Journal of Applied Crystallography

Volume 42, Part 4 (August 2009)

	Cover illustration: Three-dimensional reconstructed crystal (purple), loop (yellow) and solvent (transparent pink) for a native DNA sample. Courtesy of Brockhauser, Di Michiel, McGeehan, McCarthy & Ravelli [J. Appl. Cryst. (2008), 41, 1057-1066].

• research papers
• short communications
• CIF applications
• computer programs
• laboratory notes
• meetings

research papers

J. Appl. Cryst. (2009). 42, 553-563  [ doi:10.1107/S0021889809017361 ] Experiment and simulation on interface shapes of an yttrium aluminium garnet miniature molten zone formed using the laser-heated pedestal growth method for single-crystal fibers P. Y. Chen, C. L. Chang, K. Y. Huang, C. W. Lan, W. H. Cheng and S. L. Huang Synopsis: The melt/air and melt/solid interface shapes of the miniature molten zone formed in a laser-heated pedestal growth system are studied numerically and with experimental verification. Online 13 June 2009

J. Appl. Cryst. (2009). 42, 564-571  [ doi:10.1107/S0021889809018172 ] Transformations for monoclinic crystal symmetry in texture analysis S. Matthies and H.-R. Wenk Synopsis: Monoclinic crystals can be described in two settings: in the first setting the C2 rotation axis is parallel to the z axis and in the second setting it is parallel to the y axis. This article gives explicit transformations that need to be applied for texture analysis and for calculations of physical properties of materials with preferred orientation. Online 13 June 2009

J. Appl. Cryst. (2009). 42, 572-579  [ doi:10.1107/S0021889809006803 ] An efficient X-ray spectrometer based on thin mosaic crystal films and its application in various fields of X-ray spectroscopy H. Legall, H. Stiel, M. Schnürer, M. Pagels, B. Kanngießer, M. Müller, B. Beckhoff, I. Grigorieva, A. Antonov, V. Arkadiev and A. Bjeoumikhov Synopsis: The performance of a spectrometer based on thin mosaic crystals was investigated for different spectroscopic methods using various X-ray sources. It was found that, even with low-power X-ray sources, advanced high-resolution X-ray spectroscopy can be performed. Online 30 May 2009

J. Appl. Cryst. (2009). 42, 580-591  [ doi:10.1107/S0021889809022936 ] Twinning on pyramidal planes in hexagonal close packed crystals determined along with other defects by X-ray line profile analysis L. Balogh, G. Tichy and T. Ungár Synopsis: A systematic procedure is developed to evaluate the frequency of twinning on pyramidal planes together with dislocation densities, active slip systems and crystallite size in hexagonal close packed metals. The procedure is incorporated into the eCMWP whole powder pattern evaluation method. Online 30 June 2009

J. Appl. Cryst. (2009). 42, 592-596  [ doi:10.1107/S002188980902295X ] Morphology of polysorbate 80 (Tween 80) micelles in aqueous 1,4-dioxane solutions H. Aizawa Synopsis: Changes in the structure of micelles of the surfactant polysorbate 80 (Tween 80) in 0-50% aqueous 1,4-dioxane solutions (pH 7.2, ionic strength 2.44 mM) were measured by small-angle X-ray scattering. The polysorbate 80 micelles changed from core-shell cylindrical micelles to core-shell discus micelles between concentrations of 20 and 30% 1,4-dioxane, and from core-shell discus micelles to core-shell elliptic discus micelles between concentrations of 40 and 50% 1,4-dioxane. Online 30 June 2009

J. Appl. Cryst. (2009). 42, 597-606  [ doi:10.1107/S0021889809020378 ] Evaluation of particle statistics in powder diffractometry by a spinner-scan method T. Ida, T. Goto and H. Hibino Synopsis: The uncertainty in measured diffraction intensity caused by particle statistics has been evaluated by a step-scan measurement about the rotation angle of a specimen-spinning attachment of a laboratory powder X-ray diffractometer. Crystallite sizes of quartz powder samples ranging from 3 to 22 µm have been successfully evaluated by further statistical analysis of the measured intensity data. Online 30 June 2009

J. Appl. Cryst. (2009). 42, 607-615  [ doi:10.1107/S0021889809023528 ] Automatic multiple-zone rigid-body refinement with a large convergence radius P. V. Afonine, R. W. Grosse-Kunstleve, A. Urzhumtsev and P. D. Adams Synopsis: Systematic investigation of a large number of trial rigid-body refinements leads to an optimized multiple-zone protocol with a larger convergence radius. Online 16 July 2009

