[Dual Source RAPID II]

[ISBC Granada 2013]

Journal of Applied Crystallography

Volume 46, Part 2 (April 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Structures of polycrystals and of a Schizosaccharomyces pombe spore at different length scales. Courtesy of Reischig et al. [J. Appl. Cryst. (2013), 46, 297-311], Larson & Levine [J. Appl. Cryst. (2013), 46, 153-164] and Rodriguez et al. [J. Appl. Cryst. (2013), 46, 312-318].

editorial


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J. Appl. Cryst. (2013). 46, 295-296  [ doi:10.1107/S0021889813004160 ]

X-ray diffraction microscopy: emerging imaging techniques for nondestructive analysis of crystalline materials from the millimetre down to the nanometre scale

A. Borbély and A. R. Kaysser-Pyzalla

Synopsis: In anticipation of the International Year of Crystallography in 2014, Journal of Applied Crystallography presents a virtual issue on recent developments in X-ray diffraction microscopy. This issue is available at http://journals.iucr.org/special_issues/2013/imaging/.

Online 14 March 2013


research papers


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J. Appl. Cryst. (2013). 46, 297-311  [ doi:10.1107/S0021889813002604 ]

Advances in X-ray diffraction contrast tomography: flexibility in the setup geometry and application to multiphase materials

P. Reischig, A. King, L. Nervo, N. Viganó, Y. Guilhem, W. J. Palenstijn, K. J. Batenburg, M. Preuss and W. Ludwig

Synopsis: Recent developments in the use of the diffraction contrast tomography method to create three-dimensional grain maps of polycrystalline samples are described. These include the use of detectors in arbitrary positions, including high Bragg angles, and the application to multiphase materials.

Online 14 March 2013


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J. Appl. Cryst. (2013). 46, 312-318  [ doi:10.1107/S0021889813002471 ]

Oversampling smoothness: an effective algorithm for phase retrieval of noisy diffraction intensities

J. A. Rodriguez, R. Xu, C.-C. Chen, Y. Zou and J. Miao

Synopsis: An iterative phase retrieval algorithm, termed oversampling smoothness (OSS), has been developed to reconstruct fine features in weakly scattered objects such as biological specimens from noisy experimental data. OSS is expected to find application in the rapidly growing coherent diffraction imaging field as well as other disciplines where phase retrieval from noisy Fourier magnitudes is needed.

Online 23 February 2013


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J. Appl. Cryst. (2013). 46, 319-323  [ doi:10.1107/S0021889813003117 ]

Upsampling speckle patterns for coherent X-ray diffraction imaging

Y. Chushkin and F. Zontone

Synopsis: A new experimental method for sub-pixel resolution of speckle patterns is presented. It allows upsampling of undersampled diffraction patterns necessary for subsequent real-image reconstruction with an iterative phase-retrieval algorithm.

Online 14 March 2013


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J. Appl. Cryst. (2013). 46, 324-331  [ doi:10.1107/S0021889813000666 ]

Evaluating the polymorphic phase transition in calcium-doped Ba(Zr0.05Ti0.95)O3: a lead-free piezoelectric ceramic

G. Singh, V. S. Tiwari and P. K. Gupta

Synopsis: Structural and dielectric investigations were carried out on a perovskite lead-free (Ba1-xCax)(Zr0.05Ti0.95)O3 ferroelectric ceramic for x = 0.03, 0.05, 0.08, 0.10, 0.12 and 0.15.

Online 23 February 2013


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J. Appl. Cryst. (2013). 46, 332-336  [ doi:10.1107/S0021889812050595 ]

Quantifying amorphous and crystalline phase content with the atomic pair distribution function

J. Peterson, J. TenCate, Th. Proffen, T. Darling, H. Nakotte and K. Page

Synopsis: The application of the atomic pair distribution function for the purpose of obtaining the crystalline and amorphous phase fractions of samples with unknown phase ratios is demonstrated. The resolution of the method is established with a set of standards and recommended best practices are discussed.

Online 14 February 2013


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J. Appl. Cryst. (2013). 46, 337-345  [ doi:10.1107/S0021889812051606 ]

Liesegang-like patterns of Toll crystals grown in gel

M. Gangloff, A. Moreno and N. J. Gay

Synopsis: The observation of a repetitive pattern obtained for protein crystals formed by reaction-diffusion in capillary tubes is reported for the first time.

