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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 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion

Orf8, one of the most puzzling genes in the SARS lineage of coronaviruses, marks a unique and striking difference in genome organization between SARS-CoV-2 and SARS-CoV-1. Here, using sequence comparisons, we unequivocally reveal the distant sequence similarities between SARS-CoV-2 Orf8 with its SARS-CoV-1 counterparts and the X4-like genes of coronaviruses, including its highly divergent “paralog” gene Orf7a, whose product is a potential immune antagonist of known structure. Supervised sequence space walks unravel identity levels that drop below 10% and yet exhibit subtle conservation patterns in this novel superfamily, characterized by an immunoglobulin-like beta sandwich topology. We document the high accuracy of the sequence space walk process in detail and characterize the subgroups of the superfamily in sequence space by systematic annotation of gene and taxon groups. While SARS-CoV-1 Orf7a and Orf8 genes are most similar to bat virus sequences, their SARS-CoV-2 counterparts are closer to pangolin virus homologs, reflecting the fine structure of conservation patterns within the SARS-CoV-2 genomes. The divergence between Orf7a and Orf8 is exceptionally idiosyncratic, since Orf7a is more constrained, whereas Orf8 is subject to rampant change, a peculiar feature that may be related to hitherto-unknown viral infection strategies. Despite their common origin, the Orf7a and Orf8 protein families exhibit different modes of evolutionary trajectories within the coronavirus lineage, which might be partly attributable to their complex interactions with the mammalian host cell, reflected by a multitude of functional associations of Orf8 in SARS-CoV-2 compared to a very small number of interactions discovered for Orf7a.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Gate Set Tomography

Gate set tomography (GST) is a protocol for detailed, predictive characterization of logic operations (gates) on quantum computing processors. Early versions of GST emerged around 2012-13, and since then it has been refined, demonstrated, and used in a large number of experiments. This paper presents the foundations of GST in comprehensive detail. The most important feature of GST, compared to older state and process tomography protocols, is that it is calibration-free . GST does not rely on pre-calibrated state preparations and measurements. Instead, it characterizes all the operations in a gate set simultaneously and self-consistently, relative to each other. Long sequence GST can estimate gates with very high precision and efficiency, achieving Heisenberg scaling in regimes of practical interest. In this paper, we cover GST's intellectual history, the techniques and experiments used to achieve its intended purpose, data analysis, gauge freedom and fixing, error bars, and the interpretation of gauge-fixed estimates of gate sets. Our focus is fundamental mathematical aspects of GST, rather than implementation details, but we touch on some of the foundational algorithmic tricks used in the pyGSTi implementation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

New Data Define the Molecular Phylogeny and Taxonomy of Four Freshwater Suctorian Ciliates With Redefinition of Two Families Heliophryidae and Cyclophryidae (Ciliophora, Phyllopharyngea, Suctoria)

Four suctorian ciliates, Cyclophrya magna Gönnert, 1935, Peridiscophrya florea (Kormos & Kormos, 1958) Dovgal, 2002, Heliophrya rotunda (Hentschel, 1916) Matthes, 1954 and Dendrosoma radians Ehrenberg, 1838, were collected from a freshwater lake in Ningbo, China. The morphological redescription and molecular phylogenetic analyses of these ciliates were investigated. Phylogenetic analyses inferred from SSU rDNA sequences show that all three suctorian orders, Endogenida, Evaginogenida, and Exogenida, are monophyletic and that the latter two clusters as sister clades. The newly sequenced P. florea forms sister branches with C. magna , while sequences of D. radians group with those from H. rotunda within Endogenida. The family Heliophryidae, which is comprised of only two genera, Heliophrya and Cyclophrya , was previously assigned to Evaginogenida. There is now sufficient evidence, however, that the type genus Heliophrya reproduces by endogenous budding, which corresponds to the definitive feature of Endogenida. In line with this and with the support of molecular phylogenetic analyses, we therefore transfer the family Heliophryidae with the type genus Heliophrya to Endogenida. The other genus, Cyclophrya , still remains in Evaginogenida because of its evaginative budding. Therefore, combined with morphological and phylogenetic analysis, Cyclophyidae are reactivated, and it belongs to Evaginogenida.

