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Abstract: Determining the oxidation state of Fe through parameterization of X-ray absorption near-edge structure (XANES) spectral features is highly dependent on accurate and repeatable energy calibration between spectra. Small errors in energy calibration can lead to vastly different interpretations. While simultaneous measurement of a reference foil is often undertaken on X-ray spectroscopy beamlines, other beamlines measure XANES spectra without a reference foil and therefore lack a method for correcting energy drift. Here a method is proposed that combines two measures of Fe oxidation state taken from different parts of the spectrum to iteratively correct for an unknown energy offset between spectra, showing successful iterative self-calibration not only during individual beam time but also across different beamlines.

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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.

Open Access

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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.

Open Access

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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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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.