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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Construction of a quartz spherical analyzer: application to high-resolution analysis of the Ni K α emission spectrum

The construction and characterization of a focusing X-ray spherical analyzer based on α-quartz 4$\bar{4}$04 are presented. The performance of the analyzer was demonstrated by applying it to a high-resolution X-ray spectroscopy study of the K α 1,2 emission spectrum of Ni. An analytical representation based on physical grounds was assumed to model the shape of the X-ray emission lines. Satellite structures assigned to 3 d spectator hole transitions were resolved and determined as well as their relative contribution to the emission spectrum. The present results on 1 s -1 3 d -1 shake probabilities support a recently proposed calculation framework based on a multi-configuration atomic model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2003

Atomic-scale Modeling of the Structure and Dynamics of Dislocations in Complex Alloys at High Temperatures

We report on the progress made during the first year of the project. Most of the progress at this point has been on the theoretical and computational side. Here are the highlights: (1) A new code, tailored for high-end desktop computing, now combines modern Accelerated Dynamics (AD) with the well-tested Embedded Atom Method (EAM); (2) The new Accelerated Dynamics allows the study of relatively slow, thermally-activated processes, such as diffusion, which are much too slow for traditional Molecular Dynamics; (3) We have benchmarked the new AD code on a rather simple and well-known process: vacancy diffusion in copper; and (4) We have begun application of the AD code to the diffusion of vacancies in ordered intermetallics.

Daw, Murray S.↗
DOE OSTI2019

Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu

X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. Here, we present a bottom-up endogenous structural proteomics approach whereby near-atomic-resolution cryo electron microscopy (cryoEM) maps are reconstructed ab initio from unidentified protein complexes enriched directly from the endogenous cellular milieu, followed by identification and atomic modeling of the proteins. The proteins in each complex are identified using cryoID, a program we developed to identify proteins in ab initio cryoEM maps. As a proof of principle, we applied this approach to the malaria-causing parasite Plasmodium falciparum, an organism that has resisted conventional structural-biology approaches, to obtain atomic models of multiple protein complexes implicated in intraerythrocytic survival of the parasite. Our approach is broadly applicable for determining structures of undiscovered protein complexes enriched directly from endogenous sources.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Atomic charges for modeling metal–organic frameworks: Why and how

Atomic partial charges are parameters of key importance in the simulation of Metal–Organic Frameworks (MOFs), since Coulombic interactions decrease with the distance more slowly than van der Waals interactions. But despite its relevance, there is no method to unambiguously assign charges to each atom, since atomic charges are not quantum observables. There are several methods that allow the calculation of atomic charges, most of them starting from the electronic wavefunction or the electronic density or the system, as obtained with quantum mechanics calculations. In this work, we describe the most common methods employed to calculate atomic charges in MOFs. In order to show the influence that even small variations of structure have on atomic charges, we present the results that we obtained for DMOF-1. We also discuss the effect that small variations of atomic charges have on the predicted structural properties of IRMOF-1. - Graphical abstract: We review the different method with which to calculate atomic partial charges that can be used in force field-based calculations. We also present two examples that illustrate the influence of the geometry on the calculated charges and the influence of the charges on structural properties. - Highlights: • The choice of atomic charges is crucial in modeling adsorption and diffusion in MOFs. • Methods for calculating atomic charges in MOFs are reviewed. • We discuss the influence of the framework geometry on the calculated charges. • We discuss the influence of the framework charges on structural the properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Advances in the Application of Lasers in Materials Science, Chapter 5, Insights into Laser-Materials Interaction Through Modeling on Atomic and Macroscopic Scales

Computer simulations and theoretical analysis of laser-materials interactions are playing an increasingly important role in the advancement of modern laser technologies and broadening the range of laser applications. In this chapter, we first provide an overview of the current understanding of the laser coupling and transient variation of optical properties in metals, semiconductors and dielectrics, with the focus on the practical implications on the energy deposition and distribution in the irradiated targets. The continuum-level modeling of the dynamic evolution of laser-induced stresses, nonequilibrium phase transformations, and material redistribution within the laser spot are then discussed, and the need for the physical insights into the mechanisms and kinetics of highly nonequilibrium processes triggered by the laser excitation is highlighted. The physical insights can be provided by atomistic modeling, and several examples are discussed where large-scale molecular dynamics simulations are used for investigation of the mechanisms of the generation of crystal defects (vacancies, interstitials, dislocations, and twin boundaries) and the material redistribution responsible for the formation of laser-induced periodic surface structures in the single-pulse ablative regime. The need for the integrated computational approach fully accounting for the strong coupling between processes occurring at different time- and length-scales is highlighted.