J. Appl. Cryst. (2009). 42, 616-620  [ doi:10.1107/S0021889809023127 ] High-resolution X-ray microdiffraction analysis of NaOH-treated dentin W. Wei, M. Jing, P. Zhou, X. Jianzhong, L. Yan, G. Shiqiang, W. Dan and Z. Bin Synopsis: NaOH attacks both the mineral and the organic components of human dentin, and it is believed to cause a change in crystal sizes and crystal disorder, mainly due to the collapse of the organic scaffold. Online 16 July 2009

J. Appl. Cryst. (2009). 42, 621-628  [ doi:10.1107/S0021889809022456 ] Evaluation of incoherent scattering intensity by transmission and sample thickness M. Shibayama, T. Matsunaga and M. Nagao Synopsis: A novel method to evaluate the incoherent scattering intensity for hydrogen-containing materials is proposed. This method needs only the transmission and the sample thickness. Online 30 June 2009

J. Appl. Cryst. (2009). 42, 629-635  [ doi:10.1107/S0021889809016446 ] Structural and microstructural characterization of human kidney stones from eastern India using IR spectroscopy, scanning electron microscopy, thermal study and X-ray Rietveld analysis S. Ghosh, S. Basu, S. Chakraborty and A. K. Mukherjee Synopsis: Structural and microstructural studies of eight human urinary calculi from eastern India using IR spectroscopy, X-ray diffraction, scanning electron microscopy and thermogravimetric differential scanning calorimetry have been carried out. Quantitative X-ray diffraction phase analysis using the Rietveld method indicated exclusively calcium oxalate monohydrate in three kidney stones, while the remaining five were mixtures of calcium oxalate monohydrate, calcium oxalate dehydrate and hydroxyapatite. Online 30 May 2009

J. Appl. Cryst. (2009). 42, 636-641  [ doi:10.1107/S0021889809019177 ] Novel sample preparation technique for protein crystal X-ray crystallographic analysis combining microfluidics and acoustic manipulation S. Oberti, D. Möller, S. Gutmann, A. Neild and J. Dual Synopsis: A technique for sample preparation prior to X-ray crystallographic analysis of protein crystals involving the use of acoustic radiation forces and a micro-machined fluidic device is introduced. Crystals can be positioned in a sequence along a channel and then individually removed with a loop, which is then mounted onto a goniometer. Online 13 June 2009

J. Appl. Cryst. (2009). 42, 642-648  [ doi:10.1107/S002188980902353X ] Diffraction anomalous fine structure study of iron/iron oxide nanoparticles C. Meneghini, F. Boscherini, L. Pasquini and H. Renevier Synopsis: Diffraction anomalous fine structure measurements of Fe/Fe oxide core-shell nanoparticles are reported. It is found that such measurements can provide useful structural information despite the high degree of disorder and the nanometre-size dimensions of the investigated system. Online 16 July 2009

J. Appl. Cryst. (2009). 42, 649-659  [ doi:10.1107/S0021889809017701 ] Simulation of small-angle X-ray scattering from thylakoid membranes J. J. K. Kirkensgaard, J. K. Holm, J. K. Larsen and D. Posselt Synopsis: A novel simulation approach is presented for calculating small-angle scattering from photosynthetic membrane systems with complex geometries. Online 13 June 2009

J. Appl. Cryst. (2009). 42, 660-672  [ doi:10.1107/S0021889809017476 ] Crystal structure of defect-containing semiconductor nanocrystals - an X-ray diffraction study M. Buljan, U. V. Desnica, N. Radic, G. Drazic, Z. Matej, V. Vales and V. Holý Synopsis: A method is developed for an exact calculation of the intensity of X-ray diffraction from nanocrystals containing plane defects using a Debye-function approach. Online 13 June 2009

J. Appl. Cryst. (2009). 42, 673-680  [ doi:10.1107/S0021889809017877 ] Microbeam X-ray diffraction from twisted lamellar crystals: theory and computer simulation V. A. Luchnikov and D. A. Ivanov Synopsis: Theoretical and computer simulation approaches are developed for modelling the microbeam X-ray diffraction patterns from twisted lamellar ribbons. The angular broadening of diffraction peaks is accounted for by the varying crystal orientation caused by lamellar twisting. The proposed peak broadening analysis can be used, for example, in morphological studies of banded polymer spherulites. Online 13 June 2009

J. Appl. Cryst. (2009). 42, 681-690  [ doi:10.1107/S0021889809017919 ] Aspherical refractive lenses for small-angle neutron scattering H. Frielinghaus, V. Pipich, A. Radulescu, M. Heiderich, R. Hanslik, K. Dahlhoff, H. Iwase, S. Koizumi and D. Schwahn Synopsis: This paper discusses the testing and simulation of aspherical neutron lenses as focusing elements for small-angle neutron scattering and their transparency with respect to thermal diffuse scattering. Online 20 June 2009

