Journal of Applied Crystallography

Volume 45, Part 3 (June 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, 381-388  [ doi:10.1107/S0021889812009557 ]

Monte Carlo estimation of the structure factor for hard bodies in small-angle scattering

S. Hansen

Synopsis: A method is described for the calculation of the excluded-volume distance distribution for particles of arbitrary shape. Examples are given for ellipsoids, cylinders and cylinders with hemispherical end caps, of axial ratios between 0.1 and 10. Estimates of the structure factor using this method are compared with the hard-sphere approximation.

Online 25 April 2012


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J. Appl. Cryst. (2012). 45, 389-392  [ doi:10.1107/S0021889812009247 ]

Structure-factor statistics and crystal symmetry

U. Shmueli

Synopsis: This short article presents some applications of structure-factor statistics to the determination of crystal symmetry. It is thought that this is the first application of non-ideal structure-factor statistics to real intensity data.

Online 25 April 2012


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J. Appl. Cryst. (2012). 45, 393-397  [ doi:10.1107/S0021889812011867 ]

X-ray diffuse scattering in SrTiO3 and model of atomic displacements

M. Kopecký, J. Fábry and J. Kub

Synopsis: The scattering intensity of synchrotron radiation in a compact three-dimensional volume of the reciprocal space of an SrTiO3 single crystal has been measured. The diffuse pattern cannot be explained by a simple chain of just one of the displaced cations but is compatible with the displacements of Sr2+ along [001]cub (where the subscript cub denotes the cubic structure) correlated in the same direction and with simultaneous displacements of Ti4+ along [111]cub, or alternatively along [011]cub or [101]cub, while the displacements of Ti4+ are correlated along [001]cub.

Online 25 April 2012


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J. Appl. Cryst. (2012). 45, 398-405  [ doi:10.1107/S0021889812015075 ]

Patterson analysis for layer profile determination by neutron or X-ray reflectometry

Z. Tun

Synopsis: Although not strictly valid, Patterson analysis is a way of analysing neutron or X-ray reflectometry data. In some special cases it could even be the preferred way, especially if a strategy for minimizing the distortion caused by the breakdown of the kinematic approximation is adopted.

Online 4 May 2012


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J. Appl. Cryst. (2012). 45, 406-416  [ doi:10.1107/S0021889812012812 ]

Simple inversion formula for the small-angle X-ray scattering intensity from polydisperse systems of spheres

R. Botet and B. Cabane

Synopsis: A simple method to obtain the size distribution of a population of polydisperse spheres from small-angle scattering data is presented. The method is based on the deviations of the scattering signal from the Porod law and is optimized and stable for broad distributions.

Online 4 May 2012


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J. Appl. Cryst. (2012). 45, 417-429  [ doi:10.1107/S0021889812015191 ]

Applications of leverage analysis in structure refinement

S. Parsons, T. Wagner, O. Presly, P. A. Wood and R. I. Cooper

Synopsis: Leverage analysis can be used to investigate the importance of weak data and the effectiveness of restraints. It can also improve the precision of estimates of selected parameters: the standard uncertainty of the Flack parameter can be reduced to 0.1 or below even for light-atom crystal structures.

Online 16 May 2012


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J. Appl. Cryst. (2012). 45, 430-438  [ doi:10.1107/S0021889812008631 ]

Influence of the matrix on the fractal properties of precipitated silica in composites

G. J. Schneider, W. Hengl, K. Brandt, S. V. Roth, R. Schuster and D. Göritz

Synopsis: Small-angle X-ray scattering experiments on composites of polymers and hierarchically structured silica reveal that internal and external forces caused by mixing processes determine the particle morphology. The strength of the interaction between the polymer chains and the particle surface does not visibly affect the experimental results.

Online 31 March 2012


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J. Appl. Cryst. (2012). 45, 439-443  [ doi:10.1107/S0021889812013969 ]

Growth and electro-elastic properties of K(H1-xDx)2PO4 single crystals

B. Liu, X. Yin, X. Sun, M. Xu, S. Ji, X. Xu and J. Zhang

Synopsis: The elastic, piezoelectric and dielectric constants of K(H1-xDx)2PO4 crystals (with composition x from 0 to 0.90) were determined using the resonance technique and impedance analysis, respectively. The reasons for the composition dependence of these constants were analyzed based on the variation of the crystal structures resolved by single-crystal X-ray diffraction.

