[Dual Source RAPID II]

[ISBC Granada 2013]

Journal of Applied Crystallography

Volume 46, Part 1 (February 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, 1-13  [ doi:10.1107/S0021889812048698 ]

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source

S. Classen, G. L. Hura, J. M. Holton, R. P. Rambo, I. Rodic, P. J. McGuire, K. Dyer, M. Hammel, G. Meigs, K. A. Frankel and J. A. Tainer

Synopsis: The SIBYLS beamline of the Advanced Light Source at Lawrence Berkeley National Laboratory is a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline. Key features and capabilities are described along with implementation and performance.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 14-24  [ doi:10.1107/S0021889812047085 ]

High-pressure phase transitions and equations of state in NiSi. III. A new high-pressure phase of NiSi

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

Synopsis: A new orthorhombic high-pressure phase of NiSi has been synthesized in a multi-anvil press at 1223-1310 K and 17.5 GPa. Its crystal structure has been determined and found to be closely related to that of a tetragonal form of NiSi predicted previously to be stable at high pressure by ab initio computer simulations.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 25-29  [ doi:10.1107/S0021889812048716 ]

Improvement of crystal quality for tetragonal hen egg white lysozyme crystals under application of an external alternating current electric field

H. Koizumi, S. Uda, K. Fujiwara, M. Tachibana, K. Kojima and J. Nozawa

Synopsis: It has been observed that the FWHMs of X-ray rocking-curve profiles for crystals grown with an external electric field are smaller than those for crystals grown without. These results indicate that the crystal quality of hen egg white lysozyme crystals could be improved by application of an external alternating current electric field during growth.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 30-34  [ doi:10.1107/S0021889812048376 ]

Polarized neutron Laue diffraction on a crystal containing dynamically polarized proton spins

F. M. Piegsa, M. Karlsson, B. van den Brandt, C. J. Carlile, E. M. Forgan, P. Hautle, J. A. Konter, G. J. McIntyre and O. Zimmer

Synopsis: In a proof-of-principle polarized neutron Laue diffraction experiment it is shown that the featureless incoherent background due to hydrogen can be uniformly reduced by means of dynamic nuclear polarization of the proton spins, while the intensities of the Laue reflections can be enhanced or diminished significantly.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 35-42  [ doi:10.1107/S0021889812047346 ]

Focusing neutrons with a combination of parabolic and elliptical supermirrors

S. Désert, T. Panzner and P. Permingeat

Synopsis: The design of a neutron-focusing instrument with a combination of parabolic and elliptical supermirrors is presented and its performance is described.

Online 21 December 2012


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J. Appl. Cryst. (2013). 46, 43-47  [ doi:10.1107/S0021889812046018 ]

{111}-specific twinning structures in nonstoichiometric ZrC0.6 with ordered carbon vacancies

W. Hu, S. Liu, B. Wen, J. Xiang, F. Wen, B. Xu, J. He, D. Yu, Y. Tian and Z. Liu

Synopsis: The ordering of carbon vacancies induces the reduction of twinning interfacial energy and leads to the presence of {111} twinning structures in nonstoichiometric ZrC0.6. Two types of twinning boundaries, i.e. {111}C and {111}Zr, can be recognized.

Online 21 December 2012


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J. Appl. Cryst. (2013). 46, 48-54  [ doi:10.1107/S0021889812050522 ]

Contrast in transmission X-ray diffraction topographs of growth defects in the core of SrLaGaO4 single crystals

A. Malinowska, M. Lefeld-Sosnowska and J. Härtwig

Synopsis: Defects in the core of SrLaGaO4 single crystals were studied by transmission X-ray diffraction topography. The contrast of the defect images was analysed for various diffraction conditions and as a function of absorption. The results of the analysis confirm the model of crystal lattice deformation around rod-like volume defects in SrLaGaO4 crystals.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 55-62  [ doi:10.1107/S0021889812046705 ]

Dislocation densities and prevailing slip-system types determined by X-ray line profile analysis in a textured AZ31 magnesium alloy deformed at different temperatures

