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At least 379 records · Page 21

A deep learning-guided automated workflow in LipidOz for detailed characterization of fungal fatty acid unsaturation by ozonolysis

Understanding fungal lipid biology and metabolism is critical for antifungal target discovery as lipids play central roles in cellular processes. Nuances in lipid structural differences can significantly impact their functions, making it necessary to characterize lipids in detail to enable and understanding of their roles in these complex systems. In particular, lipid double bond (DB) locations are an important component of lipid structure that can only be determined using a few specialized analytical techniques. Ozone-induced dissociation mass spectrometry (OzID-MS) is one such technique that uses ozone to break lipid DBs, producing pairs of characteristic fragments that allow the determination of DB positions. In this work we apply OzID-MS and LipidOz software to analyze the complex lipids of Saccharomyces cerevisiae yeast strains transfected with different fatty acid desaturases from Histoplasma capsulatum to determine the specific unsaturated lipids produce. The automated data analysis in LipidOz made the determination of DB positions from this large dataset more practical, but manual verification for all targets was still time-consuming. The DL model reduces manual involvement in data analysis, but since it was trained using mammalian lipid extracts, the prediction accuracy on yeast-derived data was reduced. We addressed both shortcomings by retraining the DL model to act as a pre-filter to prioritize targets for automated analysis, providing confident manually verified results but requiring less computational time and manual effort. Our workflow resulted in the determination of novel DB positions and enzymatic specificity.

mass spectrometry, deep learning, Lipidomics, doub↗

Super-resolution model for overlapping peak detection and improved spatial resolution in high-energy diffraction microscopy

Reconstruction quality in Far-field High-Energy Diffraction Microscopy (FF-HEDM) is limited by the spatial resolution of area detectors and the frequent occurrence of overlapping diffraction spots. To address these challenges, we developed a super-resolution (SR) framework using convolutional neural networks (CNNs) to recreate 2D diffraction peaks at up to ×8 resolution from raw detector data. A specialized simulation tool was created to generate synthetic training datasets with varying degrees of peak overlap. Integrated into the Microstructural Imaging using Diffraction Analysis Software (MIDAS), the SR model improves the spatial accuracy and precision of 3D grain reconstruction by an order of magnitude. This approach provides a robust solution for investigation of complex micromechanical states and material classes where the analysis is limited by the presence of overlapping peaks. Furthermore, the methodology developed here can potentially be extended to other techniques that require sub-pixel accuracy for high-fidelity data analysis.

High-energy diffraction microscopy↗

pyEGAF: An open-source Python library for the Evaluated Gamma-ray Activation File

The Evaluated Gamma-ray Activation File (EGAF) is one of the most comprehensive resources for thermal neutron-capture data. This database contains data from prompt gamma activation analysis measurements carried out in a consistent manner using the same experimental configuration at the Budapest Research Reactor for 245 isotopes. Although these valuable datasets have been freely available for many years, one of the drawbacks is the outdated and cryptic Evaluated Nuclear Structure Data File (ENSDF) format that is currently adopted for dissemination, making it difficult for users unfamiliar with the format to access and utilize the data contained therein. Furthermore, the ENSDF format does not readily lend itself to modern computational technologies and a parser is required to interpret the complicated mixed-record format. To help overcome these challenges, we have developed a translator to convert the ENSDF-formatted datasets into an open standard JavaScript Object Notation (JSON) format enabling accessibility to applications using different programming languages running in different environments. To compliment this effort, we have also developed an open-source software package implemented in Python, pyEGAF, that is designed to interact with the JSON data structures for general purpose access, manipulation, and analysis of the neutron-capture $\gamma$-ray data in EGAF. The new format, together with the pyEGAF library, greatly enhances access to the wider applications community where EGAF data may be useful or is required.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Light Water Reactor Sustainability Program: Use of Time Distributions to Predict Operator Procedure Performance in Dynamic Human Reliability Analysis

