Journal of Synchrotron Radiation

Volume 20, Part 1 (January 2013)

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

Diamond Light Source, UK, 14-16 March 2012

A printed copy of this issue is available for purchase

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
research papers
short communications
computer programs
addenda and errata
current events
meetings

radiation damage

J. Synchrotron Rad. (2013). 20, 1-6 [ doi:10.1107/S0909049512050418 ]

Radiation damage to biological macromolecules: some answers and more questions

E. F. Garman and M. Weik

Synopsis: Introductory overview to the special issue papers on radiation damage to biological macromolecules.

Online 19 December 2012

J. Synchrotron Rad. (2013). 20, 7-13 [ doi:10.1107/S0909049512048303 ]

Global radiation damage: temperature dependence, time dependence and how to outrun it

M. Warkentin, J. B. Hopkins, R. Badeau, A. M. Mulichak, L. J. Keefe and R. E. Thorne

Synopsis: 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.

Online 29 November 2012

J. Synchrotron Rad. (2013). 20, 14-22 [ doi:10.1107/S0909049512049114 ]

A survey of global radiation damage to 15 different protein crystal types at room temperature: a new decay model

R. M. F. Leal, G. Bourenkov, S. Russi and A. N. Popov

Synopsis: 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.

Online 6 December 2012

J. Synchrotron Rad. (2013). 20, 23-36 [ doi:10.1107/S0909049512046237 ]

To scavenge or not to scavenge, that is STILL the question

E. G. Allan, M. C. Kander, I. Carmichael and E. F. Garman

Synopsis: The reasons for the conflicting results on the efficacy of scavengers in macromolecular crystallography are examined in the light of some new results.

Online 5 December 2012

J. Synchrotron Rad. (2013). 20, 37-48 [ doi:10.1107/S0909049512048807 ]

Identification of patterns in diffraction intensities affected by radiation exposure

D. Borek, Z. Dauter and Z. Otwinowski

Synopsis: 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.

Online 6 December 2012

J. Synchrotron Rad. (2013). 20, 49-57 [ doi:10.1107/S0909049512044706 ]

Optimizing the spatial distribution of dose in X-ray macromolecular crystallography

O. B. Zeldin, M. Gerstel and E. F. Garman

Synopsis: 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.

Online 29 November 2012

J. Synchrotron Rad. (2013). 20, 58-66 [ doi:10.1107/S0909049512044408 ]

Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images

F. Karimi Nejadasl, M. Karuppasamy, E. R. Newman, J. E. McGeehan and R. B. G. Ravelli

Synopsis: 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.

Online 29 November 2012

research papers

J. Synchrotron Rad. (2013). 20, 67-73 [ doi:10.1107/S0909049512041192 ]

Prediction of fatigue life of high-heat-load components made of oxygen-free copper by comparing with Glidcop

S. Takahashi, M. Sano, A. Watanabe and H. Kitamura

Synopsis: 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.

Online 10 November 2012

J. Synchrotron Rad. (2013). 20, 74-79 [ doi:10.1107/S0909049512043154 ]

Spherical analyzers and monochromators for resonant inelastic hard X-ray scattering: a compilation of crystals and reflections

T. Gog, D. M. Casa, A. H. Said, M. H. Upton, J. Kim, I. Kuzmenko, X. Huang and R. Khachatryan

Synopsis: 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.

Online 10 November 2012

J. Synchrotron Rad. (2013). 20, 80-88 [ doi:10.1107/S0909049512043415 ]

A simultaneous multiple angle-wavelength dispersive X-ray reflectometer using a bent-twisted polychromator crystal

T. Matsushita, E. Arakawa, W. Voegeli and Y. F. Yano

Synopsis: 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.

Online 15 November 2012

J. Synchrotron Rad. (2013). 20, 89-97 [ doi:10.1107/S0909049512044883 ]

Optimization of multilayer Laue lenses for a scanning X-ray microscope

H. Yan and Y. S. Chu

Synopsis: 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.

Online 22 November 2012

J. Synchrotron Rad. (2013). 20, 98-104 [ doi:10.1107/S0909049512039441 ]

The Debye-Scherrer camera at synchrotron sources: a revisit

T. Straasø, J. Becker, B. B. Iversen and J. Als-Nielsen

Synopsis: An all-in-vacuum powder diffractometer yields the fundamental background level determined by Compton scattering and is ideal for high-resolution charge density measurements.

Online 10 November 2012

J. Synchrotron Rad. (2013). 20, 105-109 [ doi:10.1107/S0909049512044457 ]

In situ synchrotron wide-angle X-ray diffraction investigation of fatigue cracks in natural rubber

P. Rublon, B. Huneau, N. Saintier, S. Beurrot, A. Leygue, E. Verron, C. Mocuta, D. Thiaudière and D. Berghezan

Synopsis: 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.

