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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The Pixel Anomaly Detection Tool : a user-friendly GUI for classifying detector frames using machine-learning approaches

Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining structure-factor amplitudes for serial crystallography or single-particle imaging experiments. Here, a new data-classification tool is reported that offers a variety of machine-learning algorithms to sort data trained either on manual data sorting by the user or by profile fitting the intensity distribution on the detector based on the experiment. This is integrated into an easy-to-use graphical user interface, specifically designed to support the detectors, file formats and software available at most X-ray free electron laser facilities. The highly modular design makes the tool easily expandable to comply with other X-ray sources and detectors, and the supervised learning approach enables even the novice user to sort data containing unwanted artefacts or perform routine data-analysis tasks such as hit finding during an experiment, without needing to write code.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Antiferromagnetic character of the quantum phase transition in the Hubbard model on the honeycomb lattice

In this work we provide a unified, comprehensive treatment of all operators that contribute to the antiferromagnetic, ferromagnetic, and charge-density-wave structure factors and order parameters of the hexagonal Hubbard Model. We use the Hybrid Monte Carlo algorithm to perform a systematic, carefully controlled analysis in the temporal Trotter error and of the thermodynamic limit. We expect our findings to improve the consistency of Monte Carlo determinations of critical exponents. We perform a data collapse analysis and determine the critical exponent β = 0.898 (37) for the semimetal-Mott insulator transition in the hexagonal Hubbard Model. Our methods are applicable to a wide range of lattice theories of strongly correlated electrons.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

An Accelerated Clip Algorithm for Unstructured Meshes: A Batch-Driven Approach

The clip technique is a popular method for visualizing complex structures and phenomena within 3D unstructured meshes. Meshes can be clipped by specifying a scalar isovalue to produce an output unstructured mesh with its external surface as the isovalue. Similar to isocontouring, the clipping process relies on scalar data associated with the mesh points, including scalar data generated by implicit functions such as planes, boxes, and spheres, which facilitates the visualization of results interior to the grid. In this paper, we introduce a novel batch-driven parallel algorithm based on a sequential clip algorithm designed for high-quality results in partial volume extraction. Our algorithm comprises five passes, each progressively processing data to generate the resulting clipped unstructured mesh. The novelty lies in the use of fixed-size batches of points and cells, which enable rapid workload trimming and parallel processing, leading to a significantly improved memory footprint and run-time performance compared to the original version. On a 32-core CPU, the proposed batch-driven parallel algorithm demonstrates a run-time speed-up of up to 32.6x and a memory footprint reduction of up to 4.37x compared to the existing sequential algorithm. The software is currently available under an open-source license in the VTK visualization system.

Tsalikis, Spiros↗
DOE OSTI2020

Finite-Temperature Structures of Supported Subnanometer Catalysts Inferred via Statistical Learning and Genetic Algorithm-Based Optimization

Single-atom catalysts (SACs) minimize noble metal utilization and can alter the activity and selectivity of supported metal nanoparticles. However, the morphology of active centers, including single atoms and subnanometer clusters of a few atoms, remains elusive due to experimental challenges. The computational cost to describe numerous cluster shapes and sizes makes direct first-principles calculations impractical. We present a computational framework to enable structure determination for single-atom and subnanometer cluster catalysts. As a case study, we obtained the low energy structures of Pd n (n = 1-21) clusters supported on CeO 2 (111), which are critical components of automobile three-way catalysts. Trained on density functional theory data, a three-dimensional cluster expansion is established using statistical learning to describe the Hamiltonian and predict energies of supported Pdn clusters of any structure. Low energy stable and metastable structures are identified using a Metropolis Monte Carlo-based genetic algorithm in the canonical ensemble at 300 K. We observe that supported single atoms sinter to form bilayer clusters and large cluster isomers share similarities in both shape and energy, and elucidate the significance of the support and microstructure on cluster stability. We discovered a simple surrogate structure-energy model, where the energy per atom scales with the square root of the average first coordination number, which can be used to estimate energies and compare the stability of clusters. Our framework, applicable to any metal/support system, fills an important methodological gap to predict the stability of supported metal catalysts in the subnanometer regime.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO , a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE . The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Computing Bottleneck Structures at Scale for High-Precision Network Performance Analysis

