Journal of Applied Crystallography

Volume 42, Part 6 (December 2009)



[Issue Author Index][Volume Author Index]
[Cover illustration] 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


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J. Appl. Cryst. (2009). 42, 981-989  [ doi:10.1107/S0021889809035353 ]

Dependence of small-angle neutron scattering contrast on the difference in thermal expansions of phases in two-phase alloys

P. Strunz, R. Gilles, D. Mukherji, M. Hofmann, D. del Genovese, J. Roesler, M. Hoelzel and V. Davydov

Synopsis: The difference in thermal expansion of the two primary phases, [gamma] and [gamma]', causes the scattering contrast to change with temperature in Ni superalloys. This feature can be used for determination of the scattering contrast without a knowledge of the compositions of the individual phases.

Online 3 October 2009


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J. Appl. Cryst. (2009). 42, 990-993  [ doi:10.1107/S0021889809035717 ]

Management of metadata and automation for mail-in measurements with the APS 11-BM high-throughput, high-resolution synchrotron powder diffractometer

B. H. Toby, Y. Huang, D. Dohan, D. Carroll, X. Jiao, L. Ribaud, J. A. Doebbler, M. R. Suchomel, J. Wang, C. Preissner, D. Kline and T. M. Mooney

Synopsis: A high-resolution and high-throughput synchrotron powder diffractometer has been automated for use with samples that are mailed in by Advanced Photon Source users.

Online 15 October 2009


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J. Appl. Cryst. (2009). 42, 994-998  [ doi:10.1107/S0021889809037777 ]

Study of structural defects in ZnGeP2 crystals by X-ray topography based on the Borrmann effect

A. O. Okunev, G. A. Verozubova, E. M. Trukhanov, I. V. Dzjuba, P. R. J. Galtier and S. A. Said Hassani

Synopsis: The effect of anomalous transmission of X-rays on ZnGeP2 crystals has been investigated, using the method of X-ray topography based on the Borrmann effect. The identification of the defects revealed in ZnGeP2 was carried out by comparison of the experimental intensity contrast with simulated images of the defects.

Online 30 October 2009


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J. Appl. Cryst. (2009). 42, 999-1003  [ doi:10.1107/S0021889809040199 ]

Detection of the standing X-ray wavefield intensity inside a thin crystal using back-diffraction topography and imaging

M. G. Honnicke and C. Cusatis

Synopsis: The standing X-ray wavefield intensity of a single crystal, under dynamical diffraction conditions, is directly measured by setting a 50 µm-thick single-crystal CCD detector chip in nondispersive back-diffraction geometry.

Online 30 October 2009


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J. Appl. Cryst. (2009). 42, 1004-1008  [ doi:10.1107/S0021889809037595 ]

Design challenges and performance of nested neutron mirrors for microfocusing on SNAP

G. E. Ice, J. W. L. Pang, C. Tulk, J. Molaison, J.-Y. Choi, C. Vaughn, L. Lytle, P. Z. Takacs, K. H. Andersen, T. Bigault and A. Khounsary

Synopsis: Kirkpatrick-Baez neutron supermirrors can efficiently focus polychromatic neutron beams to micrometre dimensions. Early results from such a system installed on the Spallation Neutrons at Pressure Beamline 3 at the Spallation Neutron Source at Oak Ridge National Laboratory are presented.

Online 30 October 2009


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J. Appl. Cryst. (2009). 42, 1009-1019  [ doi:10.1107/S0021889809036826 ]

Small-angle neutron scattering analysis of a water-based magnetic fluid with charge stabilization: contrast variation and scattering of polarized neutrons

M. V. Avdeev, E. Dubois, G. Mériguet, E. Wandersman, V. M. Garamus, A. V. Feoktystov and R. Perzynski

Synopsis: The nuclear and magnetic scattering contributions in small-angle scattering experiments on a diluted water-based magnetic fluid are separated by the contrast variation technique and scattering of polarized neutrons. The significant difference found in the nuclear and magnetic apparent particle sizes is related to different nuclear and magnetic correlation lengths in the system.

Online 30 October 2009


 

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J. Appl. Cryst. (2009). 42, 1020-1029  [ doi:10.1107/S0021889809040989 ]

Efficient calculation of a normal matrix-vector product for anisotropic full-matrix least-squares refinement of macromolecular structures

B. V. Strokopytov

Synopsis: A new set of equations for a normal matrix-vector product for the case of anisotropic refinement is given. Significantly faster methods for the calculation of a preconditioner and the normal matrix-vector product are described in detail.

