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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 OSTI2019

Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies

An array of carbohydrates masks the HIV-1 surface protein Env, contributing to the evasion of humoral immunity. In most HIV-1 isolates ‘glycan holes’ occur due to natural sequence variation, potentially revealing the underlying protein surface to the immune system. Here we computationally design epitopes that mimic such surface features (carbohydrate-occluded neutralization epitopes or CONE) of Env through ‘epitope transplantation’, in which the target region is presented on a carrier protein scaffold with preserved structural properties. Scaffolds displaying the four CONEs are examined for structure and immunogenicity. Crystal structures of two designed proteins reflect the computational models and accurately mimic the native conformations of CONEs. The sera from rabbits immunized with several CONE immunogens display Env binding activity. Our method determines essential structural elements for targets of protective antibodies. The ability to design immunogens with high mimicry to viral proteins also makes possible the exploration of new templates for vaccine development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

K-Shell photoabsorption in Si 11+ : Relativistic contributions via Breit-Pauli R-matrix calculations

As a part of the investigation of the entire Si isonuclear sequence for x-ray spectral diagnostics, we focus on the Li-like Si 11+ ion, a stable component that features prominently in x-ray astrophysical spectra. In this work, we perform R-matrix calculations for the photoabsorption cross section of Si 11+ including relativistic contributions via the use of a Breit-Pauli Hamiltonian. Relativistic effects—predominantly spin-orbit splitting of resonances and mass-velocity and one-body Darwin global shifts of energies— are shown to be tractable and of importance for accuracy in x-ray spectral modeling data banks.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies

Changing the course of the human immunodeficiency virus type I (HIV-1) pandemic is a high public health priority with approximately 39 million people currently living with HIV-1 (PLWH) and about 1.5 million new infections annually worldwide. Broadly neutralizing antibodies (bnAbs) typically target highly conserved sites on the HIV-1 envelope glycoproteins (Envs), which mediate viral entry, and block the infection of diverse HIV-1 strains. But different mechanisms of HIV-1 resistance to bnAbs prevent robust application of bnAbs for therapeutic and preventive interventions. Here we report the development of a new database that provides data and computational tools to aid the discovery of resistant features and may assist in analysis of HIV-1 resistance to bnAbs. Bioinformatic tools allow identification of specific patterns in Env sequences of resistant strains and development of strategies to elucidate the mechanisms of HIV-1 escape; comparison of resistant and sensitive HIV-1 strains for each bnAb; identification of resistance and sensitivity signatures associated with specific bnAbs or groups of bnAbs; and visualization of antibody pairs on cross-sensitivity plots. The database has been designed with a particular focus on user-friendly and interactive interface. Our database is a valuable resource for the scientific community and provides opportunities to investigate patterns of HIV-1 resistance and to develop new approaches aimed to overcome HIV-1 resistance to bnAbs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Genomes OnLine database (GOLD) v.7: updates and new features

The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project. Currently GOLD hosts information on 33 415 Studies, 49 826 Biosamples, 313 324 Organisms, 215 881 Sequencing Projects and 174 454 Analysis Projects with a total of 541 metadata fields, of which 80 are based on controlled vocabulary (CV) terms. GOLD provides a user-friendly web interface to browse sequencing projects and launch advanced search tools across four classification levels. Users submit metadata on a wide range of Sequencing and Analysis Projects in GOLD before depositing sequence data to the Integrated Microbial Genomes (IMG) system for analysis. GOLD conforms with and supports the rules set by the Genomic Standards Consortium (GSC) Minimum Information standards. The current version of GOLD (v.7) has seen the number of projects and associated metadata increase exponentially over the years. This paper provides an update on the current status of GOLD and highlights the new features added over the last two years.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Deep‐sea hydrothermal vent metagenome‐assembled genomes provide insight into the phylum Nanoarchaeota