J. Appl. Cryst. (2009). 42, 691-696  [ doi:10.1107/S0021889809020081 ] Phase transformation in nanocrystalline Sm2Co17 permanent magnet material X. Song, N. Lu, W. Xu, Z. Zhang and J. Zhang Synopsis: Phase transformations in nanocrystalline Sm2Co17 alloy were investigated systematically by a series of annealing experiments. Online 20 June 2009

J. Appl. Cryst. (2009). 42, 697-705  [ doi:10.1107/S0021889809021232 ] In situ X-ray diffraction of the transformation of gibbsite to -alumina through calcination: effect of particle size and heating rate B. K. Gan, I. C. Madsen and J. G. Hockridge Synopsis: The effect of particle size and heating rate on the transformation sequences of gibbsite to -Al2O3 has been studied using coarse-grained C31 hydrate and fine-grained Hydral 710. Online 30 June 2009

J. Appl. Cryst. (2009). 42, 706-714  [ doi:10.1107/S0021889809022924 ] High-throughput powder diffraction V: the use of Raman spectroscopy with and without X-ray powder diffraction data G. Barr, G. Cunningham, W. Dong, C. J. Gilmore and T. Kojima Synopsis: A statistically optimal method of combining Raman data with powder diffraction data is presented for use when analysing data derived from high-throughput experiments. Online 30 June 2009

J. Appl. Cryst. (2009). 42, 715-723  [ doi:10.1107/S0021889809022572 ] Analysis of focused-beam powder X-ray diffraction resolution using doubly curved crystal optics A. Bingölbali and C. A. MacDonald Synopsis: In this work, focusing doubly curved crystal X-ray optics were used in powder diffraction to produce an intense spot for use with small powder or polycrystalline samples. Online 16 July 2009

short communications

J. Appl. Cryst. (2009). 42, 724-725  [ doi:10.1107/S0021889809023504 ] Atomic pair distribution function analysis from the ARCS chopper spectrometer at the Spallation Neutron Source E. S. Bozin, P. Juhás, W. Zhou, M. B. Stone, D. L. Abernathy, A. Huq and S. J. L. Billinge Synopsis: The first use of the ARCS chopper spectrometer at the Spallation Neutron Source at Oak Ridge National Laboratory for powder-diffraction-based atomic pair distribution function analysis is reported. Its performance is benchmarked against the NPDF diffractometer at Los Alamos National Laboratory. Online 16 July 2009

CIF applications

J. Appl. Cryst. (2009). 42, 726-729  [ doi:10.1107/S0021889809016690 ] Crystallography Open Database - an open-access collection of crystal structures S. Grazulis, D. Chateigner, R. T. Downs, A. F. T. Yokochi, M. Quirós, L. Lutterotti, E. Manakova, J. Butkus, P. Moeck and A. Le Bail Synopsis: The Crystallography Open Database (COD) is an ongoing initiative by crystallographers to gather all published inorganic, metal-organic and small organic molecule structures in one database, providing a straightforward search and retrieval interface. The COD adopts an open-access model for its >80 000 structure files. Online 30 May 2009

computer programs

J. Appl. Cryst. (2009). 42, 730-733  [ doi:10.1107/S0021889809017981 ] New pole figure calculation software: 2DiffCalc U. Garbe Synopsis: 2DiffCalc is an easy to use pole figure calculation software connected to several neutron and synchrotron beam lines. Online 30 June 2009

J. Appl. Cryst. (2009). 42, 734-740  [ doi:10.1107/S0021889809019050 ] New software for the singular value decomposition of time-resolved crystallographic data Y. Zhao and M. Schmidt Synopsis: User-friendly software for the singular value decomposition of time-resolved crystallographic data has been developed. A graphical user interface guides the user through a quick and semi-automatic analysis of the data that ultimately leads to the atomic structures of reaction intermediates in conjunction with their kinetics. Online 30 June 2009

J. Appl. Cryst. (2009). 42, 741-742  [ doi:10.1107/S0021889809015921 ] MyCrystals - a simple visual data management program for laboratory-scale crystallization experiments M. N. Løvgreen, M. Løvgreen, H. E. M. Christensen and P. Harris Synopsis: MyCrystals is a simple user-friendly program developed to display and sort crystal images on the basis of the entered crystallization conditions. Online 30 May 2009

laboratory notes

J. Appl. Cryst. (2009). 42, 743-744  [ doi:10.1107/S0021889809021700 ] Rigorous filtration for protein crystallization N. E. Chayen Synopsis: The effect of filtration on the number, size and quality of protein crystals is described. Online 20 June 2009

Copyright © International Union of Crystallography
IUCr Webmaster