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
Synchrotron-based phase-sensitive imaging of leaves grown from magneto-primed seeds of soybean
Experiments were conducted to study the effects of static magnetic fields (SMFs) on the venation network of soybean leaves using the synchrotron-based X-ray micro-imaging technique. The seeds of soybean (Glycine max, variety JS-335) were pretreated with different SMFs from 50 to 300 mT in steps of 50 mT for 1 h. The phase-contrast images obtained showed that, as the strength of the SMF increased, the area, width of the midrib, area of the midrib and minor vein of the middle leaflets of third trifoliate leaves also increased up to the SMF strength of 200 mT (1 h) and decreased thereafter. Quantification ...
Source: Journal of Synchrotron Radiation - November 28, 2016 Category: Physics Authors: Fatima, A. Kataria, S. Baghel, L. Guruprasad, K.N. Agrawal, A.K. Singh, B. Sarkar, P.S. Shripathi, T. Kashyap, Y. Tags: phase-contrast imaging phase retrieval micro-imaging soybean research papers Source Type: research
On the use of flat-fields for tomographic reconstruction
Seeking for quantitative tomographic images, it is of utmost importance to limit reconstruction artifacts. Detector imperfections, inhomogeneity of the incident beam, as classically observed in synchrotron beamlines, and their variations in time are a major cause of reconstruction bias such as `ring artifacts'. The present study aims at proposing a faithful estimate of the incident beam local intensity for each acquired projection during a scan, without revisiting the process of data acquisition itself. Actual flat-fields (acquired without specimen in the beam) and sinogram borders (when the specimen is present), which are...
Source: Journal of Synchrotron Radiation - November 28, 2016 Category: Physics Authors: Jailin, C. Buffi è re, J.-Y. Hild, F. Poncelet, M. Roux, S. Tags: flat-field normalization artifact corrections computed tomography research papers Source Type: research
Determination of copper nanoparticle size distributions with total reflection X-ray fluorescence spectroscopy
In this study, two samples were intentionally contaminated with copper in non-deoxygenated and deoxygenated ultrapure water (UPW) resulting in impurity profiles that were either atomically dispersed in a thin film or particle-like, respectively. The concentration profile of the samples immersed into deoxygenated UPW was calculated using a theoretical concentration profile representative of particles, yielding a mean particle height of 16.1 nm. However, the resulting theoretical profile suggested that a distribution of particle heights exists on the surface. The fit of the angular distribution data was further refined b...
Source: Journal of Synchrotron Radiation - November 28, 2016 Category: Physics Authors: Singh, A. Luening, K. Brennan, S. Homma, T. Kubo, N. Nowak, S.H. Pianetta, P. Tags: silicon wafer surface total reflection X-ray fluorescence Cu nanoparticle grazing-incidence X-ray fluorescence research papers Source Type: research
Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
In this study, mercury single-wavelength anomalous diffraction (Hg-SAD) phasing of the luciferin regenerating enzyme (LRE) was performed using serial synchrotron rotation crystallography. The advantages of rotation and influence of dose on the data collected were evaluated. The results showed that sample rotation was effective for accurate data collection, and the optimum helical rotation step depended on multiple factors such as multiplicity and partiality of reflections, exposure time per rotation angle and the contribution from background scattering. For the LRE microcrystals, 0.25 ° was the best rotation step for t...
Source: Journal of Synchrotron Radiation - November 28, 2016 Category: Physics Authors: Hasegawa, K. Yamashita, K. Murai, T. Nuemket, N. Hirata, K. Ueno, G. Ago, H. Nakatsu, T. Kumasaka, T. Yamamoto, M. Tags: serial synchrotron crystallography mercury single-wavelength anomalous diffraction radiation damage research papers Source Type: research
Fast iterative reconstruction of data in full interior tomography
This paper introduces two novel strategies for iterative reconstruction of full interior tomography (FINT) data, i.e. when the field of view is entirely inside the object support and knowledge of the object support itself or the attenuation coefficients inside specific regions of interest are not available. The first approach is based on data edge-padding. The second technique creates an intermediate virtual sinogram, which is, then, reconstructed by a standard iterative algorithm. Both strategies are validated in the framework of the alternate direction method of multipliers plug-and-play with gridding projectors that pro...
Source: Journal of Synchrotron Radiation - November 24, 2016 Category: Physics Authors: Arcadu, F. Marone, F. Stampanoni, M. Tags: X-ray tomographic microscopy interior tomography reconstruction artifacts iterative tomographic reconstruction gridding method research papers Source Type: research
Identification of the point of diminishing returns in high-multiplicity data collection for sulfur SAD phasing
High-quality high-multiplicity X-ray diffraction data were collected on five different crystals of thaumatin using a homogeneous-profile X-ray beam at E = 8 keV to investigate the counteracting effects of increased multiplicity and increased radiation damage on the quality of anomalous diffraction data collected on macromolecular crystals. By comparing sulfur substructures obtained from subsets of the data selected as a function of absorbed X-ray dose with sulfur positions in the respective refined reference structures, the doses at which the highest quality of anomalous differences could be obtained were identified fo...