Summary Ectosymbiotic Nanoarchaeota live on the surface of diverse archaeal hosts. Despite being broadly distributed in global geothermal systems, only three Nanoarchaeota have been successfully co‐cultivated with their hosts, and until now no nanoarchaeotal cultures or genomes have been described from deep‐sea hydrothermal vents. We recovered three nanoarchaeotal metagenome‐assembled genomes (MAGs) from deep‐sea hydrothermal vent sites at the Eastern Lau Spreading Center (M10‐121), Guaymas Basin (Gua‐46) and the Mid‐Cayman Rise (MC‐1). Based on average amino acid identity analysis, M10‐121 is a novel species in the candidate genus Nanoclepta, while the other two MAGs represent novel genera in the Nanoarchaeota . Like previously sequenced Nanoarchaeota, each MAG encodes at least one split protein‐coding gene. The MAGs also contain a mosaic of key nanoarchaeotal features, including CRISPR repeat regions and marker genes for gluconeogenesis and archaeal flagella. MC‐1 also encodes the pentose bisphosphate pathway, which may allow the nanoarchaeote to bypass several steps in glycolysis and produce ATP.

St. John, Emily↗
DOE OSTI2018

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

BACKGROUND: Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis , has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley ( Hordeum vulgare ). RESULTS: The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes ( SPs ) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs , but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome. CONCLUSIONS: The characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a "one-speed" genome that differs in its architecture and (co-)evolutionary pattern from the "two-speed" genomes reported for several other filamentous phytopathogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Atomically Defined Edge-Doping of Graphene Nanoribbons for Mesoscale Electronics

The outstanding transformative potential of graphene, an infinite two-dimensional sheet of carbon atoms tightly packed into a honeycomb lattice, has been recognized mostly due to its exceptionally high electric conductivity, thermal conductivity, and tensile strength. These undeniably very desirable properties, however, represent only a very small facet of the true potential of all-sp2 carbon materials and its promise to revolutionize the field of molecular electronics. Graphene's most unusual characteristics emerge when the infinite macroscopic sheet is scaled down to nanometer dimensions. The exploration, realization, and implementation of these truly exotic magnetic and electronic properties rely on the development of innovative synthetic strategies that provide atomically precise control over the self-assembly of mesoscale objects. While traditional device architectures based on inorganic semiconductors have been fabricated using a top-down approach, we pursued a diametrically opposite strategy. Our design of a new generation of high-performance electronic materials relies on a modular bottom-up strategy. This highly multidisciplinary research program has been rooted in the synthesis of functional organic materials with precisely defined properties, their controlled assembly into hierarchical structures, and the evaluation of their performance at the molecular and the macroscopic scale. A part of this research program we have developed the chemical tools required to synthesize and to fine-tune the physical properties of graphene nanoribbons (GNR) with atomic precision. We further demonstrated that the innovative techniques and the expanded knowledge can be used to rationally tailor desired physical properties and function into nanometer-scale carbon-based electronic devices; e.g. transistors as logic gates in computing, data storage media based on electrically gated spin valves, or molecular amplifiers, all functionally integrated in atomically defined GNRs. We demonstrated the design and experimental realization of a rationally engineered graphene nanoribbon superlattice that hosts a 1D array of symmetry-protected topological states. We developed a hierarchical bottom-up fabrication strategy for graphene nanoribbons that preferentially exhibit a single heterojunction interface rather than a random statistical sequence of junctions along the ribbon. We reported the bottom-up synthesis of a series of atomically precise graphene nanoribbons featuring trigonal planar heteroatom dopants (nitrogen, oxygen, and sulfur) along the edges that induce a narrowing of the intrinsic band gap by ~0.2–0.3 eV per dopant atom. We reported the bottom-up synthesis of a graphene nanoribbon heterostructure featuring a highly tunable porphyrin quantum dot embedded at the center of a solution processable graphene nanoribbon. We reported a new technique for fabricating bottom-up graphene nanoribbon heterojunctions through a late-stage chemical transformation that results in atomically sharp heterojunction structures from a single precursor. We demonstrated the intrinsic performance enhancement of a composite material comprised of gold nanoparticles (AuNPs) embedded in a bottom-up synthesized graphene nanoribbon matrix for the electrocatalytic reduction of CO 2 . We developed a scalable, solution-based approach toward the synthesis of an exotic class of polycyclic aromatic hydrocarbons that exhibit unusual electronic and magnetic properties in the ground state. We reported the bottom-up synthesis and characterization of atomically-defined graphene nanoribbons featuring a regioregular pattern of group III dopant atoms (boron) along the backbone of the ribbon.

