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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop in this paper a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Finally, comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Variation of local atomic structure due to devitrification of Ni-Zr alloy thin films probed by EXAFS measurements

Thin film metallic glasses (TFMGs) exhibit properties superior to their bulk counterparts allowing them to be potentially useful in many practical applications. Apart from their technological interest, when converted to crystallized state (devitrification) TFMGs can also act as precursors for partially crystallized or fully crystallized forms. Such devitrified forms are attractive due to their novel structural and magnetic properties. The amorphous-to-crystalline transformation of co-sputtered Ni-Zr alloy thin films through annealing was studied using EXAFS (Extended X-ray Absorption Fine Structure) measurements. Investigation through an atomic probe gives a better insight into the local environment of the atomic species, rendering a deeper understanding of thermal evolution of such materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

High-order finite element method for atomic structure calculations

We introduce featom, an open source code that implements a high-order finite element solver for the radial Schrödinger, Dirac, and Kohn-Sham equations. The formulation accommodates various mesh types, such as uniform or exponential, and the convergence can be systematically controlled by increasing the number and/or polynomial order of the finite element basis functions. The Dirac equation is solved using a squared Hamiltonian approach to eliminate spurious states. Here, to address the slow convergence of the $κ=±1$ states due to divergent derivatives at the origin, we incorporate known asymptotic forms into the solutions. We achieve a high level of accuracy (10 -8 Hartree) for total energies and eigenvalues of heavy atoms such as uranium in both Schrödinger and Dirac Kohn-Sham solutions. We provide detailed convergence studies and computational parameters required to attain commonly required accuracies. Finally, we compare our results with known analytic results as well as the results of other methods. In particular, we calculate benchmark results for atomic numbers (Z) from 1 to 92, verifying current benchmarks. We demonstrate significant speedup compared to the state-of-the-art shooting solver dftatom. An efficient, modular Fortran 2008 implementation, is provided under an open source, permissive license, including examples and tests, wherein particular emphasis is placed on the independence (no global variables), reusability, and generality of the individual routines.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Atomic Structure and Electrical Activity of Grain Boundaries and Ruddlesden-Popper Faults in Cesium Lead Bromide Perovskite

To evaluate the role of planar defects in lead-halide perovskites—cheap, versatile semiconducting materials—it is critical to examine their structure, including defects, at the atomic scale and develop a detailed understanding of their impact on electronic properties. In this study, postsynthesis nanocrystal fusion, aberration-corrected scanning transmission electron microscopy, and first-principles calculations are combined to study the nature of different planar defects formed in CsPbBr3 nanocrystals. Two types of prevalent planar defects from atomic resolution imaging are observed: previously unreported Br-rich [001](210)Σ5 grain boundaries (GBs) and Ruddlesden–Popper (RP) planar faults. The first-principles calculations reveal that neither of these planar faults induce deep defect levels, but their Br-deficient counterparts do. It is found that the Σ5 GB repels electrons and attracts holes, similar to an n–p–n junction, and the RP planar defects repel both electrons and holes, similar to a semiconductor–insulator–semiconductor junction. Finally, the potential applications of these findings and their implications to understand the planar defects in organic–inorganic lead-halide perovskites that have led to solar cells with extremely high photoconversion efficiencies are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Atomic Structure and Cohesion Energy of ZnSe and CdSe Clusters

The first-principle calculations of the atomic and electronic structures of fullerene-like Zn{sub n}Se{sub n} and Cd{sub n}Se{sub n} have been carried out for n = 12, 36, 48, and 60. A model of two-layer fullerene-like (ZnSe){sub 60} and (CdSe){sub 60} clusters with mixed sp{sup 2}/sp{sup 3} bonds has been built for the first time. Ab initio calculations are performed in terms of the electron density functional and the hybrid B3LYP functional theory. The stability and the energy gap width of the clusters are estimated in the dependence on the number of atoms in a cluster and its geometry. It is shown that the relaxation of 1.7–1.8-nm two-layer (ZnSe){sub 60} and (CdSe){sub 60} clusters with mixed sp{sup 2}/sp{sup 3} bonds is accompanied by splitting out of the external layer.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.

