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Journal logoJOURNAL OF
APPLIED
CRYSTALLOGRAPHY
ISSN: 1600-5767

February 2016 issue

Highlighted illustration

Cover illustration: Representation of the D3 point group symmetry using two planar C3 systems, illustrating the approach taken in the protein symmetry assembly algorithm SAM. Courtesy of Ritchie & Grudinin [J. Appl. Cryst. (2016), 49, 158-167].

research papers


J. Appl. Cryst. (2016). 49, 1-14
doi: 10.1107/S1600576715021792
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This article provides a detailed technical description of the D33 small-angle neutron scattering instrument at the ILL and serves as a technical reference for users of the instrument.

J. Appl. Cryst. (2016). 49, 15-23
doi: 10.1107/S1600576715021469
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Absolute intensity calibration of a laboratory-based small-angle X-ray scattering camera equipped with an imaging plate (IP) detector is performed by means of various silica sols, serving as secondary standards. The good performance of the IP detector provides reliable data in absolute units. To test the IP detector Stöber silica nanoparticles were analyzed. The volume fractions and particle number densities show a good agreement with theoretical values predicted for the Stöber reaction.

J. Appl. Cryst. (2016). 49, 24-30
doi: 10.1107/S1600576715021378
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The geometry of graphene layers in two commercial carbon blacks has been established from powder diffraction data using refinement based on the Debye equation. The ordered regions within the layers are curved and essentially non-circular.

J. Appl. Cryst. (2016). 49, 31-39
doi: 10.1107/S1600576715022566
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Two composition-driven phase transitions are observed in the series La2−xSrxCoTiO6 (0.0 ≤ x ≤ 1.0), which can be discussed on the basis of the internal pressure associated with Sr doping using the symmetry-adapted modes formalism.

J. Appl. Cryst. (2016). 49, 40-46
doi: 10.1107/S160057671502169X
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The crystal symmetries of the parallel elements were analyzed to indicate the ambiguities in similar {hkl}/〈uvw〉 expressions of orientation relationships.

J. Appl. Cryst. (2016). 49, 47-54
doi: 10.1107/S1600576715023444
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A new, numerically efficient method has been developed to account for instrumental resolution effects on isotropic small-angle X-ray scattering with pinhole collimation.

J. Appl. Cryst. (2016). 49, 55-63
doi: 10.1107/S1600576715021573
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The spin echo modulated small-angle neutron scattering technique has been implemented using two superconducting magnetic Wollaston prisms at a reactor neutron source and used to measure the spatial correlation function of colloidal silica particles in a suspension. Monte Carlo simulation is used to understand and further improve the performance.

J. Appl. Cryst. (2016). 49, 64-68
doi: 10.1107/S1600576715022062
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A tentative phase diagram for the pseudo-binary system Nd2Fe14B–Sm2Fe14B has been constructed and no metastable phases were detected. The normalized lattice parameters and unit-cell volumes of (Nd1−xSmx)2Fe14B solid solutions decrease almost linearly with increasing Sm content.

J. Appl. Cryst. (2016). 49, 69-77
doi: 10.1107/S1600576715022608
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The article discusses misfit-induced lattice-parameter changes in two-phase systems as exposed by coherent diffraction of the assembly or incoherent diffraction by the matrix and the second-phase particles.

J. Appl. Cryst. (2016). 49, 78-84
doi: 10.1107/S160057671502261X
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This work presents the thermal evolution of the crystal structure at high temperature of Sr11Mo4O23, studied in situ by neutron powder diffraction. The crystallographic features reported here provide an interesting explanation of the increase in the ionic conductivity.

J. Appl. Cryst. (2016). 49, 85-102
doi: 10.1107/S1600576715021810
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The development of multireflection grazing-incidence X-ray diffraction to enable the determination not only of stress but also of the c/a ratio and the a0 strain-free lattice parameter in hexagonal polycrystalline materials is presented and tested.

J. Appl. Cryst. (2016). 49, 103-109
doi: 10.1107/S1600576715022633
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High-energy X-ray diffraction tomography and Rietveld refinement were used to reconstruct the quantitative differences between hydroxyapatite powders in a bone phantom.

