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Journal of Applied Crystallography

Volume 46, Part 3 (June 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: A schematic of a new X-ray scattering geometry, grazing-incidence transmission small-angle X-ray scattering. The incident beam impinges on the edge of a nanostructured surface at a grazing angle, and exits through the sample's edge. The method is demonstrated for gratings where it is shown that the Born approximation is valid with a simple and small correction. Courtesy of Lu et al. [J. Appl. Cryst. (2013), 46, 165-172].

research papers


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J. Appl. Cryst. (2013). 46, 587-593  [ doi:10.1107/S0021889813006894 ]

CCL: an algorithm for the efficient comparison of clusters

R. Hundt, J. C. Schön, S. Neelamraju, J. Zagorac and M. Jansen

Synopsis: An efficient and robust algorithm for the comparison of clusters is presented. Several illustrative example applications are given, including the screening of sets of clusters generated during global optimizations and Monte Carlo/molecular dymanics simulations, the identification of specific structure fragments inside large clusters, and the study of structure-substructure relations of periodic crystals.

Online 6 April 2013


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J. Appl. Cryst. (2013). 46, 594-600  [ doi:10.1107/S002188981300527X ]

Using GPUs to compute fast Fourier transforms for crystal structure solution and refinement

E. M. Shalaby and M. A. Oliveira

Synopsis: Fast Fourier transformation calculations, used in direct space refinement, are presented using graphical processing units (GPUs) and compared with the speed achieved using normal central processing unit calculations.

Online 6 April 2013


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J. Appl. Cryst. (2013). 46, 601-609  [ doi:10.1107/S0021889813005797 ]

Structural, optical and thermal properties of Zr-Fe co-doped congruent LiNbO3 single crystals

B. Riscob, R. Bhatt, N. Vijayan, I. Bhaumik, S. Ganesamoorthy, M. A. Wahab, Rashmi and G. Bhagavannarayana

Synopsis: High-quality single crystals of Zr-Fe co-doped lithium niobate have been grown by the Czochralski method using an automatic diameter-controlled crystal puller. The grown crystals have been assessed by various X-ray techniques to determine the lattice parameter, strain, crystalline perfection and composition variation. The optical properties were investigated and a thermal analysis was conducted to identify the potential for device fabrication.

Online 6 April 2013


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J. Appl. Cryst. (2013). 46, 610-618  [ doi:10.1107/S0021889813008340 ]

Sin2[psi]-based residual stress gradient analysis by energy-dispersive synchrotron diffraction constrained by small gauge volumes. I. Theoretical concept

M. Meixner, M. Klaus and Ch. Genzel

Synopsis: A theoretical concept for the sin2[psi]-based analysis of residual stress depth gradients providing high lateral resolution is presented. Simulations for very small gauge volumes are presented for the energy-dispersive case of diffraction.

Online 4 May 2013


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J. Appl. Cryst. (2013). 46, 619-627  [ doi:10.1107/S0021889813008364 ]

Sin2[psi]-based residual stress gradient analysis by energy-dispersive synchrotron diffraction constrained by small gauge volumes. II. Experimental implementation

M. Meixner, M. Klaus and Ch. Genzel

Synopsis: The experimental implementation of the concept introduced in part I of this series is demonstrated. The range of applications and the relevance of considering the gauge volume geometry are discussed.

Online 4 May 2013


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J. Appl. Cryst. (2013). 46, 628-638  [ doi:10.1107/S0021889813008194 ]

Analytical model for neutron diffraction peak shifts due to the surface effect

J. Saroun, J. R. Kornmeier, M. Hofmann, P. Mikula and M. Vrána

Synopsis: A new analytical model for the surface effect in strain analysis by neutron diffraction has been developed. Spurious strains are calculated from primary parameters of the instrument to a precision allowing for reliable data corrections.

Online 4 May 2013


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J. Appl. Cryst. (2013). 46, 639-643  [ doi:10.1107/S0021889813007693 ]

Surface diffraction on a [psi]-circle diffractometer using the [chi]-axis geometry

T. T. Fister, P. H. Fuoss, D. D. Fong, J. A. Eastman, C. M. Folkman, S. O. Hruszkewycz, M. J. Highland, H. Zhou and P. Fenter

Synopsis: An alternative configuration for a [psi]-circle diffractometer is discussed, such that the sample normal is along the [chi]-circle axis. Reciprocal space calculations for specular and nonspecular surface diffraction are described in detail.

