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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (M pro ) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on M pro inhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

IMS Rapid Response FY21 Summary Report for: Integrating Patterned Probes with Four-Dimensional Scanning Transmission Electron Microscopy for Unrivaled Crystallographic Structure Determination in Nanomaterials

The initial goal of our 4-dimensional scanning transmission electron microscopy (4D-STEM)-based project was to develop strain resolution two orders of magnitude better than what is now currently possible with electron-based scattering techniques, all while collecting scattering information from 7 different tilt axes at one time [multi-beam electron diffraction (MBED)1 ] through the development of a new electron probe-forming aperture with non-circular features (patterned probes 2 ). We set out to accomplish this through a collaboration with Drs. Colin Ophus and Ben Savitsky at Lawrence Berkeley Laboratory (they are the world-leading experts in developing the complex computational codes required to perform orientation analysis and quantitative strain mapping on our 4D-STEM data sets. We are motivated to invest in this area as it will be the only technique sensitive enough to perform three- dimensional automated crystallographic orientation mapping (ACOM) and strain mapping for materials exposed to external stimulus (a focus of our larger efforts).

36 MATERIALS SCIENCE↗
DOE OSTI2022

Vibrational modes and crystallographic structure of Cd 3 As 2 and (Cd 1-x Zn x ) 3 As 2 epilayers

Low-temperature Raman scattering is used to study the crystal structure of molecular-beam epitaxially grown layers of the Dirac semimetal Cd 3 As 2 and its related alloy (Cd 1-x Zn x ) 3 As 2 . The combination of narrow-linewidth spectra, multiple growth directions and full polarization analysis allows improved accuracy in identifying the irreducible representation of over 57 Raman-active vibrations. Several disagreements with previous identifications are found. Structurally, the results agree with the centrosymmetric I41/acd space group of bulk-grown Cd 3 As 2 and are clearly distinct from the Raman spectra of nanoscale platelets and wires. Three-fold twinning is seen in (112) Cd 3 As 2 grown on (111) zincblende substrates corresponding to the three possible tetragonal orientations. In dilute (Cd 1-x Zn x ) 3 As 2 , phonons have a frequency and scattering amplitude dependence on Zn concentration that is continuous with Cd 3 As 2 but at least one frequency is absent at the alloy endpoint, preventing a simple one-mode description of the alloy phonon.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Crystallographic Texture, Structure, and Stress Transmission in Nugget Sandstone Examined With X‐Ray Tomography and Diffraction Microscopy

Subsurface processes in sandstones are controlled by porosity, permeability, and deformation mechanisms, all of which are controlled by a complex interplay of crystallographic rock texture, structure, and micromechanics. Texture, structure, and micromechanics have historically been studied using optical and electron microscopy of thin-sections. Here, we employed a new combination of in situ X-ray tomography and ray diffraction microscopy to study crystallographic texture, structure, and grain stresses in 3D. We examined these features in a sample of Nugget sandstone, a sandstone constituting hydrocarbon reservoirs across the American West. Our aims are threefold. First, we demonstrate the utility of X-ray diffraction microscopy probes for revealing texture, structure, and stress transmission in 3D. Second, we apply these techniques to Nugget sandstone and discuss findings in the context of prior work. Third, we study grain stress tensor evolution during mechanical compression to examine whether their heterogeneity and orientation evolution reflect that of inter-particle forces in granular materials. Our results show: (a) larger grains featured higher intra-granular misorientations, possibly from an increased prevalence of cements; (b) pores closed parallel to the loading direction and opened normal to loading; (c) grain stresses featured heterogeneity and orientations similar to inter-particle forces in non-cohesive granular materials; (d) grains featured compressive stresses in the loading direction and tensile stresses orthogonal to the loading direction, the latter resisting sample dilation and grain separation. Our work demonstrates the first known application of multi-modal X-ray tomography and diffraction microscopy to sandstone, providing new 3D insight into the nature of quartz cement and stress evolution.

high energy diffraction microscopy↗
DOE OSTI2025

Symmetry breaking forms split-off flat bands in quantum oxides controlling metal versus insulator phases