36 MATERIALS SCIENCE↗
DOE OSTI2019

The Atomic Structure of Ti{sub 2}C and Ti{sub 3}C{sub 2} MXenes is Responsible for Their Antibacterial Activity Toward E. coli Bacteria

The expanded Ti{sub 2}C and Ti{sub 3}C{sub 2} MXene phases were synthesized from their parent Ti{sub 2}AlC and Ti{sub 3}AlC{sub 2} MAX phases using the same conditions of the classical acidic aluminum extraction method. The assumption for the study was that the expanded Ti{sub 2}C and Ti{sub 3}C{sub 2} MXenes are composed of the same atoms and if are synthesized from MAX phases using the same conditions of the classical acidic aluminum extraction method, the observed bio-effects can be related only to the changes in their structures. The scanning electron microscope investigations indicated that the expanded Ti{sub 2}C and Ti{sub 3}C{sub 2} sheets formed the specific network of slit-shaped nano-pores. The x-ray photoelectron spectroscopy for chemical analysis (ESCA-XPS) showed almost no difference in surface chemistry of Ti{sub 2}C and Ti{sub 3}C{sub 2} MXenes. The high-resolution transmission electron microscope investigations revealed, however, differences in atomic structure of the individual Ti{sub 2}C and Ti{sub 3}C{sub 2} sheets. Measured distance between Ti-C atomic layers in Ti{sub 2}C was 9.76 Å and was larger by 0.53 Å in comparison with Ti{sub 3}C{sub 2} (9.23 Å). Our investigations of bioactive properties toward model gram-negative Escherichia coli bacterial strain showed that the Ti{sub 2}C MXene did not influence the viability of bacteria. Contrarily, the Ti{sub 3}C{sub 2} MXene showed antibacterial properties. The results of the study indicate that the structure at the atomic scale may play a key role in the bioactivity of MXenes of the same chemical composition, but different stoichiometry, just like in case of Ti{sub 2}C and Ti{sub 3}C{sub 2}.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A nearsighted force-training approach to systematically generate training data for the machine learning of large atomic structures

A challenge of atomistic machine-learning (ML) methods is ensuring that the training data are suitable for the system being simulated, which is particularly challenging for systems with large numbers of atoms. Most atomistic ML approaches rely on the nearsightedness principle (“all chemistry is local”), using information about the position of an atom’s neighbors to predict a per-atom energy. Here, in this work, we develop a framework that exploits the nearsighted nature of ML models to systematically produce an appropriate training set for large structures. We use a per-atom uncertainty estimate to identify the most uncertain atoms and extract chunks centered around these atoms. It is crucial that these small chunks are both large enough to satisfy the ML’s nearsighted principle (that is, filling the cutoff radius) and are large enough to be converged with respect to the electronic structure calculation. We present data indicating when the electronic structure calculations are converged with respect to the structure size, which fundamentally limits the accuracy of any nearsighted ML calculator. These new atomic chunks are calculated in electronic structures, and crucially, only a single force—that of the central atom—is added to the growing training set, preventing the noisy and irrelevant information from the piece’s boundary from interfering with ML training. The resulting ML potentials are robust, despite requiring single-point calculations on only small reference structures and never seeing large training structures. We demonstrated our approach via structure optimization of a 260-atom structure and extended the approach to clusters with up to 1415 atoms.

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

Engineering the atomic structure of sequence-defined peptoid polymers and their assemblies

Peptoids are a family of sequence-defined, non-natural biomimetic polymers which show excellent properties including good chemical and enzymatic stability and high structural tunability. The solid-phase submonomer synthesis method allows precise control over the identity and sequence of chemically diverse side chains, enabling the atomic engineering of their chemical structures for a variety of applications. This unprecedented level of structural control enables access to atomically defined three-dimensional chain conformations and assemblies, facilitating the design and optimization of a variety of nanoscale architectures that can function in biology and materials science. In order to approach the rational design of peptoid materials in a more predictive and precise manner, it is crucial to fully understand how chemical information, in the form of the monomer sequence, encodes their folding and assembly into structurally defined, functional 3D shapes. Furthermore, this perspective focuses on recent studies into the atomic engineering of peptoid nanostructures by examining the impact of sequence variations on their secondary and three-dimensional structures, as well as their functional properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Atomic Structure and Electronic Properties of Anionic Germanium–Zirconium Clusters

This paper presents spatial structure optimization results and calculated electronic spectra for ZrGe{sub n}{sup −} (n = 8–20) anion clusters. Comparison of density-functional calculation results and available experimental data allows us to identify real spatial structures of the clusters. The formation of stable endohedral ZrGe{sub n}{sup −} clusters is possible for n ≥ 12. The clusters with a smaller number of germanium atoms predominantly have exohedral structures.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Nanotubes from the Misfit Layered Compound (SmS) 1.19 TaS 2 : Atomic Structure, Charge Transfer, and Electrical Properties

