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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 1,675 records · Page 93
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Understanding Proton Movement in [Fe-Fe] Hydrogenases

Nature uses specialized metalloenzymes to carry out small molecule activation reactions, including CO 2 fixation, O 2 activation, and proton reduction, with unparalleled efficiency, rates, and selectivity. The latter reactions are performed by hydrogenases, protein metallo-complexes that interconverts H 2 to protons and electrons (H 2 oxidation) and the reverse reaction (H 2 production) with incredibly low energy input and amazingly fast kinetics. Reproducing both the activity and efficiency of metalloenzymes in sustainable anthropogenic systems remains one of the “holy grails” of inorganic chemistry. However, identifying the precise molecular components responsible for these desirable properties has been challenging in the natural metalloenzymes, hindering efforts to develop analogous processes in synthetic compounds. Considering the inherent complexity of a metalloenzyme and the many interactions, both strong and weak, that contribute to the function of an enzyme, we have elected to model natural metalloenzymes on a biochemical platform. Towards this end, we have a developed structural, functional, and mechanistic mimic of the [Ni-Fe] hydrogenases within a robust protein scaffold, rubredoxin, to understand the influence of the secondary coordination environment on the metal center. This involved preparing a series of three rubredoxin constructs containing a single point mutation at Val positions and making the NMR chemical shift assignments for the paramagnetic (nickel-substituted) and non-paramagnetic (zinc-substituted) form. These physical studies were complemented with in silico molecular dynamic studies on proteins with [Fe-S] clusters to engineer new proton channels to test in vitro . To assist our search for new natural metalloprotein scaffolds within the vast number of sequenced genomes, we created a neural network-based program to identify proteins with specific metal-binding sites. These computational and physical studies with metalloenzymes provide direct insight into the fundamental chemical principles driving the natural systems and offer design principles for developing catalysts that utilize analogous principles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

MetaText: Compositional Generalization in Deep Language Models

Compositional generalization, the ability to infer and reason using novel combinations of previously encountered entities and structures, is a trait of great utility across a variety of deep learning tasks; it implies a certain ability to reason using consistent and therefore interpretable rules, to understand the constituent parts of its input at multiple levels of granularity, to be robust to spurious differences between semantically equivalent inputs, and more. We seek to understand the degree to which existing natural language models achieve or fall short of compositional generalization across a variety of tasks, whether there are distinct types of compositional generalization in practice, and to identify avenues of intervention through which we can improve models’ compositional generalization ability. After exploring these questions using an array of models, tasks, and potential interventions we see that large, pretrained language models have encountered sufficient training data to account for a variety of fine-grained compositional behavior but still struggle to reason at the level of phrases or larger language structures. Non-intrusive, data-based interventions in the form of augmenting individual sequences with compressed versions of themselves or deriving new examples from induced grammars prove insufficient to encourage greater levels of compositional reasoning, indicating that future work might benefit most from focusing on changes to a model’s inductive bias at the architectural or loss level, or by integrating compositionality-boosting data interventions into the large-scale pretraining process itself.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Enabling Real-time Scattering Data Analysis with Scalable Optimization [Slides]

Diffraction experiments produce datasets with rich multidimensional physics information such as microstructure, equations of state, crystal structure, elastoplastic properties, and other key inputs to LANL mission-essential multiphysics models. This information is typically extracted through a process called Rietveld refinement, which involves selecting appropriate models of the instrument, crystal structure, and microstructure, identifying suitable starting values, and then fitting often hundreds of model parameters using a sequence of empirical parameter turnon/off sequences within a non-global gradient-based optimization. Extensive user expertise is required to properly setup a refinement, identify appropriate models, and select initial parameter values close to truth, such that the refinement will yield parameter values that are optimally predictive. This is a very tedious manual process performed far after the beamline campaign has ended. As facilities have become capable of generating larger volumes of data, the limitation in throughput due to Rietveld refinement has led to a dramatic increase in unanalyzed data as opposed to an intended increase in new science. In our FY22 TED, we demonstrated an integrated toolset providing near real-time automated Rietveld analysis. If this toolset can be optimized to provide automated Rietveld analysis in real-time, this could alleviate the bottleneck in unanalyzed diffraction data, aid in decision-making during experiments, and increase efficiency of the facility.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2012

Chromosome-Specific DNA Repeats: Rapid Identification in Silico and Validation Using Fluorescence in Situ Hybridization

