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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
NASA NTRS1992

Atomic structure and chemistry of human serum albumin

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and ILIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

He, Xiao M.↗
DOE OSTI2016

Quantum Yield Heterogeneity among Single Nonblinking Quantum Dots Revealed by Atomic Structure-Quantum Optics Correlation

Physical variations in colloidal nanostructures give rise to heterogeneity in expressed optical behavior. This correlation between nanoscale structure and function demands interrogation of both atomic structure and photophysics at the level of single nanostructures to be fully understood. In this paper, by conducting detailed analyses of fine atomic structure, chemical composition, and time-resolved single-photon photoluminescence data for the same individual nanocrystals, we reveal inhomogeneity in the quantum yields of single nonblinking “giant” CdSe/CdS core/shell quantum dots (g-QDs). We find that each g-QD possesses distinctive single exciton and biexciton quantum yields that result mainly from variations in the degree of charging, rather than from volume or structure inhomogeneity. We further establish that there is a very limited nonemissive “dark” fraction (<2%) among the studied g-QDs and present direct evidence that the g-QD core must lack inorganic passivation for the g-QD to be “dark”. Finally and therefore, in contrast to conventional QDs, ensemble photoluminescence quantum yield is principally defined by charging processes rather than the existence of dark g-QDs.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Layer-Dependent Electronic Structure of Atomically Resolved Two-Dimensional Gallium Selenide Telluride

Alloying two-dimensional (2D) semiconductors provides a powerful method to tune their physical properties, especially those relevant to optoelectronic applications. However, as the crystal structure becomes more complex, it becomes increasingly difficult to accurately correlate response characteristics to detailed atomic structure. We investigate, via annular dark-field scanning transmission electron microscopy, electron energy loss spectroscopy, and second harmonic generation, the layered III-VI alloy GaSe 0.5 Te 0.5 as a function of layer number. The local atomic structure and stacking sequence for different layers is explicitly determined. We complement the measurements with first-principles calculations of the total energy and electronic band structure of GaSe 0.5 Te 0.5 for different crystal structures and layer number. The electronic band gap as well as the π and π + σ plasmons are found to be sensitive to layer number.

2D semiconductor alloys↗
DOE OSTI2017

Iron phosphate glasses: Bulk properties and atomic scale structure

Bulk properties such as glass transition temperature, density and thermal expansion of iron phosphate glass compositions, with replacement of Cs by Ba, are investigated as a surrogate for the transmutation of 137Cs to 137Ba, relevant to the immobilisation of Cs in glass. These studies are required to establish the appropriate incorporation rate of 137Cs in iron phosphate glass. Density and glass transition temperature increases with the addition of BaO indicating the shrinkage and reticulation of the iron phosphate glass network. The average thermal expansion coefficient reduces from 19.8 × 10-6 K-1 to 13.4 × 10-6 K-1, when 25 wt. % of Cs2O was replaced by 25 wt. % of BaO in caesium loaded iron phosphate glass. In addition to the above bulk properties, the role of Ba as a network modifier in the structure of iron phosphate glass is examined using various spectroscopic techniques. The FeII content and average coordination number of iron in the glass network was estimated using Mössbauer spectroscopy. The FeII content in the un-doped iron phosphate glass and barium doped iron phosphate glasses was 20, 21 and 22 ± 1% respectively and the average Fe coordination varied from 5.3 ± 0.2 to 5.7 ± 0.2 with increasing Ba content. The atomic scale structure was further probed by Fe K-edge X-ray absorption spectroscopy. The average coordination number provided by extended X-ray absorption fine structure spectroscopy and X-ray absorption near edge structure was in good agreement with that given by the Mössbauer data.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Probing the Atomic-Scale Structure of Amorphous Aluminum Oxide Grown by Atomic Layer Deposition

Atomic layer deposition (ALD) is a well-established technique for depositing nanoscale coatings with pristine control of film thickness and composition. The trimethylaluminum (TMA) and water (H 2 O) ALD chemistry is inarguably the most widely used and yet to date, we have little information about the atomic-scale structure of the amorphous aluminum oxide (AlO x ) formed by this chemistry. This lack of understanding hinders our ability to establish process-structure-property relationships and ultimately limits technological advancements employing AlOx made via ALD. In this work, we employ synchrotron high-energy X-ray diffraction (HE-XRD) coupled with pair distribution function (PDF) analysis to characterize the atomic structure of amorphous AlO x ALD coatings. We combine ex situ and in operando HE-XRD measurements on ALD AlO x and fit these experimental data using stochastic structural modeling to reveal variations in the Al-O bond length, Al and O coordination environment, and extent of Al vacancies as a function of growth conditions. In particular, the local atomic structure of ALD AlO x is found to change with the substrate and number of ALD cycles. The observed trends are consistent with the formation of bulk Al 2 O 3 surrounded by an O-rich surface layer. We deconvolute these data to reveal atomic-scale structural information for both the bulk and surface phases. Overall, this work demonstrates the usefulness of HE-XRD and PDF analysis in improving our understanding of the structure of amorphous ALD thin films and provides a pathway to evaluate how process changes impact the structure and properties of ALD films.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Modeling precursor diffusion and reaction of atomic layer deposition in porous structures