B. Jóni, T. Al-Samman, S. G. Chowdhury, G. Csiszár and T. Ungár

Synopsis: The substructure in terms of dislocation densities and prevailing slip-system types is determined by the method of X-ray line profile analysis in two different texture components of an AZ31-type Mg-base alloy after extrusion and subsequent tensile deformation at different temperatures.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 63-75  [ doi:10.1107/S0021889812050601 ]

Directional pair distribution function for diffraction line profile analysis of atomistic models

A. Leonardi, M. Leoni and P. Scardi

Synopsis: The concept of the directional pair distribution function is proposed for an atomistic level interpretation of the line profile broadening in powder diffraction patterns of nanocrystalline materials.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 76-87  [ doi:10.1107/S0021889812047620 ]

Resonant X-ray scattering studies of epitaxial complex oxide thin films

E. Perret, C. Park, D. D. Fong, K.-C. Chang, B. J. Ingram, J. A. Eastman, P. M. Baldo and P. H. Fuoss

Synopsis: The resonant anomalous X-ray reflectivity of complex oxide thin films is described.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 88-92  [ doi:10.1107/S0021889812050145 ]

Normalized structure factor analysis with the CentroMK program

M. Kowiel

Synopsis: The ideal asymptotic probability density function and the exact probability density function of the normalized structure factor are compared and a program for normalized structure factor analysis is described.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 93-98  [ doi:10.1107/S0021889812045736 ]

A preferred orientation correction to describe a fiber texture under glancing incidence

D. Simeone, D. Gosset and G. Baldinozzi

Synopsis: Preferred orientation correction of a fiber texture in asymmetric coplanar diffraction conditions is considered, with particular application to glancing-incidence X-ray scattering.

Online 21 December 2012


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J. Appl. Cryst. (2013). 46, 99-107  [ doi:10.1107/S0021889812048133 ]

Cimetidine, C10H16N6S, form C: crystal structure and modelling of polytypes using the superspace approach

A. Arakcheeva, P. Pattison, A. Bauer-Brandl, H. Birkedal and G. Chapuis

Synopsis: An efficient method for modelling a polytypic family is presented with the example of cimetidine in the form C polymorph. The method exploits the (3 + 1)-dimensional superspace model, which is a powerful tool for the description, prediction and understanding of polytype modifications in small-molecule crystallography, as illustrated with this pharmaceutical example.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 108-119  [ doi:10.1107/S0021889812044172 ]

Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals

S. W. M. Tanley, A. M. M. Schreurs, J. R. Helliwell and L. M. J. Kroon-Batenburg

Synopsis: A systematic analysis of diffraction data of 11 different lysozyme crystals (used for cisplatin and carboplatin binding studies), obtained with four diffraction data processing software packages and from two different diffractometers, serves as a pilot study for archiving raw diffraction data and associated metadata. The availability of the raw diffraction images allows for independent assessment of software packages.

Online 8 December 2012


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J. Appl. Cryst. (2013). 46, 120-127  [ doi:10.1107/S0021889812043051 ]

Study of threading dislocation density reduction in AlGaN epilayers by Monte Carlo simulation of high-resolution reciprocal-space maps of a two-layer system

S. Lazarev, M. Barchuk, S. Bauer, K. Forghani, V. Holý, F. Scholz and T. Baumbach

Synopsis: High-resolution X-ray diffraction in coplanar and noncoplanar geometries has been used to investigate the influence of an SiNx nano-mask in the reduction of the threading dislocation density of high-quality AlGaN epitaxial layers grown on sapphire substrates.

Online 8 December 2012


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J. Appl. Cryst. (2013). 46, 128-134  [ doi:10.1107/S0021889812043579 ]

Some properties of the neutron monochromatic beams obtained by multiple Bragg reflections realized in bent perfect single crystals

P. Mikula, M. Vrana, J. Saroun, F. Krejci, B.-S. Seong, W. Woo and M. Furusaka

Synopsis: A new type of high-resolution neutron monochromator based on multiple reflections realized in bent perfect crystals of Si and Ge was tested. By means of multiple reflections, a highly collimated and simultaneously highly monochromatic beam of rather large cross section can be obtained.