Online 14 February 2013


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J. Appl. Cryst. (2013). 46, 346-353  [ doi:10.1107/S0021889812050935 ]

Generation and applications of structure envelopes for porous metal-organic frameworks

A. A. Yakovenko, J. H. Reibenspies, N. Bhuvanesh and H.-C. Zhou

Synopsis: A new metal-organic framework-specific method for structure envelope construction is proposed. Structure solution from powder X-ray diffraction data of metal-organic frameworks has been demonstrated on activated and as-synthesized samples of HKUST-1 and an activated sample of PCN-200.

Online 14 February 2013


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J. Appl. Cryst. (2013). 46, 354-364  [ doi:10.1107/S0021889812050029 ]

DCD USANS and SESANS: a comparison of two neutron scattering techniques applicable for the study of large-scale structures

C. Rehm, J. Barker, W. G. Bouwman and R. Pynn

Synopsis: The capabilities of two techniques for extending the range of conventional small-angle neutron scattering (SANS) towards the micrometre length scale are compared, namely double-crystal diffraction ultra-small-angle neutron scattering (DCD USANS) and spin-echo SANS (SESANS).

Online 14 February 2013


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J. Appl. Cryst. (2013). 46, 365-371  [ doi:10.1107/S0021889813001295 ]

Improvements and considerations for size distribution retrieval from small-angle scattering data by Monte Carlo methods

B. R. Pauw, J. S. Pedersen, S. Tardif, M. Takata and B. B. Iversen

Synopsis: A method is presented and applied, capable of retrieving form-free particle size distributions complete with uncertainties from small-angle scattering patterns. Special attention is paid to particle observability in the scattering patterns, accurate estimation of data uncertainty and the effect of uncertainty on the resulting size distribution statistics.

Online 14 February 2013


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J. Appl. Cryst. (2013). 46, 372-378  [ doi:10.1107/S002188981205131X ]

Effect of the solute-solvent interface on small-angle neutron scattering from organic solutions of short alkyl chain molecules as revealed by molecular dynamics simulation

R. A. Eremin, K. Kholmurodov, V. I. Petrenko, L. Rosta and M. V. Avdeev

Synopsis: The method of classical molecular dynamics simulation is used for modeling the experimental small-angle neutron scattering from saturated monocarboxylic acids with short chain lengths in deuterated decalin solutions. It is shown that a specific organization of the solvent molecules in the solute-solvent interface area has a significant effect on the scattering.

Online 14 February 2013


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J. Appl. Cryst. (2013). 46, 379-386  [ doi:10.1107/S0021889812051175 ]

An enhancement in structural and superconducting properties of Bi2212 epitaxial thin films grown by the Pechini sol-gel method

X. Lu, T. Wang, Y. Zhang, M. B. Shahzad and Y. Qi

Synopsis: Bi2Sr2CaCu2O8+[delta] (Bi2212) thin films with excellent superconducting properties were prepared by the Pechini sol-gel method using nitrates as reactants.

Online 14 February 2013


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J. Appl. Cryst. (2013). 46, 387-390  [ doi:10.1107/S0021889812051886 ]

Indexing of multi-particle diffraction data in a high-pressure single-crystal diffraction experiment

H. Li, X. Li, M. He, Y. Li, J. Liu, G. Shen and Z. Zhang

Synopsis: A method has been proposed for the indexing of multi-particle diffraction data, in which the techniques of powder pattern indexing and genetic algorithms are applied in sequence to determine the orientation matrix.

Online 23 February 2013


 

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J. Appl. Cryst. (2013). 46, 391-395  [ doi:10.1107/S0021889812051928 ]

Dependence of the strain diffraction line broadening on (hkl) and sample direction in textured polycrystals

N. C. Popa and G. A. Lungu

Synopsis: A model describing the dependence of the strain diffraction line breadth on direction in both crystal and sample is derived. The model is appropriate for implementation in Rietveld programs.

