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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1 x Sex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated de novo cryo-EM structure modeling method. Cryo2Struct utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps, followed by an innovative Hidden Markov Model (HMM) to connect predicted atoms and build protein backbone structures. Cryo2Struct produces substantially more accurate and complete protein structural models than the widely used ab initio method Phenix. Additionally, its performance in building atomic structural models is robust against changes in the resolution of density maps and the size of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Characterization of atomic-level structure in Fe-based amorphous and nanocrystalline alloy by experimental and modeling methods

The atomic structure of Fe{sub 70}Nb{sub 10}B{sub 20} alloy in “as-cast” state and after annealing was investigated using high-energy X-ray diffraction (XRD), Mössbauer spectroscopy (MS) and high resolution transmission electron microscopy (HRTEM). The HRTEM observations allowed to indicate some medium-range order (MRO) regions about 2 nm in size and formation of some kinds of short-range order (SRO) structures represented by atomic clusters with diameter ca. 0.5 nm. The Reverse Monte Carlo (RMC) method basing on the results of XRD measurements was used in modeling the atomic structure of Fe-based alloy. The structural model was described by peak values of partial pair correlation functions and coordination numbers determined by Mössbauer spectroscopy investigations. The three-dimensional configuration box of atoms was obtained from the RMC simulation and the representative Fe-centered clusters were taken from the calculated structure. According to the Gonser et al. approach, the measured spectra of alloy studied were decomposed into 5 subspectra representing average Fe–Fe coordination numbers. Basing on the results of disaccommodation of magnetic permeability, which is sensitive to the short order of the random packing of atoms, it was stated that an occurrence of free volume is not detected after nanocrystallization process. - Highlights: • Atomic cluster model of amorphous structure was proposed for studied glassy alloy. • Short range order (ca. 0.5 nm) regions interpreted as clusters were identified by HREM. • Clusters correspond to coordination numbers (N = 4,6,8,9) calculated by using Gonser approach. • Medium-range order (ca. 2 nm) could be referred to few atomic clusters. • SRO regions are able to grow up as nuclei of crystalline bcc Fe and iron borides. • Crystalline particles have spherical morphology with an average diameter of 20 nm.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS2000

Database of non-canonical base pairs found in known RNA structures

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

NASA Discipline Exobiology↗
NASA NTRS1988

In situ chemical analyses of extraterrestrial bodies

One of the most important tasks on any sample return mission will have to be a quick sample characterization in order to guarantee a variety of collected samples. An alpha particle instrument with alpha, proton and X-ray modes can provide a quick and almost complete chemical analysis of Mars samples. This instrument is based on three interactions of the alpha particles from a radioactive source with matter: elastic scattering of the alpha particles by nuclei (alpha mode), (alpha,p) nuclear reaction with some light elements (proton mode), and excitation of the atomic structure of atoms by alpha particles, leading to emission of characteristic X-rays of the lunar surface at three sites during the Surveyor mission of 1967 to 1968. Since then the instrument has been improved and miniaturized substantially. As shown in the past, the alpha particle instrument can operate under Martian conditions without any degradation in the performance. The alpha and proton modes can provide vital information about the light elements, while the X-ray mode with its ambient temperature X-ray detector will be useful for the heavier elements. The excitation of the atomic structure is provided by the same alpha radioactive source that is used by alpha and proton modes or by an auxiliary X-ray source that is selected to enhance the sensitivity to some important geochemical elements.

