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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: 2018-04-24


SLS-2 – the upgrade of the Swiss Light Source


An upgrade of the Swiss Light Source (SLS) is planned for 2021–2024 and includes the exchange of the existing storage ring by a new one providing about 40–50 times lower emittance in user operation mode. This will extend the performance of SLS in particular in the fields of coherent imaging, full-field tomography, soft X-ray angle-resolved photoelectron spectroscopy and resonant inelastic X-ray scattering. A science case and a conceptual design for the machine have been established. As a summary of these reports, the novel lattice design, undulator developments and scientific highlights are presented.

Beam-induced redox transformation of arsenic during As K-edge XAS measurements: availability of reducing or oxidizing agents and As speciation


During X-ray absorption spectroscopy (XAS) measurements of arsenic (As), beam-induced redox transformation is often observed. In this study, the As species immobilized by poorly crystallized mackinawite (FeS) was assessed for the susceptibility to beam-induced redox reactions as a function of sample properties including the redox state of FeS and the solid-phase As speciation. The beam-induced oxidation of reduced As species was found to be mediated by the atmospheric O2 and the oxidation products of FeS [e.g. Fe(III) (oxyhydr)oxides and intermediate sulfurs]. Regardless of the redox state of FeS, both arsenic sulfide and surface-complexed As(III) readily underwent the photo-oxidation upon exposure to the atmospheric O2 during XAS measurements. With strict O2 exclusion, however, both As(0) and arsenic sulfide were less prone to the photo-oxidation by Fe(III) (oxyhydr)oxides than NaAsO2 and/or surface-complexed As(III). In case of unaerated As(V)-reacted FeS samples, surface-complexed As(V) was photocatalytically reduced during XAS measurements, but arsenic sulfide did not undergo the photo-reduction.

Influence of the core-hole effect on optical properties of magnesium oxide (MgO) near the Mg L-edge region


The influence of the core-hole effect on optical properties of magnesium oxide (MgO) is established through experimental determination of optical constants and first-principles density functional theory studies. Optical constants (δ and β) of MgO thin film are measured in the spectral region 40–300 eV using reflectance spectroscopy techniques at the Indus-1 synchrotron radiation source. The obtained optical constants show strong core exciton features near the Mg L-edge region, causing significant mismatch with Henke's tabulated values. On comparing the experimentally obtained optical constants with Henke's tabulated values, an edge shift of ∼3.0 eV is also observed. Distinct evidence of effects of core exciton on optical constants (δ and β) in the near Mg L-edge absorption spectra are confirmed through first-principles simulations.

Quantitative study of the influence of swimming therapy on osteoporosis rat models based on synchrotron radiation computed tomogaphy


Osteoporosis is a bone disease with a variety of causes, leading to bone pain and fragility to fracture. Major treatment methods include nutrition therapy, exercise therapy, drug therapy and surgical treatment, among which exercise therapy, such as swimming, is the most effective. To investigate the optimal swimming therapy regime for postmenopausal women, the effects of eight weeks of different intensity swimming exercises were studied in rat models. After the swimming program, lumbar vertebrae were dissected from all the rats and scanned by synchrotron radiation computed tomography (SRCT). Histomorphometry analysis and finite-element analysis were carried out on the trabecular structure of the L4 lumbar based on the acquired SRCT slices. Histomorphometry analysis showed that swimming can alleviate the decrease in bone strength induced by estrogen deficiency, and moderate-intensity swimming was found to have the most significant effect.

Hybrid modelling of a high-power X-ray attenuator plasma


X-ray gas attenuators act as stress-free high-pass filters for synchrotron and free-electron laser beamlines to reduce the heat load in downstream optical elements without affecting other properties of the X-ray beam. The absorption of the X-ray beam triggers a cascade of processes that ionize and heat up the gas locally, changing its density and therefore the X-ray absorption. Aiming to understand and predict the behaviour of the gas attenuator in terms of efficiency versus gas pressure, a hybrid model has been developed, combining three approaches: an analytical description of the X-ray absorption; Monte Carlo for the electron thermalization; and a fluid treatment for the electron diffusion, recombination and excited-states relaxation. The model was applied to an argon-filled attenuator prototype built and tested at the European Synchrotron Radiation Facility, at a pressure of 200 mbar and assuming stationary conditions. The results of the model showed that the electron population thermalizes within a few nanoseconds after the X-ray pulse arrival and it occurs just around the X-ray beam path, recombining in the bulk of the gas rather than diffusing to the attenuator walls. The gas temperature along the beam path reached 850 K for 770 W of incident power and 182 W m−1 of absorbed power. Around 70% of the absorbed power is released as visible and UV radiation rather than as heat to the gas. Comparison of the power absorption with the experiment showed an overall agreement both with the plasma radial profile and power absorption trend, the latter within an error smaller than 20%. This model can be used for the design and operation of synchrotron gas attenuators and as a base for a time-dependent model for free-electron laser attenuators.

