Journal of Applied Crystallography

Volume 43, Part 3 (June 2010)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: PDB_REDO optimization of the oldest structure with experimental data in the PDB [155c; Timkovich & Dickerson (1976). J. Biol. Chem. 251, 4033-4046]. Front: final structure - warmer colours show greater atomic displacement. Back: final structure model with atomic trajectories in yellow. Courtesy of Joosten et al. [J. Appl. Cryst. (2009), 42, 376-384].

research papers


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J. Appl. Cryst. (2010). 43, 385-393  [ doi:10.1107/S0021889810005625 ]

Structure of PbTe(SiO2)/SiO2 multilayers deposited on Si(111)

G. Kellermann, E. Rodriguez, E. Jimenez, C. L. Cesar, L. C. Barbosa and A. F. Craievich

Synopsis: The structure of multilayered thin films - composed of layers of spherical PbTe nanocrystals embedded in an SiO2 matrix - is studied by grazing-incidence small-angle X-ray scattering.

Online 26 March 2010


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J. Appl. Cryst. (2010). 43, 394-400  [ doi:10.1107/S0021889810008150 ]

Cation distribution in spinel (Mn,Co,Cr)3O4 at room temperature

A. Purwanto, A. Fajar, H. Mugirahardjo, J. W. Fergus and K. Wang

Synopsis: As part of a study of the long-term operation of solid-oxide fuel cells, three (Mn,Co,Cr)3O4 samples have been synthesized and characterized using X-ray and neutron diffraction on powder samples at room temperature. The data were co-refined.

Online 26 March 2010


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J. Appl. Cryst. (2010). 43, 401-406  [ doi:10.1107/S0021889810008113 ]

A benchmark method for global optimization problems in structure determination from powder diffraction data

K. Shankland, A. J. Markvardsen, C. Rowlatt, N. Shankland and W. I. F. David

Synopsis: Local minimization algorithms have been used to solve two moderately complex molecular crystal structures from powder diffraction data. The results are used to characterize the [chi]2 agreement surface and provide a benchmark against which the performance of other optimization algorithms can be assessed.

Online 26 March 2010


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J. Appl. Cryst. (2010). 43, 407-416  [ doi:10.1107/S0021889810003055 ]

Isothermal compressibility of macromolecular crystals and macromolecules derived from high-pressure X-ray crystallography

I. Ascone, R. Kahn, E. Girard, T. Prangé, A.-C. Dhaussy, M. Mezouar, N. Ponikwicki and R. Fourme

Synopsis: The compressibility of several proteins and polynucleotides was determined by high-pressure single-crystal diffraction.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 417-428  [ doi:10.1107/S0021889810007454 ]

On the coherency-controlled growth habit of precipitates in minerals

S.-L. Hwang, P. Shen, T.-F. Yui and H.-T. Chu

Synopsis: A precipitate and its parent crystal always establish a specific crystallographic relationship in which the differences in the g-vector pairs ([Delta]g) of the two structures are aligned in the same direction, and the precipitate exhibits a growth habit plane normal to [Delta]g. This normal-to-[Delta]g principle is formulated to calculate the optimum interphase boundaries in several mineral systems.

Online 30 April 2010


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J. Appl. Cryst. (2010). 43, 429-433  [ doi:10.1107/S0021889810012720 ]

Normalized one- and two-dimensional distribution functions for interatomic distance and angle data from crystallographic databases

A. Gavezzotti

Synopsis: It is demonstrated that distributions of intermolecular distances and angles should be properly normalized to highlight their chemical meaning.

Online 30 April 2010


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J. Appl. Cryst. (2010). 43, 434-447  [ doi:10.1107/S0021889810011805 ]

Structural and microstructural changes during anion exchange of CoAl layered double hydroxides: an in situ X-ray powder diffraction study

R. E. Johnsen, F. Krumeich and P. Norby

Synopsis: Anion-exchange reactions involving carbonate, chloride, nitrate and sulfate layered double hydroxides were studied in situ by synchrotron X-ray powder diffraction.

Online 30 April 2010


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J. Appl. Cryst. (2010). 43, 448-454  [ doi:10.1107/S0021889810012525 ]

A simplified invariant line analysis for face-centred cubic/body-centred cubic precipitation systems

H. Liu, E. R. Waclawik and C. Luo

Synopsis: A simplified invariant line analysis for face-centered cubic/body-centered cubic precipitation systems is proposed. This simplified analysis makes the application of phase transformation theory more understandable and highly efficient.