Online 8 December 2012


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J. Appl. Cryst. (2013). 46, 135-141  [ doi:10.1107/S0021889812044536 ]

Crystallographic relations during decomposition of the ferritic phase by isothermal ageing of duplex stainless steel

T. Berecz and P. J. Szabo

Synopsis: Orientation relations between the ferritic, austenitic and [sigma]-phase grains in duplex stainless steels were converted into mathematical (matrix) expressions and these expressions were confirmed by automated electron backscatter diffraction measurements of the orientations of single grains.

Online 8 December 2012


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J. Appl. Cryst. (2013). 46, 142-152  [ doi:10.1107/S0021889812046985 ]

Understanding cement hydration at the microscale: new opportunities from `pencil-beam' synchrotron X-ray diffraction tomography

M. Voltolini, M. C. Dalconi, G. Artioli, M. Parisatto, L. Valentini, V. Russo, A. Bonnin and R. Tucoulou

Synopsis: Improved data collection and analysis strategies concerning the `pencil-beam' synchrotron X-ray diffraction tomography technique have been used to obtain quantitative information about the spatial distribution and time evolution of all the phases present in complex systems, such as hydrated cement samples.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 153-164  [ doi:10.1107/S0021889812043737 ]

Submicrometre-resolution polychromatic three-dimensional X-ray microscopy

B. C. Larson and L. E. Levine

Synopsis: The underlying techniques and capabilities of submicrometre-resolution three-dimensional X-ray microscopy (3DXM) are reviewed. The major applications and accomplishments of 3DXM are discussed through selected examples, including investigations of local elastic strain, plastic strain, crystal structure, phase changes and microstructure evolution.

Online 21 December 2012


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J. Appl. Cryst. (2013). 46, 165-172  [ doi:10.1107/S0021889812047887 ]

Grazing-incidence transmission X-ray scattering: surface scattering in the Born approximation

X. Lu, K. G. Yager, D. Johnston, C. T. Black and B. M. Ocko

Synopsis: A new scattering geometry, grazing-incidence transmission small-angle X-ray scattering, is introduced. With this geometry the incident beam is at a grazing angle well above the critical angle and the scattered beam exits through the edge of the substrate. This geometry validates the Born approximation.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 173-180  [ doi:10.1107/S0021889812045943 ]

Advances in exploiting preferred orientation in the structure analysis of polycrystalline materials

J. Grässlin, L. B. McCusker, C. Baerlocher, F. Gozzo, B. Schmitt and L. Lutterotti

Synopsis: Improvements to the experimental setup, the data collection strategy and the data analysis procedure have simplified the method for exploiting preferred orientation in the structure analysis of polycrystalline materials.

Online 21 December 2012


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J. Appl. Cryst. (2013). 46, 181-192  [ doi:10.1107/S0021889812043531 ]

Formation of (Fe,Cr) carbides and dislocation structures in low-chromium steel studied in situ using synchrotron radiation

E. G. Dere, H. Sharma, R. M. Huizenga, G. Portale, W. Bras, V. Bliznuk, J. Sietsma and S. E. Offerman

Synopsis: The evolution of the size distribution of (Fe,Cr) carbides and the dislocation structure in low-chromium steel is studied during quenching and rapid heating by in situ small-angle X-ray scattering (SAXS). From simulations based on the theory of SAXS from dislocations, it is shown that the measured streaks in the two-dimensional SAXS patterns correspond to a dislocation structure of symmetric low-angle tilt boundaries, which in turn corresponds to the crystallographic orientation gradient in the single crystal of ferrite as measured by three-dimensional X-ray diffraction microscopy.

