Journal of Applied Crystallography

Volume 43, Part 5 Number 1 (October 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, 949-954  [ doi:10.1107/S0021889810025161 ]

Dynamical scaling in fractal structures in the aggregation of tetraethoxysilane-derived sonogels

D. R. Vollet, D. A. Donatti, A. Ibañez Ruiz and F. S. de Vicente

Synopsis: Dynamical scaling properties in fractal structures were investigated from small-angle X-ray scattering data of the kinetics of aggregation in silica-based gelling systems at different temperatures. The experimental findings are in notable agreement with the dynamical scaling properties.

Online 31 July 2010


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J. Appl. Cryst. (2010). 43, 955-958  [ doi:10.1107/S0021889810022375 ]

Determination of the optical sign of a crystal by a conoscopic method

O. Pikoul

Synopsis: Conoscopic patterns in a system of two crystal plates where the optical sign of one plate is known make it possible to identify the sense of the other crystal plate. The unknown optical sign of the crystal plate is determined by the nature of changes made to its conoscopic pattern by the plate of known optical sign.

Online 31 July 2010


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J. Appl. Cryst. (2010). 43, 959-969  [ doi:10.1107/S0021889810025379 ]

Structure of water-based ferrofluids with sodium oleate and polyethylene glycol stabilization by small-angle neutron scattering: contrast-variation experiments

M. V. Avdeev, A. V. Feoktystov, P. Kopcansky, G. Lancz, V. M. Garamus, R. Willumeit, M. Timko, M. Koneracka, V. Zavisova, N. Tomasovicova, A. Jurikova, K. Csach and L. A. Bulavin

Synopsis: The effect of the addition of polyethylene glycol (PEG) on the structure of a water-based ferrofluid (magnetite coated with sodium oleate) is followed using contrast variation in small-angle neutron scattering. A significant change in the complex aggregates, as a result of PEG adsorption by magnetite, is revealed.

Online 19 August 2010


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J. Appl. Cryst. (2010). 43, 970-980  [ doi:10.1107/S002188981002724X ]

Short-time diffusion of charge-stabilized colloidal particles: generic features

M. Heinen, P. Holmqvist, A. J. Banchio and G. Nägele

Synopsis: Short-time diffusion in charge-stabilized colloidal dispersions is studied by theory, simulation and scattering experiments. Generic features in self-diffusion, cage diffusion and sedimentation are explored.

Online 19 August 2010


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J. Appl. Cryst. (2010). 43, 981-989  [ doi:10.1107/S0021889810030451 ]

Notes on the order-of-reflection dependence of microstrain broadening

A. Leineweber and E. J. Mittemeijer

Synopsis: The reflection-order-dependent increase of the integral breadth of microstrain broadening on the d* scale is investigated. Whereas for negligible local strain gradients `usual', linear increase of the integral breadth occurs, strain gradients can lead to a nonlinear and, for the special case of uncorrelated strains, to a parabolic increase of the integral breadth in association with Lorentzian line shapes.

Online 10 September 2010


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J. Appl. Cryst. (2010). 43, 990-997  [ doi:10.1107/S0021889810031894 ]

A novel additive-free oxides-hydrothermal approach for monazite-type LaPO4 nanomaterials with controllable morphologies

J. Ma and Q. Wu

Synopsis: La2O3 and P2O5 powders are directly used as precursors for preparing monazite-type LaPO4 nanomaterials via an additive-free oxides-hydrothermal method. Many factors can affect the morphology and structure of the products, but the P/La molar ratio cannot change the composition in the given synthesis system.

Online 10 September 2010


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J. Appl. Cryst. (2010). 43, 998-1004  [ doi:10.1107/S0021889810031973 ]

Small-angle X-ray scattering of two-phase systems: significance of polydispersity

W. Ruland

Synopsis: Evaluation of the small-angle X-ray scattering of two-phase systems allows the determination of a measure of the polydispersity of the chord lengths within the dilute phase, which depends on the size distribution and the shape of the particles forming this phase.

