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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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
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↗
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↗
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↗
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↗
DOE OSTI2016

Supramolecular Gelation of Rigid Triangular Macrocycles through Rings of Multiple C–H$···$O Interactions Acting Cooperatively

When equimolar solutions of the enantiomeric naphthalenediimide-based highly rigid triangles $R-Δ$ and $S-Δ$ in ClCH 2 CH 2 Cl are mixed, the racemate $rac-Δ$ forms an organogel that is composed of interwoven fibers, resulting from the columnar stacking of the triangles in an alternating $R-Δ/S-Δ$ fashion. Under identical conditions, the pure enantiomers do not form organogels. Density functional theory calculations reveal that the racemic RS dimer is more stable than the RR dimer as a result of the enantiomeric relationship between $R-Δ$ and $S-Δ$, allowing them to act as two complementary rings comprised of 12 [C–H$···$O] interactions with an unprecedented and uninterrupted circular ADDAADDAADDA·DAADDAADDAAD alignment of hydrogen bond donors (D) and acceptors (A), in contrast with the square-wave manner in which the RR dimer forms a complementary yet interrupted ADADAD·DADADA circular sequence of six longer [C–H$···$O] hydrogen bonds. It follows that gelation is favored by weak interactions acting cooperatively in rings under precise stereoelectronic control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Superspin renormalization and slow relaxation in random spin systems

We develop an excited-state real-space renormalization group (RSRG-X) formalism to describe the dynamics of conserved densities in randomly interacting spin-12 systems. Our formalism is suitable for systems with U(1) and Z2 symmetries, and we apply it to chains of randomly positioned spins with dipolar XX+YY interactions, as arise in Rydberg quantum simulators and other platforms. The formalism generates a sequence of effective Hamiltonians that provide approximate descriptions for dynamics on successively smaller energy scales. These effective Hamiltonians involve “superspins”: two-level collective degrees of freedom constructed from (anti)aligned microscopic spins. Conserved densities can then be understood as relaxing via coherent collective spin flips. For the well-studied simpler case of randomly interacting nearest-neighbor XX+YY chains, the superspins reduce to single spins. Our formalism also leads to a numerical method capable of simulating the dynamics up to an otherwise inaccessible combination of large system size and late time. Focusing on disorder-averaged infinite-temperature autocorrelation functions, in particular the spin survival probability Sp¯(t), we demonstrate quantitative agreement between our algorithm and exact diagonalization (ED) at low but nonzero frequencies. Such agreement holds for chains with nearest-neighbor, next-nearest-neighbor, and long-range dipolar interactions. Our results indicate decay of Sp¯(t) slower than any power law and feature no significant deviation from the ∼1/ln2(t) asymptote expected from the infinite-randomness fixed-point of the nearest-neighbor model. We also apply the RSRG-X formalism to two-dimensional long-range systems of moderate size and find slow late-time decay of Sp¯(t).

Zhao, Yi J↗
DOE OSTI2020

Octet: A coherent qubit control system for trapped-ion quantum computers

This is firmware and software designed for a Zynq UltraScale+ RFSoC chip made by Xilinx, specifically targeted to laser-based individual addressing of trapped ion qubits via a multi-channel AOM. The design features 8 dual-tone outputs with frequencies up to 409 MHz that can be controlled statically or dynamically via on-chip cubic spline interpolation engines that allow one to generate sequences of output waveforms with fast modulation of frequency, phase, amplitude, and z-rotations that are smooth/discrete and can run simultaneously across all parameters/tones. It also features global phase alignment on all tones regardless of frequency and the ability to return to a known phase/frequency at any later time on a per-tone basis without the need for manual bookkeeping. Acoustic and optical cross-talk can also be destructively canceled by adding neighboring outputs with variable amplitude/phase/delay. Each tone can be optionally frequency locked to an external RF source. SAND2020-12703 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Lobser, Daniel↗
DOE OSTI2023

Insensitivity to propagation timing in a preview-enabled wind turbine control experiment

Lidar scanners are capable of taking measurements of a wind field upstream of a wind turbine. The wind turbine controller can use these measurements as a “preview” of future disturbances impacting the turbine. Such preview-enabled (or feedforward) controllers show superior performance to standard wind turbine control configurations based purely on a feedback architecture. To capitalize on the performance improvements that preview wind measurements can provide, feedforward control actions should be timed to coincide with the arrival of the wind field at the wind turbine location. However, the time of propagation of the wind field between the lidar measurement location and the wind turbine is not perfectly known. Moreover, the best time to take feedforward control action may not perfectly coincide with the true arrival time of the wind disturbance. This contribution presents results from an experiment where preview-enabled model predictive control was deployed on a fully-actuated, scaled model wind turbine operating in a wind tunnel testbed. In the study, we investigate the sensitivity of the controller performance to the assumed propagation delay using a range of wind input sequences. We find that the preview-enabled controller outperforms the feedback only case across a wide range of assumed propagation delays, demonstrating a level of robustness to the time alignment of the incoming disturbances.

17 WIND ENERGY↗