June 2015 issue
J. Appl. Cryst. (2015). 48, 620
The latest virtual special issue of Journal of Applied Crystallography includes some highlights of the 12th Conference on High-Resolution X-ray Diffraction and Imaging (XTOP), which took place in Villard-de-Lans and Grenoble in September 2014.
J. Appl. Cryst. (2015). 48, 621-644
Signature of dislocations and stacking faults of face-centred cubic nanocrystals in coherent X-ray diffraction patterns: a numerical study
Crystal defects can be identified by their fingerprint in coherent X-ray diffraction patterns. Realistic defects in face-centred cubic nanocrystals are studied numerically, revealing various signatures in diffraction patterns depending on the Miller indices and providing an identification method.
J. Appl. Cryst. (2015). 48, 645-654
Characterization of defects in mono-like silicon for photovoltaic applications using X-ray Bragg diffraction imaging
Rocking curve imaging (projection and section X-ray topography) has been used to study different kinds of defects such as precipitates, dislocations and twins in directionally solidified mono-like silicon ingots. The qualitative and quantitative information extracted from the reconstructed integrated intensity, FWHM and peak position maps provides clues about the initial stages of silicon growth.
J. Appl. Cryst. (2015). 48, 655-665
Characterization of dislocations in germanium layers grown on (011)- and (111)-oriented silicon by coplanar and noncoplanar X-ray diffraction
The generalization of the theoretical approach suggested by Kaganer et al. [Phys. Rev. B, (1997), 55, 1793–1810] to an arbitrary surface orientation, arbitrary dislocation line direction and noncoplanar measurement scheme was developed. It was applied to study the dislocation microstructure of Ge films on Si(011) and Si(111) based on a set of reciprocal space maps and profiles measured in noncoplanar geometry.
J. Appl. Cryst. (2015). 48, 666-671
Surface-treated self-standing curved crystals as high-efficiency elements for X- and γ-ray optics: theory and experiment
It is demonstrated that crystals with curved diffracting planes made of relatively light elements, such as silicon, germanium and gallium arsenide, in the Laue diffraction geometry and in an energy range between 60 and 600 keV can reach a higher diffraction efficiency than more dense mosaic crystals such as copper, silver and gold. In particular, self-standing curved crystals can be used as elements in γ-ray lenses.
J. Appl. Cryst. (2015). 48, 672-678
Inception and movement of a `subgrain boundary precursor' in ice under an applied stress, observed by X-ray synchrotron radiation Bragg imaging
Both optical microscopy with polarized light and polychromatic beam synchrotron X-ray diffraction imaging (white-beam topography) are used to study in situ the way an ice single-crystal deforms.
J. Appl. Cryst. (2015). 48, 679-689
A method for the simulation of the diffractometer instrumental function for high-resolution X-ray diffraction, applicable for coplanar and noncoplanar measurement geometry and for any combination of X-ray optical elements, is proposed. Good agreement is demonstrated between the measured and the simulated reciprocal-space maps, which account for the instrumental function.
J. Appl. Cryst. (2015). 48, 690-692
Monte Carlo simulation of the dose distribution in water around magnetite nanoparticles irradiated by monochromatic X-rays is presented.
J. Appl. Cryst. (2015). 48, 693-701
Monochromatic computed microtomography using laboratory and synchrotron sources and X-ray fluorescence analysis for comprehensive analysis of structural changes in bones
Structural changes in vertebrate bone tissues caused by bone growth or by weightlessness were studied using a combination of X-ray tomography at different wavelengths and X-ray fluorescence analysis.
J. Appl. Cryst. (2015). 48, 702-710
Quantitative evaluation of microtwins and antiphase defects in GaP/Si nanolayers for a III–V photonics platform on silicon using a laboratory X-ray diffraction setup
A laboratory X-ray diffraction setup is reported, which allows quantitative characterization of the microtwin and antiphase domain densities in epitaxial GaP/Si thin layers.
J. Appl. Cryst. (2015). 48, 711-717
In situ defect annealing of swift heavy ion irradiated CeO2 and ThO2 using synchrotron X-ray diffraction and a hydrothermal diamond anvil cell
A combination of a hydrothermal diamond anvil cell and synchrotron X-ray diffraction is utilized to perform in situ isochronal annealing and thermal expansion studies on swift heavy ion irradiated CeO2 and ThO2.
J. Appl. Cryst. (2015). 48, 718-727
A fast and fully automatic procedure for collecting electron diffraction tomography data suitable for structure solution is presented.
CCDC reference: 1052528
J. Appl. Cryst. (2015). 48, 728-735
Monolayer effect of a gemini surfactant with a rigid biphenyl spacer on its self-crystallization at the air/liquid interface
A gemini surfactant with a biphenyl spacer can spontaneously form a crystal with a lamellar character at the air/liquid interface.
