Beamline Setup Research Articles

Development of an x-ray polarimeter at the SOLEIL synchrotron.

Synchrotron radiation facilities provide highly polarized x-ray beams across a wide energy range. However, the exact type and degree of polarization vary according to the beamline and experimental setup. To accurately determine the angle and degree of linear polarization, a portable x-ray polarimeter has been developed. This setup consists of a silicon drift detector that rotates around a target made of high-density polyethylene. The imprint generated in the angular distribution of scattered photons from the target at a 90-degree angle between the incident x-rays and detector has been exploited to determine the beam polarization. Measurements were conducted at the GALAXIES beamline of the SOLEIL synchrotron. The expected angular distribution of the scattered photons for a given beam polarization was obtained through simulations using the Geant4 simulation toolkit. An excellent agreement between simulations and the collected data has been obtained, validating the setup and enabling a precise determination of the beam polarization.

High-pressure single-crystal diffraction at the Australian Synchrotron.

A new high-pressure single-crystal diffraction setup has been designed and implemented at the Australian Synchrotron for collecting molecular and protein crystal structures. The setup incorporates a modified micro-Merrill-Bassett cell and holder designed specifically to fit onto the horizontal air-bearing goniometer, allowing high-pressure diffraction measurements to be collected with little to no modification of the beamline setup compared with ambient data collections. Compression data for the amino acid, L-threonine, and the protein, hen egg-white lysozyme, were collected, showcasing the capabilities of the setup.

Time-Resolved Small-Angle X-Ray Scattering of Protein Cage Assembly.

Recent improvements in X-ray detectors and synchrotron light sources have made it possible to measure time-resolved small-angle X-ray scattering (TR-SAXS) at millisecond time resolution. As an example, in this chapter we describe the beamline setup, experimental scheme, and the points that should be noted in stopped-flow TR-SAXS experiments for investigating the ferritin assembly reaction.

Beamline setup for in situ measurements of particles in turbulent spray flames using small angle X-ray scattering

The particle formation in spray flame synthesis (SFS) is a fast and complex process involving many sub-steps that may happen simultaneously. To investigate the mechanisms that typically lead to small aggregated primary particles, a sophisticated technique for in situ measurements in the flame is necessary to provide information about primary particles and the aggregates as well. This work describes the development of an in situ measurement setup using small angle X-ray scattering (SAXS) to investigate the entire particle formation mechanism of zirconia nanoparticles in and above a turbulent spray flame. In preparation for the in situ measurements, a beamline for single crystal diffractometry at Karlsruhe Research Accelerator (KARA) was adapted for low scattering SAXS experiments including optimizations of the optics and measurement protocol. As a result, a significant dependence of scattering intensity was detected as a function of the height above the burner. A detailed analysis of the SAXS data and comparison with TEM images allow insights into the primary particle growth, the development of fractal properties and the aggregation process.

Fast wavefront sensing for X-ray optics with an alternating speckle tracking technique.

Advances in accelerator technologies have enabled the continuous development of synchrotron radiation and X-ray free electron laser (XFEL) sources. At the same time, it has been critical to perform in-situ wavefront sensing to aid delivery of high-quality X-ray beams to the end users of these facilities. The speckle-based scanning technique has obtained popularity due to its high spatial resolution and superior sensitivity compared to other wavefront sensing methods. However, these advantages often come at the expense of longer data acquisition times since multiple images have to be collected to derive the necessary wavefront information. Whereas initial speckle tracking techniques could obtain wavefront information relatively quickly, the installation of additional hardware was routinely required to do so. Here, we propose a novel speckle-based approach, termed Alternating Speckle Tracking (AST), to perform fast wavefront sensing within a conventional beamline setup. The wavefront information derived from the new technique has proven to be valuable for many applications that require temporal resolution. Importantly, both horizontal and vertical wavefront information can be simultaneously derived by moving the speckle generator along the diagonal direction. We expect this method will be widely used by the synchrotron radiation and XFEL community in the future.

