Complex modeling for the quantification of nanoscale disorder using genetic algorithms, density functional theory and line-profile analysis
Abstract not provided
Koch, Robert J.↗
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Results for “atomic structure”
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Structural and Electronic Properties of Interfaces in Graphene and Hexagonal Boron Nitride Lateral Heterostructures
The in-plane heterostructures composed of graphene and hexagonal boron nitride (G/BN), as the first kind of two-dimensional metal/semiconductor heterostructures of one-atom thickness, are attractive for both fundamental low-dimensional physics and nanoscale devices because of the tailorable electronic properties. The atomic structures and electronic properties of interfaces in lateral G/BN heterostructures are investigated by first-principles calculations. The symmetric armchair interfaces have a similar formation energy but a larger band gap compared with the nonsymmetric interfaces. G/BN heterostructures with zigzag-type interfaces constructed under the guide of Clar’s rule are found to possess a lower formation energy than those with abrupt interfaces and open a finite band gap. In addition to the zigzag and armchair interfaces, other misorientated interfaces with pentagon and heptagon rings are also stable with low formation energies of 4.4–6.8 eV/nm. These theoretical results are important to clarify the correlation between atomic structures and electronic properties of in-plane G/BN heterostructures and establish a fundamental picture for further theoretical studies and device design.
36 MATERIALS SCIENCE↗
First-principles calculations of K-shell X-ray absorption spectra for warm dense nitrogen
X-ray absorption spectrum is a powerful tool for atomic structure detection on warm dense matter. Here, we perform first-principles molecular dynamics and X-ray absorption spectrum calculations on warm dense nitrogen along a Hugoniot curve. From the molecular dynamics trajectory, the detailed atomic structures are examined for each thermodynamical condition. The K-shell X-ray absorption spectrum is calculated, and its changes with temperature and pressure along the Hugoniot curve are discussed. The warm dense nitrogen systems may contain isolated nitrogen atoms, N{sub 2} molecules, and nitrogen clusters, which show quite different contributions to the total X-ray spectrum due to their different electron density of states. The changes of X-ray spectrum along the Hugoniot curve are caused by the different nitrogen structures induced by the temperature and the pressure. Some clear signatures on X-ray spectrum for different thermodynamical conditions are pointed out, which may provide useful data for future X-ray experiments.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Au 133 (SPh - t Bu) 52 Nanomolecules: X-ray Crystallography, Optical, Electrochemical, and Theoretical Analysis
Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the "nanostructure problem". Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au-133(SPh-tBu)(52), was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than in the slightly larger Au-144(SCH2CH2Ph)(60). Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.
Dass, Amala↗
A robust synthetic data generation framework for machine learning in high-resolution transmission electron microscopy (HRTEM)
Machine learning techniques are attractive options for developing highly-accurate analysis tools for nanomaterials characterization, including high-resolution transmission electron microscopy (HRTEM). However, successfully implementing such machine learning tools can be difficult due to the challenges in procuring sufficiently large, high-quality training datasets from experiments. In this work, we introduce Construction Zone, a Python package for rapid generation of complex nanoscale atomic structures which enables fast, systematic sampling of realistic nanomaterial structures and can be used as a random structure generator for large, diverse synthetic datasets. Using Construction Zone, we develop an end-to-end machine learning workflow for training neural network models to analyze experimental atomic resolution HRTEM images on the task of nanoparticle image segmentation purely with simulated databases. Further, we study the data curation process to understand how various aspects of the curated simulated data—including simulation fidelity, the distribution of atomic structures, and the distribution of imaging conditions—affect model performance across three benchmark experimental HRTEM image datasets. Using our workflow, we are able to achieve state-of-the-art segmentation performance on these experimental benchmarks and, further, we discuss robust strategies for consistently achieving high performance with machine learning in experimental settings using purely synthetic data. Construction Zone and its documentation are available at https://github.com/lerandc/construction_zone.