Source: Journal of Synchrotron Radiation - November 24, 2016 Category: Physics Authors: Storm, S.L.S. Dall'Antonia, F. Bourenkov, G. Schneider, T.R. Tags: anomalous diffraction radiation damage SAD-phasing sulfur research papers Source Type: research
Development of tools to automate quantitative analysis of radiation damage in SAXS experiments
Biological small-angle X-ray scattering (SAXS) is an increasingly popular technique used to obtain nanoscale structural information on macromolecules in solution. However, radiation damage to the samples limits the amount of useful data that can be collected from a single sample. In contrast to the extensive analytical resources available for macromolecular crystallography (MX), there are relatively few tools to quantitate radiation damage for SAXS, some of which require a significant level of manual characterization, with the potential of leading to conflicting results from different studies. Here, computational tools hav...
Source: Journal of Synchrotron Radiation - November 24, 2016 Category: Physics Authors: Brooks-Bartlett, J.C. Batters, R.A. Bury, C.S. Lowe, E.D. Ginn, H.M. Round, A. Garman, E.F. Tags: SAXS radiation damage RADDOSE-3D radioprotectants CorMap visualization research papers Source Type: research
Fast X-ray microfluorescence imaging with submicrometer-resolution integrating a Maia detector at beamline P06 at PETRA III
The high brilliance of third-generation synchrotron sources increases the demand for faster detectors to utilize the available flux. The Maia detector is an advanced imaging scheme for energy-dispersive detection realising dwell times per image-pixel as low as 50 µ s and count rates higher than 10 × 106 s − 1. In this article the integration of such a Maia detector in the Microprobe setup of beamline P06 at the storage ring PETRA III at the Deutsches Elektronen-Synchrotron (DESY) in Hamburg, Germany, is described. The analytical performance of the complete system in terms of rate-depen...
Source: Journal of Synchrotron Radiation - October 18, 2016 Category: Physics Authors: Boesenberg, U. Ryan, C.G. Kirkham, R. Siddons, D.P. Alfeld, M. Garrevoet, J. N ú ñ ez, T. Claussen, T. Kracht, T. Falkenberg, G. Tags: Maia detector X-ray fluorescence micro-XRF beamlines Source Type: research
Nuclear incorporation of iron during the eukaryotic cell cycle
Scanning X-ray fluorescence microscopy has been used to probe the distribution of S, P and Fe within cell nuclei. Nuclei, which may have originated at different phases of the cell cycle, are found to show very different levels of Fe present with a strongly inhomogeneous distribution. P and S signals, presumably from DNA and associated nucleosomes, are high and relatively uniform across all the nuclei; these agree with X-ray phase contrast projection microscopy images of the same samples. Possible reasons for the Fe incorporation are discussed. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - October 18, 2016 Category: Physics Authors: Robinson, I. Yang, Y. Zhang, F. Lynch, C. Yusuf, M. Cloetens, P. Tags: fluorecence beamline chromosome imaging phase contrast research papers Source Type: research
X-ray analyzer-based phase-contrast computed laminography
X-ray analyzer-based phase-contrast imaging is combined with computed laminography for imaging regions of interest in laterally extended flat specimens of weak absorption contrast. The optics discussed here consist of an asymmetrically cut collimator crystal and a symmetrically cut analyzer crystal arranged in a nondispersive (+, − ) diffraction geometry. A generalized algorithm is given for calculating multi-contrast (absorption, refraction and phase contrast) images of a sample. Basic formulae are also presented for laminographic reconstruction. The feasibility of the method discussed was verified at the vertical w...
Source: Journal of Synchrotron Radiation - October 18, 2016 Category: Physics Authors: Hirano, K. Takahashi, Y. Hyodo, K. Kimura, M. Tags: X-ray phase-contrast imaging computed laminography image processing research papers Source Type: research
Nanox: a miniature mechanical stress rig designed for near-field X-ray diffraction imaging techniques
Multi-modal characterization of polycrystalline materials by combined use of three-dimensional (3D) X-ray diffraction and imaging techniques may be considered as the 3D equivalent of surface studies in the electron microscope combining diffraction and other imaging modalities. Since acquisition times at synchrotron sources are nowadays compatible with four-dimensional (time lapse) studies, suitable mechanical testing devices are needed which enable switching between these different imaging modalities over the course of a mechanical test. Here a specifically designed tensile device, fulfilling severe space constraints and p...
