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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Structure of the Receptor Binding Domain of EnvP(b)1, an Endogenous Retroviral Envelope Protein Expressed in Human Tissues

EnvP(b)1 is an endogenous retroviral envelope gene found in human and other primate genomes. We report EnvP(b)1 sequences in primate genomes consistent with an integration event between 40 and 71 million years ago. Using a highly specific polyclonal antiserum raised against the putative receptor binding domain (RBD) of human EnvP(b)1, we detected expression in human placenta, ovaries, and thymus. We found that EnvP(b)1 is proteolytically processed, and using cell-cell fusion assays in multiple primate cell lines, we demonstrated that extant EnvP(b)1 proteins from a variety of primate genomes are fusogenic. This work supports the idea that EnvP(b)1 is under purifying selection and its fusogenic activity has been maintained for over 40 million years. We determined the structure of the RBD of human EnvP(b)1, which defines structural similarities with extant leukemia viruses, despite little sequence conservation. This structure highlights a common scaffold from which novel receptor binding specificities likely evolved. The evolutionary plasticity of this domain may underlie the diversity of related Envs in circulating viruses.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2011

Dynamics of Vegetatin Indices in Tropical and Subtropical Savannas Defined by Ecoregions and Moderate Resolution Imaging Spectoradiometer (MODIS) Land Cover

In this study, we explored the capacity of vegetation indices derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) reflectance products to characterize global savannas in Australia, Africa and South America. The savannas were spatially defined and subdivided using the World Wildlife Fund (WWF) global ecoregions and MODIS land cover classes. Average annual profiles of Normalized Difference Vegetation Index, shortwave infrared ratio (SWIR32), White Sky Albedo (WSA) and the Structural Scattering Index (SSI) were created. Metrics derived from average annual profiles of vegetation indices were used to classify savanna ecoregions. The response spaces between vegetation indices were used to examine the potential to derive structural and fractional cover measures. The ecoregions showed distinct temporal profiles and formed groups with similar structural properties, including higher levels of woody vegetation, similar forest savanna mixtures and similar grassland predominance. The potential benefits from the use of combinations of indices to characterize savannas are discussed.

Hill, Michael J.↗
DOE OSTI2020

Solitary zonal structures in subcritical drift waves: a minimum model

Solitary zonal structures have recently been identified in gyrokinetic simulations of subcritical drift-wave (DW) turbulence with background shear flows. However, the nature of these structures has not been fully understood yet. Here, we show that similar structures can be obtained within a reduced model, which complements the modified Hasegawa–Mima equation with a generic primary instability and a background shear flow. We also find that these structures can be qualitatively reproduced in the modified Hasegawa–Wakatani equation, which subsumes the reduced model as a limit. In particular, we illustrate that in both cases, the solitary zonal structures approximately satisfy the same 'equation of state', which is a local relation connecting the DW envelope with the zonal-flow velocity. Due to this generality, our reduced model can be considered as a minimum model for solitary zonal structures in subcritical DWs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS1991

A model of onshore-offshore change in faunal diversity

Onshore-offshore patterns of faunal change occurred at many taxonomic scales during the Paleozoic Era, ranging from replacement of the Cambrian evolutionary fauna by the Paleozoic fauna to the environmental expansion of many orders and classes. A simple mathematical model is constructed to investigate such change. The environmental gradient across the marine shelf-slope is treated as a linear array of discrete habitats, each of which holds a set number of species, as observed in the fossil record. During any interval of time, some portion of the species in each habitat becomes extinct by background processes, with rates of extinction varying among both clades and habitats, as also observed in the record. After extinction, species are replaced from within the habitat and from immediately adjacent habitats, with proportions dependent on surviving species. This model leads to the prediction that extinction-resistant clades will always diversify at the expense of extinction-prone clades. But if extinction intensity is highest in nearshore habitats, extinction-resistant clades will expand preferentially in the onshore direction, build up diversity there, and then diversify outward toward the offshore. Thus, onshore-offshore patterns of diversification may be the expectation for faunal change quite independently of whether or not clades originate onshore. When the model is parameterized for Paleozoic trilobites and brachiopods, numerical solutions exhibit both a pattern of faunal change and a time span for diversification similar to that seen in the fossil record. They also generate structure similar to that seen in global diversification, including logistic patterns of growth, declining origination but constant extinction within clades through time, and declining overall extinction across clades through time.

