issue contents

Journal logoJOURNAL OF
SYNCHROTRON
RADIATION
ISSN: 1600-5775

September 2021 issue

Includes papers presented at the 11th International Workshop on X-ray Radiation Damage to Biological Crystalline Samples

14–16th October 2020 (online)

Highlighted illustration

Cover illustration: Artistic rendering of the photolysis of an engineered protein disulfide bond in solution by incident X-rays (see Stachowski, Snell and Snell, pages 1309–1320). This method allows perturbations to high-resolution structural features to be studied with SAXS, a low-resolution technique, by connecting these changes to observable large-scale transitions. Protein rendered with Illustrate [Goodsell, D. S., Autin, L. & Olson, A. J. (2019). Structure, 27, 1716–1720].

facility information


editorial


scientific commentaries


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Extremely bright synchrotron radiation sources give extremely strong intensities at the sample. Lawrence Bright et al. (2021) [J. Synchrotron Rad. (2021), 28, 1377–1385] dive into the details for materials science. I offer a Commentary including a historical context.

radiation damage


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An understanding of radiation damage effects suffered by biological samples during structural analysis using both X-rays and electrons is pivotal to obtain reliable molecular models of imaged molecules. This special issue on radiation damage contains six papers reporting analyses of damage from a range of biophysical imaging techniques.

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A guideline for de novo phasing with small-wedge synchrotron crystallography data collection is presented based on systematic investigations of dose and number of merged sub-datasets.

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This radiation damage study uses a hybrid approach combining molecular dynamics with non-thermal plasma simulations to follow the femtosecond dynamics and X-ray scattering from a protic ionic liquid as it is investigated by an intense XFEL pulse.

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A system engineered to produce a large-scale structural change from X-ray-induced di­sulfide bond cleavage allows residue-specific changes to be interpreted with SAXS. This system is used to investigate how radical scavengers reduce bond breakage during data collection at 10°C with the results providing insight into mitigation strategies for crystallographic and solution experiments.

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The design of a new high-throughput X-ray footprinting endstation and its application to footprinting experimental optimization is described.

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The method of X-ray footprinting mass spectrometry was used to investigate the effect of X-ray irradiation on various proteins in solution under both fully aerated and low dissolved oxygen conditions, and as a function of protein concentration.

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Alternative single-particle cryo-EM schemes are reviewed, in order to improve dose efficiency for obtaining more or complementary structure information within the limited lifetime of the sample.

photondiag2020 workshop


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Simulation results for dynamic ray-tracing software are compared with experimental data showing the impact of vibrations on sample-point X-ray beams.

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The design of an angular array of electron time-of-flight spectrometers is reported, intended for non-invasive spectral, temporal, and polarization characterization of single shots of high-repetition rate, quasi-continuous, short-wavelength free-electron lasers such as the LCLS II at SLAC.

research papers


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The high levels of flux available at a fourth-generation synchrotron are shown to have significant beam heating effects for high-energy X-rays and hard condensed matter samples, leading to temperature increases of over 400 K with a monochromatic beam.

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The development of automated sample delivery and drop on demand methods is described.


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A description of the upgraded bunch-by-bunch feedback system for time-resolved experiments at Pohang Light Source II (PLS-II) is provided. The project is part of the SPring-8 and PLS-II collaboration.

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Here, finite-element analysis is used to study the thermal deformation of a multilayer mirror due to the heat load from the undulator beam at a low-emittance synchrotron source. The energy bandwidth of the double-multilayer monochromator is larger than that of the relevant undulator harmonic, such that a considerable portion of the heat load is reflected. Optimizing the substrate geometry without considering the reflected heat load yields an incorrect depth of the `smart cut' and significant thermal bending.

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This research provides a method of designing reflective extreme ultraviolet (EUV) phase retarders using a linearly chirped Mo/Si multilayer mirror, which can achieve phase control and polarization state analysis of EUV synchrotron radiation.

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This work presents the first characterization of a thin organic semiconductor photodiode for dosimetry in microbeam radiation therapy carried out on the Australian Synchrotron Imaging and Medical Beamline.

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Exploitation of X-ray circular polarized beams to study forbidden Bragg reflections and new information that could be obtained in these experiments are discussed.

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The dynamical theory of X-ray Laue diffraction in flat and wedge sectioned multilayers is considered. Recurrence relations are obtained that describe Laue diffraction in structures that are inhomogeneous in depth.