Source: Journal of Synchrotron Radiation - October 18, 2016 Category: Physics Authors: Gueninchault, N. Proudhon, H. Ludwig, W. Tags: miniature stress rig X-ray diffraction contrast tomography topotomography crystal plasticity in situ research papers Source Type: research
High-pressure Seebeck coefficients and thermoelectric behaviors of Bi and PbTe measured using a Paris-Edinburgh cell
A new sample cell assembly design for the Paris-Edinburgh type large-volume press for simultaneous measurements of X-ray diffraction, electrical resistance, Seebeck coefficient and relative changes in the thermal conductance at high pressures has been developed. The feasibility of performing in situ measurements of the Seebeck coefficient and thermal measurements is demonstrated by observing well known solid – solid phase transitions of bismuth (Bi) up to 3 GPa and 450 K. A reversible polarity flip has been observed in the Seebeck coefficient across the Bi-I to Bi-II phase boundary. Also, successful Seebeck c...
Source: Journal of Synchrotron Radiation - October 17, 2016 Category: Physics Authors: Baker, J. Kumar, R. Park, C. Kenney-Benson, C. Cornelius, A. Velisavljevic, N. Tags: thermoelectrics Paris-Edinburgh press Seebeck coefficient thermal conductivity high pressure research papers Source Type: research
A soft XAS transmission cell for operando studies
A new cell for operando soft X-ray absorption spectroscopy in transmission mode is presented. Developed for investigations on solar water-splitting catalysts, the cell allows the study of solid films in direct contact with electrolyte solution while applying voltage and visible light. The design is optimized for fast sample exchange and the simultaneous measurement of fluorescence and transmission signal. The capability of the cell is presented on a manganese oxide (MnOx) film, where electronic structure changes are monitored during forward and backward potential changes. Detailed information about the varying contribution...
Source: Journal of Synchrotron Radiation - October 17, 2016 Category: Physics Authors: Schwanke, C. Xi, L. Lange, K.M. Tags: soft X-ray transmission mode manganese oxide in situ operando L-edge research papers Source Type: research
Analytical formula for two-dimensional ring artefact suppression
Ring artefacts are the most disturbing artefacts when reconstructed volumes are segmented. A lot of effort has already been put into better X-ray optics, scintillators and detectors in order to minimize the appearance of these artefacts. However, additional processing is often required after standard flat-field correction. Several methods exist to suppress artefacts. One group of methods is based on minimization of the Tikhonov functional. An analytical formula for processing of a single sinogram was developed. In this paper a similar approach is used and a formula for processing two-dimensional projections is found. Thus ...
Source: Journal of Synchrotron Radiation - October 17, 2016 Category: Physics Authors: Titarenko, V. Tags: X-ray tomography ring artefacts ill-posed problem convolution filter Tikhonov functional research papers Source Type: research
High-temperature tensile cell for in situ real-time investigation of carbon fibre carbonization and graphitization processes
A new high-temperature fibre tensile cell is described, developed for use at the Advanced Photon Source at Argonne National Laboratory to enable the investigation of the carbonization and graphitization processes during carbon fibre production. This cell is used to heat precursor fibre bundles to temperatures up to ∼ 2300 ° C in a controlled inert atmosphere, while applying tensile stress to facilitate formation of highly oriented graphitic microstructure; evolution of the microstructure as a function of temperature and time during the carbonization and higher-temperature graphitization processes can then be monito...
Source: Journal of Synchrotron Radiation - October 17, 2016 Category: Physics Authors: Behr, M. Rix, J. Landes, B. Barton, B. Billovits, G. Hukkanen, E. Patton, J. Wang, W. Keane, D. Weigand, S. Tags: carbon fibre scattering diffraction in situ research papers Source Type: research
XDS: a flexible beamline for X-ray diffraction and spectroscopy at the Brazilian synchrotron
The majority of the beamlines at the Brazilian Synchrotron Light Source Laboratory (LNLS) use radiation produced in the storage-ring bending magnets and are therefore currently limited in the flux that can be used in the harder part of the X-ray spectrum (above ∼ 10 keV). A 4 T superconducting multipolar wiggler (SCW) was recently installed at LNLS in order to improve the photon flux above 10 keV and fulfill the demands set by the materials science community. A new multi-purpose beamline was then installed at the LNLS using the SCW as a photon source. The XDS is a flexible beamline operating in the energy r...
Source: Journal of Synchrotron Radiation - October 14, 2016 Category: Physics Authors: Lima, F.A. Saleta, M.E. Pagliuca, R.J.S. Eleot é rio, M.A. Reis, R.D. Fonseca J ú nior, J. Meyer, B. Bittar, E.M. Souza-Neto, N.M. Granado, E. Tags: beamline X-ray diffraction X-ray absorption total X-ray scattering resonant X-ray emission beamlines Source Type: research
ShadowOui: a new visual environment for X-ray optics and synchrotron beamline simulations
A new computer environment to perform simulations on synchrotron experiments has been designed. It performs ray-tracing simulations using the popular ray-tracing code SHADOW. With this new application one can define, in a very easy and elegant way, one or several optical systems (beamlines) and perform calculations of the propagation of the X-ray beam through it. Many complementary tools and supplementary calculations improve and extend the functionality of SHADOW to deal with complex optical system optimization, including compound optical elements, iterative calculations, some sample simulations, and implementing correcti...