Online 18 April 2013


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J. Appl. Cryst. (2013). 46, 644-648  [ doi:10.1107/S0021889813010546 ]

Structural study of Yb1-xTbxMnO3 manganites: site occupancy and coexistence of hexagonal and orthorhombic phases

M. E. Bolívar Guarín, A. de M. Moreira and N. L. Speziali

Synopsis: Crystallographic changes in polycrystalline samples of Yb1-xTbxMnO3 were analyzed using the Rietveld method. Site occupancy models were tested in the double-phase cases.

Online 15 May 2013


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J. Appl. Cryst. (2013). 46, 649-655  [ doi:10.1107/S002188981300592X ]

Element-selective charge density visualization of endohedral metallofullerenes using synchrotron X-ray multi-wavelength anomalous powder diffraction data

S. Maki, E. Nishibori, D. Kawaguchi, M. Sakata, M. Takata, T. Inoue and H. Shinohara

Synopsis: An algorithm for determining the element-selective charge density is developed using multi-wavelength anomalous synchrotron X-ray powder diffraction data. The method is employed in order to resolve the disordered structure of yttrium in (Y@C82)(C6H5CH3).

Online 6 April 2013


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[HTML version][PDF version][CIF][3d view][Structure Factors][Supplementary Material]  [Buy article online]

J. Appl. Cryst. (2013). 46, 656-662  [ doi:10.1107/S0021889813006225 ]

Predicting anisotropic displacement parameters using molecular dynamics: density functional theory plus dispersion modelling of thermal motion in benzophenone

A. M. Reilly, D. A. Wann, M. J. Gutmann, M. Jura, C. A. Morrison and D. W. H. Rankin

Synopsis: The potential for first-princples molecular dynamics simulations to predict thermal-motion parameters has been illustrated by good agreement between theoretical and neutron-diffraction-determined anisotropic displacement parameters of benzophenone.

Online 18 April 2013


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J. Appl. Cryst. (2013). 46, 663-671  [ doi:10.1107/S0021889813006511 ]

Objective algorithm to separate signal from noise in a Poisson-distributed pixel data set

T. Straasø, D. Müter, H. O. Sørensen and J. Als-Nielsen

Synopsis: A method is described for the estimation of background level and separation of background pixels from signal pixels in a Poisson-distributed data set by statistical analysis.

Online 18 April 2013


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J. Appl. Cryst. (2013). 46, 672-678  [ doi:10.1107/S002188981300770X ]

Rat-tail tendon fiber SAXS high-order diffraction peaks recovered by a superbright laboratory source and a novel restoration algorithm

L. De Caro, D. Altamura, T. Sibillano, D. Siliqi, G. Filograsso, O. Bunk and C. Giannini

Synopsis: The performance of a novel synchrotron-class X-ray tabletop microsource has been tested for the collection of small-angle X-ray scattering (SAXS) data, by inspecting the nanoscale structural order of air-dried rat-tail tendon. Reciprocal space information up to the 22nd diffraction order (q = 0.21  Å-1, d = 29 Å) was retrieved for SAXS data collected over 8-10 h integration times, with a significant gain in the diffraction peak visibility found for patterns collected for only 0.5 h.

Online 18 April 2013


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J. Appl. Cryst. (2013). 46, 679-696  [ doi:10.1107/S0021889813007991 ]

McXtrace: a Monte Carlo software package for simulating X-ray optics, beamlines and experiments

E. Bergbäck Knudsen, A. Prodi, J. Baltser, M. Thomsen, P. Kjær Willendrup, M. Sanchez del Rio, C. Ferrero, E. Farhi, K. Haldrup, A. Vickery, R. Feidenhans'l, K. Mortensen, M. Meedom Nielsen, H. Friis Poulsen, S. Schmidt and K. Lefmann

Synopsis: The Monte Carlo X-ray simulation package McXtrace is described, and examples of its use for generic virtual X-ray experiments are given. These include tomography using a laboratory source, synchrotron beam evolution through compound refractive lenses, Laue protein crystallography, powder diffraction, an EXAFS and surface diffraction beamline optics study, and time-resolved disordered diffraction.

