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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 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Additional Capability Being Developed from UNF-ST&DARDS Unified Database: System Analysis and Fuel Cycle Option Analysis

The Used Nuclear Fuel Storage, Transportation & Disposal Analysis Resource and Data System (UNF-ST&DARDS) is being developed for the U.S. Department of Energy’s Office of Nuclear Energy by the national laboratories. An important part of UNF-ST&DARDS is the Unified Database (UDB), which contains information that can support a variety of activities including fuel storage, fuel transportation, and disposal-related system analysis. Currently, the main application of the UDB is to support evaluation of the characteristics of discharged spent nuclear fuel (SNF) from the U.S. commercial reactors. However, because of the extensive amount of data that has been collected and analyzed for UNF-ST&DARDS, there are many more applications that can utilize the UDB including system analysis with the Next-Generation System Analysis Model (NGSAM) and fuel cycle analysis with fuel cycle simulation codes such as ORION. Going forward, NGSAM and fuel cycle transition analysis with ORION integrate UDB data wherever possible in the UDB’s development plan. Finally, these advances in NGSAM and fuel cycle analysis can be used in conjunction with the UDB to help answer more complex questions about the optimization, utilization, storage, and eventual disposal of SNF.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2012

HIGH IONIZATION SPECIES IN THE NEARBY INTERSTELLAR MEDIUM FROM AN EXHAUSTIVE ANALYSIS OF THE IUE INES DATABASE

Main-sequence (MS) and giant late-B and early-A type stars are the best targets for searching for nearby interstellar (IS) Si IV and C IV resonance lines because they are not able to produce them, either in atmospheric layers or in their circumstellar environment, and because many stars of these spectral types are nearby and located in the local interstellar medium (LISM). In addition, the use of certain stars hotter than B6 can lead to misinterpretations (e.g., alpha Arae). This work analyzes the reliable Short-Wavelength Prime high-resolution UV spectra of 558 B6-A9 type stars observed by the International Ultraviolet Explorer at distances lower than 400 pc from the Sun. For the first time, this work utilizes the entire INES database to extract stellar and IS information in a systematic way from homogeneous data. Stars were classified into seven groups: normal (MS and subgiant), giant, peculiar, emission line, Algols, pre-main sequence or Herbig Ae/Be, and shell stars. Only 10 normal stars, located beyond 90 pc, show weak Si IV and C IV absorptions and are clustered around the direction of Sco-Cen, while 85 located closer than 90 pc, as well as another 89 beyond 90 pc, do not show any absorptions at all. We conclude that these highly ionized species originate most probably in the LISM, at 90 pc from the Sun, corresponding to the warm interaction zone (IZ), where the expanding Loop I super-shell and the Local Bubble collide. We base our results on a robust statistical analysis of both spectral types and spatial distributions of the different stellar groups we defined. Our estimated column densities N of both ions are similar to those obtained by other authors for distant stars, suggesting that these absorptions concentrate fundamentally in the IZ. A logarithmic correlation between N and the distance D confirms these results.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

EVOLUTION, NUCLEOSYNTHESIS, AND YIELDS OF LOW-MASS ASYMPTOTIC GIANT BRANCH STARS AT DIFFERENT METALLICITIES. II. THE FRUITY DATABASE

By using updated stellar low-mass stars models, we systematically investigate the nucleosynthesis processes occurring in asymptotic giant branch (AGB) stars. In this paper, we present a database dedicated to the nucleosynthesis of AGB stars: FRANEC Repository of Updated Isotopic Tables and Yields (FRUITY). An interactive Web-based interface allows users to freely download the full (from H to Bi) isotopic composition, as it changes after each third dredge-up (TDU) episode and the stellar yields the models produce. A first set of AGB models, having masses in the range 1.5 {<=}M/M{sub Sun} {<=} 3.0 and metallicities 1 Multiplication-Sign 10{sup -3} {<=} Z {<=} 2 Multiplication-Sign 10{sup -2}, is discussed. For each model, a detailed description of the physical and the chemical evolution is provided. In particular, we illustrate the details of the s-process and we evaluate the theoretical uncertainties due to the parameterization adopted to model convection and mass loss. The resulting nucleosynthesis scenario is checked by comparing the theoretical [hs/ls] and [Pb/hs] ratios to those obtained from the available abundance analysis of s-enhanced stars. On the average, the variation with the metallicity of these spectroscopic indexes is well reproduced by theoretical models, although the predicted spread at a given metallicity is substantially smaller than the observed one. Possible explanations for such a difference are briefly discussed. An independent check of the TDU efficiency is provided by the C-stars luminosity function. Consequently, theoretical C-stars luminosity functions for the Galactic disk and the Magellanic Clouds have been derived. We generally find good agreement with observations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