Ma, Mingzhen↗
DOE OSTI2023

Neutrino-driven Winds in Three-dimensional Core-collapse Supernova Simulations

Abstract In this paper, we analyze the neutrino-driven winds that emerge in 12 unprecedentedly long-duration 3D core-collapse supernova simulations done using the code F ornax . The 12 models cover progenitors with zero-age main-sequence mass between 9 and 60 solar masses. In all our models, we see transonic outflows that are at least 2 times as fast as the surrounding ejecta and that originate generically from a proto−neutron star surface atmosphere that is turbulent and rotating. We find that winds are common features of 3D simulations, even if there is anisotropic early infall. We find that the basic dynamical properties of 3D winds behave qualitatively similarly to those inferred in the past using simpler 1D models, but that the shape of the emergent wind can be deformed, very aspherical, and channeled by its environment. The thermal properties of winds for less massive progenitors very approximately recapitulate the 1D stationary solutions, while for more massive progenitors they deviate significantly owing to aspherical accretion. The Y e temporal evolution in winds is stochastic, and there can be some neutron-rich phases. Though no strong r -process is seen in any model, a weak r -process can be produced, and isotopes up to 90 Zr are synthesized in some models. Finally, we find that there is at most a few percent of a solar mass in the integrated wind component, while the energy carried by the wind itself can be as much as 10%–20% of the total explosion energy.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1979

A telescopic jib for continuous adjustment

For special space applications, e.g. for experiments distant from any orbital platforms or manipulators a new kind of jibs with extreme extension capacity has to be designed. Considering the requirements, the telescopic principle is found to be the most promising. For the choice of the stiff structure, design criteria are evaluated. Special effort deals with the drive system. An electromechanical system can satisfy the requirements. First results of the development of such a drive are presented. The most significant features are: A telescopic assembly of tubes which can be mutually moved by a short spindle in the center of the package. An elastically suspended screw is located at the bottom of each tube. For the jib extension, these screws will be linked with the spindle. The control of their sequence and the adjustment of tubes in mutual end positions are performed by latches. A functional model proved the basic idea.

Etzler, C. C.↗
NASA NTRS1981

A once-molten, coarse-grained, Ca-rich inclusion in Allende

A compact, spheroidal Type B inclusion in Allende contains melilite laths that project radially inward from the inclusion edge which show interference growth textures. The combined textural and chemical features of this object cannot be explained by independent vapor-solid condensation of grains in space, followed by random aggregation of these grains into an inclusion. Instead, it probably formed from a once-molten droplet that crystallized in response to radiative cooling from its outer surface. The crystallization sequence in this and another similar inclusion in which oxygen isotopes have been measured is melilite-spinel-anorthite-fassaite; this sequence shows that oxygen isotopic heterogeneities in coarse-grained inclusions were formed after complete solidification of these objects by partial exchange with a less O-16-rich gas, and not during or before a melting event.

Macpherson, G. J.↗
NASA NTRS2009

Evolvable Neural Software System

The Evolvable Neural Software System (ENSS) is composed of sets of Neural Basis Functions (NBFs), which can be totally autonomously created and removed according to the changing needs and requirements of the software system. The resulting structure is both hierarchical and self-similar in that a given set of NBFs may have a ruler NBF, which in turn communicates with other sets of NBFs. These sets of NBFs may function as nodes to a ruler node, which are also NBF constructs. In this manner, the synthetic neural system can exhibit the complexity, three-dimensional connectivity, and adaptability of biological neural systems. An added advantage of ENSS over a natural neural system is its ability to modify its core genetic code in response to environmental changes as reflected in needs and requirements. The neural system is fully adaptive and evolvable and is trainable before release. It continues to rewire itself while on the job. The NBF is a unique, bilevel intelligence neural system composed of a higher-level heuristic neural system (HNS) and a lower-level, autonomic neural system (ANS). Taken together, the HNS and the ANS give each NBF the complete capabilities of a biological neural system to match sensory inputs to actions. Another feature of the NBF is the Evolvable Neural Interface (ENI), which links the HNS and ANS. The ENI solves the interface problem between these two systems by actively adapting and evolving from a primitive initial state (a Neural Thread) to a complicated, operational ENI and successfully adapting to a training sequence of sensory input. This simulates the adaptation of a biological neural system in a developmental phase. Within the greater multi-NBF and multi-node ENSS, self-similar ENI s provide the basis for inter-NBF and inter-node connectivity.

