I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[14493, 19458]
Open Access
Abstract: Efficient sample delivery is an essential aspect of serial crystallography at both synchrotrons and X-ray free-electron lasers. Rastering fixed target chips through the X-ray beam is an efficient method for serial delivery from the perspectives of both sample consumption and beam time usage. Here, an approach for loading fixed targets using acoustic drop ejection is presented that does not compromise crystal quality, can reduce sample consumption by more than an order of magnitude and allows serial diffraction to be collected from a larger proportion of the crystals in the slurry.
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Sep 2019
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[18069]
Abstract: In macromolecular crystallography, a great deal of effort has been invested in understanding radiation-damage progression. While the sensitivity of protein crystals has been well characterized, crystals of DNA and of DNA–protein complexes have not thus far been studied as thoroughly. Here, a systematic investigation of radiation damage to a crystal of a DNA 16-mer diffracting to 1.8 Å resolution and held at 100 K, up to an absorbed dose of 45 MGy, is reported. The RIDL (Radiation-Induced Density Loss) automated computational tool was used for electron-density analysis. Both the global and specific damage to the DNA crystal as a function of dose were monitored, following careful calibration of the X-ray flux and beam profile. The DNA crystal was found to be fairly radiation insensitive to both global and specific damage, with half of the initial diffraction intensity being lost at an absorbed average diffraction-weighted dose, D1/2, of 19 MGy, compared with 9 MGy for chicken egg-white lysozyme crystals under the same beam conditions but at the higher resolution of 1.4 Å. The coefficient of sensitivity of the DNA crystal was 0.014 Å2 MGy−1, which is similar to that observed for proteins. These results imply that the significantly greater radiation hardness of DNA and RNA compared with protein observed in a DNA–protein complex and an RNA–protein complex could be due to scavenging action by the protein, thereby protecting the DNA and RNA in these studies. In terms of specific damage, the regions of DNA that were found to be sensitive were those associated with some of the bound calcium ions sequestered from the crystallization buffer. In contrast, moieties farther from these sites showed only small changes even at higher doses.
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Jul 2019
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I24-Microfocus Macromolecular Crystallography
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Open Access
Abstract: Temperature control is a key aspect of macromolecular crystallography, with the technique of cryocooling routinely being used to mitigate X-ray-induced damage. Beam-induced heating could cause the temperature of crystals to rise above the glass transition temperature, greatly increasing the rate of damage. X-ray-induced heating of ruby crystals of 20–40 µm in size has been quantified non-invasively by monitoring the emission wavelengths of X-ray-induced fluorescence during exposure to the X-ray beam. For the beam sizes and dose rates typically used in macromolecular crystallography, the temperature rises are of the order of 20 K. The temperature changes observed are compared with models in the literature and can be used as a validation tool for future models.
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Jul 2019
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[16022]
Open Access
Abstract: The conversion of CaSO4·0.5H2O to CaSO4·2H2O is of great importance industrially, being the reaction behind plasterboard production and the setting of medical plasters. A detailed kinetic and mechanistic study of this process was conducted using time-resolved synchrotron X-ray diffraction in this work. The CaSO4·2H2O product is very similar regardless of whether the α- or β-form of CaSO4·0.5H2O is used as the starting material, but the reaction process is very different. The induction time is usually shorter for α-CaSO4·0.5H2O than β-CaSO4·0.5H2O, and a greater conversion percentage is observed with the former (although in neither case does the reaction proceed to 100% completion). The temperature of the system, widely used in industry as an indirect measure of the extent of the hydration process, is found to be a poor proxy for this, with the maximum temperature reached well before the reaction is complete. The Avrami–Erofe'ev and Gualtieri models could both be fitted to the experimental data, with the fits being substantially closer in the case of α-CaSO4·0.5H2O. The rate of reaction in the Avrami model tends to increase with the amount of gypsum seeds added to accelerate the process, and the importance of nucleation declines. The Gualtieri analysis suggested that the rate of nucleation increases substantially with the amount of seeds added, while there are less distinct changes in the rate of crystal growth. At low seed concentrations (<0.5% w/w) the rate of crystal growth is greater than the rate of nucleation, but at concentrations above 0.5% w/w nucleation is faster. These findings represent the first synchrotron study of the conversion of CaSO4·0.5H2O to CaSO4·2H2O, and will be of importance to gypsum producers globally.