Source: Journal of Synchrotron Radiation - October 14, 2016 Category: Physics Authors: Rebuffi, L. S á nchez del R í o, M. Tags: SHADOW ShadowOui ray tracing X-ray optics research papers Source Type: research
Controlling X-ray deformable mirrors during inspection
The X-ray deformable mirror (XDM) is becoming widely used in the present synchrotron/free-electron laser facilities because of its flexibility in correcting wavefront errors or modification of the beam size at the sample location. Owing to coupling among the N actuators of an XDM, (N + 1) or (2N + 1) scans are required to learn the response of each actuator one by one. When the mirror has an important number of actuators (N) and the actuator response time including stabilization or the necessary metrology time is long, the learning process can be time consuming. In this work, a fast and accurate method is presented to driv...
Source: Journal of Synchrotron Radiation - October 14, 2016 Category: Physics Authors: Huang, L. Xue, J. Idir, M. Tags: X-ray deformable mirror active optics mirror inspection windowed Fourier transform B-spline curve fitting research papers Source Type: research
Current status of the TwinMic beamline at Elettra: a soft X-ray transmission and emission microscopy station
The current status of the TwinMic beamline at Elettra synchrotron light source, that hosts the European twin X-ray microscopy station, is reported. The X-ray source, provided by a short hybrid undulator with source size and divergence intermediate between bending magnets and conventional undulators, is energy-tailored using a collimated plane-grating monochromator. The TwinMic spectromicroscopy experimental station combines scanning and full-field imaging in a single instrument, with contrast modes such as absorption, differential phase, interference and darkfield. The implementation of coherent diffractive imaging modalit...
Source: Journal of Synchrotron Radiation - October 12, 2016 Category: Physics Authors: Gianoncelli, A. Kourousias, G. Merolle, L. Altissimo, M. Bianco, A. Tags: X-ray microscopy X-ray fluorescence STXM full-field imaging soft X-rays beamlines Source Type: research
Effect of atomic vibrations in XANES: polarization-dependent damping of the fine structure at the Cu K-edge of (creat)2CuCl4
Polarization-dependent damping of the fine structure in the Cu K-edge spectrum of creatinium tetrachlorocuprate [(creat)2CuCl4] in the X-ray absorption near-edge structure (XANES) region is shown to be due to atomic vibrations. These vibrations can be separated into two groups, depending on whether the respective atoms belong to the same molecular block; individual molecular blocks can be treated as semi-rigid entities while the mutual positions of these blocks are subject to large mean relative displacements. The effect of vibrations can be efficiently included in XANES calculations by using the same formula as for static...
Source: Journal of Synchrotron Radiation - October 12, 2016 Category: Physics Authors: Š ipr, O. Vack á ř , J. Kuzmin, A. Tags: XANES vibrations multiple-scattering formalism research papers Source Type: research
Effect of gamma irradiation on X-ray absorption and photoelectron spectroscopy of Nd-doped phosphate glass
X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy (XPS) of Nd-doped phosphate glasses have been studied before and after gamma irradiation. The intensity and the location of the white line peak of the L3-edge XANES of Nd are found to be dependent on the ratio O/Nd in the glass matrix. Gamma irradiation changes the elemental concentration of atoms in the glass matrix, which affects the peak intensity of the white line due to changes in the covalence of the chemical bonds with Nd atoms in the glass (structural changes). Sharpening of the Nd 3d5/2 peak profile in XPS spectra indicates a deficie...
Source: Journal of Synchrotron Radiation - October 12, 2016 Category: Physics Authors: Rai, V.N. Rajput, P. Jha, S.N. Bhattacharyya, D. Raja Shekhar, B.N. Deshpande, U.P. Shripathi, T. Tags: glasses XAFS photoelectron spectroscopy radiation damage defect research papers Source Type: research
Creating flat-top X-ray beams by applying surface profiles of alternating curvature to deformable piezo bimorph mirrors
Beam shaping is becoming increasingly important for synchrotron X-ray applications. Although routine for visible light lasers, this is challenging for X-rays due to the limited source coherence and extreme optical tolerances required for the shaping mirrors. In deliberate defocusing, even surface errors (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - October 12, 2016 Category: Physics Authors: Sutter, J.P. Alcock, S.G. Kashyap, Y. Nistea, I. Wang, H. Sawhney, K. Tags: X-ray bimorph mirror beam shaping re-entrant research papers Source Type: research
Automatic crystal centring procedure at the SSRF macromolecular crystallography beamline
X-ray diffraction is a common technique for determining crystal structures. The average time needed for the solution of a protein structure has been drastically reduced by a number of recent experimental and theoretical developments. Since high-throughput protein crystallography benefits from full automation of all steps that are carried out on a synchrotron beamline, an automatic crystal centring procedure is important for crystallographic beamlines. Fully automatic crystal alignment involves the application of optical methods to identify the crystal and move it onto the rotation axis and into the X-ray beam. Crystal reco...