KAPPA: A PACKAGE FOR SYNTHESIS OF OPTICALLY THIN SPECTRA FOR THE NON-MAXWELLIAN κ-DISTRIBUTIONS BASED ON THE CHIANTI DATABASE

Non-Maxwellian κ-distributions have been detected in the solar transition region and in flares. These distributions are characterized by a high-energy tail and a near-Maxwellian core and are known to have a significant impact on the resulting optically thin spectra arising from collisionally dominated astrophysical plasmas. We developed the KAPPA package for the synthesis of such line and continuum spectra. The package is based on the freely available CHIANTI database and software, and can be used in a similar manner. Ionization and recombination rates together with the ionization equilibria are provided for a range of κ values. Distribution-averaged collision strengths for excitation are obtained using an approximate method for all transitions in all ions available within CHIANTI. The validity of this approximate method is tested through a comparison with direct calculations. Typical precisions of better than 5% are found with all cases being within 10%. Tools for the calculation of synthetic line and continuum intensities are provided and described. Examples of the synthetic spectra and SDO/AIA responses to emission for the κ-distributions are given.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

LAMOST OBSERVATIONS IN THE KEPLER FIELD. I. DATABASE OF LOW-RESOLUTION SPECTRA

The nearly continuous light curves with micromagnitude precision provided by the space mission Kepler are revolutionizing our view of pulsating stars. They have revealed a vast sea of low-amplitude pulsation modes that were undetectable from Earth. The long time base of Kepler light curves allows for the accurate determination of the frequencies and amplitudes of pulsation modes needed for in-depth asteroseismic modeling. However, for an asteroseismic study to be successful, the first estimates of stellar parameters need to be known and they cannot be derived from the Kepler photometry itself. The Kepler Input Catalog provides values for the effective temperature, surface gravity, and metallicity, but not always with sufficient accuracy. Moreover, information on the chemical composition and rotation rate is lacking. We are collecting low-resolution spectra for objects in the Kepler field of view with the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (lamost, Xinglong observatory, China). All of the requested fields have now been observed at least once. In this paper, we describe those observations and provide a useful database for the whole astronomical community.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Long plasma duration operation analyses with an international multi-machine (tokamaks and stellarators) database

Combined high-fusion performance and long-pulse operation is one of the key integration challenges for fusion energy development in magnetic devices. Addressing these challenges requires an integrated vision of physics and engineering aspects with the purpose of simultaneously increasing time duration and fusion performance. Significant progress has been made in tokamaks and stellarators, including very recent achievement in duration and/or performance. This progress is reviewed by analyzing the experimental data (109 plasma pulses with a total of 3200 data points, i.e. on average 29 data per pulse) provided by ten tokamaks (in alphabetical order: Axially Symmetric Divertor Experiment Upgrade, DIII-D, Experimental Advanced Superconducting Tokamak, Joint European Torus, JT-60 Upgrade, Korea Superconducting Tokamak Advanced Research, tokamak à configuration variable, Tokamak Fusion Test Reactor, Tore Supra, W Environment in Steady-State Tokamak) and two stellarators (Large Helical Device and Wendelstein 7-X) expanding the pioneering work of Kikuchi (Kikuchi M. and Azumi M. 2015 Frontiers in Fusion Research II: Introduction to Modern Tokamak Physics (Springer)). Data have been gathered up to January 2022 and coordination has been provided by the recently created International Energy Agency-International Atomic Energy Agency international Coordination on International Challenges on Long duration OPeration group. By exploiting the multi-machine international database, recent progress in terms of injected energies (e.g. 1730 MJ in L-mode, 425 MJ in H-mode), durations (1056 s in L-mode, 101 s in H-mode), injected powers, and sustained performance will be reviewed. Progress has been made to sustain long-pulse operation in tokamaks and stellarators with superconducting coils, actively cooled components, and/or with metallic walls. The graph of the fusion triple products as a function of duration shows a dramatic reduction of, at least two orders of magnitude when increasing the plasma duration from less than 1 s to 100 s. Indeed, long-pulse operation is usually reached in dominant electron-heating modes at reduced density (current drive optimization) but with low ion temperatures ranging from 1 to 3 keV for discharges above 100 s. Difficulties in extending the duration may arise from coupling high heating powers over long durations and the evolving plasma-wall interaction towards an unstable operational domain. Possible causes limiting the duration and critical issues to be addressed prior to ITER operation and DEMO design are reported and analyzed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Security in the CernVM File System and the Frontier Distributed Database Caching System

Both the CernVM File System (CVMFS) and the Frontier Distributed Database Caching System (Frontier) distribute centrally updated data worldwide for LHC experiments using http proxy caches. Neither system provides privacy or access control on reading the data, but both control access to updates of the data and can guarantee the authenticity and integrity of the data transferred to clients over the internet. CVMFS has since its early days required digital signatures and secure hashes on all distributed data, and recently Frontier has added X.509-based authenticity and integrity checking. In this paper we detail and compare the security models of CVMFS and Frontier.

