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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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.

3D visualization↗
NASA NTRS1976

Aeroelastic characteristics of composite bearingless rotor blades

Owing to the inherent unique structural features of composite bearingless rotors, various assumptions upon which conventional rotor aeroelastic analyses are formulated, are violated. Three such features identified are highly nonlinear and time-varying structural twist, structural redundancy in bending and torsion, and for certain configurations a strongly coupled low frequency bending-torsion mode. An examination of these aeroelastic considerations and appropriate formulations required for accurate analyses of such rotor systems is presented. Also presented are test results from a dynamically scaled model rotor and complementary analytic results obtained with the appropriately reformulated aeroelastic analysis.

Bielawa, R. L.↗
NASA NTRS1983

Information contained in protein shapes

The sequence of local conformations at C-alpha atoms of a protein has been considered as an informational message string. The total self-information contents and self-information per letter have been evaluated for 83 globular proteins whose structures are known from X-ray crystallography. The derived information contents provide a method of quantitating structural specificity of proteins. This method of analysis enables repeating, intricate structural features to be recognized. Among the globular proteins whose structures have been solved, high potential iron protein stands out with the largest three-letter dependence.

Sundaram, K.↗
DOE OSTI2019

Shining a light on amorphous U 2 O 7 : A computational approach to understanding amorphous uranium materials

Mixed-phase and low-symmetry systems are widely observed among uranium oxide materials. Amorphous-U 2 O 7 forms during the calcination of studtite, a uranyl peroxide mineral. Using a genetic algorithm search for stable crystalline phases, we have identified a potentially stable phase of U2O7 that shares structural features with experimentally observed amorphous U2O7 samples. The crystalline structure is expected to undergo a solid–solid phase change around 12 GPa.

Shields, Ashley E.↗
DOE OSTI2020

Local Atomic Structure in Photo-isomerized Ruthenium Sulfur Dioxide Complexes Revealed by Pair Distribution Function Analysis

SO 2 linkage photoisomerization in crystalline ruthenium-based complexes has demonstrated nanophotonic phenomena such as optical switching and nano-optomechanical transduction. Molecular insights into these materials have been explored largely via the characterization of their photoinduced crystal structures via in situ single-crystal X-ray diffraction, known as photocrystallography. Photoinduced molecular disorder is present, which photocrystallography can model to the extent that it is confined within the periodic boundary of a unit cell. However, non-periodic molecular disorder is suspected to exist as well. In situ total scattering experiments were therefore carried out on finely powdered crystals of four ruthenium-sulfur dioxide complexes. Data were modeled using light-minus-dark' difference pair distribution function analysis, which afforded photoinduced structural changes exclusively. This revealed structural features that were first compared against models of photoinduced crystal structures known a priori from photocrystallography. Furthermore, statistical inference was then employed, which evidenced generally good agreement between the total scattering data and the photocrystallographic models, while revealing real differences that are indicative of a structure with only a short-range order. Overall, our findings demonstrate that in situ light-induced total scattering experiments on finely powdered crystals are able to reveal the photoinduced structure. Overall, the evidence suggests that such structure could include a short-range order as well as photocrystallographic content. Our demonstration experiment offers a pathway to develop studies that capture the short-range order in linkage photoisomers, while we have outlined the procedure for testing the validity of associated structural models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Structural architecture of prothrombin in solution revealed by single molecule spectroscopy

The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr 93 in kringle-1 onto Trp 547 in the protease domain that obliterates access to the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. As a result, the open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase.