36 MATERIALS SCIENCE↗
DOE OSTI2020

NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus–host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1982

The early-type component in v1 Sagittarii

Four low-resolution UV spectra of v1 Sgr (cK2) were obtained with the IUE satellite to investigate the nature of the hot component in this object, which was detected in the Astronomical Netherlands Satellite UV photometric data. The IUE results show that the spectral energy distribution of v1 Sgr in the FUV is comparable to that of a B9 star. FUV flux level, when compared with that of the mid-ultraviolet flux level, indicates that the luminosity of the hot component is roughly equivalent to that of a main-sequence star, assuming that the mid-ultraviolet flux is dominated almost entirely by a K2 I object. No discernible spectral features are present in the FUV, contrary to what may be expected in a star of B9 spectral type. Two possible interpretations are suggested: the hot component is a rapidly rotating star, or an accretion disk surrounding a central object which could be a collapsed star is being observed.

Kondo, Y.↗
NASA NTRS1983

VTOL shipboard letdown guidance system analysis

Alternative letdown guidance strategies are examined for landing of a VTOL aircraft onboard a small aviation ship under adverse environmental conditions. Off line computer simulation of shipboard landing task is utilized for assessing the relative merits of the proposed guidance schemes. The touchdown performance of a nominal constant rate of descent (CROD) letdown strategy serves as a benchmark for ranking the performance of the alternative letdown schemes. Analysis of ship motion time histories indicates the existence of an alternating sequence of quiescent and rough motions called lulls and swells. A real time algorithms lull/swell classification based upon ship motion pattern features is developed. The classification algorithm is used to command a go/no go signal to indicate the initiation and termination of an acceptable landing window. Simulation results show that such a go/no go pattern based letdown guidance strategy improves touchdown performance.

Phatak, A. V.↗
NASA NTRS1992

Efficient instruction sequencing with Inline Target Insertion

Inline target insertion, a specific compiler and pipeline implementation method for delayed branches with squashing, is defined. The method is shown to offer two important features not discovered in previous studies. First, branches inserted into branch slots are correctly executed. Second, the execution returns correctly from interrupts or exceptions with only one program counter. These two features result in better performance and less software/hardware complexity than conventional delayed branching mechanisms.

Hwu, Wen-Mei W.↗
NASA NTRS1999

Cometary Dust in the Debris Disks of HD 31648 and HD 163296: Two "Baby" (BETA) Pictoris Stars

The debris disks surrounding the pre-main-sequence stars HD 31648 and HD 163296 were observed spectroscopically between 3 and 14 microns. Both stars possess a silicate emission feature at 10 microns that resembles that of the star beta Pictoris and those observed in solar system comets. The structure of the band is consistent with a mixture of olivine and pyroxene material, plus an underlying continuum of unspecified origin. The similarity in both size and structure of the silicate band suggests that the material in these systems had a processing history similar to that in our own solar system prior to the time that the grains were incorporated into comets.

Sitko, Michael L.↗
NASA NTRS1999

Cometary Dust in the Debris of HD 31648 and HD163296: Two "Baby" Beta pictoris Stars

The debris disks surrounding the pre-main-sequence stars HD 31648 and HD 163296 were observed spectroscopically between 3 and 14 microns. Both stars possess a silicate emission feature at 10 Am that resembles that of the star P Pictoris and those observed in solar system comets. The structure of the band is consistent with a mixture of olivine and pyroxene material, plus an underlying continuum of unspecified origin. The similarity in both size and structure of the silicate band suggests that the material in these systems had a processing history similar to that in our own solar system prior to the time that the grains were incorporated into comets.