Online 23 February 2013


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J. Appl. Cryst. (2013). 46, 396-403  [ doi:10.1107/S0021889812051333 ]

Superposition twinning supported by texture in ZnO nanospikes

V. Hrkac, L. Kienle, S. Kaps, A. Lotnyk, Y. K. Mishra, U. Schürmann, V. Duppel, B. V. Lotsch and R. Adelung

Synopsis: The morphology and real structure of wurtzite-type ZnO nanospikes grown by the recently introduced flame transport synthesis have been examined by means of advanced transmission electron microscopy. The observed nanospikes show a complicated superposition of twinned domains as an intrinsic real structural feature.

Online 23 February 2013


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J. Appl. Cryst. (2013). 46, 404-414  [ doi:10.1107/S002188981300109X ]

Bayesian reconstruction of P(r) directly from two-dimensional detector images via a Markov chain Monte Carlo method

S. Paul, A. M. Friedman, C. Bailey-Kellogg and B. A. Craig

Synopsis: A new method for reconstruction of the interatomic distance distribution, P(r), directly from two-dimensional detector images of solution scattering data is developed and tested. This method employs Bayesian inference and a Markov chain Monte Carlo method to simultaneously estimate indirect transform coefficients and beam and detector parameters, while also evaluating the covariance among all parameters.

Online 5 March 2013


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J. Appl. Cryst. (2013). 46, 415-420  [ doi:10.1107/S0021889813000162 ]

Calculation of diffraction efficiency for curved crystals with arbitrary curvature radius

V. Bellucci, V. Guidi, R. Camattari and I. Neri

Synopsis: A model is proposed to calculate the diffraction efficiency of X-rays in Laue geometry for curved crystals with an arbitrary value of the curvature radius. The model generalizes the results based on the dynamical theory of diffraction, which are valid only for crystals with a radius of curvature lower than the critical curvature.

Online 5 March 2013


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J. Appl. Cryst. (2013). 46, 421-429  [ doi:10.1107/S0021889813001258 ]

A microstructural and crystallographic investigation of the precipitation behaviour of a primary Al3Zr phase under a high magnetic field

L. Li, Y. Zhang, C. Esling, K. Qin, Z. Zhao, Y. Zuo and J. Cui

Synopsis: A high magnetic field has a significant microstructural and crystallographic effect on the primary Al3Zr phase precipitated during the solidification of an Al-Zr alloy.

Online 5 March 2013


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J. Appl. Cryst. (2013). 46, 430-442  [ doi:10.1107/S0021889813001635 ]

Electron diffraction characterization of a new metastable Al2Cu phase in an Al-Cu friction stir weld

G. Ji and J.-P. Morniroli

Synopsis: The space group of a new metastable orthorhombic Al2Cu phase was unambiguously identified as Ic2m by a recently developed systematic method combining precession electron diffraction and convergent-beam electron diffraction.

Online 14 March 2013


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J. Appl. Cryst. (2013). 46, 443-447  [ doi:10.1107/S0021889813000654 ]

Spontaneous inversion of in-plane polarity of a-oriented GaN domains laterally overgrown on patterned r-plane sapphire substrates

D. Shin, S. Lee, M. Jue, W. Lee, S. Oh and C. Kim

Synopsis: The formation of inversion domain boundaries on the growth fronts of laterally overgrown domains induced spontaneously regulated inversion of in-plane polarity of a-oriented GaN domains, which is reported for the first time.

Online 23 February 2013


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J. Appl. Cryst. (2013). 46, 448-460  [ doi:10.1107/S0021889813001362 ]

P-V-T equation of state of synthetic mirabilite (Na2SO4·10D2O) determined by powder neutron diffraction

A. D. Fortes, H. E. A. Brand, L. Vocadlo, A. Lindsay-Scott, F. Fernandez-Alonso and I. G. Wood

Synopsis: A thermal equation of state for the deuterated analogue of mirabilite has been fitted to high-pressure neutron powder diffraction data and used to obtain a range of thermodynamic quantities required for modelling the structure and dynamics of icy satellite interiors.

Online 5 March 2013


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J. Appl. Cryst. (2013). 46, 461-465  [ doi:10.1107/S0021889812051357 ]

Exact and explicit expression of the atomic pair distribution function as obtained from X-ray total scattering experiments

O. Masson and P. Thomas

Synopsis: An exact and explicit expression of the pair distribution function as obtained from X-ray total scattering is derived with respect to partial functions.