Misfit layered compounds (MLCs) MX-TX 2 , where M, T = metal atoms and X = S, Se, or Te, and their nanotubes are of significant interest due to their rich chemistry and unique quasi-1D structure. In particular, LnX-TX 2 (Ln = rare-earth atom) constitute a relatively large family of MLCs, from which nanotubes have been synthesized. The properties of MLCs can be tuned by the chemical and structural interplay between LnX and TX 2 sublayers and alloying of each of the Ln, T, and X elements. In order to engineer them to gain desirable performance, a detailed understanding of their complex structure is indispensable. MLC nanotubes are a relative newcomer and offer new opportunities. In particular, like WS 2 nanotubes before, the confinement of the free carriers in these quasi-1D nanostructures and their chiral nature offer intriguing physical behavior. High-resolution transmission electron microscopy in conjunction with a focused ion beam are engaged to study SmS-TaS 2 nanotubes and their cross-sections at the atomic scale. The atomic resolution images distinctly reveal that Ta is in trigonal prismatic coordination with S atoms in a hexagonal structure. Furthermore, the position of the sulfur atoms in both the SmS and the TaS 2 sublattices is revealed. X-ray photoelectron spectroscopy, electron energy loss spectroscopy, and X-ray absorption spectroscopy are carried out. These analyses conclude that charge transfer from the Sm to the Ta atoms leads to filling of the Ta 5d z 2 level, which is confirmed by density functional theory (DFT) calculations. Transport measurements show that the nanotubes are semimetallic with resistivities in the range of 10 –4 Ω·cm at room temperature, and magnetic susceptibility measurements show a superconducting transition at 4 K.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Atomic Structure of a Fluorescent Ag8 Cluster Templated by a Multistranded DNA Scaffold

Multinuclear silver clusters encapsulated by DNA exhibit size-tunable emission spectra and rich photophysics, but their atomic organization is poorly understood. Herein, we describe the structure of one such hybrid chromophore, a green-emitting Ag8 cluster arranged in a Big Dipper-shape bound to the oligonucleotide A 2 C 4 . Three 3' cytosine metallo-base pairs stabilize a parallel A-form-like duplex with a 5' adenine-rich pocket, which binds a metallic, trapezoidal-shaped Ag5 moiety via Ag–N bonds to endo- and exocyclic nitrogens of cytosine and adenine. The unique DNA configuration, constrained coordination environment, and templated Ag8 cluster arrangement highlight the reciprocity between the silvers and DNA in adopting this structure. Overall, these first atomic details of a DNA-encapsulated Ag cluster fluorophore illuminate many aspects of biological assembly, nanoscience, and metal cluster photophysics.

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

Atomic structure and Mott nature of the insulating charge density wave phase of 1T-TaS 2

Here, using x-ray pair distribution function (PDF) analysis and computer modeling, we explore structure models for the complex charge density wave (CDW) phases of layered 1T-TaS 2 that both well capture their atomic-level features and are amenable to electronic structure calculations. The models give the most probable position of constituent atoms in terms of 3D repetitive unit cells comprising a minimum number of Ta–S layers. Structure modeling results confirm the emergence of star-of-David (SD) like clusters of Ta atoms in the high-temperature incommensurate (IC) CDW phase and show that, contrary to the suggestions of recent studies, the low-temperature commensurate (C) CDW phase expands upon cooling thus reducing lattice strain. The C-CDW phase is also found to preserve the stacking sequence of Ta–S layers found in the room temperature, nearly commensurate (NC) CDW phase to a large extent. DFT based on the PDF refined model shows that bulk C-CDW 1T-TaS 2 also preserves the insulating state of individual layers of SD clusters, favoring the Mott physics description of the metal-to-insulator (NC-CDW to C-CDW) phase transition in 1T-TaS 2 . Our work highlights the importance of using precise crystal structure models in determining the nature of electronic phases in complex materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Atomic structure of a metal-supported two-dimensional germania film