NASA Discipline Number 52-40↗
NASA NTRS1983

A linear analysis of the transition curve for the baroclinic annulus

A primitive equation linear model is shown to be capable of quantitatively predicting the neutral curve for a baroclinic annulus. Flows unstable to small nonaxisymmetric perturbations are assumed to lie on the nonaxisymmetric side of a transition curve, while the stable flows are on the axisymmetric side. The stability in the presence of perturbations is tested with linearized hydrostatic primitive equations. Attention is given to the fastest growing eigenmodes, demonstrating that the linear and nonlinear wave have similar structures at a particular point in the nonaxisymmetric regime. All the waves are similar to the Eddy wave except at the extreme to the transition curve, where the waves maintain little structure with height. The eddy kinetic energy is baroclinic with a potential energy suppresed by the large static stability of the basic state. Eddy dissipation is noted to be significant near all boundaries.

Miller, T. L.↗
NASA NTRS2022

Quantifying Structural Relationships of Metal-Binding Sites Suggests Origins of Biological Electron Transfer

Biological redox reactions drive planetary biogeochemical cycles. Using a novel, structure-guided sequence analysis of proteins, we explored the patterns of evolution of enzymes responsible for these reactions. Our analysis reveals that the folds that bind transition metal–containing ligands have similar structural geometry and amino acid sequences across the full diversity of proteins. Similarity across folds reflects the availability of key transition metals over geological time and strongly suggests that transition metal–ligand binding had a small number of common peptide origins. We observe that structures central to our similarity network come primarily from oxidoreductases, suggesting that ancestral peptides may have also facilitated electron transfer reactions. Last, our results reveal that the earliest biologically functional peptides were likely available before the assembly of fully functional protein domains over 3.8 billion years ago. Thus, life is a special, very complex form of motion of matter, but this form did not always exist, and it is not separated from inorganic nature by an impassable abyss; rather, it arose from inorganic nature as a new property in the process of evolution of the world. We must study the history of this evolution if we want to solve the problem of the origin of life.

Yana Bromberg↗
DOE OSTI2021

Optimizing FPGA-based Accelerator Design for Large-Scale Molecular Similarity Search (Special Session Paper)

Molecular similarity search has been widely used in drug discovery to rapidly identify structurally similar compounds from large molecular databases. With the increasing size of chemical libraries, there is growing interest in the efficient ac- celeration of large-scale similarity search. Existing works mainly focus on CPU and GPU to accelerate the computation of Tatimoto coefficient in measuring the pairwise similarity between different molecular fingerprints. In this paper, we propose and optimize an FPGA-based accelerator design on exhaustive and approximate search algorithms. On exhaustive search using BitBound & fold- ing, we analyze the similarity cutoff and folding level relationship with search speedup and accuracy, and propose a scalable on- the-fly query engine on FPGAs to reduce the resource utilization and pipeline interval. We achieve a 450 million compounds-per- second processing throughput for a single query engine. On approximate search using hierarchical navigable small world (HNSW), a popular algorithm with high recall and query speed, we propose an FPGA-based graph traversal engine to utilize high throughput register array based priority queue and fine- grained distance calculation engine to increase the processing capability. Experimental results show that the proposed FPGA- based HNSW implementation achieves a 35× speedup than existing works on CPU. To the best of our knowledge, our FPGA- based implementation is the first attempt to accelerate molecular similarity search on FPGA and has the highest performance among existing approaches.