Beamline setup and calibration quality control for synchrotron MX beamlines

Beamline setup and calibration quality control for synchrotron MX beamlines

Optimization of FLASH proton beams using a track-repeating algorithm.

Radiation with high dose rate (FLASH) has shown to reduce toxicities to normal tissues around the target and maintain tumor control with the same amount of dose compared to conventional radiation. This phenomenon has been widely studied in electron therapy, which is often used for shallow tumor treatment. Proton therapy is considered a more suitable treatment modality for deep-seated tumors. The feasibility of FLASH proton therapy has recently been demonstrated by a series of pre- and clinical trials. One of the challenges is to efficiently generate wide enough dose distributions in both lateral and longitudinal directions to cover the entire tumor volume. The goal of this paper is to introduce a set of automatic FLASH proton beam optimization algorithms developed recently. To develop a fast and efficient optimizer for the design of a passive scattering proton FLASH radiotherapy delivery at The University of Texas MD Anderson Proton Therapy Center, based on the fast dose calculator (FDC). A track-repeating algorithm, FDC, was validated versus Geant4 simulations and applied to calculate dose distributions in various beamline setups. The design of the components was optimized to deliver homogeneous fields with well-defined diameters between 11.0 and 20.5mm, as well as a spread-out Bragg peak (SOBP) with modulations between 8.5 and 39.0mm. A ridge filter, a high-Z material scatterer, and a collimator with range compensator were inserted in the beam path, and their shapes and sizes were optimized to spread out the Bragg peak, widen the beam, and reduce the penumbra. The optimizer was developed and tested using two proton energies (87.0 and 159.5MeV) in a variety of beamline arrangements. Dose rates of the optimized beams were estimated by scaling their doses to those of unmodified beams. The optimized 87.0-MeV beams, with a distance from the beam pipe window to the phantom surface (window-to-surface distance [WSD]) of 550mm, produced an 8.5-mm-wide SOBP (proximal 90% to distal 90% of the maximum dose); 14.5, 12.0, and 11.0-mm lateral widths at the 50%, 80%, and 90% dose location, respectively; and a 2.5-mm penumbra from 80% to 20% in the lateral profile. The 159.5-MeV beam had an SOBP of 39.0mm and lateral widths of 20.5, 15.0, and 12.5mm at 50%, 80%, and 90% dose location, respectively, when the WSD was 550mm. Wider lateral widths were obtained with increased WSD. The SOBP modulations changed when the ridge filters with different characteristics were inserted. Dose rates on the beam central axis for all optimized beams (other than the 87.0-MeV beam with 2000-mm WSD) were above that needed for the FLASH effect threshold (40Gy/s) except at the very end of the depth dose profile scaling with a dose rate of 1400Gy/s at the Bragg peak in the unmodified beams. The optimizer was able to instantly design the individual beamline components for each of the beamline setups, without the need of time intensive iterative simulations. An efficient system, consisting of an optimizer and an FDC have been developed and validated in a variety of beamline setups, comprising two proton energies, several WSDs, and SOBPs. The set of automatic optimization algorithms produces beam shaping element designs efficiently and with excellent quality.

Enabling Coarse X-ray Fluorescence Imaging Scans with Enlarged Synchrotron Beam by Means of Mosaic Crystal Defocusing Optics.

Trace elements, functionalized nanoparticles and labeled entities can be localized with sub-mm spatial resolution by X-ray fluorescence imaging (XFI). Here, small animals are raster scanned with a pencil-like synchrotron beam of high energy and low divergence and the X-ray fluorescence is recorded with an energy-dispersive detector. The ability to first perform coarse scans to identify regions of interest, followed by a close-up with a sub-mm X-ray beam is desirable, because overall measurement time and X-ray dose absorbed by the (biological) specimen can thus be minimized. However, the size of X-ray beams at synchrotron beamlines is usually strongly dependent on the actual beamline setup and can only be adapted within specific pre-defined limits. Especially, large synchrotron beams are non-trivial to generate. Here, we present the concept of graphite-based, convex reflection optics for the one-dimensional enlargement of a 1 mm wide synchrotron beam by a factor of 5 to 10 within a 1 m distance. Four different optics are tested and characterized and their reflection properties compared to ray tracing simulations. The general shape and size of the measured reflection profiles agree with expectations. Enhancements with respect to homogeneity and efficiency can be expected with improved optics manufacturing. A mouse phantom is used for a proof-of-principle XFI experiment demonstrating the applicability of coarse and fine scans with the suggested optics design.

