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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Facile hermetic TEM grid preparation for molecular imaging of hydrated biological samples at room temperature

Abstract Although structures of vitrified supramolecular complexes have been determined at near-atomic resolution, elucidating in situ molecular structure in living cells remains a challenge. Here, we report a straightforward liquid cell technique, originally developed for real-time visualization of dynamics at a liquid-gas interface using transmission electron microscopy, to image wet biological samples. Due to the scattering effects from the liquid phase, the micrographs display an amplitude contrast comparable to that observed in negatively stained samples. We succeed in resolving subunits within the protein complex GroEL imaged in a buffer solution at room temperature. Additionally, we capture various stages of virus cell entry, a process for which only sparse structural data exists due to their transient nature. To scrutinize the morphological details further, we used individual particle electron tomography for 3D reconstruction of each virus. These findings showcase this approach potential as an efficient, cost-effective complement to other microscopy technique in addressing biological questions at the molecular level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Three dimensional cluster analysis for atom probe tomography using Ripley’s K-function and machine learning

The size and structure of spatial molecular and atomic clustering can significantly impact material properties and is therefore important to accurately quantify. Ripley’s K-function (K(r)), a measure of spatial correlation, can be used to perform such quantification when the material system of interest can be represented as a marked point pattern. This work demonstrates how machine learning models based on K (r)-derived metrics can accurately estimate cluster size and intra-cluster density in simulated three dimensional (3D) point patterns containing spherical clusters of varying size; over 90% of model estimates for cluster size and intra-cluster density fall within 11% and 18% error of the true values, respectively. These K (r)-based size and density estimates are then applied to an experimental APT reconstruction to characterize MgZn clusters in a 7000 series aluminum alloy. Here we find that the estimates are more accurate, consistent, and robust to user interaction than estimates from the popular maximum separation algorithm. Using K (r) and machine learning to measure clustering is an accurate and repeatable way to quantify this important material attribute.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Fast and Universal Kohn-Sham Density Functional Theory Algorithm for Warm Dense Matter to Hot Dense Plasma

Understanding many processes, e.g., fusion experiments, planetary interiors, and dwarf stars, depends strongly on microscopic physics modeling of warm dense matter and hot dense plasma. This complex state of matter consists of a transient mixture of degenerate and nearly free electrons, molecules, and ions. This regime challenges both experiment and analytical modeling, necessitating predictive ab initio atomistic computation, typically based on quantum mechanical Kohn-Sham density functional theory (KS-DFT). However, cubic computational scaling with temperature and system size prohibits the use of DFT through much of the warm dense matter regime. A recently developed stochastic approach to KS-DFT can be used at high temperatures, with the exact same accuracy as the deterministic approach, but the stochastic error can converge slowly and it remains expensive for intermediate temperatures (< 50 eV). Here we have developed a universal mixed stochastic-deterministic algorithm for DFT at any temperature. This approach leverages the physics of KS-DFT to seamlessly integrate the best aspects of these different approaches. We demonstrate that this method significantly accelerated self-consistent field calculations for temperatures from 3 to 50 eV, while producing stable molecular dynamics and accurate diffusion coefficients.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Spectral scheme for atomic structure calculations in density functional theory

In this study, we present a spectral scheme for atomic structure calculations in pseudopotential Kohn-Sham density functional theory. In particular, after applying an exponential transformation of the radial coordinates, we employ global polynomial interpolation on a Chebyshev grid, with derivative operators approximated using the Chebyshev differentiation matrix, and integrations using Clenshaw-Curtis quadrature. We demonstrate the accuracy and efficiency of the scheme through spin-polarized and unpolarized calculations for representative atoms, while considering local, semilocal, and hybrid exchange-correlation functionals. In particular, we find that $\mathcal{O}$(200) grid points are sufficient to achieve an accuracy of 1 microhartree in the eigenvalues for optimized norm conserving Vanderbilt pseudopotentials spanning the periodic table from atomic number Ζ = 1 to 83.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

On the Development of Order and Interfaces during the Growth of Ultrathin La 2 CuO 4 Films by Molecular Beam Epitaxy