Peng, Hongwu↗
NASA NTRS1989

MEVTV Workshop on Tectonic Features on Mars

The state of knowledge of tectonic features on Mars was determined and kinematic and mechanical models were assessed for their origin. Three sessions were held: wrinkle ridges and compressional structure; strike-slip faults; and extensional structures. Each session began with an overview of the features under discussion. In the case of wrinkle ridges and extensional structures, the overview was followed by keynote addresses by specialists working on similar structures on the Earth. The first session of the workshop focused on the controversy over the relative importance of folding, faulting, and intrusive volcanism in the origin of wrinkle ridges. The session ended with discussions of the origin of compressional flank structures associated with Martian volcanoes and the relationship between the volcanic complexes and the inferred regional stress field. The second day of the workshop began with the presentation and discussion of evidence for strike-slip faults on Mars at various scales. In the last session, the discussion of extensional structures ranged from the origin of grabens, tension cracks, and pit-crater chains to the origin of Valles Marineris canyons. Shear and tensile modes of brittle failure in the formation of extensional features and the role of these failure modes in the formation of pit-crater chains and the canyons of Valles Marineris were debated. The relationship of extensional features to other surface processes, such as carbonate dissolution (karst) were also discussed.

Watters, Thomas R.↗
NASA NTRS1994

Evolution of the Southern Hemisphere subpolar middle atmosphere during summer and autumn

The evolution of zonal wind and zonal wavenumber one (wave 1) in the Southern Hemisphere subpolar middle atmosphere is described for the period December 1978 - May 1979 using temperature and ozone measurements from the Limb Infrared Monitor of the Stratosphere (LIMS) experiment. In late December maximum zonal easterlies of approx. -70 m/s are observed at 0.1 mb, 60 deg S. A zonal flow reversal occurs during late February and westerlies subsequently increase to 60-70 m/s in the upper stratosphere by April - May. LIMS zonal winds are compared with rocketsonde measurements and nadir sounder (derived) winds for summer and autumn. Although quantitative agreement is found at stratospheric levels, substantial discrepancies are evident in the mesosphere, most likely a reflection of sampling and resolution differences in the respective datasets. Stationary and traveling wave 1 temperature disturbances (amplitudes approx. 1 - 2 K at 60 deg S) are observed by LIMS during summer. The stationary wave is confined to the lower stratosphere near the level of zero zonal- mean wind flow, whereas the traveling wave is prominent in the middle stratosphere moves west at a rate similar to the zonal-mean wind, and exhibits a vertical - meridional structure similar to a P(sub 4)(sup 1) normal mode Rossby wave. A substantial intensification of wave 1 activity occurs during autumn (amplitudes approx. 5 - 10 K), which is found to be associated with an upward-directed Eliasse - Palm flux near the subpolar tropopause level. Evidence relating wave 1 activity in the lower - middle stratosphere to the occurrence of zonal ozone perturbations of 10% - 20% amplitude is presented for summer and autumn.

Miles, T.↗
DOE OSTI2023

Ultrasparse View X-ray Computed Tomography for 4D Imaging

X-ray computed tomography (CT) is a noninvasive, nondestructive approach to imaging materials, material systems, and engineered components in two and three dimensions. Acquisition of three-dimensional (3D) images requires the collection of hundreds or thousands of through-thickness X-ray radiographic images from different angles. Such 3D data acquisition strategies commonly involve suboptimal temporal sampling for in situ and operando studies (4D imaging). Herein, we introduce a sparse-view imaging approach, Tomo-NeRF, which is capable of reconstructing high-fidelity 3D images from <10 twodimensional radiographic images. Experimental 2D and 3D X-ray images were used to test the reconstruction capability in two-view, four-view, and six-view scenarios. Tomo-NeRF is capable of reconstructing 3D images with a structural similarity of 0.9971–0.9975 and a voxel-wise accuracy of 81.83–89.59% from 2D experimentally obtained images. Furthermore, the reconstruction accuracy for the experimentally obtained images is less than the synthetic structures. Experimentally obtained images demonstrate a similarity of 0.9973–0.9984 and a voxelwise accuracy of 84.31–95.77%.