Beamline setup and calibration quality control for synchrotron MX beamlines

Beamline setup and calibration quality control for synchrotron MX beamlines

VHEE beam dosimetry at CERN Linear Electron Accelerator for Research under ultra-high dose rate conditions

The aim of this work is the dosimetric characterization of a plane parallel ionization chamber under defined beam setups at the CERN Linear Electron Accelerator for Research (CLEAR). A laser driven electron beam with energy of 200 MeV at two different field sizes of approximately 3.5 mm FWHM and approximately 7 mm FWHM were used at different pulse structures. Thereby the dose-per-pulse range varied between approximately 0.2 and 12 Gy per pulse. This range represents approximately conventional dose rate range beam conditions up to ultra-high dose rate (UHDR) beam conditions. The experiment was based on a water phantom which was integrated into the horizontal beamline and radiochromic films and an Advanced Markus ionization chamber was positioned in the water phantom. In addition, the experimental setup were modelled in the Monte Carlo simulation environment FLUKA. In a first step the radiochromic film measurements were used to verify the beamline setup. Depth dose distributions and dose profiles measured by radiochromic film were compared with Monte Carlo simulations to verify the experimental conditions. Second, the radiochromic films were used for reference dosimetry to characterize the ionization chamber. In particular, polarity effects and the ion collection efficiency of the ionization chamber were investigated for both field sizes and the complete dose rate range. As a result of the study, significant polarity effects and recombination loss of the ionization chamber were shown and characterized. However, the work shows that the behavior of the ionization chamber at the laser driven beam line at the CLEAR facility is comparable to classical high dose-per-pulse electron beams. This allows the use of ionization chambers on the CLEAR system and thus enables active dose measurement during the experiment. Compared to passive dose measurement with film, this is an important step forward in the experimental equipment of the facility.

Simulation of small-angle X-ray scattering data of biological macromolecules in solution.

This article presents IMSIM, an application to simulate two-dimensional small-angle X-ray scattering patterns and, further, one-dimensional profiles from biological macromolecules in solution. IMSIM implements a statistical approach yielding two-dimensional images in TIFF, CBF or EDF format, which may be readily processed by existing data-analysis pipelines. Intensities and error estimates of one-dimensional patterns obtained from the radial average of the two-dimensional images exhibit the same statistical properties as observed with actual experimental data. With initial input on an absolute scale, [cm-1]/c[mg ml-1], the simulated data frames may also be scaled to absolute scale such that the forward scattering after subtraction of the background is proportional to the molecular weight of the solute. The effects of changes of concentration, exposure time, flux, wavelength, sample-detector distance, detector dimensions, pixel size, and the mask as well as incident beam position can be considered for the simulation. The simulated data may be used in method development, for educational purposes, and also to determine the most suitable beamline setup for a project prior to the application and use of the actual beamtime. IMSIM is available as part of the ATSAS software package (3.0.0) and is freely available for academic use (http://www.embl-hamburg.de/biosaxs/download.html).

Methods for operando coherent X-ray diffraction of battery materials at the Advanced Photon Source.

