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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 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Comparative genomics analysis of Trichoderma reesei strains

Trichoderma reesei is a key fungus for industrial production of lignocellulolytic enzymes. The genome sequences of the Trichoderma reesei hyper-cellulolytic strain RUT-C30 and its parental strain QM6a were compared at the nucleotide level. Approximately 97 % of the 87 genomic sequence scaffolds of T. reesei QM6a (33Mb) were detected to have the correspondent nucleotide in the 182 genome sequence scaffolds of RUT-C30 (32Mb). There are 455 loci within the QM6 sequence not detected in the RUT-C30 sequence. Regions at the termini of QM6a scaffolds as well as 14 small scaffolds do not have corresponding regions in RUT-C30 genomic scaffolds. Seventy-eight protein encoding genes are included within these regions. Mutated nucleotide(s) in 2,371 positions, including short insertion/deletions (indels) were detected in the aligned regions. The predicted protein coding regions of 97 gene models contain mutations, 34 of which were not previously described. Twenty-seven out of 34 newly discovered genes were found to have mutations in the peptide amino acid sequence. This is in addition to 63 genes described in a previous study based on low coverage sequencing of RUT-C30. These newly identified proteins are involved in signal transduction, transcription, RNA processing and modification, post-translational modification according to their annotations. Similar distributions of eukaryotic orthologous group (KOG) categories between the mutated and all other proteins suggest random mutation. The roles of the mutated genes and potential regulatory regions in the observed phenotype of RUT-C30 remain to be explored in a targeted fashion.

Trichoderma, genomics, biofuels, enzymes, cellulas↗
NASA NTRS2003

Effects of Two-Pulse Sequencing on Characteristics of Elementary Propellants for Ablative Laser Propulsion

This work continues on previous investigations of elementary propellants for Ablative Laser Propulsion (ALP). This paper details the experimental methods used for alignment of a non-colinear temporal pulse splitting apparatus. Spatial coincidence of the separate pulses is established, the pulses are delayed, and first data is reported on this pulse spacing effect on time-of-fight (TOF) measurements. This includes ion velocity and number density measurements, and this data is compared to results from a previous work. Also, first data on the experimental determination of the time required for the laser-induced plasma to become purely reflective to incident pulses is presented.

Thompson, M. Shane↗
DOE OSTI2016

First observation of rotational structures in Re 168

We assigned first rotational sequences to the odd-odd nucleus 168 Re. Coincidence relationships of these structures with rhenium x rays confirm the isotopic assignment, while arguments based on the γ-ray multiplicity (K-fold) distributions observed with the new bands lead to the mass assignment. Configurations for the two bands were determined through analysis of the rotational alignments of the structures and a comparison of the experimental B(M1)/B(E2) ratios with theory. Tentative spin assignments are proposed for the πh 11/2 νi 13/2 band, based on energy level systematics for other known sequences in neighboring odd-odd rhenium nuclei, as well as on systematics seen for the signature inversion feature that is well known in this region. Furthermore, the spin assignment for the πh 11/2 ν(h 9/2 /f 7/2 ) structure provides additional validation of the proposed spins and configurations for isomers in the 176 Au → 172 Ir → 168 Re α-decay chain.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

Accretion disks in the IRAS 23151+5912 region

We present observations of radio continuum emission at 1.3 and 3.6 cm and H{sub 2}O masers toward the high-mass star-forming region IRAS 23151+5912 carried out with the Very Large Array-Expanded Very Large Array (in transition phase) in configuration A. We detected one continuum source at 1.3 cm in the region, but the counterpart of this radio continuum source at 3.6 cm was not detected at a level of 3σ. We also detected 13 water maser spots toward IRAS 23151+5912, which are distributed in three groups aligned along the northeast-southwest direction. Our results suggest that the 1.3 cm emission is consistent with a hypercompact H II region, probably with an embedded zero-age main-sequence star of type B2. In particular, we find that this young star is spatially associated with a maser group, which is tracing a disk-like structure of about 460 AU. We also find that the masers of the second group are probably describing a circumstellar disk of about 86 AU, whose central protostar, still undetected, should have a mass of ∼11 M {sub ☉}. We also suggest that the third water maser group is possibly associated with the SiO outflow and the undetected driving source of the system. Finally, we noted that the 1.3 cm continuum source and the three maser groups are aligned in the northeast-southwest direction, similar to the elongation of the large ionized region, which probably is the result of shock-wave induced star formation on the densest region of the medium.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2000