Curtis, Steven A.↗
DOE OSTI2019

Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki - and Thorarchaeota

The genomes of Asgard Archaea , a novel archaeal proposed superphylum, share an enriched repertoire of eukaryotic signature genes and thus promise to provide insights into early eukaryote evolution. However, the distribution, metabolisms, cellular structures, and ecology of the members within this superphylum are not well understood. Here we provide a meta-analysis of the environmental distribution of the Asgard archaea, based on available 16S rRNA gene sequences. Metagenome sequencing of samples from a salt-crusted lagoon on the Baja California Peninsula of Mexico allowed the assembly of a new Thorarchaeota and three Lokiarchaeota genomes. Comparative analyses of all known Lokiarchaeota and Thorarchaeota genomes revealed overlapping genome content, including central carbon metabolism. Members of both groups contained putative reductive dehalogenase genes, suggesting that these organisms might be able to metabolize halogenated organic compounds. Unlike the first report on Lokiarchaeota , we identified genes encoding glycerol-1-phosphate dehydrogenase in all Loki - and Thorarchaeota genomes, suggesting that these organisms are able to synthesize bona fide archaeal lipids with their characteristic glycerol stereochemistry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage. AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.

transcription start and end sites↗
DOE OSTI2020

Source Term Reduction for Advanced and Small Modular Boiling Water Reactors

The United States Department of Energy (US DOE) is currently supporting the development of various advanced and small modular reactor (SMR) designs. Several of these designs have commenced license application with the US Nuclear Regulatory Commission (US NRC). These reactors have improved safety features that may significantly reduce radiological source terms in the event of design and beyond-design basis accidents. Specifically, some reactors feature a smaller containment volume relative to the available fission product depositional surface area, which supports increased fission product retention in the containment vessel. Pressurized water reactors (PWR) and boiling water reactors (BWR) with this feature include the integral pressurized water reactor (iPWR) and the BWRX-300 design by General Electric. A prior research program supported by the US DOE quantified the source term reduction associated with light water iPWRs and developed iPWR-specific theoretical models for fission product deposition rates. This program included a sequence of research projects that started with a feasibility study, development of theoretical models that predict higher deposition rates, and finally, development of empirical data for verification and validation of the theoretical models. The current project, which is a feasibility study, is the first step in a similar program to quantify the source term reduction associated with small and advanced light water BWRs.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Catalytic Difunctionalization of Cyclic Dienes: Direct Entry to Novel ROMP Monomers

We developed a catalytic platform to convert simple hydrocarbon feedstocks into valuable, tunable materials by leveraging nickel-catalyzed difunctionalization of cyclic dienes to access a novel class of cyclic alkene monomers. These monomers undergo ring-opening metathesis polymerization (ROMP) to yield sequence-controlled polymers with defined stereochemistry. Through mechanistic studies and catalyst optimization, we established a scalable, gram-level synthesis for selective diarylation, and expanded the reaction scope to include arylalkylation through rationally tuning the organoboron coupling partner. The resulting polymers were systematically studied to understand how steric, electronic, and stereochemical features influence polymerization behavior and bulk material properties. Functionalized derivatives bearing sulfonated groups were explored as proton-exchange membranes, and chemical recycling pathways were developed to recover monomers from the final materials. This work bridges small-molecule catalysis and macromolecular design, enabling access to tunable, recyclable polymers from abundant hydrocarbon starting materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

TCR-H: explainable machine learning prediction of T-cell receptor epitope binding on unseen datasets

Artificial-intelligence and machine-learning (AI/ML) approaches to predicting T-cell receptor (TCR)-epitope specificity achieve high performance metrics on test datasets which include sequences that are also part of the training set but fail to generalize to test sets consisting of epitopes and TCRs that are absent from the training set, i.e., are ‘unseen’ during training of the ML model. We present TCR-H, a supervised classification Support Vector Machines model using physicochemical features trained on the largest dataset available to date using only experimentally validated non-binders as negative datapoints. TCR-H exhibits an area under the curve of the receiver-operator characteristic (AUC of ROC) of 0.87 for epitope ‘hard splitting’ (i.e., on test sets with all epitopes unseen during ML training), 0.92 for TCR hard splitting and 0.89 for ‘strict splitting’ in which neither the epitopes nor the TCRs in the test set are seen in the training data. Furthermore, we employ the SHAP (Shapley additive explanations) eXplainable AI (XAI) method for post hoc interrogation to interpret the models trained with different hard splits, shedding light on the key physiochemical features driving model predictions. TCR-H thus represents a significant step towards general applicability and explainability of epitope:TCR specificity prediction.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1983

