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Quantifying stoichiometry-induced variations in structure and energy of a SrTiO 3 symmetric Σ13 {510}/<100> grain boundary
Grain boundaries (GBs) in complex oxides such as perovskites have been shown to readily accommodate nonstoichiometry changing the electrostatic potential at the boundary plane and effectively controlling material properties such as capacitance, magnetoresistance and superconductivity. Understanding and quantifying exactly how variations in atomic scale nonstoichiometry at the boundary plane extend to the practical mesoscale operating length of the system is therefore critical for improving the overall properties. Bicrystals of SrTiO 3 were fabricated to provide the model GB model structures that are analysed in this paper. We show that statistical analysis of aberration-corrected scanning transmission electron microscope images acquired from a large area of GB is an effective routine to understanding the variation in boundary structure that occurs to accommodate nonstoichiometry. In the case of the SrTiO 3 22.6° Σ13 (510)/[100] GB analysed here, the symmetric atomic structures observed from a micron-long GB can be categorized as two different competing structural arrangements, with and without a rigid-body translation along the boundary plane. How this quantified experimental approach can provide direct insights into the GB energetics is further confirmed from the first principles density functional theory, and the effect of nonstoichiometry in determining the GB energies is quantified.
Enabling liquid solvent structure analysis using hard x-ray absorption spectroscopy with a transferrable microfluidic reactor
In this study, a vacuum compatible microfluidic device, system for analysis at the liquid vacuum interface, is integrated to hard x-ray absorption spectroscopy to obtain the local structure of K 3 [Fe(CN) 6 ] in aqueous solutions with three concentrations of 0.5 M, 0.05 M, and 0.005 M. The solutions were sealed in a microchannel 500 µm wide and 300 µm deep in a portable microfluidic device. The Fe K-edge x-ray absorption spectra indicate a presence of Fe(III) in the complex in water, with an octahedral geometry coordinated with 6 C atoms in the first shell with a distance of ~1.92 Å and 6 N atoms in the second shell with a distance of ~3.10 Å. Varying the concentration has no observable influence on the structure of K 3 [Fe(CN) 6 ]. Our results demonstrate the feasibility of using microfluidic based liquid cells in large synchrotron facilities. Using portable microfludic reactors provides a viable approach to enable multifaceted measurements of liquids in the future.
Electronic Structure and Optical Properties of Cu 2 ZnGeSe 4 . First-Principles Calculations and Vacuum-Ultraviolet Spectroscopic Ellipsometric Studies
Cu 2 ZnGeSe 4 is of interest for the development of next-generation thin-film photovoltaic technologies. To understand its electronic structure and related fundamental optical properties, we perform first-principles calculations for three structural variations: kesterite, stannite, and primitive-mixed CuAu phases. The calculated data are compared with the room-temperature dielectric functionϵ=ϵ1+iϵ2 spectrum of polycrystalline Cu 2 ZnGeSe 4 determined by vacuum-ultraviolet spectroscopic ellipsometry in the photon-energy range of 0.7 to 9.0 eV. Ellipsometric data are modeled with the sum of eight Tauc-Lorentz oscillators, and the best-fit model yields the band-gap and Tauc-gap energies of 1.25 and 1.19 eV, respectively. A comparison of overall peak shapes and relative intensities between experimental spectra and the calculated ϵ data for three structural variations suggests that the sample may not have a pure (ordered) kesterite phase. We found that the complex refractive index N=n+ik, normal-incidence reflectivity R, and absorption coefficients α are calculated from the modeled ϵ spectrum, which are also compared with those of Cu 2 ZnSnSe 4 . The spectral features for Cu 2 ZnGeSe 4 appear to be weaker and broader than those for Cu 2 ZnSnSe 4 , which is possibly due to more structural imperfections presented in Cu 2 ZnGeSe 4 than Cu 2 ZnSnSe 4 .