Online 10 September 2010


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J. Appl. Cryst. (2010). 43, 1005-1011  [ doi:10.1107/S0021889810030062 ]

Structure and aggregation kinetics of vinyltriethoxysilane-derived organic/silica hybrids

D. R. Vollet, D. A. Donatti, C. M. Awano, W. Chiappim, M. R. Vicelli and A. Ibañez Ruiz

Synopsis: The aggregation kinetics of solutions of vinyltriethoxysilane-derived organic/silica species were studied by small-angle X-ray scattering (SAXS) in a strongly basic medium. The SAXS intensity was analysed using a modified Sharp-Bloomfield global function and its evolution was found to be compatible with the growth, coiling and branching of the polymeric macromolecules in solution.

Online 10 September 2010


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J. Appl. Cryst. (2010). 43, 1012-1020  [ doi:10.1107/S0021889810032644 ]

Ambiguities in the structure determination of antimony tellurides arising from almost homometric structure models and stacking disorder

M. N. Schneider, M. Seibald, P. Lagally and O. Oeckler

Synopsis: Ambiguities in the interpretation of diffraction data from layered chalcogenides arise from almost homometric non-congruent structure models, especially if mixed site occupancies are present. Further pitfalls can result from stacking disorder of distinct tetradymite and A7-type building units.

Online 11 September 2010


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J. Appl. Cryst. (2010). 43, 1021-1026  [ doi:10.1107/S0021889810030803 ]

Replacing a reservoir solution with desiccant in vapor diffusion protein crystallization screening

Q.-Q. Lu, D.-C. Yin, R.-Q. Chen, S.-X. Xie, Y.-M. Liu, X.-F. Zhang, L. Zhu, Z.-T. Liu and P. Shang

Synopsis: Using a desiccant as a substitute for a reservoir solution in the vapor diffusion technique was found to remarkably increase the success rate of crystallization, showing that it could be utilized in practical protein crystallization to yield more crystallization conditions.

Online 10 September 2010


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J. Appl. Cryst. (2010). 43, 1027-1030  [ doi:10.1107/S0021889810024829 ]

New analytical approximation of diffraction size broadened peak profile for spherical crystallites with a lognormal distribution

N. C. Popa, C. M. Teodorescu and S. Frunza

Synopsis: An analytical expression approximating the diffraction peak profile produced by spherical crystallites with a lognormal size distribution is presented. The approximation conserves the volume- and area-averaged column lengths of the exact profile, being appropriate for implementation in the whole powder pattern fitting programs.

Online 31 July 2010


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J. Appl. Cryst. (2010). 43, 1031-1035  [ doi:10.1107/S0021889810024039 ]

Reversible structural phase transition of pyridinium-4-carboxylic acid perchlorate

H.-Y. Ye, H.-L. Cai, J.-Z. Ge and R.-G. Xiong

Synopsis: A disorder-order phase transition in pyridinium-3-carboxylic acid perchlorate was studied by differential scanning calorimetry, dielectric measurement and variable-temperature X-ray single-crystal diffraction analysis.

Online 31 July 2010


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J. Appl. Cryst. (2010). 43, 1036-1039  [ doi:10.1107/S0021889810029894 ]

Dislocation sources and slip band nucleation from indents on silicon wafers

J. Wittge, A. N. Danilewsky, D. Allen, P. McNally, Z. Li, T. Baumbach, E. Gorostegui-Colinas, J. Garagorri, M. R. Elizalde, D. Jacques, M. C. Fossati, D. K. Bowen and B. K. Tanner

Synopsis: The nucleation of dislocations at controlled indents in silicon during rapid thermal annealing has been studied by in situ X-ray diffraction imaging (topography).

Online 19 August 2010


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J. Appl. Cryst. (2010). 43, 1040-1045  [ doi:10.1107/S0021889810028955 ]

Identification of single photoswitchable molecules in nanopores of silica xerogels using powder diffraction

A. Cervellino, J. Schefer, L. Keller, T. Woike and D. Schaniel

Synopsis: Identification of single photoswitchable molecules in an amorphous xerogel matrix is demonstrated using neutron powder diffraction and the Debye approach.