The application of encapsulation material stability data to photovoltaic module life assessment

For any piece of hardware that degrades when subject to environmental and application stresses, the route or sequence that describes the degradation process may be summarized in terms of six key words: LOADS, RESPONSE, CHANGE, DAMAGE, FAILURE, and PENALTY. Applied to photovoltaic modules, these six factors form the core outline of an expanded failure analysis matrix for unifying and integrating relevant material degradation data and analyses. An important feature of this approach is the deliberate differentiation between factors such as CHANGE, DAMAGE, and FAILURE. The application of this outline to materials degradation research facilitates the distinction between quantifying material property changes and quantifying module damage or power loss with their economic consequences. The approach recommended for relating material stability data to photovoltaic module life is to use the degree of DAMAGE to (1) optical coupling, (2) encapsulant package integrity, (3) PV circuit integrity or (4) electrical isolation as the quantitative criterion for assessing module potential service life rather than simply using module power loss.

Coulbert, C. D.↗
NASA NTRS1985

Geologic Interpretation of Remote Sensing Data for the Martian Volcano, Ascraeus Mons

Results of an investigation to relate remotely determined physical properties on Ascraeus Mons to the geologic history of the volcano are summarized. Products include a 1:2,000,000-scale photogeologic map of Ascraeus Mons and its environs; a 1:250,000-scale corrected thermal-inertia map of the summit caldera complex; four corrected thermal-inertia profiles across the volcano from high-resolution thermal data; fourteen low-resolution thermal sequences providing corrected thermal inertias for the volcano throughout half a Martian year; and a calibrated three-color photograph of the volcano. These data were combined with published spectral-reflectance, radar, and atmospheric water-vapor data relating to Acraeus Mons. Photogeologic mapping indicates that the sequence of events at Acraeus Mons is more complex than previously described. The plains surrounding the volcano include numerous flows, some of which can be traced to the flank of the volcano and some to different locations along the Tharsis Ridge. Surface morphology in the summit area is very distinct for features 100 m in scale, but the surface relief and tonal contrast steadily decrease toward the base of the shield, indicating modification by deposition or erosion.

Zimbelman, J.↗
NASA NTRS1987

Ground-based infrared observations of variable IRAS sources as candidates for late asymptotic giant branch stars

Analysis of the color distribution of OH/IR stars and IRAS low-resolution spectra class 30 objects suggests the presence of a well-defined evolutionary sequence which is populated by late asymptotic giant branch (LAGB) stars. The paper reports ground-based identification and infrared photometry of 10 candidates of news LAGB stars. None of the selected sources are found to have optical counterparts, and eight of the 10 show a strong 10-micron silicate absorption feature. It is suggested that these stars represent an invisible extension of extreme Mira variables and are some of the most evolved stars observed to date.

Kwok, Sun↗
NASA NTRS1988

Plume formation and lithosphere erosion - A comparison of laboratory and numerical experiments

The mechanics of thermal plume formation and intrusion into the lithosphere are investigated using a combination of laboratory and numerical simulations. The sequence of events leading to lithospheric thinning and uplift by thermal plumes is established, and some numerical estimates of the time scales for each stage in this process are derived that are applicable to the mantle. It is demonstrated that the two-dimensional finite element computations successfully reproduce the qualitative features seen in the experiments, with a quantitative discrepancy of typically 30 percent or less. The results of some calculations on plume formation and intrusion into model lithospheres with a variety of rheologies are presented.

Olson, Peter↗
NASA NTRS1996

Examples of Comet-like Spectra among Beta Pic-like Stars

Beta Pic is a nearby main-sequence star with an extended dust disk, large infrared excess, and mid-infrared emission similar to that seen in some cometary spectra. We selected a sample of stars whose infrared properties resemble Beta Pic and obtained 8 to 13 micron spectra (resolution 200). We find a variety of silicate emission features among the stars in our sample, ranging from classic interstellar dust features to spectra similar to that of comet P/Halley and the laboratory spectra of Interplanetary Dust Particles (IDP's).

Butner, H. M.↗