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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: 2017-08-21


Phase-merging enhanced harmonic generation free-electron laser with a normal modulator


A phase-merging enhanced harmonic generation free-electron laser (FEL) was proposed to increase the harmonic conversion efficiency of seeded FELs and promote the radiation wavelength towards the X-ray spectral region. However, this requires a specially designed transverse gradient undulator (TGU) as the modulator to couple the transverse and longitudinal phase space of the electron beam. In this paper, the generation of the phase-merging effect is explored using the natural field gradient of a normal planar undulator. In this method, a vertical dispersion on the electron beam is introduced and then the dispersed beam travels through a normal modulator in a vertical off-axis orbit where the vertical field gradient is selected properly in terms of the vertical dispersion strength and modulation amplitude. The phase-merging effect will be generated after passing through the dispersive chicane. Theoretical analysis and numerical simulations for a seeded soft X-ray FEL based on parameters of the Shanghai Soft X-ray FEL project are presented. Compared with a TGU modulator, using the natural gradient of a normal planar modulator has the distinct advantage that the gradient can be conveniently tuned in quite a large range by adjusting the beam orbit offset.

Temperature-dependent thermal properties of Ru/C multilayers


Multilayers made of Ru/C are the most promising candidates when working in the energy region 8–20 keV. The stability of its thermal properties, including thermal expansion and thermal conduction, needs to be considered for monochromator or focusing components. Ru/C multilayers with periodic thicknesses of 3, 4 and 5 nm were investigated in situ by grazing-incidence X-ray reflectometry and diffuse scattering in order to study their thermal expansion characteristics as a function of annealing temperature up to 400°C. The thermal conductivity of multilayers with the same structure was also measured by the transient hot-wire method and compared with bulk values.

Refurbishment of a used in-vacuum undulator from the National Synchrotron Light Source for the National Synchrotron Light Source-II ring


The National Synchrotron Light Source (NSLS) ceased operation in September 2014 and was succeeded by NSLS-II. There were four in-vacuum undulators (IVUs) in operation at NSLS. The most recently constructed IVU for NSLS was the mini-gap undulator (MGU-X25, to be renamed IVU18 for NSLS-II), which was constructed in 2006. This device was selected to be reused for the New York Structural Biology Consortium Microdiffraction beamline at NSLS-II. At the time of construction, IVU18 was a state-of-the-art undulator designed to be operated as a cryogenic permanent-magnet undulator. Due to the more stringent field quality and impedance requirements of the NSLS-II ring, the transition region was redesigned. The control system was also updated to NSLS-II specifications. This paper reports the details of the IVU18 refurbishment activities including additional magnetic measurement and tuning.

A protocol for searching the most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation


Coherent X-ray diffraction imaging (CXDI) is a technique for visualizing the structures of non-crystalline particles with size in the submicrometer to micrometer range in material sciences and biology. In the structural analysis of CXDI, the electron density map of a specimen particle projected along the direction of the incident X-rays can be reconstructed only from the diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction, relying entirely on the computational procedure, sometimes fails because diffraction patterns miss the data in small-angle regions owing to the beam stop and saturation of the detector pixels, and are modified by Poisson noise in X-ray detection. To date, X-ray free-electron lasers have allowed us to collect a large number of diffraction patterns within a short period of time. Therefore, the reconstruction of correct electron density maps is the bottleneck for efficiently conducting structure analyses of non-crystalline particles. To automatically address the correctness of retrieved electron density maps, a data analysis protocol to extract the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a single diffraction pattern is proposed. Through monitoring the variations of the phase values during PR calculations, the tendency for the PR calculations to succeed when the retrieved phase sets converged on a certain value was found. On the other hand, if the phase set was in persistent variation, the PR calculation tended to fail to yield the correct electron density map. To quantify this tendency, here a figure of merit for the variation of the phase values during PR calculation is introduced. In addition, a PR protocol to evaluate the similarity between a map of the highest figure of merit and other independently reconstructed maps is proposed. The protocol is implemented and practically examined in the structure analyses for diffraction patterns from aggregates of gold colloidal particles. Furthermore, the feasibility of the protocol in the structure analysis of organelles from biological cells is examined.