The crystal structure used as input to electronic structure calculation of conventionally bonded solids consists primarily of the standard crystallographic degrees of freedom. Quantum solids sometimes have additional microscopic degrees of freedom (m-DOF) nested within the crystallographic structure. These might include local motifs including positional (Peierls dimers, deformed octahedra, Jahn-Teller distortions), magnetic (local moment configurations) and dipolar (local ferroelectric configurations). Such motifs can be observed experimentally via local probes that avoid averaging, and theoretically as distinct total energy lowering features relative to more simplified “average crystallographic structures”. Here we examine the ability of electronic structure methods independent of strong correlation physics to explain the broad phenomenology of metal-insulator selectivity in quantum oxides by energy-lowering symmetry breaking. We do this by avoiding the restriction of considering only (i) electron-electron interactions in a fixed unresponsive lattice—as done in Mott strong correlation explanations—allowing, however, (ii) local positional and magnetic motifs that coexist within a crystallographic landscape. We find in a broad range of quantum oxides with different symmetry breaking modes the formation of split-off flat bands that can also control metallic versus insulating characteristics. The split-off band effect is common to magnetic and non-magnetic materials, including both binary and ternary oxides. One finds that when such local symmetry breaking motifs are considered in mean-field-like (e.g. density functional theory) electronic structure calculations of quantum oxides, they explain many of the observed trends in metal vs insulator phases discussed otherwise in prior literature via strong correlation in symmetry unbroken view.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Structure and properties of the Sr 2 In 1-x Sn x SbO 6 double perovskite

A series of n -type oxide double perovskite semiconductors, Sr 2 In 1-x Sn x SbO 6 (0 ≤ x ≤ 0.3) has been synthesized; Sn 4+ partially substitutes for In 3+ . 121 Sb and 119 Sn Mössbauer spectroscopy are employed to investigate the B-site cation ordering because this issue cannot be resolved by conventional diffraction techniques alone. Rigid ordering between In 3+ /Sn 4+ and Sb 5+ sites is revealed by the spectroscopic method, and hence in combination with the structural parameters extracted from the XRD structural refinements, the crystallographic structure of this series of compounds is depicted. Furthermore, the temperature dependent magnetic susceptibilities, band gaps, and carrier type are characterized, and the calculated band structure is presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure

Acetylcholinesterase (AChE) catalyzes hydrolysis of acetylcholine thereby terminating cholinergic nerve impulses for efficient neurotransmission. Human AChE (hAChE) is a target of nerve agent and pesticide organophosphorus compounds that covalently attach to the catalytic Ser203 residue. Reactivation of inhibited hAChE can be achieved with nucleophilic antidotes, such as oximes. Understanding structural and electrostatic (i.e. protonation states) determinants of the catalytic and reactivation processes is crucial to improve design of oxime reactivators. Here we report X-ray structures of hAChE conjugated with a reversible covalent inhibitor 4K-TMA (4K-TMA:hAChE) at 2.8 Å resolution and of 4K-TMA:hAChE conjugate with oxime reactivator methoxime, MMB4 (4K-TMA:hAChE:MMB4) at 2.6 Å resolution, both at physiologically relevant room temperature, as well as cryo-crystallographic structure of 4K-TMA:hAChE at 2.4 Å resolution. 4K-TMA acts as a substrate analogue reacting with the hydroxyl of Ser203 and generating a reversible tetrahedral hemiketal intermediate that closely resembles the first tetrahedral intermediate state during hAChE-catalyzed acetylcholine hydrolysis. Structural comparisons of room temperature with cryo-crystallographic structures of 4K-TMA:hAChE and published mAChE complexes with 4K-TMA, as well as the effect of MMB4 binding to the peripheral anionic site (PAS) of the 4K-TMA:hAChE complex, revealed only discrete, minor differences. The active center geometry of AChE, already highly evolved for the efficient catalysis, was thus indicative of only minor conformational adjustments to accommodate the tetrahedral intermediate in the hydrolysis of the neurotransmitter acetylcholine (ACh). To map protonation states in the hAChE active site gorge we collected 3.5 Å neutron diffraction data paving the way for obtaining higher resolution datasets that will be needed to determine locations of individual hydrogen atoms.