Online 5 March 2013


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J. Appl. Cryst. (2013). 46, 466-475  [ doi:10.1107/S0021889812050923 ]

Comprehensive synchrotron grazing-incidence X-ray scattering analysis of nanostructures in porous polymethylsilsesquioxane dielectric thin films

Y. Rho, B. Ahn, J. Yoon and M. Ree

Synopsis: A complete grazing-incidence X-ray scattering (GIXS) formula was derived for nanopores buried in a polymer dielectric thin film supported by a substrate. Using the GIXS formula, the scattering data from the nanoporous dielectric films were comprehensively analyzed, revealing structural details.

Online 23 February 2013


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J. Appl. Cryst. (2013). 46, 476-482  [ doi:10.1107/S0021889813002227 ]

RAMM: a new random-model-based method for solving ab initio crystal structure using the EXPO package

A. Altomare, C. Cuocci, A. Moliterni and R. Rizzi

Synopsis: A new method, based on the generation of random structure models, is proposed for solving ab initio crystal structures from powder diffraction data.

Online 5 March 2013


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J. Appl. Cryst. (2013). 46, 483-492  [ doi:10.1107/S0021889812052016 ]

Electron backscatter diffraction investigation of local misorientations and orientation gradients in connection with evolution of grain boundary structures in deformed and annealed zirconium. A new approach in grain boundary analysis

M. Jedrychowski, J. Tarasiuk, B. Bacroix and S. Wronski

Synopsis: The evolution of local misorientations, orientation gradients and grain boundary distribution during thermomechanical processing of zirconium samples is studied using the electron backscatter diffraction technique, kernel average misorientation and grain orientation spread statistics, and the proposed novel approach of grain boundary analysis.

Online 23 February 2013


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J. Appl. Cryst. (2013). 46, 493-504  [ doi:10.1107/S0021889813003816 ]

Three-dimensional reconstruction of liquid phases in disordered mesopores using in situ small-angle scattering

C. J. Gommes

Synopsis: In situ synchrotron small-angle X-ray scattering is used to investigate wetting transitions of liquids confined in disordered mesoporous materials. A plurigaussian stochastic model is proposed, which enables one to analyze the data in terms of changing interface areas, contact angle and triple-line length.

Online 14 March 2013


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J. Appl. Cryst. (2013). 46, 505-511  [ doi:10.1107/S0021889813004597 ]

Depth profiling of Fe-implanted Si(100) by means of X-ray reflectivity and extremely asymmetric X-ray diffraction

B. Khanbabaee, A. Biermanns, S. Facsko, J. Grenzer and U. Pietsch

Synopsis: Depth profile investigation of Fe-implanted Si(100) has been carried out using extremely asymmetric X-ray diffraction. Owing to its higher surface sensitivity compared to X-ray reflectivity, a decrease of the mass density close to the surface was found for increasing ion fluence, which is explained by the formation of ion-induced near-surface defects.

Online 14 March 2013


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J. Appl. Cryst. (2013). 46, 512-524  [ doi:10.1107/S0021889813005268 ]

Adaptive reconstruction method for three-dimensional orientation imaging

S. F. Li and R. M. Suter

Synopsis: An adaptive forward modeling orientation reconstruction algorithm is presented and illustrated. Combined with near-field high-energy X-ray diffraction microscopy measurements, the algorithm reconstructs maps of crystallographic orientations in polycrystals that include intra-granular orientation gradients, which arise in many applied materials.

Online 14 March 2013


cryocrystallography papers


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J. Appl. Cryst. (2013). 46, 525-536  [ doi:10.1107/S0021889813003348 ]

Testing commercial protein crystallography sample mounting loops for movement in a cold-stream

R. W. Alkire, F. J. Rotella and N. E. C. Duke

Synopsis: Several commercial sample mounting loops are tested for rigidity using silicon single crystals. Final testing is performed using crystals of tetragonal lysozyme to look for motion under typical data collection conditions.

Online 14 March 2013


computer programs


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J. Appl. Cryst. (2013). 46, 537-539  [ doi:10.1107/S0021889813000150 ]

FabIO: easy access to two-dimensional X-ray detector images in Python

E. B. Knudsen, H. O. Sørensen, J. P. Wright, G. Goret and J. Kieffer

Synopsis: A Python module for reading and handling data from two-dimensional X-ray detectors is presented.