The Human Unimodel for Nuclear Technology to Enhance Reliability (HUNTER) framework affords software capable of conducting human reliability analysis (HRA) using a dynamic approach built around operating procedures (OPs) from nuclear power plants (NPPs). Previous HUNTER reports document the development of this software tool, the coupling of HUNTER to the simulator code, the collection of operator performance data by using simulators to calibrate HUNTER models, and linking HUNTER to probabilistic risk assessment (PRA) software. The present report largely addresses two topics. The first is a new function in HUNTER called the HUNTER Procedure Performance Predictor (P3). HUNTER P3 uses HUNTER’s built in Monte Carlo tools featuring human performance variability to identify potential error traps in procedures. The second topic is time distribution analysis to generate time inputs for dynamic HRA. The current analysis was performed to investigate time distributions for task primitives, which are the minimum task unit of analysis used in dynamic HRA modeling. Using the time distribution data, the elapsed time for human actions in an extended loss of AC power (ELAP) scenario is then investigated. Time data and prediction are essential for modeling procedure performance.

99 GENERAL AND MISCELLANEOUS↗

MicroBooNE Public Data Sets: a Collaborative Tool for LArTPC Software Development

Among liquid argon time projection chamber (LArTPC) experiments MicroBooNE is the one that continually took physics data for the longest time (2015-2021), and represents the state of the art for reconstruction and analysis with this detector. Recently published analyses include oscillation physics results, searches for anomalies and other BSM signatures, and cross section measurements. LArTPC detectors are being used in current experiments such as ICARUS and SBND, and being planned for future experiments such as DUNE. MicroBooNE has recently released to the public two of its data sets, with the goal of enabling collaborative software developments with other LArTPC experiments and with AI or computing experts. These data sets simulate neutrino interactions on top of off-beam data, which include cosmic ray background and noise. The data sets are released in two formats: the native art/ROOT format used internally by the collaboration and familiar to other LArTPC experts, and the HDF5 format which contains reduced and simplified content and is suitable for usage by the broader community. This contribution presents the open data sets, discusses their motivation, the technical implementation, and the extensive documentation -- all inspired by FAIR principles. Finally, opportunities for collaborations are discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Combustion machine learning: Principles, progress and prospects

Progress in combustion science and engineering has led to the generation of large amounts of data from large-scale simulations, high-resolution experiments, and sensors. This corpus of data offers enormous opportunities for extracting new knowledge and insights—if harnessed effectively. Machine learning (ML) techniques have demonstrated remarkable success in data analytics, thus offering a new paradigm for data-intense analyses and scientific investigations through combustion machine learning (CombML). While data-driven methods are utilized in various combustion areas, recent advances in algorithmic developments, the accessibility of open-source software libraries, the availability of computational resources, and the abundance of data have together rendered ML techniques ubiquitous in scientific analysis and engineering. This article examines ML techniques for applications in combustion science and engineering. Starting with a review of sources of data, data-driven techniques, and concepts, we examine supervised, unsupervised, and semi-supervised ML methods. Various combustion examples are considered to illustrate and to evaluate these methods. Next, we review past and recent applications of ML approaches to problems in combustion, spanning fundamental combustion investigations, propulsion and energy-conversion systems, and fire and explosion hazards. Challenges unique to CombML are discussed and further opportunities are identified, focusing on interpretability, uncertainty quantification, robustness, consistency, creation and curation of benchmark data, and the augmentation of ML methods with prior combustion-domain knowledge.

33 ADVANCED PROPULSION SYSTEMS↗

Hardware, methodology and applications of 2 + D backscatter Mössbauer spectroscopy with simultaneous x-ray and γ-ray detection

