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Journal logoJOURNAL OF
ISSN: 1600-5767

June 2016 issue

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Cover illustration: A schematic of the experimental setup used to map the lattice bending produced by thermal strain relaxation in heteroepitaxial Ge microcrystals grown on high aspect ratio Si pillars. Courtesy of M. Meduna et al. [J. Appl. Cryst. (2016), 49, 976-986].

research papers

J. Appl. Cryst. (2016). 49, 722-735
doi: 10.1107/S1600576716003873
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This work focuses on the comparison of Mo Kα1 and Cu Kα1 radiations for the Rietveld quantitative phase analysis of challenging crystalline mixtures including amorphous content determination. The quantifications have been carried out by using calibration curves with increasing amounts of a given phase. Mo Kα1 patterns were found to yield slightly more accurate analyses than those derived from Cu Kα1 radiation.

J. Appl. Cryst. (2016). 49, 736-742
doi: 10.1107/S1600576716003940
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This article demonstrates how neutron imaging can be performed using a conventional small-angle neutron scattering instrument.

J. Appl. Cryst. (2016). 49, 743-755
doi: 10.1107/S1600576716004350
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The unique possibilities enabled by neutron imaging for in situ remote diagnostics of microstructural characteristics during crystal growth are demonstrated, even when the materials and surrounding structures are opaque to other more conventional interrogation techniques. Neutron radiography is implemented to image remotely the uniformity of elemental distribution (e.g. dopant concentration) during crystal growth, the location of the liquid/solid interface and the presence of macroscopic crystal defects (e.g. cracks), all with a temporal resolution of 5–7 s.

J. Appl. Cryst. (2016). 49, 756-761
doi: 10.1107/S1600576716004039
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A convenient data structure for the nearest-neighbor problem is discussed.

J. Appl. Cryst. (2016). 49, 762-770
doi: 10.1107/S1600576716003800
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This work suggests a method for quantifying inhomogeneity of crystal structure at the nanoscale using high-resolution transmission electron microscopy. The method can measure the lattice parameters with picometric accuracy and a spatial resolution of a few to tens of nanometres without requiring aberration correction or posing any strict requirements on the sample.

J. Appl. Cryst. (2016). 49, 771-783
doi: 10.1107/S1600576716003885
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The structure of nanocrystalline calcium silicates hydrates (C–S–H) having Ca/Si ratios ranging between 0.57 ± 0.05 and 1.47 ± 0.04 was studied. All samples are nanocrystalline and defective tobermorite. An increase of the Ca/Si ratio resulting from omission of bridging Si in the Si chains and incorporation of interlayer Ca was observed.

J. Appl. Cryst. (2016). 49, 784-797
doi: 10.1107/S1600576716003757
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A theoretical formulation for the diffraction from nonuniformly strained helical molecular assemblies is presented. The predictions of this theory are discussed in the context of double-stranded DNA and actin filaments in the presence and absence of nonuniform strains.

J. Appl. Cryst. (2016). 49, 798-805
doi: 10.1107/S1600576716004441
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A general high-accuracy method for detecting and distinguishing elastic and plastic relaxation in epitaxial layers grown on patterned substrates is applied to a Group III–nitride system. The method is based on X-ray multiple diffraction.

J. Appl. Cryst. (2016). 49, 806-813
doi: 10.1107/S1600576716004635
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An apparatus for the optimization of crystal growth using precise temperature control and dialysis combined with real-time visualization has been developed.

J. Appl. Cryst. (2016). 49, 814-822
doi: 10.1107/S1600576716004209
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This paper reports extensive testing of the Bayesian procedure for correction of systematic errors in Rietveld refinements. This testing has been performed using data collected for one sample using four X-ray and neutron diffractometers.

J. Appl. Cryst. (2016). 49, 823-834
doi: 10.1107/S1600576716004453
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This study presents a series of grazing-incidence small-angle X-ray scattering experiments on polymer line gratings, together with a quantitative analysis and comparison with the real-space structure probed by atomic force microscopy. The results provide a detailed characterization of the average profile and estimates of line-edge roughness.

J. Appl. Cryst. (2016). 49, 835-844
doi: 10.1107/S1600576716004568
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Two-dimensional small-angle X-ray scattering measurements were performed on highly oriented pyrolytic graphite. The observed radial streak patterns are discussed in the context of double Bragg scattering.

J. Appl. Cryst. (2016). 49, 845-855
doi: 10.1107/S1600576716005331
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The nanostructure of 180° ferroelectric stripe domains is analysed by diffuse X-ray scattering. The domain period, period disorder, polarization-induced strain and wall roughness are quantitatively determined.