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

Hydration and reaction mechanisms on sodium silicate glass surfaces from molecular dynamics simulations with reactive force fields

Recent development of reactive force fields have enabled molecular dynamics simulations of interactions between silicate glasses and water at the atomistic scale. While multicomponent silicate glasses encompass a wide variety of compositions and properties, one common structural feature in these glasses is the combination of the network structure that is made up of silica tetrahedra linked through corner sharing interspersed with network modifiers like alkali and alkaline-earth ions that break up the Si–O–Si linkages by forming nonbridging oxygen. In reactions with water, ion exchange between alkali ions in the glass and proton or hydronium in the solution, as well as hydrolysis reaction of the Si–O–Si linkages and subsequent silanol formation, is observed and well documented. Furthermore, we have used a set of recently developed reactive force field to investigate the reactions between water and the surfaces of silica and sodium silicate glasses of different compositions for reactions up to 8 nanoseconds. Our results indicate sodium leaching into water and diffusion of water molecules up to 25 Å into the glass surface. We examined the structural and compositional changes inside the glass and around the diffused ions and use these to explain the rates of silanol formation at the surface. We also observed proton transport in the glass which has an indirect influence on the silanol formation rates. While the surface of the glass was rough to start with, it undergoes further modification into a hydrated gel-like structure in the glass for up to 5 Å in the higher alkali containing glasses. It was found that the leached sodium ions remain close to the interface and that fragments of silicate network from the surface is capable of dislodging from the bulk glass and enter the aqueous solution. These simulations thus provide insights into the formation and structure of an alteration layers commonly observed in multicomponent silicate glasses corroded in aqueous solutions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Effects of CELF Pretreatment Severity on Lignin Structure and the Lignin-Based Polyurethane Properties

Conversion of technical lignin into performance biopolymers such as polyurethane offers environmental and economic advantages when combined with production of biofuels from biomass sugars, presenting significant interest toward studying the role of pretreatment on lignin structure and functionality. Co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment, employing acidic aqueous tetrahydrofuran (THF) mixtures, was developed to effectively break down the lignin-carbohydrate matrix and promote extraction of lignin from lignocellulosic biomass with desirable purity and yield. In this study, we report the effects of CELF pretreatment reaction severity on the molecular structure of CELF-extracted lignin and its impact toward the mechanical properties of the resulting lignin-based polyurethanes. Reaction temperature was found to play the most significant role, compared to reaction time and acidity, in manipulating structural features such as molecular weight, functionality and intra-polymer structure. At the severe reaction conditions at 180°C, the order of reactivity for primary lignin interlinkages characterized by semiquantitative HSQC NMR analysis were found to be β-ether > phenylcoumaran (β−5′) > resinol (β−β′) facilitating a high degree of depolymerization and yielding a high frequency of free phenolics and reduced aliphatic hydroxyl groups. All side-chain interlinkages were depleted converting guaiacyl subunits into condensed forms, while still retaining uncondensed syringyl subunits. Under the mild 150°C temperature reaction, CELF lignin had higher molecular weight and retained more β-ether interlinkages. The results from CELF lignin-based polyurethane synthesis indicated that the tensile properties depended on the miscibility of CELF lignin with other components and low molecular weight cuts improved the dispersion of lignin in the polyurethane network. Pre-mixing of CELF with poly(ethylene glycol) (PEG) reduced the brittleness and improved the ductility of the CELF lignin-PEG polyurethanes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1975

Airborne remote sensors applied to engineering geology and civil works design investigations

The usefulness of various airborne remote sensing systems in the detection and identification of regional and specific geologic structural features that may affect the design and location of engineering structures on major civil works projects is evaluated. The Butler Valley Dam and Blue Lake Project in northern California was selected as a demonstration site. Findings derived from the interpretation of various kinds of imagery used are given.

Gelnett, R. H.↗
NASA NTRS1976

Coronal X-ray enhancements associated with H-alpha filament disappearances

The X-ray telescope experiment aboard the Skylab/ATM mission provided high-resolution soft X-ray images of the lower corona away from active regions, revealing frequent large-scale transient X-ray enhancements which could often be associated with the disappearance of H-alpha filaments. The X-ray emitting structures featured peak brightnesses similar to those of nonflaring active region structures, durations from 3 to 40 hours, shapes that in general outlined the preexisting H-alpha filaments to as large as 400,000 km, apparent expansion velocities of the order of tens of km/sec, and observed peak temperatures of the order of a few million degrees. One such event is described and analyzed in detail. Two explanations of the events are discussed: (1) excess cool material is present in the filament cavity, contributing to the X-ray enhancement, and (2) the enhancement is due to the compression of preexisting material by a changing magnetic field.