Online 19 August 2010


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J. Appl. Cryst. (2010). 43, 1046-1052  [ doi:10.1107/S0021889810030281 ]

Strain-profile determination in ion-implanted single crystals using generalized simulated annealing

A. Boulle and A. Debelle

Synopsis: The strain profiles in ion-implanted single crystals are determined using high-resolution X-ray diffraction and the generalized simulated annealing algorithm.

Online 10 September 2010


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J. Appl. Cryst. (2010). 43, 1053-1061  [ doi:10.1107/S0021889810025860 ]

Recrystallization of Cu-In-S thin films studied in situ by energy-dispersive X-ray diffraction

H. Rodriguez-Alvarez, R. Mainz, B. Marsen, D. Abou-Ras and H. W. Schock

Synopsis: In situ monitoring of the recrystallization of Cu-In-S thin films by means of X-ray diffraction reveals that the process is composed of three steps: consumption of the CuIn5S8 phase, growth of CuInS2 grains, and a transition from the Cu-Au-type to the chalcopyrite-type ordering of CuInS2.

Online 19 August 2010


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J. Appl. Cryst. (2010). 43, 1062-1067  [ doi:10.1107/S0021889810026646 ]

Investigation of high-temperature phase transformation in one-dimensional Ta2O5 nanorods

R. S. Devan, J.-H. Lin, W.-D. Ho, S. Y. Wu, Y. Liou and Y.-R. Ma

Synopsis: Variable-temperature X-ray diffraction data from the [alpha](1 0 11), [alpha](200), [alpha](2 0 10), [beta](3 11 1) and [beta](2 21 1) lattice planes of one-dimensional Ta2O5 nanorods reveal complex and polymorphic thermochromic phase transformations, which incorporate [beta] to [alpha] ([beta]-[alpha]), [beta] to [beta] ([beta]-[beta]), [alpha] to [alpha] ([alpha]-[alpha]) and [alpha] to [beta] ([alpha]-[beta]) phase transitions at elevated temperatures ranging from 300 to 750 K.

Online 19 August 2010


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J. Appl. Cryst. (2010). 43, 1068-1077  [ doi:10.1107/S002188981002217X ]

The extended Q-range small-angle neutron scattering diffractometer at the SNS

J. K. Zhao, C. Y. Gao and D. Liu

Synopsis: This paper describes the design, construction and initial operation of the extended Q-range SANS instrument at the Spallation Neutron Source (SNS). It also introduces a novel frame-skipping mode of operation on the instrument.

Online 31 July 2010


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J. Appl. Cryst. (2010). 43, 1078-1083  [ doi:10.1107/S0021889810027378 ]

Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization system

C. J. Gerdts, G. L. Stahl, A. Napuli, B. Staker, J. Abendroth, T. E. Edwards, P. Myler, W. Van Voorhis, P. Nollert and L. J. Stewart

Synopsis: The Microcapillary Protein Crystallization System (MPCS) is used to successfully optimize protein crystals from 28 out of 29 tested proteins. Six protein structures have been determined from diffraction-ready crystals grown inside and harvested directly from the MPCS CrystalCards, which are compatible with the recently commercialized and automated MPCS Plug Maker instrument.

Online 19 August 2010


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J. Appl. Cryst. (2010). 43, 1084-1091  [ doi:10.1107/S0021889810026257 ]

An analytical model for the small-angle scattering of polyethylene glycol-modified liposomes

L. Arleth and C. Vermehren

Synopsis: A full analytical model for analysing small-angle neutron scattering data from polymer-modified liposomes is derived. It is demonstrated that the model provides a more accurate structural description of the experimental data than conventional centrosymmetric shell models.

Online 19 August 2010


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J. Appl. Cryst. (2010). 43, 1092-1099  [ doi:10.1107/S0021889810032358 ]

Minimization of absorption contrast for accurate amorphous phase quantification: application to ZrO2 nanoparticles

T. Suzuki-Muresan, P. Deniard, E. Gautron, V. Petrícek, S. Jobic and B. Grambow

Synopsis: This paper highlights the importance of thoroughly characterizing commercial products by complementary methods. The presence of impurities in such products could become a non-negligible parameter for physical and chemical properties studies.