4K-TMA↗
DOE OSTI2026

Machine learning approaches for crystallographic classification from synthetic 2D X-ray diffraction data

Crystallographic structure identification is crucial for understanding material properties; however, current methodologies often depend on labor-intensive and time-consuming analyses of 2D X-ray diffraction (XRD) patterns. To address these limitations, this study employs synthetic 2D XRD patterns combined with deep learning (DL) techniques to enable automated and high-throughput classification of the seven crystal systems and 230 space groups. We introduce the novel Auto Diffraction Pipeline, designed to generate synthetic 2D XRD spot patterns from crystallographic information files under diverse conditions, including varying zone axes, atomic substitution, atomic depletion and mechanical loading. These conditions enhance the realism of synthetic data, mitigating the scarcity of experimental datasets and enabling the creation of large representative training sets. Convolutional neural networks were trained and validated on these synthetic datasets to classify crystallographic structures across multiple scenarios. Our results demonstrate that integrating synthetic 2D XRD patterns with DL facilitates rapid, accurate and automated crystallographic classification, promoting the wider adoption of data-driven approaches in materials science.

Shahnazari, Ayoub [Univ. of Rochester, NY (United ↗
DOE OSTI2024

Electron diffraction intensity from single crystal silicon in a photoinjector

A method includes simulating diffraction in a transmission geometry of relativistic electron bunches from a crystallographic structure of a crystal thereby simulating diffraction of the relativistic electron bunches into a plurality of Bragg peaks. The method includes selecting a range of angles between a direction of propagation of the relativistic electron bunches and a normal direction of crystal including an angle at which a diffraction portion is maximized. The method includes sequentially accelerating a plurality of physical electron bunches to relativistic energies toward a physical crystal having the crystallographic structure and diffracting the plurality of physical electron bunches off the physical crystal at different angles and measuring the diffraction portion into the respective Bragg peak at the different angles. The method includes selecting a final angle based on the measured diffraction portion into the respective Bragg peak at the different angles and generating a pulse of light.

Graves, William↗
DOE OSTI2025

Unveiling the role of halide mixing in the crystallization kinetics and charge transfer mechanisms of wide-bandgap organic–inorganic halide perovskites

Understanding the crystallization kinetics of Br–I mixed-halide WBG perovskite films, and their correlation to the crystallographic structure and charge transfer dynamics, is critical for advancing WBG perovskite devices. Despite many efforts to increase the photovoltaic performances of wide-bandgap (WBG, with a Br content above 20%) perovskite solar cells based on bromine–iodine (Br–I) mixed-halide perovskites, understanding the crystallization kinetics of WBG perovskite films, as well as the role of Br mixing in the crystallization kinetics, is still lacking. Furthermore, an overlooked aspect is the correlation of the halide compositions, crystallization kinetics, crystallographic structure, and charge transfer dynamics. Here, we unveil that Br–I mixed-halide WBG perovskite films undergo two intrinsically different crystallization kinetic processes. One is the intermediate solvent-complex phase-assisted growth (I-rich), and the other is top-to-bottom downward growth (Br-rich). Such downward growth (including high Br concentrations) correlates with the formation of a highly vertically oriented perovskite film, which is accompanied by defect formation caused by a dissolving and recrystallization process coupled with halide homogenization. Consequently, Br-rich WBG perovskite films exhibit enhanced charge carrier transport, but are concurrently plagued by non-radiative charge recombination. Addressing this fundamental perspective is critical to precisely tailor Br-related crystallization, which significantly affects the structure and optoelectronic properties of WBG perovskite films and devices.