Dykstra, D.↗
DOE OSTI2011

MapReduce Implementation of a Hybrid Spectral Library-Database Search Method for Large-Scale Peptide Identification

A MapReduce-based implementation called MR- MSPolygraph for parallelizing peptide identification from mass spectrometry data is presented. The underlying serial method, MSPolygraph, uses a novel hybrid approach to match an experimental spectrum against a combination of a protein sequence database and a spectral library. Our MapReduce implementation can run on any Hadoop cluster environment. Experimental results demonstrate that, relative to the serial version, MR-MSPolygraph reduces the time to solution from weeks to hours, for processing tens of thousands of experimental spectra. Speedup and other related performance studies are also reported on a 400-core Hadoop cluster using spectral datasets from environmental microbial communities as inputs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species

Major feedstock sources for future biofuel production are likely to be high biomass producing plant species such as poplar, pine, switchgrass, sorghum and maize. One active area of research in these species is genome-enabled improvement of lignocellulosic biofuel feedstock quality and yield. To facilitate genomic-based investigations in these species, we developed the Biofuel Feedstock Genomic Resource (BFGR), a database and web-portal that provides high-quality, uniform and integrated functional annotation of gene and transcript assembly sequences from species of interest to lignocellulosic biofuel feedstock researchers. The BFGR includes sequence data from 54 species and permits researchers to view, analyze and obtain annotation at the gene, transcript, protein and genome level. Annotation of biochemical pathways permits the identification of key genes and transcripts central to the improvement of lignocellulosic properties in these species. The integrated nature of the BFGR in terms of annotation methods, orthologous/paralogous relationships and linkage to seven species with complete genome sequences allows comparative analyses for biofuel feedstock species with limited sequence resources.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9

We report the Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute (DOE-JGI) continues to maintain its role as one of the flagship genomic metadata repositories of the world. The ever-increasing number of projects and metadata are freely available to the user community world-wide. GOLD’s metadata is consumed by scientists and remains an important source for large-scale comparative genomics analysis initiatives. Encouraged by this active user engagement and growth, GOLD has continued to add new components and capabilities. The new features such as a public Application Programming Interface (API) and Ecosystem landing page as well as the growth of different entities in this current GOLD v.9 edition are described in detail in this manuscript.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

PATRIC, the bacterial bioinformatics database and analysis resource

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein– protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

ModBase, a database of annotated comparative protein structure models and associated resources

ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modeller/). ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. ModBase allows users to compute or update comparative models on demand, through an interface to the ModWeb modeling server (http://salilab.org/ modweb). ModBase models are also available through the Protein Model Portal (http://www.prote inmodelportal.org/). Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics (http://salilab.org/ allosmod), the AllosMod-FoXS server for predicting a structural ensemble that fits an SAXS profile (http://salilab.org/allosmod-foxs), the FoXSDock server for protein–protein docking filtered by an SAXS profile (http://salilab.org/foxsdock), the SAXS Merge server for automatic merging of SAXS profiles (http://salilab.org/saxsmerge) and the Pose & Rank server for scoring protein–ligand complexes (http://salilab.org/poseandrank). In this update, we also highlight two applications of ModBase: a PSI:Biology initiative to maximize the structural coverage of the human alpha-helical transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Disease Ontology 2015 update: An expanded and updated database of human diseases for linking biomedical knowledge through disease data

The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years. These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language. In conclusion, this will enable closer collaboration with the Human Phenotype Ontology, EBI's Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DO's current asserted view and multiple inferred views through reasoning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes

Genomic islands are mobile DNAs that are major agents of bacterial and archaeal evolution. Integration into prokaryotic chromosomes usually occurs site-specifically at tRNA or tmRNA gene (together, tDNA) targets, catalyzed by tyrosine integrases. This splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm identifies tDNAs, finds fragments of those tDNAs in the same replicon and removes unlikely candidate islands through a series of filters. A search for islands in 2168 whole prokaryotic genomes produced 3919 candidates. The website Islander (recently moved to http://bioinformatics.sandia.gov/islander/) presents these precisely mapped candidate islands, the gene content and the island sequence. The algorithm further insists that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

FOAM (Functional Ontology Assignments for Metagenomes): A Hidden Markov Model (HMM) database with environmental focus

A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Rice SNP-seek database update: new SNPs, indels, and queries

We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Webservice calls were implemented to access most data. These features enable seamless querying of SNPSeek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org.

59 BASIC BIOLOGICAL SCIENCES↗