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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗
DOE OSTI2022

Molecular structural dataset of lignin macromolecule elucidating experimental structural compositions

Abstract Lignin is one of the most abundant biopolymers in nature and has great potential to be transformed into high-value chemicals. However, the limited availability of molecular structure data hinders its potential industrial applications. Herein, we present the Lignin Structural (LGS) Dataset that includes the molecular structure of milled wood lignin focusing on two major monomeric units (coniferyl and syringyl), and the six most common interunit linkages (phenylpropane β-aryl ether, resinol, phenylcoumaran, biphenyl, dibenzodioxocin, and diaryl ether). The dataset constitutes a unique resource that covers a part of lignin’s chemical space characterized by polymer chains with lengths in the range of 3 to 25 monomer units. Structural data were generated using a sequence-controlled polymer generation approach that was calibrated to match experimental lignin properties. The LGS dataset includes 60 K newly generated lignin structures that match with high accuracy (~90%) the experimentally determined structural compositions available in the literature. The LGS dataset is a valuable resource to advance lignin chemistry research, including computational simulation approaches and predictive modelling.

Scientific data↗
NASA NTRS2014

Cross Flow Parameter Calculation for Aerodynamic Analysis

A system and method for determining a cross flow angle for a feature on a structure. A processor unit receives location information identifying a location of the feature on the structure, determines an angle of the feature, identifies flow information for the location, determines a flow angle using the flow information, and determines the cross flow angle for the feature using the flow angle and the angle of the feature. The flow information describes a flow of fluid across the structure. The flow angle comprises an angle of the flow of fluid across the structure for the location of the feature.

Norman, David, Jr.↗
NASA NTRS1975

Prediction and verification of creep behavior in metallic materials and components for the space shuttle thermal protection system. Volume 2: Phase 2 subsize panel cyclic creep predictions

A method for predicting permanent cyclic creep deflections in stiffened panel structures was developed. The resulting computer program may be applied to either the time-hardening or strain-hardening theories of creep accumulation. Iterative techniques were used to determine structural rotations, creep strains, and stresses as a function of time. Deflections were determined by numerical integration of structural rotations along the panel length. The analytical approach was developed for analyzing thin-gage entry vehicle metallic-thermal-protection system panels subjected to cyclic bending loads at high temperatures, but may be applied to any panel subjected to bending loads. Predicted panel creep deflections were compared with results from cyclic tests of subsize corrugation and rib-stiffened panels. Empirical equations were developed for each material based on correlation with tensile cyclic creep data and both the subsize panels and tensile specimens were fabricated from the same sheet material. For Vol. 1, see N75-21431.

Cramer, B. A.↗
NASA NTRS1975

Creep analysis capability for stiffened panel structures

A method of analysis developed for predicting permanent cyclic creep deflections in stiffened panel structures is presented. The resulting computer program (TPSC, for Thermal Protection System Creep) applies either the time hardening or strain hardening theories of creep accumulation, using iterative techniques to determine structural rotations, creep strains, and stresses as a function of time. Deflections are determined by numerical integration of structural rotations along the panel length. The analytical approach was developed for purposes of analyzing thin gage entry vehicle metallic thermal protection system panels subjected to cyclic bending loads at high temperatures. The method is applicable to any panel subjected to bending loads. Predicted panel creep deflections are compared with results from cyclic tests of subsize and full size corrugation and rib stiffened panels. Empirical equations used in the analysis were developed for each material based on correlation with tensile cyclic creep data.

Cramer, B. A.↗
DOE OSTI2024

Twins in rotational spectroscopy: Does a rotational spectrum uniquely identify a molecule?

Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique “fingerprint” of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. Here we demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Machine learning for interpreting coherent X-ray speckle patterns

Speckle patterns produced by coherent X-ray have a close relationship with the internal structure of materials but quantitative inversion of the relationship to determine structure from speckle patterns is challenging. Here, in this work, we investigate the link between coherent X-ray speckle patterns and sample structures using a model 2D disk system and explore the ability of machine learning to learn aspects of the relationship. Specifically, we train a deep neural network to classify the coherent X-ray speckle patterns according to the disk number density in the corresponding structure. It is demonstrated that the classification system is accurate for both non-disperse and disperse size distributions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Instability of Rock-Salt Cubic NbN in Density Functional Calculations

All-nitride semiconductor/superconductor heterojunctions utilizing cubic niobium nitride (NbN) are a promising approach to superconducting quantum circuits for next-generation quantum-information systems. However, there are fundamental open questions on the atomic structure of NbN. In calculations with several levels of density functional theory (DFT), we find that the cubic rocksalt structure NbN (Fm-3m, 225) is energetically very unstable against the ground state hexagonal NbN in a tungsten carbide (P-6m2, 187) type lattice. To better understand the appearance of a cubic phase in numerous experiments, we perform a DFT study on possible NbN structures, determining the energy ordering between different polymorphs from databases and structure prediction. We perform supercell calculations of disordered NbN, finding that the rocksalt structure is dynamically unstable and relaxes to a lower energy monoclinic phase (C2/m, 12), which retains an approximate average cubic symmetry. However, the associated energy gain is not substantial enough for a plausible explanation for cubic NbN. We further investigate the role of external factors such as in-plane strain during epitaxial growth as well as the presence of off-stoichiometry and impurity doping on the energy ordering.

CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SU↗
NASA NTRS1972

Determinants of Market Structure and the Airline Industry

The general economic determinants of market structure are outlined with special reference to the airline industry. Included are the following facets: absolute size of firms; distributions of firms by size; concentration; entry barriers; product and service differentiation; diversification; degrees of competition; vertical integration; market boundaries; and economies of scale. Also examined are the static and dynamic properties of market structure in terms of mergers, government policies, and economic growth conditions.

Raduchel, W.↗
NASA NTRS1992

The atmospheric structures of the companion stars of eclipsing binary x ray sources

This investigation was aimed at determining structural features of the atmospheres of the massive early-type companion stars of eclipse x-ray pulsars by measurement of the attenuation of the x-ray spectrum during eclipse transitions and in deep eclipse. Several extended visits were made to ISAS in Japan by G. Clark and his graduate student, Jonathan Woo to coordinate the Ginga observations and preliminary data reduction, and to work with the Japanese host scientist, Fumiaki Nagase, in the interpretation of the data. At MIT extensive developments were made in software systems for data interpretation. In particular, a Monte Carlo code was developed for a 3-D simulation of the propagation of x-rays from the neutron star through the ionized atmosphere of the companion. With this code it was possible to determine the spectrum of Compton-scattered x-rays in deep eclipse and to subtract that component from the observed spectra, thereby isolating the software component that is attributable in large measure to x-rays that have been scattered by interstellar grains. This research has culminated in the submission of paper to the Astrophysical Journal on the determination of properties of the atmosphere of QV Nor, the BOI companion of 4U 1538-52, and the properties of interstellar dust grains along the line of sight from the source. The latter results were an unanticipated byproduct of the investigation. Data from Ginga observations of the Magellanic binaries SMC X-1 and LMC X-4 are currently under investigation as the PhD thesis project of Jonathan Woo who anticipated completion in the spring of 1993.

Clark, George W.↗
DOE OSTI2024

Structure of an RNA G-quadruplex from the West Nile virus genome

Potential G-quadruplex sites have been identified in the genomes of DNA and RNA viruses and proposed as regulatory elements. The genus Orthoflavivirus contains arthropod-transmitted, positive-sense, single-stranded RNA viruses that cause significant human disease globally. Computational studies have identified multiple potential G-quadruplex sites that are conserved across members of this genus. Subsequent biophysical studies established that some G-quadruplexes predicted in Zika and tickborne encephalitis virus genomes can form and known quadruplex binders reduced viral yields from cells infected with these viruses. The susceptibility of RNA to degradation and the variability of loop regions have made structure determination challenging. Despite these difficulties, we report a high-resolution structure of the NS5-B quadruplex from the West Nile virus genome. Analysis reveals two stacked tetrads that are further stabilized by a stacked triad and transient noncanonical base pairing. This structure expands the landscape of solved RNA quadruplex structures and demonstrates the diversity and complexity of biological quadruplexes. We anticipate that the availability of this structure will assist in solving further viral RNA quadruplexes and provides a model for a conserved antiviral target in Orthoflavivirus genomes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication

Remdesivir (RDV) prodrug can be metabolized into a triphosphate form nucleotide analogue (RDV-TP) to bind and insert into the active site of viral RNA dependent RNA polymerase (RdRp) to further interfere with viral genome replication. Here in this work, we computationally studied how RDV-TP binds and inserts to the SARS-CoV-2 RdRp active site, in comparison with natural nucleotide substrate adenosine triphosphate (ATP). To do that, we first constructed atomic structural models of an initial binding complex (active site open) and a substrate insertion complex (active site closed), based on high-resolution cryo-EM structures determined recently for SARS-CoV-2 RdRp or non-structural protein (nsp) 12, in complex with accessory protein factors nsp7 and nsp8. By conducting all-atom molecular dynamics simulation with umbrella sampling strategies on the nucleotide insertion between the open and closed state RdRp complexes, our studies show that RDV-TP can initially bind in a comparatively stabilized state to the viral RdRp active site, as it primarily forms base stacking with the template uracil nucleotide (nt +1), which under freely fluctuations supports a low free energy barrier of the RDV-TP insertion (~1.5 kcal mol -1 ). In comparison, the corresponding natural substrate ATP binds initially to the RdRp active site in Watson–Crick base pairing with the template nt, and inserts into the active site with a medium low free energy barrier (~2.6 kcal mol -1 ), when the fluctuations of the template nt are well quenched. The simulations also show that the initial base stacking of RDV-TP with the template can be specifically stabilized by motif C-S759, S682 (near motif B) with the base, and motif G-K500 with the template backbone. Although the RDV-TP insertion can be hindered by motif F-R555/R553 interaction with the triphosphate, the ATP insertion seems to be facilitated by such interactions. The inserted RDV-TP and ATP can be further distinguished by specific sugar interaction with motif B-T687 and motif A-D623, respectively.

36 MATERIALS SCIENCE↗
NASA NTRS1994

Preliminary crystallographic studies of four crystal forms of serum albumin

Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure.

Serum Albumin/chemistry↗
NASA NTRS1988

Satellite/radiosonde comparison

Collocated measurements of radiosonde and TIROS Operational Vertical Sounder (TOVS) data are compared to determine whether significant latitudinal, seasonal, or instrumental biases exist. Long-wave structure determined by each system is being examined for correlation. Because U.S. radiosonde data are archived uncorrected, an effort to correct the measurements is being considered. These corrections will be applied to 7 years of measurements. New comparisons will then be made using corrected radiosonde and TOVS data. A regression method is used to retrieve temperatures, and radiosonde zonal means are used to update the regression coefficients. Preliminary results of auto-correlation analysis indicate that detection of long-wave structure in each set of data is slightly different with some levels and locations experiencing different wave periods or amplitudes. Scatter diagrams and linear regression for each layer show bias in the mean temperatures. Winter-time measurements show poorer correlations due to noisy measurements.

Schmidlin, F. J.↗
NASA NTRS2000

An Innovative Structural Mode Selection Methodology: Application for the X-33 Launch Vehicle Finite Element Model

An innovative methodology for determining structural target mode selection and mode selection based on a specific criterion is presented. An effective approach to single out modes which interact with specific locations on a structure has been developed for the X-33 Launch Vehicle Finite Element Model (FEM). We presented Root-Sum-Square (RSS) displacement method computes resultant modal displacement for each mode at selected degrees of freedom (DOF) and sorts to locate modes with highest values. This method was used to determine modes, which most influenced specific locations/points on the X-33 flight vehicle such as avionics control components, aero-surface control actuators, propellant valve and engine points for use in flight control stability analysis and for flight POGO stability analysis. Additionally, the modal RSS method allows for primary or global target vehicle modes to also be identified in an accurate and efficient manner.

Hidalgo, Homero, Jr.↗