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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 OSTI2023

Multilevel atomic structural model for interstratified opal materials

The structure of opal has long fascinated scientists. It occurs in a number of structural states, ranging from amorphous to exhibiting features of stacking disorder. Opal-CT, where C and T signify cristobalite- and tridymite-like interstratification, represents an important link in the length scales between amorphous and crystalline states. However, details about local atomic (dis)order and arrangements extending to long-range stacking faults in opal polymorphs remain incompletely understood. Here, a multilevel modeling approach is reported that considers stacking states in correlation with the abundance of C and T segments as a high-level structural parameter (i.e. not each atom). Optimization accounting for inter-tetrahedral bond lengths and angles and the regularity of the silicate tetrahedra is included as lower levels of structural parameters. Together, a set of parameters with both coarse-grained and atomistic features for different levels of structural details is refined. Structural disorder at the ~10–100 Å distance scale is evaluated using experimental pair distribution function and diffraction datasets, comparing peak intensities, widths and asymmetry. Here this work presents a complete multilevel structural description of natural opal-CT and explains many of the unusual features observed in X-ray powder diffraction patterns. This modeling approach can be adopted generally for analyzing layered materials and their assembly into 3D structures.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Electron density distribution and disordered crystal structure of 15R-SiAlON, SiAl{sub 4}O{sub 2}N{sub 4}

The crystal structure of SiAl{sub 4}O{sub 2}N{sub 4} was characterized by laboratory X-ray powder diffraction (CuKα{sub 1}). The title compound is trigonal with space group R3-bar m. The hexagonal unit-cell dimensions (Z=3) are a=0.301332(3) nm, c=4.18616(4) nm and V=0.3291825(5) nm{sup 3}. The initial structural model was successfully derived by the charge-flipping method and further refined by the Rietveld method. The final structural model showed the positional disordering of one of the three (Si,Al) sites. The maximum-entropy method-based pattern fitting (MPF) method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. The reliability indices calculated from the MPF were R{sub wp}=5.05%, S (=R{sub wp}/R{sub e})=1.21, R{sub p}=3.77%, R{sub B}=1.29% and R{sub F}=1.01%. The disordered crystal structure was successfully described by overlapping three types of domains with ordered atom arrangements. The distribution of atomic positions in one of the three types of domains can be achieved in the space group R3-bar m. The atom arrangements in the other two types of domains are noncentrosymmetrical with the space group R3m. These two structural configurations are related by the pseudo-symmetry inversion. -- Graphical abstract: A bird's eye view of electron densities up to 75.3% (0.133 nm{sup −3}) of the maximum on the plane parallel to (110) with the corresponding atomic arrangements of SiAl{sub 4}O{sub 2}N{sub 4}. Highlights: • Crystal structure of SiAl{sub 4}O{sub 2}N{sub 4} is determined by laboratory X-ray powder diffraction. • The atom arrangements are represented by the split-atom model. • The maximum-entropy method-based pattern fitting method is used to confirm the validity of the model. • The disordered structure is described by overlapping three types of domains with ordered atom arrangements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Electron density distribution and disordered crystal structure of 8H-SiAlON, Si{sub 3−x}Al{sub 1+x}O{sub x}N{sub 5−x} (x∼2.2)

The 8H-SiAlON crystal with general formula Si{sub 3−x}Al{sub 1+x}O{sub x}N{sub 5−x} was characterized using laboratory X-ray powder diffraction (CuKα{sub 1}), transmission electron microscopy and energy dispersive X-ray spectroscopy. The [Si: Al] molar ratios were determined to be [0.21(1): 0.79(1)], corresponding to x=2.2(1). The Si{sub 0.8(1)}Al{sub 3.2(1)}O{sub 2.2(1)}N{sub 2.8(1)} compound is hexagonal with space group P6{sub 3}/mmc (Z=2). The unit-cell dimensions are a=0.298877(8) nm, c=2.30872(5) nm and V=0.178602(8) nm{sup 3}. The initial structural model was successfully derived by the charge-flipping method and further refined by the Rietveld method. The final structural model showed the positional disordering of two of the three (Si,Al) sites. The maximum-entropy method-based pattern fitting (MPF) method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. The reliability indices calculated from the MPF were R{sub wp}=4.74%, S (=R{sub wp}/R{sub e})=1.30, R{sub p}=3.40%, R{sub B}=1.04% and R{sub F}=0.74%. The disordered crystal structure was successfully described by overlapping four types of domains with ordered atom arrangements. The distribution of atomic positions in each of the domains can be achieved in the space group P6{sub 3}mc. Two of the four types of domains are related by a pseudo-symmetry inversion, and the two remaining domains also have each other the inversion pseudo-symmetry. - Graphical abstract: Bird's eye view of electron densities up to 49.3% (0.071 nm{sup −3}) of the maximum on the plane parallel to (110) with the corresponding atomic arrangements of Si{sub 0.8}Al{sub 3.2}O{sub 2.2}N{sub 2.8}. - Highlights: • Crystal structure of Si{sub 0.8}Al{sub 3.2}O{sub 2.2}N{sub 2.8} is determined by laboratory X-ray powder diffraction. • The atom arrangements are represented by the split-atom model. • The maximum-entropy method-based pattern fitting method is used to confirm the validity of the model. • The disordered structure is described by overlapping four types of domains with ordered atom arrangements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Tartarus: A relativistic Green's function quantum average atom code

