) at micrometre resolution is presented. The implementation includes a low-cost instrument setup installed at the 2-BM micro-CT beamline of the Advanced Photon Source. Additionally, sample mounting, scanning techniques, data stitching procedures, a fast reconstruction algorithm with low computational complexity, and accelerated reconstruction on multi-GPU systems for processing large-scale datasets are presented. The applicability of the whole laminography pipeline was demonstrated by imaging four sequential slabs throughout an entire mouse brain sample stained with osmium, in total generating approximately 12 TB of raw data for reconstruction.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Production of alternate realizations of DESI fiber assignment for unbiased clustering measurement in data and simulations

A critical requirement of spectroscopic large scale structure analyses is correcting for selection of which galaxies to observe from an isotropic target list. This selection is often limited by the hardware used to perform the survey which will impose angular constraints of simultaneously observable targets, requiring multiple passes to observe all of them. In SDSS this manifested solely as the collision of physical fibers and plugs placed in plates. In DESI, there is the additional constraint of the robotic positioner which controls each fiber being limited to a finite patrol radius. A number of approximate methods have previously been proposed to correct the galaxy clustering statistics for these effects, but these generally fail on small scales. To accurately correct the clustering we need to upweight pairs of galaxies based on the inverse probability that those pairs would be observed (Bianchi & Percival 2017). This paper details an implementation of that method to correct the Dark Energy Spectroscopic Instrument (DESI) survey for incompleteness. To calculate the required probabilities, we need a set of alternate realizations of DESI where we vary the relative priority of otherwise identical targets. These realizations take the form of alternate Merged Target Ledgers (AMTL), the files that link DESI observations and targets. We present the method used to generate these alternate realizations and how they are tracked forward in time using the real observational record and hardware status, propagating the survey as though the alternate orderings had been adopted. We detail the first applications of this method to the DESI One-Percent Survey (SV3) and the DESI year 1 data. We include evaluations of the pipeline outputs, estimation of survey completeness from this and other methods, and validation of the method using mock galaxy catalogs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Mass Spectrometer Transient Analysis

This software implements a complete preprocessing pipeline for transient mass spectrometry (MS) data collected during TAP (Temporal Analysis of Products) experiments. It is designed to extract chemically meaningful fluxes from overlapping ion signals by applying a calibrated defragmentation matrix and solving the resulting linear system using non-negative least squares (NNLS) regression. The core script, preprocess_mass_spec.py, performs the following operations: Gain correction: Applies amplifier gain scalars derived from inert-packed calibration pulses to normalize signal intensities across AMUs and acquisition settings. Background subtraction: Removes experiment baselines using user-defined time windows, ensuring compatibility with slow-diffusing species and preventing negative values that would interfere with NNLS. Options to subtract before and after defragmentation. Defragmentation: Constructs a fragmentation matrix A from zeroth moments of calibration pulses (equal molar gas:inert mixtures) and solves Ax=b at each time point, where b is the raw MS signal and x is the estimated species flux. The matrix is normalized to inert signals and accounts for instrument-specific fragmentation behavior. Pulse-mode handling: Supports both averaged and individual pulse modes, enabling statistical treatment of fluxes and calculation of standard deviations. Integration and output: Computes zeroth moments (integrated fluxes) and exports time-resolved and integrated data in CSV format, suitable for downstream kinetic modeling. The software is validated using both virtual TAP simulations (VTAP) and experimental data from propane dehydrogenation (PDH) on CrOx/Al2O3 catalysts. It preserves temporal resolution by applying NNLS point-by-point across the pulse duration (typically 6,000+ time slices per pulse), leveraging the linear superposition principle to reconstruct full flux profiles. The defragmented outputs are compatible with kinetic extraction methods such as the G and Y procedures, which are used to derive rate–concentration relationships from TAP data. The details of these validations are discussed in detail in the supporting manuscript and supporting information. Example data and output files are also included. The methodology is robust to experimental noise and drift, with calibration protocols that account for pulse size effects, MS aging, and inert gas normalization. The software is modular, reproducible, and tailored for high-throughput TAP-MS workflows in catalysis research.