Online 30 April 2010


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J. Appl. Cryst. (2010). 43, 455-465  [ doi:10.1107/S0021889810010642 ]

Dynamical theory calculations of spin-echo resolved grazing-incidence scattering from a diffraction grating

R. Ashkar, P. Stonaha, A. L. Washington, V. R. Shah, M. R. Fitzsimmons, B. Maranville, C. F. Majkrzak, W. T. Lee, W. L. Schaich and R. Pynn

Synopsis: A dynamical theory calculation, based on Bloch wave expansion, is developed to explain spin-scho resolved grazing incidence scattering measurements on a diffraction grating. The theory provides a detailed description of the scattering process and the behavior of the neutron wavefunction in the vicinity of the grating.

Online 30 April 2010


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J. Appl. Cryst. (2010). 43, 466-472  [ doi:10.1107/S0021889810008484 ]

An investigation of goethite-seeded Al(OH)3 precipitation using in situ X-ray diffraction and Rietveld-based quantitative phase analysis

N. A. S. Webster, I. C. Madsen, M. J. Loan, R. B. Knott, F. Naim, K. S. Wallwork and J. A. Kimpton

Synopsis: In situ X-ray diffraction has been used to investigate goethite-seeded Al(OH)3 precipitation from synthetic Bayer liquor at 343 K. Rietveld-based quantitative phase analysis has allowed for the determination of the absolute phase abundances of the precipitated phases and for the determination of kinetic information.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 473-482  [ doi:10.1107/S0021889810009313 ]

Effect of mechanical vibration on protein crystallization

Q.-Q. Lu, D.-C. Yin, Y.-M. Liu, X.-K. Wang, P.-F. Yang, Z.-T. Liu and P. Shang

Synopsis: Mechanical vibration was found to affect crystal morphology and crystallization screening, showing that it could be utilized in practical protein crystallization to obtain better faceted crystals and yield more crystallization conditions.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 483-490  [ doi:10.1107/S0021889810008460 ]

Atomic structure analysis at the nanoscale using the pair distribution function: simulation studies of simple elemental nanoparticles

K. Mullen, V. Krayzman and I. Levin

Synopsis: Estimation of the features of an ensemble of Au nanoparticles using pair distribution function data is investigated via optimization of a model function calculated by simulation of an ensemble of particles.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 491-497  [ doi:10.1107/S0021889810008745 ]

Enhancement of second harmonic generation, optical and dielectric properties in L-asparagine monohydrate single crystals due to an improvement in crystalline perfection by annealing

M. Shakir, S. K. Kushawaha, K. K. Maurya, S. Kumar, M. A. Wahab and G. Bhagavannarayana

Synopsis: Significant improvement of crystalline perfection in L-asparagine monohydrate single crystals was achieved by annealing. As a result of the improvement in crystalline perfection, remarkable enhancement in second harmonic generation efficiency, optical transparency, fluorescence intensity and dielectric properties was observed.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 498-503  [ doi:10.1107/S002188981000796X ]

Low-temperature phase transformation and phonon confinement in one-dimensional Ta2O5 nanorods

R. S. Devan, W.-D. Ho, S. Y. Wu and Y.-R. Ma

Synopsis: The variable-temperature X-ray diffraction results of the [beta](001), [alpha](101) and [alpha](103) lattice planes of one-dimensional Ta2O5 nanorods showed complex and polymorphic thermochromic phase transformations, which incorporate [alpha]-to-[alpha] ([alpha]-[alpha]), [alpha]-[alpha]-[beta] and [alpha]-[beta] phase transitions at elevated temperatures ranging from 80 to 300 K. The d-spacing expansions of the lattice planes can explain the thermochromic phase transformations between [alpha]- and [beta]-phase crystals.

Online 26 March 2010


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J. Appl. Cryst. (2010). 43, 504-510  [ doi:10.1107/S0021889810005856 ]

Parametric Rietveld refinement for the evaluation of powder diffraction patterns collected as a function of pressure

I. Halasz, R. E. Dinnebier and R. Angel

Synopsis: Parametric Rietveld refinement is extended to variable-pressure powder diffraction data. Different approaches to parameterization are described and compared.

Online 26 March 2010


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J. Appl. Cryst. (2010). 43, 511-519  [ doi:10.1107/S0021889810006990 ]

A thermosyphon-driven hydrothermal flow-through cell for in situ and time-resolved neutron diffraction studies

F. Xia, B. O'Neill, Y. Ngothai, J. Peak, C. Tenailleau, B. Etschmann, G. Qian, J. Brugger, A. Studer, S. Olsen and A. Pring

Synopsis: A thermosyphon-driven flow-through cell has been designed and constructed for hydrothermal crystallization studies by the in situ and time-resolved neutron diffraction technique, and has been demonstrated by the hydrothermal transformations between KAlSi2O6 and NaAlSi2O6·H2O on the high-intensity powder diffraction beamline WOMBAT at the Australian Nuclear Science and Technology Organization (ANSTO). The cell is located at ANSTO and is open to worldwide users.