Online 4 May 2012


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J. Appl. Cryst. (2012). 45, 444-452  [ doi:10.1107/S0021889812008217 ]

Observation of a low-symmetry phase in Na0.5Bi0.5TiO3 crystals by optical birefringence microscopy

S. Gorfman, A. M. Glazer, Y. Noguchi, M. Miyayama, H. Luo and P. A. Thomas

Synopsis: Single crystals of Na0.5Bi0.5TiO3 were investigated by optical birefringence microscopy as a function of temperature. Evidence of a temperature-driven rotation of the axis of the optical indicatrix within a monoclinic plane was obtained.

Online 31 March 2012


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J. Appl. Cryst. (2012). 45, 453-457  [ doi:10.1107/S0021889812010722 ]

Single-crystal CVD diamonds as small-angle X-ray scattering windows for high-pressure research

S. Wang, Y. Meng, N. Ando, M. Tate, S. Krasnicki, C. Yan, Q. Liang, J. Lai, H. Mao, S. M. Gruner and R. J. Hemley

Synopsis: Single-crystal chemical vapor deposition (CVD) diamonds have been investigated using small-angle X-ray scattering, X-ray topography and photoluminescence techniques. An undoped single-crystal CVD diamond proved to be an excellent window material in the characterization of protein unfolding at high pressures.

Online 25 April 2012


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J. Appl. Cryst. (2012). 45, 458-470  [ doi:10.1107/S0021889812011569 ]

Patterson selectivity by modulation-enhanced diffraction

R. Caliandro, D. Chernyshov, H. Emerich, M. Milanesio, L. Palin, A. Urakawa, W. van Beek and D. Viterbo

Synopsis: The difficulties of phasing experimental diffraction patterns obtained by the novel modulation-enhanced diffraction (MED) technique are described. Once these difficulties are overcome, MED results are better than those obtained by standard phasing methods. Indications are given for future developments.

Online 4 May 2012


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J. Appl. Cryst. (2012). 45, 471-481  [ doi:10.1107/S0021889812015154 ]

A Bayesian approach for denoising one-dimensional data

C. Hogg III, K. Mullen and I. Levin

Synopsis: A Bayesian approach is presented to quantify uncertainty in the true signal underlying noisy count data. A free software implementation has been developed.

Online 16 May 2012


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J. Appl. Cryst. (2012). 45, 482-488  [ doi:10.1107/S0021889812016159 ]

Pair distribution function analysis of molecular compounds: significance and modeling approach discussed using the example of p-terphenyl

N. Rademacher, L. L. Daemen, E. L. Chronister and Th. Proffen

Synopsis: Specific features in pair distribution functions of molecular crystals are discussed and modeling procedures introduced. As an example, the short-range order in p-terphenyl is investigated using total scattering methods.

Online 16 May 2012


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J. Appl. Cryst. (2012). 45, 489-495  [ doi:10.1107/S0021889812013490 ]

Instrumental setup for high-throughput small- and wide-angle solution scattering at the X33 beamline of EMBL Hamburg

C. E. Blanchet, A. V. Zozulya, A. G. Kikhney, D. Franke, P. V. Konarev, W. Shang, R. Klaering, B. Robrahn, C. Hermes, F. Cipriani, D. I. Svergun and M. Roessle

Synopsis: An experimental setup is presented for automated high-throughput small- and wide-angle synchrotron X-ray scattering studies of macromolecular solutions at EMBL Hamburg.

Online 4 May 2012


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J. Appl. Cryst. (2012). 45, 496-502  [ doi:10.1107/S0021889812008953 ]

Strain analysis in Si micro-electromechanical systems by dynamical X-ray diffraction

T. Saka

Synopsis: Long-range strain can be detected by rotating a specimen along the scattering vector. This method is applied to Si devices.

Online 31 March 2012


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J. Appl. Cryst. (2012). 45, 503-506  [ doi:10.1107/S0021889812011545 ]

Regularly branched InN nanostructures: zinc-blende nanocore and polytypic transition

I. Jung, S. Lee, D. Shin, H. Park, M. Y. Ju and C. Kim

Synopsis: On the basis of the crystallographic analysis of regularly branched InN tetrapods, it is proposed that the polytypic transition at four {111} faces of a truncated tetrahedral nanocore plays an important role in the branching regularity.