Pulse intensity characterization of the LCLS nanosecond double-bunch mode of operation


The recent demonstration of the `nanosecond double-bunch' operation mode, i.e. two X-ray pulses separated in time between 0.35 and hundreds of nanoseconds and by increments of 0.35 ns, offers new opportunities to investigate ultrafast dynamics in diverse systems of interest. However, in order to reach its full potential, this mode of operation requires the precise characterization of the intensity of each X-ray pulse within each pulse pair for any time separation. Here, a transmissive single-shot diagnostic that achieves this goal for time separations larger than 0.7 ns with a precision better than 5% is presented. It also provides real-time monitoring feedback to help tune the accelerator parameters to deliver double pulse intensity distributions optimized for specific experimental goals.

First-principles X-ray absorption dose calculation for time-dependent mass and optical density


A dose integral of time-dependent X-ray absorption under conditions of variable photon energy and changing sample mass is derived from first principles starting with the Beer–Lambert (BL) absorption model. For a given photon energy the BL dose integral D(e, t) reduces to the product of an effective time integral T(t) and a dose rate R(e). Two approximations of the time-dependent optical density, i.e. exponential A(t) = c + aexp(−bt) for first-order kinetics and hyperbolic A(t) = c + a/(b + t) for second-order kinetics, were considered for BL dose evaluation. For both models three methods of evaluating the effective time integral are considered: analytical integration, approximation by a function, and calculation of the asymptotic behaviour at large times. Data for poly(methyl methacrylate) and perfluorosulfonic acid polymers measured by scanning transmission soft X-ray microscopy were used to test the BL dose calculation. It was found that a previous method to calculate time-dependent dose underestimates the dose in mass loss situations, depending on the applied exposure time. All these methods here show that the BL dose is proportional to the exposure time D(e, t) ≃ K(e)t.

XFEL experiments: jitter of pump–probe time delays and pulse intensities


Jitter of XFEL signals due to fluctuations in shot-to-shot time delays and intensities are explored in the frame of a statistical theory of X-ray diffraction from liquids. Deformed signals are calculated at different levels of pump–probe jitter. A new method is proposed to eliminate these distortions.

Effects of soft X-ray radiation damage on paraffin-embedded rat tissues supported on ultralene: a chemical perspective


Radiation damage is an important aspect to be considered when analysing biological samples with X-ray techniques as it can induce chemical and structural changes in the specimens. This work aims to provide new insights into the soft X-ray induced radiation damage of the complete sample, including not only the biological tissue itself but also the substrate and embedding medium, and the tissue fixation procedure. Sample preparation and handling involves an unavoidable interaction with the sample matrix and could play an important role in the radiation-damage mechanism. To understand the influence of sample preparation and handling on radiation damage, the effects of soft X-ray exposure at different doses on ultralene, paraffin and on paraffin-embedded rat tissues were studied using Fourier-transform infrared (FTIR) microspectroscopy and X-ray microscopy. Tissues were preserved with three different commonly used fixatives: formalin, glutaraldehyde and Karnovsky. FTIR results showed that ultralene and paraffin undergo a dose-dependent degradation of their vibrational profiles, consistent with radiation-induced oxidative damage. In addition, formalin fixative has been shown to improve the preservation of the secondary structure of proteins in tissues compared with both glutaraldehyde and Karnovsky fixation. However, conclusive considerations cannot be drawn on the optimal fixation protocol because of the interference introduced by both substrate and embedding medium in the spectral regions specific to tissue lipids, nucleic acids and carbohydrates. Notably, despite the detected alterations affecting the chemical architecture of the sample as a whole, composed of tissue, substrate and embedding medium, the structural morphology of the tissues at the micrometre scale is essentially preserved even at the highest exposure dose.