A Tool for Automatic Data Distribution for CFD Applications on Structured Grids

Development of HPF versions of NPB and ARC3D has shown that HPF provides an efficient, concise way to express parallelism and to organize data traffic. The use of HPF, as noted in the papers, requires an intimate knowledge of the applications and a detailed analysis of data affinity, data movement, and data granularity. To simplify and accelerate the task of developing HPF versions of existing CFD applications we have designed and implemented ADAPT (Automatic Data Alignment and Placement Tool). ADAPT analyzes a CFD application working on a single structured grid and generates HPF TEMPLATE, (RE)DISTRIBUTION, ALIGNMENT, and INDEPENDENT directives. The directives can be generated on the nest level, subroutine level, application level, or on the application interface level. ADAPT annotates an existing CFD FORTRAN application, performing computations on single or multiple grids. On each grid the application is considered as a sequence of operators, each applied to a set of variables defined in a particular grid domain. ADAPT automatically detects implicit operators (i.e., having data dependences) and explicit operators (without data dependences). For parallelization of an explicit operator ADAPT creates a template for the operator domain, aligns arrays used in the operator with the template, distributes the template, and declares the loops over the distributed dimensions as INDEPENDENT. For parallelization of an implicit operator, the distribution of the operator's domain should be consistent with the operator's dependences. Any dependence between sections distributed on different processors would preclude parallelization if the compiler does not have an ability to pipeline computations. If a data distribution is "orthogonal" to the dependences of an implicit operator, then the loop which implements the operator can be declared as INDEPENDENT. ADAPT starts with an analysis of array index expressions of the loop nests. For each pair of arrays referenced in an assignment statement, it generates an arc in the alignment graph and annotates it with an affinity relation. The template, alignment, and distribution directives for a particular loop nest are then derived from a transitive closure of the affinity relation. A compromise of data distributions in different nests and subroutines is achieved by merging annotated alignment graphs for adjacent nests/stibroutine calls in the nest/call graph of the application in the process called distribution lifting. ADAPT has been implemented as a C++ program running in conjunction with a parallelization tool called CAPTools. ADAPT uses the parse tree, interprocedural analysis and application database generated by CAPTools. It also uses the Directed Graph class, initially implemented in p2d2 (parallel debugger oi distributed programs), and some other classes supporting symbolic computations. ADAPT uses data distribution techniques described. ADAPT was tested with ARC3D and the FT benchmark and has demonstrated a code performance within a factor of 1.5 of handwritten versions.