The Theory of Bottleneck Structures is a recently-developed framework for studying the performance of data networks. It describes how local perturbations in one part of the network propagate and interact with others. This framework is a powerful analytical tool that allows network operators to make accurate predictions about network behavior and thereby optimize performance. Previous work implemented a software package for bottleneck structure analysis, but applied it only to toy examples. In this work, we introduce the first software package capable of scaling bottleneck structure analysis to production-size networks. Here, we benchmark our system using logs from ESnet, the Department of Energy's high-performance data network that connects research institutions in the U.S. Using the previously published tool as a baseline, we demonstrate that our system achieves vastly improved performance, constructing the bottleneck structure graphs in 0.21 s and calculating link derivatives in 0.09 s on average. We also study the asymptotic complexity of our core algorithms, demonstrating good scaling properties and strong agreement with theoretical bounds. These results indicate that our new software package can maintain its fast performance when applied to even larger networks. They also show that our software is efficient enough to analyze rapidly changing networks in real time. Overall, we demonstrate the feasibility of applying bottleneck structure analysis to solve practical problems in large, real-world data networks.

benchmark↗
DOE OSTI2025

The System for Classification of Low-Pressure Systems (SyCLoPS): An All-In-One Objective Framework for Large-Scale Data Sets

We propose the first unified objective framework (SyCLoPS) for detecting and classifying all types of low-pressure systems (LPSs) in a given data set. We use the state-of-the-art automated feature tracking software TempestExtremes (TE) to detect and track LPS features globally in ERA5 and compute 16 parameters from commonly found atmospheric variables for classification. A Python classifier is implemented to classify all LPSs at once. The framework assigns 16 different labels (classes) to each LPS data point and designates four different types of high-impact LPS tracks, including tracks of tropical cyclone (TC), monsoonal system, subtropical storm and polar low. The classification process involves disentangling high-altitude and drier LPSs, differentiating tropical and non-tropical LPSs using novel criteria, and optimizing for the detection of the four types of high-impact LPS. A comparison of our labels with those in the International Best Track Archive for Climate Stewardship (IBTrACS) revealed an overall accuracy of 95% in distinguishing between tropical systems, extratropical cyclones, and disturbances. SyCLoPS produces a better TC detection skill compared to the previous algorithms, highlighted by an approximately 6% reduction in the false alarm rate compared to the previous TE algorithm. The vertical cross section composite of the four types of high-impact LPS we detect each shows distinct structural characteristics. Finally, we demonstrate that SyCLoPS is valuable for investigating various aspects of LPSs in climate data, such as the evolution of a single LPS track, patterns of LPS frequencies, and precipitation or wind influence associated with a particular LPS class.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Mapping nanocrystal orientations via scanning Laue diffraction microscopy for multi-peak Bragg coherent diffraction imaging

The recent commissioning of a movable monochromator at the 34-ID-C endstation of the Advanced Photon Source has vastly simplified the collection of Bragg coherent diffraction imaging (BCDI) data from multiple Bragg peaks of sub-micrometre scale samples. Laue patterns arising from the scattering of a polychromatic beam by arbitrarily oriented nanocrystals permit their crystal orientations to be computed, which are then used for locating and collecting several non-co-linear Bragg reflections. The volumetric six-component strain tensor is then constructed by combining the projected displacement fields that are imaged using each of the measured reflections via iterative phase retrieval algorithms. Complications arise when the sample is heterogeneous in composition and/or when multiple grains of a given lattice structure are simultaneously illuminated by the polychromatic beam. Here, a workflow is established for orienting and mapping nanocrystals on a substrate of a different material using scanning Laue diffraction microscopy. The capabilities of the developed algorithms and procedures with both synthetic and experimental data are demonstrated. The robustness is verified by comparing experimental texture maps obtained with Laue diffraction microscopy at the beamline with maps obtained from electron back-scattering diffraction measurements on the same patch of gold nanocrystals. Such tools provide reliable indexing for both isolated and densely distributed nanocrystals, which are challenging to image in three dimensions with other techniques.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Identifying chemically similar multiphase nanoprecipitates in compositionally complex non-equilibrium oxides via machine learning

