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Preview: Journal of Synchrotron Radiation

Journal of Synchrotron Radiation

Synchrotron radiation research is rapidly expanding with many new sources of radiation being created globally. Synchrotron radiation plays a leading role in pure science and in emerging technologies. The Journal of Synchrotron Radiation provides comprehen

Published: 2017-06-29


Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL


The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on the Xmipp software package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy.

Numerical simulations of the hard X-ray pulse intensity distribution at the Linac Coherent Light Source


Numerical simulations of the current and future pulse intensity distributions at selected locations along the Far Experimental Hall, the hard X-ray section of the Linac Coherent Light Source (LCLS), are provided. Estimates are given for the pulse fluence, energy and size in and out of focus, taking into account effects due to the experimentally measured divergence of the X-ray beam, and measured figure errors of all X-ray optics in the beam path. Out-of-focus results are validated by comparison with experimental data. Previous work is expanded on, providing quantitatively correct predictions of the pulse intensity distribution. Numerical estimates in focus are particularly important given that the latter cannot be measured with direct imaging techniques due to detector damage. Finally, novel numerical estimates of improvements to the pulse intensity distribution expected as part of the on-going upgrade of the LCLS X-ray transport system are provided. We suggest how the new generation of X-ray optics to be installed would outperform the old one, satisfying the tight requirements imposed by X-ray free-electron laser facilities.

Using refractive optics to broaden the focus of an X-ray mirror


X-ray mirrors are widely used at synchrotron radiation sources for focusing X-rays into focal spots of size less than 1 µm. The ability of the beamline optics to change the size of this spot over a range up to tens of micrometres can be an advantage for many experiments such as X-ray microprobe and X-ray diffraction from micrometre-scale crystals. It is a requirement that the beam size change should be reproducible and it is often essential that the change should be rapid, for example taking less than 1 s, in order to allow high data collection rates at modern X-ray sources. In order to provide a controlled broadening of the focused spot of an X-ray mirror, a series of refractive optical elements have been fabricated and installed immediately before the mirror. By translation, a new refractive element is moved into the X-ray beam allowing a variation in the size of the focal spot in the focusing direction. Measurements using a set of prefabricated refractive structures with a test mirror showed that the focused beam size could be varied from less than 1 µm to over 10 µm for X-rays in the energy range 10–20 keV. As the optics is in-line with the X-ray beam, there is no effect on the centroid position of the focus. Accurate positioning of the refractive optics ensures reproducibility in the focused beam profile and no additional re-alignment of the optics is required.

Very efficient spin polarization analysis (VESPA): new exchange scattering-based setup for spin-resolved ARPES at APE-NFFA beamline at Elettra


Complete photoemission experiments, enabling measurement of the full quantum set of the photoelectron final state, are in high demand for studying materials and nanostructures whose properties are determined by strong electron and spin correlations. Here the implementation of the new spin polarimeter VESPA (Very Efficient Spin Polarization Analysis) at the APE-NFFA beamline at Elettra is reported, which is based on the exchange coupling between the photoelectron spin and a ferromagnetic surface in a reflectometry setup. The system was designed to be integrated with a dedicated Scienta-Omicron DA30 electron energy analyzer allowing for two simultaneous reflectometry measurements, along perpendicular axes, that, after magnetization switching of the two targets, allow the three-dimensional vectorial reconstruction of the spin polarization to be performed while operating the DA30 in high-resolution mode. VESPA represents the very first installation for spin-resolved ARPES (SPARPES) at the Elettra synchrotron in Trieste, and is being heavily exploited by SPARPES users since autumn 2015.

Structural variation in a synchrotron-induced contamination layer (a-C:H) deposited on a toroidal Au mirror surface


