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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 955 records · Page 53
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Exceptional Thermochemical Stability of Graphene on N-Polar GaN for Remote Epitaxy

In this study, we investigate the thermochemical stability of graphene on the GaN substrate for metal–organic chemical vapor deposition (MOCVD)-based remote epitaxy. Despite excellent physical properties of GaN, making it a compelling choice for high-performance electronic and light-emitting device applications, the challenge of thermochemical decomposition of graphene on a GaN substrate at high temperatures has obstructed the achievement of remote homoepitaxy via MOCVD. Our research uncovers an unexpected stability of graphene on N-polar GaN, thereby enabling the MOCVD-based remote homoepitaxy of N-polar GaN. Our comparative analysis of N- and Ga-polar GaN substrates reveals markedly different outcomes: while a graphene/N-polar GaN substrate produces releasable microcrystals (μCs), a graphene/Ga-polar GaN substrate yields nonreleasable thin films. We attribute this discrepancy to the polarity-dependent thermochemical stability of graphene on the GaN substrate and its subsequent reaction with hydrogen. Evidence obtained from Raman spectroscopy, electron microscopic analyses, and overlayer delamination points to a pronounced thermochemical stability of graphene on N-polar GaN during MOCVD-based remote homoepitaxy. Molecular dynamics simulations, corroborated by experimental data, further substantiate that the thermochemical stability of graphene is reliant on the polarity of GaN, due to different reactions with hydrogen at high temperatures. In conclusion, based on the N-polar remote homoepitaxy of μCs, the practical application of our findings was demonstrated in fabrication of flexible light-emitting diodes composed of p–n junction μCs with InGaN heterostructures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes

Abstract McrBC complexes are motor-driven nucleases functioning in bacterial self-defense by cleaving foreign DNA. The GTP-specific AAA + protein McrB powers translocation along DNA and its hydrolysis activity is stimulated by its partner nuclease McrC. Here, we report cryo-EM structures of Thermococcus gammatolerans McrB and McrBC, and E. coli McrBC. The McrB hexamers, containing the necessary catalytic machinery for basal GTP hydrolysis, are intrinsically asymmetric. This asymmetry directs McrC binding so that it engages a single active site, where it then uses an arginine/lysine-mediated hydrogen-bonding network to reposition the asparagine in the McrB signature motif for optimal catalytic function. While the two McrBC complexes use different DNA-binding domains, these contribute to the same general GTP-recognition mechanism employed by all G proteins. Asymmetry also induces distinct inter-subunit interactions around the ring, suggesting a coordinated and directional GTP-hydrolysis cycle. Our data provide insights into the conserved molecular mechanisms governing McrB family AAA + motors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Fast mass spectrometry search and clustering of untargeted metabolomics data

The throughput of mass spectrometers and the amount of publicly available metabolomics data are growing rapidly, but analysis tools such as molecular networking and Mass Spectrometry Search Tool do not scale to searching and clustering billions of mass spectral data in metabolomics repositories. To address this limitation, we designed MASST+ and Networking+, which can process datasets that are up to three orders of magnitude larger than those processed by state-of-the-art tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Computational insights into the interaction of water with the UiO-66 metal–organic framework and its functionalized derivatives

The UiO-66 metal–organic framework (MOF) has been identified as a promising hydrophilic material for water harvesting. Recent studies show that its water uptake ability at low relative humidity (RH) can be improved by incorporating hydrophilic functional groups into the framework. In this work, we provide computational insights into the adsorption of water in UiO-66 and its functionalized derivatives to reveal the role played by different adsorption sites and functional groups in the adsorption mechanism. We started by developing molecular models for UiO-66, UiO-66-NH 2 , UiO-66-OH, and UiO-66-(OH) 2 compatible with the MB-pol data-driven many-body potential of water. We then benchmarked these models against ab initio data. Here we used these models to perform molecular dynamics simulations and calculate radial distribution functions, IR spectra, and two-dimensional density distribution maps for water in the MOFs. These results consistently show that the μ 3 -OH sites are the preferential interaction sites for water in UiO-66 and all its variants, and the formation of localised water clusters inside the octahedral pores is responsible for the abrupt step in the experimental adsorption isotherms. Furthermore, the presence of functional groups in the framework allows water to cluster in the octahedral pores at lower RH, thus making the MOF a more efficient water harvester. Overall, this study provides molecular-level insights into the pore filling process of UiO-66 and its functionalized derivatives, which are needed for the design of efficient water harvesting materials based on MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

P SI4 1.4: Open-source software for high-throughput quantum chemistry

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree–Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4 's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. We announce a rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