Frumkin, Michael↗
NASA NTRS2007

CEV Trajectory Design Considerations for Lunar Missions

The Crew Exploration Vehicle (CEV) translational maneuver Delta-V budget must support both the successful completion of a nominal lunar mission and an "anytime" emergency crew return with the potential for much more demanding orbital maneuvers. This translational Delta-V budget accounts for Earth-based LEO rendezvous with the lunar surface access module (LSAM)/Earth departure stage (EDS) stack, orbit maintenance during the lunar surface stay, an on-orbit plane change to align the CEV orbit for an in-plane LSAM ascent, and the Moon-to-Earth trans-Earth injection (TEI) maneuver sequence as well as post-TEI TCMs. Additionally, the CEV will have to execute TEI maneuver sequences while observing Earth atmospheric entry interface objectives for lunar high-latitude to equatorial sortie missions as well as near-polar sortie and long duration missions. The combination of these objectives places a premium on appropriately designed trajectories both to and from the Moon to accurately size the translational V and associated propellant mass in the CEV reference configuration and to demonstrate the feasibility of anytime Earth return for all lunar missions. This report examines the design of the primary CEV translational maneuvers (or maneuver sequences) including associated mission design philosophy, associated assumptions, and methodology for lunar sortie missions with up to a 7-day surface stay and with global lunar landing site access as well as for long duration (outpost) missions with up to a 210-day surface stay at or near the polar regions. The analyses presented in this report supports the Constellation Program and CEV project requirement for nominal and anytime abort (early return) by providing for minimum wedge angles, lunar orbit maintenance maneuvers, phasing orbit inclination changes, and lunar departure maneuvers for a CEV supporting an LSAM launch and subsequent CEV TEI to Earth return, anytime during the lunar surface stay.

Condon, Gerald L.↗
DOE OSTI2019

Aftershocks of the 2012 Off-Coast of Sumatra Earthquake Sequence

Aftershocks of the 2012 Off-Coast of Sumatra Earthquake Sequence exhibit a complex and diffuse spatial distribution. The first-order complexity in aftershock distribution is clear and well beyond the influence of typical earthquake location uncertainty. The sequence included rupture of multiple fault segments, spatially separated. We use surface-wave based relative centroid locations to examine whether, at the small scale, the distribution of the aftershocks was influenced by location errors. Surface-wave based relative location has delineated precise oceanic transform fault earthquake locations in multiple regions. However, the relocated aftershocks off the coast of Sumatra seldom align along simple linear trends that are compatible with the corresponding fault strikes as estimated for the GCMT catalog. The relocation of roughly 60 moderate-earthquake epicentroids suggests that the faulting involved in the 2012 earthquake aftershock sequence included strain release along many short fault segments. Statistical analysis and temporal variations of aftershocks show a typical decay of the aftershocks but a relatively low number of aftershocks, as is common for intraplate oceanic earthquakes. Coulomb stress calculations indicate that most of the moderate-magnitude aftershocks are compatible with stress changes predicted by the large-event slip models. Furthermore the patterns in the aftershocks suggest that the formation of the boundary and eventual localization of deformation between the Indian and Australian plate is a complicated process.

2012 Sumatra Earthquake↗
DOE OSTI2014

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

One of the major goals in metagenomics is to identify the organisms present in a microbial community from unannotated shotgun sequencing reads. Taxonomic profiling has valuable applications in biological and medical research, including disease diagnostics. Most currently available approaches do not scale well with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing. Here we introduce FOCUS, an agile composition based approach using non-negative least squares (NNLS) to report the organisms present in metagenomic samples and profile their abundances. FOCUS was tested with simulated and real metagenomes, and the results show that our approach accurately predicts the organisms present in microbial communities. FOCUS was implemented in Python. The source code and web-sever are freely available at http://edwards.sdsu.edu/FOCUS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

IDENTIFICATION OF NICOTINAMIDE MONONUCLEOTIDE DEAMIDASE OF THE BACTERIAL PYRIDINE NUCLEOTIDE CYCLE REVEALS A NOVEL BROADLY CONSERVED AMIDOHYDROLASE FAMILY

