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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The 3D magnetic topology and plasma dynamics in open stochastic magnetic field lines

We report the thermal quench triggered by locked modes is known to be mainly due to open stochastic magnetic field lines connected to the wall boundary. It is essential to understand the 3D structure of open stochastic field lines since it determines the overall plasma dynamics in the system. In this study, we analyze the 3D magnetic topology for two key concepts, the connection length L c and the effective magnetic mirror ratio M eff , and present a comprehensive picture of electron and ion dynamics related to the magnetic topology. The connection length determines the 3D structure of the ambipolar potential, and a sharp potential drop across distinct L c regions induces the E × B transport and mixing across the field line. The confinement of electrons and ions along the field line is determined by the ambipolar potential and [Formula: see text] configuration. Electron and ion temperatures in magnetic hills (M eff < 1) are lower than in magnetic wells (M eff > 1) because particles in magnetic hills are more likely to escape toward the wall boundary along the field line. The mixing between the magnetic wells and hills by E × B and magnetic drift motions results in collisionless detrapping of electrons and ions, which reduces their temperature efficiently. Numerical simulations of two different magnetic configurations demonstrate the importance of the collisionless detrapping mechanism, which could be the main cause of plasma temperature drop during the thermal quench.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Protection of the Queuosine Biosynthesis Enzyme QueF from Irreversible Oxidation by a Conserved Intramolecular Disulfide

QueF enzymes catalyze the nicotinamide adenine dinucleotide phosphate (NADPH)‐dependent reduction of the nitrile group of 7‐cyano‐7‐deazaguanine (preQ 0 ) to 7‐aminomethyl‐7‐deazaguanine (preQ 1 ) in the biosynthetic pathway to the tRNA modified nucleoside queuosine. The QueF‐catalyzed reaction involves the formation of a covalent thioimide intermediate with a conserved active site cysteine (Cys55) that is prone to oxidation in vivo under different conditions. Here, we report the crystal structure of a mutant of Bacillus subtilis QueF, which reveals an unanticipated intramolecular disulfide bond formed between the catalytically active Cys55 and a conserved Cys99 located near the active site. When compared to the substrate‐bound structure, this structure is more symmetric and exhibits major rearrangement of the loops responsible for substrate binding. It has been demonstrated that the disulfide does not play a catalytic role because mutation of Cys99 to Ala/Ser does not compromise enzyme activity. Inactivation of the wild‐type enzyme via peroxidation is reversible with thioredoxin, while such inactivation of the Cys99Ala/Ser mutants is irreversible. This is consistent with protection of Cys55 from irreversible oxidation by disulfide formation with Cys99. Conservation of the cysteine pair, and the reported in vivo interaction of QueF with the thioredoxin‐like hydroperoxide reductase AhpC in Escherichia coli suggest that regulation by the thioredoxin disulfide‐thiol exchange system may constitute a general protective mechanism of QueF from oxidative stress in vivo. Docking of QueF onto this enzyme complex sheds structural light on the mechanism of redox control and may inform future mutagenesis experiments. Support or Funding Information This project was supported by National Science Foundation grant CHE‐1309323 to D. Iwata‐Reuyl and M.A. Swairjo, National Institutes of Health (NIH) grant GM110588 to M.A. Swairjo and D. Iwata‐Reuyl, and NIH grant GM70641 to D. Iwata‐Reuyl. Use of the Stanford Synchrotron Radiation Lightsource (SSRL), Stanford Linear Accelerator Center National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE‐AC02‐76SF00515. The SSRL Structural Molecular Biology Program is supported by the Department of Energy Office of Biological and Environmental Research, by the NIH, and the National Institute of General Medical Sciences (NIGMS) (including grant P41GM103393). This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Mohammad, Adeba↗
DOE OSTI2016