36 MATERIALS SCIENCE↗
Atomic Number Dependent “Structural Transitions” in Ordered Lanthanide Monolayers: Role of the Hydration Shell
When lanthanide ions are present in the aqueous subphase of a floating monolayer (Langmuir film), the ions attracted to the interface will in many cases form commensurate and/or incommensurate two-dimensional structures. These lattices depend not only on the molecules forming the monolayer, but also on the atomic number of the lanthanide, with a sudden change between the lattice formed by lighter ions and that formed by heavier ions under a given monolayer. Since there are few other relevant differences between the lanthanides, we attribute the Z-dependent “transition” to the number of water molecules associated with each ion. Finally, the first hydration shell is thought to vary continuously from ~9 in lighter lanthanides to ~8 in heavier lanthanides.
Miller, Mitchell↗
Studies of Nucleation and Growth, Specific Heat and Viscosity of Undercooled Melts of Quasicrystals and Polytetrahedral-Phase-Forming Alloys
The local atomic structures of undercooled liquid metals are presumed to be icosahedral; this order is incompatible with translational periodicity, constituting a barrier to the nucleation of the crystal phase. The extended atomic structure of the icosahedral quasicrystal (i-phase) is similar to that presumed in the undercooled liquid. Therefore, a comparison of the maximum undercooling in alloys that form the i-phase with those that form crystal phases provides a probe of the liquid structure.
Kelton, K. F.↗
Pressure-induced nonmonotonic cross-over of steady relaxation dynamics in a metallic glass
Relaxation dynamics, as a key to understand glass formation and glassy properties, remains an elusive and challenging issue in condensed matter physics. In this work, in situ high-pressure synchrotron high-energy X-ray photon correlation spectroscopy has been developed to probe the atomic-scale relaxation dynamics of a cerium-based metallic glass during compression. Although the sample density continuously increases, the collective atomic motion initially slows down as generally expected and then counterintuitively accelerates with further compression (density increase), showing an unusual nonmonotonic pressure-induced steady relaxation dynamics cross-over at ~3 GPa. Furthermore, by combining in situ high-pressure synchrotron X-ray diffraction, the relaxation dynamics anomaly is evidenced to closely correlate with the dramatic changes in local atomic structures during compression, rather than monotonically scaling with either sample density or overall stress level. In conclusion, these findings could provide insight into relaxation dynamics and their relationship with local atomic structures of glasses.
36 MATERIALS SCIENCE↗
Relativistic R -matrix calculations for the electron-impact excitation of neutral molybdenum
A recent PISCES-B Mod experiment [Nishijima et al., J. Phys. B 43, 225701 (2010)] has revealed up to a factor of 5 discrepancy between measurement and the two existing theoretical models [Badnell et al., J. Phys. B 29, 3683 (1996); Bartschat et al., J. Phys. B 35, 2899 (2002)], providing important diagnostics for M O I . In the following paper we address this issue by employing a relativistic atomic structure and R -matrix scattering calculations to improve upon the available models for future applications and benchmark results against a recent Compact Toroidal Hybrid experiment [Hartwell et al., Fusion Sci. Technol. 72, 76 (2017)]. We determine the atomic structure of M O I using GRASP 0 , which implements the multiconfigurational Dirac-Fock method. Fine structure energies and radiative transition rates are presented and compared to existing experimental and theoretical values. The electron-impact excitation of M O I is investigated using the relativistic R -matrix method and the parallel versions of the Dirac atomic R -matrix codes. Electron-impact excitation cross sections are presented and compared to the few available theoretical cross sections. Throughout, our emphasis is on improving the results for the z 5 P$^{o}_{1, 2, 3}$ → a 5 S 2 , z 7 P$^{o}_{2, 3, 4}$ → a 7 S 3 and y 7 P$^{o}_{2, 3, 4}$ → a 7 S 3 electric dipole transitions of particular relevance for diagnostic work.