Bragg coherent X-ray diffraction imaging has become valuable for visualization of the structural, morphological and strain evolution of crystals in operando electrode materials. As the electrode material particles (either in a single-crystal form or an aggregation form of single crystals) are evenly dispersed and randomly oriented in the electrode laminate, the submicrometer-sized coherentX-ray beam can be used to probe the local properties of electrode material crystals using two approaches. Coherent multi-crystal diffraction provides collective structural information of phase transitions in tens of crystals simultaneously as well as the individual behavior from single crystals, which are oriented at the Bragg condition in the X-ray illumination volume. Bragg coherent diffractive imaging enables one to monitor the evolution of the morphology and strain in individual crystals. This work explores and highlights the Bragg coherent X-ray diffraction measurements of battery electrode materials in operando conditions at the 34-ID-C beamline at the Advanced Photon Source. The experiment is demonstrated with NaNi1/3Fe1/3Mn1/3O2, a sodium-ion cathode material loaded in a half cell. The paper will discuss, in detail, the beamline setup, sample mounting and handling, alignment strategies and the data acquisition protocols.

Flexible sample cell for real-time GISAXS, GIWAXS and XRR: design and construction.

Since the properties of functional materials are highly dependent on their specific structure, and since the structural changes, for example during crystallization, induced by coating and annealing processes are significant, the study of structure and its formation is of interest for fundamental and applied science. However, structure analysis is often limited to ex situ determination of final states due to the lack of specialized sample cells that enable real-time investigations. The lack of such cells is mainly due to their fairly complex design and geometrical restrictions defined by the beamline setups. To overcome this obstacle, an advanced sample cell has been designed and constructed; it combines automated doctor blading, solvent vapor annealing and sample hydration with real-time grazing-incidence wide- and small-angle scattering (GIWAXS/GISAXS) and X-ray reflectivity (XRR). The sample cell has limited spatial requirements and is therefore widely usable at beamlines and laboratory-scale instruments. The cell is fully automatized and remains portable, including the necessary electronics. In addition, the cell can be used by interested scientists in cooperation with the Institute for Crystallography and Structural Physics and is expandable with regard to optical secondary probes. Exemplary research studies are presented, in the form of coating of P3HT:PC61PM thin films, solvent vapor annealing of DRCN5T:PC71BM thin films, and hydration of supported phospholipid multilayers, to demonstrate the capabilities of the in situ cell.

Morphological Evolution of Lithium Electrode in Lithium-Based Cells: Investigated By Synchrotron X-Ray Phase Contrast Tomography

Lithium (Li) metal, due to its high theoretical specific capacity (3860 mA h/g), low density (0.59 g/cm3) and the lowest negative electrochemical potential (-3.04 V vs. the standard hydrogen electrode), is widely considered as the most promising candidate for the next generation energy storage systems such as lithium-sulfur and lithium-air batteries. In addition, it has been currently used as a standard counter electrode for the evolution of new cathode or anode materials in half-cells. Unfortunately, the commercialization of Li metal as a negative electrode has not been succeeded due to the intrinsically uncontrolled growth of Lithium micro-Structures (LmSs, eg., dendrites, fibers) since the early investigation in 1970s. Although various characterization techniques such as optical microscopy, atomic force microscopy (AFM), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and magnetic resonance imaging (MRI) have been employed to characterize the morphological changes of Li electrodes, our understanding towards the evolution of Li during operational cycling has not greatly improved owing to these inherently limited analytical tools. The challenge of a detailed nondestructive characterization way and a comprehensive analysis of correlation between the evolution of Li electrodes and the battery electrochemical performance still remains. In the present demonstration, the powerful characterization tool, synchrotron X-ray phase contrast tomography imaging technique will be employed to characterize the evolution of Li electrodes during cycling. To this end, we have designed and fabricated a tomography cell (tomo-cell) for the three-dimensional nondestructive investigation, as shown in Fig. 1, along with a schematic illustration of the beamline set-up. Fig. 1. a) Photograph of the fabricated proof-of-concept cell. b) Corresponding schematic representation of the cell consisting of a polyamide-imide housing (brown), two screw electrodes and retaining screws each on top (light grey), two sealing rings (yellow), a porous separator (white) sandwiched between two electrodes (blue and green). c) Schematic representation of the experimental setup of the tomography station at the BAMline at BESSY II, Helmholtz-Zentrum Berlin, Germany. This figure has been adapted from ACS Energy Lett., 2017, 2, pp 94–104, with permission by the American Chemical Society. Selected results of our previous investigations using this tomo-cell about the evolution of Li electrodes in half-cells (lithium-silicon, lithium-sulfur and lithium-lithium cobalt oxide) and symmetrical cells (Li-Li) will be briefly demonstrated. The morphological evolution of Li electrodes based on these measurements will also be summarized. These unprecedented findings, which were not accessible from conventional microscopic characterizations and electrochemical measurements, fundamentally deepen our understanding of the evolution mechanism of Li electrodes during battery cycling. The insights obtained could open up the way toward design principles and opportunities to accelerate the commercialization of Li metal. Figure 1