Chromosome enumeration in interphase and metaphase cells using fluorescence in situ hybridization (FISH) is an established procedure for the rapid and accurate cytogenetic analysis of cell nuclei and polar bodies, the unambiguous gender determination, as well as the definition of tumor-specific signatures. Present bottlenecks in the procedure are a limited number of commercial, non-isotopically labeled probes that can be combined in multiplex FISH assays and the relatively high price and effort to develop additional probes. We describe a streamlined approach for rapid probe definition, synthesis and validation, which is based on the analysis of publicly available DNA sequence information, also known as “database mining”. Examples of probe preparation for the human gonosomes and chromosome 16 as a selected autosome outline the probe selection strategy, define a timeline for expedited probe production and compare this novel selection strategy to more conventional probe cloning protocols.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Predicting Drug Resistance Using Deep Mutational Scanning

Drug resistance is a major healthcare challenge, resulting in a continuous need to develop new inhibitors. The development of these inhibitors requires an understanding of the mechanisms of resistance for a critical mass of occurrences. Recent genome editing technologies based on high-throughput DNA synthesis and sequencing may help to predict mutations resulting in resistance by testing large mutagenesis libraries. Here we describe the rationale of this approach, with examples and relevance to drug development and resistance in malaria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

YOUNG STELLAR CLUSTERS CONTAINING MASSIVE YOUNG STELLAR OBJECTS IN THE VVV SURVEY

The purpose of this research is to study the connections of the global properties of eight young stellar clusters projected in the Vista Variables in the Via Lactea (VVV) ESO Large Public Survey disk area and their young stellar object (YSO) populations. The analysis is based on the combination of spectroscopic parallax-based reddening and distance determinations with main-sequence and pre-main-sequence ishochrone fitting to determine the basic parameters (reddening, age, distance) of the sample clusters. The lower mass limit estimations show that all clusters are low or intermediate mass (between 110 and 1800 M {sub ⊙}), the slope Γ of the obtained present-day mass functions of the clusters is close to the Kroupa initial mass function. The YSOs in the cluster’s surrounding fields are classified using low resolution spectra, spectral energy distribution fits with theoretical predictions, and variability, taking advantage of multi-epoch VVV observations. All spectroscopically confirmed YSOs (except one) are found to be massive (more than 8 M {sub ⊙}). Using VVV and GLIMPSE color–color cuts we have selected a large number of new YSO candidates, which are checked for variability and 57% are found to show at least low-amplitude variations. In few cases it was possible to distinguish between YSO and AGB classifications on the basis of light curves.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

GALEX–SDSS–WISE Legacy Catalog (GSWLC): Star formation rates, stellar masses, and dust attenuations of 700,000 low-redshift galaxies

In this paper, we present the GALEX–SDSS–WISE Legacy Catalog (GSWLC), a catalog of physical properties (stellar masses, dust attenuations, and star formation rates [SFRs]) for ∼700,000 galaxies with Sloan Digital Sky Survey (SDSS) redshifts below 0.3. GSWLC contains galaxies within the Galaxy Evolution Explorer footprint, regardless of a UV detection, covering 90% of SDSS. The physical properties were obtained from UV/optical spectral energy distribution (SED) fitting following Bayesian methodology of Salim et al., with improvements such as blending corrections for low-resolution UV photometry, flexible dust attenuation laws, and emission-line corrections. GSWLC also includes mid-IR SFRs derived from IR templates based on 22 μm Wide-field Infrared Survey Explorer observations. These estimates are independent of UV/optical SED fitting, in order to separate possible systematics. The paper argues that the comparison of specific SFRs (sSFRs) is more informative and physically motivated than the comparison of SFRs. The sSFRs resulting from the UV/optical SED fitting are compared to the mid-IR sSFRs and to sSFRs from three published catalogs. For “main-sequence” galaxies with no active galactic nucleus (AGN) all sSFRs are in very good agreement (within 0.1 dex on average). In particular, the widely used aperture-corrected SFRs from the MPA/JHU catalog show no systematic offsets, in contrast to some integral field spectroscopy results. For galaxies below the main sequence (log sSFR <−11), mid-IR (s)SFRs based on fixed luminosity–SFR conversion are severely biased (up to 2 dex) because the dust is primarily heated by old stars. Furthermore, mid-IR (s)SFRs are overestimated by up to 0.6 dex for galaxies with AGNs, presumably due to nonstellar dust heating. UV/optical (s)SFRs are thus preferred to IR-based (s)SFRs for quenched galaxies and those that host AGNs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Collisions of Terrestrial Worlds: The Occurrence of Extreme Mid-infrared Excesses around Low-mass Field Stars