A carbon layer deposited on an optical component is the result of complex interactions between the optical surface, adsorbed hydrocarbons, photons and secondary electrons (photoelectrons generated on the surface of optical elements). In the present study a synchrotron-induced contamination layer on a 340 mm × 60 mm Au-coated toroidal mirror has been characterized. The contamination layer showed a strong variation in structural properties from the centre of the mirror to the edge region (along the long dimension of the mirror) due to the Gaussian distribution of the incident photon beam intensity/power on the mirror surface. Raman scattering measurements were carried out at 12 equidistant (25 mm) locations along the length of the mirror. The surface contamination layer that formed on the Au surface was observed to be hydrogenated amorphous carbon film in nature. The effects of the synchrotron beam intensity/power distribution on the structural properties of the contamination layer are discussed. The I(D)/I(G) ratio, cluster size and disordering were found to increase whereas the sp2:sp3 ratio, G peak position and H content decreased with photon dose. The structural parameters of the contamination layer in the central region were estimated (thickness ≃ 400 Å, roughness ≃ 60 Å, density ≃ 72% of bulk graphitic carbon density) by soft X-ray reflectivity measurements. The amorphous nature of the layer in the central region was observed by grazing-incidence X-ray diffraction.

Normal tracing deflectometry using a secondary light source


Scanning deflectometric profilers based on an f–θ system are typical optical tools used to measure mirror profiles at many synchrotron facilities. Unlike these profilers, which are based on a pencil beam, here a secondary light source and a pinhole are used to construct a system that automatically selects a beam that will always pass through the pinhole and propagate along the normal direction of the measured area on the surface under test. By measuring the angle variation of the selected beam, slope variations of the surface under test can be measured. Systematic errors introduced by manufacturing defects or aberrations of an optical element, which greatly degrade the performance of traditional profilers, could be minimized by using the developed method. Simulation values of the proposed method and a conventional method are compared.

Protective radiolucent aluminium oxide coatings for beryllium X-ray optics


Beryllium, being one of the most transparent materials to X-ray radiation, has become the material of choice for X-ray optics instrumentation at synchrotron radiation sources and free-electron laser facilities. However, there are concerns due to its high toxicity and, consequently, there is a need for special safety regulations. The authors propose to apply protective coatings in order to seal off beryllium from the ambient atmosphere, thus preventing degradation processes providing additional protection for users and prolonging the service time of the optical elements. This paper presents durability test results for Be windows coated with atomic-layer-deposition alumina layers run at the European Synchrotron Radiation Facility. Expositions were performed under monochromatic, pink and white beams, establishing conditions that the samples could tolerate without radiation damage. X-ray treatment was implemented in various environments, i.e. vacuum, helium, nitrogen, argon and dry air at different pressures. Post-process analysis revealed their efficiency for monochromatic and pink beams.

A method to stabilize the incident X-ray energy for anomalous diffraction measurements


A method to calibrate and stabilize the incident X-ray energy for anomalous diffraction data collection is provided and has been successfully used at the single-crystal diffraction beamline 1W2B at the Beijing Synchrotron Radiation Facilities. Employing a feedback loop to control the movement of the double-crystal monochromator, this new method enables the incident X-ray energy to be kept within a 0.2 eV range at the inflection point of the absorption edge.

In situ electrochemical high-energy X-ray diffraction using a capillary working electrode cell geometry


The ability to generate new electrochemically active materials for energy generation and storage with improved properties will likely be derived from an understanding of atomic-scale structure/function relationships during electrochemical events. Here, the design and implementation of a new capillary electrochemical cell designed specifically for in situ high-energy X-ray diffraction measurements is described. By increasing the amount of electrochemically active material in the X-ray path while implementing low-Z cell materials with anisotropic scattering profiles, an order of magnitude enhancement in diffracted X-ray signal over traditional cell geometries for multiple electrochemically active materials is demonstrated. This signal improvement is crucial for high-energy X-ray diffraction measurements and subsequent Fourier transformation into atomic pair distribution functions for atomic-scale structural analysis. As an example, clear structural changes in LiCoO2 under reductive and oxidative conditions using the capillary cell are demonstrated, which agree with prior studies. Accurate modeling of the LiCoO2 diffraction data using reverse Monte Carlo simulations further verifies accurate background subtraction and strong signal from the electrochemically active material, enabled by the capillary working electrode geometry.

