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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 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response

Rhodopseudomonas palustris encodes 16 extracytoplasmic function (ECF) σ factors. In this paper, to begin to investigate the regulatory network of one of these ECF σ factors, the whole proteome of R. palustris CGA010 was quantitatively analyzed by tandem mass spectrometry from cultures episomally expressing the ECF σ RPA4225 (ecfT) versus a WT control. Among the proteins with the greatest increase in abundance were catalase KatE, trehalose synthase, a DPS-like protein, and several regulatory proteins. Alignment of the cognate promoter regions driving expression of several upregulated proteins suggested a conserved binding motif in the -35 and -10 regions with the consensus sequence GGAAC-18N-TT. Additionally, the putative anti-σ factor RPA4224, whose gene is contained in the same predicted operon as RPA4225, was identified as interacting directly with the predicted response regulator RPA4223 by mass spectrometry of affinity-isolated protein complexes. Furthermore, another gene (RPA4226) coding for a protein that contains a cytoplasmic histidine kinase domain is located immediately upstream of RPA4225. The genomic organization of orthologs for these four genes is conserved in several other strains of R. palustris as well as in closely related α-Proteobacteria. Finally, taken together, these data suggest that ECF σ RPA4225 and the three additional genes make up a sigma factor mimicry system in R. palustris.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

BANYAN. II. Very low mass and substellar candidate members to nearby, young kinematic groups with previously known signs of youth

We present Bayesian Analysis for Nearby Young AssociatioNs II (BANYAN II), a modified Bayesian analysis for assessing the membership of later-than-M5 objects to any of several Nearby Young Associations (NYAs). In addition to using kinematic information (from sky position and proper motion), this analysis exploits 2MASS-WISE color-magnitude diagrams in which old and young objects follow distinct sequences. As an improvement over our earlier work, the spatial and kinematic distributions for each association are now modeled as ellipsoids whose axes need not be aligned with the Galactic coordinate axes, and we use prior probabilities matching the expected populations of the NYAs considered versus field stars. We present an extensive contamination analysis to characterize the performance of our new method. We find that Bayesian probabilities are generally representative of contamination rates, except when a parallax measurement is considered. In this case contamination rates become significantly smaller and hence Bayesian probabilities for NYA memberships are pessimistic. We apply this new algorithm to a sample of 158 objects from the literature that are either known to display spectroscopic signs of youth or have unusually red near-infrared colors for their spectral type. Based on our analysis, we identify 25 objects as new highly probable candidates to NYAs, including a new M7.5 bona fide member to Tucana-Horologium, making it the latest-type member. In addition, we reveal that a known L2γ dwarf is co-moving with a bright M5 dwarf, and we show for the first time that two of the currently known ultra red L dwarfs are strong candidates to the AB Doradus moving group. Several objects identified here as highly probable members to NYAs could be free-floating planetary-mass objects if their membership is confirmed.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Genome-based evolutionary history of Pseudomonas spp

Pseudomonas is a large and diverse genus of Gammaproteobacteria. To provide a framework for discovery of evolutionary and taxonomic relationships of these bacteria, we compared the genomes of type strains of 163 species and 3 additional subspecies of Pseudomonas, including 118 genomes sequenced herein. A maximum likelihood phylogeny of the 166 type strains based on protein sequences of 100 single-copy orthologous genes revealed thirteen groups of Pseudomonas, composed of two to sixty three species each. Pairwise average nucleotide identities and alignment fractions were calculated for the data set of the 166 type strains and 1224 genomes of Pseudomonas available in public databases. Results revealed that 394 of the 1224 genomes were distinct from any type strain, suggesting that the type strains represent only a fraction of the genomic diversity of the genus. The core genome of Pseudomonas was determined to contain 794 genes conferring primarily housekeeping functions. Here, the results of this study provide a phylogenetic framework for future studies aiming to resolve the classification and phylogenetic relationships, identify new gene functions and phenotypes, and explore the ecological and metabolic potential of the Pseudomonas spp.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Nanocrystal Geometry Governs Phase Transformation Pathways in Palladium Hydride