Kristy, Stephen [Idaho National Laboratory (INL), ↗

DOE OSTI2024

Complete and Correct Transfer of Information (CACTI)

Many distributed systems, file transfer mechanisms, and message passing systems offer reliability mechanisms such as acknowledgements, retries, and durability. While these tools may be “good enough” for their typical use cases, they may not offer sufficient coverage for the wide range of faults that impact data transfers and communication. A gap in the reliability measures may lead to some small amount of data loss. Some high-consequence systems cannot tolerate the loss or corruption of even a single record. We present seven principles that will counter a wide range of faults and protect against data loss and corruption. These principles bring together lessons learned from a wide range of technologies and can inform appropriate system design and application usage. These principles will help readers reason on how prevent data loss in a multi-hop pipeline and how to properly use tools that may have a deficiency in reliability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Prioritizing Uncertainties in Hydrogen Contribution to Risk in Post-Crash Outcomes for Rail

This report presents analysis from Sandia National Laboratories predicting contributions to risk associated with the use of hydrogen technology for rail. Event sequence diagrams are used to describe possible accident scenarios and progressions. Initiating event frequencies and branch event probabilities for each scenario are quantified with uncertainty using distributions fit to Federal Railroad Administration and U.S. Department of Transportation Pipeline and Hazardous Materials Safety Administration data on applicable accidents from 2000 to 2020. Uncertainty is propagated through the event sequence diagram to estimate the frequency and conditional probability of accident end states. The analysis identifies four scenarios with significant contributions to risk from hydrogen that are predicted to occur relatively frequently, which may inform priorities for reducing uncertainty. These scenarios are 1) overpressure events resulting from collisions with hydrogen release due to mechanical damage and delayed ignition, 2) jet fire events resulting from collisions with hydrogen release due to mechanical damage and immediate ignition, 3) jet fires resulting from fire or explosion initiating events involving the hydrogen tank and correct operation of the thermally-activated pressure relief device (TPRD) subsequent to the thermal insult, and 4) pressure burst resulting from fire or explosion initiating events involving the hydrogen tank and failure of the TPRD. Delayed and immediate hydrogen ignition probabilities are identified as being highly uncertain and potential candidates for reducing conservatism in the predicted frequencies for these two scenarios.

08 HYDROGEN↗

DOE OSTI2022

Multiphysics Simulation of the NASA SIRIUS-CAL Fuel Experiment in the Transient Test Reactor Using Griffin

After approximately 50 years, NASA is restarting efforts to develop nuclear thermal propulsion (NTP) for interplanetary missions. Building upon nuclear engine tests performed from the late 1950s to the early 1970s, the present research and testing focuses on advanced materials and fabrication methods. A number of transient tests have been performed to evaluate materials performance under high-temperature, high-flux conditions, with several more experiments in the pipeline for future testing. The measured data obtained from those tests are being used to validate the Griffin reactor multiphysics code for this particular type of application. Griffin was developed at Idaho National Laboratory (INL) using the MOOSE framework. This article describes the simulation results of the SIRIUS-CAL calibration experiment in the Transient Reactor Test Facility (TREAT). SIRIUS-CAL was the first transient test conducted on NASA fuels, and although the test was performed with a relatively low core peak power, the test specimen survived a temperature exceeding 900 K. Griffin simulations of the experiment successfully matched the reactor’s power transient after calibrating the initial control rod position to match the initial reactor period. The thermal-hydraulics model largely matches the time-dependent response of a thermocouple located within the experiment specimen to within the uncertainty estimate. However, the uncertainty range is significant and must be reduced in the future.