Economou, Thanasis E.↗
DOE OSTI2018

Single-layer TiO x reconstructions on SrTiO 3 (111): (√7 × √7)R19.1°, (√13 × √13)R13.9°, and related structures

The atomic structures of two reconstructions, (√7 × √7)R19.1° and (√13 × √13)R13.9°, on the SrTiO 3 (111) surface were determined using a combination of density functional theory and scanning tunneling microscopy data and simulations. The combination of these methods allows for potential surface structures to be generated and verified in the absence of diffraction data, providing another tool for solving surface reconstructions. These reconstructions belong to the same stoichiometric, nSrTiO 3 • mTiO 2 , structural family made up of an interconnected, single layer of edge-sharing TiO 6 and TiO 5 [] octahedra. This family is found to include the previously-solved (2 × 2)a reconstruction as its smallest unit-cell sized member and serves as a tool for better understanding and predicting the structure of other reconstructions of arbitrary surface unit-cell size on SrTiO 3 (111). This reconstruction family and the calculations of surface energies for different hypothesis structures also shed light on the structure of Schottky defects observed on these reconstructed SrTO 3 (111) surfaces.

Andersen, Tassie K. (ORCID:0000000295444995)↗
DOE OSTI2024

Generalized representative structures for atomistic systems

A new method is presented to generate atomic structures that reproduce the essential characteristics of arbitrary material systems, phases, or ensembles. Previous methods allow one to reproduce the essential characteristics (e.g. the chemical disorder) of a large random alloy within a small crystal structure. The ability to generate small representations of random alloys, along with the restriction to crystal systems, results from using the fixed-lattice cluster correlations to describe structural characteristics. A more general description of the structural characteristics of atomic systems is obtained using complete sets of atomic environment descriptors. These are used within for generating representative atomic structures without restriction to fixed lattices. A general data-driven approach is provided here utilizing the atomic cluster expansion (ACE) basis. The N-body ACE descriptors are a complete set of atomic environment descriptors that span both chemical and spatial degrees of freedom and are used within for describing atomic structures. The generalized representative structure (GRS) method presented within generates small atomic structures that reproduce ACE descriptor distributions corresponding to arbitrary structural and chemical complexity. It is shown that systematically improvable representations of crystalline systems on fixed parent lattices, amorphous materials, liquids, and ensembles of atomic structures may be produced efficiently through optimization algorithms. With the GRS method, we highlight reduced representations of atomistic machine-learning training datasets that contain similar amounts of information and small 40–72 atom representations of liquid phases. The ability to use GRS methodology as a driver for informed novel structure generation is also demonstrated. The advantages over other data-driven methods and state-of-the-art methods restricted to high-symmetry systems are highlighted.

atomic cluster expansion↗
DOE OSTI2021

Materials Fingerprinting Classification

Significant progress in many classes of materials could be made with the availability of experimentally-derived large datasets composed of atomic identities and three-dimensional coordinates. Methods for visualizing the local atomic structure, such as atom probe tomography (APT), which routinely generate datasets comprised of millions of atoms, are an important step in realizing this goal. However, state-of-the-art APT instruments generate noisy and sparse datasets that provide information about elemental type, but obscure atomic structures, thus limiting their subsequent value for materials discovery. The application of a materials fingerprinting process, a machine learning algorithm coupled with topological data analysis, provides an avenue by which here-to-fore unprecedented structural information can be extracted from an APT dataset. As a proof of concept, the material fingerprint is applied to high-entropy alloy APT datasets containing body-centered cubic (BCC) and face-centered cubic (FCC) crystal structures. A local atomic configuration centered on an arbitrary atom is assigned a topological descriptor, with which it can be characterized as a BCC or FCC lattice with near perfect accuracy, despite the inherent noise in the dataset. Finally, this successful identification of a fingerprint is a crucial first step in the development of algorithms which can extract more nuanced information, such as chemical ordering, from existing datasets of complex materials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Polarization-Controlled Structural Modulation in the Single Atomic Layer at the PbZr 0.2 Ti 0.8 O 3 /LaNiO 3 Interface