Online 7 November 2009


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J. Appl. Cryst. (2009). 42, 1030-1034  [ doi:10.1107/S0021889809040126 ]

Scherrer grain-size analysis adapted to grazing-incidence scattering with area detectors

D.-M. Smilgies

Synopsis: Various aspects of the application of the Scherrer formula to grain-size analysis in thin films of soft materials are discussed within the methodology of grazing-incidence small- and wide-angle scattering and in conjunction with the use of area detectors.

Online 15 October 2009


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J. Appl. Cryst. (2009). 42, 1035-1042  [ doi:10.1107/S0021889809042022 ]

The MORPHEUS protein crystallization screen

F. Gorrec

Synopsis: MORPHEUS is an initial protein crystallization screen with a unique organization which integrates components and ligands selected after analysing all crystal structure data deposited with the Protein Data Bank and local data gathered at the MRC Laboratory of Molecular Biology, Cambridge, England (MRC-LMB). Three challenging proteins from the MRC-LMB have already been crystallized exclusively using MORPHEUS.

Online 7 November 2009


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J. Appl. Cryst. (2009). 42, 1043-1053  [ doi:10.1107/S0021889809033147 ]

Aspherical electron scattering factors and their parameterizations for elements from H to Xe

J.-C. Zheng, L. Wu and Y. Zhu

Synopsis: The formalism for and the parameterizations of aspherical electron scattering factors using relativistic wavefunctions are presented.

Online 3 October 2009


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J. Appl. Cryst. (2009). 42, 1054-1061  [ doi:10.1107/S0021889809035705 ]

The crystal structure of perdeuterated methanol monoammoniate (CD3OD·ND3) determined from neutron powder diffraction data at 4.2 and 180 K

A. D. Fortes, I. G. Wood and K. S. Knight

Synopsis: The crystal structure of perdeuterated methanol monoammoniate, CD3OD·ND3, has been solved from neutron powder diffraction data collected at 4.2 and 180 K.

Online 3 October 2009


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J. Appl. Cryst. (2009). 42, 1062-1067  [ doi:10.1107/S002188980903739X ]

Simulation of the powder diffraction pattern of randomly restacked Ca2Nb3O10 nanosheets

M. Onoda, Y. Ebina and T. Sasaki

Synopsis: The matrix method for diffuse scattering has been effectively used to simulate the X-ray powder diffraction pattern of randomly restacked Ca2Nb3O10 nanosheets connected by K ions.

Online 15 October 2009


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J. Appl. Cryst. (2009). 42, 1068-1072  [ doi:10.1107/S002188980904196X ]

Basal plane bending of 6H-SiC single crystals observed by synchrotron radiation X-ray topography

L. Ning, X. Hu, Y. Wang, X. Xu, Y. Gao, Y. Peng, X. Chen, W. Huang and Q. Yuan

Synopsis: Basal plane bending was observed by synchrotron white-beam X-ray topography. The shapes of Laue spots for different reflections were simulated based on a spherical curvature model, and the simulation results fit well with the experimental images.

Online 7 November 2009


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J. Appl. Cryst. (2009). 42, 1073-1084  [ doi:10.1107/S0021889809037376 ]

In situ diffraction strain analysis of elastically deformed polycrystalline thin films, and micromechanical interpretation

D. Faurie, O. Castelnau, R. Brenner, P.-O. Renault, E. Le Bourhis and Ph. Goudeau

Synopsis: In situ tensile tests on polycrystalline Au thin films have been carried out under synchrotron radiation. The 2[theta] shift of diffraction lines, which reflects the elastic strain (and its heterogeneity) within the specimen, is analysed by means of several micromechanical approaches.

Online 15 October 2009


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J. Appl. Cryst. (2009). 42, 1085-1091  [ doi:10.1107/S002188980903475X ]

Structural characterization of manganese-substituted nanocrystalline zinc oxide using small-angle neutron scattering and high-resolution transmission electron microscopy

B. Roy, B. Karmakar, J. Bahadur, S. Mazumder, D. Sen and M. Pal

Synopsis: Structural characterization of nanocrystalline Mn-substituted ZnO has been carried out using X-ray diffraction, high-resolution transmission electron microscopy and small-angle neutron scattering in order to check the growth of secondary phases, particle size and size distribution which are the prime issues for analyzing different physical properties.

