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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Surface and electronic structure at atomic length scales of the nonsymmorphic antiferromagnet Eu 5 In 2 Sb 6

We performed scanning tunneling microscopy and spectroscopy (STM/STS) measurements to investigate the Zintl phase Eu 5 ⁢In 2 ⁢Sb 6 , a nonsymmorphic antiferromagnet. The theoretical prediction of a nontrivial Fermi surface topology stabilized by the nonsymmorphic symmetry motivated our research. On the cleaved (010) plane, we obtained striped patterns that can be correlated to the stacking of the [In 2 ⁢Sb 6 ] 10- double chains along the crystallographic c axis. The attempted cleavage along the a axis revealed a more complex pattern. We combined the STS measurement on nonreconstructed (010) and (081) surfaces with DFT calculations to further elucidate the electronic structure of Eu 5 ⁢In 2 ⁢Sb 6 . From our investigations so far, direct experimental evidence of the predicted topological surface states remains elusive.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Radiative properties of quantum emitters in boron nitride from excited state calculations and Bayesian analysis

Abstract Point defects in hexagonal boron nitride (hBN) have attracted growing attention as bright single-photon emitters. However, understanding of their atomic structure and radiative properties remains incomplete. Here we study the excited states and radiative lifetimes of over 20 native defects and carbon or oxygen impurities in hBN using ab initio density functional theory and GW plus Bethe-Salpeter equation calculations, generating a large data set of their emission energy, polarization and lifetime. We find a wide variability across quantum emitters, with exciton energies ranging from 0.3 to 4 eV and radiative lifetimes from ns to ms for different defect structures. Through a Bayesian statistical analysis, we identify various high-likelihood charge-neutral defect emitters, among which the native V N N B defect is predicted to possess emission energy and radiative lifetime in agreement with experiments. Our work advances the microscopic understanding of hBN single-photon emitters and introduces a computational framework to characterize and identify quantum emitters in 2D materials.

Chemistry↗
DOE OSTI2023

The N‐terminal intrinsically disordered region of Ncb5or docks with the cytochrome b 5 core to form a helical motif that is of ancient origin

Abstract NADH cytochromeb 5 oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochromeb 5 (b 5 ) and cytochromeb 5 reductase (b 5 R) domains separated by a CHORD‐Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter‐domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full‐length human Ncb5or has proven resistant to crystallization, we have succeeded in obtaining high‐resolution atomic structures of theb 5 domain and a construct containing the CS andb 5 R domains (CS/b 5 R). Ncb5or also contains an N‐terminal intrinsically disordered region of 50 residues that has no homologs in other protein families in animals but features a distinctive, conserved L 34 MDWIRL 40 motif also present in reduced lateral root formation (RLF) protein in rice and increased recombination center 21 in baker's yeast, all attaching to ab 5 domain. After unsuccessful attempts at crystallizing a human Ncb5or construct comprising the N‐terminal region naturally fused to theb 5 domain, we were able to obtain a high‐resolution atomic structure of a recombinant rice RLF construct corresponding to residues 25–129 of human Ncb5or (52% sequence identity; 74% similarity). The structure reveals Trp 120 (corresponding to invariant Trp 37 in Ncb5or) to be part of an 11‐residue α‐helix (S 116 QMDWLKLTRT 126 ) packing against two of the four helices in theb 5 domain that surround heme (α2 and α5). The Trp 120 side chain forms a network of interactions with the side chains of four highly conserved residues corresponding to Tyr 85 and Tyr 88 (α2), Cys 124 (α5), and Leu 47 in Ncb5or. Circular dichroism measurements of human Ncb5or fragments further support a key role of Trp 37 in nucleating the formation of the N‐terminal helix, whose location in the N/b 5 module suggests a role in regulating the function of this multi‐domain redox enzyme. This study revealed for the first time an ancient origin of a helical motif in the N/b 5 module as reflected by its existence in a class of cytochromeb 5 proteins from three kingdoms among eukaryotes.

Biochemistry & Molecular Biology↗
DOE OSTI2025

CuXASNet: Rapid and accurate prediction of copper L-edge x-ray absorption spectra using machine learning

In this work, we have developed CuXASNet, a dense neural network that predicts simulated Cu -edge x-ray absorption spectra (XAS) from atomic structures. Featurization of the Cu local environment is performed using a component of M3GNet, a graph neural network developed for predicting the potential energy surface. CuXASNet is trained on simulated spectra from FEFF9 at the multiple scattering level of theory, and can predict the and edges for Cu sites to quantitative accuracy. To validate our approach, we compare 14 experimental spectra extracted from the literature with the predictions of CuXASNet. The agreement of CuXASNet with experiments is shown by an average mean absolute error of 0.125 and an average Spearman's correlation coefficient of 0.891, which is comparable to FEFF9's values of 0.131 and 0.898 for the same metrics. As such, CuXASNet can rapidly predict a large number of -edge XAS spectra at the same accuracy as FEFF9 simulations. This can be used as a drop-in replacement for multiple scattering codes for fast screening of candidate atomic structure models of a measured system. This model establishes a general framework for Cu XAS prediction, and can be extended to more computationally expensive levels of theory and to other transition metal edges.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Temperature-induced structural evolution in liquid Ag-Ga alloys