J. Appl. Cryst. (2016). 49, 856-865
doi: 10.1107/S1600576716004969
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The density distribution is estimated from small-angle scattering data from symmetrical objects without using the distance distribution function as an explicit intermediate.

J. Appl. Cryst. (2016). 49, 866-872
doi: 10.1107/S1600576716004957
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A detailed structural investigation of (Na0.5Bi0.5TiO3)(1−x)(BaZrO3)x (x = 0.00, 0.01, 0.03, 0.05 and 0.07) was carried out as a function of composition using Rietveld analysis of powder X-ray diffraction data.

J. Appl. Cryst. (2016). 49, 873-879
doi: 10.1107/S1600576716005355
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Buried seeding is developed to strengthen the thermal stability of YBa2Cu3O7−δ (YBCO) films, leading to an enhancement of endurable maximum processing temperature of over 30 K in low supersaturation. Furthermore, the buried-seeding mode was successfully applied in growing single crystals of other REBCO (RE = Nd, Sm, Gd) oxides.

J. Appl. Cryst. (2016). 49, 880-890
doi: 10.1107/S1600576716005136
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A method for analyzing radiation damage experiments in biological small-angle X-ray scattering is presented. This method allows direct comparison between results obtained at different beamlines and by different experimenters.

J. Appl. Cryst. (2016). 49, 891-901
doi: 10.1107/S1600576716005197
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A low- to high-temperature neutron diffraction study of some (KxNa1−x)NbO3-based ceramics has been carried out. The structure of these ceramic compositions has been determined using Rietveld refinement.

J. Appl. Cryst. (2016). 49, 902-908
doi: 10.1107/S1600576716005574
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By the combination of small-angle X-ray scattering with tomographic techniques, the spatially varying preferred orientation of micrometre-sized talc particles embedded in injection-moulded isotactic polypropylene has been retrieved nondestructively.

J. Appl. Cryst. (2016). 49, 909-917
doi: 10.1107/S1600576716005483
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On the basis of the film structure of a Pt/AlN multilayer film which exhibits a superlattice peak after annealing, a disc-shaped nanocrystal model is proposed for simulating the diffraction profile from a one-dimensional superlattice, and the effects of the in-plane crystal size and the orientation distribution on the profile are discussed.

J. Appl. Cryst. (2016). 49, 918-922
doi: 10.1107/S1600576716006282
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In spite of the low absolute values of the resonant contribution at high energy, accurate measurements of the Bragg intensities up to high Q values are capable of providing data sufficient for absolute structure determination.

J. Appl. Cryst. (2016). 49, 923-933
doi: 10.1107/S1600576716005744
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The nuclear fuel candidate U–8 wt%Mo has been investigated by means of neutron and hard X-ray diffraction, revealing the isothermal transformation kinetics of the high-temperature γ-UMo phase into its thermal equilibrium microstructures.

J. Appl. Cryst. (2016). 49, 934-943
doi: 10.1107/S1600576716005586
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A method is given for converting slit-smeared azimuthally asymmetric data collected on a double-crystal diffractometer for concatenation with the usual pinhole-geometry small-angle neuton scattering data.

J. Appl. Cryst. (2016). 49, 944-952
doi: 10.1107/S1600576716006233
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This article reports the incorporation of a fast continuous grid scan with both still and oscillation images into the Swiss Light Source macromolecular crystallography beamlines and its application in visualization of protein crystals with scanning transmission X-ray microscopy.

J. Appl. Cryst. (2016). 49, 953-960
doi: 10.1107/S1600576716005793
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A method utilizing a spherical harmonics representation of the scattering amplitudes for a rapid superposition of three-dimensional models is developed.

J. Appl. Cryst. (2016). 49, 961-967
doi: 10.1107/S1600576716006385
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A solution for X-ray experiments in an asymmetric skew geometry with a constant angle of incidence is described. It enables mapping of the three-dimensional reciprocal space of a sample by a single motor scan.

J. Appl. Cryst. (2016). 49, 968-975
doi: 10.1107/S1600576716006348
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A micro-patterned sample holder of single-crystalline silicon, loaded with multiple protein crystals which are exposed to a humidified gas stream, allows high-quality room-temperature data collection.

J. Appl. Cryst. (2016). 49, 976-986
doi: 10.1107/S1600576716006397
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The scanning X-ray nanodiffraction technique is used to map the lattice bending in heteroepitaxial Ge microcrystals grown on high aspect ratio Si pillars produced by thermal strain relaxation. The simulated three-dimensional reciprocal space maps based on finite element calculations are in a good agreement with the measured ones.