Simulated sample heating from a nanofocused X-ray beam


Recent developments in synchrotron brilliance and X-ray optics are pushing the flux density in nanofocusing experiments to unprecedented levels, which increases the risk of different types of radiation damage. The effect of X-ray induced sample heating has been investigated using time-resolved and steady-state three-dimensional finite-element modelling of representative nanostructures. Simulations of a semiconductor nanowire indicate that the heat generated by X-ray absorption is efficiently transported within the nanowire, and that the temperature becomes homogeneous after about 5 ns. The most important channel for heat loss is conduction to the substrate, where the heat transfer coefficient and the interfacial area are limiting the heat transport. While convective heat transfer to air is significant, the thermal radiation is negligible. The steady-state average temperature in the nanowire is 8 K above room temperature at the reference parameters. In the absence of heat transfer to the substrate, the temperature increase at the same flux reaches 55 K in air and far beyond the melting temperature in vacuum. Reducing the size of the X-ray focus at constant flux only increases the maximum temperature marginally. These results suggest that the key strategy for reducing the X-ray induced heating is to improve the heat transfer to the surrounding.

Analysis of the microvascular morphology and hemodynamics of breast cancer in mice using SPring-8 synchrotron radiation microangiography


Tumor vasculature is characterized by morphological and functional abnormalities. However, analysis of the dynamics in blood flow is still challenging because of limited spatial and temporal resolution. Synchrotron radiation (SR) microangiography above the K-edge of the iodine contrast agent can provide high-contrast imaging of microvessels in time orders of milliseconds. In this study, mice bearing the human breast cancer cell lines MDAMB231 and NOTCH4 overexpression in MDAMB231 (MDAMB231NOTCH4+) and normal mice were assessed using SR microangiography. NOTCH is transmembrane protein that has crucial roles for vasculogenesis, angiogenesis and tumorigenesis, and NOTCH4 is considered to be a cause of high-flow arteriovenous shunting. A subgroup of mice received intravenous eribulin treatment, which is known to improve intratumor core circulation (MDAMB231_eribulin). Microvessel branches from approximately 200 µm to less than 20 µm in diameter were observed within the same visual field. The mean transition time (MTT) was measured as a dynamic parameter and quantitative analysis was performed. MTT in MDAMB231 was longer than that in normal tissue, and MDAMB231NOTCH4+ showed shorter MTT [5.0 ± 1.4 s, 3.6 ± 1.0 s and 3.6 ± 1.1 s (mean ± standard deviation), respectively]. After treatment, average MTT was correlated to tumor volume (r = 0.999) in MDAMB231_eribulin, while in contrast there was no correlation in MDAMB231 (r = −0.026). These changes in MTT profile are considered to be driven by the modulation of intratumoral circulation dynamics. These results demonstrate that a SR microangiography approach enables quantitative analysis of morphological and dynamic characteristics of tumor vasculature in vivo. Further studies will reveal new findings concerning vessel function in tumors.

Electron-bunch lengthening on higher-harmonic oscillations in storage-ring free-electron lasers


The influence of higher-harmonic free-electron laser (FEL) oscillations on an electron beam have been studied by measuring its bunch length at the NIJI-IV storage ring. The bunch length and the lifetime of the electron beam were measured, and were observed to have become longer owing to harmonic lasing, which is in accord with the increase of the FEL gain. It was demonstrated that the saturated FEL power could be described by the theory of bunch heating, even for the harmonic lasing. Cavity-length detuning curves were measured for the harmonic lasing, and it was found that the width of the detuning curve was proportional to a parameter that depended on the bunch length. These experimental results will be useful for developing compact resonator-type FELs by using higher harmonics in the extreme-ultraviolet and the X-ray regions.

Flyscan opportunities in medicine: the case of quantum rattle based on gold quantum dots


The new rapid scan method, Flyscan mode, implemented on the DiffAbs beamline at Synchrotron SOLEIL, allows fast micro-X-ray fluorescence data acquisition. It paves the way for applications in the biomedical field where a large amount of data is needed to generate meaningful information for the clinician. This study presents a complete set of data acquired after injection of gold-cluster-enriched mesoporous silica nanospheres, used as potential theranostic vectors, into rats. While classical X-ray fluorescence investigations (using step-by-step acquisitions) are based on a limited number of samples (approximately one per day at the DiffAbs beamline), the Flyscan mode has enabled gathering information on the interaction of nanometer-scale vectors in different organs such as liver, spleen and kidney at the micrometer scale, for five rats, in only a single five-day synchrotron shift. Moreover, numerous X-ray absorption near-edge structure spectra, which are beam-time-consuming taking into account the low concentration of these theranostic vectors, were collected.

