Uranium XAFS analysis of kidney from rats exposed   to uranium
The kidney is the critical target of uranium exposure because uranium accumulates in the proximal tubules and causes tubular damage, but the chemical nature of uranium in kidney, such as its chemical status in the toxic target site, is poorly understood. Micro-X-ray absorption fine-structure ( µ XAFS) analysis was used to examine renal thin sections of rats exposed to uranyl acetate. The U LIII-edge X-ray absorption near-edge structure spectra of bulk renal specimens obtained at various toxicological phases were similar to that of uranyl acetate: their edge position did not shift compared with that of uranyl acetate ...
Source: Journal of Synchrotron Radiation - February 20, 2017 Category: Physics Authors: Kitahara, K. Numako, C. Terada, Y. Nitta, K. Shimada, Y. Homma-Takeda, S. Tags: uranium µ XAFS elemental mapping kidney research papers Source Type: research

Establishment of new design criteria for GlidCop ® X-ray absorbers
An engineering research program has been conducted at the Advanced Photon Source (APS) in order to determine the thermomechanical conditions that lead to crack formation in GlidCop ® , a material commonly used to fabricate X-ray absorbers at X-ray synchrotron facilities. This dispersion-strengthened copper alloy is a proprietary material and detailed technical data of interest to the synchrotron community is limited. The results from the research program have allowed new design criteria to be established for GlidCop ® X-ray absorbers based upon the thermomechanically induced fatigue behavior of the material. X-ray ...
Source: Journal of Synchrotron Radiation - February 20, 2017 Category: Physics Authors: Collins, J.T. Nudell, J. Navrotski, G. Liu, Z. Den Hartog, P. Tags: GlidCop ® thermal fatigue life photon absorbers high heat load front-ends design criteria transient non-linear FEA research papers Source Type: research

Simulating and optimizing compound refractive lens-based X-ray microscopes
A comprehensive optical description of compound refractive lenses (CRLs) in condensing and full-field X-ray microscopy applications is presented. The formalism extends ray-transfer matrix analysis by accounting for X-ray attenuation by the lens material. Closed analytical expressions for critical imaging parameters such as numerical aperture, spatial acceptance (vignetting), chromatic aberration and focal length are provided for both thin- and thick-lens imaging geometries. These expressions show that the numerical aperture will be maximized and chromatic aberration will be minimized at the thick-lens limit. This limit may...
Source: Journal of Synchrotron Radiation - February 20, 2017 Category: Physics Authors: Simons, H. Ahl, S.R. Poulsen, H.F. Detlefs, C. Tags: X-ray imaging X-ray microscopy X-ray optics compound refractive lens ray transfer matrix research papers Source Type: research

A large-solid-angle X-ray Raman scattering spectrometer at ID20 of the European Synchrotron Radiation Facility
An end-station for X-ray Raman scattering spectroscopy at beamline ID20 of the European Synchrotron Radiation Facility is described. This end-station is dedicated to the study of shallow core electronic excitations using non-resonant inelastic X-ray scattering. The spectrometer has 72 spherically bent analyzer crystals arranged in six modular groups of 12 analyzer crystals each for a combined maximum flexibility and large solid angle of detection. Each of the six analyzer modules houses one pixelated area detector allowing for X-ray Raman scattering based imaging and efficient separation of the desired signal from the samp...
Source: Journal of Synchrotron Radiation - February 16, 2017 Category: Physics Authors: Huotari, S. Sahle, C.J. Henriquet, C. Al-Zein, A. Martel, K. Simonelli, L. Verbeni, R. Gonzalez, H. Lagier, M.-C. Ponchut, C. Moretti Sala, M. Krisch, M. Monaco, G. Tags: inelastic x-ray scattering X-ray Raman spectroscopy beamline spectrometer ESRF beamlines Source Type: research

Magnetic design and modelling of a 14   mm-period prototype superconducting undulator
The magnetic design of a ten-period (each period 14   mm) prototype superconducting undulator is reported using RADIA. The results of modelling the magnetic flux density are presented in an analytical formula. The dependence of the field integrals and phase error on the current density and undulator gap has been calculated, and temperature curves are determined for the models and are compared with earlier reported Moser – Rossmanith fits. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - February 16, 2017 Category: Physics Authors: Mishra, G. Gehlot, M. Sharma, G. Trillaud, F. Tags: superconducting undulator research papers Source Type: research

Probe reconstruction for holographic X-ray imaging
In X-ray holographic near-field imaging the resolution and image quality depend sensitively on the beam. Artifacts are often encountered due to the strong focusing required to reach high resolution. Here, two schemes for reconstructing the complex-valued and extended wavefront of X-ray nano-probes, primarily in the planes relevant for imaging (i.e. focus, sample and detection plane), are presented and compared. Firstly, near-field ptychography is used, based on scanning a test pattern laterally as well as longitudinally along the optical axis. Secondly, any test pattern is dispensed of and the wavefront reconstructed only ...
Source: Journal of Synchrotron Radiation - February 16, 2017 Category: Physics Authors: Hagemann, J. Robisch, A.-L. Osterhoff, M. Salditt, T. Tags: X-ray near-field imaging ptychography probe characterization research papers Source Type: research