We present the results of an investigation into the occurrence and properties (stellar age and mass trends) of low-mass field stars exhibiting extreme mid-infrared (MIR) excesses (L{sub IR}/L{sub ∗}≳0.01). Stars for the analysis were initially selected from the Motion Verified Red Stars (MoVeRS) catalog of photometric stars with Sloan Digital Sky Survey, 2MASS, and WISE photometry and significant proper motions. We identify 584 stars exhibiting extreme MIR excesses, selected based on an empirical relationship for main-sequence W1−W3 colors. For a small subset of the sample, we show, using spectroscopic tracers of stellar age (Hα and Li i) and luminosity class, that the parent sample is most likely comprised of field dwarfs (≳1 Gyr). We also develop the Low-mass Kinematics (LoKi) galactic model to estimate the completeness of the extreme MIR excess sample. Using Galactic height as a proxy for stellar age, the completeness-corrected analysis indicates a distinct age dependence for field stars exhibiting extreme MIR excesses. We also find a trend with stellar mass (using r − z color as a proxy). Our findings are consistent with the detected extreme MIR excesses originating from dust created in a short-lived collisional cascade (≲100,000 years) during a giant impact between two large planetismals or terrestrial planets. These stars with extreme MIR excesses also provide support for planetary collisions being the dominant mechanism in creating the observed Kepler dichotomy (the need for more than a single mode, typically two, to explain the variety of planetary system architectures Kepler has observed), rather than different formation mechanisms.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

Distinct p53 genomic binding patterns in normal and cancer-derived human cells

We report here genome-wide analysis of the tumor suppressor p53 binding sites in normal human cells. 743 high-confidence ChIP-seq peaks representing putative genomic binding sites were identified in normal IMR90 fibroblasts using a reference chromatin sample. More than 40% were located within 2 kb of a transcription start site (TSS), a distribution similar to that documented for individually studied, functional p53 binding sites and, to date, not observed by previous p53 genome-wide studies. Nearly half of the high-confidence binding sites in the IMR90 cells reside in CpG islands, in marked contrast to sites reported in cancer-derived cells. The distinct genomic features of the IMR90 binding sites do not reflect a distinct preference for specific sequences, since the de novo developed p53 motif based on our study is similar to those reported by genome-wide studies of cancer cells. More likely, the different chromatin landscape in normal, compared with cancer-derived cells, influences p53 binding via modulating availability of the sites. We compared the IMR90 ChIPseq peaks to the recently published IMR90 methylome1 and demonstrated that they are enriched at hypomethylated DNA. Our study represents the first genome-wide, de novo mapping of p53 binding sites in normal human cells and reveals that p53 binding sites reside in distinct genomic landscapes in normal and cancer-derived human cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

pnnl/hundo

:bar_chart: Snakemake-based amplicon processing protocol for 16S and ITS sequences.

Brown, Joe↗
DOE OSTI2015

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.

Life Sciences & Biomedicine - Other Topics↗
NASA NTRS1970

Simple data-smoothing and noise-suppression technique

Algorithm, based on the Borel method of summing divergent sequences, is used for smoothing noisy data where knowledge of frequency content is not required. Technique's effectiveness is demonstrated by a series of graphs.

Duty, R. L.↗
NASA NTRS1973

The NASA computer aided design and test system

A family of computer programs facilitating the design, layout, evaluation, and testing of digital electronic circuitry is described. CADAT (computer aided design and test system) is intended for use by NASA and its contractors and is aimed predominantly at providing cost effective microelectronic subsystems based on custom designed metal oxide semiconductor (MOS) large scale integrated circuits (LSIC's). CADAT software can be easily adopted by installations with a wide variety of computer hardware configurations. Its structure permits ease of update to more powerful component programs and to newly emerging LSIC technologies. The components of the CADAT system are described stressing the interaction of programs rather than detail of coding or algorithms. The CADAT system provides computer aids to derive and document the design intent, includes powerful automatic layout software, permits detailed geometry checks and performance simulation based on mask data, and furnishes test pattern sequences for hardware testing.