Online 18 April 2013


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J. Appl. Cryst. (2013). 46, 697-708  [ doi:10.1107/S002188981300681X ]

Development and applications of a new neutron single-crystal diffractometer based on a two-dimensional large-area curved position-sensitive detector

C.-H. Lee, Y. Noda, Y. Ishikawa, S. A. Kim, M. Moon, H. Kimura, M. Watanabe and Y. Dohi

Synopsis: A new reactor-based neutron single-crystal diffractometer was developed based on a large-area curved position-sensitive detector with a delay-line readout method. The instrumentation details are presented, including diffractometer construction, measurement method, raw data treatment and calibration, and various applications for structural studies are given to exploit the strengths of the diffractometer.

Online 4 May 2013


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J. Appl. Cryst. (2013). 46, 709-715  [ doi:10.1107/S0021889813008182 ]

Growth of a three-dimensional anisotropic lattice of Ge quantum dots in an amorphous alumina matrix

M. Buljan, O. Roshchupkina, A. Santic, V. Holý, C. Baehtz, A. Mücklich, L. Horák, V. Vales, N. Radic, S. Bernstorff and J. Grenzer

Synopsis: A self-assembly process is demonstrated that results in the formation of an anisotropic lattice of regularly ordered Ge quantum dots in an amorphous alumina matrix. The prepared material shows a strong anisotropy of the electrical transport properties.

Online 4 May 2013


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J. Appl. Cryst. (2013). 46, 716-725  [ doi:10.1107/S0021889813008522 ]

Analysis of variant selection in friction-stir-processed high-strength low-alloy steels

M. Abbasi, T. W. Nelson and C. D. Sorensen

Synopsis: Variant selection in friction-stir-welded high-strength low-alloy steels has been studied using electron backscatter diffraction and prior austenite reconstruction techniques. A hypothesis for variant selection has been proposed on the basis of grain-boundary interfacial energy and misorientation.

Online 15 May 2013


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J. Appl. Cryst. (2013). 46, 726-735  [ doi:10.1107/S002188981300890X ]

Contrast enhancement of data measured with area detectors: a way to generalize the use of neutron diffraction for thin-film studies

A. M. Bataille, V. Auvray, C. Gatel and A. Gukasov

Synopsis: A denoising method is reported for the treatment of neutron scattering data obtained with position-sensitive detectors, which enhances the information obtained from weak and very weak Bragg peaks.

Online 15 May 2013


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J. Appl. Cryst. (2013). 46, 736-739  [ doi:10.1107/S0021889813005785 ]

Thermal expansion and enhanced heat transfer in high-entropy alloys

C.-L. Lu, S.-Y. Lu, J.-W. Yeh and W.-K. Hsu

Synopsis: Alloys made from equimolar mixtures of more than five elements exhibit an improved thermal diffusivity at elevated temperatures, and the improvement reaches 20% at 423 K and 50% at 573 K. This phenomenon is identified from the lengthened mean free path upon thermal expansion, and lengthening scales with lattice dilation over a wide range of temperatures.

Online 4 May 2013


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J. Appl. Cryst. (2013). 46, 740-745  [ doi:10.1107/S002188981301008X ]

A geometrical approach for semi-automated crystal centering and in situ X-ray diffraction data collection

M. Y. H. Heidari Khajepour, H. Lebrette, X. Vernede, P. Rogues and J.-L. Ferrer

Synopsis: Visual analysis with a motorized microscope coupled to image processing software is used to measure the positions of crystals in their crystallization plates. Crystals, still in their crystallization drop, can then be rapidly centered in the beam for in situ X-ray analysis.

Online 15 May 2013


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J. Appl. Cryst. (2013). 46, 746-751  [ doi:10.1107/S002188981301025X ]

A new technique to grow incongruent melting Ga:YIG crystals: the edge-defined film-fed growth method

N. Zhuang, W. Chen, L. Shi, J. Nie, X. Hu, B. Zhao, S. Lin and J. Chen

Synopsis: A system for growing Ga-doped yttrium iron garnet (YIG) single crystals by the edge-defined film-fed growth method was designed and constructed, and the mechanism of crystal growth was also preliminarily studied. The Ga3+ dopant concentration, the Curie temperature and the transmission spectra of as-grown crystals were investigated to evaluate their potential application in magneto-optical devices.