Structure of siderite FeCO[subscript 3] to 56 GPa and hysteresis of its spin-pairing transition
The structure of siderite, FeCO{sub 3}, was determined to 56 GPa, beyond the spin-pairing transition of its iron d electrons. Fe{sup 2+} in the siderite structure is in the high-spin state at low pressures and transforms to the low-spin (LS) state over a narrow pressure range, 44 to 45 GPa, that is concomitant with a shrinkage of the octahedral bond distance by 4%, and a volume collapse of 10%. The structural rearrangements associated with the electronic transition are nearly isotropic in contrast with other properties of siderite, which mostly are highly anisotropic. Robust refinements of the crystal structure from single-crystal x-ray diffraction data were performed at small pressure intervals in order to accurately evaluate the variation in the interatomic distances and to define the geometry of the carbonate hosting LS-Fe{sup 2+}. Thermal vibrations are remarkably lowered in the LS-Sd as shown by atomic displacement parameters. The formation of like-spin domains at the transition shows a hysteresis of more than 3 GPa, compatible with a strong cooperative contribution of neighboring clusters to the transition.
Nanoscale imaging of the electronic and structural transitions in vanadium dioxide
Not Available
Magnetic and structural phase transitions in erbium at low temperatures and high pressures
Electrical resistance and crystal structure measurements have been carried out on polycrystalline erbium (Er) at temperatures down to 10 K and pressures up to 20 GPa. An abrupt change in the slope of the resistance is observed with decreasing temperature below 84 K, which is associated with the c-axis modulated (CAM) antiferromagnetic (AFM) ordering of the Er moments. With increasing pressure the temperature of the resistance slope change and the corresponding AFM ordering temperature decrease until vanishing above 10.6 GPa. The disappearance of the slope change in the resistance occurs at similar pressures where the hcp structural phase of Er is transformed to a nine-layer {alpha}-Sm structural phase, as confirmed by our high-pressure synchrotron x-ray diffraction studies. These results suggest that the disappearance in the AFM ordering of Er moments is strongly correlated to the structural phase transition at high pressures and low temperatures.
Nonlinear Excitations of Zonal Structures by Toroidal Alfvén Eigenmodes
Zonal flows and, more generally, zonal structures are known to play important self-regulatory roles in the dynamics of microscopic drift-wave-type turbulences. Since toroidal Alfvén eigenmode (TAE) plays crucial roles in the Alfvén wave instabilities in burning fusion plasmas, it is, thus, important to understand and assess the possible roles of zonal flow and structures on the nonlinear dynamics of TAE. It is shown that zonal flow or structure spontaneous excitation is more easily induced by finite amplitude TAEs including the proper trapped-ion responses, causing the zonal structure to be dominated by the zonal current instead of the usual zonal flow. This work shows that proper accounting for plasma equilibrium geometry as well as including kinetic thermal ion treatment in the nonlinear simulations of Alfvénic modes are important ingredients for realistic comparisons with experimental measurements, where the existence of zonal fields has been clearly observed.
What Determines the fcc-bcc Structural Transformation in Shock Compressed Noble Metals?
Abstract not provided
Structural characterization of V57D and V57P mutants of human cystatin C, an amyloidogenic protein
Abstract not provided
Structural Consequences of Cutting a Binding Loop: Two Circularly Permuted Variants of Streptavidin
Abstract Not Provided
Automated identification of elemental ions in macromolecular crystal structures
The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions. Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed.
Solution NMR Structures of Oxidized and Reduced Ehrlichia chaffeensis thioredoxin: NMR-Invisible Structure Owing to Backbone Dynamics
Thioredoxins (Trxs) are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site, CGPC. Here, we describe the NMR solution structures of a Trx from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, in both the oxidized and reduced states. The overall topology of the calculated structures is similar in both redox states and similar to other Trx structures, a five-strand, mixed -sheet (1:3:2:4:5) surrounded by four -helices. Unlike other Trxs studied by NMR in both redox states, the 1H-15N HSQC spectra of reduced Ec-Trx was missing eight amide cross peaks relative to the spectra of oxidized Ec-Trx. These missing amides correspond to residues C32-E39 in the active site containing helix (2) and S72-I75 in a loop near the active site and suggest a substantial change in the backbone dynamics associated with the formation of an intramolecular C32-C35 disulfide bond.