The pyridine nucleotide cycle (PNC) is a network of salvage and recycling routes maintaining homeostasis of NAD(P) cofactor pool in the cell. Nicotinamide mononucleotide (NMN) deamidase (EC 3.5.1.42), one of the key enzymes of the bacterial PNC was originally described in Enterobacteria, but the corresponding gene eluded identification for over 30 years. A genomics-based reconstruction of NAD metabolism across hundreds bacterial species suggested that NMN deamidase reaction is the only possible way of nicotinamide salvage in the marine bacterium Shewanella oneidensis. This prediction was verified via purification of native NMN deamidase from S. oneidensis followed by the identification of the respective gene, termed pncC. Enzymatic characterization of the PncC protein, as well as phenotype analysis of deletion mutants, confirmed its proposed biochemical and physiological function in S. oneidensis. Of the three PncC homologs present in E. coli, NMN deamidase activity was confirmed only for the recombinant purified product of the ygaD gene. A comparative analysis at the level of sequence and three dimensional structure, which is available for one of the PncC family member, shows no homology with any previously described amidohydrolases. Multiple alignment analysis of functional and non functional PncC homologs, together with NMN docking experiments, allowed us to tentatively identify the active site area and conserved residues therein. An observed broad phylogenomic distribution of predicted functional PncCs in bacterial kingdom is consistent with a possible role in detoxification of NMN, resulting from NAD utilization by DNA ligase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure of the Core Postfusion Porcine Endogenous Retrovirus Fusion Protein

Retroviral elements from endogenous retroviruses have functions in mammalian physiology. The best-known examples are the envelope proteins that function in placenta development and immune suppression. Porcine endogenous retroviruses (PERVs) are an understudied class of endogenous retroviruses that infect cultured human cells, raising concern regarding porcine xenografts. The PERV envelope glycoprotein has also been proposed as a possible swine syncytin with a role in placental development. Despite the growing interest in PERVs, their envelope glycoproteins remain poorly characterized. Here, we successfully determined the postfusion crystal structure of the PERV core fusion ectodomain. The PERV fusion protein structure reveals a conserved class I viral fusion protein six-helix bundle. Biophysical experiments demonstrated that the thermodynamic stability of the PERV fusion protein secondary structure was the same at physiological and acidic pHs. A conserved surface analysis highlights the high degree of sequence conservation among retroviral fusogens in the chain reversal region that facilitates the large-scale conformational change required for membrane fusion. Further structural alignment of class I viral fusogens revealed a phylogenetic clustering that shows evolution into various lineages that correlate with virus mechanisms of cell entry. Our work indicates that structural dendrograms can be used to qualitatively infer insights into the fusion mechanisms of newly discovered class I viral fusogen structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea

We report that the basidiomycete fungus Coprinopsis cinerea is an important model system for multicellular development. Fruiting bodies of C. cinerea are typical mushrooms, which can be produced synchronously on defined media in the laboratory. To investigate the transcriptome in detail during fruiting body development, high-throughput sequencing (RNA-seq) was performed using cDNA libraries strand-specifically constructed from 13 points (stages/tissues) with two biological replicates. The reads were aligned to 14,245 predicted transcripts, and counted for forward and reverse transcripts. Differentially expressed genes (DEGs) between two adjacent points and between vegetative mycelium and each point were detected by Tag Count Comparison (TCC). To validate RNA-seq data, expression levels of selected genes were compared using RPKM values in RNA-seq data and qRT-PCR data, and DEGs detected in microarray data were examined in MA plots of RNA-seq data by TCC. We discuss events deduced from GO analysis of DEGs. In addition, we uncovered both transcription factor candidates and antisense transcripts that are likely to be involved in developmental regulation for fruiting.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1988

Geology and geochemistry of the Middle Proterozoic Eastern Ghat mobile belt and its comparison with the lower crust of the Southern Peninsular shield

Two prominent rock suites constitute the lithology of the Eastern Ghat mobile belt: (1) the khondalite suite - the metapelites, and (2) the charnockite suite. Later intrusives include ultramafic sequences, anorthosites and granitic gneisses. The chief structural element in the rocks of the Eastern Ghats is a planar fabric (gneissosity), defined by the alignment of platy minerals like flattened quartz, garnet, sillimanite, graphite, etc. The parallelism between the foliation and the lithological layering is related to isoclinal folding. The major structural trend (axial plane foliation trend) observed in the belt is NE-SW. Five major tectonic events have been delineated in the belt. A boundary fault along the western margin of the Eastern Ghats, bordering the low grade terrain has been substantiated by recent gravity and the deep seismic sounding studies. Field evidence shows that the pyroxene granulites (basic granulites) post-date the khondalite suite, but are older than the charnockites as well as the granitic gneisses. Polyphase metamorphism, probably correlatable with different periods of deformation is recorded. The field relations in the Eastern Ghats point to the intense deformation of the terrain, apparently both before, during and after metamorphism.