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May 2019
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[9396]
Open Access
Abstract: X-ray computed tomography and, specifically, time-resolved volumetric tomography data collections (4D datasets) routinely produce terabytes of data, which need to be effectively processed after capture. This is often complicated due to the high rate of data collection required to capture at sufficient time-resolution events of interest in a time-series, compelling the researchers to perform data collection with a low number of projections for each tomogram in order to achieve the desired `frame rate'. It is common practice to collect a representative tomogram with many projections, after or before the time-critical portion of the experiment without detrimentally affecting the time-series to aid the analysis process. For this paper these highly sampled data are used to aid feature detection in the rapidly collected tomograms by assisting with the upsampling of their projections, which is equivalent to upscaling the θ-axis of the sinograms. In this paper, a super-resolution approach is proposed based on deep learning (termed an upscaling Deep Neural Network, or UDNN) that aims to upscale the sinogram space of individual tomograms in a 4D dataset of a sample. This is done using learned behaviour from a dataset containing a high number of projections, taken of the same sample and occurring at the beginning or the end of the data collection. The prior provided by the highly sampled tomogram allows the application of an upscaling process with better accuracy than existing interpolation techniques. This upscaling process subsequently permits an increase in the quality of the tomogram's reconstruction, especially in situations that require capture of only a limited number of projections, as is the case in high-frequency time-series capture. The increase in quality can prove very helpful for researchers, as downstream it enables easier segmentation of the tomograms in areas of interest, for example. The method itself comprises a convolutional neural network which through training learns an end-to-end mapping between sinograms with a low and a high number of projections. Since datasets can differ greatly between experiments, this approach specifically develops a lightweight network that can easily and quickly be retrained for different types of samples. As part of the evaluation of our technique, results with different hyperparameter settings are presented, and the method has been tested on both synthetic and real-world data. In addition, accompanying real-world experimental datasets have been released in the form of two 80 GB tomograms depicting a metallic pin that undergoes corruption from a droplet of salt water. Also a new engineering-based phantom dataset has been produced and released, inspired by the experimental datasets.
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May 2019
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Optics
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Abstract: Cr/C multilayer optics are a suitable choice for the tender X-ray range (1–4 keV) that covers the K absorption edges of P, S, Cl and 3d transition metals as well as the L absorption edges of 4d transition metals. In particular, these optics are studied in order to optimize the optical properties of collimated plane-grating monochromators. In this paper, the structure, stress and optical properties of Cr/C multilayers (fabricated using direct-current magnetron sputtering) with bi-layer number of 20 and the same period (about 11.64 nm) but different Cr thickness ratio (0.20–0.80) are investigated. Firstly, the grazing-incidence X-ray reflectivity at 8.04 keV was measured. These measurements were fitted assuming a multilayer structure with a four-layer and non-periodic model. Results and fitting show that interface widths increase with the Cr thickness ratio. The results obtained from X-ray diffraction at 8.04 keV were consistent with high-resolution transmission electron microscopy which showed an increase in grain size of the Cr layers. In addition, the stresses of the Cr/C multilayers have been measured and the results show that the stress value approaches zero when the Cr thickness ratio is about 0.45. The reflectivity of a Cr/C multilayer with Cr thickness ratio of 0.37 was measured and reaches 26.6% at 1.04 keV. The measured reflectivity matches very well with the predicted value using the four-layer and non-periodic model, which confirmed the viability of the prediction. Thus, the reflectivity at 1.04 keV of a Cr/C multilayer with different Cr thickness ratio was predicted and was found to drastically decrease when the Cr thickness ratio is larger than 0.37. It has been determined that a Cr thickness ratio value of 0.37 is the best choice for a Cr/C multilayer in view of high reflectivity and low stress.
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May 2019
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I05-ARPES
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Diamond Proposal Number(s):
[16764, 14488]
Open Access
Abstract: This article reports on the fabrication and testing of dedicated Fresnel zone plates for use at the nano-ARPES branch of the I05-ARPES beamline of Diamond Light Source to perform angle-resolved photoelectron spectroscopy with sub-micrometre resolution in real space. The aim of the design was to provide high photon flux combined with sub-micrometre spot sizes. The focusing lenses were tested with respect to efficiency and spatial resolution in the extreme ultraviolet between 50 eV and 90 eV. The experimentally determined diffraction efficiencies of the zone plates are as high as 8.6% at 80 eV, and a real-space resolution of 0.4 µm was demonstrated. Using the zone-plate-based setup, monolayer flakes of the two-dimensional semiconductor WS2 were investigated. This work demonstrates that the local electronic structure can be obtained from an area of a few micrometres across a two-dimensional heterostructure.