Online 3 October 2009


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J. Appl. Cryst. (2009). 42, 1092-1101  [ doi:10.1107/S0021889809036498 ]

Characterization of order domains in [bold gamma]-TiAl by orientation microscopy based on electron backscatter diffraction

C. Zambaldi, S. Zaefferer and S. I. Wright

Synopsis: The slight tetragonality of only about 2% in ordered [gamma]-TiAl makes it difficult to discriminate the order variants in orientation mapping by electron backscatter diffraction. A successful approach, based on high-accuracy measurement and a newly developed indexing scheme, is presented and validated.

Online 15 October 2009


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J. Appl. Cryst. (2009). 42, 1102-1109  [ doi:10.1107/S0021889809035857 ]

Measurement of stress factors and residual stress of a film by in situ X-ray diffraction during four-point bending

M. Ortolani, C. L. Azanza Ricardo and P. Scardi

Synopsis: Stress factors and residual stress in a film are simultaneously measured by in-situ X-ray diffraction during four-point bending. The procedure, here applied to a galvanic nickel coating, can be used for virtually any polycrystalline layer, without previous knowledge of single-crystal elastic constants or grain interaction models.

Online 15 October 2009


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J. Appl. Cryst. (2009). 42, 1110-1121  [ doi:10.1107/S0021889809034621 ]

Towards extracting the charge density from normal-resolution data

B. Dittrich, C. B. Hübschle, J. J. Holstein and F. P. A. Fabbiani

Synopsis: It is shown that the charge density of a molecule in a crystal can be obtained from normal-resolution data when thermal motion and electron density are de-convoluted. This can be achieved by incorporating fixed atomic displacement parameters from a preceding invariom refinement.

Online 3 October 2009


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J. Appl. Cryst. (2009). 42, 1122-1128  [ doi:10.1107/S0021889809036280 ]

Structural studies on carbon nanotube fibres by synchrotron radiation microdiffraction and microfluorescence

R. J. Davies, C. Riekel, K. K. Koziol, J. J. Vilatela and A. H. Windle

Synopsis: This study reports on the characterization of a carbon nanotube fibre using synchrotron radiation microbeam small- and wide-angle X-ray scattering in combination with microfluorescence.

Online 15 October 2009


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J. Appl. Cryst. (2009). 42, 1129-1138  [ doi:10.1107/S0021889809040990 ]

Grating-based holographic X-ray diffraction: theory and application to confined fluids

K. Nygård, D. K. Satapathy, O. Bunk, E. Perret, J. Buitenhuis, C. David and J. F. van der Veen

Synopsis: A grating-based holographic X-ray diffraction technique has been developed which allows reconstruction of the density profiles of confined nano-scale fluids.

Online 30 October 2009


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J. Appl. Cryst. (2009). 42, 1139-1146  [ doi:10.1107/S0021889809039867 ]

Energy-dispersive Laue diffraction by means of a frame-store pnCCD

S. Send, M. von Kozierowski, T. Panzner, S. Gorfman, K. Nurdan, A. H. Walenta, U. Pietsch, W. Leitenberger, R. Hartmann and L. Strüder

Synopsis: The crystallographic unit cell of [gamma]-LiAlO2 is determined without a priori information by means of an energy-dispersive X-ray Laue diffraction experiment using a frame-store pn-junction CCD detector.

Online 30 October 2009


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J. Appl. Cryst. (2009). 42, 1147-1157  [ doi:10.1107/S0021889809041685 ]

Comparison of X-ray and electron backscatter diffraction textures for back-annealed Al-Mg alloys

O. Engler

Synopsis: The potential of electron backscatter diffraction (EBSD) to determine integral macrotexture data is explored by comparing EBSD-derived textures with standard X-ray textures for the Al-Mg alloy AA 5005 in the cold-rolled and various back-annealed states. In particular, the effect of EBSD filtering tools and the impact of sampling step size on the statistical significance of EBSD data are investigated.