Smyth, R. T.↗
A NEW GENERATION OF LOS ALAMOS OPACITY TABLES
We present a new, publicly available set of Los Alamos OPLIB opacity tables for the elements hydrogen through zinc. Our tables are computed using the Los Alamos ATOMIC opacity and plasma modeling code, and make use of atomic structure calculations that use fine-structure detail for all the elements considered. Our equation of state model, known as ChemEOS, is based on the minimization of free energy in a chemical picture and appears to be a reasonable and robust approach to determining atomic state populations over a wide range of temperatures and densities. In this paper we discuss in detail the calculations that we have performed for the 30 elements considered, and present some comparisons of our monochromatic opacities with measurements and other opacity codes. We also use our new opacity tables in solar modeling calculations and compare and contrast such modeling with previous work.
79 ASTRONOMY AND ASTROPHYSICS↗
Status Report on the Development of Cladding Inner-wall and Outer-wall Coatings
Advanced cladding is critical for nuclear reactors with enhanced performance in radiation tolerance, neutron transparency and reactor safety. Using advanced cladding will ensure the adequate thermal conductivity and mechanical stability of the cladding base material, corrosion resistance and high-temperature coolant compatibility of the cladding surface, and chemical stability in the cladding inner wall against fuel cladding chemical interaction (FCCI). An innovative cladding with a three-layer structure (i.e., a modified outer surface, a robust clad base material, and a modified inner wall) promises to meet all these requirements. In this status report, the initial efforts on the development of cladding inner-wall and outer-wall coatings are summarized. The activities covered in this report are (1) High-resolution TEM studies of TiN/HT-9 interface atomic structure and chemistry after ion irradiation, (2) High-resolution TEM studies of TiN/14YWT ODS interface atomic structure after thermal cycling, (3) Inner-wall TiN coating for an experimental 14YWT ODS cladding, and (4) Corrosion test of TiN coated Ziracloy-4 bar samples.
36 - MATERIALS SCIENCE↗
Perspective: Emerging strategies for determining atomic-resolution structures of macromolecular complexes within cells
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Atomic Decay Data for Modeling K Lines of Iron Peak and Light Odd-Z Elements*
Complete data sets of level energies, transition wavelengths, A-values, radiative and Auger widths and fluorescence yields for K-vacancy levels of the F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu and Zn isonuclear sequences have been computed by a Hartree-Fock method that includes relativistic corrections as implemented in Cowan's atomic structure computer suite. The atomic parameters for more than 3 million fine-structure K lines have been determined. Ions with electron number N greater than 9 are treated for the first time, and detailed comparisons with available measurements and theoretical data for ions with N less than or equal to 9 are carried out in order to estimate reliable accuracy ratings.
modeling K lines↗
Operando XAS/SAXS: Guiding Design of Single-Atom and Subnanocluster Catalysts
Single-atom and subnanocluster catalysts (SSCs) represent a highly promising class of low-cost materials with high catalytic activity and high atom-utilization efficiency. However, SSCs are susceptible to undergo restructuring during the reactions. Exploring the active sites of catalysts through in situ characterization techniques plays a critical role in studying reaction mechanism and guiding the design of optimum catalysts. In situ X-ray absorption spectroscopy/small-angle X-ray scattering (XAS/SAXS) is promising and widely used for monitoring electronic structure, atomic configuration, and size changes of SSCs during real-time working conditions. Unfortunately, there is no detailed summary of XAS/SAXS characterization results of SSCs. The recent advances in applying in situ XAS/SAXS to SSCs are thoroughly summarized in this review, including the atomic structure and oxidation state variations under open circuit and realistic reaction conditions. Furthermore, the reversible transformation of single-atom catalysts (SACs) to subnanoclusters/nanoparticles and the application of in situ XAS/SAXS in subnanoclusters are discussed. To conlcude, the outlooks in modulating the SSCs and developing operando XAS/SAXS for SSCs are highlighted.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Large-angle illumination STEM: Toward three-dimensional atom-by-atom imaging
To completely understand and control materials and their properties, it is of critical importance to determine their atomic structures in all three dimensions. Recent revolutionary advances in electron optics – the inventions of geometric and chromatic aberration correctors as well as electron source monochromators – have provided fertile ground for performing optical depth sectioning at atomic-scale dimensions. In this study we theoretically demonstrate the imaging of top/sub-surface atomic structures and identify the depth of single dopants, single vacancies and the other point defects within materials by large-angle illumination scanning transmission electron microscopy (LAI-STEM). The proposed method also allows us to measure specimen properties such as thickness or three-dimensional surface morphology using observations from a single crystallographic orientation.
