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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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Sequence of Silicon Monolayer Structures Grown on a Ru Surface: from a Herringbone Structure to Silicene

Silicon-based two-dimensional (2D) materials are uniquely suited for integration in Si-based electronics. Silicene, an analogue of graphene, was recently fabricated on several substrates and was used to make a field-effect transistor. Here, we report that when Ru(0001) is used as a substrate, a range of distinct monolayer silicon structures forms, evolving toward silicene with increasing Si coverage. Low Si coverage produces a herringbone structure, a hitherto undiscovered 2D phase of silicon. With increasing Si coverage, herringbone elbows evolve into silicene-like honeycomb stripes under tension, resulting in a herringbone-honeycomb 2D superlattice. At even higher coverage, the honeycomb stripes widen and merge coherently to form silicene in registry with the substrate. Scanning tunneling microscopy (STM) was used to image the structures. The structural stability and electronic properties of the Si 2D structures, the interaction between the Si 2D structures and the Ru substrate, and the evolution of the distinct monolayer Si structures were elucidated by density functional theory (DFT) calculations. This work paves the way for further investigations of monolayer Si structures, the corresponding growth mechanisms, and possible functionalization by impurities.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Same Precursor, Two Different Products: Comparing the Structural Evolution of In–Ga–O “Gel-Derived” Powders and Solution-Cast Films Using Pair Distribution Function Analysis

Amorphous metal oxides are central to a variety of technological applications. In particular, indium gallium oxide has garnered attention as a thin-film transistor channel layer material. In this work we examine the structural evolution of indium gallium oxide gel-derived powders and thin films using infrared vibrational spectroscopy, X-ray diffraction, and pair distribution function (PDF) analysis of X-ray total scattering from standard and normal incidence thin-film geometries (tfPDF). We find that the gel-derived powders and films from the same aqueous precursor evolve differently with temperature, forming mixtures of Ga-substituted In2O3 and In-substituted β-Ga2O3 with different degrees of substitution. X-ray total scattering and PDF analysis indicate that the majority phase for both the powders and films is an amorphous/nanocrystalline β-Ga2O3 phase, with a minor constituent of In2O3 with significantly larger coherence lengths. This amorphous β-Ga2O3 phase could not be identified using the conventional Bragg diffraction techniques traditionally used to study crystalline metal oxide thin films. The combination of Bragg diffraction and tfPDF provides a much more complete description of film composition and structure, which can be used to detail the effect of processing conditions and structure–property relationships. This study also demonstrates how structural features of amorphous materials, traditionally difficult to characterize by standard diffraction, can be elucidated using tfPDF.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Stripe-like nanoscale structural phase separation in superconducting BaPb 1-x Bi x O 3

The phase diagram of BaPb 1-x Bi x O 3 exhibits a superconducting dome in the proximity of a charge density wave phase. For the superconducting compositions, the material coexists as two structural polymorphs. Here we show, via high-resolution transmission electron microscopy, that the structural dimorphism is accommodated in the form of partially disordered nanoscale stripes. Identification of the morphology of the nanoscale structural phase separation enables determination of the associated length scales, which we compare with the Ginzburg–Landau coherence length. We find that the maximum T c occurs when the superconducting coherence length matches the width of the partially disordered stripes, implying a connection between the structural phase separation and the shape of the superconducting dome.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

State-of-the-art of non-destructive testing methods and technologies for application to nuclear power plant safety-related concrete structures

The inspection of nuclear power plant concrete structures presents challenges different from conventional civil engineering structures. Wall thicknesses can be in excess of one meter and the structures often have increased steel reinforcement density with more complex detailing. The accessibility for any testing method may be limited due to the presence of liners and other components and there can be a number of penetrations or cast-in-place items present. The objective of the report is to present the state-of-the art of non-destructive testing methods and technologies for the inspection of thick, heavily-reinforced nuclear power plant concrete cross-sections with particular respect to: •locating steel reinforcement and identification of its cover depth •locating tendon ducts and identification of the condition of the grout materials •detection of cracking, voids, delamination, and honeycombing in concrete structures •detection of inclusions of different materials or voids adjacent to the concrete side of the containment liner •methods capable of identification of corrosion occurrence on the concrete side of the containment liner.