Shugaev, Maxim V.↗
DOE OSTI2016

FREQUENCY REDISTRIBUTION OF POLARIZED LIGHT IN THE Λ-TYPE MULTI-TERM POLARIZED ATOM

We study the effects of Rayleigh and Raman scattering on the formation of polarized spectral lines in a Λ-type multi-term atom. We fully take into account the partial redistribution of frequency and the presence of atomic polarization in the lower states of the atomic model. Problems that can be modeled with this formalism include, for example, the formation of the Ca ii H–K and IR triplet, the analogous system of Ba ii, and the Ly β –H α system of hydrogenic ions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Crystallographic and Molecular Dynamics Simulation Analysis of Escherichia Coli Dihydroneopterin Aldolase

To understand the structural basis for the biochemical differences and further investigate the catalytic mechanism of DHNA, we have determined the structure of EcDHNA complexed with NP at 1.07-Å resolution [PDB:2O90], built an atomic model of EcDHNA complexed with the substrate DHNP, and performed molecular dynamics (MD) simulation analysis of the substrate complex. EcDHNA has the same fold as SaDHNA and also forms an octamer that consists of two tetramers, but the packing of one tetramer with the other is significantly different between the two enzymes. Furthermore, the structures reveal significant differences in the vicinity of the active site, particularly in the loop that connects strands β3 and β4, mainly due to the substitution of nearby residues. The building of an atomic model of the complex of EcDHNA and the substrate DHNP and the MD simulation of the complex show that some of the hydrogen bonds between the substrate and the enzyme are persistent, whereas others are transient. The substrate binding model and MD simulation provide the molecular basis for the biochemical behaviors of the enzyme, including noncooperative substrate binding, indiscrimination of a pair of epimers as the substrates, proton wire switching during catalysis, and formation of epimerization product.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Atomic-scale modeling of the dissolution of oxidized platinum nanoparticles in an explicit water environment

Pt nanoparticles (NPs) are currently being investigated for use in fuel cells; however, Pt NP oxidation as a function of size, morphology, and temperature is not well understood or currently quantified. In this study, the stability and dissolution of oxidized platinum NPs is examined via classical molecular dynamics in an explicit water environment. The NPs considered range in size from 1.35 to 2.92 nm in diameter and included five different monolayer (ML) coverages of O*. The simulations were performed at 300, 450, and 600 K with the many-body, reactive third-generation charge-optimized many-body or COMB3 potentials and examine the kinetics of NP dissolution in water. The Pt–O layer, which reduces the kinetic activity for Pt atom dissolution, is projected to make dissolution more favorable for O* MLs smaller than 0.5. The simulations further indicate that the Pt NPs' kinetic rates of dissolution are slowed by an increase in the number of adsorbed species caused by the dissociation of water molecules at the reconstructed facets of the Pt NPs. Furthermore, these findings quantify the effect of oxygen and temperature on the stability and dissolution of oxidized platinum NP in an explicit water environment similar to the conditions in fuel cells and electrocatalysis.

08 HYDROGEN↗
DOE OSTI2021

A Model for Atomic Precision p-Type Doping with Diborane on Si(100)-2×1

Diborane (B 2 H 6 ) is a promising molecular precursor for atomic precision p-type doping of silicon that has recently been experimentally demonstrated. In this study, we use density functional theory (DFT) calculations to determine the reaction pathway for diborane dissociating into a species that will incorporate as electrically active substitutional boron after adsorbing onto the Si(100)-2×1 surface. Our calculations indicate that diborane must overcome an energy barrier to adsorb, explaining the experimentally observed low sticking coefficient (<1 × 10 –4 at room temperature) and suggesting that heating can be used to increase the adsorption rate. Upon sticking, diborane has an ≈50% chance of splitting into two BH 3 fragments versus merely losing hydrogen to form a dimer such as B 2 H 4 . As boron dimers are likely electrically inactive, whether this latter reaction occurs is shown to be predictive of the incorporation rate. The dissociation process proceeds with significant energy barriers, necessitating the use of high temperatures for incorporation. Using the barriers calculated from DFT, we parameterize a Kinetic Monte Carlo model that predicts the incorporation statistics of boron as a function of the initial depassivation geometry, dose, and anneal temperature. Our results suggest that the dimer nature of diborane inherently limits its doping density as an acceptor precursor and furthermore that heating the boron dimers to split before exposure to silicon can lead to poor selectivity on hydrogen and halogen resists. This suggests that, while diborane works as an atomic precision acceptor precursor, other non-dimerized acceptor precursors may lead to higher incorporation rates at lower temperatures.

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

Analytical Model for Atomic Relaxation in Twisted Moiré Materials

By virtue of being atomically thin, the electronic properties of heterostructures built from two-dimensional materials are strongly influenced by atomic relaxation. The atomic layers behave as flexible membranes rather than rigid crystals. Here we develop an analytical theory of lattice relaxation in twisted moiré materials. We obtain analytical results for the lattice displacements and corresponding pseudo gauge fields, as a function of twist angle. We benchmark our results for twisted bilayer graphene and twisted WSe 2 bilayers using large-scale molecular dynamics simulations. Our single-parameter theory is valid in graphene bilayers for twist angles 𝜃 ≳ 0.7°, and in twisted WSe 2 for 𝜃 ≳ 1.6°. Furthermore, we also investigate how relaxation alters the electronic structure in twisted bilayer graphene, providing a simple extension to the continuum model to account for lattice relaxation.