Online 7 November 2009


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J. Appl. Cryst. (2009). 42, 1158-1164  [ doi:10.1107/S0021889809042678 ]

Depth-dependent local structures in thin films unraveled by grazing-incidence X-ray absorption spectroscopy

N. M. Souza-Neto, A. Y. Ramos, H. C. N. Tolentino, A. Martins and A. D. Santos

Synopsis: A method of using X-ray absorption spectroscopy together with resolved grazing-incidence geometry for depth profiling of atomic, electronic or chemical local structures in thin films is presented. Surface oxidation and local structural depth profiles in nanometric FePt films are determined, exemplifying the application of the method.

Online 17 November 2009


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J. Appl. Cryst. (2009). 42, 1165-1175  [ doi:10.1107/S0021889809042277 ]

Development of a shutterless continuous rotation method using an X-ray CMOS detector for protein crystallography

K. Hasegawa, K. Hirata, T. Shimizu, N. Shimizu, T. Hikima, S. Baba, T. Kumasaka and M. Yamamoto

Synopsis: A shutterless continuous rotation method using an X-ray complementary metal-oxide semiconductor (CMOS) detector has been developed for high-speed, precise data collection in protein crystallography. The new method and detector were applied to the structure determination of three proteins by multi- and single-wavelength anomalous diffraction phasing and have thereby been proved to be applicable in protein crystallography.

Online 17 November 2009


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J. Appl. Cryst. (2009). 42, 1176-1188  [ doi:10.1107/S0021889809043210 ]

Neutron powder diffraction in materials with incoherent scattering: an illustration of Rietveld refinement quality from nondeuterated gypsum

P. F. Henry, M. T. Weller and C. C. Wilson

Synopsis: This work presents an investigation of nondeuterated gypsum using the current generation of constant-wavelength neutron powder diffraction instruments at the Institut Laue-Langevin.

Online 17 November 2009


computer programs


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J. Appl. Cryst. (2009). 42, 1189-1193  [ doi:10.1107/S0021889809034207 ]

PeckCryst: a program for structure determination from powder diffraction data using a particle swarm optimization algorithm

Z. J. Feng, C. Dong, R. R. Jia, X. D. Deng, S. X. Cao and J. C. Zhang

Synopsis: PeckCryst has been developed and released for molecular crystal structure determination from powder diffraction data and uses a particle swarm optimization algorithm. The distributed releases can run on Windows and Linux (32- and 64-bit) platforms.

Online 3 October 2009


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J. Appl. Cryst. (2009). 42, 1194-1196  [ doi:10.1107/S0021889809040424 ]

VIBRATE! A program to compute irreducible representations for atomic vibrations in crystals

A. M. Glazer

Synopsis: A computer program has been written to carry out factor group analysis of normal modes of vibration for crystal structures.

Online 15 October 2009


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J. Appl. Cryst. (2009). 42, 1197-1202  [ doi:10.1107/S0021889809042915 ]

EXPO2009: structure solution by powder data in direct and reciprocal space

A. Altomare, M. Camalli, C. Cuocci, C. Giacovazzo, A. Moliterni and R. Rizzi

Synopsis: Ab initio crystal structure solution by powder diffraction data can be performed by EXPO2009 both in direct and in reciprocal space. The main applications and novel features of EXPO2009 are described.

Online 17 November 2009


laboratory notes


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J. Appl. Cryst. (2009). 42, 1203-1204  [ doi:10.1107/S0021889809036218 ]

A method for the indexation of back-reflection Laue X-ray photographs

F. A. Sidokhine, E. F. Sidokhine and A. F. Sidokhine

Synopsis: This article proposes an alternative approach to indexing X-ray Laue back-photographs with the emphasis on imperfect metallic single crystals.

Online 3 October 2009


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J. Appl. Cryst. (2009). 42, 1205  [ doi:10.1107/S0021889809036188 ]

Test tube for obtaining crystals

B. Cabric and N. Danilovic

Synopsis: A model of an air-cooled test tube (`crystallization socket-outlet adaptor') in a laboratory furnace, for simultaneous regulation of different crystallization parameters in crucible columns, is presented. This design enables fast studies of crystal growth.

Online 3 October 2009


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J. Appl. Cryst. (2009). 42, 1206-1208  [ doi:10.1107/S0021889809036164 ]

A robotic arm as a simple sample changer for a diffractometer with very low component costs

D. Lian, I. P. Swainson, L. M. D. Cranswick and R. Donaberger

Synopsis: Cheap model robots can be used to automate simple sample changing for less than the cost of a linear drive with far more flexibility of design.

Online 15 October 2009


 

J. Appl. Cryst. (2009). 42, 1209-1212

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