Atomic layer deposition (ALD) is a technique for depositing thin films of materials with a precise thickness control and uniformity using the self-limitation of the underlying reactions. Usually, it is difficult to predict the result of the ALD process for given external parameters, e.g., the precursor exposure time or the size of the precursor molecules. Therefore, a deeper insight into ALD by modeling the process is needed to improve process control and to achieve more economical coatings. In this paper, a detailed, microscopic approach based on the model developed by Yanguas-Gil and Elam is presented and additionally compared with the experiment. Precursor diffusion and second-order reaction kinetics are combined to identify the influence of the porous substrate's microstructural parameters and the influence of precursor properties on the coating. The thickness of the deposited film is calculated for different depths inside the porous structure in relation to the precursor exposure time, the precursor vapor pressure, and other parameters. Good agreement with experimental results was obtained for ALD zirconiumdioxide (ZrO{sub 2}) films using the precursors tetrakis(ethylmethylamido)zirconium and O{sub 2}. The derivation can be adjusted to describe other features of ALD processes, e.g., precursor and reactive site losses, different growth modes, pore size reduction, and surface diffusion.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Electronic structure and dynamics of confined atoms

Confined atomic systems are of great importance owing a multitude of possible applications in various areas of science and technology. Of particular interest are atoms encaged in the C 60 molecule, A@C 60 , since the near-spherical symmetry of C 60 simplifies theoretical studies, and the stability of C 60 renders it amenable to experimental examination. Herein a review of investigations of the electronic structure and dynamics of A@C 60 is presented in this manuscript focusing on developments in the last decade. Addressed mainly are how the confinement affects electronic structure properties such as ionization potentials, localization of atomic electrons, Shannon entropy, correlation effects, relativistic interactions, and others. In the area of dynamics, photoionization and e-A@C 60 scattering are reviewed and summarized, and the major effects of confinement on the dynamical properties, e.g., confinement resonances, hybridization, Wigner time delay, are delineated.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Atomic-Level Structural Dynamics of Polyoxoniobates during DMMP Decomposition

Ambient pressure in situ synchrotron-based spectroscopic techniques have been correlated to illuminate atomic-level details of bond breaking and formation during the hydrolysis of a chemical warfare nerve agent simulant over a polyoxometalate catalyst. Specifically, a Cs 8 [Nb 6 O 19 ] polyoxoniobate catalyst has been shown to react readily with dimethyl methylphosphonate (DMMP). The atomic-level transformations of all reactant moieties, the [Nb 6 O 19 ] 8- polyanion, its Cs + counterions, and the DMMP substrate, were tracked under ambient conditions by a combination of X-ray absorption fine structure spectroscopy, Raman spectroscopy, and X-ray diffraction. Results reveal that the reaction mechanism follows general base (in contrast to specific base) hydrolysis. Together with computational results, the work demonstrates that the ultimate fate of DMMP hydrolysis at the Cs 8 [Nb 6 O 19 ] catalyst is strong binding of the (methyl) methylphosphonic acid ((M)MPA) product to the polyanions, which ultimately inhibits catalytic turnover.

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

Structural trends in atomic nuclei from laser spectroscopy of tin

Tin is the chemical element with the largest number of stable isotopes. Its complete proton shell, comparable with the closed electron shells in the chemically inert noble gases, is not a mere precursor to extended stability; since the protons carry the nuclear charge, their spatial arrangement also drives the nuclear electromagnetism. We report high-precision measurements of the electromagnetic moments and isomeric differences in charge radii between the lowest 1/2 + , 3/2 + , and 11/2 - states in 117–131 Sn, obtained by collinear laser spectroscopy. Supported by state-of-the-art atomic-structure calculations, the data accurately show a considerable attenuation of the quadrupole moments in the closed-shell tin isotopes relative to those of cadmium, with two protons less. Linear and quadratic mass-dependent trends are observed. While microscopic density functional theory explains the global behaviour of the measured quantities, interpretation of the local patterns demands higher-fidelity modelling.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Imaging the atomic surface structures of CeO2 nanoparticles

Atomic surface structures of CeO2 nanoparticles are under debate owing to the lack of clear experimental determination of the positions of the surface oxygen atoms. Particularly controversial is the (100) surface structure of this material. In this study, with oxygen atoms clearly observed using aberration corrected high resolution electron microscopy, we determined the atomic structures of the (100), (110) and (111) surfaces of CeO2 nanocubes. The predominantly exposed (100) surface has a mixture of Ce, O, and reduced CeO terminations, underscoring the complex structures of this polar surface that previously was often oversimplified. The (110) surface shows saw-like (111) nanofacets and flat CeO2-x terminations with oxygen vacancies. The (111) surface has an O termination. As these three low index surfaces are the most often exposed facets in the majority of CeO2 nanoparticles, these findings can be extended to the surfaces of differently shaped CeO2 nanoparticles as well as provide insight about face-selective catalysis.

Lin, Yuyuan↗