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Mar 2019
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I20-Scanning-X-ray spectroscopy (XAS/XES)
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Abstract: In order to provide adequate cryogenic cooling of both existing and next-generation crystal monochromators, a new approach to produce an optimum thermal interface between the first crystal and its copper heat exchanger is proposed. This will ensure that the increased heat load deposited by higher X-ray powers can be properly dissipated. Utilizing a cylindrical silicon crystal, a tubular copper heat exchanger and by exploiting the differing thermal and mechanical properties of the two, a very good thermal interface was achieved at liquid-nitrogen temperatures. The surface flatness of the diffracting plane at one end of the cylindrical crystal was measured at room temperature while unconstrained. The crystal was then placed into the copper heat exchanger, a slide fit at room temperature, and then cooled to liquid-nitrogen temperature. At −200°C the slide fit became an interference fit. This room-temperature `loose' fit was modelled using finite-element analysis to obtain the desired fit at cryogenic temperatures by prescribing the fit at room temperature. Under these conditions, the diffraction surface was measured for distortion due to thermal and mechanical clamping forces. The total deformation was measured to be 30 nm, an order of magnitude improvement over deformation caused by cooling alone with the original side-clamped design this concept method is set to replace. This new methodology also has the advantage that it is repeatable and does not require macro-scale tools to acquire a nanometre-accuracy mounting.
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Mar 2019
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Open Access
Abstract: Full-field transmission X-ray microscopy (TXM) is a well established technique, available at various synchrotron beamlines around the world as well as by laboratory benchtop devices. One of the major TXM challenges, due to its nanometre-scale resolution, is the overall instrument stability during the acquisition of the series of tomographic projections. The ability to correct for vertical and horizontal distortions of each projection image during acquisition is necessary in order to achieve the effective 3D spatial resolution. The effectiveness of such an image alignment is also heavily influenced by the absorption properties and strong contrast of specific features in the scanned sample. Here it is shown that nanoporous gold (NPG) can be used as an ideal 3D test pattern for evaluating and optimizing the performance of a TXM instrument for hard X-rays at a synchrotron beamline. Unique features of NPG, such as hierarchical structures at multiple length scales and high absorbing capabilities, makes it an ideal choice for characterization, which involves a combination of a rapid-alignment algorithm applied on the acquired projections followed by the extraction of a set of both 2D- and 3D-descriptive image parameters. This protocol can be used for comparing the efficiency of TXM instruments at different synchrotron beamlines in the world or benchtop devices, based on a reference library of scanned NPG samples, containing information about the estimated horizontal and vertical alignment values, 2D qualitative parameters and quantitative 3D parameters. The possibility to tailor the ligament sizes of NPG to match the achievable resolution in combination with the high electron density of gold makes NPG an ideal 3D test pattern for evaluating the status and performance of a given synchrotron-based or benchtop-based TXM setup.
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Jan 2019
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Metrology
Optics
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Open Access
Abstract: Piezoelectric bimorph deformable mirrors (`bimorphs') are routinely used on many synchrotron and free-electron laser beamlines to provide active variation in the size and shape of the X-ray beam. However, the time-domain potential of such optics has never been fully exploited. For the first time, the fast dynamic bending response of bimorphs is investigated here using Fizeau interferometry. Automated scripts for acquisition and analysis were developed to collect Fizeau data at a rate of 0.1 Hz to record dynamic changes in the optical surface as voltages were applied to the electrodes of the piezoelectric actuators. It is demonstrated that residual drift in the tangential radius of curvature of a bimorph can be significantly reduced using enhanced opto-mechanical holders and a fast programmable high-voltage power supply. Further improvements are achieved by applying small opposing voltages to compensate for piezoelectric creep. The present study shows that bimorphs can truly be used as high-speed adaptive optics for the X-ray domain, even without closed-loop feedback correction. This opens the possibility for relatively simple real-time tuning of the profile of X-ray bimorphs. Part II of this study [Alcock, Nistea, Signorato, Owen, Axford, Sutter, Foster & Sawhney (2019), J. Synchrotron Rad. 26, this issue] builds upon these results and demonstrates how bimorphs can rapidly provide customisable sizes and shapes of synchrotron X-ray beams, specifically tailored to suit the experimental samples being investigated.
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Dec 2018
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