42 ENGINEERING↗
DOE OSTI2016

Structural crossover in a supercooled metallic liquid and the link to a liquid-to-liquid phase transition

Time-resolved synchrotron measurements were carried out to capture the structure evolution of an electrostatically levitated metallic-glass-forming liquid during free cooling. The experimental data shows a crossover in the liquid structure at ~1000 K, about 115 K below the melting temperature and 150 K above the crystallization temperature. The structure change is characterized by a dramatic growth in the extended-range order below the crossover temperature. Molecular dynamics simulations have identified that the growth of the extended-range order was due to an increased correlation between solute atoms. These results provide structural evidence for a liquid-to-liquid-phase-transition in the supercooled metallic liquid.

Glass transitions↗
DOE OSTI2020

Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data

In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in the solvent exposed area, such as unfolding. Utilization of the graphics processing unit allows for an efficient all-atom calculation of scattering patterns on-the-fly, even for large biomolecules, resulting in a speed-up of the calculation of the associated driving force. The utility of the methodology is demonstrated on two model protein systems, the structural transition of lysine-, arginine-, ornithine-binding protein and the folding of deca-alanine. We discuss how the present approach will aid in the interpretation of dynamical scattering experiments on protein folding and association.

Hsu, Darren J.↗
DOE OSTI2018

Crystal structure of the human NK 1 tachykinin receptor

The NK 1 tachykinin G-protein–coupled receptor (GPCR) binds substance P, the first neuropeptide to be discovered in mammals. Through activation of NK 1 R, substance P modulates a wide variety of physiological and disease processes including nociception, inflammation, and depression. Human NK 1 R (hNK 1 R) modulators have shown promise in clinical trials for migraine, depression, and emesis. However, the only currently approved drugs targeting hNK 1 R are inhibitors for chemotherapy-induced nausea and vomiting (CINV). To better understand the molecular basis of ligand recognition and selectivity, we solved the crystal structure of hNK 1 R bound to the inhibitor L760735, a close analog of the drug aprepitant. Our crystal structure reveals the basis for antagonist interaction in the deep and narrow orthosteric pocket of the receptor. We used our structure as a template for computational docking and molecular-dynamics simulations to dissect the energetic importance of binding pocket interactions and model the binding of aprepitant. Furthermore, the structure of hNK 1 R is a valuable tool in the further development of tachykinin receptor modulators for multiple clinical applications.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

Structural Classification of Proteins—extended (SCOPe, http://scop.berkeley.edu) is a database of protein structural relationships that extends the SCOP database. SCOP is a manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. Development of the SCOP 1.x series concluded with SCOP 1.75. The ASTRAL compendium provides several databases and tools to aid in the analysis of the protein structures classified in SCOP, particularly through the use of their sequences. SCOPe extends version 1.75 of the SCOP database, using automated curation methods to classify many structures released since SCOP 1.75. We have rigorously benchmarked our automated methods to ensure that they are as accurate as manual curation, though there are many proteins to which our methods cannot be applied. SCOPe is also partially manually curated to correct some errors in SCOP. SCOPe aims to be backward compatible with SCOP, providing the same parseable files and a history of changes between all stable SCOP and SCOPe releases. SCOPe also incorporates and updates the ASTRAL database. The latest release of SCOPe, 2.03, contains 59 514 Protein Data Bank (PDB) entries, increasing the number of structures classified in SCOP by 55% and including more than 65% of the protein structures in the PDB.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

From cluster structures to nuclear molecules: The role of nodal structure of the single-particle wave functions

In this study, the nodal structure of the density distributions of the single-particle states occupied in rod-shaped, hyper- and megadeformed structures of non-rotating and rotating N ~ Z nuclei has been investigated in detail. The single-particle states with the Nilsson quantum numbers of the [NN0]1/2 (with N from 0 to 5) and [N,N – 1,1]Ω (with N from 1 to 3 and Ω = 1/2, 3/2) types are considered. These states are building blocks of extremely deformed shapes in the nuclei with mass numbers A ≤ 50. Because of (near) axial symmetry and large elongation of such structures, the wave functions of the single-particle states occupied are dominated by a single basis state in cylindrical basis. This basis state defines the nodal structure of the single-particle density distribution. The nodal structure of the single-particle density distributions allows us to understand in a relatively simple way the necessary conditions for α clusterization and the suppression of the α clusterization with the increase of mass number. It also explains in a natural way the coexistence of ellipsoidal mean-field-type structures and nuclear molecules at similar excitation energies and the features of particle-hole excitations connecting these two types of the structures. Lastly, our analysis of the nodal structure of the single-particle density distributions does not support the existence of quantum liquid phase for the deformations and nuclei under study.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Structure of the Fc fragment of the NIST reference antibody RM8671