Temperature-dependent atomic structural evolutions of liquid Ag 60 Ga 40 and Ag 70 Ga 30 alloys have been studied by in situ high-energy x-ray-diffraction (HEXRD) experiments combined with ab initio molecular-dynamics simulations. The experimental data show a reversible structural crossover at about 1050 ~ 1100 (± 50) K in both liquid Ag 60 Ga 40 and Ag 70 Ga 30 alloys. Obvious changes of the electrical resistivity, absolute thermoelectric power, and atomic diffusivity around the similar temperature range for both Ag-Ga liquids strongly support the HEXRD results. The origin of the liquid-to-liquid crossover in both Ag-Ga liquids was suggested to link with the rearrangements of Ag and Ga atoms, i.e., Ag and Ga atoms prefer to associate with themselves in the higher temperature range above 1100 K, consistent with the accelerated increase of the strong covalently bonded Ga–Ga dimers in both Ag-Ga liquids. In addition, more studies from the energy aspect are still desirable to understand the rearrangements of Ag and Ga atoms in the higher temperature range in both Ag-Ga liquids.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Three-dimensional atomic packing in amorphous solids with liquid-like structure

Liquids and solids are two fundamental states of matter. However, our understanding of their three-dimensional atomic structure is mostly based on physical models. Here we use atomic electron tomography to experimentally determine the three-dimensional atomic positions of monatomic amorphous solids, namely a Ta thin film and two Pd nanoparticles. We observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Instead of forming icosahedra, the majority of pentagonal bipyramids arrange into pentagonal bipyramid networks with medium-range order. Molecular dynamics simulations further reveal that pentagonal bipyramid networks are prevalent in monatomic metallic liquids, which rapidly grow in size and form more icosahedra during the quench from the liquid to the glass state. Furthermore, these results expand our understanding of the atomic structures of amorphous solids and will encourage future studies on amorphous–crystalline phase and glass transitions in non-crystalline materials with three-dimensional atomic resolution.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A general synthesis of single atom catalysts with controllable atomic and mesoporous structures

The control of single metal atomic sites has been extensively studied in the field of single atom catalysts. By contrast, the precise control of the mesoporous structure in the matrix material, which directly correlates with mass diffusions and may play a dominant role in delivering industrially relevant reaction rates, has been overlooked. In this work, we report a general method for the synthesis of a single atom catalyst with control of the atomic structure of the single atomic site as well as the mesoporous structure of the carbon support for optimized catalytic performance. Various combinations of metal centres (Ni, Co, Mn, Zn, Cu, Sc and Fe) and mass diffusion channels in two dimensions and three dimensions were achieved. Using CO 2 reduction to CO as an example, our Ni single atom catalyst with three-dimensional diffusion channels delivered a practical current of 350 mA cm –2 while maintaining a 93% CO Faradaic efficiency, representing a sixfold improvement in turnover frequency compared to two-dimensional counterparts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Unravelling Disorder in Aperiodic Crystals – Diffuse Scattering and Atomic Resolution Holography

The atomic–scale disorder of aperiodic crystals, and quasicrystals in particular, is inherently difficult to explore by experimental methods due to their complex atomic arrangements. Two advanced characterization techniques, a revived and an emerging one, offer direct experimental access even to such complex atomic structures: Diffuse Scattering and Atomic Resolution Holography. Finally, in this overview, we introduce their specific application to aperiodic crystals and discuss their merits and difficulties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Dependence of simulated radiation damage on crystal structure and atomic misfit in metals

This study investigates the evolution of radiation damage in three metals in the low temperature and high radiant flux regime using molecular statics and a Frenkel pair accumulation method to simulate up to 2.0 displacements per atom. The metals considered include Fe, equiatomic CrCoNi, and a fictitious metal with similar bulk properties to the CrCoNi composed of a single atom type referred to as an A-atom. CrCoNi is found to sustain higher concentrations of dislocations than either the Fe or A-atom systems and more stacking faults than the A-atom system. The results suggest that the difference between the concentrations of vacancies and interstitials is substantially smaller for CrCoNi than the A-atom system, perhaps reflecting that the sink capture radius is smaller in CrCoNi due to the roughened potential energy landscape. A model that partitions the major contributions from defects to the stored energy is described, and serves to highlight a general need for higher fidelity approaches to point defect identification.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Real-Time Atomic-Scale Structural Analysis Resolves the Amorphous to Crystalline CaCO 3 Mechanism Controversy