J. Appl. Cryst. (2016). 49, 110-119
doi: 10.1107/S1600576715022621
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A cooling system compatible with in-vacuum operation is reported. The temperature has been calibrated by comparison of the unit-cell and thermal displacement parameters of copper. Furthermore, the high-quality diffraction data of copper allowed a detailed modelling of the electron density and the anharmonic atomic displacement.

J. Appl. Cryst. (2016). 49, 120-127
doi: 10.1107/S1600576715022943
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SENJU, a time-of-flight Laue-type single-crystal neutron diffractometer, was developed at the Materials and Life Science Experimental Facility of the Japan Accelerator Research Complex (J-PARC). Molecular structure analysis of a sub-millimetre taurine crystal and magnetic structure analysis of an MnF2 crystal were performed to evaluate its performance.

J. Appl. Cryst. (2016). 49, 128-138
doi: 10.1107/S1600576715022797
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A multi-tube area detector, composed of 96 position-sensitive detector tubes, has been recently developed for the small-angle neutron scattering spectrometer SANS-J-II at the research reactor JRR-3, Tokai, Japan. A data acquisition system identical to the J-PARC time-of-flight spectrometer (event data mode) has been deployed.

J. Appl. Cryst. (2016). 49, 139-148
doi: 10.1107/S1600576715021731
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The effect of a strong magnetic field on the morphology and orientation of the Al2Cu dendrite and Al–Al2Cu eutectic in Al–Cu alloys was studied using electron backscatter diffraction (EBSD) technology. The applied magnetic field modified the morphology and orientation of both the Al2Cu dendrite and the Al–Al2Cu eutectic significantly.

J. Appl. Cryst. (2016). 49, 149-157
doi: 10.1107/S1600576715023195
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High-pressure cryocooling using a pressure above 300 MPa can reduce disorder such as nonmerohedral twinning and high mosaicity in protein crystals.

J. Appl. Cryst. (2016). 49, 158-167
doi: 10.1107/S1600576715022931
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A method is described for the fast Fourier transform-based assembly of protein complexes having any of the naturally occurring point group symmetry types.

J. Appl. Cryst. (2016). 49, 168-174
doi: 10.1107/S1600576715023845
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Morphology-controlled BiFeO3 aggregates composed of oriented building units were prepared by a simple one-pot hydrothermal synthesis without any additives. The shape of the building units, the size distribution of the aggregates and the internal structure of the aggregates were controlled by the supersaturation condition of the precursor solution, and the formation mechanism of the aggregates is discussed on the basis of these structure analyses.

J. Appl. Cryst. (2016). 49, 175-181
doi: 10.1107/S1600576715022906
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Thanks to cross analysis using three techniques of characterization, linear relationships are found between the oxygen content, the microhardness and the α-phase lattice parameters in a titanium alloy resistant to creep

J. Appl. Cryst. (2016). 49, 182-187
doi: 10.1107/S1600576715023419
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X-ray nanodiffraction is used to evaluate axial and tangential residual stress distributions in a W thin film deposited on the scalloped inner wall of a through-silicon via. The results reveal oscillatory stress distributions which correlate well with the scallop wavelength and morphology.

J. Appl. Cryst. (2016). 49, 188-194
doi: 10.1107/S1600576715023924
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This article provides a description and validation of a detailed Monte Carlo X-ray transport simulation technique that utilizes user-provided cross sections to describe X-ray interaction in virtual samples and to explore small-angle X-ray scattering instrument design choices for in vivo molecular imaging applications.

J. Appl. Cryst. (2016). 49, 195-202
doi: 10.1107/S1600576715023353
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Novel neutron imaging techniques utilize diffraction, phase and magnetic contrasts for materials characterization. The recently upgraded instrument for neutron imaging at the Helmholtz-Zentrum Berlin (CONRAD-2) presents the full suite of innovative techniques in combination with outstanding spatial resolution.

J. Appl. Cryst. (2016). 49, 203-212
doi: 10.1107/S1600576715024462
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Low-latency small-angle X-ray scattering (SAXS) data reduction for bioSAXS and real-time feedback to the users is implemented.

J. Appl. Cryst. (2016). 49, 213-221
doi: 10.1107/S1600576715023663
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A phase transition of nanostructured SnSe at high pressure is reported. The transition occurs from a higher to a lower orthorhombic symmetry structure.