Source: Journal of Synchrotron Radiation - October 11, 2016 Category: Physics Authors: Wang, Z. Pan, Q. Yang, L. Zhou, H. Xu, C. Yu, F. Wang, Q. Huang, S. He, J. Tags: crystal centre algorithm recognition crystallography loop centre research papers Source Type: research
Optical performance of materials for X-ray refractive optics in the energy range 8 – 100 keV
A quantitative analysis of the crucial characteristics of currently used and promising materials for X-ray refractive optics is performed in the extended energy range 8 – 100 keV. According to the examined parameters, beryllium is the material of choice for X-ray compound refractive lenses (CRLs) in the energy range 8 – 25 keV. At higher energies the use of CRLs made of diamond and the cubic phase of boron nitride (c-BN) is beneficial. It was demonstrated that the presence of the elements of the fourth (or higher) period has a fatal effect on the functional X-ray properties even if low-Z elements domina...
Source: Journal of Synchrotron Radiation - October 11, 2016 Category: Physics Authors: Serebrennikov, D. Clementyev, E. Semenov, A. Snigirev, A. Tags: X-ray optics refractive lenses X-ray windows optical performance research papers Source Type: research
A high-accuracy complex-phase method of simulating X-ray propagation through a multi-lens system
The propagation of X-ray waves through an optical system consisting of many X-ray refractive lenses is considered. For solving the problem for an electromagnetic wave, a finite-difference method is applied. The error of simulation is analytically estimated and investigated. It was found that a very detailed difference grid is required for reliable and accurate calculations of the propagation of X-ray waves through a multi-lens system. The reasons for using a very detailed difference grid are investigated. It was shown that the wave phase becomes a function, very quickly increasing with increasing distance from the optical ...
Source: Journal of Synchrotron Radiation - October 10, 2016 Category: Physics Authors: Kshevetskii, S. Wojda, P. Maximov, V. Tags: X-ray wave X-ray optic lens non-uniform medium focusing numerical method simulation finite-difference stability numerical error research papers Source Type: research
Interaction of a relativistic dense electron beam with a laser wiggler in a vacuum: self-field effects on the electron orbits and free-electron laser gain
Employing laser wigglers and accelerators provides the potential to dramatically cut the size and cost of X-ray light sources. Owing to recent technological developments in the production of high-brilliance electron beams and high-power laser pulses, it is now conceivable to make steps toward the practical realisation of laser-pumped X-ray free-electron lasers (FELs). In this regard, here the head-on collision of a relativistic dense electron beam with a linearly polarized laser pulse as a wiggler is studied, in which the laser wiggler can be realised using a conventional quantum laser. In addition, an external guide magne...
Source: Journal of Synchrotron Radiation - October 10, 2016 Category: Physics Authors: Abbasi, E. Jafari, S. Hedayati, R. Tags: dense electron beam laser wiggler self-fields stability analysis free-electron laser research papers Source Type: research
A multi-MHz single-shot data acquisition scheme with high dynamic range: pump – probe X-ray experiments at synchrotrons
The technical implementation of a multi-MHz data acquisition scheme for laser – X-ray pump – probe experiments with pulse limited temporal resolution (100 ps) is presented. Such techniques are very attractive to benefit from the high-repetition rates of X-ray pulses delivered from advanced synchrotron radiation sources. Exploiting a synchronized 3.9 MHz laser excitation source, experiments in 60-bunch mode (7.8 MHz) at beamline P01 of the PETRA III storage ring are performed. Hereby molecular systems in liquid solutions are excited by the pulsed laser source and the total X-ray fluorescence yiel...
Source: Journal of Synchrotron Radiation - October 10, 2016 Category: Physics Authors: Britz, A. Assefa, T.A. Galler, A. Gawelda, W. Diez, M. Zalden, P. Khakhulin, D. Fernandes, B. Gessler, P. Sotoudi Namin, H. Beckmann, A. Harder, M. Yava ş , H. Bressler, C. Tags: time-resolved X-ray absorption spectroscopy data acquisition instrumentation ultrafast detection multi-photon counting research papers Source Type: research
Augmentation of the step-by-step Energy-Scanning EXAFS beamline BL-09 to continuous-scan EXAFS mode at INDUS-2 SRS
An innovative scheme to carry out continuous-scan X-ray absorption spectroscopy (XAS) measurements similar to quick-EXAFS mode at the Energy-Scanning EXAFS beamline BL-09 at INDUS-2 synchrotron source (Indore, India), which is generally operated in step-by-step scanning mode, is presented. The continuous XAS mode has been implemented by adopting a continuous-scan scheme of the double-crystal monochromator and on-the-fly measurement of incident and transmitted intensities. This enabled a high signal-to-noise ratio to be maintained and the acquisition time was reduced to a few seconds from tens of minutes or hours. The quali...