Online 26 March 2010


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J. Appl. Cryst. (2010). 43, 520-530  [ doi:10.1107/S0021889810012197 ]

Coherent and diffuse X-ray scattering in crystals modulated by a surface acoustic wave

V. I. Punegov, Y. I. Nesterets and D. V. Roshchupkin

Synopsis: A new theory describing the coherent and diffuse X-ray scattering in non-ideal crystals modulated by a surface acoustic wave is presented. The calculated reciprocal space maps and rocking curves are compared with the corresponding experimental results.

Online 30 April 2010


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J. Appl. Cryst. (2010). 43, 531-538  [ doi:10.1107/S0021889810009131 ]

Long-range ordering in anodic alumina films: a microradian X-ray diffraction study

K. S. Napolskii, I. V. Roslyakov, A. A. Eliseev, A. V. Petukhov, D. V. Byelov, N. A. Grigoryeva, W. G. Bouwman, A. V. Lukashin, K. O. Kvashnina, A. P. Chumakov and S. V. Grigoriev

Synopsis: Microradian X-ray diffraction shows that the porous structure of anodic alumina films possesses long-range orientational order and very extended longitudinal self-correlations, while the interpore positional order is rather short-range, not more than ~10 interpore distances.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 539-549  [ doi:10.1107/S0021889810012963 ]

Determining grain resolved stresses in polycrystalline materials using three-dimensional X-ray diffraction

J. Oddershede, S. Schmidt, H. F. Poulsen, H. O. Sørensen, J. Wright and W. Reimers

Synopsis: A new algorithm to extend three-dimensional X-ray diffraction analysis of grain resolved properties to include the characterization of grain resolved stresses is presented. The algorithm has been applied to both simulated and experimental data to validate the obtained results.

Online 30 April 2010


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J. Appl. Cryst. (2010). 43, 550-559  [ doi:10.1107/S0021889810009143 ]

Implementation of statistical dynamic diffraction theory for defective semiconductor heterostructure modelling

P. K. Shreeman and R. J. Matyi

Synopsis: A modified method for implementing statistical dynamic diffraction theory is presented, along with its application to structurally defective semiconductor heterostructures.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 560-569  [ doi:10.1107/S0021889810006400 ]

Powder diffraction by fixed incident angle reflection using a curved position-sensitive detector

R. P. Haggerty, P. Sarin, J.-F. Bérar, Z. D. Apostolov and W. M. Kriven

Synopsis: The corrections necessary to conduct and analyze fixed incident angle reflection geometry experiments with a curved position-sensitive detector are provided.

Online 26 March 2010


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J. Appl. Cryst. (2010). 43, 570-577  [ doi:10.1107/S0021889810008587 ]

The macromolecular neutron diffractometer (MaNDi) at the Spallation Neutron Source, Oak Ridge: enhanced optics design, high-resolution neutron detectors and simulated diffraction

L. Coates, A. D. Stoica, C. Hoffmann, J. Richards and R. Cooper

Synopsis: A newly designed neutron guide system for the macromolecular diffractometer (MaNDi) at the Spallation Neutron Source is described, along with large-area high-resolution neutron detectors. Monte Carlo techniques used to simulate diffraction from large unit cells are also detailed.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 578-586  [ doi:10.1107/S0021889810008873 ]

Theory of geometrical broadening of diffraction peaks from twisted lamellar crystals for interpretation of X-ray microbeam and selected-area electron diffraction experiments

V. A. Luchnikov and D. A. Ivanov

Synopsis: The broadening of X-ray and electron diffraction peaks due to helicoidal twist of lamellar crystals is analyzed in the limit of small natural reflection width. The proposed approach can be useful for interpretation of microbeam diffractograms measured on banded polymer spherulites.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 587-595  [ doi:10.1107/S0021889810008459 ]

Modeling of kinematic diffraction from a thin silicon film illuminated by a coherent, focused X-ray nanobeam

A. Ying, B. Osting, I. C. Noyan, C. E. Murray, M. Holt and J. Maser

Synopsis: Simulation of kinematic diffraction from a thin Si film illuminated by a coherent, focused X-ray nanobeam is presented and compared with experimental data measured at the nanoprobe instrument at Sector 26 of the Advanced Photon Source.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 596-602  [ doi:10.1107/S0021889810008228 ]

Misorientations induced by deformation twinning in titanium

N. Bozzolo, L. Chan and A. D. Rollett

Synopsis: All possible misorientations induced in commercially pure titanium during cold-rolling as a result of the combination of two twinning systems have been calculated and compared with the experimentally observed twin configurations. A 41° misorientation has been identified as resulting from the development of tensile twins inside primary compressive twins.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 603-610  [ doi:10.1107/S0021889810006163 ]

Simulating and evaluating small-angle X-ray scattering of micro-voids in polypropylene during mechanical deformation

S. Fischer, T. Diesner, B. Rieger and O. Marti

Synopsis: A model is introduced to evaluate the scattering of randomly distributed micro-voids which are aligned along a given direction and show a log-normal size distribution.

