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Journal of Applied Crystallography

Volume 45, Part 2 (April 2012)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Example of a three-dimensional reciprocal-space map recorded from a sample of GaAs nanowires grown on GaAs. Courtesy of Schlepütz et al. [J. Appl. Cryst. (2011), 44, 73-83].

research papers


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J. Appl. Cryst. (2012). 45, 157-165  [ doi:10.1107/S0021889812001616 ]

Validating classical line profile analyses using microbeam diffraction from individual dislocation cell walls and cell interiors

L. E. Levine, P. Geantil, B. C. Larson, J. Z. Tischler, M. E. Kassner and W. Liu

Synopsis: Depth-resolved microbeam diffraction was used to measure diffraction line profiles from numerous individual dislocation cell walls and cell interiors in a heavily deformed Cu single crystal, allowing the construction of the cell-interior and cell-wall subprofiles that have been approximated in the line profile analysis literature for the past 30 years. Comparison of the reconstructed subprofiles and the macroscopic asymmetric line profile from the same sample allows the first direct tests of many of the assumptions that have been used in such analyses.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 166-173  [ doi:10.1107/S0021889812002300 ]

Single-pass flow-through reaction cell for high-temperature and high-pressure in situ neutron diffraction studies of hydrothermal crystallization processes

F. Xia, J. Brugger, G. Qian, Y. Ngothai, B. O'Neill, J. Zhao, S. Pullen, S. Olsen and A. Pring

Synopsis: A versatile flow-through reaction cell, featuring independent and accurate controls of temperature (up to 673 K), pressure (up to 46 MPa), fluid volume ([greater-than or equal to]65 ml) and flow rate (0.01-10 ml min-1), has been developed and commissioned for in situ neutron diffraction investigation of crystallization under mild to extreme hydrothermal conditions (e.g. supercritical).

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 174-181  [ doi:10.1107/S0021889812001690 ]

A high-resolution synchrotron powder diffraction study of substituted gallium ferrites using flat-plate fixed angle of incidence geometry on beamline I11 at Diamond

S. H. M. Ryding, F. Azough, R. Freer, R. J. Cernik, C. C. Tang and S. P. Thompson

Synopsis: This paper outlines a data collection strategy and the necessary corrections for synchrotron powder data collected in flat-plate geometry. A number of solid solutions in multiferroic Ga(2-x)FexO3 have been used to deliver very accurate crystal structures suitable for modelling material functionality.

Online 9 February 2012


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J. Appl. Cryst. (2012). 45, 182-185  [ doi:10.1107/S0021889812001665 ]

Synthesis and characterization of one-dimensional vertically aligned Sb-doped ZnO nanowires

W. E. Mahmoud, F. Al-Marzouki, S. Al-Ameer and F. Al-Hazmi

Synopsis: The morphology, structure and luminescence properties of one-dimensional vertically aligned Sb-doped ZnO nanowires on a silicon substrate have been studied. The results show that the use of Si(111) is a critical factor for the growth of vertically aligned nanowires.

Online 9 February 2012


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J. Appl. Cryst. (2012). 45, 186-196  [ doi:10.1107/S0021889812000337 ]

High-pressure phase transitions and equations of state in NiSi. I. Ab initio simulations

L. Vocadlo, I. G. Wood and D. P. Dobson

Synopsis: The relative stability of high-pressure phases of NiSi has been determined by ab initio calculations. Above ~250 GPa, NiSi adopts the CsCl structure and therefore at the pressures of the Earth's inner core it will be isostructural with FeSi.

Online 25 February 2012


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J. Appl. Cryst. (2012). 45, 197-206  [ doi:10.1107/S0021889812002221 ]

A model for calculating diffraction elastic constants

T. Gnäupel-Herold, A. A. Creuziger and M. Iadicola

Synopsis: A model is proposed to calculate the diffraction elastic constants that convert lattice strain into macroscopic stress.