A novel molten-salt electrochemical cell for investigating   the reduction of uranium dioxide to uranium metal by lithium using in situ synchrotron radiation
A novel electrochemical cell has been designed and built to allow for in situ energy-dispersive X-ray diffraction measurements to be made during reduction of UO2 to U metal in LiCl – KCl at 500 ° C. The electrochemical cell contains a recessed well at the bottom of the cell into which the working electrode sits, reducing the beam path for the X-rays through the molten-salt and maximizing the signal-to-noise ratio from the sample. Lithium metal was electrodeposited onto the UO2 working electrode by exposing the working electrode to more negative potentials than the Li deposition potential of the LiCl – KCl e...
Source: Journal of Synchrotron Radiation - February 16, 2017 Category: Physics Authors: Brown, L.D. Abdulaziz, R. Jervis, R. Bharath, V. Mason, T.J. Atwood, R.C. Reinhard, C. Connor, L.D. Inman, D. Brett, D.J.L. Shearing, P.R. Tags: cell design molten-salt reduction spent fuel reprocessing energy-dispersive X-ray diffraction research papers Source Type: research

A modified equally sloped algorithm based on the total variation algorithm in computed tomography for insufficient data
Computed tomography (CT) has become an important technique for analyzing the inner structures of material, biological and energy fields. However, there are often challenges in the practical application of CT due to insufficient data. For example, the maximum rotation angle of the sample stage is limited by sample space or image reconstruction from the limited number of views required to reduce the X-ray dose delivered to the sample. Therefore, it is difficult to acquire CT images with complete data. In this work, an iterative reconstruction algorithm based on the minimization of the image total variation (TV) has been util...
Source: Journal of Synchrotron Radiation - February 16, 2017 Category: Physics Authors: Wang, L. Guan, Y. Liang, Z. Guo, L. Wei, C. Luo, R. Liu, G. Tian, Y. Tags: computed tomography total variation minimization equally sloped tomography limited-angle few-view noisy data research papers Source Type: research

Ultra-short and ultra-intense X-ray free-electron laser single pulse in one-dimensional photonic crystals
The propagation within a one-dimensional photonic crystal of a single ultra-short and ultra-intense pulse delivered by an X-ray free-electron laser is analysed with the framework of the time-dependent coupled-wave theory in non-linear media. It is shown that the reflection and the transmission of an ultra-short pulse present a transient period conditioned by the extinction length and also the thickness of the structure for transmission. For ultra-intense pulses, non-linear effects are expected: they could give rise to numerous phenomena, bi-stability, self-induced transparency, gap solitons, switching, etc., which have bee...
Source: Journal of Synchrotron Radiation - February 16, 2017 Category: Physics Authors: Andr é , J.-M. Jonnard, P. Tags: X-ray free electron laser one-dimensional photonic crystal non-linear processes research papers Source Type: research

RixsToolBox: software for the analysis of soft X-ray RIXS data acquired with 2D detectors
A software with a graphical user interface has been developed with the aim of facilitating the data analysis for users of a new resonant inelastic X-ray scattering (RIXS) spectrometer installed at the ESRF beamline ID32. The software is organized in modules covering all relevant steps in the data reduction from a stack of several hundred two-dimensional CCD images to a single RIXS spectrum. It utilizes both full charge integration and single-photon centroiding to cope with high-flux and high-resolution requirements. Additional modules for further data analysis and the extraction of instrumental parameters are available. Th...
Source: Journal of Synchrotron Radiation - February 2, 2017 Category: Physics Authors: Kummer, K. Tamborrino, A. Amorese, A. Minola, M. Braicovich, L. Brookes, N.B. Ghiringhelli, G. Tags: RixsToolBox resonant inelastic X-ray scattering software ESRF computer programs Source Type: research

A compact permanent-magnet system for measuring magnetic circular dichroism in resonant inelastic soft X-ray scattering
A compact and portable magnet system for measuring magnetic dichroism in resonant inelastic soft X-ray scattering (SX-RIXS) has been developed at the beamline BL07LSU in SPring-8. A magnetic circuit composed of Nd – Fe – B permanent magnets, which realised ∼ 0.25   T at the center of an 11   mm gap, was rotatable around the axis perpendicular to the X-ray scattering plane. Using the system, a SX-RIXS spectrum was obtained under the application of the magnetic field at an angle parallel, nearly 45 ° or perpendicular to the incident X-rays. A dedicated sample stage was also designed to be as compact a...
Source: Journal of Synchrotron Radiation - February 2, 2017 Category: Physics Authors: Miyawaki, J. Suga, S. Fujiwara, H. Niwa, H. Kiuchi, H. Harada, Y. Tags: soft X-ray RIXS magnetic circular dichroism Nd – Fe B permanent magnet sample transfer system research papers Source Type: research

Nondestructive imaging of the internal microstructure of vessels and nerve fibers in rat spinal cord using phase-contrast synchrotron radiation microtomography
In this study, this method has been employed for nondestructive imaging of the internal microstructure of rat spinal cord. Furthermore, digital virtual slices based on phase-contrast synchrotron radiation were compared with conventional histological sections. The three-dimensional internal microstructure of the intramedullary arteries and nerve fibers was vividly detected within the same spinal cord specimen without the application of a stain or contrast agent or sectioning. With the aid of image post-processing, an optimization of vessel and nerve fiber images was obtained. The findings indicated that phase-contrast synch...
Source: Journal of Synchrotron Radiation - February 1, 2017 Category: Physics Authors: Hu, J. Li, P. Yin, X. Wu, T. Cao, Y. Yang, Z. Jiang, L. Hu, S. Lu, H. Tags: synchrotron radiation imaging virtual slices three-dimensional microstructure phase-contrast imaging spinal cord research papers Source Type: research