Online 15 May 2013


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J. Appl. Cryst. (2013). 46, 752-757  [ doi:10.1107/S0021889813009023 ]

Advances in small-angle X-ray scattering for the study of supported catalysts

Y. V. Larichev and F. V. Tuzikov

Synopsis: Ru particle sizes in supported ruthenium catalysts have been studied by small-angle X-ray scattering (SAXS). Using new masking liquids with a relatively low X-ray radiation absorption, it was possible to achieve practically quantitative agreement between SAXS and transmission electron microscopy data.

Online 15 May 2013


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J. Appl. Cryst. (2013). 46, 758-768  [ doi:10.1107/S0021889813010509 ]

New insight into pressure-induced phase transitions of amorphous silicon: the role of impurities

B. Haberl, M. Guthrie, D. Sprouster, J. Williams and J. Bradby

Synopsis: The pressure-induced phase transformations up to 40 GPa of a well characterized form of amorphous silicon were examined using in situ synchrotron X-ray radiation. The phase-transformation pathway was found to be critically dependent on the impurity content, which explains the diversity in phase-transformation pathways reported in previous high-pressure studies on amorphous silicon.

Online 15 May 2013


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J. Appl. Cryst. (2013). 46, 769-778  [ doi:10.1107/S0021889813008923 ]

Determination of the distribution of elements with similar electron counts: a practical guide for resonant X-ray scattering

S. Welzmiller, P. Urban, F. Fahrnbauer, L. Erra and O. Oeckler

Synopsis: General guidelines are given for the application of resonant X-ray diffraction in order to determine the element distribution in compounds lacking X-ray scattering contrast, including cases where more than two `similar' elements are involved.

Online 15 May 2013


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J. Appl. Cryst. (2013). 46, 779-787  [ doi:10.1107/S0021889813010571 ]

The hybrid big bang-big crunch method for solving crystal structure from powder diffraction data

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

Synopsis: The big bang-big crunch optimization method has been revised, combined with the simulated annealing technique and implemented in the latest version of the EXPO program for solving crystal structure from powder diffraction data.

Online 15 May 2013


short communications


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J. Appl. Cryst. (2013). 46, 788-790  [ doi:10.1107/S0021889813005402 ]

Autocorrelation function of the spin misalignment in magnetic small-angle neutron scattering: application to nanocrystalline metals

A. Michels and J.-P. Bick

Synopsis: Real-space magnetic small-angle neutron scattering data from nanocrystalline cobalt and nickel have been analysed in terms of a recently developed micromagnetic theory for the autocorrelation function of the spin misalignment.

Online 6 April 2013


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J. Appl. Cryst. (2013). 46, 791-794  [ doi:10.1107/S0021889813005888 ]

Using a non-monochromatic microbeam for serial snapshot crystallography

C. Dejoie, L. B. McCusker, C. Baerlocher, R. Abela, B. D. Patterson, M. Kunz and N. Tamura

Synopsis: The proof of concept for using a 4% broad-bandpass beam, which is planned for the new SwissFEL facility, for the structural characterization of nonbiological materials is shown.

Online 6 April 2013


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J. Appl. Cryst. (2013). 46, 795-797  [ doi:10.1107/S0021889813008030 ]

The current approach to initial crystallization screening of proteins is under-sampled

F. Gorrec

Synopsis: Forty-seven main reagents included in a large set of macromolecular crystallization conditions are shown to have a similar impact overall on the yield of crystal structures. It is also shown that the conditions formulated with such reagents are under-sampled.

Online 18 April 2013


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J. Appl. Cryst. (2013). 46, 798-800  [ doi:10.1107/S0021889813009126 ]

Determination of crystal symmetry for Bi4Ti3O12-based ferroelectrics by using electron diffraction

W. Ye, C. Lu, P. You, K. Liang and Y. Zhou

Synopsis: The electron diffraction technique was employed to unambiguously clarify the crystal symmetries of ferroelectric Bi4Ti3O12 and Bi3.15Nd0.85Ti3O12 single crystals at room temperature. On the basis of the monoclinic space group B1a1, the lattice parameters of both the ferroelectrics were calculated by the Rietveld refinement of powder X-ray diffraction data.