Online 25 February 2012


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J. Appl. Cryst. (2012). 45, 207-212  [ doi:10.1107/S002188981200249X ]

Control of Gibbs free energy relationship between hen egg white lysozyme polymorphs under application of an external alternating current electric field

Y. Tomita, H. Koizumi, S. Uda, K. Fujiwara and J. Nozawa

Synopsis: The Gibbs free energy relationship between bulk (tetragonal structure) and spherulitic crystals of hen egg white lysozyme was controlled under application of an external alternating current electric field. The distribution of phases differed depending on differences in the magnitude of the electrostatic energy contribution to the respective chemical potentials of the two solid phases.

Online 25 February 2012


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J. Appl. Cryst. (2012). 45, 213-223  [ doi:10.1107/S0021889812000957 ]

High-throughput biological small-angle X-ray scattering with a robotically loaded capillary cell

S. S. Nielsen, M. Møller and R. E. Gillilan

Synopsis: A high-throughput biological small-angle X-ray scattering facility is described, which combines single-channel robotic pipetting with a capillary-based sample cell. The design parameters, sample rinsing protocol and effects of fluid dynamics on radiation damage are examined.

Online 9 February 2012


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J. Appl. Cryst. (2012). 45, 224-233  [ doi:10.1107/S002188981200091X ]

On the multiple orientation relationship of the Mg/[gamma]-Mg17Al12 precipitation system

H. Liu, J. Liu, L. Ouyang and C. Luo

Synopsis: The origin of the multiple orientation relationship found in the Mg/[gamma]-Mg17Al12 precipitation system has been rationally interpreted by a simplified invariant line analysis with consideration of the pseudo-twinning relationship between close-packed planes ({\\overline 8}\\hskip.75{\\overline 7}\\hskip.75{\\overline 7}), ({\\overline 4}11), (033), (411) and ({8}{\\overline 7}\\hskip.75{\\overline 7}) in the precipitate phase [gamma]-Mg12Al17.

Online 9 February 2012


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J. Appl. Cryst. (2012). 45, 234-238  [ doi:10.1107/S0021889812003585 ]

Upgrade of automated sample exchanger SPACE

H. Murakami, G. Ueno, N. Shimizu, T. Kumasaka and M. Yamamoto

Synopsis: SPACE is an automated sample exchanger for cryo-cooled protein crystals, developed at SPring-8. This article reports the upgrading of SPACE.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 239-244  [ doi:10.1107/S0021889812003007 ]

Structural polytypism and residual strain in GaAs nanowires grown on Si(111) probed by single-nanowire X-ray diffraction

A. Biermanns, S. Breuer, A. Davydok, L. Geelhaar and U. Pietsch

Synopsis: Using nanowire-resolved X-ray diffraction with a focused synchrotron beam, the structural composition, phase arrangement and residual strain of individual GaAs nanowires grown on Si(111) have been investigated.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 245-254  [ doi:10.1107/S0021889812002324 ]

Analysis of randomly oriented structures by grazing-incidence small-angle neutron scattering

D. Korolkov, P. Busch, L. Willner, E. Kentzinger, U. Rücker, A. Paul, H. Frielinghaus and T. Brückel

Synopsis: A formalism is presented which allows the quantitative evaluation of grazing-incidence small-angle neutron scattering patterns from randomly oriented one-dimensional paracrystal domains with lamellar structure.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 255-262  [ doi:10.1107/S0021889812003366 ]

Dispersive spread of virtual sources by asymmetric X-ray monochromators

X. R. Huang, A. T. Macrander, M. G. Honnicke, Y. Q. Cai and P. Fernandez

Synopsis: From the principles of X-ray dispersion in asymmetric Bragg reflections, typical dispersive multiple-crystal monochromators are analyzed to show that they may produce millimetre-sized virtual sources. Possible schemes to mitigate this problem for microfocusing are proposed.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 263-271  [ doi:10.1107/S002188981200516X ]