Data catalog project—A browsable, searchable, metadata system

Modern experiments are typically conducted by large, extended groups, where researchers rely on other team members to produce much of the data they use. The experiments record very large numbers of measurements that can be difficult for users to find, access and understand. Here. we are developing a system for users to annotate their data products with structured metadata, providing data consumers with a discoverable, browsable data index. Machine understandable metadata captures the underlying semantics of the recorded data, which can then be consumed by both programs, and interactively by users. Collaborators can use these metadata to select and understand recorded measurements. The data catalog project is a data dictionary and index which enables users to record general descriptive metadata, use cases and rendering information as well as providing them a transparent data access mechanism (URI). Users describe their diagnostic including references, text descriptions, units, labels, example data instances, author contact information and data access URIs. The list of possible attribute labels is extensible, but limiting the vocabulary of names increases the utility of the system. The data catalog is focused on the data products and complements process-based systems like the Metadata Ontology Provenance project [Greenwald, 2012; Schissel, 2015]. This system can be coupled with MDSplus to provide a simple platform for data driven display and analysis programs. Sites which use MDSplus can describe tree branches, and if desired create ‘processed data trees’ with homogeneous node structures for measurements. Sites not currently using MDSplus can either use the database to reference local data stores, or construct an MDSplus tree whose leaves reference the local data store. A data catalog system can provide a useful roadmap of data acquired from experiments or simulations making it easier for researchers to find and access important data and understand the meaning of the data and how it was obtained. This is particularly useful in research facilities that study the results of many different experiments or simulations and may not know the intricacies of the data organization in use where the data was generated. It is also possible to store a local copy of key data items in local MDSplus trees and then add processed data to the local catalog.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Author Correction: An autonomous laboratory for the accelerated synthesis of inorganic materials

Following publication of this article, concerns were raised about the unambiguous identification of the compound structures using diffraction as well as the original claims of material novelty. We acknowledge that the original claims of material novelty were subject to misinterpretation—their intention was to indicate that the materials were new to the prediction platform, not necessarily new to science. The article text has been updated to reflect this in the HTML and PDF versions of the article.

Szymanski, Nathan J. [University of California, Be↗
DOE OSTI2021

Helical versus collinear antiferromagnetic order tuned by magnetic anisotropy in polar and chiral (Ni,Mn) 3 TeO 6

In this work, polar and chiral Ni 3 TeO 6 was found to exhibit a colossal magnetoelectric (ME) effect associated with collinear antiferromagnetic order. We have investigated the evolution of its magnetic state with the substitution of the Ni 2+ spins by isotropic Mn 2+ spins, namely (Ni, Mn) 3 TeO 6 (NMTO). The ground state of NMTO maintains an Ising nature, but a new phase with XY-type magnetic anisotropy is discovered at an intermediate temperature range. Neutron powder diffraction experiments reveal that (1) Mn ions tend to occupy a specific transition-metal site, consistent with the first-principle calculation, and (2) the intermediate phase is an incommensurate (IC) helical magnetic state propagating along the $\textit{c}$ axis with $\vec q_{\text{IC}}$ = (0, 0, 1.5 ± δ). We also found that the balance between these two magnetic states can be readily manipulated with magnetic fields, which results in significant ME effects. This selective site occupancy of NMTO allows for a unique competition between collinear and helical magnetic structures with minimal chemical disorder. Thus, NMTO serves as a model system to study site-specific chemical control of noncollinear magnetism and ME coupling.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Higher spin partition functions via the quasinormal mode method in de Sitter quantum gravity