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

Trace Compound Analysis in TATB by Liquid Chromatography coupled with Spectroscopic and Spectrometric Detection

Accurate quantitation of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is important because of its strategic use as an energetic material. A purity determination is also needed for the proper assessment of performance. A fast and sensitive method has been developed to measure the purity of TATB in polymer-bonded materials. The target material is extracted with DMSO, and the extract is separated on a reversed-phase chromatography column. The column effluent is monitored by diode array detection (DAD) at 354 nm. The characteristic UV-Vis response and retention time identify the individual components when compared to pure compound standards. The chemical structures of compounds with no pure standards available have been determined by high-resolution mass spectrometry (MS) and MS/MS. The major component, TATB, along with 1-chloro-3,5-dinitro-2,4,6-triaminobenzene (T4A) and mono-benzofuroxan (FX1) were quantitated directly from pure compound standards. Several trace concentration components, mono-benzofurazan (F1), 1-bromo-3,5-dinitro-2,4,6-triaminobenzene (Br-T4A), 2,4,6-triamino-1-nitroso-3,5-dinitrobenzene (MN-TATB), 2,4,6-triamino-1-hydroxyl-3,5-dinitrobenzene (HO-TATB), and 2,4,6-triamino-1-nitrile-3,5-dinitrobenzene (Nitrile-TATB) were also detected and structures verified via MS/MS. Approximate concentrations were determined using calibrations from standards of similar structures. Additional trace components were also detected by MS. Contained herein are the results of analyses of TATB-based materials characterized for polymer-bonded formulations compared to different preparations of TATB. The accuracy, details, and process of developing this method are reported here.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea

Abstract Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr -like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis . Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Introducing a multiscale feature integration network for inpainting with applications to enhanced CMB map reconstruction

We introduce a novel neural network, SkyReconNet, which combines the expanded receptive fields of dilated convolutional layers along with standard convolutions, to capture both the global and local features for reconstructing the missing information in an image. We implement our network to inpaint the masked regions in a full-sky cosmic microwave background (CMB) map. Inpainting CMB maps is a particularly formidable challenge when dealing with extensive and irregular masks, such as galactic masks which can obscure substantial fractions of the sky. The hybrid design of SkyReconNet leverages the strengths of standard and dilated convolutions to accurately predict CMB fluctuations in the masked regions by effectively utilizing the information from surrounding unmasked areas. During training, the network optimizes its weights by minimizing a composite loss function that combines the structural similarity index measure (SSIM) and mean squared error (MSE). SSIM preserves the essential structural features of the CMB, ensuring an accurate and coherent reconstruction of the missing CMB fluctuations, while MSE minimizes the pixelwise deviations, thus enhancing the overall accuracy of the predictions. The predicted CMB maps and their corresponding angular power spectra align closely with the targets, achieving the performance limited only by the fundamental uncertainty of cosmic variance. The network’s generic architecture enables application to other physics-based challenges involving data with missing or defective pixels, systematic artifacts, etc. In conclusion, our results demonstrate its effectiveness in addressing the challenges posed by large irregular masks, offering a significant inpainting tool not only for CMB analyses but also for image-based experiments across disciplines where such data imperfections are prevalent.

Cosmic microwave background↗
NASA NTRS1973

Evaluation of forming and manufacturing characterisitics of boron/aluminum materials

Low cost techniques were evaluated for forming boron-reinforced aluminum structural shapes from diffusion-bonded flat sheet and plate. Successful forming was accomplished on fully consolidated material up to .46 cm (0.180) in thick. Five hot section 12 in long were formed from 0.100 thick flat plates 12 in long by 7 in wide. Three of the hat sections were tested in cyclic compression to demonstrate the performance capability of structures by this type of low-cost secondary fabrication. The structural efficiency of these hats was found to be equal or superior to similar structures fabricated by more costly techniques.

Dolowy, J. F., Jr.↗
NASA NTRS1999

Characterizing the Small Scale Structure in Clusters of Galaxies

We have applied a wavelet transform analysis to quantify the small-scale (less than a few arcminutes) X-ray structure of clusters of galaxies to several clusters. Three of these clusters show interesting structure. In addition to the small scale structure in surface brightness, we have searched for temperature structure using Advanced Satellite for Cosmology and Astrophysics (ASCA) observations. For A754, we find a filamentary structure, similar to that previously detected in A85. For A119, we find small scale structure associated with both cool and hot regions with a hot filament extending to the northeast. For A1750, one of the first clusters to show substructure from Einstein, we have a rederived the substructure from the ROSAT observations. The ASCA observations show a hot region between the two small scale features - sub-clusters. The hot region shows that the two subclusters are merging and producing a shock wave at the leading edge of the interaction. This analysis had been applied to a sample of 17 clusters to determine the radial distribution of substructure in a sample. The number of detected substructures was rather small and it was decided to select a different cluster sample at larger redshift. This provided a larger radial range over which substructure could be detected. This new cluster sample also includes about 20 clusters and is being analyzed. Finally, we are considering how to compare the substructure parameters of nearby clusters with a more distant sample to see if one can extract cosmological information. Since substructure frequency should depend on the cosmological density parameter, it may be possible to derive new constraints by comparing nearby and distant clusters.