Online 25 April 2012


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J. Appl. Cryst. (2012). 45, 507-512  [ doi:10.1107/S0021889812008928 ]

Optimization of the thickness of a ZnS/6LiF scintillator for a high-resolution detector installed on a focusing small-angle neutron scattering spectrometer (SANS-U)

H. Iwase, M. Katagiri and M. Shibayama

Synopsis: The high-resolution detector on the SANS-U spectrometer at the Japan Atomic Energy Agency has been upgraded by improving experimental efficiency with the optimization of the thickness of a ZnS/6LiF scintillator.

Online 31 March 2012


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J. Appl. Cryst. (2012). 45, 513-516  [ doi:10.1107/S0021889812015804 ]

An analytical scattering function for polydisperse spherical core-shell particles with Schulz-Flory size distributions of both core size and shell thickness

J. Wagner

Synopsis: A closed analytical expression for the form factor of spherical core-shell particles, with independent Schulz-Flory size distribution functions for both the core size and the shell thickness, is derived. The results of the analytical expression are identical to numerical results and existing analytical expressions for homogeneous spheres.

Online 16 May 2012


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J. Appl. Cryst. (2012). 45, 517-522  [ doi:10.1107/S0021889812015038 ]

Analysis of polycrystallinity in hen egg-white lysozyme using a pnCCD

S. Send, A. Abboud, W. Leitenberger, M. S. Weiss, R. Hartmann, L. Strüder and U. Pietsch

Synopsis: An analysis of polycrystallinity in tetragonal hen egg-white lysozyme by means of energy-dispersive Laue diffraction techniques using a pnCCD detector is presented.

Online 4 May 2012


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J. Appl. Cryst. (2012). 45, 523-534  [ doi:10.1107/S0021889812014847 ]

The P-V-T equation of state of D2O ice VI determined by neutron powder diffraction in the range 0 < P < 2.6 GPa and 120 < T < 330 K, and the isothermal equation of state of D2O ice VII from 2 to 7 GPa at room temperature

A. D. Fortes, I. G. Wood, M. G. Tucker and W. G. Marshall

Synopsis: Ice VI is an important rock-forming mineral phase in icy planetary bodies; the pressure and temperature dependence of its density have been measured using powder neutron diffraction, throughout the high-pressure stability field, to obtain an accurate equation of state parameterization. These data are used to derive other thermodynamic quantities of use in planetary modelling.

Online 16 May 2012


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J. Appl. Cryst. (2012). 45, 535-545  [ doi:10.1107/S002188981201607X ]

In situ studies into the formation kinetics of potassium jarosite

H. E. A. Brand, N. V. Y. Scarlett and I. E. Grey

Synopsis: This paper reports the results of time-resolved synchrotron powder diffraction and small-angle scattering experiments designed to investigate the formation of potassium jarosite.

Online 16 May 2012


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J. Appl. Cryst. (2012). 45, 546-553  [ doi:10.1107/S0021889812003445 ]

Polarization-analyzed small-angle neutron scattering. I. Polarized data reduction using Pol-Corr

K. Krycka, W. Chen, J. Borchers, B. Maranville and S. Watson

Synopsis: Efficiency corrections for polarized small-angle neutron scattering are presented and the accompanying software, Pol-Corr, is described.

Online 16 May 2012


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J. Appl. Cryst. (2012). 45, 554-565  [ doi:10.1107/S0021889812010114 ]

Polarization-analyzed small-angle neutron scattering. II. Mathematical angular analysis

K. Krycka, J. Borchers, Y. Ijiri, R. Booth and S. Majetich

Synopsis: Algorithms for the separation of nuclear and magnetic polarized small-angle neutron scattering at all angles, including the case of anisotropic samples, are presented.

Online 16 May 2012


computer programs


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J. Appl. Cryst. (2012). 45, 566-567  [ doi:10.1107/S0021889812014318 ]

BayesApp: a web site for indirect transformation of small-angle scattering data

S. Hansen

Synopsis: A web site for indirect transformation of small-angle scattering data is presented. No user input is necessary beyond the experimental data.

Online 4 May 2012


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J. Appl. Cryst. (2012). 45, 568-572  [ doi:10.1107/S0021889812011715 ]

XDSAPP: a graphical user interface for the convenient processing of diffraction data using XDS

M. Krug, M. S. Weiss, U. Heinemann and U. Mueller

Synopsis: XDSAPP, a graphical user interface for the easy and convenient processing of diffraction data sets using XDS, is described.