33 ADVANCED PROPULSION SYSTEMS↗

NASA NTRS1980

Outline of a fast hardware implementation of Winograd's DFT algorithm

The main characteristics of the discrete Fourier transform (DFT) algorithm considered by Winograd (1976) is a significant reduction in the number of multiplications. Its primary disadvantage is a higher structural complexity. It is, therefore, difficult to translate the reduced number of multiplications into faster execution of the DFT by means of a software implementation of the algorithm. For this reason, a hardware implementation is considered in the current study, taking into account a design based on the algorithm prescription discussed by Zohar (1979). The hardware implementation of a FORTRAN subroutine is proposed, giving attention to a pipelining scheme in which 5 consecutive data batches are being operated on simultaneously, each batch undergoing one of 5 processing phases.

Zohar, S.↗

NASA NTRS2004

Searching for Pulsations from CEN X-4

The goal of this proposal is to detect or place sensitive upper limits on pulsations from the quiescent neutron-star X-ray binary Cen X-4. The observations were obtained on 1 March 2003. Unfortunately, due to problems with the standard pipeline processing of this observation, the data were not delivered until more than one year later, on 21 April 2004. No pulsations have yet been found in the data set. However, new optical spectra have been obtained which will lead to better constraints on the orbital period of Cen X-4 and which may enable detection of pulsations.

Kaaret, Philip↗

NASA NTRS2005

The Nature of the Enigmatic 10-Minute Accreting Binary System ES CET

ES Cet is one of the most compact binary systems known with an orbital period of only 10.3 minutes. Our allocated observations with the XMM-Newton X-ray satellite were performed in January and July 2004, with the data being delivered to the PI in August 2004. Preliminary results were presented by the PI in September 2004 and January 2005. We have also secured supporting optical observations of ES Ceti using the Magellan telescopes (November 2004). The team is currently performing a thorough and final analysis of the X-ray, UV and optical data sets with the latest XMM pipeline software and our own analysis packages.

Steeghs, Daniel↗

NASA NTRS2014

The Spitzer Survey of Interstellar Clouds in the Gould Belt. VI. The Auriga-California Molecular Cloud Observed with IRAC and MIPS

We present observations of the Auriga-California Molecular Cloud (AMC) at 3.6, 4.5, 5.8, 8.0, 24, 70 and 160 micrometers observed with the IRAC and MIPS detectors as part of the Spitzer Gould Belt Legacy Survey. The total mapped areas are 2.5 deg(exp 2) with IRAC and 10.47 deg2 with MIPS. This giant molecular cloud is one of two in the nearby Gould Belt of star-forming regions, the other being the Orion A Molecular Cloud (OMC). We compare source counts, colors and magnitudes in our observed region to a subset of the SWIRE data that was processed through our pipeline. Using color-magnitude and color-color diagrams, we find evidence for a substantial population of 166 young stellar objects (YSOs) in the cloud, many of which were previously unknown. Most of this population is concentrated around the LkH(alpha) 101 cluster and the filament extending from it. We present a quantitative description of the degree of clustering and discuss the fraction of YSOs in the region with disks relative to an estimate of the diskless YSO population. Although the AMC is similar in mass, size and distance to the OMC, it is forming about 15 - 20 times fewer stars.

Orion A Molecular Cloud (OMC)↗

NASA NTRS2019

Creating Data-Driven Vector Visualizations of Satellite Orbit Tracks Using NASA GIBS and Worldview

NASA Earth Observing System (EOS) currently operates dozens of remote sensing satellites, many of which can be viewed directly in NASA’s open-source Worldview application. Much of this satellite imagery can be viewed in near-real time as it is processed and served by NASA’s Global Imagery Browse Service (GIBS). To better educate users on the time and location of imagery, GIBS serves orbit track specific layers for each satellite. Worldview has historically served these layers as raster images but recent updates have enabled the application to now serve these layers using vector tiles. With the release of Worldview v3.0, orbit track layers can be displayed using mapbox vector tiles (MVT). This visualization format allows users to not only view and change the color of orbit track layers, as they could do previously with rasters, but also inspect individual vector points and filter layers by specific parameters such as time. The data contained within a MVT is further enhanced in Worldview with the combination of a JSON description file served from GIBS used to describe the MVT data. This presentation will provide an overview of the process of consuming orbit track vector tiles and data files from GIBS using a pipeline to configure, build and ultimately display the orbit tracks in Worldview. Furthermore, the presentation aims to describe how others can leverage our open-source code to display and enhance vector layers in their own applications.