Development of new CdZnTe detectors for room-temperature high-flux radiation measurements
Recently, CdZnTe (CZT) detectors have been widely proposed and developed for room-temperature X-ray spectroscopy even at high fluxes, and great efforts have been made on both the device and the crystal growth technologies. In this work, the performance of new travelling-heater-method (THM)-grown CZT detectors, recently developed at IMEM-CNR Parma, Italy, is presented. Thick planar detectors (3   mm thick) with gold electroless contacts were realised, with a planar cathode covering the detector surface (4.1   mm × 4.1   mm) and a central anode (2   mm × 2   mm) surrounded by a guard-ring electrode. The...
Source: Journal of Synchrotron Radiation - February 1, 2017 Category: Physics Authors: Abbene, L. Gerardi, G. Raso, G. Principato, F. Zambelli, N. Benassi, G. Bettelli, M. Zappettini, A. Tags: X-ray and γ -ray detectors CdZnTe detectors travelling heater method gold electroless contact high flux digital pulse shape analysis energy-resolved photon-counting detectors research papers Source Type: research

Computer-assisted area detector masking
Area detectors have become the predominant type of detector for the rapid acquisition of X-ray diffraction, small-angle scattering and total scattering. These detectors record the scattering for a large area, giving each shot good statistical significance to the resulting scattered intensity I(Q) pattern. However, many of these detectors have pixel level defects, which cause error in the resulting one-dimensional patterns. In this work, new software to automatically find and mask these dead pixels and other defects is presented. This algorithm is benchmarked with both ideal simulated and experimental datasets. (Source: Jou...
Source: Journal of Synchrotron Radiation - January 30, 2017 Category: Physics Authors: Wright, C.J. Zhou, X.-D. Tags: masking area detector Python short communications Source Type: research

Performance on absolute scattering intensity calibration and protein molecular weight determination at BL16B1, a dedicated SAXS beamline at SSRF
The optical system and end-station of bending-magnet beamline BL16B1, dedicated to small-angle X-ray scattering (SAXS) at the Shanghai Synchrotron Radiation Facility, is described. Constructed in 2009 and upgraded in 2013, this beamline has been open to users since May 2009 and supports methodologies including SAXS, wide-angle X-ray scattering (WAXS), simultaneous SAXS/WAXS, grazing-incidence small-angle X-ray scattering (GISAXS) and anomalous small-angle X-ray scattering (ASAXS). Considering that an increasing necessity for absolute calibration of SAXS intensity has been recognized in in-depth investigations, SAXS intensi...
Source: Journal of Synchrotron Radiation - January 24, 2017 Category: Physics Authors: Zeng, J. Bian, F. Wang, J. Li, X. Wang, Y. Tian, F. Zhou, P. Tags: beamline SAXS absolute intensity calibration molecular weight beamlines Source Type: research

Improving the spatial and statistical accuracy in X-ray Raman scattering based direct tomography
An algorithm to simultaneously increase the spatial and statistical accuracy of X-ray Raman scattering (XRS) based tomographic images is presented. Tomography that utilizes XRS spectroscopy signals as a contrast for the images is a new and promising tool for investigating local atomic structure and chemistry in heterogeneous samples. The algorithm enables the spatial resolution to be increased based on a deconvolution of the optical response function of the spectrometer and, most importantly, it allows for the combination of data collected from multiple analyzers and thus enhances the statistical accuracy of the measured i...
Source: Journal of Synchrotron Radiation - January 24, 2017 Category: Physics Authors: Sahle, Ch.J. Mirone, A. Vincent, T. Kallonen, A. Huotari, S. Tags: inelastic X-ray scattering imaging direct tomography XRS research papers Source Type: research

Compact IR synchrotron beamline design
Third-generation storage rings are massively evolving due to the very compact nature of the multi-bend achromat (MBA) lattice which allows amazing decreases of the horizontal electron beam emittance, but leaves very little place for infrared (IR) extraction mirrors to be placed, thus prohibiting traditional IR beamlines. In order to circumvent this apparent restriction, an optimized optical layout directly integrated inside a SOLEIL synchrotron dipole chamber that delivers intense and almost aberration-free beams in the near- to mid-IR domain (1 – 30   µ m) is proposed and analyzed, and which can be integrate...
Source: Journal of Synchrotron Radiation - January 24, 2017 Category: Physics Authors: Moreno, T. Tags: infrared synchrotron beamline multi-bend achromat storage ring bending-magnet source optical aberrations integrating magnetic and photonic synchrotron beamline components research papers Source Type: research

A convolutional neural network approach to calibrating the rotation axis for X-ray computed tomography
This paper presents an algorithm to calibrate the center-of-rotation for X-ray tomography by using a machine learning approach, the Convolutional Neural Network (CNN). The algorithm shows excellent accuracy from the evaluation of synthetic data with various noise ratios. It is further validated with experimental data of four different shale samples measured at the Advanced Photon Source and at the Swiss Light Source. The results are as good as those determined by visual inspection and show better robustness than conventional methods. CNN has also great potential for reducing or removing other artifacts caused by instrument...
Source: Journal of Synchrotron Radiation - January 24, 2017 Category: Physics Authors: Yang, X. De Carlo, F. Phatak, C. G ü rsoy, D. Tags: tomography reconstruction rotation axis convolutional neural network open-source Python research papers Source Type: research