Source: Journal of Synchrotron Radiation - October 7, 2016 Category: Physics Authors: Poswal, A.K. Agrawal, A. Poswal, H.K. Bhattacharyya, D. Jha, S.N. Sahoo, N.K. Tags: time-resolved EXAFS chemical processes. quick-XAS beamlines Source Type: research
Design and performance of BOREAS, the beamline for resonant X-ray absorption and scattering experiments at the ALBA synchrotron light source
The optical design of the BOREAS beamline operating at the ALBA synchrotron radiation facility is described. BOREAS is dedicated to resonant X-ray absorption and scattering experiments using soft X-rays, in an unusually extended photon energy range from 80 to above 4000 eV, and with full polarization control. Its optical scheme includes a fixed-included-angle, variable-line-spacing grating monochromator and a pair of refocusing mirrors, equipped with benders, in a Kirkpatrick – Baez arrangement. It is equipped with two end-stations, one for X-ray magnetic circular dichroism and the other for resonant magnetic sca...
Source: Journal of Synchrotron Radiation - October 7, 2016 Category: Physics Authors: Barla, A. Nicol á s, J. Cocco, D. Valvidares, S.M. Herrero-Mart í n, J. Gargiani, P. Moldes, J. Ruget, C. Pellegrin, E. Ferrer, S. Tags: soft X-ray beamlines X-ray magnetic circular dichroism grating monochromator Source Type: research
KB scanning of X-ray beam for Laue microdiffraction on accelero-phobic samples: application to in situ mechanically loaded nanowires
A mapping technique has been developed where a sub-micrometer focused polychromatic X-ray beam is scanned across a stationary sample instead of scanning the sample in front of the X-ray microbeam. This method is applied to a gold nanowire during its mechanical loading using the tip of an atomic force microscope. During the loading process, such a sample is `accelero-phobic', i.e. the sample scanning stages must not to be moved to avoid parasitic additional load. Without beam scanning, only one single position within the sample can be probed during the test. The probed material point may even change because of drifts or mov...
Source: Journal of Synchrotron Radiation - October 7, 2016 Category: Physics Authors: Leclere, C. Cornelius, T.W. Ren, Z. Robach, O. Micha, J.-S. Davydok, A. Ulrich, O. Richter, G. Thomas, O. Tags: Laue microdiffraction nanowire in situ mechanical test atomic force microscope research papers Source Type: research
X-ray powder diffraction at the XRD1 beamline at LNLS
Various upgrades have been completed at the XRD1 beamline at the Brazilian synchrotron light source (LNLS). The upgrades are comprehensive, with changes to both hardware and software, now allowing users of the beamline to conduct X-ray powder diffraction experiments with faster data acquisition times and improved quality. The main beamline parameters and the results obtained for different standards are presented, showing the beamline ability of performing high-quality experiments in transmission geometry. XRD1 operates in the 5.5 – 14 keV range and has a photon flux of 7.8 × 109 photons s − 1 ...
Source: Journal of Synchrotron Radiation - October 6, 2016 Category: Physics Authors: Carvalho, A.M.G. Ara ú jo, D.H.C. Canova, H.F. Rodella, C.B. Barrett, D.H. Cuffini, S.L. Costa, R.N. Nunes, R.S. Tags: X-ray diffraction beamline bending magnet beamlines Source Type: research
Measuring the criticality of the `magic condition' for a beam-expanding monochromator
It has been established that for cylindrically bent crystals the optimal beam characteristics occur when the geometric and single-ray foci are matched. In the beam-expanding monochromator developed for the BioMedical Imaging and Therapy beamlines at the Canadian Light Source, it was unclear how critical this `magic condition' was for preserving the transverse coherence of the beam. A study was conducted to determine whether misalignments away from the ideal conditions would severely affect the transverse coherence of the beam, thereby limiting phase-based imaging techniques. The results were that the magic condition has en...
Source: Journal of Synchrotron Radiation - October 6, 2016 Category: Physics Authors: Martinson, M. Chapman, D. Tags: magic condition bent Laue double-crystal monochromator geometric and polychromatic focus short communications Source Type: research
Using irregularly spaced current peaks to generate an isolated attosecond X-ray pulse in free-electron lasers
A method is proposed to generate an isolated attosecond X-ray pulse in free-electron lasers, using irregularly spaced current peaks induced in an electron beam through interaction with an intense short-pulse optical laser. In comparison with a similar scheme proposed in a previous paper, the irregular arrangement of current peaks significantly improves the contrast between the main and satellite pulses, enhances the attainable peak power and simplifies the accelerator layout. Three different methods are proposed for this purpose and achievable performances are computed under realistic conditions. Numerical simulations carr...