While the atomic structure of interfaces in complex oxide heterostructures created by epitaxial growth has been investigated extensively, few studies have been conducted on how interfaces form and restructure at the initial stage of film growth. The dynamic aspects of the growth behavior can strongly influence the final interfacial atomic structure, which may lead to the emergence of interface-specific properties, such as the rise of interfacial superconductivity between certain Ruddlesden-Popper oxide materials. In this report, the structural development of La2CuO 4 thin films grown by molecular beam epitaxy on a LaSrAlO 4 substrate is investigated by X-ray diffraction measurements with rapid scans over a volume of reciprocal space. This method provides far more detailed information on interface formation than traditional fixed-point measurements. The results show that the atomic structure of the interface becomes fully established after just a single unit cell of growth. Interestingly, restructuring continues to occur within the topmost half to one unit cell of the film during the deposition process. However, diffraction intensity oscillations from both reflection high-energy electron and X-ray measurements stabilize only after the growth of two unit cells, indicating that the growth front morphology continues to evolve until the start of the third unit cell. This multimodal investigation provides insights into the atomic processes taking place during layered oxide interface formation, including the dynamical rearrangement of LaO and CuO 2 layers. Such information is not only relevant to the engineering and optimization of functional layer structures but can also be critical for ultrathin films.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Synthetic Pathways to gamma-Graphyne and Related Allotropes of Carbon

Graphynes, two-dimensional carbon lattices combining sp 1 and sp 2 hybridized atoms, were predicted theoretically more than three decades ago, but few structures have been realized to date. These carbons are believed to possess remarkable mechanical and electronic properties, including high charge carrier mobilities comparable to those in graphene (10 4 to 10 5 cm 2 V -1 s -1 ). Unlike graphene, certain graphynes are predicted to be intrinsic semiconductors. Among these intriguing structures, γ-graphyne stands out as the structurally simplest and most symmetric sp 1 /sp 2 lattice. γ-Graphyne was first theorized in 1987. In contrast with graphene, γ-graphyne will be a semiconductor with a small band gap suitable for fabrication of electronic devices. This solves one of the fundamental problems of carbon-based electronics, the necessity for inducing a band gap in graphene. γ-Graphyne has the potential to form the basis for the next generation of carbon-based electronics operating at speeds unattainable by traditional silicon chips. Unlike silicon, γ-graphyne is a direct band gap semiconductor, and it will feature exceptional strength comparable to that of other 2D carbon allotropes. Such combination of properties may enable a new generation of highly efficient, ultra-light and flexible solar cells. Despite being a potentially “magical” material, γ-graphyne remained synthetically elusive for over three decades. The primary goals of this project were: (1) Synthesis of bulk γ-graphyne phases through solution-phase 2D polymerizations; (2) Experimental exploration of the physical and chemical properties of γ-graphyne; and (3) Mechanistic and theoretical studies of the novel chemical transformations developed in Goal 1. Common pyrolytic and vapor-deposition methodologies used for the synthesis of graphitic allotropes are unsuitable for graphyne and other sp 1 -contaning structures, as acetylenes readily convert to graphene and amorphous carbon at high temperatures. In contrast, this proposal is based on solution-based 2D polymerization. The major advantages of this approach over the traditional high temperature techniques are the potential to adjust the structure of the material with atomic precision, and the possibility of using structurally complex and relatively fragile repeat units. The outcomes of this research can revolutionize carbon nanotechnology, expanding the field’s structural toolbox beyond primarily graphitic and benzenoid structures. Understanding the chemistry of sp 1 carbon allotropes can lead to entirely new classes of structures with unique properties, including graphyne ribbons, nanotubes, quantum dots, and heterostructures with other 2D materials. Furthermore, the development of reliable and robust synthetic pathways towards periodic covalent molecular sheets with atomically precise structures shall have a profound impact on chemistry and materials science.

2D polymerization↗
DOE OSTI2022

Atomic layer epitaxy of kagome magnet Fe 3 Sn 2 and Sn-modulated heterostructures

Magnetic materials with kagome crystal structure exhibit rich physics, such as frustrated magnetism, skyrmion formation, topological flat bands, and Dirac/Weyl points. Until recently, most studies on kagome magnets have been performed on bulk crystals or polycrystalline films. Here, we report the atomic layer molecular beam epitaxy synthesis of high-quality thin films of topological kagome magnet Fe 3 Sn 2 . The structural and magnetic characterization of Fe 3 Sn 2 on epitaxial Pt(111) identifies highly ordered films with c-plane orientation and an in-plane magnetic easy axis. Studies on the local magnetic structure by anomalous Nernst effect imaging reveal in-plane oriented micrometer size domains. Superlattice structures consisting of Fe 3 Sn 2 and Fe 3 Sn are also synthesized by atomic layer molecular beam epitaxy, demonstrating the ability to modulate the sample structure at the atomic level. The realization of high-quality films by atomic layer molecular beam epitaxy opens the door to explore the rich physics of this system and investigate novel spintronic phenomena by interfacing Fe 3 Sn 2 with other materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Vanadium Substitution Dictates H Atom Uptake at Lindqvist-type Polyoxotungstates