Pathways and structural dynamics of phase transformations impact performance of materials in energy and information storage technologies. Palladium hydride (PdH x ) nanocrystals are an ideal model system for studying solute-induced phase transformations, where elastic energy from lattice mismatch between α-PdH x and β-PdH x phases is often considered a key to determining the transformation pathways. α/β-PdH x interfacial elastic energy is affected by the confined geometry of a nanocrystal. However, how nanocrystal geometry influences phase transformation pathways is largely unknown. Using in situ liquid phase transmission electron microscopy, we directly visualize hydrogenation in Pd nanocrystals with two geometries, a nanocube and a hexagonal nanoplate. Both follow similar sequences of an initially curved nucleus, interface flattening, and reverse-stage nucleation; however, their evolving α/β-PdH x interfaces exhibit geometry-dependent crystallographic alignments. In nanocubes, {100}-aligned configurations conform to static elastic energy ordering, representing a pathway that maintains a local mechanical equilibrium, whereas nanoplates display both {110}- and {211}-aligned interfaces. Theoretical simulations show that geometry determines the accessibility of alternative phase transformation pathways as the system is driven far from equilibrium during hydrogenation. In conclusion, these findings identify geometry as a fundamental parameter for directing phase transformation pathways, offering design principles for accessing atypical configurations and improving properties of intercalation-based devices.

Lee, Daewon [Lawrence Berkeley National Laboratory↗
NASA NTRS1989

Chip Advancer For GPS Receiver

Instrument errors made negligible. For each integration interval, both delay and rate of change of delay initialized to small fraction of chip - for example, to order of 10 to the negative 7th power - thereby making feedback control and extraction of delay highly accurate and flexible. With appropriate selection of sampling rate relative to chip rate, commensurability errors reduced to extremely small levels. In Global Positioning System (GPS) receiver, pseudorandom code sequence generated by simple digital logic incorporating effects of time, delay, and rate of change of delay. Flexibility in starting time and sum interval very useful in aligning correlation interval with beginnings and endings of data bits.

Meehan, Thomas K.↗
NASA NTRS1993

Generating local addresses and communication sets for data-parallel programs

Generating local addresses and communication sets is an important issue in distributed-memory implementations of data-parallel languages such as High Performance Fortran. We show that for an array A affinely aligned to a template that is distributed across p processors with a cyclic(k) distribution, and a computation involving the regular section A, the local memory access sequence for any processor is characterized by a finite state machine of at most k states. We present fast algorithms for computing the essential information about these state machines, and extend the framework to handle multidimensional arrays. We also show how to generate communication sets using the state machine approach. Performance results show that this solution requires very little runtime overhead and acceptable preprocessing time.

Chatterjee, Siddhartha↗
NASA NTRS2011

Telemetry-Based Ranging

A telemetry-based ranging scheme was developed in which the downlink ranging signal is eliminated, and the range is computed directly from the downlink telemetry signal. This is the first Deep Space Network (DSN) ranging technology that does not require the spacecraft to transmit a separate ranging signal. By contrast, the evolutionary ranging techniques used over the years by NASA missions, including sequential ranging (transmission of a sequence of sinusoids) and PN-ranging (transmission of a pseudo-noise sequence) whether regenerative (spacecraft acquires, then regenerates and retransmits a noise-free ranging signal) or transparent (spacecraft feeds the noisy demodulated uplink ranging signal into the downlink phase modulator) relied on spacecraft power and bandwidth to transmit an explicit ranging signal. The state of the art in ranging is described in an emerging CCSDS (Consultative Committee for Space Data Systems) standard, in which a pseudo-noise (PN) sequence is transmitted from the ground to the spacecraft, acquired onboard, and the PN sequence is coherently retransmitted back to the ground, where a delay measurement is made between the uplink and downlink signals. In this work, the telemetry signal is aligned with the uplink PN code epoch. The ground station computes the delay between the uplink signal transmission and the received downlink telemetry. Such a computation is feasible because symbol synchronizability is already an integral part of the telemetry design. Under existing technology, the telemetry signal cannot be used for ranging because its arrival-time information is not coherent with any Earth reference signal. By introducing this coherence, and performing joint telemetry detection and arrival-time estimation on the ground, a high-rate telemetry signal can provide all the precision necessary for spacecraft ranging.