Magnetic assessment and modelling of the Aramis undulator beamline


Within the SwissFEL project at the Paul Scherrer Institute (PSI), the hard X-ray line (Aramis) has been equipped with short-period in-vacuum undulators, known as the U15 series. The undulator design has been developed within the institute itself, while the prototyping and the series production have been implemented through a close collaboration with a Swiss industrial partner, Max Daetwyler AG, and several subcontractors. The magnetic measurement system has been built at PSI, together with all the data analysis tools. The Hall probe has been designed for PSI by the Swiss company SENIS. In this paper the general concepts of both the mechanical and the magnetic properties of the U15 series of undulators are presented. A description of the magnetic measurement equipment is given and the results of the magnetic measurement campaign are reported. Lastly, the data reduction methods and the associated models are presented and their actual implementation in the control system is detailed.

The fractional Fourier transform as a simulation tool for lens-based X-ray microscopy


The fractional Fourier transform (FrFT) is introduced as a tool for numerical simulations of X-ray wavefront propagation. By removing the strict sampling requirements encountered in typical Fourier optics, simulations using the FrFT can be carried out with much decreased detail, allowing, for example, on-line simulation during experiments. Moreover, the additive index property of the FrFT allows the propagation through multiple optical components to be simulated in a single step, which is particularly useful for compound refractive lenses (CRLs). It is shown that it is possible to model the attenuation from the entire CRL using one or two effective apertures without loss of accuracy, greatly accelerating simulations involving CRLs. To demonstrate the applicability and accuracy of the FrFT, the imaging resolution of a CRL-based imaging system is estimated, and the FrFT approach is shown to be significantly more precise than comparable approaches using geometrical optics. Secondly, it is shown that extensive FrFT simulations of complex systems involving coherence and/or non-monochromatic sources can be carried out in minutes. Specifically, the chromatic aberrations as a function of source bandwidth are estimated, and it is found that the geometric optics greatly overestimates the aberration for energy bandwidths of around 1%.

Quick X-ray reflectivity using monochromatic synchrotron radiation for time-resolved applications


A new technique for the parallel collection of X-ray reflectivity (XRR) data, compatible with monochromatic synchrotron radiation and flat substrates, is described and applied to the in situ observation of thin-film growth. The method employs a polycapillary X-ray optic to produce a converging fan of radiation, incident onto a sample surface, and an area detector to simultaneously collect the XRR signal over an angular range matching that of the incident fan. Factors determining the range and instrumental resolution of the technique in reciprocal space, in addition to the signal-to-background ratio, are described in detail. This particular implementation records ∼5° in 2θ and resolves Kiessig fringes from samples with layer thicknesses ranging from 3 to 76 nm. The value of this approach is illustrated by showing in situ XRR data obtained with 100 ms time resolution during the growth of epitaxial La0.7Sr0.3MnO3 on SrTiO3 by pulsed laser deposition at the Cornell High Energy Synchrotron Source (CHESS). Compared with prior methods for parallel XRR data collection, this is the first method that is both sample-independent and compatible with the highly collimated, monochromatic radiation typical of third-generation synchrotron sources. Further, this technique can be readily adapted for use with laboratory-based sources.

Development of an X-ray imaging system to prevent scintillator degradation for white synchrotron radiation


The high flux of the white X-ray beams from third-generation synchrotron light sources can significantly benefit the development of high-speed X-ray imaging, but can also bring technical challenges to existing X-ray imaging systems. One prevalent problem is that the image quality deteriorates because of dust particles accumulating on the scintillator screen during exposure to intense X-ray radiation. Here, this problem has been solved by embedding the scintillator in a flowing inert-gas environment. It is also shown that the detector maintains the quality of the captured images even after days of X-ray exposure. This modification is cost-efficient and easy to implement. Representative examples of applications using the X-ray imaging system are also provided, including fast tomography and multimodal phase-contrast imaging for biomedical and geological samples.