Rice, Zachary↗

DOE OSTI2023

Natural Language Processing for Text Based Event Extraction: Identifying Events of Interest Related to Worldwide State-Sponsored Civil Nuclear Power

Beginning in FY20, SRNL was funded by the National Nuclear Security Administration’s Office of Defense Nuclear Non-Proliferation Research and Development to develop a prototype natural language processing/natural language understating machine learning-based modeling and analysis pipeline to extract and forecast events of interest from massive open data sources. The working hypothesis within the approach is that contextual shifts in key words and phrases act as indicators of events of interest over time. Therefore, by identifying points in time where contextual shifts occur, events of interest can be extracted along with explicit and implicit connections of entities and activities. The development of the preliminary prototype pipeline proved successful, meriting further testing of the pipeline on more broad topical domains and in a worldwide data environment. Therefore, SRNL, in collaboration with the Sanghani Center for Artificial Intelligence and Data Analytics at Virginia Tech, have continued development with a test case of identifying events of interest related to worldwide state-sponsored civil nuclear power in open data sources. In the first year of this follow-on effort, the team has curated domain-specific data corpuses using an automated scheme and applied the modeling and analysis pipeline. This robust, focused, and efficient approach consists of an ensemble of analyses applied to time dependent word embedding models that are trained on the data corpuses. In this report, the team has demonstrated the capability of the existing pipeline (as development has continued in parallel) by exploring several specific case-studies centered around Rosatom’s international activities regarding the planning, construction, operation, and/or shutdown of nuclear reactors. A basic timeline events has been generated by manually cataloging known “milestone” events that have occurred at reactors in Turkey, Finland, Hungary, and Egypt and compared with the output of the modeling pipeline. In this approach, the team has characterized the lead time using the prototype pipeline, as well as the ability to capture relevant information, which proved 100% successful. A deep dive example of the Akkuyu reactor (Turkey) is presented that shows the breadth of information that can be captured using the approach. In this case study, events were extracted pertaining to the planning/construction of Akkuyu including protests from the population, information campaigns in response to the protests, forged regulatory documents and lawsuits, budgetary/shareholder information, geopolitical tensions, and the various construction milestones. This has demonstrated the pipeline’s utility as a research aid or real-time event extraction tool, where summary-level information and detailed text extractions from millions of articles or Tweets across long time periods can be generated with significantly less effort than current techniques.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

PNNL-Predictive-Phenomics/ProteoMeter

ProteoMeter is a Python package that assists in the statistical analysis of global proteomics, protein post-translation modification (PTM), and limited proteolysis (LiP) data. It contains batch correction, normalization, and statistical testing methods, as well as functions that "roll up" peptide-level data to the single-site level. It has a robust user configuration system, allowing it to flexibly integrate different types of experiment designs. For basic usage, a simple configuration file provides the essential functionality. Advanced users have access to the entire statistical pipeline for fine-tuning analyses. Processed data is easily exported to many common spreadsheet and data-frame formats.