Rao, M. V. Subba↗
NASA NTRS1999

Automatic Data Distribution for CFD Applications on Structured Grids

Development of HPF versions of NPB and ARC3D showed that HPF has potential to be a high level language for parallelization of CFD applications. The use of HPF requires an intimate knowledge of the applications and a detailed analysis of data affinity, data movement and data granularity. Since HPF hides data movement from the user even with this knowledge it is easy to overlook pieces of the code causing low performance of the application. In order to simplify and accelerate the task of developing HPF versions of existing CFD applications we have designed and partially implemented ADAPT (Automatic Data Distribution and Placement Tool). The ADAPT analyzes a CFD application working on a single structured grid and generates HPF TEMPLATE, (RE)DISTRIBUTION, ALIGNMENT and INDEPENDENT directives. The directives can be generated on the nest level, subroutine level, application level or inter application level. ADAPT is designed to annotate existing CFD FORTRAN application performing computations on single or multiple grids. On each grid the application can considered as a sequence of operators each applied to a set of variables defined in a particular grid domain. The operators can be classified as implicit, having data dependences, and explicit, without data dependences. In order to parallelize an explicit operator it is sufficient to create a template for the domain of the operator, align arrays used in the operator with the template, distribute the template, and declare the loops over the distributed dimensions as INDEPENDENT. In order to parallelize an implicit operator, the distribution of the operator's domain should be consistent with the operator's dependences. Any dependence between sections distributed on different processors would preclude parallelization if compiler does not have an ability to pipeline computations. If a data distribution is "orthogonal" to the dependences of an implicit operator then the loop which implements the operator can be declared as INDEPENDENT.

Frumkin, Michael↗
DOE OSTI2014

Recruiting Human Microbiome Shotgun Data to Site-Specific Reference Genomes

The human body consists of innumerable multifaceted environments that predispose colonization by a number of distinct microbial communities, which play fundamental roles in human health and disease. In addition to community surveys and shotgun metagenomes that seek to explore the composition and diversity of these microbiomes, there are significant efforts to sequence reference microbial genomes from many body sites of healthy adults. To illustrate the utility of reference genomes when studying more complex metagenomes, we present a reference-based analysis of sequence reads generated from 55 shotgun metagenomes, selected from 5 major body sites, including 16 sub-sites. Interestingly, between 13% and 92% (62.3% average) of these shotgun reads were aligned to a then-complete list of 2780 reference genomes, including 1583 references for the human microbiome. However, no reference genome was universally found in all body sites. For any given metagenome, the body site-specific reference genomes, derived from the same body site as the sample, accounted for an average of 58.8% of the mapped reads. While different body sites did differ in abundant genera, proximal or symmetrical body sites were found to be most similar to one another. The extent of variation observed, both between individuals sampled within the same microenvironment, or at the same site within the same individual over time, calls into question comparative studies across individuals even if sampled at the same body site. This study illustrates the high utility of reference genomes and the need for further site-specific reference microbial genome sequencing, even within the already well-sampled human microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

pGraph: Efficient Parallel Construction of Large-Scale Protein Sequence Homology Graphs