Online 29 November 2012

J. Synchrotron Rad. (2013). 20, 110-115 [ doi:10.1107/S0909049512040617 ]

Electronic structure and hybridization of CaS by means of X-ray absorption spectroscopy at Ca and S K-edges

W. Xu, L. Liu, M. Cui, L. Zheng, Y. Hu, A. Marcelli and Z. Wu

Synopsis: A discussion on the electronic structure and particular hybridization of CaS via ab initio calculations of X-ray absorption spectra is presented.

Online 10 November 2012

J. Synchrotron Rad. (2013). 20, 116-124 [ doi:10.1107/S0909049512041301 ]

Towards high-resolution synchrotron radiation imaging with statistical iterative reconstruction

E. A. Rashed and H. Kudo

Synopsis: A statistical iterative image reconstruction algorithm is developed for the local tomography problem in synchrotron radiation X-ray micro-computed tomography.

Online 10 November 2012

J. Synchrotron Rad. (2013). 20, 125-136 [ doi:10.1107/S0909049512041568 ]

Optimizing a flow-through X-ray transmission cell for studies of temporal and spatial variations of ion distributions at mineral-water interfaces

S. S. Lee, P. Fenter and C. Park

Synopsis: 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.

Online 13 November 2012

J. Synchrotron Rad. (2013). 20, 137-144 [ doi:10.1107/S090904951204157X ]

Ascertaining the nanocluster formation within an ion-irradiated Pt/Ni/C multi-trilayer with X-ray absorption spectroscopy

N. Ramanan, S. Roy, D. Lahiri, S. M. Sharma and B. N. Dev

Synopsis: 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.

Online 15 November 2012

J. Synchrotron Rad. (2013). 20, 145-152 [ doi:10.1107/S0909049512039301 ]

A preliminary design of a knot undulator

F. Xi, T. Shi, Q. Fan, S. Prestemon, W. Wan, Z. An and S. Qiao

Synopsis: 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.

Online 10 November 2012

J. Synchrotron Rad. (2013). 20, 153-159 [ doi:10.1107/S0909049512044366 ]

High-resolution high-efficiency X-ray imaging system based on the in-line Bragg magnifier and the Medipix detector

P. Vagovic, D. Korytár, A. Cecilia, E. Hamann, L. Svéda, D. Pelliccia, J. Härtwig, Z. Záprazný, P. Oberta, I. Dolbnya, K. Shawney, U. Fleschig, M. Fiederle and T. Baumbach

Synopsis: 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.

Online 10 November 2012

J. Synchrotron Rad. (2013). 20, 160-165 [ doi:10.1107/S0909049512041337 ]

Measurements of spatial variations in response of ionization chambers

W. E. B. Miller and A. L. Kastengren

Synopsis: 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.

Online 10 November 2012

J. Synchrotron Rad. (2013). 20, 166-171 [ doi:10.1107/S0909049512042197 ]

Local and electronic structure around Ga in CdTe: evidence of DX- and A-centers

V. Koteski, J. Belosevic-Cavor, P. Fochuk and H.-E. Mahnke

Synopsis: 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.

Online 22 November 2012

J. Synchrotron Rad. (2013). 20, 172-180 [ doi:10.1107/S0909049512044354 ]

A comparative study of X-ray tomographic microscopy on shales at different synchrotron facilities: ALS, APS and SLS

W. Kanitpanyacharoen, D. Y. Parkinson, F. De Carlo, F. Marone, M. Stampanoni, R. Mokso, A. MacDowell and H.-R. Wenk

Synopsis: 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.

Online 22 November 2012

J. Synchrotron Rad. (2013). 20, 181-189 [ doi:10.1107/S0909049512041325 ]

Two-dimensional resonant magnetic soft X-ray scattering set-up for extreme sample environment

S. Stanescu, C. Mocuta, F. Merlet and A. Barbier

Synopsis: 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.

Online 10 November 2012

short communications

J. Synchrotron Rad. (2013). 20, 190-193 [ doi:10.1107/S0909049512041556 ]

Concepts for flexible and efficient monochromatization of X-rays by refraction to a relative bandwidth of the order of 0.5%

W. Jark

Synopsis: 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.

Online 10 November 2012

J. Synchrotron Rad. (2013). 20, 194-196 [ doi:10.1107/S0909049512039246 ]

In situ reaction furnace for real-time XRD studies

P. Riello, A. Lausi, J. Macleod, J. R. Plaisier, G. Zerauschek and P. Fornasiero

Synopsis: 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.

Online 10 November 2012

J. Synchrotron Rad. (2013). 20, 197-199 [ doi:10.1107/S0909049512041763 ]

Beam-induced oxidation of monomeric U(IV) species

D. S. Alessi, B. Uster, C. N. Borca, D. Grolimund and R. Bernier-Latmani

Synopsis: 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.

Online 22 November 2012