In this note we compute the 1-loop partition function of spin- s s fields on Euclidean de Sitter space S^{2n+1} S 2 n + 1 using the quasinormal mode method. Instead of computing the quasinormal mode frequencies from scratch, we use the analytic continuation prescription L_{\text{AdS}}\to iL_{\text{dS}} L AdS → i L dS , appearing in the dS/CFT correspondence, and Wick rotate the normal mode frequencies of fields on thermal \text{AdS}_{2n+1} AdS 2 n + 1 into the quasinormal mode frequencies of fields on de Sitter space. We compare the quasinormal mode and heat kernel methods of calculating 1-loop determinants, finding exact agreement, and furthermore explicitly relate these methods via a sum over the conformal dimension. We discuss how the Wick rotation of normal modes on thermal \text{AdS}_{2n+1} AdS 2 n + 1 can be generalized to calculating 1-loop partition functions on the thermal spherical quotients S^{2n+1}/\mathbb{Z}_{p} S 2 n + 1 / ℤ p . We further show that the quasinormal mode frequencies encode the group theoretic structure of the spherical spacetimes in question, analogous to the analysis made for thermal AdS in [1-3] .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Structure-property correlations and scaling in the magnetic and magnetocaloric properties of GdCrO 3 particles

The structure, magnetic, and magnetocaloric (MC) properties of orthorhombic nanocrystalline GdCrO 3 with six particle sizes: < d > = 87, 103, 145, 224, 318, and 352 nm are reported. The particle size was tailored by annealing under different temperatures and estimated by scanning electron microscopy. With increase in < d >, Goldschmidt tolerance factor t, orthorhombic strain s, and out-of-plane Cr–O 1 –Cr bond angle first decrease, reaching minimum values for < d > = 224 nm, and then increase for sample with < d > = 318 nm and 352 nm, thus showing a V-shaped variation. Temperature dependence of the magnetization (M) reveals an antiferromagnetic transition at ${T}_{\text{N}}^{\text{Cr}}\sim 168$ K for < d > ≥ 224 nm and ${T}_{\text{N}}^{\text{Cr}}\sim 167$ K for < d > < 224 nm and an essentially d-independent spin-reorientation at T SR = 9 K. M measured at 5 K and 7 T first increases with increase in < d >, reaching maximum value for sample with < d > = 224 nm, and then decreases for samples with < d > = 318 nm and 352 nm, showing an inverted-V variation with < d >. Similar < d >-dependence is observed for the magnetic entropy change (MEC) and relative cooling power (RCP) showing a close relationship between the structural and magnetic properties of GdCrO 3 nanoparticles investigated here. The 224 nm sample with the minimum values of t, s, and Cr–O 1 –Cr bond angle exhibits the maximum value of MEC (–ΔS) = 37.8 J kg –1 K –1 at 5 K under a field variation (ΔH) of 7 T and its large estimated RCP of 623.6 J Kg –1 is comparable with those of typical MC materials. Both (–ΔS) and RCP are shown to scale with the saturation magnetization MS, suggesting that MS is the crucial factor controlling their magnitudes. Assuming (–ΔS) ~ (ΔH) n , the temperature dependence of n for the six samples are determined, n varying between 1.3 at 5 K to n = 2.2 at 130 K in line with its expected magnitudes based on mean-field theory. Furthermore, these results on structure-property correlations and scaling in GdCrO 3 suggest that its MC properties are tunable for potential low-temperature magnetic refrigeration applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Nuclear Data Sheets for A=100

Here, evaluated experimental data are presented for 15 known nuclides of mass 100 (Kr, Rb, Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn). Recommended values are given for level parameters, γ and β radiations, and other spectroscopic information. No excited states are known in 100 Rb and 100 Sn. Except for isotopic identification, no information is available for the decay of the 100 Kr isotope, and limited information is known about the decay properties of the 100 Sn isotope. According to Fig. 2 (A/Q versus counts plot) and as mentioned in the text in 2021Su01, 100 Br isotope was not observed, although, discovery of 101 Br was claimed in this work. In the case of 100 Pd, the agreement in the orderings of the γ-ray cascades and γ-ray inventory between various studies of high-spin structures remains poor at high excitation energies (>9 MeV). For 100 Y, the assignments of the two previously known half-lives to the respective states (g.s. and the 145-keV isomer) remain to be established. Here, this work supersedes earlier full evaluations of A=100 by 2008Si01, 1997Si09, 1990Si05 and 1974Ko37.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1976