Surface EXAFS via differential electron yield
Surface-sensitive analysis via extended X-ray absorption fine-structure (EXAFS) spectroscopy is demonstrated using a thickness-defined SiO2   (12.4   nm)/Si sample. The proposed method exploits the differential electron yield (DEY) method wherein Auger electrons escaping from a sample surface are detected by an electron analyzer. The DEY method removes local intensity changes in the EXAFS spectra caused by photoelectrons crossing the Auger peak during X-ray energy sweeps, enabling EXAFS analysis through Fourier transformation of wide-energy-range spectral oscillations. The Si K-edge DEY X-ray absorption near-edge struc...
Source: Journal of Synchrotron Radiation - January 24, 2017 Category: Physics Authors: Isomura, N. Murai, T. Nomoto, T. Kimoto, Y. Tags: XAS EXAFS silicon dioxide partial electron yield surface-sensitive research papers Source Type: research

Current events
(Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - December 23, 2016 Category: Physics Authors: , Tags: current events Source Type: research

A practical local tomography reconstruction algorithm based on a known sub-region
A new method to reconstruct data acquired in a local tomography setup is proposed. This method uses an initial reconstruction and refines it by correcting the low-frequency artifacts, known as the cupping effect. A basis of Gaussian functions is used to correct the initial reconstruction. The coefficients of this basis are found by optimizing iteratively a fidelity term under the constraint of a known sub-region. Using a coarse basis reduces the degrees of freedom of the problem while actually correcting the cupping effect. Simulations show that the known region constraint yields an unbiased reconstruction, in accordance w...
Source: Journal of Synchrotron Radiation - December 23, 2016 Category: Physics Authors: Paleo, P. Desvignes, M. Mirone, A. Tags: tomography reconstruction algorithm interior problem research papers Source Type: research

X-ray radiation damage to biological macromolecules: further insights
Despite significant progress made over more than 15 years of research, structural biologists are still grappling with the issue of radiation damage suffered by macromolecular crystals which is induced by the resultant radiation chemistry occurring during X-ray diffraction experiments. Further insights into these effects and the possible mitigation strategies for use in both diffraction and SAXS experiments are given in eight papers in this volume. In particular, damage during experimental phasing is addressed, scavengers for SAXS experiments are investigated, microcrystals are imaged, data collection strategies are optimiz...
Source: Journal of Synchrotron Radiation - December 23, 2016 Category: Physics Authors: Garman, E.F. Weik, M. Tags: X-ray radiation damage macromolecular crystallography SAXS dose imaging scavengers editorial Source Type: research

AI-BL1.0: a program for automatic on-line beamline optimization using the evolutionary algorithm
In this report, AI-BL1.0, an open-source Labview-based program for automatic on-line beamline optimization, is presented. The optimization algorithms used in the program are Genetic Algorithm and Differential Evolution. Efficiency was improved by use of a strategy known as Observer Mode for Evolutionary Algorithm. The program was constructed and validated at the XAFCA beamline of the Singapore Synchrotron Light Source and 1W1B beamline of the Beijing Synchrotron Radiation Facility. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - December 22, 2016 Category: Physics Authors: Xi, S. Borgna, L.S. Zheng, L. Du, Y. Hu, T. Tags: automatic beamline optimization evolutionary algorithm Labview computer programs Source Type: research

Surface science at the PEARL beamline of the Swiss Light Source
The Photo-Emission and Atomic Resolution Laboratory (PEARL) is a new soft X-ray beamline and surface science laboratory at the Swiss Light Source. PEARL is dedicated to the structural characterization of local bonding geometry at surfaces and interfaces of novel materials, in particular of molecular adsorbates, nanostructured surfaces, and surfaces of complex materials. The main experimental techniques are soft X-ray photoelectron spectroscopy, photoelectron diffraction, and scanning tunneling microscopy (STM). Photoelectron diffraction in angle-scanned mode measures bonding angles of atoms near the emitter atom, and thus ...
Source: Journal of Synchrotron Radiation - December 22, 2016 Category: Physics Authors: Muntwiler, M. Zhang, J. Stania, R. Matsui, F. Oberta, P. Flechsig, U. Patthey, L. Quitmann, C. Glatzel, T. Widmer, R. Meyer, E. Jung, T.A. Aebi, P. Fasel, R. Greber, T. Tags: X-ray photoelectron spectroscopy X-ray photoelectron diffraction scanning tunneling microscopy beamlines Source Type: research

Conformational variation of proteins at room temperature is not dominated by radiation damage
Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100   K and below, the immobilization of free radicals increases the lifetime of the crystals by approximately 100-fold. Recent studies have shown that flash-cooling decreases the heterogeneity of the conformational ensemble and can hide important functional mechanisms from observation. These discoveries have motivated increasing numbers of experiments to be carried out at room temperature. However, the trade-offs between increased risk of radiation ...
Source: Journal of Synchrotron Radiation - December 22, 2016 Category: Physics Authors: Russi, S. Gonz á lez, A. Kenner, L.R. Keedy, D.A. Fraser, J.S. Bedem, H. van den Tags: radiation damage room temperature cryo-temperature conformational dynamics research papers Source Type: research

Design of a prototype split-and-delay unit for XFEL pulses, and their evaluation by synchrotron radiation X-rays
A prototype split-and-delay unit (SDU) for X-ray free-electron laser (XFEL) pulses is proposed based on the Graeff – Bonse four-Bragg-reflection interferometer by installing 12.5 ° slopes. The SDU can continuously provide a delay time from approximately − 20 to 40   ps with a resolution of less than 26   fs. Because the SDU was constructed from a monolithic silicon crystal, alignment is straightforward. The obtained thoroughputs of the SDU reached 0.7% at 7.46   keV and 0.02% at 14.92   keV. The tunability of the delay time using the proposed SDU was demonstrated by finding the interference effects ...
Source: Journal of Synchrotron Radiation - December 20, 2016 Category: Physics Authors: Sakamoto, J. Ohwada, K. Ishino, M. Mizuki, J. Ando, M. Namikawa, K. Tags: split-and-delay unit Bragg case interferometer XFEL synchrotron radiation X-rays research papers Source Type: research