Conductivity modulation via ferroelectric polarization coupling with LaNiO 3 (LNO) is demonstrated at an epitaxial ferroelectric–LNO interface. Conductivity measurements, varying the thickness of the LNO channel, show that this phenomenon is confined to a few atomic layers at the interface. Combining in situ biasing and off-axis holography, we mapped out electrostatic potentials at the PbZr 0.2 Ti 0.8 O 3 (PZT)/LNO/SrTiO 3 (STO) heterostructure upon polarization switching. Using aberration-corrected STEM, the interfacial atomic structures were investigated for the two different PZT polarization states. Polarization in PZT induces a significant change in the in-plane O–Ni–O bond angles, with a 37° modulation in the topmost 1 or 2 LNO unit cells, driven by strain in the oxygen sublattice for the two opposite polarization directions in PZT. Both oxygen and cation sublattices exhibit strain responses exceeding 10% upon switching. This atomic-layer structural modulation highlights a mechanism for functional oxide heterostructure development, offering pathways for advancements in nonvolatile memory, sensors, and energy-efficient transistors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Atomic Gradient Structure Alters Electronic Structure in 3D across the Bulk and Enhances Photoactivity

Abstract Understanding structure–function relationships enables the design of materials with tailored functionalities. The long‐standing challenge is to design materials with high active volume to improve efficiency. Tailored grain boundaries and lattice defects are traditionally used to tune the electronic structure near interfaces or defects to promote electron and hole separation. However, the active volume of point defect sites or interfaces in these traditional photocatalysts is extremely low. This study reports a structure with continuous atomic positional deformation across the bulk, altering the electronic structure in 3D and creating a significantly higher active volume. Such a structure in anatase is obtained and tuned by phase transformation during the heating process. Transmission electron microscopy and density functional theory results reveal that atomic deformations result in continuous band bending across the particles, facilitating electron–hole separation, inhibiting their recombination, and inducing dramatically enhanced photoactivity. These findings enable a different materials design paradigm that can potentially be harnessed for a broad range of applications.

Ren, Peng↗
DOE OSTI2017

Atomic-level structural correlations across the morphotropic phase boundary of a ferroelectric solid solution: xBiMg 1/2 Ti 1/2 O 3 -(1$-$x)PbTiO 3

Revelation of unequivocal structural information at the atomic level for complex systems is uniquely important for deeper and generic understanding of the structure property connections and a key challenge in materials science. Here in this paper we report an experimental study of the local structure by applying total elastic scattering and Raman scattering analyses to an important non-relaxor ferroelectric solid solution exhibiting the so-called composition-induced morphotropic phase boundary (MPB), where concomitant enhancement of physical properties have been detected. The powerful combination of static and dynamic structural probes enabled us to derive direct correspondence between the atomic-level structural correlations and reported properties. The atomic pair distribution functions obtained from the neutron total scattering experiments were analysed through big-box atom-modelling implementing reverse Monte Carlo method, from which distributions of magnitudes and directions of off-centred cationic displacements were extracted. We found that an enhanced randomness of the displacement-directions for all ferroelectrically active cations combined with a strong dynamical coupling between the A- and B-site cations of the perovskite structure, can explain the abrupt amplification of piezoelectric response of the system near MPB. Finally, altogether this provides a more fundamental basis in inferring structure-property connections in similar systems including important implications in designing novel and bespoke materials.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Structural and Magnetic Evolution of Bimetallic MnAu Clusters Driven by Asymmetric Atomic Migration

The nanoscale structural, compositional, and magnetic properties are examined for annealed MnAu nanoclusters. The MnAu clusters order into the L10 structure, and monotonic size-dependences develop for the composition and lattice parameters, which are well reproduced by our density functional theory calculations. Simultaneously, Mn diffusion forms 5 Å nanoshells on larger clusters inducing significant magnetization in an otherwise antiferromagnetic system. The differing atomic mobilities yield new cluster nanostructures that can be employed generally to create novel physical properties.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Atomic-scale e-beam sculptor

A system and method (referred to as the system) fabricates controllable atomic assemblies in two and three dimensions. The systems identify by a non-invasive imager, a local atomic structure, distribution of vacancies, and dopant atoms and modify, by a microscopic modifier, the local atomic structure, via electron beam irradiation. The systems store, by a knowledge base, cause-and-effect relationships based on a non-invasive imaging and electron scans. The systems detect, by detectors, changes in the local atomic structure induced by the electron irradiation; and fabricate, a modified atomic structure by a beam control software and feedback.