Online 21 December 2012


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J. Appl. Cryst. (2013). 46, 193-209  [ doi:10.1107/S0021889812047917 ]

Short-range and long-range order of phyllomanganate nanoparticles determined using high-energy X-ray scattering

A. Manceau, M. A. Marcus, S. Grangeon, M. Lanson, B. Lanson, A.-C. Gaillot, S. Skanthakumar and L. Soderholm

Synopsis: High-energy X-ray scattering data from turbostratic phyllomanganate nanosheets are analyzed in real-space by pair distribution function analysis and in reciprocal space by the Bragg-rod method and the Debye equation. The elastic deformation of the two-dimensional nanocrystals is modeled with (1) a new empirical strain function in Bragg-rod calculations and (2) explicit spherical and cylindrical mandrels implemented in the Debye equation.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 210-215  [ doi:10.1107/S002188981204914X ]

Back calculation of parent austenite orientation using a clustering approach

V. Tari, A. D. Rollett and H. Beladi

Synopsis: A new approach is presented for calculating the parent orientation from sets of variants of orientations produced by phase transformation.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 216-223  [ doi:10.1107/S0021889812047553 ]

Twin and topotactic growth of [beta]-eucryptite dendrites and their lattice coincidence analysed by the reticular theory

S.-R. Zhao, H.-J. Xu, R. Liu, Q.-Y. Wang and X.-Y. Liu

Synopsis: The crystallographic orientation of [beta]-eucryptite dendrites has been analysed by the electron backscatter diffraction technique, and a twin relationship and a topotactic relationship between dendrites have been found. The twin index n = 2 and the obliquity [omega] = 3.2877°.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 224-233  [ doi:10.1107/S0021889812050042 ]

On the determination of the helical structure parameters of amyloid protofilaments by small-angle neutron scattering and atomic force microscopy

M. V. Avdeev, V. L. Aksenov, Z. Gazová, L. Almásy, V. I. Petrenko, H. Gojzewski, A. V. Feoktystov, K. Siposova, A. Antosova, M. Timko and P. Kopcansky

Synopsis: Various models to describe small-angle neutron scattering data from helices of amyloid protofilaments (hen egg white lysozyme) in solution were analyzed. The found parameters were compared with those obtained by atomic force microscopy of the dried adsorbed state of amyloid fibrils.

Online 17 January 2013


cryocrystallography papers


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J. Appl. Cryst. (2013). 46, 234-241  [ doi:10.1107/S0021889812045013 ]

A high-pressure cryocooling method for protein crystals and biological samples with reduced background X-ray scatter

C. U. Kim, J. L. Wierman, R. Gillilan, E. Lima and S. M. Gruner

Synopsis: A new crystal-hydration method has been developed for high-pressure cryocooling of protein crystals.

Online 21 December 2012


teaching and education


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J. Appl. Cryst. (2013). 46, 242-247  [ doi:10.1107/S0021889812049151 ]

The prolific polytypism of silicon carbide

A. L. Ortiz, F. Sánchez-Bajo, F. L. Cumbrera and F. Guiberteau

Synopsis: A worked example of polytypism is presented to motivate undergraduates in the study and instructors in the teaching of this crystallography topic.

Online 17 January 2013


short communications


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J. Appl. Cryst. (2013). 46, 248-251  [ doi:10.1107/S0021889812044974 ]

Merohedral twin interpretation spreadsheet, including command lines for SHELXL

H. D. Flack and M. Wörle

Synopsis: The spreadsheet described provides much necessary information for undertaking and interpreting least-squares refinements on crystals twinned by merohedry.

Online 8 December 2012


computer programs


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J. Appl. Cryst. (2013). 46, 252-254  [ doi:10.1107/S0021889812048431 ]

ABSORB-7 and ABSORB-GUI for single-crystal absorption corrections

R. Angel and J. Gonzalez-Platas

Synopsis: ABSORB, a program to calculate and apply absorption corrections to single-crystal X-ray intensity data, has been reconfigured to allow it to be called directly from external data processing programs. ABSORB-GUI has been developed to allow much easier specification of standard experiments.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 255-258  [ doi:10.1107/S0021889812045967 ]

SrRietveld: a program for automating Rietveld refinements for high-throughput powder diffraction studies

