issue contents

Journal logoJOURNAL OF
ISSN: 1600-5775

January 2013 issue

Includes papers presented at the Seventh International Workshop on X-ray Damage to Biological Crystalline Samples

Diamond Light Source, UK, 14-16 March 2012

Highlighted illustration

Cover illustration: Radiation damage montage: the background shows an overlay of the first and last image of an exposure series of cryo-electron microscopy images. The sample suffered from beam-induced motions; these motions were tracked using gold fiducial markers (in red). A Voronoi diagram, shown in blue, is used for non-rigid registration of the images (see Karimi Nejadasl, Karuppasamy, Newman, McGeehan and Ravelli, pages 58-66). In the foreground, absorbed dose isosurfaces (0.11, 1.8 and 2.5 MGy) for a cuboid crystal, exposed during an X-ray diffraction experiment ten times along its length using a translation data collection strategy to spread dose more evenly, as calculated by Zeldin, Gerstel and Garman (pages 49-57).

facility information

radiation damage

J. Synchrotron Rad. (2013). 20, 1-6
doi: 10.1107/S0909049512050418
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Introductory overview to the special issue papers on radiation damage to biological macromolecules.

J. Synchrotron Rad. (2013). 20, 7-13
doi: 10.1107/S0909049512048303
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The temperature and time dependence of global radiation damage are discussed in the context of outrunning damage at or near room temperature using synchrotron X-ray sources.

J. Synchrotron Rad. (2013). 20, 14-22
doi: 10.1107/S0909049512049114
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A systematic study of the sensitivity to radiation damage of crystals held at room temperature for a large set of model macromolecular structures is presented.

J. Synchrotron Rad. (2013). 20, 23-36
doi: 10.1107/S0909049512046237
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The reasons for the conflicting results on the efficacy of scavengers in macromolecular crystallography are examined in the light of some new results.

J. Synchrotron Rad. (2013). 20, 37-48
doi: 10.1107/S0909049512048807
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Singular value decomposition of a matrix is a versatile tool used in multivariate data analysis. Here, its use is presented to test the validity of physical models applied when scaling diffraction data affected by radiation-induced changes.

J. Synchrotron Rad. (2013). 20, 49-57
doi: 10.1107/S0909049512044706
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Simulated dose distributions for helical and translational macromolecular crystallography data-collection strategies are compared with that of a `standard' protocol as a step towards giving robust definitive guidelines to experimenters for optimizing the diffraction lifetime of crystals.

J. Synchrotron Rad. (2013). 20, 58-66
doi: 10.1107/S0909049512044408
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Cryo-electron microscopy images of vitrified large macromolecular complexes can become blurred due to beam-induced specimen alterations. Exposure series are examined, and rigid and non-rigid image registration schemes are applied to reduce such blurring.

research papers

J. Synchrotron Rad. (2013). 20, 67-73
doi: 10.1107/S0909049512041192
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By using the strain-range partitioning method, the fatigue life of high-heat-load components made of oxygen-free copper have been successfully predicted within a factor of two.

J. Synchrotron Rad. (2013). 20, 74-79
doi: 10.1107/S0909049512043154
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Resonant inelastic X-ray scattering (RIXS) experiments require special sets of near-backscattering spherical diced analyzers and high-resolution monochromators for every distinct absorption-edge energy or emission line. For the purpose of aiding the design and planning of efficient RIXS experiments, a compilation of suitable crystal materials and viable reflections for hard X-rays, together with energy resolution and throughput information, is presented.

J. Synchrotron Rad. (2013). 20, 80-88
doi: 10.1107/S0909049512043415
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Using a convergent X-ray beam having continuously varying energy and glancing angle as a function of direction, the whole profile of a specular X-ray reflectivity curve is measured with no need for any mechanical motion during the measurement.

J. Synchrotron Rad. (2013). 20, 89-97
doi: 10.1107/S0909049512044883
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The optimal design of multilayer Laue lenses for a scanning X-ray microscope based on practical considerations of the apodization effect, monochromaticity requirement and working distance is presented.

J. Synchrotron Rad. (2013). 20, 98-104
doi: 10.1107/S0909049512039441
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An all-in-vacuum powder diffractometer yields the fundamental background level determined by Compton scattering and is ideal for high-resolution charge density measurements.

J. Synchrotron Rad. (2013). 20, 105-109
doi: 10.1107/S0909049512044457
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An original procedure, coupling synchrotron radiation with a mechanical device, is proposed in order to evaluate the strain-induced crystallization phenomenon at a crack tip in natural rubber during uninterrupted fatigue tests.