(Invited) Novel in-Situ Operando X-Ray Absorption Spectroscopy Techniques for the Characterization of the Electrochemical Growth of Metal Oxides

In-situ Operando X-ray Absorption Spectroscopy (XAS) has been widely adopted to understand materials modification under working conditions. Under appropriate conditions, In-situ operando XAS provides surface information, being a tool of primary importance to study electrochemical growth. In the present talk we will describe the application of a recently developed XAS technique to the electrochemical growth of metal oxides. This technique, known as FEXRAV (Fixed Energy X-ray Absorption Voltammetry), is an experimental method that couples cyclic voltammetry (CV) with the acquisition of the XAS signal at a fixed energy diagnostic of a chemical and/or structural modification of the material. This approach is extraordinary powerful and we propose it as a new tool to understand the formation of oxide thin films on metals relevant to electrochemical energy conversion and storage. This contribution reviews the fundamental principles, the electrochemical cell design, and the synchrotron beamline set-up that enable the collection of FEXRAV data. As a case study, we report the investigation of the formation of palladium oxides on palladium nanoparticles in alkaline media, a subject of extreme importance for alkaline fuel cells. With our investigation we have discovered that palladium oxidation occurs at potential larger than 0.65 V (RHE) and that the passivation layer blocks out the capability of palladium to oxidize alcohols. Remarkably, these conditions happen in real systems and are responsible of the loss of efficiency of direct alcohol fuel cells. We have also found that the presence of promoting metal oxide in contact with Pd accelerate the oxidation and, ultimately are detrimental for the stability of the devices. Finally, the description of a novel experimental set-up with enanched surface sensitivity based on grazing incidence FEXRAV experiments will be given, together with preliminary results on the in-situ electro-oxidation of palladium thin films thae have been obtained at the LISA BM08 beamline of the European Synchrotron Radiation Facility.

Single proton counting at the RIKEN cell irradiation facility.

We present newly developed tapered capillaries with a scintillator window, which enable us to count single protons at the RIKEN cell irradiation setup. Their potential for performing single proton irradiation experiments at our beamline setup is demonstrated with CR39 samples, showing a single proton detection fidelity of 98%.

DATASW, a tool for HPLC-SAXS data analysis.

Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement the high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS experiments using a sliding window of a user-specified size, calculates overall parameters [I(0), Rg, Dmax and molecular weight] and predicts the folding state (folded/unfolded) of the sample. Applications of DATASW are illustrated for several proteins with various oligomerization behaviours recorded on different beamlines. DATASW binaries for major operating systems can be downloaded from http://datasw.sourceforge.net/.