Webb, D. F.↗
NASA NTRS1986

Deformational sequence of a portion of the Michipicoten greenstone belt, Chabanel Township, Ontario

Detailed mapping at a scale of one inch = 400 feet is being carried out within a fume kill, having excellent exposure, located in the southwestern portion of the Michipicoten Greenstone Belt near Wawa, Ontario. The rocks are metasediments and metavolcanics of lower greenschist facies. U-Pb geochronology indicates that they are at least 2698 + or - 11 Ma old. The lithologic packages strike northeast to northwest, but the dominant strike is approximately east-west. Sedimentary structures and graded bedding are well preserved, aiding in the structural interpretation of this multiply deformed area. At least six phases of deformation within a relatively small area of the Michipicoten Greenstone Belt have been tentatively identified. These include the following structural features in approximate order of occurrence: (0) soft-sediment structures; (1) regionally overturned rocks, flattened pebbles, bedding parallel cleavage, and early, approximately bedding parallel faults; (2) northwest to north striking cleavage; (3) northeast striking cleavage and associated folds, and at least some late movement on approximately bedding parallel faults; (4) north-northwest and northeast trending faults; and (5) diabase dikes and associated fracture cleavages. Minor displacement of the diabase dikes occurs on faults that appear to be reactivated older structures.

Shrady, C. H.↗
DOE OSTI2016

The Dimerization of H 2 NO

H 2 NO is the prototype of aminoxyls, kinetically persistent free radicals. The potential dimerization and reaction modes of H 2 NO are examined. The dimer potential energy surface features a barely metastable O–O bound species and several locally bound dimeric structures. One of these, a rectangular or rhomboid O–N–O-N ring, is a characteristic structural feature of more stable aminoxyls in the solid state. Its electronic structure is related to other four-center six-electron systems. A general picture of the weak dimer binding is constructed for these and other H 2 NO dimers from a balance of four-electron repulsions between NO π electrons, and two-electron attractive interaction between the singly occupied π* orbitals of the diradical. The most stable diradical structure is a surprisingly strongly hydrogen bonded dimer diradical. Lastly, the barriers separating the other isomers from this global minimum are calculated to be small.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Controlling the intermediate structure of an ionic liquid for f-block element separations

Recent research has revealed molecular structure beyond the inner coordination sphere is essential in defining the performance of separations processes, but nevertheless remains largely unexplored. Here we apply small angle neutron scattering (SANS) and x-ray absorption fine structure (XAFS) spectroscopy to investigate the structure of an ionic liquid system studied for f-block element separations. SANS data reveal dramatic changes in the ionic liquid microstructure (~150 Å) which we demonstrate can be controlled by judicious selection of counter ion. Mesoscale structural features (> 500 Å) are also observed as a function of metal concentration. XAFS analysis supports formation of extended aggregate structures, similar to those observed in traditional solvent extraction processes, and suggest additional parallels may be drawn from further study. As a result, achieving precise tunability over the intermediate features is an important development in controlling mesoscale structure and realizing advanced new forms of soft matter.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Zwitterionic Photocurable Resin for High‐Resolution 3D Printing of Ultralow‐Fouling Microstructures

High‐resolution 3D printing technologies are enabling a new generation of microstructured materials for applications where biocompatibility is critical. However, most conventional 3D‐printable resins yield materials that exhibit trade‐offs between antifouling properties and mechanical robustness, limiting their applicability in living systems. In nature, zwitterionic surface groups form tightly bound hydration layers that act as effective barriers against protein and cell attachment. Inspired by this strategy, a zwitterionic acrylamide‐based photoresist—carboxybetaine di‐methacrylamide (CBDA)—is developed for projection‐based vat photopolymerization, enabling the fabrication of complex microarchitectures with exceptional antifouling properties. The bifunctional monomer allows the formation of dense, cross‐linked networks that resist swelling while maintaining a high density of zwitterionic groups. Printed structures exhibit strong resistance to protein and cell adhesion, as confirmed by porcine blood assays, alongside robust mechanical performance. As a demonstration, a tubular structure featuring a negative Poisson's ratio lattice is printed to showcase structural fidelity and versatility. This resin formulation offers a broadly applicable strategy for fabricating microscale devices and surfaces where antifouling performance and structural integrity are both essential—spanning biomedical interfaces, soft robotics, and beyond.