Amorphous calcium carbonate (ACC) occurs as a precursor to geological and biogenic calcium carbonate (CaCO 3 ), yet its transformation pathways and reaction mechanisms remain inconsistent and controversial. In this study, we investigated the transformation of ACC to calcite under both solution and dry conditions, in the presence and absence of impurity ions, utilizing operando time-resolved synchrotron X-ray diffraction (TRXRD) and reactive transport modeling. Results demonstrate that TRXRD techniques allow us to differentiate dissolution-reprecipitation versus solid-state transformation mechanisms for amorphous to crystalline phase transitions. Specifically, we observe that in environments with abundant water, ACC transforms to calcite through a dissolution-reprecipitation mechanism. This features an activation energy of 63 ± 2 kJ/mol and unit cell volume contraction during calcite crystal growth. Conversely, under water-limited conditions, ACC to calcite transformation proceeds via a solid-state transformation mechanism, with an activation energy of 210 ± 2 kJ/mol, three times greater than the dissolution-reprecipitation route, and a unit cell expansion during crystalline calcite growth. Further, to illustrate the magnitude of these effects, the rates of calcite growth were similar during dissolution-reprecipitation at 3 °C [0.00207(35) s –1 ] and solid-state transformation at 280 °C [0.00134(11) s –1 ]. Moreover, the incorporation of an impurity, strontium, significantly retards the rate of calcite growth while expanding its unit cell but whose incorporation is history dependent. Reactive transport modeling of the dissolution–precipitation kinetics suggests that ACC must be dissolving as compact aggregates. These various transformation mechanisms drive diverse geological and biological carbonate formations, impacting their use as paleoenvironmental markers and functional materials synthesis.

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

Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel–Ligand Docking

The identification of promising lead compounds showing pharmacological activities toward a biological target is essential in early stage drug discovery. With the recent increase in available small-molecule databases, virtual high-throughput screening using physics-based molecular docking has emerged as an essential tool in assisting fast and cost-efficient lead discovery and optimization. However, the best scored docking poses are often suboptimal, resulting in incorrect screening and chemical property calculation. We address the pose classification problem by leveraging data-driven machine learning approaches to identify correct docking poses from AutoDock Vina and Glide screens. To enable effective classification of docking poses, we present two convolutional neural network approaches: a three-dimensional convolutional neural network (3D-CNN) and an attention-based point cloud network (PCN) trained on the PDBbind refined set. We demonstrate the effectiveness of our proposed classifiers on multiple evaluation data sets including the standard PDBbind CASF-2016 benchmark data set and various compound libraries with structurally different protein targets including an ion channel data set extracted from Protein Data Bank (PDB) and an in-house KCa3.1 inhibitor data set. Our experiments show that excluding false positive docking poses using the proposed classifiers improves virtual high-throughput screening to identify novel molecules against each target protein compared to the initial screen based on the docking scores.

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

Prediction of Structures and Atomization Energies of Coinage Metals, (M)n, n < 20: Extrapolation of Normalized Clustering Energies to Predict the Cohesive Energy

The geometries of the group 11 coinage metals (n = 2-20) were optimized to determine the lowest energy isomers for each cluster size, singlets for even numbers and doublets for odd numbers. For copper and silver, 2-D (planar) geometries were favored up to n = 6. For gold, 2D (planar) geometries were favored up to n = 13. Normalized clustering energies were plotted as a function of cluster size (n-1/3, for n = 4-20) with various DFT functionals and the CCSD(T)-F12b method and were extrapolated to predict the bulk cohesive energy. In the case of copper and silver, there is excellent agreement between the cohesive energies predicted at the CCSD(T)-F12b level of theory and the experimental values. For gold, the CCSD(T)-F12b values needed to be corrected for spin-orbit relativistic effects to obtain good agreement with experiment. Electronic properties including the HOMO-LUMO gaps for the even clusters and the spin densities for the odd clusters were calculated. The lowest gap is predicted to occur for n = 16 where the HOMO and LUMO are very similar in shape.

Persuad, Rudradatt R.↗
DOE OSTI2020

Electronic Structure of Atomically Dispersed Supported Iridium Catalyst Controls Iridium Aggregation

Supported iridium complexes, Ir(C 2 H 4 ) 2 /support, were characterized by X-ray absorption spectroscopy during a temperature ramp to 120 °C in flowing H 2 . Iridium in complexes bonded to weak and moderate electron-donor supports, SiO 2 and γ-Al 2 O 3 , underwent aggregation, forming nanoparticles and clusters, respectively. When the support was a strong electron-donor (MgO), iridium remained site-isolated. Density functional theory calculations confirm the dependence of iridium–support bond strength on the support’s electron-donor character. Coating the SiO 2 -supported complexes with 1-n-ethyl-3-methyl-imidazolium acetate enhanced electron density on the iridium, hindering its aggregation. Finally, these results demonstrate opportunities for stabilizing atomically dispersed supported noble metals under reducing conditions by choice of support/ionic liquid sheath combinations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