Micro-beam Laue alignment of multi-reflection Bragg coherent diffraction imaging measurements


Multi-reflection Bragg coherent diffraction imaging has the potential to allow three-dimensional (3D) resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here a different approach is demonstrated, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focused ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples.

Observation of an optical vortex beam from a helical undulator in the XUV region


The observation of an optical vortex beam at 60 nm wavelength, produced as the second-harmonic radiation from a helical undulator, is reported. The helical wavefront of the optical vortex beam was verified by measuring the interference pattern between the vortex beam from a helical undulator and a normal beam from another undulator. Although the interference patterns were slightly blurred owing to the relatively large electron beam emittance, it was possible to observe the interference features thanks to the helical wavefront of the vortex beam. The experimental results were well reproduced by simulation.

The EIGER detector for low-energy electron microscopy and photoemission electron microscopy


EIGER is a single-photon-counting hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland. It is designed for applications at synchrotron light sources with photon energies above 5 keV. Features of EIGER include a small pixel size (75 µm × 75 µm), a high frame rate (up to 23 kHz), a small dead-time between frames (down to 3 µs) and a dynamic range up to 32-bit. In this article, the use of EIGER as a detector for electrons in low-energy electron microscopy (LEEM) and photoemission electron microscopy (PEEM) is reported. It is demonstrated that, with only a minimal modification to the sensitive part of the detector, EIGER is able to detect electrons emitted or reflected by the sample and accelerated to 8–20 keV. The imaging capabilities are shown to be superior to the standard microchannel plate detector for these types of applications. This is due to the much higher signal-to-noise ratio, better homogeneity and improved dynamic range. In addition, the operation of the EIGER detector is not affected by radiation damage from electrons in the present energy range and guarantees more stable performance over time. To benchmark the detector capabilities, LEEM experiments are performed on selected surfaces and the magnetic and electronic properties of individual iron nanoparticles with sizes ranging from 8 to 22 nm are detected using the PEEM endstation at the Surface/Interface Microscopy (SIM) beamline of the Swiss Light Source.

Characterization of individual stacking faults in a wurtzite GaAs nanowire by nanobeam X-ray diffraction


Coherent X-ray diffraction was used to measure the type, quantity and the relative distances between stacking faults along the growth direction of two individual wurtzite GaAs nanowires grown by metalorganic vapour epitaxy. The presented approach is based on the general property of the Patterson function, which is the autocorrelation of the electron density as well as the Fourier transformation of the diffracted intensity distribution of an object. Partial Patterson functions were extracted from the diffracted intensity measured along the [000\bar{1}] direction in the vicinity of the wurtzite 00\bar{1}\bar{5} Bragg peak. The maxima of the Patterson function encode both the distances between the fault planes and the type of the fault planes with the sensitivity of a single atomic bilayer. The positions of the fault planes are deduced from the positions and shapes of the maxima of the Patterson function and they are in excellent agreement with the positions found with transmission electron microscopy of the same nanowire.

Confocal depth-resolved fluorescence micro-X-ray absorption spectroscopy for the study of cultural heritage materials: a new mobile endstation at the Beijing Synchrotron Radiation Facility


A confocal fluorescence endstation for depth-resolved micro-X-ray absorption spectroscopy is described. A polycapillary half-lens defines the incident beam path and a second polycapillary half-lens at 90° defines the probe sample volume. An automatic alignment program based on an evolutionary algorithm is employed to make the alignment procedure efficient. This depth-resolved system was examined on a general X-ray absorption spectroscopy (XAS) beamline at the Beijing Synchrotron Radiation Facility. Sacrificial red glaze (AD 1368–1644) china was studied to show the capability of the instrument. As a mobile endstation to be applied on multiple beamlines, the confocal system can improve the function and flexibility of general XAS beamlines, and extend their capabilities to a wider user community.