A systematic approach to advanced cockpit warning systems for air transport operations: Line pilot preferences

Line pilots (fifty captains, first officers, and flight engineers) from 8 different airlines were administered a structured questionnaire relating to future warning system design and solutions to current warning system problems. This was followed by a semantic differential to obtain a factor analysis of 18 different cockpit warning signals on scales such as informative/distracting, annoying/soothing. Half the pilots received a demonstration of the experimental text and voice synthesizer warning systems before answering the questionnaire and the semantic differential. A control group answered the questionnaire and the semantic differential first, thus providing a check for the stability of pilot preferences with and without actual exposure to experimental systems. Generally, the preference data obtained revealed much consistency and strong agreement among line pilots concerning advance cockpit warning system design.

Williams, D. H.↗
NASA NTRS1989

Isolating contour information from arbitrary images

Aspects of natural vision (physiological and perceptual) serve as a basis for attempting the development of a general processing scheme for contour extraction. Contour information is assumed to be central to visual recognition skills. While the scheme must be regarded as highly preliminary, initial results do compare favorably with the visual perception of structure. The scheme pays special attention to the construction of a smallest scale circular difference-of-Gaussian (DOG) convolution, calibration of multiscale edge detection thresholds with the visual perception of grayscale boundaries, and contour/texture discrimination methods derived from fundamental assumptions of connectivity and the characteristics of printed text. Contour information is required to fall between a minimum connectivity limit and maximum regional spatial density limit at each scale. Results support the idea that contour information, in images possessing good image quality, is (centered at about 10 cyc/deg and 30 cyc/deg). Further, lower spatial frequency channels appear to play a major role only in contour extraction from images with serious global image defects.

Jobson, Daniel J.↗
NASA NTRS1993

Collisionless shock structures of Earth and other planets

This report summarizes the closing segment of our multi-spacecraft, multi-instrument study of collisionless shock structure. In this last year of our study, we have necessarily concentrated on subjects that limited time and remaining resources could be expected to bring to reasonable stopping points, if not full conclusions. Our attention has been focused therefore on matters that were either well underway when the year began or that could be expected to yield rapidly completed reports publishable quickly in abbreviated versions. Contemporary publication delays prevent any new initiatives from reaching the literature within the year in the best of circumstances. The topics that fell into these categories were detailed plasma wave (pw) phenomenology in slow shocks in the Earth's distant geomagnetic tail, instantaneous orientations of theta(sub Bn) in quasiparallel (Q(sub parallel)) shock structure, and a comprehensive overview of the relationship between structural ULF waves in the Qll shock environment and waves in the magnetosphere, i.e. geomagnetic ULF pulsations. The remainder of this report describes our freshly completed results, discusses two related investigations of pw waves in the foreshock and magnetosheath, and appends the abstracts of published papers and the texts of papers in press.

Greenstadt, Eugene W.↗
DOE OSTI2025

Informing Plant Asset Reliability and Availability Through AI-Driven Analysis of Operator Logs

The availability and reliability of nuclear power plant (NPP) structures, systems, and components (SSCs) are critical parameters for NPP safety. Tracking these parameters is necessary but costly and labor-intensive, requiring the collection and evaluation of SSC event data such as shutdowns, startups, and failures. To show how these events are needed for the parameters an example is given: one measure of reliability is based on the number of equipment failure events and the number of run hours (i.e., the time from a startup event to a shutdown event). Here, this work investigates using artificial intelligence (AI) to mine NPP operator log entry texts for SSC event data. Four AI approaches were explored for identifying these events, including natural language processing (NLP) methods, generative AI, generative AI combined with NLP, and topic modeling. A key challenge addressed with all four approaches is the brevity of operator log entries. Among these four a neural network–based NLP method was shown to be the most promising for this application, achieving F1 scores of 86.0% for shutdowns, 92.2% for startups, and 80.4% for failures on a subject-matter-expert-curated dataset from NPP operator logs, compared to a baseline of 66.6% for a random classifier. This shows that NLP methods can perform better than generative AI. Additionally, the NLP methods combined with generative AI were shown to perform better than generative AI alone. Generative AI was most successful at providing the background information for the NLP methods to use. This work demonstrates the potential to use AI to automate parameter collection from NPP operator log entries and other records.