Design of a multilayer-based collimated plane-grating monochromator for tender X-ray range
Collimated plane-grating monochromators (cPGMs), consisting of a plane mirror and plane diffraction grating, are essential optics in synchrotron radiation sources for their remarkable flexibility and good optical characteristics in the soft X-ray region. However, the poor energy transport efficiency of a conventional cPGM (single-layer-coated) degrades the source intensity and leaves reduced flux at the sample, especially for the tender X-ray range (1 – 4   keV) that covers a large number of K- and L-edges of medium-Z elements, and M-edges of high-Z elements. To overcome this limitation, the use of a multilayer-bas...
Source: Journal of Synchrotron Radiation - December 20, 2016 Category: Physics Authors: Yang, X. Wang, H. Hand, M. Sawhney, K. Kaulich, B. Kozhevnikov, I.V. Huang, Q. Wang, Z. Tags: X-ray optics monochromator diffraction grating multilayer research papers Source Type: research

Automatic processing of multimodal tomography datasets
With the development of fourth-generation high-brightness synchrotrons on the horizon, the already large volume of data that will be collected on imaging and mapping beamlines is set to increase by orders of magnitude. As such, an easy and accessible way of dealing with such large datasets as quickly as possible is required in order to be able to address the core scientific problems during the experimental data collection. Savu is an accessible and flexible big data processing framework that is able to deal with both the variety and the volume of data of multimodal and multidimensional scientific datasets output such as th...
Source: Journal of Synchrotron Radiation - December 20, 2016 Category: Physics Authors: Parsons, A.D. Price, S.W.T. Wadeson, N. Basham, M. Beale, A.M. Ashton, A.W. Mosselmans, J.F.W. Quinn, P.D. Tags: big data multimodal imaging mapping tomography research papers Source Type: research

Protein crystallography beamline BL2S1 at the Aichi synchrotron
The protein crystallography beamline BL2S1, constructed at one of the 5   T superconducting bending-magnet ports of the Aichi synchrotron, is available to users associated with academic and industrial organizations. The beamline is mainly intended for use in X-ray diffraction measurements of single-crystals of macromolecules such as proteins and nucleic acids. Diffraction measurements for crystals of other materials are also possible, such as inorganic and organic compounds. BL2S1 covers the energy range 7 – 17   keV (1.8 – 0.7   Å ) with an asymmetric-cut curved single-crystal monochromator [Ge(111...
Source: Journal of Synchrotron Radiation - December 20, 2016 Category: Physics Authors: Watanabe, N. Nagae, T. Yamada, Y. Tomita, A. Matsugaki, N. Tabuchi, M. Tags: protein crystallography superbend beamline high pressure beamlines Source Type: research

Direct tomography imaging for inelastic X-ray scattering experiments at high pressure
A method to separate the non-resonant inelastic X-ray scattering signal of a micro-metric sample contained inside a diamond anvil cell (DAC) from the signal originating from the high-pressure sample environment is described. Especially for high-pressure experiments, the parasitic signal originating from the diamond anvils, the gasket and/or the pressure medium can easily obscure the sample signal or even render the experiment impossible. Another severe complication for high-pressure non-resonant inelastic X-ray measurements, such as X-ray Raman scattering spectroscopy, can be the proximity of the desired sample edge energy...
Source: Journal of Synchrotron Radiation - December 20, 2016 Category: Physics Authors: Sahle, C.J. Rosa, A.D. Rossi, M. Cerantola, V. Spiekermann, G. Petitgirard, S. Jacobs, J. Huotari, S. Moretti Sala, M. Mirone, A. Tags: inelastic X-ray scattering direct tomography diamond anvil cell high pressure research papers Source Type: research

Bunch-by-bunch position measurement and analysis   at PLS-II
A bunch-by-bunch measurement system has been developed at Pohang Light Source II. The system consists of a four-channel button pick-up, 20   GHz sampling oscilloscope and an 800   MHz low-pass digital filter. Upon measuring a bunch-by-bunch spatio-temporal beam motion matrix over many turns, singular-value decomposition analysis is used to reveal the dominant coupled-bunch modes. The system can diagnose injection oscillations due to kicker errors and the effect of resistive-wall impedance that gives rise to instability during operation. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - December 20, 2016 Category: Physics Authors: Lee, J. Chun, M.H. Kim, G.-J. Shin, D.-C. Kim, D.-T. Shin, S. Tags: instability bunch by bunch position research papers Source Type: research

X-ray grating interferometer for in   situ and at-wavelength wavefront metrology
A wavefront metrology setup based on the X-ray grating interferometry technique for spatially resolved, quantitative, in   situ and at-wavelength measurements of the wavefront at synchrotron radiation and hard X-ray free-electron laser beamlines is reported. Indeed, the ever-increasing demands on the optical components to preserve the wavefront shape and the coherence of the delivered X-ray beam call for more and more sensitive diagnostic instruments. Thanks to its angular sensitivity, X-ray grating interferometry has been established in recent years as an adequate wavefront-sensing technique for quantitatively assess...
Source: Journal of Synchrotron Radiation - December 16, 2016 Category: Physics Authors: Kayser, Y. David, C. Flechsig, U. Krempasky, J. Schlott, V. Abela, R. Tags: X-ray grating interferometry wavefront metrology X-ray optics XFELs research papers Source Type: research