Investigation of the multiplet features of SrTiO3 in X-ray absorption spectra based on configuration interaction calculations


Synchrotron-based L2,3-edge absorption spectra show strong sensitivities to the local electronic structure and chemical environment. However, detailed physical information cannot be extracted easily without computational aids. Here, using the experimental Ti L2,3-edges absorption spectrum of SrTiO3 as a fingerprint and considering full multiplet effects, calculations yield different energy parameters characterizing local ground state properties. The peak splitting and intensity ratios of the L3 and L2 set of peaks are carefully analyzed quantitatively, giving rise to a small hybridization energy around 1.2 eV, and the different hybridization energy values reported in the literature are further addressed. Finally, absorption spectra with different linearly polarized photons under various tetragonal crystal fields are investigated, revealing a non-linear orbital–lattice interaction, and a theoretical guidance for material engineering of SrTiO3-based thin films and heterostructures is offered. Detailed analysis of spectrum shifts with different tetragonal crystal fields suggests that the eg crystal field splitting is a necessary parameter for a thorough analysis of the spectra, even though it is not relevant for the ground state properties.

Wavelet processing and digital interferometric contrast to improve reconstructions from X-ray Gabor holograms


In this work, the application of an undecimated wavelet transformation together with digital interferometric contrast to improve the resulting reconstructions in a digital hard X-ray Gabor holographic microscope is shown. Specifically, the starlet transform is used together with digital Zernike contrast. With this contrast, the results show that only a small set of scales from the hologram are, in effect, useful, and it is possible to enhance the details of the reconstruction.

High-speed tomography under extreme conditions at the PSICHE beamline of the SOLEIL Synchrotron


In situ microtomography at high pressure and temperature has developed rapidly in the last decade, driven by the development of new high-pressure apparatus. It is now routinely possible to characterize material under high pressure with acquisition times for tomograms of the order of tens of minutes. Here, advantage was taken of the possibility to combine the use of a pink beam projected through a standard Paris–Edinburgh press in order to demonstrate the possibility to perform high-speed synchrotron X-ray tomography at high pressure and temperature allowing complete high-resolution tomograms to be acquired in about 10 s. This gives direct visualization to rapidly evolving or unstable systems, such as flowing liquids or reacting components, and avoids assumptions in the interpretation of quenched samples. Using algebraic reconstruction techniques allows the missing angle artefacts that result from the columns of the press to be minimized.

Synchrotron X-ray microbeam dosimetry with a 20 micrometre resolution scintillator fibre-optic dosimeter


Cancer is one of the leading causes of death worldwide. External beam radiation therapy is one of the most important modalities for the treatment of cancers. Synchrotron microbeam radiation therapy (MRT) is a novel pre-clinical therapy that uses highly spatially fractionated X-ray beams to target tumours, allowing doses much higher than conventional radiotherapies to be delivered. A dosimeter with a high spatial resolution is required to provide the appropriate quality assurance for MRT. This work presents a plastic scintillator fibre optic dosimeter with a one-dimensional spatial resolution of 20 µm, an improvement on the dosimeter with a resolution of 50 µm that was demonstrated in previous work. The ability of this probe to resolve microbeams of width 50 µm has been demonstrated. The major limitations of this method were identified, most notably the low-light signal resulting from the small sensitive volume, which made valley dose measurements very challenging. A titanium-based reflective paint was used as a coating on the probe to improve the light collection, but a possible effect of the high-Z material on the probes water-equivalence has been identified. The effect of the reflective paint was a 28.5 ± 4.6% increase in the total light collected; it did not affect the shape of the depth-dose profile, nor did it explain an over-response observed when used to probe at low depths, when compared with an ionization chamber. With improvements to the data acquisition, this probe design has the potential to provide a water-equivalent, inexpensive dosimetry tool for MRT.

Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources


Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic–plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spectrum bandwidth and realistic detector size. Diffraction patterns and reciprocal space nodes are obtained from atomic configurations for different loading (elastic and plastic) and detection conditions, and interpretation of the diffraction patterns is discussed.