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

Cold gas mass measurements for the era of large optical spectroscopic surveys

ABSTRACT Gas plays an important role in many processes in galaxy formation and evolution, but quantifying the importance of gas has been hindered by the challenge to measure gas masses for large samples of galaxies. Data sets of direct atomic and molecular gas measurements are sufficient to establish simple scaling relations, but often not large enough to quantify three-parameter relations, or second-order dependences. As an alternative approach, we derive here indirect cold gas measurements from optical emission lines using photoionization models for galaxies in the Sloan Digital Sky Survey (SDSS) main galaxy sample and the PHANGS-MUSE survey. We calibrate the gas surface density measurements using xCOLD GASS and PHANGS-ALMA molecular gas measurements to ensure that our measurements are reliable. We demonstrate the importance of taking into account the scale dependence of the relation between optical depth (τ V ) and gas surface density (Σ gas ) and provide a general prescription to estimate Σ gas from τ V , metallicity, and the dust-to-metal ratio, at any arbitrary physical resolution. To demonstrate that the indirect cold gas masses are accurate enough to quantify the role of gas in galaxy evolution, we study the mass–metallicity relation of SDSS galaxies and show that as a third parameter gas mass is better than star formation rate at reducing the scatter of the relation, as predicted by models and simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Thick filament activation is different in fast- and slow-twitch skeletal muscle

The contractile properties of fast-twitch and slow-twitch skeletal muscles are primarily determined by the myosin isoform content and modulated by a variety of sarcomere proteins. X-ray diffraction studies of regulatory mechanisms in muscle contraction have focused predominately on fast- or mixed-fibre muscle with slow muscle being much less studied. Here, we used time-resolved X-ray diffraction to investigate the dynamic behaviour of the myofilament proteins in relatively pure slow-twitch-fibre rat soleus (SOL) and pure fast-twitch-fibre rat extensor digitorum longus (EDL) muscle during twitch and tetanic contractions at optimal length. During twitch contractions the diffraction signatures indicating a transition in the myosin heads from ordered OFF states, where heads are held close to the thick filament backbone, to disordered ON states, where heads are free to bind to thin filaments, were found in EDL and not in SOL muscle. During tetanic contraction, changes in the disposition of myosin heads as active tension develops is a quasi-stepwise process in EDL muscle whereas in SOL muscle this relationship appears to be linear. The observed reduced extensibility of the thick filaments in SOL muscle as compared to EDL muscles indicates a molecular basis for this behaviour. These data indicate that for the EDL, thick filament activation is a cooperative strain-induced mechano-sensing mechanism, whereas for the SOL, thick filament activation has a more graded response. Further, these different approaches to thick filament regulation in fast- and slow-twitch muscles may be adaptations for short-duration, strong contractions versus sustained, finely controlled contractions, respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management

3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression—factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure of the Diphtheria Toxin at Acidic pH: Implications for the Conformational Switching of the Translocation Domain

Diphtheria toxin, an exotoxin secreted by Corynebacterium that causes disease in humans by inhibiting protein synthesis, enters the cell via receptor-mediated endocytosis. The subsequent endosomal acidification triggers a series of conformational changes, resulting in the refolding and membrane insertion of the translocation (T-)domain and ultimately leading to the translocation of the catalytic domain into the cytoplasm. Here, we use X-ray crystallography along with circular dichroism and fluorescence spectroscopy to gain insight into the mechanism of the early stages of pH-dependent conformational transition. For the first time, we present the high-resolution structure of the diphtheria toxin at a mildly acidic pH (5–6) and compare it to the structure at neutral pH (7). We demonstrate that neither catalytic nor receptor-binding domains change their structure upon this acidification, while the T-domain undergoes a conformational change that results in the unfolding of the TH2–3 helices. Surprisingly, the TH1 helix maintains its conformation in the crystal of the full-length toxin even at pH 5. This contrasts with the evidence from the new and previously published data, obtained by spectroscopic measurements and molecular dynamics computer simulations, which indicate the refolding of TH1 upon the acidification of the isolated T-domain. The overall results imply that the membrane interactions of the T-domain are critical in ensuring the proper conformational changes required for the preparation of the diphtheria toxin for the cellular entry.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1974

Rotationsal and vibrational spectra of molecular ions: Feasibility of laboratory and astrophysical observation

The rotational spectra of a number of small molecular ions should be detectable in the microwave or millimeter wave regions in laboratory experiments using currently available techniques. The dipole moments and absorption coefficients of polar diatomics CO(+) and NO(+) as well as asymmetric isotopically enriched species, like O-18O-16(+), NE-20NE-22(+), and OC-18 O-16(+) are calculated to be sufficiently large to allow observation of their spectra. In addition to the detailed molecular structure information which such spectral data would provide, precise knowledge of the transition frequencies would render likely the detection of certain of these ions in the interstellar sources or in planetary atmospheres. All of these ions also possess vibrational spectra which should be detectable in the infrared region in laboratory or astrophysical sources.