Abstract A unique method is presented for the acquisition and analysis of 57 Fe backscatter Mössbauer spectra with simultaneous detection of the resonant 14.4 keV γ -rays and the characteristic 6.4 keV x-rays, using a custom-built multi-parameter analyser constructed on the basis of commercial analogue to digital converters and high-speed digital latches. The system allows for the simultaneous registration of Doppler-modulation velocities and photon energies, with up to 4096 and 8192 digital channels respectively. This arrangement is in contrast to most related systems, which detect at a single narrow energy window per detector. Samples of arbitrary atomic structure, morphology and surface topography can be studied without altering the setup or the analysis procedure, provided that the samples are at least micrometre sized. The hardware and software that are used to acquire data with minimal dead time are described and the custom and self-contained methods for post-measurement energy discrimination, background correction and velocity-axis folding are discussed. The data are fit using a general Hamiltonian model for the nuclear energy levels of 57 Fe and a quantum mechanical description of the angular momentum coupling is utilised, with consideration of the crystalline and chemical disorder of the sample under examination. Three examples of distinct magnetic systems, with thicknesses ranging from 5 μ m to 6 mm, that were studied using this method are presented, these are: an amorphous CoFeB-based ribbon with ultra-soft coercivity for high-frequency applications, magnetically hard Nd-Fe-B thick films on Si substrates, examined in both as-deposited and annealed states, and a sample from the nickel-rich iron meteorite NWA 6259 that contains the atomically ordered, elevated coercivity, L 1 0 phase of FeNi, tetrataenite. The wide applicability and usefulness of this method is thus demonstrated on three distinct sample morphologies that required little to no surface preparation prior to examination.

Engineering↗

Collaboration 51 Correlation Function Analysis Suite (c51_corr_analysis) v0.1.0

This is a data analysis package designed for analyzing correlation functions generated with lattice QCD calculations. The purpose is to make a centralized software suite for use by all members of my collaboration, so that various members can spend less time developing their own analysis codes, and more time extracting the interesting physics from our calculations. There are also 3 independent collaborations that have expressed interest in using this code, so there is some expectation it will be used in the broader international lattice QCD community.

Walker-Loud, Andre↗

Ascribe XR v0.1.0

Ascribe XR is an immersive visualization software designed for scientists and engineers working with 3D data sets. Its key features include interactive exploration, multi-user collaboration, and flexible data import capabilities, supporting various formats such as meshes, volumes, and terrain maps. The software utilizes Godot, OpenXR and PC-VR technology to provide an immersive experience. Ascribe XR is used for data analysis, visualization, and collaboration in various fields, enabling users to gain deeper insights into complex data sets. Its advantages over similar technologies include its flexibility, customizability, and ease of use. Ascribe XR's interactive and immersive environment facilitates collaboration and accelerates the discovery process. Compared to traditional 2D visualization tools, Ascribe XR offers a more engaging and intuitive experience, allowing users to explore complex data sets in a more natural and interactive way. Its ability to support multi-user collaboration and flexible data import capabilities make it a versatile tool for various applications. Overall, Ascribe XR provides a unique combination of features, usability, and performance, making it an attractive solution for scientists and engineers working with 3D data sets.

Pandolfi, Ronald [Lawrence Berkeley National Labor↗

Human Host Cellular Response to HCoV-229E Infection Proteomics (ACS-JM-DP2)

The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection. Sample data was obtained for mock and infected immortalized human lung epithelial cells (A549) (MOI 5) nuclear extracts, immortalized human lung fibroblasts cells (MRC5) (MOI5) nuclear extracts, and primary human airway epithelial (HAE) (MOI 3) cells from lung tissue and processed for proteome analysis. Processed datasets are openly accessible from the download button and contain secondary processed proteomic results files and supporting metadata materials. Experimental proteomics samples were prepared using Limited Proteolysis (LiP) methods for Label-free quantification (LFQ) and global proteomic evaluation. Sample data was acquired using a Q-Exactive HF-X mass spectrometer and was processed and compiled using MaxQuant software (v.1.6.17.0). Processed proteomic data downloads include a sample naming key, processed MaxQuant results/parameters, and protein annotated relative abundance files. See corresponding primary data accessions below and Viral Experiment LiP Analysis source code supporting data transparency and reuse. Experimental transcriptomics samples were collected in parallel and processed for RNA sequencing (RNA-Seq) as summarized under ACS-DP1 (https://data.pnnl.gov/group/nodes/dataset/34069).