Online 25 April 2012


 

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J. Appl. Cryst. (2012). 45, 573-574  [ doi:10.1107/S0021889812014252 ]

ISODEC: software for calculating diffraction elastic constants

T. Gnäupel-Herold

Synopsis: ISODEC is a program for the calculation of diffraction elastic constants for aggregates with and without preferred orientation. It also calculates stress from lattice strain and vice versa.

Online 4 May 2012


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J. Appl. Cryst. (2012). 45, 575-580  [ doi:10.1107/S0021889812016068 ]

EDMA: a computer program for topological analysis of discrete electron densities

L. Palatinus, S. J. Prathapa and S. van Smaalen

Synopsis: A computer program for topological analysis of discrete electron densities is presented. Test calculations demonstrate the accuracy of the applied methods.

Online 16 May 2012


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J. Appl. Cryst. (2012). 45, 581-586  [ doi:10.1107/S0021889812017293 ]

Graphical tools for macromolecular crystallography in PHENIX

N. Echols, R. W. Grosse-Kunstleve, P. V. Afonine, G. Bunkóczi, V. B. Chen, J. J. Headd, A. J. McCoy, N. W. Moriarty, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. D. Adams

Synopsis: The foundations and current features of a widely used graphical user interface for macromolecular crystallography are described.

Online 16 May 2012


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J. Appl. Cryst. (2012). 45, 587-593  [ doi:10.1107/S0021889812015786 ]

The Small Angle Scattering ToolBox (SASTBX): an open-source software for biomolecular small-angle scattering

H. Liu, A. Hexemer and P. H. Zwart

Synopsis: A novel software platform for the analysis of biological small-angle scattering is presented.

Online 16 May 2012


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J. Appl. Cryst. (2012). 45, 594-597  [ doi:10.1107/S0021889812014859 ]

XBroad: program for extracting basic microstructure information from X-ray diffraction patterns in few clicks

Z. Skoko, J. Popovic, K. Dekanic, V. Kolbas and S. Popovic

Synopsis: The Stokes deconvolution method followed by Warren-Averbach-Bertaut and/or Williamson-Hall analysis is implemented in easy-to-use program, XBroad, for quick extraction of basic microstructural information from powder X-ray diffraction data.

Online 4 May 2012


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J. Appl. Cryst. (2012). 45, 598-602  [ doi:10.1107/S002188981201775X ]

PROSPERO: online prediction of crystallographic success from experimental results and sequence

F. H. Zucker, H. Y. Kim and E. A. Merritt

Synopsis: The PROSPERO server analyzes sequence and experimental protein characterization results, then uses that analysis to predict crystallization outcome and suggest priorities for futher work on difficult targets. The server allows users to upload data from six types of experiment, to organize those data by sample and project, and to share those data with collaborators.

Online 16 May 2012


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J. Appl. Cryst. (2012). 45, 603-607  [ doi:10.1107/S0021889812016056 ]

nxs: a program library for neutron cross section calculations

M. Boin

Synopsis: A reusable program library to compute cold and thermal neutron cross sections and examples of its application for Bragg edge imaging are presented.

Online 16 May 2012


laboratory notes


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J. Appl. Cryst. (2012). 45, 608-610  [ doi:10.1107/S0021889812012332 ]

A compact, transportable, thermoelectrically cooled cold stage for reflection geometry X-ray powder diffraction

I. G. Wood, N. J. Hughes, F. Browning and A. D. Fortes

Synopsis: A thermoelectrically cooled sample stage for X-ray powder diffraction in the range from about 250 to 300 K is described. The stage is constructed in such a way that it may be removed from the diffractometer and pre-cooled to its base temperature before the sample is loaded.

Online 25 April 2012


crystallographers


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J. Appl. Cryst. (2012). 45, 611  [ doi:10.1107/S0021889812015725 ]

Valentin Ivanovich Simonov (1930-2012)

Online 25 April 2012


book reviews


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J. Appl. Cryst. (2012). 45, 612  [ doi:10.1107/S0021889812014434 ]

Materials Science of DNA

Online 16 May 2012


books received


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J. Appl. Cryst. (2012). 45, 613  [ doi:10.1107/S0021889812006607 ]

Introduction to Nonlinear Optics

Online 31 March 2012


 

J. Appl. Cryst. (2012). 45, 614-620

forthcoming meetings and short courses


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