Hamkins, Jon↗
NASA NTRS2013

Modeling Delamination in Postbuckled Composite Structures Under Static and Fatigue Loads

The ability of the Abaqus progressive Virtual Crack Closure Technique (VCCT) to model delamination in composite structures was investigated for static, postbuckling, and fatigue loads. Preliminary evaluations were performed using simple Double Cantilever Beam (DCB) and Mixed-Mode Bending (MMB) specimens. The nodal release sequences that describe the propagation of the delamination front were investigated. The effect of using a sudden or a gradual nodal release was evaluated by considering meshes aligned with the crack front as well as misaligned meshes. Fatigue simulations were then performed using the Direct Cyclic Fatigue (DCF) algorithm. It was found that in specimens such as the DCB, which are characterized by a nearly linear response and a pure fracture mode, the algorithm correctly predicts the Paris Law rate of propagation. However, the Abaqus DCF algorithm does not consider different fatigue propagation laws in different fracture modes. Finally, skin/stiffener debonding was studied in an aircraft fuselage subcomponent in which debonding occurs deep into post-buckling deformation. VCCT was shown to be a robust tool for estimating the onset propagation. However, difficulties were found with the ability of the current implementation of the Abaqus progressive VCCT to predict delamination propagation within structures subjected to postbuckling deformations or fatigue loads.

Bisagni, Chiara↗
DOE OSTI2014

Microbial species delineation using whole genome sequences

Species assignments in prokaryotes use a manual, poly-phasic approach utilizing both phenotypic traits and sequence information of phylogenetic marker genes. With thousands of genomes being sequenced every year, an automated, uniform and scalable approach exploiting the rich genomic information in whole genome sequences is desired, at least for the initial assignment of species to an organism. We have evaluated pairwise genome-wide Average Nucleotide Identity (gANI) values and alignment fractions (AFs) for nearly 13,000 genomes using our fast implementation of the computation, identifying robust and widely applicable hard cut-offs for species assignments based on AF and gANI. Using these cutoffs, we generated stable species-level clusters of organisms, which enabled the identification of several species mis-assignments and facilitated the assignment of species for organisms without species definitions.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2014

Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs

Assembly of metagenomic samples is a very complex process, with algorithms designed to address sequencing platform-specific issues, (read length, data volume, and/or community complexity), while also faced with genomes that differ greatly in nucleotide compositional biases and in abundance. To address these issues, we have developed a post-assembly process: MetaGenomic Assembly by Merging (MeGAMerge). We compare this process to the performance of several assemblers, using both real, and in-silico generated samples of different community composition and complexity. MeGAMerge consistently outperforms individual assembly methods, producing larger contigs with an increased number of predicted genes, without replication of data. MeGAMerge contigs are supported by read mapping and contig alignment data, when using synthetically-derived and real metagenomic data, as well as by gene prediction analyses and similarity searches. Ultimately, MeGAMerge is a flexible method that generates improved metagenome assemblies, with the ability to accommodate upcoming sequencing platforms, as well as present and future assembly algorithms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