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The first X-ray Extended Range Technique (XERT)-like experiment at the Australian Synchrotron measured 496 energies from 8.51 keV to 11.59 keV for zinc metal to 0.023–0.036% accuracy. Systematics are quantified.

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Zinc metal XAFS to high accuracy determined K-edge jump ratio and jump factors, revealing significant issues in theory and experiment. Nanostructure of zinc is determined to high accuracy with bond lengths with uncertainties from 0.1% to 0.3% or 0.003 to 0.008 ÅA, suggesting local dynamic motion of the crystal lattice.

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Sputter deposition is combined with in situ N K-edge absorption measurements to study thin films of magnetic nitrides (Fe-N, Co-N, Ni-N) ranging from sub-monolayer to bulk. Ultra-thin films of these nitrides were found to demonstrate a different behavior that can be coupled with structural changes taking place with the increasing film thickness.

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This article evaluates the utility of pre-edge analysis of X-ray absorption near-edge structure spectra for studying materials with variable amounts of disorder using two examples: a unimodal distribution of nearest neighbors of homogeneously distributed metal centers (Ti in Ti oxide nanocomposites) and a bimodal distribution due to the local structural heterogeneities around V in V oxide nanocomposites. In the latter case, both the pre-edge analysis and conventional EXAFS analysis are combined to detect the presence of local structural heterogeneities.

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The local chemical state of a model Pt/Al2O3 catalyst is visualized operando by rapid 2D XANES imaging during the catalytic partial oxidation of methane to synthesis gas.

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Beam stability and sample drift compensation schemes are presented for use on I14, the Hard X-ray Nanoprobe at Diamond Light Source.

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Nuclear resonant reflectivity (NRR) was measured from an Fe60Al40 film irradiated by 20 keV Ne+ ions with gradually varying fluences of 0–3.0 × 1014 ions cm−2. The evolution of the ferromagnetic onset, starting from the central part of the film and propagating towards the interfaces, was revealed by the fit of the NRR time spectra.

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The temperature and wavenumber dependence of the EXAFS oscillation of hexagonal close-packed crystals have been calculated and analyzed under the effect of the non-ideal axial ratio c/a based on the extended anharmonic correlated Debye model.

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A feasible implementation of a novel X-ray detector for highly energetic X-ray photons with a large solid angle coverage, optimal for the detection of Compton X-ray scattered photons, is described. The device, consisting of a 20 cm-thick sensitive volume filled with xenon at atmospheric pressure, forms photoelectron images by resorting to the electroluminescence produced in a custom-made multi-hole acrylic structure.

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In an off-axis geometry, a circular multilayer zone disc is used to locally generate X-ray beam induced currents inside a single InP nanowire. This allows to spatially probe local electric fields at practical working distances and very low background signal.

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Dissimilar hardware and software conventions at various synchrotrons lead to quantitative differences in experimental results. This paper proposes a method to improve reproducibility of tomographic reconstructions by optimizing the filtering step in commonly used reconstruction algorithms.

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A practical step-by-step guide to high-speed X-ray computed tomography is presented, from the collection of computed tomography images and their reconstruction to performing quantitative analysis, while accounting for the constraints imposed by high-pressure and high-temperature experimentation.

short communications


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A ptychographic coherent diffraction imaging (CDI) system with pinhole or Fresnel zone-plate optics for use in the tender X-ray region (2–5 keV) has been developed on the BL27SU beamline at SPring-8. A resolution of approximately 50 nm was achieved in ptychographic CDI of a 200 nm thick Ta test chart, and a sulfur polymer material was successfully observed.

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A correlation-based semi-synthetic computational optical approach has been applied to assess the possibilities of exploiting the spatio-spectral aberrations of the Infrared Microspectroscopy Beamline to perform rapid imaging.

beamlines



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A new experimental station has been developed at BL25SU of SPring-8 for angle-resolved photoemission spectroscopy using a soft X-ray microbeam.

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The commissioning and first experiments on the white beam imaging facility at the imaging beamline Indus-2 to allow high-resolution imaging at high frame rates and higher penetration are presented.


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The Brain Imaging Beamline (BIB) of the Taiwan Photon Source (TPS) and its endstation, designed to take advantage of bright unmonochromatized synchrotron X-rays and targeting fast 3D imaging and high spatial resolution, have been commissioned and opened to users.

laboratory notes


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A wide-acceptance-angle spherical grid with numerous micro cylindrical holes was developed for a high-resolution retarding field analyzer.
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