A relativistic Green’s Function quantum average atom model is implemented in the Tartarus code for the calculation of equation of state data in dense plasmas. We first present the relativistic extension of the quantum Green’s Function average atom model described by Starrett [1]. The Green’s Function approach addresses the numerical challenges arising from resonances in the continuum density of states without the need for resonance tracking algorithms or adaptive meshes, though there are still numerical challenges inherent to this algorithm. We discuss how these challenges are addressed in the Tartarus algorithm. The outputs of the calculation are shown in comparison to PIMC/DFT-MD simulations of the Principal Shock Hugoniot in Silicon. Finally, we also present the calculation of the Hugoniot for Silver coming from both the relativistic and nonrelativistic modes of the Tartarus code.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Molecular Models of Atomically Dispersed Uranium at MoS 2 Surfaces Reveal Cooperative Mechanism of Water Reduction

Single atoms of uranium supported on molybdenum sulfide surfaces (U@MoS 2 ) have been recently demonstrated to facilitate the hydrogen evolution reaction (HER) through electrocatalysis. Theoretical calculations have predicted uranium hydroxide moieties bound to edge-sulfur atoms of MoS 2 as a proposed transition state involved in the HER process. However, the isolation of relevant intermediates involved in this process remains a challenge, rendering mechanistic hypotheses unverified. The present work describes the isolation and characterization of a uranium-hydroxide intermediate on molybdenum sulfide surfaces using [(Cp* 3 Mo 3 S 4 )UCp*], a molecular model of a reduced uranium center supported at MoS 2 . Mechanistic investigations highlight the metalloligand cooperativity with uranium involved in the water activation pathway. The corresponding uranium-oxo analogue, [(Cp* 3 Mo 3 S 4 )Cp*U(═O)], was also accessed from the hydroxide cluster via hydrogen atom transfer and from [(Cp* 3 Mo 3 S 4 )UCp*] through an alternative direct oxygen atom transfer. These results provide an atomistic perspective on the reactivity of low-valent uranium at molybdenum sulfide surfaces toward water, modeling key intermediates associated with the HER of U@MoS 2 catalysts.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Improving dynamic collision frequencies: Impacts on dynamic structure factors and stopping powers in warm dense matter

Simulations and diagnostics of high-energy-density plasmas and warm dense matter rely on models of material response properties, both static and dynamic (frequency-dependent). Here, in this work, we systematically investigate variations in dynamic electron–ion collision frequencies ν(ω) in warm dense matter using data from a self-consistent-field average-atom model. We show that including the full quantum density of states, strong collisions, and inelastic collisions lead to significant changes in ν(ω). These changes result in red shifts and broadening of the plasmon peak in the dynamic structure factor, an effect observable in x-ray Thomson scattering spectra, and modify stopping powers around the Bragg peak. These changes improve the agreement of computationally efficient average-atom models with first-principles time-dependent density functional theory in warm dense aluminum, carbon, and deuterium.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Atomic structure and bonding of the interfacial bilayer between Au nanoparticles and epitaxially regrown MgAl{sub 2}O{sub 4} substrates

A unique metal/oxide interfacial bilayer formed between Au nanoparticles and MgAl{sub 2}O{sub 4} substrates following thermal treatment is reported. Associated with the formation of the bilayer was the onset of an abnormal epitaxial growth of the substrate under the nanoparticle. According to the redistribution of atoms and the changes of their electronic structure probed across the interface by a transmission electron microscopy, we suggest two possible atomic models of the interfacial bilayer.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
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↗