MO-FG-202-07: Real-Time EPID-Based Detection Metric For VMAT Delivery Errors

Purpose: To create and test an accurate EPID-frame-based VMAT QA metric to detect gross dose errors in real-time and to provide information about the source of error. Methods: A Swiss cheese model was created for an EPID-based real-time QA process. The system compares a treatmentplan- based reference set of EPID images with images acquired over each 2° gantry angle interval. The metric utilizes a sequence of independent consecutively executed error detection Methods: a masking technique that verifies infield radiation delivery and ensures no out-of-field radiation; output normalization checks at two different stages; global image alignment to quantify rotation, scaling and translation; standard gamma evaluation (3%, 3 mm) and pixel intensity deviation checks including and excluding high dose gradient regions. Tolerances for each test were determined. For algorithm testing, twelve different types of errors were selected to modify the original plan. Corresponding predictions for each test case were generated, which included measurement-based noise. Each test case was run multiple times (with different noise per run) to assess the ability to detect introduced errors. Results: Averaged over five test runs, 99.1% of all plan variations that resulted in patient dose errors were detected within 2° and 100% within 4° (∼1% of patient dose delivery). Including cases that led to slightly modified but clinically equivalent plans, 91.5% were detected by the system within 2°. Based on the type of method that detected the error, determination of error sources was achieved. Conclusion: An EPID-based during-treatment error detection system for VMAT deliveries was successfully designed and tested. The system utilizes a sequence of methods to identify and prevent gross treatment delivery errors. The system was inspected for robustness with realistic noise variations, demonstrating that it has the potential to detect a large majority of errors in real-time and indicate the error source. J. V. Siebers receives funding support from Varian Medical Systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Phase transitions and octahedral rotations in epitaxial Ag(Ta x Nb 1-x )O 3 thin films under tensile strain

In this paper, epitaxial Ag(Ta 0.5 Nb 0.5 )O 3 (ATN) films under tensile strain were deposited on (Ba 0.4 Sr 0.6 )TiO 3 /LaAlO 3 (001) p and KTaO 3 (001) substrates. These films exhibited a domain structure with the c-axis aligned primarily along the in-plane direction in contrast with the poly-domain nature of bulk ATN ceramics or relaxed films. While the generic phase transition sequence of the tensile films was qualitatively similar to bulk, the tetragonal and orthorhombic phase field regions expanded by ~270 °C in ATN/(Ba 0.4 Sr 0.6 )TiO 3 /LaAlO 3 . Furthermore, the films were found to be in the M 3 (complex octahedral tilting with disordered Nb/Ta displacements) phase at room temperature with either significantly reduced tilt angles or a suppression of the long range order of the complex tilt as compared to bulk materials. It was observed that the octahedral tilt domains were oriented with the complex tilt axes lying in the plane of the film due to the tensile strain. Finally, this work demonstrates that tensile strain can be used to strain-engineer materials with complex tilt systems and thereby modify functional properties.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

HIV Sequence Compendium 2018

This compendium is an annual summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics

Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calculates the percent bases aligned between two bacterial genomes and their corresponding ANI values, to set threshold values for determining species consistent with the conventional identification methods of known species. The performance of species identification was evaluated using two datasets: the Reference Genome Dataset v2 (RGDv2), consisting of 43 enteric genome assemblies representing 32 species, and the Test Genome Dataset (TGDv1), comprising 454 genome assemblies which is designed to represent all species needed to query for identification, as well as rare and closely related species. The RGDv2 contains six Campylobacter spp., three Escherichia/Shigella spp., one Grimontia hollisae, six Listeria spp., one Photobacterium damselae, two Salmonella spp., and thirteen Vibrio spp., while the TGDv1 contains 454 enteric bacterial genomes representing 42 different species. The analysis showed that, when a standard minimum of 70% genome bases alignment existed, the ANI threshold values determined for these species were ≥95 for Escherichia/Shigella and Vibrio species, ≥93% for Salmonella species, and ≥92% for Campylobacter and Listeria species. Using these metrics, the RGDv2 accurately classified all validation strains in TGDv1 at the species level, which is consistent with the classification based on previous gold standard methods.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1982

Reverse draping of magnetic field lines in the boundary layer

An unexpected orientation of field lines has been found by ISEE satellite measurements of the earth magnetosphere boundary layer, perhaps indicating a reverse draping. Three-dimensional plasma flow measurements by ISEE 1 and 2 show the tailward flow in the boundary layer to have an equatorward component which suggests high-latitude plasma entry. Simultaneous magnetic field measurements with the two satellites during a boundary crossing sequence yielded data on the boundary layer electric currents and the boundary layer interface with plasma sheet and magnetosheath. The currents are found to be largely field-aligned, with intensities in the 0.03-0.06 microampere/sq m range.