In situ quantitative analysis of stress and texture development in forsterite aggregates deformed at 6 GPa and 1373 K

C. Bollinger, S. Merkel and P. Raterron

Synopsis: This paper presents a new protocol for the in situ investigation of differential stress, principal stress direction and lattice preferred orientation in low-symmetry materials deformed at high pressure and high temperature. The method has been successfully applied to data collected on the D-DIA deformation press at the X17B2 beamline of the National Synchrotron Light Source.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 272-278  [ doi:10.1107/S0021889812003081 ]

Modulation of quartz-like GeO2 structure by Si substitution: an X-ray diffraction study of Ge1-xSixO2 (0 [less-than or equal to] x < 0.2) flux-grown single crystals

A. Lignie, D. Granier, P. Armand, J. Haines and P. Papet

Synopsis: Using X-ray diffraction, the high purity and high crystalline quality of millimetre-sized GeO2-based crystals obtained using the flux method have been revealed. The effect of Ge replacement by Si on the distortion of the [alpha]-quartz-type GeO2 structure was assessed by following the evolution of the intra-tetrahedral angle and other structural parameters.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 279-291  [ doi:10.1107/S0021889812006085 ]

Reckoning electromagnetic principles with polarimetric measurements of anisotropic optically active crystals

O. Arteaga, J. Freudenthal and B. Kahr

Synopsis: The problem of light propagation in optically active anisotropic crystals is studied with a unified theory of electromagnetic plane waves transmitted in a layered homogeneous bianisotropic system. The combined analytical and experimental methods described are applicable to the determination of the spectroscopic optical activity tensor of crystals.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 292-298  [ doi:10.1107/S0021889812000702 ]

Masquerade: removing non-sample scattering from integrated reflection intensities

J. A. Coome, A. E. Goeta, J. A. K. Howard and M. R. Probert

Synopsis: A new technique is introduced to remove non-sample scattering from integrated reflection intensities by utilizing changes in relative scattering vectors. This approach is found to improve data quality.

Online 9 February 2012


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J. Appl. Cryst. (2012). 45, 299-308  [ doi:10.1107/S0021889812003998 ]

Application of matrix decomposition algorithms for singular matrices to the Pawley method in Z-Rietveld

R. Oishi-Tomiyasu, M. Yonemura, T. Morishima, A. Hoshikawa, S. Torii, T. Ishigaki and T. Kamiyama

Synopsis: Improvements have been made to the nonlinear least-squares algorithms of the powder diffraction analysis program Z-Rietveld so that it can deal with singular matrices and intensity non-negativity constraints. Owing to these improvements, Z-Rietveld successfully executes the Pawley method without requiring any constraints on the integrated intensities, even in the case of severely or exactly overlapping peaks.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 309-315  [ doi:10.1107/S0021889812007546 ]

Application of constrained real-space refinement of flexible molecular fragments to automatic model building of RNA structures

F. Pavelcik

Synopsis: New methods have been developed for locating phosphate groups and nucleic acid bases in the electron density of RNA structures. A program, RSR, has been created for the constrained refinement of molecular fragments in model-building methods based on a phased rotation-conformation-translation function, and the programs NUT, HEL and DHL have been upgraded and organized into a program system.

Online 15 March 2012


CIF applications


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J. Appl. Cryst. (2012). 45, 316-323  [ doi:10.1107/S0021889812006462 ]

CrystalEye: automated aggregation, semantification and dissemination of the world's open crystallographic data

N. Day, J. Downing, S. Adams, N. W. England and P. Murray-Rust

Synopsis: An automatic system for the aggregation, semantification and presentation of open crystallographic data is presented.