Forman, William R.↗
NASA NTRS1985

Middle atmosphere (60-110 km) tidal oscillations at Saskatoon, Canada (52 deg N, 107 deg W) during 1983/84

Since mid-1978, the medium frequency (2.2 MHz; M.F.) radar at Saskatoon has run continuously, measuring winds by the spaced antenna method in the upper middle atmosphere. As there is so much dynamics activity during the years of MAP it seems very important to establish the features of the tidal field at Saskatoon during 1983 to 1984, and compare these with the climatology from the four years 1978 to 1979 and 1981 to 1982. Wind profiles with 60 to 110 km (80 to 110 km at night) with 3 km resolution are obtained every 5 minutes by means of a full-correlation analysis. Hourly means are formed and harmonic analysis applied to sets of data to obtain the mean winds and tidal oscillation amplitudes and phases. The zonal wind field at Saskatoon is structurally similar to CIRA-72; however, the wind eastward cell is weaker and much more structured, and the summer eastward cell above 85 km is also weaker. For the semidiurnal tide, a strong seasonal change exists, with larger amplitudes and shorter wavelengths, in winter-like months and the reverse in summer-like months. A summary of the tidal parameters at 90 km is given, where mean values from 1978 to 1982 are also shown. This seasonal variation of tides is a midlatitude climatology, as comparisons with Monpazier, France and Christchurch, New Zealand show very similar behavior, as does Durham; and requires antisymmetric tidal modes such as 2,3 and 2,5. Considering the diurnal tide, for most months centered on summer there are long wavelength modes, or superposition of several models. However, some winter months show a short wavelength mode. A summary of the 90 km characteristics is presented.

Manson, A. H.↗
NASA NTRS1977

The trapped mercury ion frequency standard

Singly ionized mercury atoms have a structure similar to neutral alkali atoms. They can be maintained as ions for very long times in an RF quadrupole ion trap. Thus, their ground state hyperfine structure can be used to make a frequency standard using optical pumping techniques similar to the well-known rubidium standard. The mass 199 isotope of mercury has an ionic hyperfine structure of 40.5 GHz. In a trap system a linewidth of 10 Hz has been measured. An expression is presented for the short-term stability of a proposed mercury standard as set by the achieved signal to noise ratio. There is prospect of further improvement. Long-term stability is affected by second order doppler effect, and by pressure, light, and Stark shifts. However, these appear either sufficiently small or sufficiently controlable that the proposed mercury ion standard would be competitive with existing standards.

Mcguire, M. D.↗
DOE OSTI2022

Grain incompatibility determines the local structure of amorphous grain boundary complexions

Amorphous grain boundary complexions lack long-range crystalline order but are not featureless, as distinct gradients in structural short-range order have been reported through their thickness. In this work, we test the hypothesis that the distribution of short-range order is determined by the confining crystals using atomistic simulations of both Cu-Zr bicrystals and a random polycrystal. Voronoi polyhedra with structures similar to that of perfect face-centered cubic serve as signatures of high structural order and are only found at the amorphous-crystalline transition regions. The density of the ordered structural motifs within a specific amorphous-crystalline transition region is found to not be directly determined by the orientation and symmetry of the grain which touches it, but rather by the incompatibility between the two confining grains. Further, ordered polyhedra density is found to be inversely related to grain incompatibility, meaning that large incompatibilities between the confining crystals lead to less order in the amorphous-crystalline transition region. The finding that the entire grain-film-grain system must be considered to understand local structure unequivocally demonstrates that amorphous complexions are not simply a collection of independent phases which happen to nucleate at a grain boundary. Rather, an amorphous grain boundary complexion is a single entity that finds a local equilibrium configuration.

36 MATERIALS SCIENCE↗