36 MATERIALS SCIENCE↗
Insights on the origin of the Tb5Ge4 magnetocaloric effect
In this report the magnetic, atomic structures and spin-lattice coupling have been thoroughly studied through high magnetic field magnetometry, Synchrotron X-ray diffraction under applied magnetic field and magnetostriction measurements in the Tb5Ge4 compounds. A field induced phase transition from an antiferromagnetic towards a ferromagnetic ordering was confirmed but with absence of structural transformation. This absence has been confirmed experimentally through synchrotron x-ray diffraction under applied field (up to 30 T). Moreover, this absence was explained via a thermodynamic free energy model: first principles calculations determined a large energy gap (ΔE=0.65 eV) between the two possible structures, O(I) and O(II). From magnetic and structural properties, a H-T phase diagram has been proposed for Tb5Ge4. Finally it was observed a large magnetostriction (up to 600 ppm) induced by ΔH=7 T.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Prediction of Structures and Atomization Energies of Small Silver Clusters, (Ag) n , n < 100
Neutral silver clusters, Ag n , were studied using density functional theory (DFT) followed by high level coupled cluster CCSD(T) calculations to determine the low energy isomers for each cluster size for small clusters. The normalized atomization energy, heats of formation, and average bond lengths were calculated for each of the different isomeric forms of the silver clusters. For n = 2–6, the preferred geometry is planar, and the larger n = 7–8 clusters prefer higher symmetry, three-dimensional geometries. The low spin state is predicted to be the ground state for every cluster size. A number of new low energy isomers for the heptamer and octamer were found. Additional larger Ag n structures, n < 100, were initially optimized using a tree growth-hybrid genetic algorithm with an embedded atom method (EAM) potential. Finally, for n ≤ 20, DFT was used to optimize the geometries. DFT with benchmarked functionals were used to predict that the normalized atomization energies ((AE)s) for Ag n start to converge slowly to the bulk at n = 55. The (AE) for Ag 99 is predicted to be ~50 kcal/mol.
Environmental Molecular Sciences Laboratory↗
High‐Resolution Electron Tomography of Ultrathin Boerdijk–Coxeter–Bernal Nanowire Enabled by Superthin Metal Surface Coating
Abstract The rapid advancement of transmission electron microscopy has resulted in revolutions in a variety of fields, including physics, chemistry, and materials science. With single‐atom resolution, 3D information of each atom in nanoparticles is revealed, while 4D electron tomography is shown to capture the atomic structural kinetics in metal nanoparticles after phase transformation. Quantitative measurements of physical and chemical properties such as chemical coordination, defects, dislocation, and local strain have been made. However, due to the incompatibility of high dose rate with other ultrathin morphologies, such as nanowires, atomic electron tomography has been primarily limited to quasi‐spherical nanoparticles. Herein, the 3D atomic structure of a complex core–shell nanowire composed of an ultrathin Boerdijk–Coxeter–Bernal (BCB) core nanowire and a noble metal thin layer shell deposited on the BCB nanowire surface is discovered. Furthermore, it is demonstrated that a new superthin noble metal layer deposition on an ultrathin BCB nanowire could mitigate electron beam damage using an in situ transmission electron microscope and atomic resolution electron tomography. The colloidal coating method developed for electron tomography can be broadly applied to protect the ultrathin nanomaterials from electron beam damage, benefiting both the advanced material characterizations and enabling fundamental in situ mechanistic studies.
Song, Xiaohui↗