As the link between antigen binding and immune activation, the antibody Fc region has received extensive structural study. In this report, the structure of the Fc fragment of the NIST IgG1 mAb (reference material 8671) is described at 2.1 Å resolution in space group P 2 1 2 1 2 1 , with approximate unit-cell parameters a = 50, b = 80, c = 138 Å. Prior Fc structures with a wide variety of modifications are also surveyed, focusing on those in the same crystal form. To facilitate the analysis of conformations, a reference frame and a two-parameter metric are proposed, considering the CH 2 domains as mobile with respect to a fixed dimeric CH 3 core. Over several human Fc structures, a significant variation in Fc elbow conformations is observed, which may serve to facilitate the regulation of Fc effector signaling.

Gallagher, D. Travis↗
DOE OSTI2015

The structure of PccH from Geobactersulfurreducens-a novel low reduction potential monoheme cytochrome essential for accepting electrons from an electrode

The structure of cytochrome c (GSU3274) designated as PccH from Geobactersulfurreducens was determined at a resolution of 2.0 angstrom. PccH is a small (15kDa) cytochrome containing one c-type heme, found to be essential for the growth of G.sulfurreducens with respect to accepting electrons from graphite electrodes poised at -300mV versus standard hydrogen electrode. with fumarate as the terminal electron acceptor. The structure of PccH is unique among the monoheme cytochromes described to date. The structural fold of PccH can be described as forming two lobes with the heme sandwiched in a cleft between the two lobes. In addition, PccH has a low reduction potential of -24mV at pH7, which is unusual for monoheme cytochromes. Based on difference in structure, together with sequence phylogenetic analysis, we propose that PccH can be regarded as a first characterized example of a new subclass of class I monoheme cytochromes. The low reduction potential of PccH may enable the protein to be redox active at the typically negative potential ranges encountered by G. sulfurreducens. Because PccH is predicted to be located in the periplasm of this bacterium, it could not be involved in the first step of accepting electrons from the electrode but is very likely involved in the downstream electron transport events in the periplasm.

Dantas, Joana↗
DOE OSTI2015

Structural, Functional, and Immunogenic Insights on Cu,Zn Superoxide Dismutase Pathogenic Virulence Factors from Neisseria meningitidis and Brucella abortus

ABSTRACT Bacterial pathogens Neisseria meningitidis and Brucella abortus pose threats to human and animal health worldwide, causing meningococcal disease and brucellosis, respectively. Mortality from acute N. meningitidis infections remains high despite antibiotics, and brucellosis presents alimentary and health consequences. Superoxide dismutases are master regulators of reactive oxygen and general pathogenicity factors and are therefore therapeutic targets. Cu,Zn superoxide dismutases (SODs) localized to the periplasm promote survival by detoxifying superoxide radicals generated by major host antimicrobial immune responses. We discovered that passive immunization with an antibody directed at N. meningitidis SOD (NmSOD) was protective in a mouse infection model. To define the relevant atomic details and solution assembly states of this important virulence factor, we report high-resolution and X-ray scattering analyses of NmSOD and of SOD from B. abortus (BaSOD). The NmSOD structures revealed an auxiliary tetrahedral Cu-binding site bridging the dimer interface; mutational analyses suggested that this metal site contributes to protein stability, with implications for bacterial defense mechanisms. Biochemical and structural analyses informed us about electrostatic substrate guidance, dimer assembly, and an exposed C-terminal epitope in the NmSOD dimer. In contrast, the monomeric BaSOD structure provided insights for extending immunogenic peptide epitopes derived from the protein. These collective results reveal unique contributions of SOD to pathogenic virulence, refine predictive motifs for distinguishing SOD classes, and suggest general targets for antibacterial immune responses. The identified functional contributions, motifs, and targets distinguishing bacterial and eukaryotic SOD assemblies presented here provide a foundation for efforts to develop SOD-specific inhibitors of or vaccines against these harmful pathogens. IMPORTANCE By protecting microbes against reactive oxygen insults, SODs aid survival of many bacteria within their hosts. Despite the ubiquity and conservation of these key enzymes, notable species-specific differences relevant to pathogenesis remain undefined. To probe mechanisms that govern the functioning of Neisseria meningitidis and Brucella abortus SODs, we used X-ray structures, enzymology, modeling, and murine infection experiments. We identified virulence determinants common to the two homologs, assembly differences, and a unique metal reservoir within meningococcal SOD that stabilizes the enzyme and may provide a safeguard against copper toxicity. The insights reported here provide a rationale and a basis for SOD-specific drug design and an extension of immunogen design to target two important pathogens that continue to pose global health threats.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2017