Online 15 March 2012


computer programs


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J. Appl. Cryst. (2012). 45, 324-328  [ doi:10.1107/S0021889812004037 ]

Nika: software for two-dimensional data reduction

J. Ilavsky

Synopsis: Nika is a free open-source Igor Pro-based program for reduction of two-dimensional scattering data from area-detector small- and wide-angle scattering instruments to one-dimensional lineouts. It can be used in transmission and grazing-incidence geometries.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 329-331  [ doi:10.1107/S0021889812004979 ]

MossA: a program for analyzing energy-domain Mössbauer spectra from conventional and synchrotron sources

C. Prescher, C. McCammon and L. Dubrovinsky

Synopsis: This paper introduces a new program for analyzing 57Fe conventional and synchrotron energy-domain Mössbauer spectra.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 332-334  [ doi:10.1107/S0021889812001501 ]

Fragment Finder 2.0: a computing server to identify structurally similar fragments

R. Nagarajan, S. Siva Balan, R. Sabarinathan, M. Kirti Vaishnavi and K. Sekar

Synopsis: The proposed web server is an updated version of a previously developed search engine and is useful for identifying structurally similar peptide fragments.

Online 9 February 2012


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J. Appl. Cryst. (2012). 45, 335-341  [ doi:10.1107/S0021889812002312 ]

CrystFEL: a software suite for snapshot serial crystallography

T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman

Synopsis: A new suite of software is described, for processing data acquired from many small crystals illuminated `serially' by an X-ray free-electron laser.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 342-350  [ doi:10.1107/S0021889812007662 ]

New developments in the ATSAS program package for small-angle scattering data analysis

M. V. Petoukhov, D. Franke, A. V. Shkumatov, G. Tria, A. G. Kikhney, M. Gajda, C. Gorba, H. D. T. Mertens, P. V. Konarev and D. I. Svergun

Synopsis: The paper presents new developments and amendments to the ATSAS package (version 2.4) for processing and analysis of isotropic small-angle scattering data.

Online 15 March 2012


 

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J. Appl. Cryst. (2012). 45, 351-356  [ doi:10.1107/S0021889812003317 ]

Automated determination of the extinction symbol via electron diffraction data

M. Camalli, B. Carrozzini, G. L. Cascarano and C. Giacovazzo

Synopsis: A new statistical method for the automatic determination of the extinction symbol from electron diffraction data is described.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 357-361  [ doi:10.1107/S0021889812001124 ]

SIR2011: a new package for crystal structure determination and refinement

M. C. Burla, R. Caliandro, M. Camalli, B. Carrozzini, G. L. Cascarano, C. Giacovazzo, M. Mallamo, A. Mazzone, G. Polidori and R. Spagna

Synopsis: The main features of the program SIR2011 are described.

Online 9 February 2012


laboratory notes


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J. Appl. Cryst. (2012). 45, 362-366  [ doi:10.1107/S002188981200756X ]

A fibre-based crystal mounting technique for protein cryocrystallography

M. Sugahara

Synopsis: A fibre-based crystal mounting technique for protein cryocrystallography has been developed.

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 367-370  [ doi:10.1107/S0021889812000908 ]

Grazing-incidence in-plane X-ray diffraction on ultra-thin organic films using standard laboratory equipment

M. Neuschitzer, A. Moser, A. Neuhold, J. Kraxner, B. Stadlober, M. Oehzelt, I. Salzmann, R. Resel and J. Novák

Synopsis: A setup for grazing-incidence in-plane X-ray diffraction using standard laboratory equipment and its application for organic thin-film and monolayer characterization is described.

Online 9 February 2012


crystallographers


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J. Appl. Cryst. (2012). 45, 371-372  [ doi:10.1107/S0021889812005213 ]

Alexander McLeod Mathieson (1920-2011)

Online 15 March 2012


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J. Appl. Cryst. (2012). 45, 373  [ doi:10.1107/S0021889812006668 ]

Hans Dachs (1927-2011)

Online 15 March 2012


books received


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J. Appl. Cryst. (2012). 45, 374  [ doi:10.1107/S0021889812001938 ]

Crystal Engineering. A Textbook

Online 9 February 2012


 

J. Appl. Cryst. (2012). 45, 375-380

forthcoming meetings and short courses


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