X-ray reflectivity measurement of interdiffusion in metallic multilayers during rapid heating


A technique for measuring interdiffusion in multilayer materials during rapid heating using X-ray reflectivity is described. In this technique the sample is bent to achieve a range of incident angles simultaneously, and the scattered intensity is recorded on a fast high-dynamic-range mixed-mode pixel array detector. Heating of the multilayer is achieved by electrical resistive heating of the silicon substrate, monitored by an infrared pyrometer. As an example, reflectivity data from Al/Ni heated at rates up to 200 K s−1 are presented. At short times the interdiffusion coefficient can be determined from the rate of decay of the reflectivity peaks, and it is shown that the activation energy for interdiffusion is consistent with a grain boundary diffusion mechanism. At longer times the simple analysis no longer applies because the evolution of the reflectivity pattern is complicated by other processes, such as nucleation and growth of intermetallic phases.

Accuracy of stress measurement by Laue microdiffraction (Laue-DIC method): the influence of image noise, calibration errors and spot number


Laue microdiffraction, available at several synchrotron radiation facilities, is well suited for measuring the intragranular stress field in deformed materials thanks to the achievable submicrometer beam size. The traditional method for extracting elastic strain (and hence stress) and lattice orientation from a microdiffraction image relies on fitting each Laue spot with an analytical function to estimate the peak position on the detector screen. The method is thus limited to spots exhibiting ellipsoidal shapes, thereby impeding the study of specimens plastically deformed. To overcome this difficulty, the so-called Laue-DIC method introduces digital image correlation (DIC) for the evaluation of the relative positions of spots, which can thus be of any shape. This paper is dedicated to evaluating the accuracy of this Laue-DIC method. First, a simple image noise model is established and verified on the data acquired at beamline BM32 of the European Synchrotron Radiation Facility. Then, the effect of image noise on errors on spot displacement measured by DIC is evaluated by Monte Carlo simulation. Finally, the combined effect of the image noise, calibration errors and the number of Laue spots used for data treatment is investigated. Results in terms of the uncertainty of stress measurement are provided, and various error regimes are identified.

Alternative difference analysis scheme combining R-space EXAFS fit with global optimization XANES fit for X-ray transient absorption spectroscopy


Time-resolved X-ray absorption spectroscopy (TR-XAS), based on the laser-pump/X-ray-probe method, is powerful in capturing the change of the geometrical and electronic structure of the absorbing atom upon excitation. TR-XAS data analysis is generally performed on the laser-on minus laser-off difference spectrum. Here, a new analysis scheme is presented for the TR-XAS difference fitting in both the extended X-ray absorption fine-structure (EXAFS) and the X-ray absorption near-edge structure (XANES) regions. R-space EXAFS difference fitting could quickly provide the main quantitative structure change of the first shell. The XANES fitting part introduces a global non-derivative optimization algorithm and optimizes the local structure change in a flexible way where both the core XAS calculation package and the search method in the fitting shell are changeable. The scheme was applied to the TR-XAS difference analysis of Fe(phen)3 spin crossover complex and yielded reliable distance change and excitation population.

Insight into growth of Au–Pt bimetallic nanoparticles: an in situ XAS study


Au–Pt bimetallic nanoparticles have been synthesized through a one-pot synthesis route from their respective chloride precursors using block copolymer as a stabilizer. Growth of the nanoparticles has been studied by simultaneous in situ measurement of X-ray absorption spectroscopy (XAS) and UV–Vis spectroscopy at the energy-dispersive EXAFS beamline (BL-08) at Indus-2 SRS at RRCAT, Indore, India. In situ XAS spectra, comprising both X-ray near-edge structure (XANES) and extended X-ray absorption fine-structure (EXAFS) parts, have been measured simultaneously at the Au and Pt L3-edges. While the XANES spectra of the precursors provide real-time information on the reduction process, the EXAFS spectra reveal the structure of the clusters formed in the intermediate stages of growth. This insight into the formation process throws light on how the difference in the reduction potential of the two precursors could be used to obtain the core–shell-type configuration of a bimetallic alloy in a one-pot synthesis method. The core–shell-type structure of the nanoparticles has also been confirmed by ex situ energy-dispersive spectroscopy line-scan and X-ray photoelectron spectroscopy measurements with in situ ion etching on fully formed nanoparticles.