Hones, E. W., Jr.↗
DOE OSTI2023

The Dark Energy Survey Year 3 and eBOSS: constraining galaxy intrinsic alignments across luminosity and colour space

ABSTRACT We present direct constraints on galaxy intrinsic alignments (IAs) using the Dark Energy Survey Year 3 (DES Y3), the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and its precursor, the Baryon Oscillation Spectroscopic Survey (BOSS). Our measurements incorporate photometric red sequence (redMaGiC) galaxies from DES with median redshift z ∼ 0.2–1.0, luminous red galaxies from eBOSS at z ∼ 0.8, and also an SDSS-III BOSS CMASS sample at z ∼ 0.5. We measure two-point IA correlations, which we fit using a model that includes lensing, magnification, and photometric redshift error. Fitting on scales 6 Mpc h−1 < rp < 70 Mpc h−1, we make a detection of IAs in each sample, at 5σ–22σ (assuming a simple one-parameter model for IAs). Using these red samples, we measure the IA–luminosity relation. Our results are statistically consistent with previous results, but offer a significant improvement in constraining power, particularly at low luminosity. With this improved precision, we see detectable dependence on colour between broadly defined red samples. It is likely that a more sophisticated approach than a binary red/blue split, which jointly considers colour and luminosity dependence in the IA signal, will be needed in future. We also compare the various signal components at the best-fitting point in parameter space for each sample, and find that magnification and lensing contribute $\sim 2\!-\!18~{{\ \rm per\ cent}}$ of the total signal. As precision continues to improve, it will certainly be necessary to account for these effects in future direct IA measurements. Finally, we make equivalent measurements on a sample of emission-line galaxies from eBOSS at z ∼ 0.8. We constrain the non-linear alignment amplitude to be $A_1=0.07^{+0.32}_{-0.42}$ (|A1| < 0.78 at 95 per cent CL).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2014

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

HUBBLE SPACE TELESCOPE SNAPSHOT SURVEY FOR RESOLVED COMPANIONS OF GALACTIC CEPHEIDS

We have conducted an imaging survey with the Hubble Space Telescope Wide Field Camera 3 (WFC3) of 70 Galactic Cepheids, typically within 1 kpc, with the aim of finding resolved physical companions. The WFC3 field typically covers the 0.1 pc area where companions are expected. In this paper, we identify 39 Cepheids having candidate companions, based on their positions in color–magnitude diagrams, and having separations ≥5{sup "} from the Cepheids. We use follow-up observations of 14 of these candidates with XMM-Newton, and of one of them with ROSAT, to separate X-ray-active young stars (probable physical companions) from field stars (chance alignments). Our preliminary estimate, based on the optical and X-ray observations, is that only 3% of the Cepheids in the sample have wide companions. Our survey easily detects resolved main-sequence companions as faint as spectral type K. Thus the fact that the two most probable companions (those of FF Aql and RV Sco) are earlier than type K is not simply a function of the detection limit. We find no physical companions having separations larger than 4000 au in the X-ray survey. Two Cepheids are exceptions in that they do have young companions at significantly larger separations (δ Cep and S Nor), but both belong to a cluster or a loose association, so our working model is that they are not gravitationally bound binary members, but rather cluster/association members. All of these properties provide constraints on both star formation and subsequent dynamical evolution. The low frequency of true physical companions at separations >5{sup "} is confirmed by examination of the subset of the nearest Cepheids and also the density of the fields.

79 ASTRONOMY AND ASTROPHYSICS↗