Kalinin, Sergei V.↗
DOE OSTI2017

Intermetallic structures with atomic precision for selective hydrogenation of nitroarenes

It is essential to bridge the structure-properties relationship of bimetallic catalysts for the rational design of heterogeneous catalysts. Different from random alloys, intermetallic compounds (IMCs) present atomically-ordered structures, which is advantageous for catalytic mechanism studies. Here, we used Pt-based intermetallic nanoparticles (iNPs), individually encapsulated in mesoporous silica shells, as catalysts for the hydrogenation of nitroarenes to functionalized anilines. With the capping-free nature and ordered atomic structure, PtSn iNPs show >99% selectivity to hydrogenate the nitro group of 3-nitrostyrene albeit with a lower activity, in contrast to Pt 3 Sn iNPs and Pt NPs. The geometric structure of PtSn iNPs in eliminating Pt threefold sites hampers the adsorption/dissociation of molecular H 2 and leads to a non-Horiuti-Polanyi hydrogenation pathway, while Pt 3 Sn and Pt surfaces are saturated by atomic H. Calculations using density functional theory (DFT) suggest a preferential adsorption of the nitro group on the intermetallic PtSn surface contributing to its high selectivity.

3-Nitrostyrene↗
DOE OSTI2017

Atomic-scale structural and electronic properties of SrTiO 3 / GaAs interfaces: A combined STEM-EELS and first-principles study

The electronic properties of epitaxial oxide thin films grown on compound semiconductors are largely determined by the interfacial atomic structure, as well as the thermodynamic conditions during synthesis. Ferroelectric polarization and Fermi-level pinning in SrTiO 3 films have been attributed to the presence of oxygen vacancies at the oxide/semiconductor interface. Here, we present scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy analyses of GaAs films grown on SrTiO 3 combined with first-principles calculations to determine the atomic and electronic structures of the SrTiO 3 /GaAs interfaces. In this work, an atomically abrupt SrO/As interface is observed and the interfacial SrO layer is found to be O-deficient. First-principles density functional theory (DFT) calculations show SrO/Ga and Sr/As interfaces are favorable under O-rich and O-poor conditions, respectively. The SrO/Ga interface is reconstructed via the formation of Ga-Ga dimers while the Sr/As interface is abrupt and consistent with the experiment. DFT calculations further reveal that intrinsic two-dimensional electron gas (2DEG) forms in both SrO/Ga and Sr/As interfaces, and the Fermi level is pinned to the localized 2DEG states. Interfacial O vacancies can enhance the 2DEG density while it is possible for Ga/As vacancies to unpin the Fermi level from the 2DEG states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