Woods, R. C.↗
NASA NTRS1986

Para hydrogen equilibration in the atmospheres of the outer planets

The thermodynamic behavior of the atmospheres of the Jovian planets is strongly dependent on the extent to which local thermal equilibration of the ortho and para states of molecular hydrogen is achieved. Voyager IRIS data from Jupiter imply substantial departures of the para hydrogen fraction from equilibrium in the upper troposphere at low latitudes, but with values approaching equilibrium at higher latitudes. Data from Saturn are less sensitive to the orth-para ratio, but suggest para hydrogen fractions near the equilibrium value. Above approximately the 200 K temperature level, para hydrogen conversion can enhance the efficiency of convection, resulting in a substantial increase in overturning times on all of the outer planets. Currently available data cannot definitively establish the ortho-para ratios in the atmospheres of Uranus and Neptune, but suggest values closer to local equilibrium than to the 3.1 normal ratio. Modeling of sub-millimeter wavelength measurements of these planets suggest thermal structures with frozen equilibrium lapse rates in their convective regions.

Conrath, Barney J.↗
NASA NTRS1988

Effect of thermal spike on composite moisture capacity

As part of a continuing study of the effects of thermal spike on composite physical properties, severals sets of 16-ply TGDDM-DDS epoxy/graphite fiber composites were first saturated with moisture, and then individual specimens were subjected to thermal spikes of up to 240 C for periods of up to 25 minutes. At the cure temperature, 177 C, all sets show a change in rate of mass lost during spike. Post-spike moisture reabsorption capacity data provides evidence of temperature dependent molecular structural dilation and consolidation of the epoxide matrix. This evidence suggests that either a thermoreversible phenomenon such as physical aging or a nonreversible additional cure becomes active near the upper limit of the aircraft supersonic flight profile. These and other important observations suggest that one or more of several mechanisms may be active during thermal spike.

Adamson, M. J.↗
NASA NTRS1990

An infrared study of Orion Molecular Cloud-2 (OMC-2)

This paper reports 1.2-23 micron photometry for 11 discrete sources in Orion Molecular Cloud-2 (OMC-2). These data, combined with H and K photometric and K polarimetric images, are used to model the cluster sources. Most appear to be young stars of roughly solar mass. Some have circumstellar dust reradiation or reflection nebulosity. A model based on single scattering of light from an exciting star explains some features of the IRS 1 nebula, the largest reflection nebula in OMC-2. However, the red colors and high surface brightness of the IRS 1 nebula require a cool excitation source that is more luminous than far-infrared observations would indicate.

Johnson, J. J.↗
NASA NTRS1991

The pituitary - Aging and spaceflown rats

Decrements in growth hormone (GH) release we observed in two spaceflight experiments and four tail-suspended rat studies mimic age-associated changes in the mammalian pituitary GH system seen by Meites and others. The spaceflight data suggest that formation of high molecular weight bioactive disulfide-linked aggregates of the 20 and 22K monomeric GH forms may be reduced in microgravity, thereby, reducing target tissue activity. Correlative studies to confirm spaceflight as a model for pituitary GH system aging should include: (1) investigation of mechanisms of intracellular hormone packaging, (2) consequences to biological activity of the hormone molecule, and (3) study of intracellular microtubule dynamics.

Hymer, W. C.↗
NASA NTRS1996

Experimental Modification of Rat Pituitary Prolactin Cell Function During and After Spaceflight

Experimental modification of rat pituitary prolactin cell function during and after spaceflight. This study was done to evaluate the effects of microgravity on prolactin (PRL) cells of the male rat pituitary gland. We used the identical passive closed-vial cell culture system that was described for the culture of growth hormone cells (W C. Hymer, R. E. Grindeland, T. Salada, P. Nye, E. Grossman, and R Lane). After an 8-day spaceflight, all flight media (containing released PRL), as well as extracts (containing intracellular PRL), contained significantly lower amounts of immunoreactive PRL than their corresponding ground control samples. On the other hand, these same samples, when assessed for their biological activities by two different in vitro lymphocyte assays, yielded disparate results that may reflect posttranslational modifications to the hormone molecule. Other data showed that: (1) the apparent molecular weights of released PRL molecules were not altered by microgravity; but (2) the region from which the PRL cells came (dorsal or ventral) made a significant difference in the amount and activity of PRL released from the flight cells. Because there is much current interest in the role that PRL may play in the regulation of the immune system and because changes in both cellular and humoral immunity accompany spaceflight, this study could help define future microgravity research in this area.

Hymer, W. C.↗