Online 14 February 2013


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J. Appl. Cryst. (2013). 46, 540-543  [ doi:10.1107/S0021889813002173 ]

CLUSTERGEN: a program for molecular cluster generation from crystallographic data

R. Kaminski, K. N. Jarzembska and S. Domagala

Synopsis: A new program, CLUSTERGEN, for molecular cluster generation is introduced. CLUSTERGEN provides the quantum mechanics/molecular mechanics input files for program packages such as ADF or GAUSSIAN and, in general, facilitates file-format manipulation.

Online 5 March 2013


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J. Appl. Cryst. (2013). 46, 544-549  [ doi:10.1107/S0021889813003531 ]

GSAS-II: the genesis of a modern open-source all purpose crystallography software package

B. H. Toby and R. B. Von Dreele

Synopsis: The new open-source GSAS-II package is intended to offer all stages of crystallographic analysis on all types of X-ray and neutron single-crystal and powder diffraction data.

Online 14 March 2013


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J. Appl. Cryst. (2013). 46, 550-553  [ doi:10.1107/S0021889813002938 ]

CTEAS: a graphical-user-interface-based program to determine thermal expansion from high-temperature X-ray diffraction

Z. A. Jones, P. Sarin, R. P. Haggerty and W. M. Kriven

Synopsis: The CTEAS software for calculating thermal expansion of crystalline materials in three dimensions is presented.

Online 14 March 2013


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J. Appl. Cryst. (2013). 46, 554-559  [ doi:10.1107/S0021889812052065 ]

Detection of alternative conformations: Shift_plot and AC_prediction programs

O. V. Sobolev

Synopsis: Programs for visual and automatic detection of alternative conformations in protein structures are presented. The detection procedure is based on features of atomic mobility in unrestrained refinement.

Online 5 March 2013


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J. Appl. Cryst. (2013). 46, 560-566  [ doi:10.1107/S0021889813005190 ]

PDFgetX3: a rapid and highly automatable program for processing powder diffraction data into total scattering pair distribution functions

P. Juhás, T. Davis, C. L. Farrow and S. J. L. Billinge

Synopsis: This paper presents the PDFgetX3 program for extracting an atomic pair distribution function from X-ray powder diffraction data.

Online 14 March 2013


laboratory notes


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J. Appl. Cryst. (2013). 46, 567-569  [ doi:10.1107/S0021889813003178 ]

Measuring radioactive powder samples on the high-resolution powder diffraction beamline at the European Synchrotron Radiation Facility

A. H. Hill, T. Klimczuk, R. Springell and H. C. Walker

Synopsis: A sample preparation technique has been developed to enable the safe measurement of radioactive powders on the high-resolution powder diffraction beamline, ID31, at the European Synchrotron Radiation Facility.

Online 5 March 2013


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J. Appl. Cryst. (2013). 46, 570-572  [ doi:10.1107/S0021889813000629 ]

A new gas system for automated in situ powder diffraction studies at the European Synchrotron Radiation Facility

A. H. Hill

Synopsis: A new rig at the European Synchrotron Radiation Facility for dosing fixed pressures of absorbent gas up to 100 bar (107 Pa) into a powder sample is described. The system is fully integrated into the beamline control software.

Online 14 February 2013


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J. Appl. Cryst. (2013). 46, 573-576  [ doi:10.1107/S002188981205162X ]

Development of powder diffraction apparatus for small-angle X-ray scattering measurements

A. Bóta

Synopsis: A novel type of X-ray collimation system attached to commercial powder diffractometers makes the structural characterization of nanomaterials possible in a wide size range from <0.1 to 100 nm by combination of the small- and wide-angle X-ray scattering techniques. This device can be attached to any existing `[theta]/[theta]' powder diffractometer, providing a multi-functional small- and wide-angle X-ray scattering/diffraction apparatus.

Online 23 February 2013


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J. Appl. Cryst. (2013). 46, 577-579  [ doi:10.1107/S0021889813002628 ]

Accurate measurements of intrinsic scattering from window materials by use of a vacuum camera

H. Masunaga, K. Sakurai, I. Akiba, K. Ito and M. Takata

Synopsis: Window materials for small-angle X-ray scattering measurements have been evaluated using a vacuum camera. It is shown that window materials vary in how they scatter the background signal depending on the q range.

Online 14 March 2013


 

J. Appl. Cryst. (2013). 46, 580-586

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