P. Tian, W. Zhou, J. Liu, Y. Shang, C. L. Farrow, P. Juhás and S. J. L. Billinge

Synopsis: SrRietveld, a Python-based Rietveld refinement program, is described. SrRietveld extends and automates the popular existing Rietveld programs FullProf and GSAS to facilitate studies that involve many refinements, such as the analysis of large numbers of data sets.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 259-261  [ doi:10.1107/S0021889812045025 ]

ReX.Cell: a user-friendly program for powder diffraction indexing

M. Bortolotti and I. Lonardelli

Synopsis: ReX.Cell is a multi-platform open-source program aimed at the automation of powder diffraction data indexing, providing an interactive environment and a simple user interface.

Online 21 December 2012


laboratory notes


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J. Appl. Cryst. (2013). 46, 262-266  [ doi:10.1107/S0021889812042781 ]

An X-ray diffractometer coupled with diffuse reflectance infrared Fourier transform spectroscopy and gas chromatography for in situ and in operando characterization: an innovative analytical laboratory instrument

L. Braconnier, I. Clémençon, C. Legens, V. Moizan, F. Diehl, H. Pillière, P. Echegut, D. De Sousa Meneses and Y. Schuurman

Synopsis: An innovative analytical tool combining X-ray diffraction, diffuse reflectance infrared Fourier transform spectroscopy and gas chromatography using a dedicated reaction cell for in situ and in operando characterization has for the first time been developed for laboratory-scale application. The use of this multitechnique device is illustrated by the study of the thermal decomposition of calcium oxalate.

Online 8 December 2012


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J. Appl. Cryst. (2013). 46, 267-269  [ doi:10.1107/S0021889812046912 ]

A compact device for loading diamond anvil cells with low-boiling pressure-transmitting media

B. A. Zakharov and A. F. Achkasov

Synopsis: A new compact device for loading diamond anvil cells with low-boiling pressure-transmitting media is described.

Online 21 December 2012


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J. Appl. Cryst. (2013). 46, 270-275  [ doi:10.1107/S0021889812046948 ]

Fast acquisition of extensive X-ray diffraction patterns of a gas-liquid interface in grazing-incidence geometry

O. V. Konovalov and A. A. Vorobiev

Synopsis: A collimationless setup for grazing-incidence X-ray diffraction on liquid surfaces and its application for behenic acid Langmuir monolayer characterization is described.

Online 21 December 2012


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J. Appl. Cryst. (2013). 46, 276-278  [ doi:10.1107/S0021889812050297 ]

Effect of crucible design on crystalline perfection and the enhanced optical properties of benzimidazole single crystals grown by the vertical Bridgman technique

B. Riscob, N. Vijayan, M. Shakir, M. A. Wahab and G. Bhagavannarayana

Synopsis: The reported investigations reveal that the crystalline perfection and optical properties of crystals grown by the vertical Bridgman technique with a specially designed double-walled ampoule are better than those of the usually used single-walled ampoule-grown crystals.

Online 17 January 2013


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J. Appl. Cryst. (2013). 46, 279-285  [ doi:10.1107/S0021889812048388 ]

Thermal equilibration of samples for neutron scattering

T. K. Herman, S. C. Parks and J. Scherschligt

Synopsis: Thermal equilibration rates are determined for typical powder samples used in neutron scattering experiments, at temperatures from 5 to 300 K.

Online 17 January 2013


addenda and errata


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J. Appl. Cryst. (2013). 46, 286  [ doi:10.1107/S0021889812050054 ]

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

D.-M. Smilgies

Synopsis: A poor divergence value in the paper by Smilgies [J. Appl. Cryst. (2009), 42, 1030-1034] is corrected.

Online 17 January 2013


book reviews


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J. Appl. Cryst. (2013). 46, 287-288  [ doi:10.1107/S0021889812050716 ]

Advanced Solid State Physics

Online 17 January 2013


 

J. Appl. Cryst. (2013). 46, 289-294

forthcoming meetings and short courses


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