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Preview: Forthcoming article in Journal of Applied Crystallography

Forthcoming article in Journal of Applied Crystallography



Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer



 



The Shift_and_Fix procedure in EXPO: Advances for solving ab-initio crystal structure by powder diffraction data
The Shift_and_Fix procedure is a new automatic computational process which has been developed and introduced in the EXPO package for optimizing a structure model and increasing the probability of succeeding in the ab-initio powder solution by Direct Methods.



Hierarchical clustering for multiple crystal macromolecular crystallography experiments: the ccCluster program
The ccCluster program provides an easy-to-use interface to perform hierarchical cluster analysis on protein diffraction datasets.



Combinatorial appraisal of transition states for in situ pair distribution function analysis
A method and software tool are introduced to fit a series of pair distribution function data through a phase transition or to detect and track a specific structural feature of interest using a linear combination of two end-member states. The misfit between the model combination and the data can reveal underlying details regarding the nature and length scale of intermediate structures.



The modular small-angle X-ray scattering data correction sequence
A data correction sequence is presented, consisting of ordered elementary steps that extract the small-angle X-ray scattering cross section from the original detector signal(s). It is applicable to a wide range of samples, including solids and dispersions.



CarbonXS GUI: a graphical front-end for CarbonXS
CarbonXS GUI is a graphical user interface to CarbonXS. It is used to fit the X-ray diffraction patterns of disordered and graphitized carbon materials to extract structural parameters such as coherence size and strain.



A method to perform modulated structure studies using the program ZMC
A relatively simple method for users new to modulated structures to implement such structural features in an atomistic Monte Carlo modelling program (ZMC) is described. The relevance and usefulness of such a method is outlined.






Full elastic strain tensor determination at the phase scale in a powder metallurgy nickel-based superalloy using X-ray Laue microdiffraction
Laue microdiffraction coupled with energy measurements is used to determine the full elastic strain tensor related to the γ and γ′ phases in a coarse-grained nickel-based superalloy. Model microstructures with a 200 or 2000 nm average precipitate size are investigated.



Spherical harmonics analysis based on the Reuss model in elastic macro strain and stress determination by powder diffraction
This article presents a stress tensor spherical harmonics expansion with the Reuss ground state, which is used for macro strain/stress investigation by powder diffraction.



Characteristic diffuse scattering from distinct line roughnesses
The impact of the edge roughness of laterally periodic nanostructures on the scattering pattern is investigated. The applicability of existing analytical approaches for the description of real samples is discussed.



Protein crystals ablated from aqueous solution at high velocity retain their diffractive properties: applications in high-speed serial crystallography
This paper describes a proof-of-principle study demonstrating that protein crystals ablated by a picosecond infrared laser retain their diffractive properties. The crystals were ejected at high velocity from an aqueous solution, collected and then used for structure determination by serial synchrotron crystallography.



A combined characterization of clusters in naturally aged Al–Cu–(Li, Mg) alloys using small-angle neutron and X-ray scattering and atom probe tomography
Compositional fluctuations arising from Cu-rich solute clusters in Al–Cu alloys with additions of Li and Mg are characterized by combined small-angle neutron and X-ray scattering.



Implications of X-ray thermal diffuse scattering in integrated Bragg intensities of silicon and cubic boron nitride
The thermal diffuse scattering (TDS) contribution to the integrated Bragg intensities is calculated and quantified, and the implications of uncorrected TDS for crystallographic models investigated.



A peak-finding algorithm based on robust statistical analysis in serial crystallography
This manuscript addresses the problem of peak finding and, by extension, `hit finding' in crystallographic X-ray free-electron laser datasets, by exploiting recent developments in robust statistical analysis.



Effect of phenol red dye on monocrystal growth, crystalline perfection, and optical and dielectric properties of zinc (tris) thio­urea sulfate
In this article, the effect of phenol red dye on key structural, crystalline perfection, optical, photoluminescence and dielectric properties of zinc (tris) thio­urea sulfate single crystals is reported.