Understanding how modification of molecular structures changes the thermochemistry of H atom uptake can provide design criteria for the formation of highly active catalysts for reductive transformations. Herein, we describe the effect of doping an atomically precise polyoxotungstate with vanadium on proton-coupled electron transfer (PCET) reactivity. The Lindqvist-type polyoxotungstate [W 6 O 19 ] 2– displays reversible redox chemistry, which was found to be unchanged in the presence of acid, indicating an inability to couple reduction with protonation. However, the incorporation of a single vanadium center into the structure significantly changes the reactivity, and the potential required for one-electron reduction of [VW 5 O 19 ] 3– was shown to vary with the strength of the acid added. Construction of a potential-pK a diagram allowed assessment of the thermodynamics of H atom uptake, indicating BDFE(O–H) ≈ 64 kcal/mol, while chemical synthesis of the reduced/protonated derivative (TBA) 3 [VW 5 O 19 H] was used to probe the position of protonation.

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

Molecular simulation of the structural and thermodynamic properties of n-alkane/brine interfacial systems with nonionic surfactants

All-atom molecular dynamics (MD) simulations are used to study the structural and thermodynamic properties of water + n-heptane interfacial systems in the presence of salinity (NaCl, NaI, KCl, and KI) and two different nonionic surfactants. Excellent qualitative and quantitative agreement with interfacial tension experimental data is obtained, but this requires applying a charge scaling factor to the ionic species, suggesting the likely role of polarizability effects. Tensoactive behavior is observed for the NaI and KI systems, coinciding with layering of the iodide species near the interface. Further, there are significant interaction differences between the surfactants and the different ionic species, but the structural and thermodynamic behavior of the surfactant molecules is relatively unaffected by the specific salt species. Our analysis suggest that the surfactant-surfactant interactions play a critical role in determining the interfacial behavior, with a much smaller impact associated with the composition of the brine phase.

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

The importance of correlation in the molecular orbital picture

The molecular orbital picture plays a fundamental role in analyzing and interpreting the electronic structure of atoms and molecules. Evaluation of molecular orbitals obtained from the Hartree–Fock method and other one-electron Hamiltonian models is routine for quantum-chemical studies. Although these analyses have proven to be useful for identifying different patterns in electronic structure and reactivity, in many cases, the chosen set of orbitals do not incorporate many of the fundamental electron correlation effects needed to accurately describe the atom or molecule under study. This work addresses the question of whether or not the inclusion of electron correlation is essential for the orbital picture by contrasting the differences between canonical Hartree–Fock orbitals and the correlated, normalized Dyson orbitals.

Hernandez Corzo, Hector↗
DOE OSTI2020

Roles for Countercharge in the Voltage Sensor Domain of Ion Channels

Voltage-gated ion channels share a common structure typified by peripheral, voltage sensor domains. Their S4 segments respond to alteration in membrane potential with translocation coupled to ion permeation through a central pore domain. The mechanisms of gating in these channels have been intensely studied using pioneering methods such as measurement of charge displacement across a membrane, sequencing of genes coding for voltage-gated ion channels, and the development of all-atom molecular dynamics simulations using structural information from prokaryotic and eukaryotic channel proteins. One aspect of this work has been the description of the role of conserved negative countercharges in S1, S2, and S3 transmembrane segments to promote sequential salt-bridge formation with positively charged residues in S4 segments. These interactions facilitate S4 translocation through the lipid bilayer. In this review, we describe functional and computational work investigating the role of these countercharges in S4 translocation, voltage sensor domain hydration, and in diseases resulting from countercharge mutations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks

Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational heterogeneity. Here we present a model refinement protocol that automatically generates series of molecular models from CryoEM datasets, which describe the dynamics of the macromolecular system and have near-perfect geometry scores. This method makes it easier to interpret the movement of the protein complex from heterogeneity analysis and to compare the structural dynamics observed from CryoEM data with results from other experimental and simulation techniques.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Combined Experimental and Computational Study of Molybdenum and Niobium for Nuclear Sensor Application

Due to their novel electromagnetic and thermal properties, molybdenum (Mo) and niobium (Nb) become optimal temperature sensor materials for nuclear energy applications. We leveraged voltage recorded during a heat ramp to tune a computational method to predict the Seebeck electromotive force (EMF) of Mo and Nb. Using a combined Density Functional Theory (DFT) and Boltzmann Transport Equations (BTE) method the voltage was predicted but did not include the effects of temperature on atomic structure. Combining Ab Initio Molecular Dynamics (AIMD) and BTE included temperature effects on structure optimization and yielded voltages in a good agreement with experiment. Lanthanum (La) and Phosphorus (P) additives in Mo and Nb, respectively, could increase the EMF compared to those of the pure metals. The presence of oxygen (O) in Mo increases the EMF while O in Nb slightly reduces the EMF. Furthermore, our studies suggested that heat treatment-induced structural changes that lead to a reduction in voltage occur not only at the mesoscale as previously understood but also at the atomic scale.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