Estimating the absolute flux distribution for a synchrotron X-ray beam using ionization-chamber measurements with various filters


It is shown that an extensive set of accurate ionization-chamber measurements with a primary polychromatic synchrotron X-ray beam transmitted through various filter combinations/thicknesses can be used to quite effectively estimate the absolute flux distribution. The basic technique is simple but the `inversion' of the raw data to extract the flux distribution is a fundamentally ill-posed problem. It is demonstrated, using data collected at the Imaging and Medical Beamline (IMBL) of the Australian Synchrotron, that the absolute flux can be quickly and reliably estimated if a suitable choice of filters is made. Results are presented as a function of the magnetic field (from 1.40 to 4.00 T) of the superconducting multi-pole wiggler insertion device installed at IMBL. A non-linear least-squares refinement of the data is used to estimate the incident flux distribution and then comparison is made with calculations from the programs SPECTRA, XOP and spec.exe. The technique described is important not only in estimating flux itself but also for a variety of other, derived, X-ray properties such as beam quality, power density and absorbed-dose rate. The applicability of the technique with a monochromatic X-ray beam for which there is significant harmonic contamination is also demonstrated. Whilst absolute results can also be derived in this monochromatic beam case, relative (integrated) flux values are sufficient for our primary aim of establishing reliable determinations of the percentages of the various harmonic components.

In operando quantitation of Li concentration for a commercial Li-ion rechargeable battery using high-energy X-ray Compton scattering


Compton scattering is one of the most promising probes for quantitating Li under in operando conditions, since high-energy X-rays, which have high penetration power, are used as the incident beam and the Compton-scattered energy spectrum has specific line-shapes for each element. An in operando quantitation method to determine the Li composition in electrodes has been developed by using line-shape (S-parameter) analysis of the Compton-scattered energy spectrum. In this study, S-parameter analysis has been applied to a commercial coin cell Li-ion rechargeable battery and the variation of the S-parameters during the charge/discharge cycle at the positive and negative electrodes has been obtained. By using calibration curves for Li composition in the electrodes, the change in Li composition of the positive and negative electrodes has been determined using the S-parameters simultaneously.

Characterization of enamel caries lesions in rat molars using synchrotron X-ray microtomography


Dental caries is a ubiquitous infectious disease with a nearly 100% lifetime prevalence. Rodent caries models are widely used to investigate the etiology, progression and potential prevention or treatment of the disease. To explore the suitability of these models for deeper investigations of intact surface zones during enamel caries, the structures of early-stage carious lesions in rats were characterized and compared with previous reports on white spot enamel lesions in humans. Synchrotron X-ray microcomputed tomography non-destructively mapped demineralization in carious rat molar specimens across a range of caries severity, identifying 52 lesions across the 30 teeth imaged. Of these lesions, 13 were shown to have intact surface zones. Depth profiles of fractional mineral density were qualitatively similar to lesions in human teeth. However, the thickness of the surface zone in the rat model ranges from 10 to 58 µm, and is therefore significantly thinner than in human enamel. These results indicate that a fraction of lesions in rat caries possess an intact surface zone and are qualitatively similar to human lesions at the micrometer scale. This suggests that rat caries models may be a suitable analog through which to investigate the structure of surface zone enamel and its role during dental caries.

Mutual optical intensity propagation through non-ideal mirrors


The mutual optical intensity (MOI) model is extended to include the propagation of partially coherent radiation through non-ideal mirrors. The propagation of the MOI from the incident to the exit plane of the mirror is realised by local ray tracing. The effects of figure errors can be expressed as phase shifts obtained by either the phase projection approach or the direct path length method. Using the MOI model, the effects of figure errors are studied for diffraction-limited cases using elliptical cylinder mirrors. Figure errors with low spatial frequencies can vary the intensity distribution, redistribute the local coherence function and distort the wavefront, but have no effect on the global degree of coherence. The MOI model is benchmarked against HYBRID and the multi-electron Synchrotron Radiation Workshop (SRW) code. The results show that the MOI model gives accurate results under different coherence conditions of the beam. Other than intensity profiles, the MOI model can also provide the wavefront and the local coherence function at any location along the beamline. The capability of tuning the trade-off between accuracy and efficiency makes the MOI model an ideal tool for beamline design and optimization.