CCDC reference: 1053701
J. Appl. Cryst. (2015). 48, 736-746
Appropriate zone-axis orientations for the determination of crystal polarity by convergent-beam electron diffraction
The appropriate zone-axis orientations for polarity determination via a single zone-axis convergent-beam electron diffraction (CBED) pattern are deduced for 19 of the 25 polar point groups. The validity of the CBED method is confirmed both by experiment and by calculation of CBED patterns.
J. Appl. Cryst. (2015). 48, 747-757
A look-up table based approach to characterize crystal twinning for synchrotron X-ray Laue microdiffraction scans
An automated method has been developed to characterize the type and spatial distribution of twinning in crystal orientation maps from synchrotron X-ray Laue microdiffraction results.
J. Appl. Cryst. (2015). 48, 758-762
Recrystallization can be an effective method for improving the quality of protein crystals. Experimental studies have verified that recrystallization not only enhanced the morphology of the crystals but also improved crystal quality. Therefore, it is proposed that recrystallization might be a useful alternative method for obtaining protein crystals with enhanced diffraction.
J. Appl. Cryst. (2015). 48, 763-768
X-ray powder diffraction has been used to evaluate the influence of sample preparation on the microstructure of dental hydroxyapatite. These results point out the most appropriate extraction technique for enamel specimens.
J. Appl. Cryst. (2015). 48, 769-775
Differential ultracentrifugation coupled to small-angle X-ray scattering on macromolecular complexes
A new method is described for collecting small-angle X-ray scattering data from samples while they are fractionated after differential ultracentrifugation. This may enable solution structural studies on a host of large macromolecular complexes for the first time.
J. Appl. Cryst. (2015). 48, 776-785
Rotation contour contrast reconstruction using electron backscatter diffraction in a scanning electron microscope
This paper presents the rotation contour contrast (RCC) in backscattered electron (BSE) micrographs of a deformed specimen. Using electron backscatter diffraction, a model was developed and validated to link the rotation of crystal planes to the channeling contrast in the channeling pattern and. consequently, RCC in the BSE micrograph.
J. Appl. Cryst. (2015). 48, 786-796
Element-specific structural studies of Si/B4C buried interfaces were carried out using resonant soft X-ray reflectivity. This approach enabled us to construct a quantitative interfacial map of the element-sensitive structural profile with a precision of a few atomic percent on the nanometre length scale.
J. Appl. Cryst. (2015). 48, 797-813
Error analysis of the crystal orientations and disorientations obtained by the classical electron backscatter diffraction technique
The fidelity of the crystal orientations and disorientations obtained by the classical two-dimensional Hough-transform-based EBSD method is investigated.
J. Appl. Cryst. (2015). 48, 814-826
X-ray diffraction line profile analysis of acid-resistant goethite in Western Australian nickel laterite ore
A bimodal size distribution of goethite crystals is estimated from their X-ray powder diffraction line profile. This enables monitoring of the acid-leaching performance for two distinct goethite size fractions.
J. Appl. Cryst. (2015). 48, 827-835
Kinetic model for calcium sulfate α-hemihydrate produced hydrothermally from gypsum formed by flue gas desulfurization
In order to interpret the transformation kinetics of gypsum, formed by flue gas desulfurization, to the hemihydrate in an isothermal batch crystallizer, nonlinear optimization was employed to solve a model based on horizontally translating the crystal size distribution during the transformation process.
J. Appl. Cryst. (2015). 48, 836-843
Influence of doping on crystal growth, structure and optical properties of nanocrystalline CaTiO3: a case study using small-angle neutron scattering
This article presents a detailed micro/mesoscopic structural analysis of doped calcium titanate nanoparticles using small-angle neutron scattering and X-ray diffraction techniques. The effects of doping on the optical properties are also investigated.
J. Appl. Cryst. (2015). 48, 844-852
Hydrogen-bonded supramolecular architecture in nonlinear optical ammonium 2,4-dinitrophenolate hydrate
A hydrogen-bonded supramolecular architecture, leading to superior nonlinear optical activity, is observed in ammonium 2,4-dinitrophenolate hydrate.
CCDC reference: 1012355
J. Appl. Cryst. (2015). 48, 853-856
X-ray diffraction method for determination of interplanar spacing and temperature distribution in crystals under an external temperature gradient
An X-ray diffraction method is developed for the determination of the distribution of temperature and interplanar spacing in a single-crystal plate.
J. Appl. Cryst. (2015). 48, 857-868
Considerations on the model-free shape retrieval of inorganic nanocrystals from small-angle scattering data
New methods for the quantitative evaluation of averaged dummy atom models resulting from small-angle X-ray scattering ab initio shape retrieval programs such as DAMMIN are presented. The techniques are validated for model systems with distinct shapes and size distributions, enabling the use of bead-modelling software for inorganic nanocrystals.
J. Appl. Cryst. (2015). 48, 869-875
Calculating millions of Gaussians three orders of magnitude faster than alternative methods should allow for the refinement of large structural models using the atomic pair distribution function. Central to the success of the method are very accurate representations of Gaussians and fast convolutions.