59 BASIC BIOLOGICAL SCIENCES↗

Pyrolysis Molecular Beam Mass Spectrometry_Analysis_of_Natural_Variants_of_Poplulus_Trichocarpa_Leaves

Select leaves from natural variants of Poplar (Populus Trichocarpa) grown in a greenhouse at Oak Ridge National Laboratory were analyzed by Pyrolysis-Molecular Beam Mass Spectrometry (Py-MBMS). Leaves were harvested, cryomilled and kept frozen until analysis. Py-MBMS analysis was conducted using approximately 4 mg of biomass and each sample was analyzed in duplicate. A Frontier PY2020 unit pyrolyzed samples at 500°C for 30 s in 80 µL deactivated stainless steel cups. An Extrel Super-Sonic MBMS Model Max 1000 was used to collect mass spectral data fromm/z30 to 450 at 17 eV and processed using Merlin Automation software (V3). Spectral ion intensities were normalized to the total ion chromatogram signal for each sample for analysis of spectral variance. Lignin content (wt %) was estimated based on relative responses from standards of known Klason lignin content using mean-normalized ion intensities ofm/z120, 124 (G), 137 (G), 138 (G), 150 (G), 152, 154 (S), 164 (G), 167 (S), 168 (S), 178 (G), 180, 181, 182 (S), 194 (S), 208 (S) and 210 (S) where G indicates guaiacyl-derived ions, S indicates syringyl-derived ions, and other ions either derive from other lignin monomers or multiple sources. Ratios of S and G lignin monomer units (S/G) were obtained by dividing the sum of S-based ions by the sum of G-based ions using mean-normalized ion intensities.

CBI↗

Pyrolysis_Molecular_Beam_Mass_Spectrometry_Analysis_of_Specific_Switchgrass_Genotypes

Select natural variant switchgrass genotypes grown in Tifton, GA were analyzed by Pyrolysis-Molecular Beam Mass Spectrometry (Py-MBMS). Biomass was harvested, milled, several genotypes were analyzed with and without being destarched and extracted with ethanol prior to analysis (indicated with -DE if destarched and extracted). Py-MBMS analysis was conducted using approximately 4 mg of biomass and each sample was analyzed in duplicate. A Frontier PY2020 unit pyrolyzed samples at 500°C for 30 s in 80 µL deactivated stainless steel cups. An Extrel Super-Sonic MBMS Model Max 1000 was used to collect mass spectral data fromm/z30 to 450 at 17 eV and processed using Merlin Automation software (V3). Spectral ion intensities were normalized to the total ion chromatogram signal for each sample for analysis of spectral variance. Lignin content (wt %) was estimated based on relative responses from standards of known Klason lignin content using mean-normalized ion intensities ofm/z120, 124 (G), 137 (G), 138 (G), 150 (G), 152, 154 (S), 164 (G), 167 (S), 168 (S), 178 (G), 180, 181, 182 (S), 194 (S), 208 (S) and 210 (S) where G indicates guaiacyl-derived ions, S indicates syringyl-derived ions, and other ions either derive from other lignin monomers or multiple sources. Ratios of S and G lignin monomer units (S/G) were obtained by dividing the sum of S-based ions by the sum of G-based ions using mean-normalized ion intensities.

CBI↗

HL-LHC Analysis With ROOT: ROOT Project Input to the HL-LHC Computing Review (Stage 2)

ROOT is high energy physics' software for storing and mining data in a statistically sound way, to publish results with scientific graphics. It is evolving since 25 years, now providing the storage format for more than one exabyte of data; virtually all high energy physics experiments use ROOT. With another significant increase in the amount of data to be handled scheduled to arrive in 2027, ROOT is preparing for a massive upgrade of its core ingredients. As part of a review of crucial software for high energy physics, the ROOT team has documented its R&D plans for the coming years.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Pyrolysis_Molecular_Beam_Mass_Spectrometry_Analysis_of_hybrid_cross_of_Populus_tremula_x_P_alba_717-1B4_and_overexpression_of_a_lectin_receptor-like_kinase_(PtLecRLK1)