97 - MATHEMATICS AND COMPUTING↗
NASA NTRS2004

Geographic Information Systems and Web Page Development

The Facilities Engineering and Architectural Branch is responsible for the design and maintenance of buildings, laboratories, and civil structures. In order to improve efficiency and quality, the FEAB has dedicated itself to establishing a data infrastructure based on Geographic Information Systems, GIs. The value of GIS was explained in an article dating back to 1980 entitled "Need for a Multipurpose Cadastre which stated, "There is a critical need for a better land-information system in the United States to improve land-conveyance procedures, furnish a basis for equitable taxation, and provide much-needed information for resource management and environmental planning." Scientists and engineers both point to GIS as the solution. What is GIS? According to most text books, Geographic Information Systems is a class of software that stores, manages, and analyzes mapable features on, above, or below the surface of the earth. GIS software is basically database management software to the management of spatial data and information. Simply put, Geographic Information Systems manage, analyze, chart, graph, and map spatial information. At the outset, I was given goals and expectations from my branch and from my mentor with regards to the further implementation of GIs. Those goals are as follows: (1) Continue the development of GIS for the underground structures. (2) Extract and export annotated data from AutoCAD drawing files and construct a database (to serve as a prototype for future work). (3) Examine existing underground record drawings to determine existing and non-existing underground tanks. Once this data was collected and analyzed, I set out on the task of creating a user-friendly database that could be assessed by all members of the branch. It was important that the database be built using programs that most employees already possess, ruling out most AutoCAD-based viewers. Therefore, I set out to create an Access database that translated onto the web using Internet Explorer as the foundation. After some programming, it was possible to view AutoCAD files and other GIS-related applications on Internet Explorer, while providing the user with a variety of editing commands and setting options. I was also given the task of launching a divisional website using Macromedia Flash and other web- development programs.

Reynolds, Justin↗
DOE OSTI2016

A novel procedure on next generation sequencing data analysis using text mining algorithm

Background: Next-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for large scale comparative and evolutional studies to be performed on the large amounts of data derived from NGS projects. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. Methods: We report a novel procedure to analyse NGS data using topic modeling. It consists of four major procedures: NGS data retrieval, preprocessing, topic modeling, and data mining using Latent Dirichlet Allocation (LDA) topic outputs. The NGS data set of the Salmonella enterica strains were used as a case study to show the workflow of this procedure. The perplexity measurement of the topic numbers and the convergence efficiencies of Gibbs sampling were calculated and discussed for achieving the best result from the proposed procedure. Results: The output topics by LDA algorithms could be treated as features of Salmonella strains to accurately describe the genetic diversity of fliC gene in various serotypes. The results of a two-way hierarchical clustering and data matrix analysis on LDA-derived matrices successfully classified Salmonella serotypes based on the NGS data. The implementation of topic modeling in NGS data analysis procedure provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data. Conclusion: The implementation of topic modeling in NGS data analysis provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Pseudonymization at Scale: OLCF’s Summit Usage Data Case Study