Abstract Characterizing oxide nuclear fuels is difficult due to complex fission products, which result from time-evolving system chemistry and extreme operating environments. Here, we report a machine learning-enhanced approach that accelerates the characterization of spent nuclear fuels and improves the accuracy of identifying nanophase fission products and bubbles. We apply this approach to commercial, high-burnup, irradiated light-water reactor fuels, demonstrating relationships between fission product precipitates and gases. We also gain understanding of the fission versus decay pathways of precipitates across the radius of a fuel pellet. An algorithm is provided for quantifying the chemical segregation of the fission products with respect to the high-burnup structure, which enhances our ability to process large amounts of microscopy data, including approaching the atomistic-scale. This may provide a faster route for achieving physics-based fuel performance modeling.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The Pristine survey – XVI. The metallicity of 26 stellar streams around the Milky Way detected with the STREAMFINDER in Gaia EDR3

ABSTRACT We use the photometric metallicities provided by the panoramic Pristine survey to study the veracity and derive the metallicities of the numerous stellar streams found by the application of the STREAMFINDER algorithm to the Gaia Early Data Release 3 data. All 26 streams present in Pristine show a clear metallicity distribution function, which provides an independent check of the reality of these structures, supporting the reliability of STREAMFINDER in finding streams and the power of Pristine to measure precise metallicities. We further present six candidate structures with coherent phase-space and metallicity signals that are very likely streams. The majority of studied streams are very metal-poor (14 structures with [Fe/H] < −2.0) and include three systems with [Fe/H] < −2.9 (C-11, C-19, and C-20). These streams could be the closest debris of low-luminosity dwarf galaxies or may have originated from globular clusters of significantly lower metallicity than any known current Milky Way globular cluster. Our study shows that the promise of the Gaia data for Galactic Archeology studies can be substantially strengthened by quality photometric metallicities, allowing us to peer back into the earliest epochs of the formation of our Galaxy and its stellar halo constituents.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

PDBspheres: a method for finding 3D similarities in local regions in proteins

Abstract We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (‘spheres’) adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. PDBspheres uses the LGA (Local–Global Alignment) structure alignment algorithm as the main engine for detecting structural similarities between the protein of interest and template spheres from the library, which currently contains >2 million spheres. To assess confidence in structural matches, an all-atom-based similarity metric takes side chain placement into account. Here, we describe the PDBspheres method, demonstrate its ability to detect and characterize binding sites in protein structures, show how PDBspheres—a strictly structure-based method—performs on a curated dataset of 2528 ligand-bound and ligand-free crystal structures, and use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of 4876 structures in the ‘refined set’ of the PDBbind 2019 dataset.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Imaging interfacial topography with coherent x-ray reflectivity

The use of coherent x-ray reflectivity to image interfaces is illustrated using model calculations for three cases: a thin film, a semi-infinite substrate, and a coherently strained epitaxial thin film. The intensities and phases of the coherent scattering signals are calculated based on a fully atomistic model (where the phases are assumed to have been recovered by a phasing algorithm). Here, we describe the characteristics of the effective density that are obtained by direct inverse Fourier transformation of the complex structure factors, using a window function to define the data range. These effective densities include significant artifacts like oscillations and negative values derived from the finite vertical momentum transfer of the window function. Two approaches are described to extract the surface topography from the effective densities for three-dimensional visualization: (i) multiplying the effective density by a phase factor and (ii) analyzing the data as a hybrid structure factor F(x, Q z ). The explicit surface sensitivity and specificity of measurements is illustrated when the film or substrate Bragg peaks are excluded. These considerations show that images of interfacial topography can be obtained using currently available experimental capabilities with parameters corresponding to epitaxial thin films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

New approach to QCD final-state evolution in processes with massive partons

We present an algorithm for massive parton evolution which is based on the differentially accurate simulation of soft-gluon radiation by means of a nontrivial azimuthal angle dependence of the splitting functions. The kinematics mapping is chosen such as to reflect the symmetry of the final state in soft-gluon radiation and collinear splitting processes. We compute the counterterms needed for a fully differential next-to-leading order matching and discuss the analytic structure of the parton shower in the next-to-leading logarithmic limit. We implement the new algorithm in the numerical code Alaric and present a first comparison to experimental data. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Sequential Inference of Hospitalization Electronic Health Records Using Probabilistic Models