Rotatable high-resolution ARPES system for tunable linear-polarization geometry


A rotatable high-resolution angle-resolved photoemission spectroscopy (ARPES) system has been developed to utilize tunable linear-polarization geometries on the linear undulator beamline (BL-1) at Hiroshima Synchrotron Radiation Center. By rotating the whole ARPES measurement system, the photoelectron detection plane can be continuously changed from parallel to normal against the electric field vector of linearly polarized undulator radiation. This polarization tunability enables us to identify the symmetry of the initial electronic states with respect to the mirror planes, and to selectively observe the electronic states based on the dipole selection rule in the photoemission process. Specifications of the rotatable high-resolution ARPES system are described, as well as its capabilities with some representative experimental results.

Potential of propagation-based synchrotron X-ray phase-contrast computed tomography for cardiac tissue engineering


Hydrogel-based cardiac tissue engineering offers great promise for myocardial infarction repair. The ability to visualize engineered systems in vivo in animal models is desired to monitor the performance of cardiac constructs. However, due to the low density and weak X-ray attenuation of hydrogels, conventional radiography and micro-computed tomography are unable to visualize the hydrogel cardiac constructs upon their implantation, thus limiting their use in animal systems. This paper presents a study on the optimization of synchrotron X-ray propagation-based phase-contrast imaging computed tomography (PCI-CT) for three-dimensional (3D) visualization and assessment of the hydrogel cardiac patches. First, alginate hydrogel was 3D-printed into cardiac patches, with the pores filled by fibrin. The hydrogel patches were then surgically implanted on rat hearts. A week after surgery, the hearts including patches were excised and embedded in a soft-tissue-mimicking gel for imaging by using PCI-CT at an X-ray energy of 25 keV. During imaging, the sample-to-detector distances, CT-scan time and the region of interest (ROI) were varied and examined for their effects on both imaging quality and radiation dose. The results showed that phase-retrieved PCI-CT images provided edge-enhancement fringes at a sample-to-detector distance of 147 cm that enabled visualization of anatomical and microstructural features of the myocardium and the implanted patch in the tissue-mimicking gel. For visualization of these features, PCI-CT offered a significantly higher performance than the dual absorption-phase and clinical magnetic resonance (3 T) imaging techniques. Furthermore, by reducing the total CT-scan time and ROI, PCI-CT was examined for lowering the effective dose, meanwhile without much loss of imaging quality. In effect, the higher soft tissue contrast and low-dose potential of PCI-CT has been used along with an acceptable overall animal dose to achieve the high spatial resolution needed for cardiac implant visualization. As a result, PCI-CT at the identified imaging parameters offers great potential for 3D assessment of microstructural features of hydrogel cardiac patches.

Preclinical radiotherapy at the Australian Synchrotron's Imaging and Medical Beamline: instrumentation, dosimetry and a small-animal feasibility study


Therapeutic applications of synchrotron X-rays such as microbeam (MRT) and minibeam (MBRT) radiation therapy promise significant advantages over conventional clinical techniques for some diseases if successfully transferred to clinical practice. Preclinical studies show clear evidence that a number of normal tissues in animal models display a tolerance to much higher doses from MRT compared with conventional radiotherapy. However, a wide spread in the parameters studied makes it difficult to make any conclusions about the associated tumour control or normal tissue complication probabilities. To facilitate more systematic and reproducible preclinical synchrotron radiotherapy studies, a dedicated preclinical station including small-animal irradiation stage was designed and installed at the Imaging and Medical Beamline (IMBL) at the Australian Synchrotron. The stage was characterized in terms of the accuracy and reliability of the vertical scanning speed, as this is the key variable in dose delivery. The measured speed was found to be within 1% of the nominal speed for the range of speeds measured by an interferometer. Furthermore, dose measurements confirm the expected relationship between speed and dose and show that the measured dose is independent of the scan direction. Important dosimetric parameters such as peak dose, valley dose, the collimator output factor and peak-to-valley dose ratio are presented for 5 mm × 5 mm, 10 mm × 10 mm and 20 mm × 20 mm field sizes. Finally, a feasibility study on three glioma-bearing rats was performed. MRT and MBRT doses were prescribed to achieve an average dose of 65 Gy in the target, and magnetic resonance imaging follow-up was performed at various time points after irradiation to follow the tumour volume. Although it is impossible to draw conclusions on the different treatments with such a small number of animals, the feasibility of end-to-end preclinical synchrotron radiotherapy studies using the IMBL preclinical stage is demonstrated.