Source: Journal of Synchrotron Radiation - October 6, 2016 Category: Physics Authors: Tanaka, T. Parc, Y.W. Kida, Y. Kinjo, R. Shim, C.H. Ko, I.S. Kim, B. Kim, D.E. Prat, E. Tags: free electron laser attosecond pulse terawatt power level research papers Source Type: research
Fabrication and testing of a newly designed slit system for depth-resolved X-ray diffraction measurements
A new system of slits called `spiderweb slits' have been developed for depth-resolved powder or polycrystalline X-ray diffraction measurements. The slits act on diffracted X-rays to select a particular gauge volume of sample, while absorbing diffracted X-rays from outside of this volume. Although the slit geometry is to some extent similar to that of previously developed conical slits or spiral slits, this new design has advantages over the previous ones in use for complex heterogeneous materials and in situ and operando diffraction measurements. For example, the slits can measure a majority of any diffraction cone for any...
Source: Journal of Synchrotron Radiation - October 6, 2016 Category: Physics Authors: Sinsheimer, J. Bouet, N. Ghose, S. Dooryhee, E. Conley, R. Tags: synchrotron X-ray powder diffraction depth-resolved slits ray-tracing research papers Source Type: research
Brownian and advective dynamics in microflow studied by coherent X-ray scattering experiments
Combining microfluidics with coherent X-ray illumination offers the possibility to not only measure the structure but also the dynamics of flowing samples in a single-scattering experiment. Here, the power of this combination is demonstrated by studying the advective and Brownian dynamics of colloidal suspensions in microflow of different geometries. Using an experimental setup with a fast two-dimensional detector and performing X-ray correlation spectroscopy by calculating two-dimensional maps of the intensity auto-correlation functions, it was possible to evaluate the sample structure and furthermore to characterize the ...
Source: Journal of Synchrotron Radiation - October 6, 2016 Category: Physics Authors: Urbani, R. Westermeier, F. Banusch, B. Sprung, M. Pfohl, T. Tags: microfluidics X-ray scattering photon correlation spectroscopy flow profiles flow geometries particle dynamics research papers Source Type: research
Determination of the packing fraction in photonic glass using synchrotron radiation nanotomography
Photonic glass is a material class that can be used as photonic broadband reflectors, for example in the infrared regime as thermal barrier coating films. Photonic properties such as the reflectivity depend on the ordering and material packing fraction over the complete film thickness of up to 100 µ m. Nanotomography allows acquiring these key parameters throughout the sample volume at the required resolution in a non-destructive way. By performing a nanotomography measurement at the PETRA III beamline P05 on a photonic glass film, the packing fraction throughout the complete sample thickness was analyzed. Th...
Source: Journal of Synchrotron Radiation - October 6, 2016 Category: Physics Authors: Ogurreck, M. Rosario, J.J. do Leib, E.W. Laipple, D. Greving, I. Marschall, F. Last, A. Schneider, G.A. Vossmeyer, T. Weller, H. Beckmann, F. M ü ller, M. Tags: nanotomography photonic glass X-ray microscopy research papers Source Type: research
X-ray third-order nonlinear plane-wave Bragg-case dynamical diffraction effects in a perfect crystal. Erratum
Formulae in the paper by Balyan (2015) [J. Synchrotron Rad. 22, 1410 – 1418] are corrected. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - August 30, 2016 Category: Physics Authors: Balyan, M.K. Tags: nonlinear diffraction Bragg case reflection region third-order nonlinearity two-wave diffraction addenda and errata Source Type: research
CTM4DOC: electronic structure analysis from X-ray spectroscopy
Two electronic structure descriptions, one based on orbitals and the other based on term symbols, have been implemented in a new Matlab-based program, CTM4DOC. The program includes a graphical user interface that allows the user to explore the dependence of details of electronic structure in transition metal systems, both in the ground and core-hole excited states, on intra-atomic electron – electron, crystal-field and charge-transfer interactions. The program can also track the evolution of electronic structure features as the crystal-field parameters are systematically varied, generating Tanabe – Sugano-type ...