Role of structure imperfection in the formation of the magnetotransport properties of rare-earth manganites with a perovskite structure

The structure, the structure imperfection, and the magnetoresistance, magnetotransport, and microstructure properties of rare-earth perovskite La{sub 0.3}Ln{sub 0.3}Sr{sub 0.3}Mn{sub 1.1}O{sub 3–δ} manganites are studied by X-ray diffraction, thermogravimetry, electrical resistivity measurement, magnetic, {sup 55}Mn NMR, magnetoresistance measurement, and scanning electron microscopy. It is found that the structure imperfection increases, and the symmetry of a rhombohedrally distorted R3̅c perovskite structure changes into its pseudocubic type during isovalent substitution for Ln = La{sup 3+}, Pr{sup 3+}, Nd{sup 3+}, Sm{sup 3+}, or Eu{sup 3+} when the ionic radius of an A cation decreases. Defect molar formulas are determined for a real perovskite structure, which contains anion and cation vacancies. The decrease in the temperatures of the metal–semiconductor (T{sub ms}) and ferromagnet–paramagnet (T{sub C}) phase transitions and the increase in electrical resistivity ρ and activation energy E{sub a} with increasing serial number of Ln are caused by an increase in the concentration of vacancy point defects, which weaken the double exchange 3d{sup 4}(Mn{sup 3+})–2p{sup 6}(O{sup 2–})–3d{sup 3}(Mn{sup 4+})–V{sup (a)}–3d{sup 4}(Mn{sup 3+}). The crystal structure of the compositions with Ln = La contains nanostructured planar clusters, which induce an anomalous magnetic hysteresis at T = 77 K. Broad and asymmetric {sup 55}Mn NMR spectra support the high-frequency electronic double exchange Mn{sup 3+}(3d{sup 4}) ↔ O{sup 2–}(2p{sup 6}) ↔ Mn{sup 4+}(3d{sup 3}) and indicate a heterogeneous surrounding of manganese by other ions and vacancies. A correlation is revealed between the tunneling magnetoresistance effect and the crystallite size. A composition–structure imperfection–property experimental phase diagram is plotted. This diagram supports the conclusion about a strong influence of structure imperfection on the formation of the magnetic, magnetotransport, and magnetoresistance properties of rare-earth perovskite manganites.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Strain-dependence Of The Structure And Ferroic Properties Of Epitaxial NiTiO3 Thin Films Grown On Different Substrates

Polarization-induced weak ferromagnetism has been predicted a few years back in perovskite MTiO3 (M = Fe, Mn, Ni) [Fennie, Phys. Rev. Lett. 100, 167203 (2008)]. We set out to stabilize this metastable perovskite structure by growing NiTiO3 epitaxially on different substrates, and to investigate the dependence of polar and magnetic properties on strain. Epitaxial NiTiO3 films were deposited on Al2O3, Fe2O3, and LiNbO3 substrates by pulsed laser deposition, and characterized using several techniques. The effect of substrate choice on lattice strain, film structure, and physical properties was investigated. Our structural data from x-ray diffraction and electron microscopy shows that substrate-induced strain has a marked effect on the structure and crystalline quality of the films. Physical property measurements reveal a dependence of the weak ferromagnetism and lattice polarization on strain, and highlight our ability to control the ferroic properties in NiTiO3 thin films by the choice of substrate. Our results are also consistent with the theoretical prediction that the ferromagnetism in acentric NiTiO3 is polarization-induced. From the substrates studied here, the perovskite substrate LiNbO3 proved to be the most promising one for strong multiferroism.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2014

Structural Health Monitoring for Impact Damage in Composite Structures.