In the dynamic hospital setting, decision support can be a valuable tool for improving patient outcomes. Data-driven inference of future outcomes is challenging in this dynamic setting, where long sequences such as laboratory tests and medications are updated frequently. This is due in part to heterogeneity of data types and mixed-sequence types contained in variable length sequences. In this work we design a probabilistic unsupervised model for multiple arbitrary-length sequences contained in hospitalization Electronic Health Record (EHR) data. The model uses a latent variable structure and captures complex relationships between medications, diagnoses, laboratory tests, neurological assessments, and medications. It can be trained on original data, without requiring any lossy transformations or time binning. Inference algorithms are derived that use partial data to infer properties of the complete sequences, including their length and presence of specific values. We train this model on data from subjects receiving medical care in the Kaiser Permanente Northern California integrated healthcare delivery system. The results are evaluated against held-out data for predicting the length of sequences and presence of Intensive Care Unit (ICU) in hospitalization bed sequences. Our method outperforms a baseline approach, showing that in these experiments the trained model captures information in the sequences that is informative of their future values.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination

To understand the dynamic structure–function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Robust clustering of the local Milky Way stellar kinematic substructures with Gaia eDR3

Understanding local stellar kinematic substructures in the solar neighbourhood helps build a complete picture of the formation of the Milky Way, as well as an empirical phase space distribution of dark matter that would inform detection experiments. We apply the clustering algorithm HDBSCAN on the Gaia early third data release to identify a list of stable clusters in velocity space and action-angle space by taking into account the measurement uncertainties and studying the stability of the clustering results. We find 1405 (497) stars in 23 (6) robust clusters in velocity space (action-angle space) that are consistently not associated with noise. We discuss the kinematic properties of these structures and study whether many of the small clusters belong to a similar larger cluster based on their chemical abundances. They are attributed to the known structures: the Gaia Sausage-Enceladus, the Helmi Stream, and globular cluster NGC 3201 are found in both spaces, while NGC 104 and the thick disc (Sequoia) are identified in velocity space (action-angle space). Although we do not identify any new structures, we find that the HDBSCAN member selection of already known structures is unstable to input kinematics of the stars when resampled within their uncertainties. We therefore present the stable subset of local kinematic structures, which are consistently identified by the clustering algorithm, and emphasize the need to take into account error propagation during both the manual and automated identification of stellar structures, both for existing ones as well as future discoveries.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Physics in the Machine: Integrating Physical Knowledge in Autonomous Phase-Mapping

Application of artificial intelligence (AI), and more specifically machine learning, to the physical sciences has expanded significantly over the past decades. In particular, science-informed AI, also known as scientific AI or inductive bias AI, has grown from a focus on data analysis to now controlling experiment design, simulation, execution and analysis in closed-loop autonomous systems. The CAMEO (closed-loop autonomous materials exploration and optimization) algorithm employs scientific AI to address two tasks: learning a material system’s composition-structure relationship and identifying materials compositions with optimal functional properties. By integrating these, accelerated materials screening across compositional phase diagrams was demonstrated, resulting in the discovery of a best-in-class phase change memory material. Key to this success is the ability to guide subsequent measurements to maximize knowledge of the composition-structure relationship, or phase map. In this work we investigate the benefits of incorporating varying levels of prior physical knowledge into CAMEO’s autonomous phase-mapping. This includes the use of ab-initio phase boundary data from the AFLOW repositories, which has been shown to optimize CAMEO’s search when used as a prior.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

GraphAlign: Graph-Enabled Machine Learning for Seismic Event Filtering

This report summarizes results from a 2 year effort to improve the current automated seismic event processing system by leveraging machine learning models that can operated over the inherent graph data structure of a seismic sensor network. Specifically, the GraphAlign project seeks to utilize prior information on which stations are more likely to detect signals originating from particular geographic regions to inform event filtering. To date, the GraphAlign team has developed a Graphical Neural Network (GNN) model to filter out false events generated by the Global Associator (GA) algorithm. The algorithm operates directly on waveform data that has been associated to an event by building a variable sized graph of station waveforms nodes with edge relations to an event location node. This builds off of previous work where random forest models were used to do the same task using hand crafted features. The GNN model performance was analyzed using an 8 week IMS/IDC dataset, and it was demonstrated that the GNN outperforms the random forest baseline. We provide additional error analysis of which events the GNN model performs well and poorly against concluded by future directions for improvements.

58 GEOSCIENCES↗