Comparison of phantom materials for use in quality assurance of microbeam radiation therapy


Microbeam radiation therapy (MRT) is a promising radiotherapy modality that uses arrays of spatially fractionated micrometre-sized beams of synchrotron radiation to irradiate tumours. Routine dosimetry quality assurance (QA) prior to treatment is necessary to identify any changes in beam condition from the treatment plan, and is undertaken using solid homogeneous phantoms. Solid phantoms are designed for, and routinely used in, megavoltage X-ray beam radiation therapy. These solid phantoms are not necessarily designed to be water-equivalent at low X-ray energies, and therefore may not be suitable for MRT QA. This work quantitatively determines the most appropriate solid phantom to use in dosimetric MRT QA. Simulated dose profiles of various phantom materials were compared with those calculated in water under the same conditions. The phantoms under consideration were RMI457 Solid Water (Gammex-RMI, Middleton, WI, USA), Plastic Water (CIRS, Norfolk, VA, USA), Plastic Water DT (CIRS, Norfolk, VA, USA), PAGAT (CIRS, Norfolk, VA, USA), RW3 Solid Phantom (PTW Freiburg, Freiburg, Germany), PMMA, Virtual Water (Med-Cal, Verona, WI, USA) and Perspex. RMI457 Solid Water and Virtual Water were found to be the best approximations for water in MRT dosimetry (within ±3% deviation in peak and 6% in valley). RW3 and Plastic Water DT approximate the relative dose distribution in water (within ±3% deviation in the peak and 5% in the valley). PAGAT, PMMA, Perspex and Plastic Water are not recommended to be used as phantoms for MRT QA, due to dosimetric discrepancies greater than 5%.

Effects of temperature, mechanical motion and source positional jitter on the resolving power of beamline 02B at the SSRF


A detailed analysis of the effects of temperature excursions, instrumental mechanical motion and source position jitter on the energy-resolving power of beamline 02B at the Shanghai Synchrotron Radiation Facility (SSRF) is presented in this study. This beamline uses a bending-magnet-based source and includes a variable-line-spacing grating monochromator with additional optics. Expressions are derived for the monochromator output photon energy shifts for each of the performance challenges considered. The calculated results indicate that measured temperature excursions of ±1 K produce an energy shift of less than 11% of the system's energy resolution. Mechanical displacements and vibrations measured at amplitudes of less than 0.5 µm produce changes of less than 5%, while measured source location jitter results in a change of less than 10%. Spectroscopic test experiments at 250 and 400 eV provide energy resolutions of over 104. This analysis, combined with the measured results, confirms the operational stability of the beamline, indicating that it meets the performance requirements for experimental use.

Pump−probe experiments at the TEMPO beamline using the low-α operation mode of Synchrotron SOLEIL


The SOLEIL synchrotron radiation source is regularly operated in special filling modes dedicated to pump–probe experiments. Among others, the low-α mode operation is characterized by shorter pulse duration and represents the natural bridge between 50 ps synchrotron pulses and femtosecond experiments. Here, the capabilities in low-α mode of the experimental set-ups developed at the TEMPO beamline to perform pump–probe experiments with soft X-rays based on photoelectron or photon detection are presented. A 282 kHz repetition-rate femtosecond laser is synchronized with the synchrotron radiation time structure to induce fast electronic and/or magnetic excitations. Detection is performed using a two-dimensional space resolution plus time resolution detector based on microchannel plates equipped with a delay line. Results of time-resolved photoelectron spectroscopy, circular dichroism and magnetic scattering experiments are reported, and their respective advantages and limitations in the framework of high-time-resolution pump–probe experiments compared and discussed.

The relativistic foundations of synchrotron radiation


Special relativity (SR) determines the properties of synchrotron radiation, but the corresponding mechanisms are frequently misunderstood. Time dilation is often invoked among the causes, whereas its role would violate the principles of SR. Here it is shown that the correct explanation of the synchrotron radiation properties is provided by a combination of the Doppler shift, not dependent on time dilation effects, contrary to a common belief, and of the Lorentz transformation into the particle reference frame of the electromagnetic field of the emission-inducing device, also with no contribution from time dilation. Concluding, the reader is reminded that much, if not all, of our argument has been available since the inception of SR, a research discipline of its own standing.

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