Online 11 September 2010


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J. Appl. Cryst. (2010). 43, 1100-1107  [ doi:10.1107/S0021889810025598 ]

CRYSTALS enhancements: dealing with hydrogen atoms in refinement

R. I. Cooper, A. L. Thompson and D. J. Watkin

Synopsis: The implementation of hydrogen treatment functionality in the software suite CRYSTALS is described.

Online 19 August 2010


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J. Appl. Cryst. (2010). 43, 1108-1112  [ doi:10.1107/S0021889810029493 ]

Crystallographic features of the primary Al3Fe phase in as-cast Al-3.31wt% Fe alloy

L. Li, Y. Zhang, C. Esling, H. Jiang, Z. Zhao, Y. Zuo and J. Cui

Synopsis: Al-3.31wt% Fe was solidified to form the primary Al3Fe phase. The crystallographic features (the extension directions, the complete twinning elements and the surface planes binding the primary phase in the extension directions) of the primary phase were investigated experimentally by electron backscatter diffraction.

Online 10 September 2010


cryocrystallography papers


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J. Appl. Cryst. (2010). 43, 1113-1120  [ doi:10.1107/S0021889810027111 ]

Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase

E. Oksanen, F. Dauvergne, A. Goldman and M. Budayova-Spano

Synopsis: A new Peltier cooling device has allowed the collection of neutron diffraction data from temperature-sensitive crystals of inorganic pyrophosphatase.

Online 19 August 2010


short communications


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J. Appl. Cryst. (2010). 43, 1121-1123  [ doi:10.1107/S0021889810022491 ]

Use of linear scans to obtain |Fhkl|2 and the integrated intensity

R. Shayduk

Synopsis: An alternative method for determining the structure factor of a Bragg reflection is described. It is shown that, for broad reflections, the structure factor can be obtained from linear scans through the reflection in reciprocal space, and the necessary correction factors and diffractometer slit settings are pointed out.

Online 31 July 2010


 

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J. Appl. Cryst. (2010). 43, 1124-1125  [ doi:10.1107/S0021889810021199 ]

Efficiency in the calculation of absorption corrections for cylinders

T. Ida

Synopsis: Efficiency in the calculation of absorption corrections for cylinders has been examined. Application of the Gauss-Legendre quadrature to the formula proposed by Thorkildsen and Larsen gives results having a relative error [less-than or equal to]10-6 with 12 × 12 terms in the numerical integrals.

Online 31 July 2010


computer programs


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J. Appl. Cryst. (2010). 43, 1126-1128  [ doi:10.1107/S0021889810030499 ]

Fityk: a general-purpose peak fitting program

M. Wojdyr

Synopsis: Fityk is portable, open-source, graphical software for nonlinear curve fitting, with an add-on for Pawley refinement of powder patterns.

Online 10 September 2010


 

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J. Appl. Cryst. (2010). 43, 1129-1130  [ doi:10.1107/S0021889810029900 ]

LASER - a program for response-ratio refinement of time-resolved diffraction data

I. Vorontsov, S. Pillet, R. Kaminski, M. S. Schmøkel and P. Coppens

Synopsis: The program LASER for refinement of time-resolved X-ray diffraction data uses the externally-induced intensity changes, rather than the individual intensities, as the data to be refined.

Online 19 August 2010


laboratory notes


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J. Appl. Cryst. (2010). 43, 1131-1133  [ doi:10.1107/S0021889810027901 ]

A laboratory X-ray microbeam for combined X-ray diffraction and fluorescence measurements

S. Rouzière, E. Jourdanneau, B. Kasmi, P. Joly, D. Petermann and P. A. Albouy

Synopsis: A laboratory apparatus is presented that delivers an X-ray microbeam to perform simultaneous X-ray fluorescence and diffraction measurements. The instrument combines specific detectors and optics to optimize performance.

Online 10 September 2010


crystallographers


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J. Appl. Cryst. (2010). 43, 1134  [ doi:10.1107/S0021889810035971 ]

Lachlan M. D. Cranswick (1968-2010)

Online 10 September 2010


 

J. Appl. Cryst. (2010). 43, 1135-1136

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