Application of forward models to crystal orientation refinement
Two algorithms reliant on physics-based forward models are proposed to refine crystal orientations: a multi-resolution brute-force local search and a derivative-free optimization. The efficacy of these methods is evaluated for the electron backscatter diffraction and electron channeling pattern modalities using simulated patterns with known orientations.



Modeling the polarized X-ray scattering from periodic nanostructures with molecular anisotropy
A modeling framework to relate the molecular orientation of nanostructures to polarized resonant soft X-ray scattering measurements using the Born approximation and a full tensor treatment is described.



ECCI, EBSD and EPSC characterization of rhombohedral twinning in polycrystalline α-alumina deformed in a D-DIA apparatus
This study presents rhombohedral twin characterization in plastically deformed alumina at high-pressure and -temperature conditions using electron channeling contrast imaging (ECCI) in a field emission scanning electron microscope, electron backscatter diffraction (EBSD) and elastic plastic self-consistent (EPSC) numerical modeling on synchrotron X-ray diffraction data.



Variant selection in surface martensite
Variant selection is reported in martensite formed on the surface of an Fe–30% Ni sample. Predictive models of the phenomenon based on different crystallographic descriptions of the transformation are proposed and compared.



The electrostatic potential of dynamic charge densities
The electrostatic potential (ESP) is computed for dynamic charge densities corresponding to multipole models and maximum-entropy densities. Convergence of the reciprocal-space summation is guaranteed by the Gaussian form of the Debye–Waller factor. Applications to serine demonstrate only a weak temperature dependence of the ESP on molecular surfaces relevant to intermolecular interactions.



Generalized skew-symmetric interfacial probability distribution in reflectivity and small-angle scattering analysis
Generalized skew-symmetric interfacial probability density functions are used to model arbitrary interfacial density profiles for the analysis of reflectivity and small-angle scattering.



Whole-nanoparticle atomistic modeling of the schwertmannite structure from total scattering data
A single-particle structural model of schwertmannite is proposed from a combined multi-technique approach, using a novel reverse Monte Carlo/Debye scattering equation parallel code.



Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements
Reverse Monte Carlo software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference.



NanoPDF64: software package for theoretical calculation and quantitative real-space analysis of powder diffraction data of nanocrystals
NanoPDF64 is a software package for analysis of pair distribution functions of nanocrystals. It is also capable of calculating theoretical powder diffraction patterns and pair distribution functions for atomistic models of nanocrystals.



Advancing reverse Monte Carlo structure refinements to the nanoscale
The computing speed of reverse Monte Carlo structure refinements has been improved by up to two orders of magnitude, which significantly expands the capabilities of this method.



Melting and freezing temperatures of confined Bi nanoparticles over a wide size range
The size dependences of the melting and crystallization temperatures of spherical Bi nanoparticles embedded in glass were determined using combined small- and wide-angle X-ray scattering measurements for nanoparticle radii ranging from 1 to 11 nm. The results provide additional and stronger evidence supporting previous conclusions showing that, below the melting temperature, Bi nanocrystals with radii larger than 1.8 nm consist of a crystalline core surrounded by a disordered shell.



Phase retrieval of coherent diffractive images with global optimization algorithms
Phase-retrieval algorithms combined with global optimization techniques have been shown to be robust and reliable, and to outperform phase-retrieval algorithms used in coherent diffractive imaging.



Improved orientation sampling for indexing diffraction patterns of polycrystalline materials
A method for generating high-quality discretizations of SO(3) is described and compared with existing methods.



A valence-selective X-ray fluorescence holography study of an yttrium oxide thin film
The first direct valence-selective structure determination by X-ray fluorescence holography is presented. This method uses the fluorescence intensity variation of specific elements close to the K absorption edge. Thereby, the different crystal structures in a mixed Y2+/Y3+ thin film of yttrium oxide are distinguished.