Structural Characterization of Heparin-induced Glyceraldehyde-3-phosphate Dehydrogenase Protofibrils Preventing α-Synuclein Oligomeric Species Toxicity

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a multifunctional enzyme that has been associated with neurodegenerative diseases. GAPDH colocalizes with α-synuclein in amyloid aggregates in post-mortem tissue of patients with sporadic Parkinson disease and promotes the formation of Lewy body-like inclusions in cell culture. In a previous work, we showed that glycosaminoglycan-induced GAPDH prefibrillar species accelerate the conversion of α-synuclein to fibrils. However, it remains to be determined whether the interplay among glycosaminoglycans, GAPDH, and α-synuclein has a role in pathological states. Here, we demonstrate that the toxic effect exerted by α-synuclein oligomers in dopaminergic cell culture is abolished in the presence of GAPDH prefibrillar species. Structural analysis of prefibrillar GAPDH performed by small angle x-ray scattering showed a particle compatible with a protofibril. This protofibril is shaped as a cylinder 22 nm long and a cross-section diameter of 12 nm. Using biocomputational techniques, we obtained the first all-atom model of the GAPDH protofibril, which was validated by cross-linking coupled to mass spectrometry experiments. Because GAPDH can be secreted outside the cell where glycosaminoglycans are present, it seems plausible that GAPDH protofibrils could be assembled in the extracellular space kidnapping α-synuclein toxic oligomers. Thus, the role of GAPDH protofibrils in neuronal proteostasis must be considered. The data reported here could open alternative ways in the development of therapeutic strategies against synucleinopathies like Parkinson disease.

Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning

Confocal microscopy, a technique that has been extensively applied in cellular biological studies, may also be applied to the visualization and three-dimensional imaging of protein crystals at high resolution on synchrotron beamlines. Protein crystal samples are examined using a commercially available confocal microscope adapted for cryogenic use. A preliminary test using a custom confocal design adapted for beamline use is also presented. The confocal optics configuration is compatible with nonlinear imaging techniques such as two-photon excited fluorescence imaging and second harmonic generation. The possibilities of this method are explored using two modes: fluorescence and reflection confocal. In fluorescence mode, small amounts of dye are introduced into the crystal through soaking or growth conditions. Under such conditions, protein crystals are easily resolved from salts and amorphous precipitates, which do not generally take up dye. Reflection mode, which does not require dye, still exhibits greater resolution and sensitivity to surface detail than conventional wide-field microscopy as a result of the confocal optics configuration. The inherent three-dimensional nature of the method means that on-axis sample views (along the direction of the X-ray beam) can be reconstructed from an off-axis configuration, simplifying the beamline setup and providing uniquely detailed views of cryogenically cooled crystals.

VUV Spectroscopic Study of the D 1Π u State of Molecular Deuterium

The D 1Π u – absorption system of molecular deuterium has been re-investigated using the VUV Fourier-Transform (FT) spectrometer at the DESIRS beamline of the synchrotron SOLEIL and photon-induced fluorescence spectrometry (PIFS) using the 10 m normal incidence monochromator at the synchrotron BESSY II. Using the FT spectrometer absorption spectra in the range 72–82 nm were recorded in quasi static gas at 100 K and in a free flowing jet at a spectroscopic resolution of 0.50 and 0.20 cm−1 respectively. The narrow Q-branch transitions, probing states of Π− symmetry, were observed up to vibrational level v = 22. The states of Π+ symmetry, known to be broadened due to predissociation and giving rise to asymmetric Beutler–Fano resonances, were studied up to v = 18. The 10 m normal incidence beamline setup at BESSY II was used to simultaneously record absorption, dissociation, ionization and fluorescence decay channels from which information on the line intensities, predissociated widths, and Fano q-parameters were extracted. R-branch transitions were observed up to v = 23 for J = 1–3 as well as several transitions for J = 4 and 5 up to v = 22 and 18 respectively. The Q-branch transitions are found to weakly predissociate and were observed from v = 8 to the final vibrational level of the state v = 23. The spectroscopic study is supported by two theoretical frameworks. Results on the Π− symmetry states are compared to ab initio multi-channel-quantum defect theory (MQDT) calculations, demonstrating that these calculations are accurate to within 0.5 cm−1. Furthermore, the calculated line intensities of Q-lines agree well with measured values. For the states of Π+ symmetry a perturbative model based on a single bound state interacting with a predissociation continuum was explored, yielding good agreement for predissociation widths, Fano q-parameters and line intensities.