36 MATERIALS SCIENCE↗
DOE OSTI2017

NLTE ANALYSIS OF HIGH-RESOLUTION H -BAND SPECTRA. II. NEUTRAL MAGNESIUM

Aiming at testing the validity of our magnesium atomic model and investigating the effects of non-local thermodynamical equilibrium (NLTE) on the formation of the H -band neutral magnesium lines, we derive the differential Mg abundances from selected transitions for 13 stars either adopting or relaxing the assumption of local thermodynamical equilibrium (LTE). Our analysis is based on high-resolution and high signal-to-noise ratio H -band spectra from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) and optical spectra from several instruments. The absolute differences between the Mg abundances derived from the two wavelength bands are always less than 0.1 dex in the NLTE analysis, while they are slightly larger for the LTE case. This suggests that our Mg atomic model is appropriate for investigating the NLTE formation of the H -band Mg lines. The NLTE corrections for the Mg i H -band lines are sensitive to the surface gravity, becoming larger for smaller log g values, and strong lines are more susceptible to departures from LTE. For cool giants, NLTE corrections tend to be negative, and for the strong line at 15765 Å they reach −0.14 dex in our sample, and up to −0.22 dex for other APOGEE stars. Our results suggest that it is important to include NLTE corrections in determining Mg abundances from the H -band Mg i transitions, especially when strong lines are used.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

X-ray absorption spectroscopy measurements of radiatively ionized argon gas

X-ray absorption spectroscopy is a diagnostic tool that can characterize the temperature and ionization state of a plasma. This technique requires experiments to characterize the platform, careful data calibration, and comparison with atomic models to understand the plasma parameters. We performed ionizing radiation wave experiments at the OMEGA Laser Facility that used an ∼ 80 eV X-ray source to heat an Argon (Ar) gas cell at fill pressures of 3 atm. To diagnose the Ar plasma, we used a capsule backlighter offset 10 mm from the gas cell, to produce X-rays that were absorbed by the ionized Ar gas. The absorption analysis was calibrated using the significant line structure in the backlighter spectrum, which served as independent energy fiducials enabling definitive measurements of a 50-eV shift in the energy of the Ar K-edge due to ionization. We compare the measured absorption spectra to two independent atomic models, PrismSPECT and SCRAM, and show that the observed K-edge shift in the heated gas is consistent with ionization up to Ar 4+ and temperatures of 10 eV.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

On the possibility to detect multipolar order in URu 2 Si 2 by the electric quadrupolar transition of resonant elastic x-ray scattering

Resonant elastic x-ray scattering is a powerful technique for measuring multipolar order parameters. In this paper, we theoretically and experimentally study the possibility of using this technique to detect the proposed multipolar order parameters in URu 2 Si 2 at the U- L 3 edge with the electric quadrupolar transition. Based on an atomic model, we calculate the azimuthal dependence of the quadrupolar transition at the U- L 3 edge. Our results illustrate the potential of this technique for distinguishing different multipolar order parameters. We then perform experiments on ultraclean single crystals of URu 2 Si 2 at the U- L 3 edge to search for the predicted signal, but do not detect any indications of multipolar moments within the experimental uncertainty. We also theoretically estimate the orders of magnitude of the cross section and the expected count rate of the quadrupolar transition and compare them to the dipolar transitions at the U- M 4 and U- L 3 edges, clarifying the difficulty in detecting higher order multipolar order parameters in URu 2 Si 2 in the current experimental setup.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies

Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum – Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited for structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data. - Highlights: • We solved a 4.1 Å resolution crystal structure of Mdm12, the soluble subunit of ERMES. • The two Mdm12 apo monomers differ in the conformation of their N-terminal β-strands. • We reconstituted and crystallized two distinct Mdm12/Mmm1 complexes. • SAXS analysis of the complexes agrees with our previous electron microscopy data. • The structure suggests a head-to-tail association in the Mdm12/Mmm1 complex.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Extending continuum models for atom probe simulation

Highlights: • Demonstration of 3D curvature level set methods for APT simulations • Demonstration of non-rotationally symmetric tip shape simulations • Optimised speed for simulations, calculations achievable on minute timescales This work describes extensions to existing level-set algorithms developed for application within the field of atom probe tomography (APT). We present a new simulation tool for the simulation of 3D tomographic volumes, using advanced level set methods. By combining narrow-band, B-Tree and particle-tracing approaches from level-set methods, we demonstrate a practical tool for simulating shape changes to APT samples under applied electrostatic fields, in three dimensions. This work builds upon our previous studies by allowing for non-axially symmetric solutions, with minimal loss in computational speed, whilst retaining numerical accuracy.

36 MATERIALS SCIENCE↗