Local structure around In atoms in coherently grown m-plane InGaN film


The local structure around In atoms in an m-plane In0.06Ga0.94N film coherently grown on a freestanding m-plane GaN substrate was investigated by polarization-dependent X-ray absorption fine-structure. A step-by-step fitting procedure was proposed for the m-plane wurtzite structure. The interatomic distance for the first nearest neighbour In—N atomic pairs was almost isotropic. For the second nearest In—Ga pairs, the interatomic distances along the m- and a-axes were longer and shorter, respectively, than that in strain-free virtual crystals as expected for the m-plane compressive strain. In contrast, the In—Ga interatomic distance in the c-direction was elongated in spite of the compressive strain, which was explained in terms of the anisotropic atomic structure on the m-plane. The local strain in the m-plane film was more relaxed than that in coherently grown c-plane single quantum wells. A few In atoms were atomically localized in all directions, and thus localized excitonic emission is expected as in the case of c-plane InGaN.

Investigation of nanoparticulate silicon as printed layers using scanning electron microscopy, transmission electron microscopy, X-ray absorption spectroscopy and X-ray photoelectron spectroscopy


The presence of native oxide on the surface of silicon nanoparticles is known to inhibit charge transport on the surfaces. Scanning electron microscopy (SEM) studies reveal that the particles in the printed silicon network have a wide range of sizes and shapes. High-resolution transmission electron microscopy reveals that the particle surfaces have mainly the (111)- and (100)-oriented planes which stabilizes against further oxidation of the particles. X-ray absorption spectroscopy (XANES) and X-ray photoelectron spectroscopy (XPS) measurements at the O 1s-edge have been utilized to study the oxidation and local atomic structure of printed layers of silicon nanoparticles which were milled for different times. XANES results reveal the presence of the +4 (SiO2) oxidation state which tends towards the +2 (SiO) state for higher milling times. Si 2p XPS results indicate that the surfaces of the silicon nanoparticles in the printed layers are only partially oxidized and that all three sub-oxide, +1 (Si2O), +2 (SiO) and +3 (Si2O3), states are present. The analysis of the change in the sub-oxide peaks of the silicon nanoparticles shows the dominance of the +4 state only for lower milling times.

Strategies for high-throughput focused-beam ptychography


X-ray ptychography is being utilized for a wide range of imaging experiments with a resolution beyond the limit of the X-ray optics used. Introducing a parameter for the ptychographic resolution gain Gp (the ratio of the beam size over the achieved pixel size in the reconstructed image), strategies for data sampling and for increasing imaging throughput when the specimen is at the focus of an X-ray beam are considered. The tradeoffs between large and small illumination spots are examined.

Non-uniform nanosecond gate-delay of hybrid pixel detectors


A simple experiment to characterize the gating properties of X-ray area detectors using pulsed X-ray sources is presented. For a number of time-resolved experiments the gating uniformity of area detectors is important. Relative gating delays between individual modules and readout chips of PILATUS2 series area X-ray detectors have been observed. For three modules of a PILATUS 300K-W unit the maximum gating offset between the modules is found to be as large as 30 ns. On average, the first photosensor module is found to be triggered 15 ns and 30 ns later than the second and the third modules, respectively.

Atomic pair distribution function at the Brazilian Synchrotron Light Laboratory: application to the Pb1–xLaxZr0.40Ti0.60O3 ferroelectric system


This work reports the setting up of the X-ray diffraction and spectroscopy beamline at the Brazilian Synchrotron Light Laboratory for performing total scattering experiments to be analyzed by atomic pair distribution function (PDF) studies. The results of a PDF refinement for Al2O3 standard are presented and compared with data acquired at a beamline of the Advanced Photon Source, where it is common to perform this type of experiment. A preliminary characterization of the Pb1–xLaxZr0.40Ti0.60O3 ferroelectric system, with x = 0.11, 0.12 and 0.15, is also shown.

WIFIP: a web-based user interface for automated synchrotron beamlines


The beamline control software, through the associated graphical user interface (GUI), is the user access point to the experiment, interacting with synchrotron beamline components and providing automated routines. FIP, the French beamline for the Investigation of Proteins, is a highly automatized macromolecular crystallography (MX) beamline at the European Synchrotron Radiation Facility. On such a beamline, a significant number of users choose to control their experiment remotely. This is often performed with a limited bandwidth and from a large choice of computers and operating systems. Furthermore, this has to be possible in a rapidly evolving experimental environment, where new developments have to be easily integrated. To face these challenges, a light, platform-independent, control software and associated GUI are required. Here, WIFIP, a web-based user interface developed at FIP, is described. Further than being the present FIP control interface, WIFIP is also a proof of concept for future MX control software.