Uridine as a new scavenger for synchrotron-based structural biology techniques
Macromolecular crystallography (MX) and small-angle X-ray scattering (SAXS) studies on proteins at synchrotron light sources are commonly limited by the structural damage produced by the intense X-ray beam. Several effects, such as aggregation in protein solutions and global and site-specific damage in crystals, reduce the data quality or even introduce artefacts that can result in a biologically misguiding structure. One strategy to reduce these negative effects is the inclusion of an additive in the buffer solution to act as a free radical scavenger. Here the properties of uridine as a scavenger for both SAXS and MX expe...
Source: Journal of Synchrotron Radiation - December 16, 2016 Category: Physics Authors: Crosas, E. Castellvi, A. Crespo, I. Fulla, D. Gil-Ortiz, F. Fuertes, G. Kamma-Lorger, C.S. Malfois, M. Aranda, M.A.G. Juanhuix, J. Tags: radiation damage reactive oxygen species free radical scavenger macromolecular crystallography methods SAXS methods research papers Source Type: research

Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography
The proliferation of extremely intense synchrotron sources has enabled ever higher-resolution structures to be obtained using data collected from smaller and often more imperfect biological crystals (Helliwell, 1984). Synchrotron beamlines now exist that are capable of measuring data from single crystals that are just a few micrometres in size. This provides renewed motivation to study and understand the radiation damage behaviour of small protein crystals. Reciprocal-space mapping and Bragg coherent diffractive imaging experiments have been performed on cryo-cooled microcrystals of hen egg-white lysozyme as they undergo r...
Source: Journal of Synchrotron Radiation - December 16, 2016 Category: Physics Authors: Coughlan, H.D. Darmanin, C. Kirkwood, H.J. Phillips, N.W. Hoxley, D. Clark, J.N. Vine, D.J. Hofmann, F. Harder, R.J. Maxey, E. Abbey, B. Tags: radiation damage dose protein crystallography micro-crystallography Bragg coherent diffractive imaging research papers Source Type: research

Medium-energy microprobe station at the SXRMB of the CLS
Micro-XAFS and chemical imaging techniques have been widely applied for studies of heterogeneously distributed systems, mostly in hard X-ray (>5   keV) or in soft X-ray ( (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - December 15, 2016 Category: Physics Authors: Xiao, Q. Maclennan, A. Hu, Y. Hackett, M. Leinweber, P. Sham, T.-K. Tags: medium-energy beamline micro-XAFS micro-XRF beamlines Source Type: research

Generation of apodized X-ray illumination and its application to scanning and diffraction microscopy
X-ray science has greatly benefited from the progress in X-ray optics. Advances in the design and the manufacturing techniques of X-ray optics are key to the success of various microscopic and spectroscopic techniques practiced today. Here the generation of apodized X-ray illumination using a two-stage deformable Kirkpatrick – Baez mirror system is presented. Such apodized illumination is marked by the suppression of the side-lobe intensities of the focused beam. Thus generated apodized illumination was employed to improve the image quality in scanning X-ray fluorescence microscopy. Imaging of a non-isolated object b...
Source: Journal of Synchrotron Radiation - December 15, 2016 Category: Physics Authors: Khakurel, K.P. Kimura, T. Nakamori, H. Goto, T. Matsuyama, S. Sasaki, T. Takei, M. Kohmura, Y. Ishikawa, T. Yamauchi, K. Nishino, Y. Tags: X-ray deformable mirrors apodized X-ray illumination hard X-ray microscopy research papers Source Type: research

Performance of photoelectron spin polarimeters with continuous and pulsed sources: from storage rings to free electron lasers
In this work the experimental uncertainties concerning electron spin polarization (SP) under various realistic measurement conditions are theoretically derived. The accuracy of the evaluation of the SP of the photoelectron current is analysed as a function of the detector parameters and specifications, as well as of the characteristics of the photoexcitation sources. In particular, the different behaviour of single counter or twin counter detectors when the intensity fluctuations of the source are considered have been addressed, leading to a new definition of the SP detector performance. The widely used parameter called th...
Source: Journal of Synchrotron Radiation - December 15, 2016 Category: Physics Authors: Pincelli, T. Grasselli, F. Petrov, V.N. Torelli, P. Rossi, G. Tags: spin-resolved photoemission spin-polarimetry statistics intensity fluctuations pulsed source continuous source research papers Source Type: research

Miniature diamond anvils for X-ray Raman scattering spectroscopy experiments at high pressure
X-ray Raman scattering (XRS) spectroscopy is an inelastic scattering method that uses hard X-rays of the order of 10   keV to measure energy-loss spectra at absorption edges of light elements (Si, Mg, O etc.), with an energy resolution below 1   eV. The high-energy X-rays employed with this technique can penetrate thick or dense sample containers such as the diamond anvils employed in high-pressure cells. Here, we describe the use of custom-made conical miniature diamond anvils of less than 500   µ m thickness which allow pressure generation of up to 70   GPa. This set-up overcomes the limitations of the XRS ...
Source: Journal of Synchrotron Radiation - December 15, 2016 Category: Physics Authors: Petitgirard, S. Spiekermann, G. Weis, C. Sahle, C. Sternemann, C. Wilke, M. Tags: X-ray Raman scattering high pressure miniature diamond anvils SiO2 glass research papers Source Type: research