Composite structures are increasing in prevalence throughout the aerospace, wind, defense, and transportation industries, but the many advantages of these materials come with unique challenges, particularly in inspecting and repairing these structures. Because composites of- ten undergo sub-surface damage mechanisms which compromise the structure without a clear visual indication, inspection of these components is critical to safely deploying composite re- placements to traditionally metallic structures. Impact damage to composites presents one of the most signi fi cant challenges because the area which is vulnerable to impact damage is generally large and sometimes very dif fi cult to access. This work seeks to further evolve iden- ti fi cation technology by developing a system which can detect the impact load location and magnitude in real time, while giving an assessment of the con fi dence in that estimate. Fur- thermore, we identify ways by which impact damage could be more effectively identi fi ed by leveraging impact load identi fi cation information to better characterize damage. The impact load identi fi cation algorithm was applied to a commercial scale wind turbine blade, and results show the capability to detect impact magnitude and location using a single accelerometer, re- gardless of sensor location. A technique for better evaluating the uncertainty of the impact estimates was developed by quantifying how well the impact force estimate meets the assump- tions underlying the force estimation technique. This uncertainty quanti fi cation technique was found to reduce the 95% con fi dence interval by more than a factor of two for impact force estimates showing the least uncertainty, and widening the 95% con fi dence interval by a fac- tor of two for the most uncertain force estimates, avoiding the possibility of understating the uncertainty associated with these estimates. Linear vibration based damage detection tech- niques were investigated in the context of structural stiffness reductions and impact damage. A method by which the sensitivity to damage could be increased for simple structures was presented, and the challenges of applying that technique to a more complex structure were identi fi ed. The structural dynamic changes in a weak adhesive bond were investigated, and the results showed promise for identifying weak bonds that show little or no static reduction in stiffness. To address these challenges in identifying highly localized impact damage, the possi- bility of detecting damage through nonlinear dynamic characteristics was also identi fi ed, with a proposed technique which would leverage impact location estimates to enable the detection of impact damage. This nonlinear damage identi fi cation concept was evaluated on a composite panel with a substructure disbond, and the results showed that the nonlinear dynamics at the damage site could be observed without a baseline healthy reference. By further developing impact load identi fi cation technology and combining load and damage estimation techniques into an integrated solution, the challenges associated with impact detection in composite struc- tures can be effectively solved, thereby reducing costs, improving safety, and enhancing the operational readiness and availability of high value assets.

Roach, Dennis P.↗
DOE OSTI2017

Crystal structure of the receptor-binding domain of botulinum neurotoxin type HA, also known as type FA or H

Botulinum neurotoxins (BoNTs), which have been exploited as cosmetics and muscle-disorder treatment medicines for decades, are well known for their extreme neurotoxicity to humans. They pose a potential bioterrorism threat because they cause botulism, a flaccid muscular paralysis-associated disease that requires immediate antitoxin treatment and intensive care over a long period of time. In addition to the existing seven established BoNT serotypes (BoNT/A–G), a new mosaic toxin type termed BoNT/HA (aka type FA or H) was reported recently. Sequence analyses indicate that the receptor-binding domain (HC) of BoNT/HA is ~84% identical to that of BoNT/A1. However, BoNT/HA responds differently to some potent BoNT/A-neutralizing antibodies (e.g., CR2) that target the HC. Therefore, it raises a serious concern as to whether BoNT/HA poses a new threat to our biosecurity. In this study, we report the first high-resolution crystal structure of BoNT/HA-HC at 1.8 Å. Sequence and structure analyses reveal that BoNT/HA and BoNT/A1 are different regarding their binding to cell-surface receptors including both polysialoganglioside (PSG) and synaptic vesicle glycoprotein 2 (SV2). Furthermore, the new structure also provides explanations for the ~540-fold decreased affinity of antibody CR2 towards BoNT/HA compared to BoNT/A1. Altogether, these new findings advance our understanding of the structure and function of this newly identified toxin at the molecular level, and pave the way for the future development of more effective countermeasures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structure-based analysis of CysZ-mediated cellular uptake of sulfate

Sulfur, most abundantly found in the environment as sulfate (SO 4 2- ), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO 4 2- at the molecular level is limited. CysZ has been described as a SO 4 2- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO 4 2- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO 4 2- across membranes. CysZ structures from three different bacterial species display a hitherto unknown fold and have subunits organized with inverted transmembrane topology. CysZ from Pseudomonas denitrificans assembles as a trimer of antiparallel dimers and the CysZ structures from two other species recapitulate dimers from this assembly. In conclusion, mutational studies highlight the functional relevance of conserved CysZ residues.

59 BASIC BIOLOGICAL SCIENCES↗