The growth and microscopic characterization of two-dimensional germania films is presented. Germanium oxide monolayer films were grown on Ru(0001) by physical vapor deposition and subsequent annealing in oxygen. We obtain a comprehensive image of the germania film structure by combining intensity-voltage low-energy electron diffraction (I/V-LEED) and ab initio density functional theory (DFT) analysis with atomic-resolution scanning tunneling microscopy (STM) imaging. For benchmarking purposes, the bare Ru(0001) substrate and the (2×2)3O covered Ru(0001) were analyzed with I/V-LEED with respect to previous reports. STM topographic images of the germania film reveal a hexagonal network where the oxygen and germanium atom positions appear in different imaging contrasts. For quantitative LEED, the best agreement has been achieved with DFT structures where the germanium atoms are located preferentially on the top and fcc hollow sites of the Ru(0001) substrate. Moreover, in these atomically flat germania films, local site geometries, i.e., tetrahedral building blocks, ring structures, and domain boundaries, have been identified, indicating possible pathways towards two-dimensional amorphous networks.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Atomic Structure, Dynamics, Changes in Chemical Bonding and Semiconductor-Metal Transition in Sb 2 Se 3 : A Remarkable Material for Quantum Networks and Energy Applications

Antimony sesquiselenide has become an outstanding functional material for photovoltaics, energy storage and transformation, memory and photonic applications. Sb 2 Se 3 is one of the most successful emerging solar light absorbers and has also been identified as a highly promising ultralow-loss phase-change material (PCM) for next-generation coherent nanophotonic processors, photonic tensor cores, quantum and neuromorphic networks. Unlike benchmark telluride PCMs, Sb 2 Se 3 features a quasi-one-dimensional (1D) crystalline structure consisting of (Sb 4 Se 6 ) ∞ ribbons, lacks the typical PCM chemical bonding, and undergoes an extended semiconductor-metal transition above the melting point. Consequently, the origin of high optical contrast between crystalline (SET) and amorphous (RESET) logic states remains elusive and presents a significant challenge. Using high-energy X-ray diffraction and Raman spectroscopy over a wide temperature range, supported by first-principles simulations and complemented by thermal, optical and electrical measurements, as well as by 121 Sb-Mossbauer spectroscopy, the quasi-1D network of orthorhombic antimony sesquiselenide was found to undergo significant evolution in amorphous and supercooled Sb 2 Se 3 , leading to lower coordination, shorter interatomic distances and a higher p-electron density on antimony, indicating changes in chemical bonding. The observed novel Sb 2 Se 3 nanocrystalline polymorph, characterized by trigonal antimony coordination and more isolated Sb-Se ribbons, could help reduce multiple trapping defect states in the bandgap, which are typical of orthorhombic Sb 2 Se 3 , thereby enhancing the power-conversion efficiency of photovoltaic devices. Semimetallic and metallic liquid Sb 2 Se 3 exhibit a gradual transformation into a denser 2D and/or 3D network with higher antimony coordination. Localized electron states in the pseudogap are becoming extended, leading to an increase in electronic conductivity σ following the relationship σ ∝ N(E F ) 2 . Liquid Sb 2 Se 3 also appears to be strongly fragile, with a nonmonotonic change in viscosity and higher atomic mobility in the metallic liquid. Furthermore, these results explain extraordinary functionalities of Sb 2 Se 3 for photonic and energy applications.

antimony↗
DOE OSTI2025

Atomic Structural Features of Stacking Faults and Domain Connections in the Li- and Mn-Rich Cathode

Li- and Mn-rich layered oxides (LMRs), a class of earth-abundant materials for rechargeable Li-ion battery cathodes, crystallize into layered structures of two different symmetries: C2/m represented by Li 2 MnO 3 and R$\overline{3}$m represented by LiMn 0.5 Ni 0.5 O 2 . Fundamental questions about how the C2/m and R$\overline{3}$m domains spatially correlate within the same oxide grain and how the C2/m stacking faults arrange themselves when this happens still remain. Here, by using integrated differential phase contrast imaging in scanning transmission electron microscopy (STEM-iDPC), we probe the structural and compositional details of a prototypical, cobalt-free LMR material, 0.3Li 2 MnO 3 •0.7LiMn 0.5 Ni 0.5 O 2 (Li 1.13 Mn 0.57 Ni 0.3 O 2 ). The connection between the C2/m and R$\overline{3}$m domains is found to be abrupt, facilitated by the small lattice mismatch between the two structures. Stacking faults in the C2/m domains feature atomic plane shifting that accommodates stacking sequence changes, which explains why the stacking faults form in a random manner. Furthermore, a local disordering mechanism was identified to correlate with the C2/m stacking faults. Chemically, it is found that Ni coexists with Mn at the transition metal sites within the nominal Li 2 MnO 3 domain. As a result, this study demonstrates that STEM-iDPC is a very useful tool for capturing all the elements in a single image, revealing atomic details on domain connections and stacking faults in the LMRs.

Li-rich and Mn-rich oxides↗