Rozum, Jordan [Pacific Northwest National Lab]↗

NASA NTRS2019

A Chromaticity Analysis and PSF Subtraction Techniques for SCExAO/CHARIS Data

We present an analysis of instrument performance using new observations taken with the Coronagraphic High Angular Resolution Imaging Spectrograph (CHARIS) instrument and the Subaru Coronagraphic Extreme Adaptive Optics (SCExAO) system. In a correlation analysis of our data sets (which use the broadband mode covering the J band through the K band in a single spectrum), we find that chromaticity in the SCExAO/CHARIS system is generally worse than temporal stability. We also develop a point-spread function (PSF) subtraction pipeline optimized for the CHARIS broadband mode, including a forward modeling-based exoplanet algorithmic throughput correction scheme. We then present contrast curves using this newly developed pipeline. An analogous subtraction of the same data sets using only the H-band slices yields the same final contrasts as the full JHK sequences; this result is consistent with our chromaticity analysis, illustrating that PSF subtraction using spectral differential imaging (SDI) in this broadband mode is generally not more effective than SDI in the individual J, H, or K bands. In the future, the data processing framework and analysis developed in this paper will be important to consider for additional SCExAO/CHARIS broadband observations and other ExAO instruments which plan to implement a similar integral field spectrograph broadband mode.

Benjamin L. Gerard↗

DOE OSTI2026

Opportunities in AI/ML for the Rubin LSST Dark Energy Science Collaboration

The Vera C. Rubin Observatory's Legacy Survey of Space and Time (LSST) will produce unprecedented volumes of heterogeneous astronomical data (images, catalogs, and alerts) that challenge traditional analysis pipelines. The LSST Dark Energy Science Collaboration (DESC) aims to derive robust constraints on dark energy and dark matter from these data, requiring methods that are statistically powerful, scalable, and operationally reliable. Artificial intelligence and machine learning (AI/ML) are already embedded across DESC science workflows, from photometric redshifts and transient classification to weak lensing inference and cosmological simulations. Yet their utility for precision cosmology hinges on trustworthy uncertainty quantification, robustness to covariate shift and model misspecification, and reproducible integration within scientific pipelines. This white paper surveys the current landscape of AI/ML across DESC's primary cosmological probes and cross-cutting analyses, revealing that the same core methodologies and fundamental challenges recur across disparate science cases. Since progress on these cross-cutting challenges would benefit multiple probes simultaneously, we identify key methodological research priorities, including Bayesian inference at scale, physics-informed methods, validation frameworks, and active learning for discovery. With an eye on emerging techniques, we also explore the potential of the latest foundation model methodologies and LLM-driven agentic AI systems to reshape DESC workflows, provided their deployment is coupled with rigorous evaluation and governance. Finally, we discuss critical software, computing, data infrastructure, and human capital requirements for the successful deployment of these new methodologies, and consider associated risks and opportunities for broader coordination with external actors.

Aubourg, Eric [APC, Paris] (ORCID:000000025592023X↗

DOE OSTI2025

Extraction and Analysis of Time Series Data from Building Automation Systems Using Large Language Models

Semantic schemas like Haystack 4, Brick and ASHRAE standard 223 enable the structured, standardized, and machine-readable representation of building data, facilitating interoperability, data integration, and advanced analytics. However, extracting information from these models requires specialized expertise in SPARQL and other programming languages, skills that are not commonly found among building professionals. Recent advancements in Large Language Models (LLMs), such as ChatGPT, enable the construction of queries using natural language, making it easier for individuals to interact with these systems in a manner that resembles everyday speech. However, these methods have not yet been tested on building semantic ontologies. This paper introduces a novel workflow and tool for enabling users to ask questions about a specific building's data, using natural language and receive answers automatically generated by GPT-4o. Our approach integrates semantic ontologies with advanced LLM capabilities to automate three critical steps: (1) generating SPARQL queries to retrieve time series references from ontological models, (2) extracting the corresponding time series data from the Building Automation System, and (3) performing computations and visualizations tailored to the user's query. The proposed method simplifies access to BAS data, allowing both domain experts and non-specialists to conduct sophisticated analyses without needing extensive technical knowledge of semantic web technologies. By demonstrating this pipeline, we facilitate more accessible and scalable data-driven decision-making in building operations and management.

Mulayim, Ozan Baris↗

DOE OSTI2025

Extraction and Analysis of Time Series Data from Building Automation Systems Using Large Language Models

Mulayim, Ozan Baris↗