J. Appl. Cryst. (2016). 49, 987-996
doi: 10.1107/S1600576716006713
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The plastic deformation modes and stress/strain partitioning between parent and child grains resulting from different types of twinning are discussed. Insight into the effect of deformation twinning on the plastic deformation behavior of Zr-4 alloy is provided.

J. Appl. Cryst. (2016). 49, 997-1008
doi: 10.1107/S1600576716006415
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A combination of neutron and X-ray diffraction together with pair distribution function and EXAFS analysis is shown to solve the crystal structure for the highly disordered proton and electron conductor La5.6WO12−δ on average and local length scales.

J. Appl. Cryst. (2016). 49, 1009-1015
doi: 10.1107/S160057671600710X
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The crystallographic origin of ultralow superelastic fatigue in NiTi-based shape memory alloys is explored. Ti-rich precipitates are coupled to austenite and martensite, and serve as epitaxial seeds during the repeated phase transformations.

J. Appl. Cryst. (2016). 49, 1016-1020
doi: 10.1107/S1600576716007147
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The X-ray diffuse scattering pattern of SrTiO3 has been measured and simulated. It is shown that the structural model based on the displacement of the Sr2+ and Ti4+ cations is ambiguous, whereas the method of multi-energy anomalous diffuse scattering yields an unambiguous solution.

J. Appl. Cryst. (2016). 49, 1021-1028
doi: 10.1107/S1600576716005471
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In serial crystallography, CC1/2 may be used as an optimization target, and outlier datasets can be identified on the basis of their influence on the average CC1/2 of the merged data. This leads to the ΔCC1/2 method presented here.

J. Appl. Cryst. (2016). 49, 1029-1034
doi: 10.1107/S1600576716007196
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A procedure is presented to model the truncated low pixel counts in micro-electron diffraction (MicroED) images. The correction could extend to any conventional macromolecular X-ray crystallography or X-ray free-electron laser measurements.

computer programs

J. Appl. Cryst. (2016). 49, 1035-1041
doi: 10.1107/S1600576716005720
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A data processing pipeline for SACLA was developed, based on Cheetah and CrystFEL. Real-time analysis and rapid structure solution were enabled.

J. Appl. Cryst. (2016). 49, 1042-1047
doi: 10.1107/S1600576716005926
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Hummingbird is an open-source scalable Python-based software tool for real-time analysis of diffraction data with the purpose of giving users immediate feedback during their experiments.

J. Appl. Cryst. (2016). 49, 1048-1056
doi: 10.1107/S1600576716006014

J. Appl. Cryst. (2016). 49, 1057-1064
doi: 10.1107/S1600576716006683
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An integration optimization, triage and analysis tool (IOTA) is presented, which uses a grid-search approach to maximize the success of indexing and integrating serial X-ray free-electron laser diffraction images. IOTA also includes several useful tools for on-site diffraction data processing.

J. Appl. Cryst. (2016). 49, 1065-1072
doi: 10.1107/S1600576716006981
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Here cppxfel, a software package for integration and post-refinement of serial femtosecond crystallography data, is released.

J. Appl. Cryst. (2016). 49, 1073-1080
doi: 10.1107/S1600576716007469
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This article describes the software package OnDA: online data analysis and feedback for serial X-ray imaging.

J. Appl. Cryst. (2016). 49, 1081-1084
doi: 10.1107/S1600576716004428
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DCC is a wrapper for third-party software packages to aid in structure factor analysis and validation. As the results are recorded in PDBx/mmCIF format, the output from DCC can be used in automatic data pipelines.

J. Appl. Cryst. (2016). 49, 1085-1092
doi: 10.1107/S1600576716004416
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A new version of XDSAPP, an expert system and graphical user interface for the automated processing of diffraction images using XDS, is presented.

J. Appl. Cryst. (2016). 49, 1093-1098
doi: 10.1107/S1600576716006208
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This article describes an online database on the interactions of nucleobase compounds in macromolecular structures.

J. Appl. Cryst. (2016). 49, 1099-1106
doi: 10.1107/S1600576716006075
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This article introduces a free and open-source program, PTCLab, for calculating phase transformation crystallography.

J. Appl. Cryst. (2016). 49, 1107-1114
doi: 10.1107/S1600576716006932
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The program SUNBIM, here presented, is a novel suite of programs designed for scientists who make use of small- and wide-angle X-ray scattering (SAXS/WAXS) and grazing-incidence SAXS/WAXS (GISAXS/GIWAXS) techniques for the structural characterization of artificial or natural materials. It consists of four sections: (1) Calibration; (2) Batch Script & 2D Mesh Composite; (3) multi-scan SAXS and WAXS data analysis (M-SAWANA); (4) single-scan SAXS and WAXS data analysis (S-SAWANA).

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