Characterization of the surface contamination of deep X-ray lithography mirrors exposed to synchrotron radiation


In deep X-ray lithography (DXRL), synchrotron radiation is applied to pattern polymer microstructures. At the Synchrotron Laboratory for Micro and Nano Devices (SyLMAND), Canadian Light Source, a chromium-coated grazing-incidence X-ray double-mirror system is applied as a tunable low-pass filter. In a systematic study, the surface conditions of the two mirrors are analyzed to determine the mirror reflectivity for DXRL process optimization, without the need for spectral analysis or surface probing: PMMA resist foils were homogeneously exposed and developed to determine development rates for mirror angles between 6 mrad and 12 mrad as well as for white light in the absence of the mirrors. Development rates cover almost five orders of magnitude for nominal exposure dose (deposited energy per volume) values of 1 kJ cm−3 to 6 kJ cm−3. The rates vary from case to case, indicating that the actual mirror reflectivity deviates from that of clean chromium assumed for the experiments. Fitting the mirror-based development rates to the white-light case as a reference, reflectivity correction factors are identified, and verified by experimental and numerical results of beam calorimetry. The correction factors are related to possible combinations of a varied chromium density, chromium oxidation and a carbon contamination layer. The best fit for all angles is obtained assuming 7.19 g cm−3 nominal chromium density, 0.5 nm roughness for all involved layers, and an oxide layer thickness of 25 nm with a carbon top coat of 50 nm to 100 nm. A simulation tool for DXRL exposure parameters was developed to verify that the development rates for all cases do coincide within a small error margin (achieving a reduction of the observed errors by more than two orders of magnitude) if the identified mirror surface conditions are considered when calculating the exposure dose.

A convolutional neural network-based screening tool for X-ray serial crystallography


A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization.

X-ray beam-position feedback system with easy-to-use beam-position monitor


X-ray beam-position stability is indispensable in cutting-edge experiments using synchrotron radiation. Here, for the first time, a beam-position feedback system is presented that utilizes an easy-to-use X-ray beam-position monitor incorporating a diamond-fluorescence screen. The acceptable range of the monitor is above 500 µm and the feedback system maintains the beam position within 3 µm. In addition to being inexpensive, the system has two key advantages: it works without a scale factor for position calibration, and it has no dependence on X-ray energy, X-ray intensity, beam size or beam shape.

A scanning transmission X-ray microscope at the Pohang Light Source


A scanning transmission X-ray microscope is operational at the 10A beamline at the Pohang Light Source. The 10A beamline provides soft X-rays in the photon energy range 100–2000 eV using an elliptically polarized undulator. The practically usable photon energy range of the scanning transmission X-ray microscopy (STXM) setup is from ∼150 to ∼1600 eV. With a zone plate of 25 nm outermost zone width, the diffraction-limited space resolution, ∼30 nm, is achieved in the photon energy range up to ∼850 eV. In transmission mode for thin samples, STXM provides the element, chemical state and magnetic moment specific distributions, based on absorption spectroscopy. A soft X-ray fluorescence measurement setup has been implemented in order to provide the elemental distribution of thicker samples as well as chemical state information with a space resolution of ∼50 nm. A ptychography setup has been implemented in order to improve the space resolution down to 10 nm. Hardware setups and application activities of the STXM are presented.

MX2: a high-flux undulator microfocus beamline serving both the chemical and macromolecular crystallography communities at the Australian Synchrotron


MX2 is an in-vacuum undulator-based crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range 4.8–21 keV to a focal spot of 22 × 12 µm FWHM (H × V). At 13 keV the flux at the sample is 3.4 × 1012 photons s−1. The beamline endstation allows robotic handling of cryogenic samples via an updated SSRL SAM robot. This beamline is ideal for weakly diffracting hard-to-crystallize proteins, virus particles, protein assemblies and nucleic acids as well as smaller molecules such as inorganic catalysts and organic drug molecules. The beamline is now mature and has enjoyed a full user program for the last nine years. This paper describes the beamline status, plans for its future and some recent scientific highlights.

Sample cell for studying liquid interfaces with an in situ electric field using X-ray reflectivity and application to clay particles at oil–oil interfaces


Commissioning results of a liquid sample cell for X-ray reflectivity studies with an in situ applied electrical field are presented. The cell consists of a Plexiglas container with lateral Kapton windows for air–liquid and liquid–liquid interface studies, and was constructed with grooves to accept plate electrodes on the walls parallel to the direction of the beam. Both copper and ITO plate electrodes have been used, the latter being useful for simultaneous optical studies. Commissioning tests were made at the I07 beamline of the Diamond Light Source.