Detecting sequence homology between protein sequences is a fundamental problem in computational molecular biology, with a pervasive application in nearly all analyses that aim to structurally and functionally characterize protein molecules. While detecting the homology between two protein sequences is relatively inexpensive, detecting pairwise homology for a large number of protein sequences can become computationally prohibitive for modern inputs, often requiring millions of CPU hours. Yet, there is currently no robust support to parallelize this kernel. In this paper, we identify the key characteristics that make this problemparticularly hard to parallelize, and then propose a new parallel algorithm that is suited for detecting homology on large data sets using distributed memory parallel computers. Our method, called pGraph, is a novel hybrid between the hierarchical multiple-master/worker model and producer-consumer model, and is designed to break the irregularities imposed by alignment computation and work generation. Experimental results show that pGraph achieves linear scaling on a 2,048 processor distributed memory cluster for a wide range of inputs ranging from as small as 20,000 sequences to 2,560,000 sequences. In addition to demonstrating strong scaling, we present an extensive report on the performance of the various system components and related parametric studies.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2023

SCALE depletion capabilities for molten salt reactors and other liquid-fueled systems

Nuclear reactor systems that use fuel dissolved in a liquid have the potential for enhanced safety characteristics, improved fuel-cycle outcomes, and more efficient isotope-production configurations. In these reactor systems, the fueled liquid may simultaneously undergo irradiation, physical and chemical removal processes, and fueling. The modeling and simulation of this transmutation and decay with material additions and removals is an ongoing research area. An accurate simulation tool is critical to the reactor and fuel-cycle design, reactor deployment, and source-term characterization for these advanced reactor systems. The work described herein involved implementing, testing, and applying the capability to perform reactor physics simulations within the Oak Ridge National Laboratory-developed SCALE suite for nuclear systems analyses and design, leveraging much of its pedigree in quality-assurance and reactor-analysis capabilities. The functionalities to simulate irradiation with material feeds and removals had been added in ORIGEN, and the TRITON reactor physics sequence was extended to calculate the total removed material and track external nonirradiated mixtures to estimate separate processing or waste streams. Results from these capabilities align with analytical expectations obtained from ORIGEN for simplified test cases and with expectations for a molten salt reactor application. This implementation, available with the SCALE 6.3 release, provides for a more efficient and accurate material accountability methodology, allowing for the characterization, design, and analysis of the complete isotopic material inventory of advanced liquid-fueled systems for a variety of applications.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Identifying DQ-Domain Admittance Models of a 2.3-MVA Commercial Grid-Following Inverter Via Frequency-Domain and Time-Domain Data

Here, we present two methods to identify the admittance of a 2.3-MVA commercial grid-following inverter through frequency-domain data and time-domain data. In addition to the well-known harmonic injection method to obtain the admittance at frequency points followed by vector fitting, we adopt a step response-based method where the step response data of the converter are collected and their s-domain expressions are obtained. In turn, the s-domain admittance model of the converter is found. The two methods can be used for cross validation. Step responses and frequency-domain responses obtained from the two methods are compared. Results show that the time- domain data-based method leads to an admittance comparable with that from the frequency-domain measurement in the range less than 60 Hz. In addition, two insights are obtained from the frequency-domain admittance measurements. First, when the dq- frame is aligned to the point of common coupling (PCC) voltage, the per unit DQ-domain admittance directly reflects operating conditions. Second, existence of negative-sequence control can be detected via sequence-domain admittances.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2012

Using Comparative Genomics for Inquiry-Based Learning to Dissect Virulence of Escherichia coli O157:H7 and Yersinia pestis

Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of Genomes database. In the second module, students use an alignment of five Yersinia pestis genomes to analyze single-nucleotide polymorphisms of three genes to classify strains into biovar groups. Students are then given sequences of bacterial DNA amplified from the teeth of corpses from the first and second pandemics of the bubonic plague and asked to classify these new samples. Learning-assessment results reveal student improvement in self-efficacy and content knowledge, as well as students' ability to use BLAST to identify genomic islands and conduct analyses of virulence factors from E. coli O157:H7 or Y. pestis. Each of these educational modules offers educators new ready-to-implement resources for integrating comparative genomic topics into their curricula.

59 BASIC BIOLOGICAL SCIENCES↗