Stem tissues from the hybrid poplarPopulus tremula × P. albaclone 717-1B4 and from lectin receptor-like kinase overexpression lines PP7 and PP19 were individually colonized with the ectomycorrhizal fungiLaccaria bicolorstrain S238N,Hyaloscypha finlandicastrain PMI746, orUmbelopsis vinaceastrain PMI3018, as well as with a mixed fungal inoculum; non-inoculated plants served as controls. Plants were grown in a greenhouse at Oak Ridge National Laboratory and harvested in January 2025. Stem samples were analyzed using Pyrolysis–Molecular Beam Mass Spectrometry (Py-MBMS). Stems were harvested, debarked, dried, milled, destarched and ethanol extracted prior to analysis. Py-MBMS analysis was conducted using approximately 4 mg of wood from biomass and each sample was analyzed in duplicate. A Frontier PY2020 unit pyrolyzed samples at 500°C for 30 s in 80 µL deactivated stainless steel cups. An Extrel Super-Sonic MBMS Model Max 1000 was used to collect mass spectral data fromm/z30 to 450 at 17 eV and processed using Merlin Automation software (V3). Spectral ion intensities were normalized to the total ion chromatogram signal for each sample for analysis of spectral variance. Lignin content (wt %) was estimated based on relative responses from standards of known Klason lignin content using mean-normalized ion intensities ofm/z120, 124 (G), 137 (G), 138 (G), 150 (G), 152, 154 (S), 164 (G), 167 (S), 168 (S), 178 (G), 180, 181, 182 (S), 194 (S), 208 (S) and 210 (S) where G indicates guaiacyl-derived ions, S indicates syringyl-derived ions, and other ions either derive from other lignin monomers or multiple sources. Ratios of S and G lignin monomer units (S/G) were obtained by dividing the sum of S-based ions by the sum of G-based ions using mean-normalized ion intensities.

CBI↗

SSTDR and FDR Detection of Un-Energized and Energized Cable Anomalies Including Thermal Degradation Using Machine Learning

Historically, cables are initially qualified for nuclear power plant use for 40 years. As plants extend their operating license to 60 and 80 years, continued use of these cables must shift to a performance-based approach since it is cost prohibitive to completely replace cables that are likely still capable of performing their design function. A variety of cable tests are available and are commonly applied during outages when the cables can be taken out of service. Frequency domain reflectometry (FDR) is one of these test methods that is being more broadly accepted and used because it not only detects anomalies along the cable with a low-voltage signal that does not stress the cable insulation, but the technique also locates the anomalies. This supports follow-up local inspection and local repair or partial replacement of a damaged cable segment. Currently, FDR testing is only applied to cables that are taken out of service since the test instrument would be damaged by operational voltages. A related technology that has found some acceptance in the aircraft and rail industry is spread spectrum time domain reflectometry (SSTDR). This technology has been implemented with a custom commercial instrument by LiveWire Innovation that is designed to operate on live cables up to 1000 volts and with a bandwidth of 48 MHz. Initial evaluation by the Pacific Northwest National Laboratory (PNNL) of the Live Wire system indicated that a broader bandwidth (BW) SSTDR may be better for many kinds of flaws. This led PNNL to develop an SSTDR laboratory instrument suitable for tests up to 500 MHz bandwidth. Testing on energized cables is also desirable for online monitoring systems so an inductive clamshell coupler was developed that allows energized cables to be tested up to at least 5 kV and likely higher voltage levels. Dielectric spectroscopy and tan delta testing plus various laboratory destructive tests were included in this data acquisition campaign directed to feed a machine learning (ML) study. With these kinds of developments, online energized cable tests may be possible with industrial adoption of such hardware advances but it will be completely impractical to have highly skilled data analysts continually examine these complex signals for indications of damage or compromised conditions. If online testing is to be implemented in new test hardware, it must be accompanied by software that can interpret the signals and alert plant operators of changing or degraded conditions. The thermally aged, shielded cable investigated here was separately treated for ML analysis. Visual analysis of electrical data showed generally increasing peaks where the cable entered and exited the oven. These peaks were not exactly aligned with expected locations, but these differences were attributed to velocity of propagation calibration errors. Only supervised ML was applied to the thermally aged data as this data was only available shortly before the committed publication date of this report. The supervised ML was structured to divide the 0 to 70-day responses as ‘normal’ from 0 to 35 days or ‘anomalous’ from 36 to 70 days, based on cable tensile elongation at break (EAB) insulation characterization. Using 80% of the data for training and 20% for testing, the supervised ML predicted normal versus anomalous was 70% accurate. Important conclusions include: • Accuracy to predict the presence of cable damage is improved from the 2023 effort by more training data. Weighted accuracies for comparisons among the instruments ranged from 67 to 89 % for unsupervised ML and 71 to 99% for supervised ML. • Based on the synthetic data tests, the unsupervised models are more generalizable to unseen anomalies. The Multi-Layer Perceptron classifier (MLP) model reported as high as 99.7% accuracy on the test data, but this dropped to 58.3% when tested on the synthetic data. In contrast, the unsupervised Pointwise model only achieved 89.7% accuracy on the experimental data but reported 78.3% accuracy on the synthetic data. • The best anomaly indicators are higher frequency (400 MHz BW) FDR data. Other tests may be interesting but for this study, this was the best predicter.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Drilling Down I/O Bottlenecks with Cross-layer I/O Profile Exploration