Li, Nian↗
DOE OSTI2021

Comparative Studies of Optoelectronic Properties, Structures, and Surface Morphologies for Phosphorus-Doped Poly-Si/SiOx Passivating Contacts

We investigated and compared optoelectronic properties, crystallographic structures, and nanoscale surface morphologies of ex-situ phosphorus-doped polycrystalline silicon (poly-Si)/SiO x passivating contacts, formed by different deposition methods (sputtering, plasma-enhanced chemical vapour deposition (PECVD), and low-pressure chemical vapour deposition (LPCVD)). Across all these deposition technologies, a similar trend is observed: higher diffusion temperatures yield films that are more crystalline but have rougher surface morphologies due to bigger surface crystal grains. Also, the recrystallization process of the as-deposited Si films starts from the SiO x interface, rather than from the film surface and bulk. However, there are some distinct differences among these technologies. Firstly, the LPCVD method yields the roughest surface and smallest degree of crystallinity on finished poly-Si films. In contrast, the PECVD method has the smoothest surface for both as-deposited Si and annealed poly-Si films. Secondly, as-deposited sputtered and PECVD Si films contain only an amorphous phase whereas as-deposited LPCVD films has already had some crystalline phase. Thirdly, the LPCVD phosphorus in-diffusion into the substrate depends strongly on the initial film thickness, whereas for the other two methods it is weakly dependent on thickness.

crystallographic structures↗
DOE OSTI2021

Morphology, microstructure, and doping behaviour: A comparison between different deposition methods for poly-Si/SiO x passivating contacts

In this work, we study how crystallographic structures, optoelectronic properties, and nanoscale surface morphologies of ex situ phosphorus-doped polycrystalline silicon (poly-Si)/SiO x passivating contacts, formed by different deposition methods (sputtering, plasma-enhanced chemical vapour deposition [PECVD], and low-pressure chemical vapour deposition [LPCVD]), are investigated and compared. Across all these deposition technologies, we noted the same trend: higher diffusion temperatures yield films that are more crystalline but that have rougher surface morphologies due to bigger surface crystal grains. Also, the recrystallization process of the as-deposited Si films starts from the SiO x interface, rather than from the film surface and bulk. However, there are some distinct differences among these technologies. First, the LPCVD method yields the lowest deposition rate, roughest surfaces, and smallest degree of crystallinity on finished poly-Si films. In contrast, the PECVD method has the highest deposition rate and smoothest surfaces for both as-deposited Si and annealed poly-Si films. Second, as-deposited sputtered and PECVD Si films contain only an amorphous phase, whereas as-deposited LPCVD films already has some crystalline phase. Third, the LPCVD phosphorus in-diffusion into the substrate depends strongly on the initial film thickness, whereas for the other two methods, it is weakly dependent on thickness. Finally, the passivation quality of every poly-Si film type has different responses to the film thickness and diffusion temperature, suggesting that the ex situ doping optimization should be performed independently.

14 SOLAR ENERGY↗
DOE OSTI2024

Exploring the impact of Cr-doping on the crystallographic and magnetic structure of Mn 5 Si 3 antiferromagnetic alloy

Here, the role of Cr-doping on the structural and magnetic ground states of Mn 5 Si 3 alloy has been investigated through temperature-dependent neutron powder diffraction (NPD) and X-ray absorption fine structure (XAFS) techniques. All the Cr-doped alloys of nominal composition Mn 5-x Cr x Si 3 (for x = 0.05, 0.1, and 0.2) undergo two first-order magneto-structural phase transitions from hexagonal (space group: P6 3 /mcm) paramagnetic → orthorhombic (space group: Ccmm) collinear antiferromagnetic → orthorhombic (space group: Cc2m) non-collinear antiferromagnetic phase on cooling from room temperature. NPD studies at different constant temperatures indicate that both anti ferromagnetic phases are commensurate in nature and can be represented by q = (0,1,0) magnetic propagation vector for all the Cr-doped alloys. Such doping at the Mn-site results in a significant modification of the non-collinear antiferromagnetic structure (both moment size and orientation) and hence affects the unusual magnetic properties, like inverted hysteresis loop, thermomagnetic irreversibility, etc. The XAFS measurements were performed to interpret the local environment of doped Cr atoms in detail, which is critical for a microscopic understanding of the unusual properties of this class of Cr-doped Mn 5 Si 3 alloys. The analysis confirms the elemental state of Cr in the doped alloys and indicates a high degree of preservation of local crystallographic structure with varying Cr concentration and sample temperature. Doping induces intriguing changes in XAFS patterns, elucidated through different types of scattering mechanisms associated with the central absorbing Cr atom.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus–programmed ribosomal frameshifting element