Comparison of helical scan and standard rotation methods in single-crystal X-ray data collection strategies
X-ray radiation in macromolecular crystallography can chemically alter the biological material and deteriorate the integrity of the crystal lattice with concomitant loss of resolution. Typical alterations include decarboxylation of glutamic and aspartic residues, breaking of disulfide bonds and the reduction of metal centres. Helical scans add a small translation to the crystal in the rotation method, so that for every image the crystal is shifted to expose a fresh part. On beamline PROXIMA 2A at Synchrotron SOLEIL, this procedure has been tested with various parameters in an attempt to understand how to mitigate the effec...
Source: Journal of Synchrotron Radiation - December 15, 2016 Category: Physics Authors: Polsinelli, I. Savko, M. Rouanet-Mehouas, C. Ciccone, L. Nencetti, S. Orlandini, E. Stura, E.A. Shepard, W. Tags: helical scans radiation damage bromophenyl ligands micro-focus PROXIMA 2A research papers Source Type: research

Quantitative characterization of the X-ray beam at the Australian Synchrotron Imaging and Medical Beamline (IMBL)
A critical early phase for any synchrotron beamline involves detailed testing, characterization and commissioning; this is especially true of a beamline as ambitious and complex as the Imaging& Medical Beamline (IMBL) at the Australian Synchrotron. IMBL staff and expert users have been performing precise experiments aimed at quantitative characterization of the primary polychromatic and monochromatic X-ray beams, with particular emphasis placed on the wiggler insertion devices (IDs), the primary-slit system and any in   vacuo and ex vacuo filters. The findings from these studies will be described herein. These res...
Source: Journal of Synchrotron Radiation - December 13, 2016 Category: Physics Authors: Stevenson, A.W. Crosbie, J.C. Hall, C.J. H ä usermann, D. Livingstone, J. Lye, J.E. Tags: ionization chambers dosimetry X-ray beam quality research papers Source Type: research

Analytic expressions for the angular and the spectral fluxes at Compton X-ray sources
The goal of this paper is to express simply the number of photons impinging on a target in the framework of accelerator-based Compton X-ray sources. From the basic kinematics of Compton sources, analytic formulas for the angular and the spectral fluxes are established as functions of the energy spread or/and the angular divergence of the electron and the laser beams. Their detailed predictions are compared with Monte Carlo simulations. These analytic expressions allow one to compute in a simple and precise way the X-ray flux in a given angular acceptance and a given energy bandwidth, knowing the characteristics of the inco...
Source: Journal of Synchrotron Radiation - December 13, 2016 Category: Physics Authors: Jacquet, M. Bruni, C. Tags: Compton scattering angular flux spectral flux electron beam divergence energy spread research papers Source Type: research

P13, the EMBL macromolecular crystallography beamline at the low-emittance PETRA III ring for   high- and low-energy phasing with variable beam focusing
The macromolecular crystallography P13 beamline is part of the European Molecular Biology Laboratory Integrated Facility for Structural Biology at PETRA III (DESY, Hamburg, Germany) and has been in user operation since mid-2013. P13 is tunable across the energy range from 4 to 17.5   keV to support crystallographic data acquisition exploiting a wide range of elemental absorption edges for experimental phase determination. An adaptive Kirkpatrick – Baez focusing system provides an X-ray beam with a high photon flux and tunable focus size to adapt to diverse experimental situations. Data collections at energies as lo...
Source: Journal of Synchrotron Radiation - December 9, 2016 Category: Physics Authors: Cianci, M. Bourenkov, G. Pompidor, G. Karpics, I. Kallio, J. Bento, I. Roessle, M. Cipriani, F. Fiedler, S. Schneider, T.R. Tags: phasing sulfur SAD variable beam low-energy data collection 2 θ -detector arm softer X-rays tunability beamlines Source Type: research

Development of synchrotron X-ray micro-tomography under extreme conditions of pressure and   temperature
X-ray tomography is a non-destructive three-dimensional imaging/microanalysis technique selective to a wide range of properties such as density, chemical composition, chemical states and crystallographic structure with extremely high sensitivity and spatial resolution. Here the development of in situ high-pressure high-temperature micro-tomography using a rotating module for the Paris – Edinburgh cell combined with synchrotron radiation is described. By rotating the sample chamber by 360 ° , the limited angular aperture of ordinary high-pressure cells is surmounted. Such a non-destructive high-resolution probe pr...
Source: Journal of Synchrotron Radiation - December 9, 2016 Category: Physics Authors: Á lvarez-Murga, M. Perrillat, J.P. Le Godec, Y. Bergame, F. Philippe, J. King, A. Guignot, N. Mezouar, M. Hodeau, J.L. Tags: X-ray absorption tomography diffraction scattering tomography high pressure basalt glass C60 polymerization research papers Source Type: research

Synchrotron radiation micro X-ray fluorescence spectroscopy of thin structures in bone samples: comparison of confocal and color X-ray camera setups
In the quest for finding the ideal synchrotron-radiation-induced imaging method for the investigation of trace element distributions in human bone samples, experiments were performed using both a scanning confocal synchrotron radiation micro X-ray fluorescence (SR- µ XRF) (FLUO beamline at ANKA) setup and a full-field color X-ray camera (BAMline at BESSY-II) setup. As zinc is a trace element of special interest in bone, the setups were optimized for its detection. The setups were compared with respect to count rate, required measurement time and spatial resolution. It was demonstrated that the ideal method depends on...
Source: Journal of Synchrotron Radiation - December 9, 2016 Category: Physics Authors: Rauwolf, M. Turyanskaya, A. Roschger, A. Prost, J. Simon, R. Scharf, O. Radtke, M. Schoonjans, T. Guilherme Buzanich, A. Klaushofer, K. Wobrauschek, P. Hofstaetter, J.G. Roschger, P. Streli, C. Tags: SR- µ XRF color X-ray camera confocal human bone research papers Source Type: research