Sitko, Michael L.↗
NASA NTRS2008

The Fredegonde (V-57) Quadrangle, Venus: Characterization of the Venus Midlands

The Fredegonde quadrangle (V-57, 50-75degS, 60-120degE) in the southern hemisphere of Venus represents a typical region of midlands (0-2 km above MPR). Midlands are the most widespread topographic province on Venus (approx.80%) and display the richest variety of features. Geological mapping in the V-57 quadrangle provides the possibility of defining and characterizing units that make up a region of midlands and to establish the general sequence of events there and thus address questions about the modes of formation and chronology of midlands on Venus. The map area is in contact with the uplands in the central portion of Lada Terra to the west and the lowlands of Aino Planitia to the northeast. This position also provides a transitional zone between the other two major topographic provinces, similar to that of the Meskhent Tessera (V-3) area. Here we report on the results of our mapping in the V-57 quadrangle, describe the major features, units, and structural assemblages exposed there, and outline the main episodes of geologic history.

Ivanov, M. A.↗
DOE OSTI2024

Invariant Features for Accurate Predictions of Quantum Chemical UV-vis Spectra of Organic Molecules

Including invariance of global properties of a phys-ical system as an intrinsic feature in graph neural networks (GNNs) enhances the model's robustness and generalizability and reduces the amount of training data required to obtain a desired accuracy for predictions of these properties. Existing open source GNN libraries construct invariant features only for specific GNN architectures. This precludes the generalization of invariant features to arbitrary message passing neural network (MPNN) layers which, in turn, precludes the use of these libraries for new, user-specified predictive tasks. To address this limitation, we implement invariant MPNNs into the flexible and scalable HydraGNN architecture. HydraGNN enables a seamless switch between various MPNNs in a unified layer sequence and allows for a fair comparison between the predictive performance of different MPNNs. We trained this enhanced HydraGNN archi-tecture on the ultraviolet-visible (UV-vis) spectrum of GDB-9 molecules, a feature that describes the molecule's electronic exci-tation modes, computed with time-dependent density functional tight binding (TD-DFTB) and available open source through the GDB-9-Ex dataset. We assess the robustness (i.e., accuracy and generalizability) of the predictions obtained using different invariant MPNNs with respect to different values of the full width at half maximum (FWHM) for the Gaussian smearing of the theoretical peaks. Our numerical results show that incorporating invariance in the HydraGNN architecture significantly enhances both accuracy and generalizability in predicting UV-vis spectra of organic molecules.

Baker, Justin↗
DOE OSTI2022

Sequentially regular polymer acceptors featuring flexible spacers for high-performance and mechanically robust all-polymer solar cells

Developing high-performance and mechanically robust polymer solar cells (PSCs) is crucial for realizing wearable power sources. While efficient all-polymer solar cells (all-PSCs) can be fabricated from polymerized small-molecule acceptors (PSMAs) with high optical absorption and electron mobilities, they still show limited mechanical robustness. Here, we achieve highly efficient and mechanically robust all-PSCs by designing a PSMA (PYFS-Reg) containing sequence-regular flexible spacers (FSs). The regular incorporation of the FS units into PSMAs is essential in simultaneously improving the electrical and mechanical properties of blend films. As a result, all-PSCs featuring PYFS-Reg achieve a high power conversion efficiency (PCE = 16.1%) and stretchability (crack onset strain (COS) = 22.4%), outperforming PSMAs without FSs (i.e., PYBDT, PCE = 12.6% and COS = 11.7%) or with randomly distributed FSs (i.e., PYFS-Ran, PCE = 12.2% and COS = 18.1%). Importantly, these all-PSCs are fabricated by an environmentally benign, non-halogenated solvent process. To further demonstrate their feasible applications in wearable devices, we construct intrinsically stretchable (IS) all-PSCs by using PYFS-Reg-based active layers, which exhibit a high PCE (10.6%) and excellent device stretchability (strain at PCE 80% = 36.7%).