J. Appl. Cryst. (2016). 49, 222-233
doi: 10.1107/S1600576715023997
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A pnCCD detector is applied for energy-dispersive Laue diffraction on GaAs with white synchrotron radiation in the energy range between 40 and 140 keV. Despite the low quantum efficiency of the pnCCD in this energy range the unit-cell parameters and kinematical structure factors of GaAs are extracted from the three-dimensional data volume with an adequate accuracy.

J. Appl. Cryst. (2016). 49, 234-240
doi: 10.1107/S160057671502419X
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Protein crystals exhibit temperature-dependent autofluorescence when excited with visible light. The intensity of visible-light-excited autofluorescence is tenfold higher at cryogenic temperatures owing to temperature-dependent chromophore stabilization.

J. Appl. Cryst. (2016). 49, 241-249
doi: 10.1107/S160057671600128X
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An improvement in X-ray stress measurement using Debye–Scherrer rings is proposed. Even if the specimen is coarse grained, in-plane averaging can improve the accuracy of the measurement.

J. Appl. Cryst. (2016). 49, 250-259
doi: 10.1107/S1600576715024620
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The origin of asterism in X-ray diffraction images of cracks in silicon is shown to be associated with tilted material just prior to breakout. Cracks around indentations reflect the indenter tip geometry, not the specimen crystallography, and surface-breaking Palmqvist cracks are found to be directly connected to the median sub-surface cracks, the presence of extensive lateral cracks being a prerequisite for material breakout.

J. Appl. Cryst. (2016). 49, 260-276
doi: 10.1107/S160057671502258X
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The scattering intensities of thread-like and film-like systems, respectively, behave as {\cal P}_{{\cal C}}/q and {\cal P}_{{\cal S}}/q^2 in an intermediate range of the scattering vector magnitude q. The {\cal P}_{{\cal C}} and {\cal P}_{{\cal S}} expressions are reported.

CIF applications


J. Appl. Cryst. (2016). 49, 277-284
doi: 10.1107/S1600576715021871

J. Appl. Cryst. (2016). 49, 285-291
doi: 10.1107/S1600576715021883
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A C-language application programming interface and implementation are described that enable software developers to readily incorporate CIF 2.0 (and earlier) support into their applications.

J. Appl. Cryst. (2016). 49, 292-301
doi: 10.1107/S1600576715022396
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A syntax-correcting CIF parser, COD::CIF::Parser, is described that can parse CIF 1.1 files and accurately report the position and nature of the discovered syntactic problems while automatically correcting the most common and the most obvious syntactic deficiencies.

J. Appl. Cryst. (2016). 49, 302-310
doi: 10.1107/S1600576715024942
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An extension of the sasCIF format is intended for representation, storage and exchange of SAS data and SAS-based models. Open-source sasCIFtools are developed for convenient data conversion, and for deposition into and retrieval from databases and data-processing pipelines.

computer programs


J. Appl. Cryst. (2016). 49, 311-316
doi: 10.1107/S1600576715021019
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RaDMaX is a program that allows the retrieval of strain and damage profiles in ion-irradiated materials from the simulation of X-ray diffraction data recorded in symmetric θ–2θ geometry. It can be downloaded from http://aboulle.github.io/RaDMaX.

J. Appl. Cryst. (2016). 49, 317-321
doi: 10.1107/S1600576715024814
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A new version of the CHARDI software to compute the effective coordination number and charge distribution in non-molecular structures is presented, now with a CIF parser and graphical user interface.

J. Appl. Cryst. (2016). 49, 322-329
doi: 10.1107/S1600576715024656
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New software and some algorithms for analysis of digitally stored Kossel diffraction patterns are described. The program is designed to facilitate the refinement of lattice parameters and determination of lattice strains.

J. Appl. Cryst. (2016). 49, 330-339
doi: 10.1107/S1600576716000108
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The free software application Aurore, allowing comprehensive analysis of neutron reflectometry data and especially designed for thin bio-films, is described.

laboratory notes


J. Appl. Cryst. (2016). 49, 340-345
doi: 10.1107/S1600576715022165
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A novel integrated high-throughput sample holder for in situ X-ray powder diffraction of coin cell batteries was developed and successfully tested for precision and reliability with a silicon standard and spinel-based positive electrode materials for Li-ion batteries.

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