Gould, J. M.↗
NASA NTRS1974

Vectorcardiographic results from Skylab medical experiment M092: Lower body negative pressure

Vectorcardiograms were recorded via a modified Frank lead system from all crewmen of the three Skylab missions in conjuction with the Lower Body Negative Pressure - M092 Experiment. Data were analyzed by a specially developed computer program (VECTAN). Design of the test sequences allowed direct comparisons of supine resting, Earth based (reference) vectorcardiograms with those taken during lower body negative pressure stress and those obtained at rest in orbit, as well as combinations of these conditions. Results revealed several statistically significant space flight related changes; namely, increased testing and lower body negative pressure stressed heart rates, modestly increased PR interval and corrected QTC interval, and greatly increased P and QPS loop maximal amplitudes. In addition, orientation changes in the QRS maximum vector and the J-vector at rest in space seem quite consistent among crewmen and different from those caused by the application of lower body negative pressure. No clinical abnormalities were observed. Etiology of these findings is conjectured to be, at least in part, related to fluid mass shifts occurring in weightlessness and attendant alterations in cardiovascular dynamics and myocardial autonomic control mechanisms.

Hoffler, G. W.↗
NASA NTRS1974

The engineering design integration (EDIN) system

A digital computer program complex for the evaluation of aerospace vehicle preliminary designs is described. The system consists of a Univac 1100 series computer and peripherals using the Exec 8 operating system, a set of demand access terminals of the alphanumeric and graphics types, and a library of independent computer programs. Modification of the partial run streams, data base maintenance and construction, and control of program sequencing are provided by a data manipulation program called the DLG processor. The executive control of library program execution is performed by the Univac Exec 8 operating system through a user established run stream. A combination of demand and batch operations is employed in the evaluation of preliminary designs. Applications accomplished with the EDIN system are described.

Glatt, C. R.↗
NASA NTRS1977

Inclusion of explicit thermal requirements in optimum structural design

A finite-element based procedure is described for obtaining minimum mass designs of structures subjected to combined thermal and mechanical loading and both strength and thermal constraints. The procedure is based on a mathematical programming method using the Sequence of Unconstrained Minimizations Technique (SUMT) in which design requirements are incorporated by an exterior penalty function. The procedure is limited to steady-state temperatures which are controlled by structural sizing only. The optimization procedure is demonstrated by the design of a structural wing box with both mechanical loading and external heating, subject to design constraints on stress, minimum gage, and temperature. The final design for these conditions is compared with a corresponding design in which temperature constraints are omitted.

Adelman, H. M.↗
NASA NTRS1976

Theoretical models of Beta Cephei stars constructed with new radiative opacities

Equilibrium models for the main-sequence and early post-main-sequence phases of evolution are constructed for stars of 10.9 and 15 solar masses with two different initial hydrogen and metals abundances. Carson's (1976) radiative opacities are used in the calculations. It is found that the models which lie off the zero-age main sequence have cooler effective temperatures than corresponding models based on other opacities and cross the observed Beta Cephei strip in the H-R diagram only during the main phase of core hydrogen burning. The stability of radial and nonradial pulsations is studied by applying linear nonadiabatic perturbations to the models. The results show that all the modes examined are stable and that the margin of stability decreases with advancing evolution. It is suggested that the closeness of the periods of the two lowest nonradial quadrupole p-modes may be responsible for the 'beat' phenomenon observed in many Beta Cephei stars, if these modes are somehow excited. Possible instability mechanisms are evaluated, particularly the ultimate ionization of CNO elements.

Stothers, R.↗
NASA NTRS1980

Early photosynthetic microorganisms and environmental evolution

Microfossils which are preserved as shrivelled kerogenous residues provide little information about cellular organization and almost none about the metabolic properties of the organisms. The distinction between prokaryotic vs eukaryotic, and phototrophic vs chemo- and organotrophic fossil microorganisms rests entirely on morphological comparisons with recent counterparts. The residual nature of the microbial fossil record promotes the conclusion that it must be biased toward (a) most abundant organisms, (b) those most resistant to degradation, and (c) those inhabiting environments with high preservation potential e.g., stromatolites. These criteria support the cyanophyte identity of most Precambrian microbial fossils on the following grounds: (1) as primary producers they dominate prokaryotic communities in modern extreme environments, e.g., intertidal zone; (2) several morphological counterparts of modern cyanophytes and microbial fossils have been established based on structure, cell division patterns and degradation sequences. The impact of anaerobic and oxygenic microbial photosynthesis on the evolution of Precambrian environments is discussed.

Golubic, S.↗