The analysis of vast amounts of data and the processing of complex computational jobs have traditionally relied upon high performance computing (HPC) systems, which offer reliable and efficient management of large-scale computational and data resources. Understanding these analyses’ needs is paramount for designing solutions that can lead to better science, and similarly, understanding the characteristics of the user behavior on those systems is important for improving user experiences on HPC systems. A common approach to gathering data about user behavior is to extract workload characteristics from system log data available only to system administrators. Recently at Oak Ridge Leadership Computing Facility (OLCF), however, we unveiled user behavior about the Summit supercomputer by collecting data from a user’s point of view with ordinary Unix commands.In this paper, we discuss the process, challenges, and lessons learned while preparing this dataset for publication and submission to an open data challenge. The original dataset contains personal identifiable information (PII) about the users of OLCF which needed be masked prior to publication, and we determined that anonymization, which scrubs PII completely, destroyed too much of the structure of the data to be interesting for the data challenge. We instead chose to pseudonymize the dataset, which reduced the linkability of the dataset to the users’ identities. Pseudonymization is significantly more computationally expensive than anonymization, and the size of our dataset, which is approximately 175 million lines of raw text, necessitated the development of a parallelized workflow that could be reused on different HPC machines. We demonstrate the scaling behavior of the workflow on two leadership class HPC systems at OLCF, and we show that we were able to bring the overall makespan time from an impractical 20+ hours on a single node down to around 2 hours. As a result of this work, we release the entire pseudonymized dataset and make the workflows and source code publicly available.

Maheshwari, Ketan↗
DOE OSTI2020

Hypergraph Random Walks, Laplacians, and Clustering

We propose a flexible framework for clustering hypergraph-structured data based on recently proposed random walks utilizing edge-dependent vertex weights. When incorporating edge-dependent vertex weights (EDVW), a weight is associated with each vertex-hyperedge pair, yielding a weighted incidence matrix of the hypergraph. Such weightings have been utilized in term-document representations of text data sets. We explain how random walks with EDVW serve to construct different hypergraph Laplacian matrices, and then develop a suite of clustering methods that use these incidence matrices and Laplacians for hypergraph clustering. Using 20Newsgroup, U.S. patent, Reuters' Corpus Volume 1, and genetics data sets, we compare the performance of these clustering algorithms experimentally against a variety of existing hypergraph clustering methods. We show that the proposed methods produce higher-quality clusters.

hypergraphs, clustering, laplacian, random walk, M↗
DOE OSTI2026

First constraints on the nonperturbative gluon Collins-Soper kernel

The gluon Collins-Soper kernel, which encodes the rapidity evolution of transverse-momentum-dependent gluon distributions, is constrained for the first time in the nonperturbative regime, for transverse momentum scales $q_{T} \in [ 300\text{ MeV}, 1.3\text{ GeV}]$. The constraints are determined in lattice QCD at a close-to-physical pion mass $M_π= 172(3)\text{ MeV}$, a single lattice spacing $a=0.15\text{ fm}$, and next-to-next-to-leading logarithmic matching in Large-Momentum Effective Theory. These results represent the first step toward a controlled determination of the gluon Collins-Soper kernel in QCD, with eventual phenomenological import and relevance to present and future experiments sensitive to the gluon structure of hadronic matter.

Avkhadiev, Artur [Argonne; MIT, Cambridge, CTP]↗
DOE OSTI2015

Citing a Data Repository: A Case Study of the Protein Data Bank

The Protein Data Bank (PDB) is the worldwide repository of 3D structures of proteins, nucleic acids and complex assemblies. The PDB’s large corpus of data (> 100,000 structures) and related citations provide a well-organized and extensive test set for developing and understanding data citation and access metrics. In this paper, we present a systematic investigation of how authors cite PDB as a data repository. We describe a novel metric based on information cascade constructed by exploring the citation network to measure influence between competing works and apply that to analyze different data citation practices to PDB. Based on this new metric, we found that the original publication of RCSB PDB in the year 2000 continues to attract most citations though many follow-up updates were published. None of these follow-up publications by members of the wwPDB organization can compete with the original publication in terms of citations and influence. Meanwhile, authors increasingly choose to use URLs of PDB in the text instead of citing PDB papers, leading to disruption of the growth of the literature citations. A comparison of data usage statistics and paper citations shows that PDB Web access is highly correlated with URL mentions in the text. The results reveal the trend of how authors cite a biomedical data repository and may provide useful insight of how to measure the impact of a data repository.

59 BASIC BIOLOGICAL SCIENCES↗