3D printing↗
DOE OSTI2014

Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride

Ionic liquids have become a popular solvent for cellulose pretreatment in biorefineries due to their efficiency in dissolution and their reusability. Understanding the interactions between cations, anions, and cellulose is key to the development of better solvents and the improvement of pretreatment conditions. While previous studies described the interactions between ionic liquids and cellulose fibers, shedding light on the initial stages of the cellulose dissolution process, we study the end state of that process by exploring the structure and dynamics of a single cellulose decamer solvated in 1-butyl-3-methyl-imidazolium chloride (BmimCl) and in water using replica-exchange molecular dynamics. In both solvents, global structural features of the cellulose chain are similar. However, analyses of local structural properties show that cellulose explores greater conformational variability in the ionic liquid than in water. For instance, in BmimCl the cellulose intramolecular hydrogen bond O3H'••• O5 is disrupted more often resulting in greater flexibility of the solute. Our results indicate that the cellulose chain is more dynamic in BmimCl than in water, which may play a role in the favorable dissolution of cellulose in the ionic liquid. Here, the calculation of the configurational entropy of the cellulose decamer confirms its higher conformational flexibility in BmimCl than in water at elevated temperatures.

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

Tuning chemical precompression: Theoretical design and crystal chemistry of novel hydrides in the quest for warm and light superconductivity at ambient pressures

Over the past decade, a combination of crystal structure prediction techniques and experimental synthetic work has thoroughly explored the phase diagrams of binary hydrides under pressure. The fruitfulness of this dual approach is demonstrated in the recent identification of several superconducting hydrides with T c s approaching room temperature. We start with an overview of the computational procedures for predicting stable structures and estimating their propensity for superconductivity. A survey of phases with high T c reveals some common structural features that appear conducive to the strong coupling of the electronic structure with atomic vibrations that leads to superconductivity. We discuss the stability and superconducting properties of phases containing two of these—molecular H 2 units mixed with atomic H and hydrogenic clathrate-like cages—as well as more unique motifs. Lastly, we argue that ternary hydride phases, whose exploration is still in its infancy, are a promising route to achieve simultaneous superconductivity at high temperatures and stability at low pressures. Several ternary hydrides arise from the addition of a third element to a known binary hydride structure through site mixing or onto a new site, and several more are based on altogether new structural motifs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Estimation of elastic properties of an additively manufactured lattice using resonant ultrasound spectroscopy

Development of improved approaches in the characterization of additively manufactured structures continues to be a topic of interest for the advanced manufacturing community. This article will investigate an approach using resonant ultrasound spectroscopy (RUS) to determine the effective elastic constants of an orthotropic lattice structure. The evaluation is performed on a cube shaped 316 L stainless steel test specimen, constructed using selective laser melting techniques. The approach uses RUS techniques in conjunction with the assumption that in the frequency regime of interest, the wavelength of the diagnostic ultrasound is greater than the discrete structural features of the unit cell of the lattice; thus, the AM structure can be treated as an anisotropic continuum with effective material properties and symmetry inherited from the unit cell. The RUS analysis estimates the nine elastic coefficients associated with orthotropic sample symmetry, which, in turn, are used to determine the elastic moduli and Poisson ratios. Current results show good agreement between experiments and modeled data. Comparisons to published results are also in good agreement, indicating the potential applicability of this characterization technique for estimating the linear elastic properties of innovative additive manufactured metal lattice structures.

36 MATERIALS SCIENCE↗