Online 30 April 2010


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J. Appl. Cryst. (2010). 43, 611-616  [ doi:10.1107/S0021889810010782 ]

Autoindexing with outlier rejection and identification of superimposed lattices

N. K. Sauter and B. K. Poon

Synopsis: After autoindexing, Bragg spot candidates that do not fit on the model lattice can be identified, providing a potentially useful measure of sample quality and giving an avenue for indexing a second lattice, if one is present.

Online 30 April 2010


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J. Appl. Cryst. (2010). 43, 617-622  [ doi:10.1107/S002188981000868X ]

New approach to twin interfaces of modulated martensite

Z. Li, Y. Zhang, C. Esling, X. Zhao, Y. Wang and L. Zuo

Synopsis: Using automated electron backscatter diffraction, a new approach is presented for the comprehensive and unambiguous determination of twin relationships in a 7M modulated Ni-Mn-Ga alloy.

Online 30 April 2010


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J. Appl. Cryst. (2010). 43, 623-629  [ doi:10.1107/S002188981000988X ]

Crystal structure solution from experimentally determined atomic pair distribution functions

P. Juhás, L. Granlund, S. R. Gujarathi, P. M. Duxbury and S. J. L. Billinge

Synopsis: A method is presented for crystal structure solution from atomic pair distribution function data.

Online 30 April 2010


short communications


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J. Appl. Cryst. (2010). 43, 630-631  [ doi:10.1107/S002188981000779X ]

Morphology of polysorbate 80 (Tween 80) micelles in aqueous dimethyl sulfoxide solutions

H. Aizawa

Synopsis: A study of the structure of micelles of the surfactant polysorbate 80 in aqueous dimethyl sulfoxide solutions shows that the micelles change from core-shell cylinder micelles to core-shell discus micelles between concentrations of 20 and 30% dimethyl sulfoxide.

Online 26 March 2010


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J. Appl. Cryst. (2010). 43, 632-634  [ doi:10.1107/S0021889810007673 ]

Whole-pattern profile fitting of powder diffraction data collected in parallel-beam flat-plate asymmetric reflection geometry

M. R. Rowles and I. C. Madsen

Synopsis: A simple, physically-based model which uses up to three refinable parameters to fit peak profiles is presented. The use of this model reduces the total number of parameters required to fit the observed peak profiles, hence leading to increased stability during profile analysis.

Online 26 March 2010


computer programs


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J. Appl. Cryst. (2010). 43, 635-638  [ doi:10.1107/S0021889810009155 ]

Extracting differential pair distribution functions using MIXSCAT

C. Wurden, K. Page, A. Llobet, C. E. White and Th. Proffen

Synopsis: MIXSCAT is a user-friendly program to extract differential pair distribution functions from neutron and X-ray data.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 639-646  [ doi:10.1107/S0021889810008289 ]

Scatter: software for the analysis of nano- and mesoscale small-angle scattering

S. Förster, L. Apostol and W. Bras

Synopsis: Scatter is a new software for analysis, modeling and fitting of scattering curves and scattering patterns of non-ordered, partially ordered or fully ordered nano- and mesoscale structures.

Online 15 April 2010


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J. Appl. Cryst. (2010). 43, 647-653  [ doi:10.1107/S0021889810005133 ]

Real-space calculation of powder diffraction patterns on graphics processing units

L. Gelisio, C. L. Azanza Ricardo, M. Leoni and P. Scardi

Synopsis: This paper shows how the power of graphics processing units can be exploited to compute the powder diffraction pattern of nano-sized objects.

Online 30 April 2010


laboratory notes


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J. Appl. Cryst. (2010). 43, 654-658  [ doi:10.1107/S0021889810008551 ]

Optimization of a bent perfect Si(111) monochromator at a small take-off angle for use in a stress instrument

B.-S. Seong, V. Em, P. Mikula, J. Saroun and M.-H. Kang

Synopsis: It is shown that for a stress instrument with small monochromator take-off angle (~30°) the maximum figure of merit for angular accuracy of the diffraction line position, which is comparable to the instrument having a take-off angle of ~55°, can be achieved by optimizing a focusing Si(111) bent perfect crystal monochromator.

Online 15 April 2010


crystallographers


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J. Appl. Cryst. (2010). 43, 659  [ doi:10.1107/S0021889810006941 ]

Aaron Joseph Kalb (Gilboa) (1937-2009)

Online 26 March 2010


book reviews


 

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J. Appl. Cryst. (2010). 43, 660-661  [ doi:10.1107/S0021889810009702 ]

Two-dimensional X-ray diffraction

Online 30 April 2010


 

J. Appl. Cryst. (2010). 43, 662-664

forthcoming meetings and short courses


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