I/O performance monitoring tools such as Darshan and Recorder collect I/O-related metrics on production systems and help understand the applications' behavior. However, some gaps prevent end-users from seeing the whole picture when it comes to detecting and drilling down to the root causes of I/O performance slowdowns and where those problems originate. These gaps arise from limitations in the available metrics, their collection strategy, and the lack of translation to actionable items that could advise on optimizations. This paper highlights such gaps and proposes solutions to drill down to the source code level to pinpoint the root causes of I/O bottlenecks scientific applications face by relying on cross-layer analysis combining multiple performance metrics related to I/O software layers. We demonstrate with two real applications how metrics collected in high-level libraries (which are closer to the data models used by an application), enhanced by source-code insights and natural language translations, can help streamline the understanding of I/O behavior and provide guidance to end-users, developers, and supercomputing facilities on how to improve I/O performance. Using this cross-layer analysis and the heuristic recommendations, we attained up to 6.9× speedup from run-as-is executions.

Ather, Hammad↗

Empirical Validation of UBEM: An Assessment of Bias in Urban Building Energy Modeling for Chicago

Residential and commercial buildings currently account for 30% of total global final energy consumption. Urban-scale building energy modeling (UBEM) can enable scalable investments and unlock building improvements by quantifying energy, demand, emissions, and cost reductions of specific measures or packages for building-specific technologies in large geographic regions. While the sophistication of UBEM data sources and technologies have increased dramatically in the past decade, there remains a knowledge gap for empirical validation and sources of bias between building-specific energy models and measured data at varying geographic scales.As UBEM continues to develop, systemic analysis of accuracy, bias, and limitations of the resulting models is necessary to inform best practices and move toward standardization. These are characterized for the Automatic Building Energy Modeling (AutoBEM) software suite with an initial case study involving metered electricity consumption data from 247,188 buildings in Chicago, Illinois, USA - averaged across years 2019-2021 - compared to the following datasets: (1) the AutoBEM-generated nation-scale Model America version 2 (MAv2) data for 596,064 buildings, (2) tax assessor data for 579,829 buildings, (3) tax assessor data filled with MAv2, and (4) 102 representative dynamic archetypes. The accuracy is reported for every building type and vintage combination, along with multiple sources of bias for unique building descriptors. The AutoBEM simulation workflow produced energy consumption estimates that closely match aggregated metered electricity consumption data for different types of buildings constructed during various time periods at the city scale - with initial normalized mean bias error of 10.9%, and 1.1% after removing outliers. Contribution of statistically significant factors including building type, land use, age, and size to variance in UBEM bias is quantified.

Garg, Ankur↗

Vulnerabilities in Artificial Intelligence and Machine Learning Applications and Data

Artificial intelligence (AI) applications driven by machine learning (ML) are transformational technologies within the international nuclear security regime. Advancements realized by AI—faster and improved data insights, more efficient and automated processes, reductions in human error—enable nuclear security applications such as behavior analysis for insider threat mitigation, source tracking of stolen nuclear material, and facial recognition software for physical protection. In addition to the advantages, however, there are also inherent vulnerabilities and threats associated with its use and risk mitigations must be built into any AI/ML-enabled systems. This work provides a background on AI and ML and different data types used in the field, including open-source intelligence information (OSINT) that is discoverable by AI tools and application data that are used by AI tools for decision-making and automation. Current and potential AI applications and vulnerabilities related to their use within the nuclear security regime are also discussed.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