Source: Journal of Synchrotron Radiation - August 23, 2016 Category: Physics Authors: Delgado-Jaime, M.U. Zhang, K. Vura-Weis, J. de Groot, F.M.F. Tags: multiplet simulations electronic structure differential orbital covalency X-ray spectroscopy computer programs Source Type: research
Development of a speckle-based portable device for in situ metrology of synchrotron X-ray mirrors
A portable device for in situ metrology of synchrotron X-ray mirrors based on the near-field speckle scanning technique has been developed. Ultra-high angular sensitivity is achieved by scanning a piece of abrasive paper or filter membrane in the X-ray beam. In addition to the compact setup and ease of implementation, a user-friendly graphical user interface has been developed to ensure that optimizing active X-ray mirrors is simple and fast. The functionality and feasibility of this device have been demonstrated by characterizing and optimizing X-ray mirrors. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - August 16, 2016 Category: Physics Authors: Kashyap, Y. Wang, H. Sawhney, K. Tags: speckle X-ray optics metrology research papers Source Type: research
The SwissFEL Experimental Laser facility
The hard X-ray laser SwissFEL at the Paul Scherrer Institute is currently being commissioned and will soon become available for users. In the current article the laser facility is presented, an integral part of the user facility, as most time-resolved experiments will require a versatile optical laser infrastructure and precise information about the relative delay between the X-ray and optical pulse. The important key parameters are a high availability and long-term stability while providing advanced laser performance in the wavelength range from ultraviolet to terahertz. The concept of integrating a Ti:sapphire laser ampl...
Source: Journal of Synchrotron Radiation - August 16, 2016 Category: Physics Authors: Erny, C. Hauri, C.P. Tags: FEL pump – probe experiment user laser research papers Source Type: research
Simultaneous X-ray fluorescence and scanning X-ray diffraction microscopy at the Australian Synchrotron XFM beamline
Owing to its extreme sensitivity, quantitative mapping of elemental distributions via X-ray fluorescence microscopy (XFM) has become a key microanalytical technique. The recent realisation of scanning X-ray diffraction microscopy (SXDM) meanwhile provides an avenue for quantitative super-resolved ultra-structural visualization. The similarity of their experimental geometries indicates excellent prospects for simultaneous acquisition. Here, in both step- and fly-scanning modes, robust, simultaneous XFM-SXDM is demonstrated. (Source: Journal of Synchrotron Radiation)
Source: Journal of Synchrotron Radiation - August 11, 2016 Category: Physics Authors: Jones, M.W.M. Phillips, N.W. Riessen, G.A. van Abbey, B. Vine, D.J. Nashed, Y.S.G. Mudie, S.T. Afshar, N. Kirkham, R. Chen, B. Balaur, E. de Jonge, M.D. Tags: X-ray fluorescence scanning X-ray diffraction microscopy ptychography research papers Source Type: research
A robust method for high-precision quantification of the complex three-dimensional vasculatures acquired by X-ray microtomography
The quantification of micro-vasculatures is important for the analysis of angiogenesis on which the detection of tumor growth or hepatic fibrosis depends. Synchrotron-based X-ray computed micro-tomography (SR- µ CT) allows rapid acquisition of micro-vasculature images at micrometer-scale spatial resolution. Through skeletonization, the statistical features of the micro-vasculature can be extracted from the skeleton of the micro-vasculatures. Thinning is a widely used algorithm to produce the vascular skeleton in medical research. Existing three-dimensional thinning methods normally emphasize the preservation of topol...
Source: Journal of Synchrotron Radiation - August 11, 2016 Category: Physics Authors: Tan, H. Wang, D. Li, R. Sun, C. Lagerstrom, R. He, Y. Xue, Y. Xiao, T. Tags: 3D image analysis quantitative analysis thinning end-point skeleton geometric properties vasculature research papers Source Type: research
A new optical scheme for large-extraction small-aberration vacuum-ultraviolet synchrotron radiation beamlines
Vacuum-ultraviolet radiation delivered by bending-magnet sources is used at numerous synchrotron radiation facilities worldwide. As bending-magnet radiation is inherently much less collimated compared with undulator sources, the generation of high-quality intense bending-magnet vacuum-ultraviolet photon beams is extremely demanding in terms of the optical layout due to the necessary larger collection apertures. In this article, an optimized optical layout which takes into account both the optical and electron beam properties is proposed. This layout delivers an improved beam emittance of over one order of magnitude compare...
Source: Journal of Synchrotron Radiation - August 10, 2016 Category: Physics Authors: Moreno, T. Tags: vacuum-ultraviolet synchrotron beamline bending magnet optical aberrations integration of magnetic and photonic synchrotron beamline components research papers Source Type: research
Large-surface-area diamond (111) crystal plates for applications in high-heat-load wavefront-preserving X-ray crystal optics
Fabrication and results of high-resolution X-ray topography characterization of diamond single-crystal plates with large surface area (10 mm × 10 mm) and (111) crystal surface orientation for applications in high-heat-load X-ray crystal optics are reported. The plates were fabricated by laser-cutting of the (111) facets of diamond crystals grown using high-pressure high-temperature methods. The intrinsic crystal quality of a selected 3 mm × 7 mm crystal region of one of the studied samples was found to be suitable for applications in wavefront-preserving high-heat-load crystal optics. Wavefront ...
Source: Journal of Synchrotron Radiation - August 10, 2016 Category: Physics Authors: Stoupin, S. Antipov, S. Butler, J.E. Kolyadin, A.V. Katrusha, A. Tags: X-ray monochromator high heat load diamond crystal wavefront preservation research papers Source Type: research