NbTaV_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution ternary alloys niobium-tantalum-vanadium (Nb-Ta-V). The first-principle code that has been used to run the calculations is the closed-source Vienna Ab-Initio Simulation Package (VASP). The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 8. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 10,500 randomized atomic structures over 105 chemical compositions. The calculations have been collected on NERSC-Perlmutter using the VASP 6.3.2. The VASP calculations for every atomic structure have been performed in 2 main steps: 1. Starting from an ideal body-centered-cubic (BCC) structure, geometry optimization with low precision has been executed to perform a preliminary optimization of the atomic structure. The output for this calculations is available in the files 0.CONTCAR, 0.OUTCAR, rlx1.out. 2. Using the atomic structure resulting from the preliminary geometry optimization, a second geometry optimization has been performed using normal precision. The output for this calculations is available in the files CONTCAR, OUTCAR, rlx2.out, vaspout.h5, and vasprun.xml. Every chemical composition sampled across the composition range in the dataset has its own directory. The convention used to name the directories for ternary alloys is AXBYCZ, where A, B, and C refer to the constituents, and X, Y, and Z are positive integers that represent the number of atoms for each constituent and their values still sum up to 128. Each atomic structure associated with a specific chemical composition has its own sub-directory within the directory of the corresponding chemical composition. The sub-directories for each atomic structure for each chemical composition are named 'case-*', where * is a positive integer that spans all the values from 1 through 100, extremes included. The files contained in each sub-directory 'case-*' for each atomic structure are as follows: 1. INCAR: input file that contains various parameters and settings for controlling the behavior of the electronic structure calculations 2. 0.POSCAR: input file that defines the atomic structure of a system 3. 0.CONTCAR: output file that provides the atomic positions and cell parameters after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 4. 0.OUTCAR: output file that contains detailed information about the progress of a calculation after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 5. rlx1.out: file with diagnostic information about the execution of the first geometry optimization with precision variable set to PREC=Low in the INCAR file 6. POSCAR: input file that defines the atomic structure of a system after the first geometry optimization has been run at low precision. This represents the input for the second geometry optimization run with the precision variable set to PREC=Normal in the INCAR file 7. CONTCAR: output file that provides the atomic positions and cell parameters after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 8. OUTCARL: output file that contains detailed information about the progress of a calculation after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 9. rlx2.out: file with diagnostic information about the execution of the second geometry optimization with precision variable set to PREC=Normal in the INCAR file 10. vaspout.h5: hierarchical HDF5 file containing the inputs and outputs of a VASP calculation. To analyze the data in this file we recommend using py4vasp. This file is only produced if the VASP version used is compiled with HDF5 support 11. vasprun.xml: contains similar information to OUTCAR, but in an xml format. This research is sponsored by the Artificial Intelligence Initiative as part of the Laboratory Directed Research and Development (LDRD) Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the US Department of Energy under contract DE-AC05-00OR22725. This work used resources of the Oak Ridge Leadership Computing Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725, under Directorate Discretionary awards MAT025 (Materials Science) and LRN026 (Machine Learning), and INCITE award MAT201. This work also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, under award ERCAP0025216.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Atomic-Scale Structure and Stress Release Mechanism in Core–Shell Nanoparticles

According to the article, core–shell nanoparticles find applications in catalysts, sensors, and theranostics. The full internal 3D atomic structure, however, cannot be resolved by current imaging and diffraction techniques. We analyzed the atomic positions and stress-release mechanism in a cubic Au–Pd core–shell nanoparticle in approximately 1000 times higher resolution than current experimental techniques using large-scale molecular dynamics simulation to overcome these limitations. The core–shell nanocube of 73 nm size was modeled similarly to solution synthesis by random epitaxial deposition of a 4 nm thick shell of Pd atoms onto a Au core of 65 nm side length using reliable interatomic potentials. The internal structure reveals specific deformations and stress relaxation mechanisms that are caused by the +4.8% lattice mismatch of gold relative to palladium and differential confinement of extended particle facets, edges, and corners by one, two, or three Au–Pd interfaces, respectively. The three-dimensional lattice strain causes long-range, arc-like bending of atomic rows along the faces and edges of the particle, especially near the Au–Pd interface, a bulging deformation of the Pd shell, and stacking faults in the Pd shell at the corners of the particle. The strain pattern and mechanism of stress release were further characterized by profiles of the atomic layer spacing in the principal crystallographic directions. Accordingly, strain in the Pd shell is several times larger in the extended facets than near the edges and corners of the nanoparticle, which likely affects adsorption, optical, and electrochemical properties. The findings are consistent with available experimental data, including 3D reconstructions of the same cubic nanoparticle by coherent diffractive imaging (CDI) and may be verified by more powerful experimental techniques in the future. The stress release mechanisms are representative for cubic core–shell nanoparticles with fcc structure and can be explored for different shapes by the same methods.

Chemistry↗