In-plane Wilson loop for measurement of quantized non-Abelian Berry flux

Band topology of anomalous quantum Hall insulators can be precisely addressed by computing the Chern numbers of constituent nondegenerate bands, describing the presence of quantized, Abelian Berry flux through the two-dimensional Brillouin zone. Can Berry flux be captured for the SU (2) Berry connection of two -fold degenerate bands in spinful materials preserving space -inversion ($\mathscr{P}$) and time -reversal ($\mathscr{T}$) symmetries without detailed knowledge of underlying basis? We address this question by investigating the correspondence between a non -Abelian generalization of Stokes' theorem and the manifestly gauge -invariant eigenvalues of Wilson loops computed along in -plane contours which preserve the underlying crystalline symmetry. The importance of this correspondence is elucidated by performing natural number resolved classification of ab initio band structures of three-dimensional, Dirac materials. Further, our work underscores how identification of quantized Berry flux, both Abelian and non -Abelian, offers a unified framework for addressing first -order and higher -order topology of insulators and semimetals.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

A new self-adaptive reconstruction method to identify defects through Wigner–Seitz approach

A new self-adaptive reconstruction method based on local atomic structure at any given molecular dynamics (MD) step has been developed in this article. The method can be used in Wigner–Seitz defect analysis approach to correctly and efficiently explore the information of both point defects and complex defect clusters (e.g. dislocation loops and voids) formed after a displacement cascade where the cascade interacts with grain boundaries and/or dislocations. The algorithm and validation are provided in detail. Results for identification of radiation defects during and after cascades interacting with a dislocation network show that the new method can well recognize all simple and complex defects and defect clusters. Thus, this new method provides a totally new way to explore the density and size of radiation defects at atomic scale after complex MD evolution processes, providing correct information to understand and predict radiation damage in materials through atomic simulations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Atomic Structure and Dynamics of Unusual and Wide-Gap Phase-Change Chalcogenides: A GeTe 2 Case

Brain-inspired computing, reconfigurable optical metamaterials, photonic tensor cores, and many other advanced applications require next-generation phase-change materials (PCMs) with better energy efficiency and a wider thermal and spectral range for reliable operations. Germanium ditelluride (GeTe 2 ), with higher thermal stability and a larger bandgap compared to current benchmark PCMs, appears promising for THz metasurfaces and the controlled crystallization of atomically thin 2D materials. Using high-energy X-Ray diffraction supported by first-principles simulation, the atomic structure in semiconducting pulsed laser deposition films and metallic high-temperature liquids is investigated. The results suggest that the structural and chemical metastability of GeTe 2 , leading to disproportionation into GeTe and Te, is related to high internal pressure during a semiconductor–metal transition, presumably occurring in the supercooled melt. Similar phenomena are expected for canonical GeS 2 and GeSe 2 under high temperatures and pressures.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Laser spectroscopy of indium Rydberg atom bunches by electric field ionization

This work reports on the application of a novel electric field-ionization setup for high-resolution laser spectroscopy measurements on bunched fast atomic beams in a collinear geometry. In combination with multi-step resonant excitation to Rydberg states using pulsed lasers, the field ionization technique demonstrates increased sensitivity for isotope separation and measurement of atomic parameters over previous non-resonant laser ionization methods. The setup was tested at the Collinear Resonance Ionization Spectroscopy experiment at ISOLDE-CERN to perform high-resolution measurements of transitions in the indium atom from the 5s 2 5d 2 D 5/2 and 5s 2 5d 2 D 3/2 states to 5s 2 np 2 P and 5s 2 nf 2 F Rydberg states, up to a principal quantum number of n=72 . The extracted Rydberg level energies were used to re-evaluate the ionization potential of the indium atom to be 46,670.107(4)cm -1 . The nuclear magnetic dipole and nuclear electric quadrupole hyperfine structure constants and level isotope shifts of the 5s 2 5d 2 D 5/2 and 5s 2 5d 2 D 3/2 states were determined for 113,115 In. The results are compared to calculations using relativistic coupled-cluster theory. A good agreement is found with the ionization potential and isotope shifts, while disagreement of hyperfine structure constants indicates an increased importance of electron correlations in these excited atomic states. With the aim of further increasing the detection sensitivity for measurements on exotic isotopes, a systematic study of the field-ionization arrangement implemented in the work was performed at the same time and an improved design was simulated and is presented. The improved design offers increased background suppression independent of the distance from field ionization to ion detection.

74 ATOMIC AND MOLECULAR PHYSICS↗