J. Synchrotron Rad. (2013). 20, 110-115
doi: 10.1107/S0909049512040617
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A discussion on the electronic structure and particular hybridization of CaS via ab initio calculations of X-ray absorption spectra is presented.

J. Synchrotron Rad. (2013). 20, 116-124
doi: 10.1107/S0909049512041301
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A statistical iterative image reconstruction algorithm is developed for the local tomography problem in synchrotron radiation X-ray micro-computed tomography.

J. Synchrotron Rad. (2013). 20, 125-136
doi: 10.1107/S0909049512041568
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An X-ray transmission cell was optimized for high-resolution in situ X-ray reflectivity measurements of the kinetics and thermodynamics of reactions at mineral–solution interfaces and its performance was tested using both optical and X-ray based measurements.

J. Synchrotron Rad. (2013). 20, 137-144
doi: 10.1107/S090904951204157X
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X-ray absorption spectroscopy, in conjunction with the X-ray standing-wave technique, is employed to characterize nanoclusters formed within a Pt/Ni/C multilayer by ion-irradiation.

J. Synchrotron Rad. (2013). 20, 145-152
doi: 10.1107/S0909049512039301
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A preliminary design of a knot undulator is presented. The characteristics of the radiation match the theoretical prediction well. The impact of the undulator on beam dynamics is benign.

J. Synchrotron Rad. (2013). 20, 153-159
doi: 10.1107/S0909049512044366
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A full-field X-ray imaging system based on the in-line germanium Bragg magnifier and Medipix detector is presented. A theoretical and experimental study of the imaging performance of the crystals–detector combination and a comparison with a standard indirect detector typically used in high-resolution X-ray imaging schemes are reported.

J. Synchrotron Rad. (2013). 20, 160-165
doi: 10.1107/S0909049512041337
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Measurements of the spatial variations in the response of three ionization chamber designs were tested as a function of chamber bias voltage, incident X-ray flux and fill gas.

J. Synchrotron Rad. (2013). 20, 166-171
doi: 10.1107/S0909049512042197
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EXAFS on Ga in CdTe complemented by DFT calculations with LAPW+lo methods provide evidence for DX- and A-centers as defect structures besides substitutional incorporation of Ga in CdTe〈Ga〉 grown crystals.

J. Synchrotron Rad. (2013). 20, 172-180
doi: 10.1107/S0909049512044354
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The 3D microstructure of shales is important to assess elastic anisotropic characteristics. In this study, microporosity and mineral components in two shale samples were investigated with X-ray tomographic microscopy at three synchrotron facilities: ALS, APS and SLS, and excellent agreement was observed.

J. Synchrotron Rad. (2013). 20, 181-189
doi: 10.1107/S0909049512041325
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A description of a new optical-transport-based set-up dedicated to soft X-ray magnetic resonant scattering in extreme sample environment, i.e. ultra-high vacuum, high magnetic fields and very low temperatures, is given.

short communications

J. Synchrotron Rad. (2013). 20, 190-193
doi: 10.1107/S0909049512041556
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It is shown that differently shaped prism arrays can provide spectral bandwidth for X-rays of the order of 0.5% under practically feasible experimental conditions.

J. Synchrotron Rad. (2013). 20, 194-196
doi: 10.1107/S0909049512039246
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A reaction furnace has been designed and built for use at the Materials Characterization by X-ray Diffraction beamline at the Elettra synchrotron source (Trieste, Italy). The furnace provides an atmosphere- and temperature-controlled environment for powders in capillaries and a temperature-controlled environment for thin-film samples.

J. Synchrotron Rad. (2013). 20, 197-199
doi: 10.1107/S0909049512041763
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The use of microbeams in X-ray absorption spectroscopy may lead to the oxidation of monomeric U(IV) species in environmental samples. Thus, care should be taken when analyzing samples that may contain monomeric U(IV) with X-ray microprobes.

computer programs

J. Synchrotron Rad. (2013). 20, 200-204
doi: 10.1107/S0909049512044007
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A program for deconvoluting multiple neighbouring absorption edges and computing values of f ′ and f ′′ is presented.

addenda and errata

current events

J. Synchrotron Rad. (2013). 20, 206-207
doi: 10.1107/S0909049512050285

J. Synchrotron Rad. (2013). 20, 208
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