Online 15 May 2013


computer programs


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J. Appl. Cryst. (2013). 46, 801-803  [ doi:10.1107/S0021889813009746 ]

Twiny: from morphology to twin element and vice versa

M. Nespolo and C. Iordache

Synopsis: Software to compute the angle between corresponding directions in a twinned crystal from a known twin element or vice versa is presented.

Online 4 May 2013


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J. Appl. Cryst. (2013). 46, 804-810  [ doi:10.1107/S0021889813006195 ]

Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF

S. Monaco, E. Gordon, M. W. Bowler, S. Delagenière, M. Guijarro, D. Spruce, O. Svensson, S. M. McSweeney, A. A. McCarthy, G. Leonard and M. H. Nanao

Synopsis: A system for the automatic reduction of single- and multi-position macromolecular crystallography data is presented.

Online 15 May 2013


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J. Appl. Cryst. (2013). 46, 811-816  [ doi:10.1107/S0021889813005426 ]

SOWOS: an open-source program for the three-dimensional Wulff construction

D. Scopece

Synopsis: An open-source Fortran90 program is presented for creating the Wulff construction (resulting from a user-defined list of facets) in a general and efficient way using a simple algorithm, which is explained. The output files contain all the detailed structural information required to define the solid completely. The code is made freely available to the crystallographic community for immediate use.

Online 18 April 2013


laboratory notes


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J. Appl. Cryst. (2013). 46, 817-822  [ doi:10.1107/S0021889813009734 ]

Fast preparation of a desiccant array for the gradual desiccation method in protein crystallization screening

Q.-Q. Lu, X.-Z. Xie, Y.-M. Liu, H.-M. Lu, D. Chen, X.-S. Wang and D.-C. Yin

Synopsis: The preparation of a desiccant array by dispensing and then drying droplets of aqueous salt solutions on a tape is presented as a means of enhancing the efficiency and the applicability of the gradual desiccation method in protein crystallization screening.

Online 15 May 2013


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J. Appl. Cryst. (2013). 46, 823-825  [ doi:10.1107/S0021889813005955 ]

A cautionary tale on the use of GE-7031 varnish: low-temperature thermal expansion studies of ScF3

C. R. Morelock, M. R. Suchomel and A. P. Wilkinson

Synopsis: An unexpected phase transition observed during low-temperature X-ray diffraction measurements of the negative thermal expansion material ScF3 is a result of stresses arising from the large thermal expansion mismatch with the GE-7031 varnish used as a thermally conducting sample matrix.

Online 6 April 2013


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J. Appl. Cryst. (2013). 46, 826-828  [ doi:10.1107/S0021889813006912 ]

Low-temperature Debye-Scherrer powder diffraction on Beamline I11 at Diamond

J. Potter, J. E. Parker, A. R. Lennie, S. P. Thompson and C. C. Tang

Synopsis: A bespoke capillary sample holder is described that attaches to the cold head of a commercially manufactured (PheniX) closed-cycle helium cryostat originally intended for flat-plate geometry. The new holder allows high-resolution synchrotron powder diffraction data to be collected from samples in Debye-Scherrer geometry over the temperature range 11-295 K.

Online 4 May 2013


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J. Appl. Cryst. (2013). 46, 829-831  [ doi:10.1107/S0021889813006742 ]

An efficient nanolitre-volume multi-channel device for highly viscous materials used in membrane protein crystallization

J. Luo, R. Zwier and J. P. Abrahams

Synopsis: A straightforward low-cost device with a specially engineered multi-channel tip allows the dispensing of very small volumes of viscous lipidic cubic phases (LCPs) more efficiently. The device lowers the threshold for LCP crystallization of membrane proteins/peptides

Online 4 May 2013


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J. Appl. Cryst. (2013). 46, 832-834  [ doi:10.1107/S0021889813010558 ]

An electrically assisted device for protein crystallization in a vapor-diffusion setup

E. Flores-Hernández, V. Stojanoff, R. Arreguín-Espinosa, A. Moreno and N. Sánchez-Puig

Synopsis: This article describes protein crystallization under the influence of an electric field using a sitting-drop and vapor-diffusion experimental setup.

Online 15 May 2013


 

J. Appl. Cryst. (2013). 46, 835-840

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