J. Appl. Cryst. (2015). 48, 876-881
A wide field of view X-ray microscope based on grazing incidence diffraction on bent perfect silicon wafers has been developed and tested.
J. Appl. Cryst. (2015). 48, 882-889
Quantitative grain-scale ferroic domain volume fractions and domain switching strains from three-dimensional X-ray diffraction data
An algorithm for the extraction of grain-by-grain domain volume fractions in polycrystalline ferroic materials using the three-dimensional X-ray diffraction method is presented. Here, the volume fraction information is used to calculate a grain-scale non-180° ferroelectric domain switching strain in two example electroceramic materials.
J. Appl. Cryst. (2015). 48, 890-900
The grain-refining mechanism of cast zinc through copper inoculation is described, and the hexagonal close packing orientation relationship in zinc–copper alloys is identified using electron backscatter diffraction, an Euler-based numerical method and the edge-to-edge crystallographic matching model.
teaching and education
J. Appl. Cryst. (2015). 48, 901-905
A teaching tool for X-ray crystallography using a one dimensional approach is presented.
J. Appl. Cryst. (2015). 48, 906-908
Fully ab initio crystal structure prediction of NiSi was carried out and a new high-pressure phase was discovered. This phase is a tetragonal distortion of the CsCl-type structure and it is stable in the pressure range 213–522 GPa.
J. Appl. Cryst. (2015). 48, 909-912
A simple Schiff base molecule was found to form different types of crystalline framework, which show potential selectivity for uptake of small guest molecules.
J. Appl. Cryst. (2015). 48, 913-916
Protein crystals have been subjected to a vacuum pressure of 10−5 mbar prior to flash-cooling, and data acquired at either 7 or 13 keV.
J. Appl. Cryst. (2015). 48, 917-926
GIXSGUI: a MATLAB toolbox for grazing-incidence X-ray scattering data visualization and reduction, and indexing of buried three-dimensional periodic nanostructured films
A MATLAB-based toolbox was developed to visualize and process grazing-incidence X-ray scattering data from surfaces and thin films. Three-dimensional nanostructures in thin films can also be indexed.
J. Appl. Cryst. (2015). 48, 927-932
SynchWeb significantly simplifies sample registration and is targeted towards live data collection monitoring and remote access for macromolecular crystallography.
J. Appl. Cryst. (2015). 48, 933-938
The new computer program DSR enables semi-automatic modelling of disordered or well ordered moieties in crystal structures via a placement procedure of molecular fragments and corresponding stereochemical restraints from a database.
J. Appl. Cryst. (2015). 48, 939-942
An online server has been created to compute the diffraction precision index and thereby estimate the atomic coordinate errors of non-covalent interactions in a given three-dimensional structure. The widespread false-precision representation of protein crystal structures could be considered an issue for the field of protein crystallography and the aim of this work is to try to ensure that this practice is eradicated.
J. Appl. Cryst. (2015). 48, 943-949
A code named AniCryDe to calculate the anisotropic elastic properties in a silicon or germanium crystal has been released. For the selected crystallographic orientation, AniCryDe calculates several key mechanical parameters. The program has a user-friendly interface that makes it readily operational and intuitive.
J. Appl. Cryst. (2015). 48, 950-952
X-ray Intermolecular Structure Factor (XISF): separation of intra- and intermolecular interactions from total X-ray scattering data
XISF is a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids.
J. Appl. Cryst. (2015). 48, 953-961
The SCT suite of tools for the atomistic modelling of X-ray and neutron scattering curves has resulted in 77 macromolecular structures to date. SCT is now made publicly available as open source, alongside an easier-to-use reimplementation of the same algorithms in Python.
J. Appl. Cryst. (2015). 48, 962-969
A user-friendly open-source Monte Carlo regression package (McSAS) is presented, which aids in the analysis of scattering patterns from uncorrelated, shape-similar scatterers. The Monte Carlo nature necessitates an assumption on the elementary shape of the scatterer, but can resolve the shape-defining parameter distributions without restrictions on the mathematical form of the distribution.
J. Appl. Cryst. (2015). 48, 970-974
Combining high time and angular resolutions: time-resolved X-ray powder diffraction using a multi-channel analyser detector
The new stroboscopic MAD-STROBO data acquisition system was developed to measure profiles of high-resolution X-ray powder diffraction under a dynamically applied electric field. The possibility of detecting sub-millidegree shifts of Bragg reflections with a microsecond time resolution is demonstrated.
addenda and errata
J. Appl. Cryst. (2015). 48, 975
Calculation of scattering patterns from phase-shifting objects using the Radon transform. Corrigendum
The affiliations for the authors of J. Appl. Cryst. (2011), 44, 1157–1163 are corrected.
J. Appl. Cryst. (2015). 48, 976