Linear parabolic single-crystal diamond refractive lenses for synchrotron X-ray sources
Linear parabolic diamond refractive lenses are presented, designed to withstand high thermal and radiation loads coming from upgraded accelerator X-ray sources. Lenses were manufactured by picosecond laser treatment of a high-quality single-crystal synthetic diamond. Twelve lenses with radius of curvature at parabola apex R = 200   µ m, geometrical aperture A = 900   µ m and length L = 1.5   mm were stacked as a compound refractive lens and tested at the ESRF ID06 beamline. A focal spot of size 2.2   µ m and a gain of 20 were measured at 8   keV. The lens profile and surface quality were estimat...
Source: Journal of Synchrotron Radiation - December 9, 2016 Category: Physics Authors: Terentyev, S. Polikarpov, M. Snigireva, I. Di Michiel, M. Zholudev, S. Yunkin, V. Kuznetsov, S. Blank, V. Snigirev, A. Tags: X-ray optics refractive lenses diamond laser ablation beam conditioning research papers Source Type: research

OH cleavage from tyrosine: debunking a myth
During macromolecular X-ray crystallography experiments, protein crystals held at 100   K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100   K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Further...
Source: Journal of Synchrotron Radiation - December 9, 2016 Category: Physics Authors: Bury, C.S. Carmichael, I. Garman, E.F. Tags: tyrosine specific damage radiation chemistry electron density loss Fourier difference maps research papers Source Type: research

X-ray fluorescence at nanoscale resolution for multicomponent layered structures: a solar cell case   study
The study of a multilayered and multicomponent system by spatially resolved X-ray fluorescence microscopy poses unique challenges in achieving accurate quantification of elemental distributions. This is particularly true for the quantification of materials with high X-ray attenuation coefficients, depth-dependent composition variations and thickness variations. A widely applicable procedure for use after spectrum fitting and quantification is described. This procedure corrects the elemental distribution from the measured fluorescence signal, taking into account attenuation of the incident beam and generated fluorescence fr...
Source: Journal of Synchrotron Radiation - December 2, 2016 Category: Physics Authors: West, B.M. Stuckelberger, M. Jeffries, A. Gangam, S. Lai, B. Stripe, B. Maser, J. Rose, V. Vogt, S. Bertoni, M.I. Tags: thin film characterization X-ray fluorescence CIGS multilayered structure solar cell research papers Source Type: research

An endstation for resonant inelastic X-ray scattering studies of solid and liquid samples
A novel experimental setup is presented for resonant inelastic X-ray scattering investigations of solid and liquid samples in the soft X-ray region for studying the complex electronic configuration of (bio)chemical systems. The uniqueness of the apparatus is its high flexibility combined with optimal energy resolution and energy range ratio. The apparatus enables investigation of chemical analyses, which reflects the chemical imprints. The endstation is composed of a main sample chamber, a sample holder for either solid or liquid jet delivery system, and a soft X-ray grating spectrometer for 210 – 1250   eV with a ...
Source: Journal of Synchrotron Radiation - December 1, 2016 Category: Physics Authors: Yin, Z. Peters, H.-B. Hahn, U. Gonschior, J. Mierwaldt, D. Rajkovic, I. Viefhaus, J. Jooss, C. Techert, S. Tags: RIXS varied line spacing liquid jet XAS XES FEL research papers Source Type: research

1s2p resonant inelastic X-ray scattering combined dipole and quadrupole analysis method
In this study an analysis strategy towards using the resonant inelastic X-ray scattering (RIXS) technique more effectively compared with X-ray absorption spectroscopy (XAS) is presented. In particular, the question of when RIXS brings extra information compared with XAS is addressed. To answer this question the RIXS plane is analysed using two models: (i) an exciton model and (ii) a continuum model. The continuum model describes the dipole pre-edge excitations while the exciton model describes the quadrupole excitations. Applying our approach to the experimental 1s2p RIXS planes of VO2 and TiO2, it is shown that only in th...
Source: Journal of Synchrotron Radiation - November 30, 2016 Category: Physics Authors: Bagger, A. Haarman, T. Puig Molina, A. Moses, P.G. Ishii, H. Hiraoka, N. Wu, Y.-H. Tsuei, K.-D. Chorkendorff, I. De Groot, F. Tags: resonant inelestic X-ray scattering RIXS X-ray absorption X-ray emission research papers Source Type: research

Dynamic X-ray diffraction sampling for protein crystal positioning
A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which ...
Source: Journal of Synchrotron Radiation - November 30, 2016 Category: Physics Authors: Scarborough, N.M. Godaliyadda, G.M.D.P. Ye, D.H. Kissick, D.J. Zhang, S. Newman, J.A. Sheedlo, M.J. Chowdhury, A.U. Fischetti, R.F. Das, C. Buzzard, G.T. Bouman, C.A. Simpson, G.J. Tags: dynamic sampling supervised learning approach X-ray diffraction nonlinear optical microscopy two-photon-excited fluorescence second-harmonic generation research papers Source Type: research