14 SOLAR ENERGY↗
NASA NTRS2008

The Origin of the Terra Meridiani Sediments: Volatile Transport and the Formation of Sulfate Bearing Layered Deposits on Mars

The chemistry, sedimentology, and geology of the Meridiani sedimentary deposits are best explained by eolian reworking of the sublimation residue of a large scale ice/dust deposit. This large ice deposit was located in close proximity to Terra Meridiani and incorporated large amounts of dust, sand, and SO2 aerosols generated by impacts and volcanism during early martian history. Sulfate formation and chemical weathering of the initial igneous material is hypothesized to have occurred inside of the ice when the darker mineral grains were heated by solar radiant energy. This created conditions in which small films of liquid water were created in and around the mineral grains. This water dissolved the SO2 and reacted with the mineral grains forming an acidic environment under low water/rock conditions. Subsequent sublimation of this ice deposit left behind large amounts of weathered sublimation residue which became the source material for the eolian process that deposited the Terra Meridiani deposit. The following features of the Meridiani sediments are best explained by this model: The large scale of the deposit, its mineralogic similarity across large distances, the cation-conservative nature of the weathering processes, the presence of acidic groundwaters on a basaltic planet, the accumulation of a thick sedimentary sequence outside of a topographic basin, and the low water/rock ratio needed to explain the presence of very soluble minerals and elements in the deposit. Remote sensing studies have linked the Meridiani deposits to a number of other martian surface features through mineralogic similarities, geomorphic similarities, and regional associations. These include layered deposits in Arabia Terra, interior layered deposits in the Valles Marineris system, southern Elysium/Aeolis, Amazonis Planitia, and the Hellas basin, Aram Chaos, Aureum Chaos, and Ioni Chaos. The common properties shared by these deposits suggest that all of these deposits share a common formation process which must have acted over a large area of Mars. The results of this study suggest a mechanism for volatile transport on Mars without invoking an early greenhouse. They also imply a common formation mechanism for most of the sulfate minerals and layered deposits on Mars, which explains their common occurrence.

Niles, P.B.↗
NASA NTRS1990

The growth of short cracks in 4340 steel and aluminum-lithium 2090

The objectives were to investigate crack initiation characteristics and short crack growth behavior for Al-Li 2090 and for 4340 steel and to evaluate the ability of a closure-based crack-growth model to predict fatigue crack growth rates and total fatigue lives for the steel. Single-edge-notched tension specimens of each alloy were used to obtain the short crack growth rate information via an acetate replica technique. In addition to constant amplitude loading, tests on the steel were conducted using the Felix/28 variable amplitude spectrum (a shortened form of a standard loading sequence for fixed or semi-rigid helicopter rotors). The short crack growth rates were compared to those for long cracks grown under similar loading conditions. Metallurgical features associated with crack initiation are discussed. For Al-Li 2090 under R = -1 loading, the short cracks grew well below the long crack threshold and grew at acute angles to the loading axis. For 4340 steel under constant amplitude loading at R = 0.5 and 0 and for the Felix/28 spectrum loading, short-crack growth rates agreed well with long-crack growth rates, even near the long-crack threshold. A slight short-crack effect, growth below the long-crack threshold, was observed at R = -1. Fatigue lives were found to depend on the size and type of initiation site, especially for the Felix/28 loading sequence. A semi-empirical crack-growth model incorporating crack-closure effects was used to predict crack growth rates and total fatigue lives of notched 4340 steel specimens. An initial defect size and shape typical of those identified in this steel was assumed for the life predictions. For all loading conditions, reasonable agreement was found between measured and predicted values for both crack growth rates and fatigue lives.

Swain, M. H.↗