A hallmark of retrovirus replication is the translation of two different polyproteins from one RNA through programmed –1 frameshifting. This is a mechanism in which the actively translating ribosome is induced to slip in the 5′ direction at a defined codon and then continues translating in the new reading frame. Programmed frameshifting controls the stoichiometry of viral proteins and is therefore under stringent evolutionary selection. Forty years ago, the first frameshifting stimulatory element was discovered in the Rous sarcoma virus. The ~120 nt RNA segment was predicted to contain a pseudoknot, but its 3D structure has remained elusive. Now, we have determined cryoEM and X-ray crystallographic structures of this classic retroviral element, finding that it adopts a butterfly-like double-pseudoknot fold. One “wing” contains a dynamic pyrimidine-rich helix, observed crystallographically in two conformations and in a third conformation via cryoEM. The other wing encompasses the predicted pseudoknot, which interacts with a second unexpected pseudoknot through a toggle residue, A2546. This key purine switches conformations between structural states and tunes the stability of interacting residues in the two wings. We find that its mutation can modulate frameshifting by as much as 50-fold, likely by altering the relative abundance of different structural states in the conformational ensemble of the RNA. Taken together, our structure–function analyses reveal how a dynamic double pseudoknot junction stimulates frameshifting by taking advantage of conformational heterogeneity, supporting a multistate model in which high Shannon entropy enhances frameshifting efficiency.

Science & Technology - Other Topics↗
DOE OSTI2026

Assessing Metal Ion Assignment Accuracy in Protein Data Bank Models via Elemental Spectroscopy

Accurate representation of metal ions in macromolecular structures is critical for chemical interpretation, computational modeling, and machine-learning methods that rely on Protein Data Bank (PDB) entries. However, the elemental identity of metals modeled in crystallographic structures is often inferred indirectly and rarely validated experimentally. Here, we combine Particle Induced X-ray Emission (PIXE) and X-ray Fluorescence Spectroscopy (XRFS) to determine the elemental composition of protein samples used to generate 70 deposited metalloprotein crystal structures. By analyzing the original protein material employed for crystallization, but before the addition of crystallization buffer solutions, we assess whether the modeled metal ions in deposited structures are consistent with experimentally detectable elemental content. We find that in a majority of cases, the metals modeled in the corresponding PDB entries are inconsistent with the metals present in the protein samples before crystallization, or that additional metals are present but not represented in the structural models. Spectroscopic results were integrated with automated crystallographic validation metrics, including real-space Z-difference (RSZD) analysis and systematic rerefinement, to evaluate atomic-number mismatch at metal sites. PIXE and XRFS show strong agreement for dominant elemental signals and provide complementary, scalable approaches for identifying suspect metal assignments. This work does not address physiological or functional metalation but instead highlights a widespread data integrity issue in deposited macromolecular structures, PDB-wide. These results establish an experimentally corroborated link between elemental identity and crystallographic validation metrics, enabling the large-scale detection of chemically inconsistent annotations in structural databases used for computational modeling and machine learning.

Crystallization↗
DOE OSTI2023

Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation

The assembly of the autophagy initiation machinery nucleates autophagosome biogenesis, including in the PINK1- and Parkin-dependent mitophagy pathway implicated in Parkinson’s disease. The structural interaction between the sole transmembrane autophagy protein, autophagy-related protein 9A (ATG9A), and components of the Unc-51–like autophagy activating kinase (ULK1) complex is one of the major missing links needed to complete a structural map of autophagy initiation. We determined the 2.4-Å x-ray crystallographic structure of the ternary structure of ATG9A carboxyl-terminal tail bound to the ATG13:ATG101 Hop1/Rev7/Mad2 (HORMA) dimer, which is part of the ULK1 complex. We term the interacting portion of the extreme carboxyl-terminal part of the ATG9A tail the “HORMA dimer–interacting region” (HDIR). This structure shows that the HDIR binds to the HORMA domain of ATG101 by β sheet complementation such that the ATG9A tail resides in a deep cleft at the ATG13:ATG101 interface. Disruption of this complex in cells impairs damage-induced PINK1/Parkin mitophagy mediated by the cargo receptor NDP52.

59 BASIC BIOLOGICAL SCIENCES↗