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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: 2016-12-02


Development of tools to automate quantitative analysis of radiation damage in SAXS experiments


Biological small-angle X-ray scattering (SAXS) is an increasingly popular technique used to obtain nanoscale structural information on macromolecules in solution. However, radiation damage to the samples limits the amount of useful data that can be collected from a single sample. In contrast to the extensive analytical resources available for macromolecular crystallography (MX), there are relatively few tools to quantitate radiation damage for SAXS, some of which require a significant level of manual characterization, with the potential of leading to conflicting results from different studies. Here, computational tools have been developed to automate and standardize radiation damage analysis for SAXS data. RADDOSE-3D, a dose calculation software utility originally written for MX experiments, has been extended to account for the cylindrical geometry of the capillary tube, the liquid composition of the sample and the attenuation of the beam by the capillary material to allow doses to be calculated for many SAXS experiments. Furthermore, a library has been written to visualize and explore the pairwise similarity of frames. The calculated dose for the frame at which three subsequent frames are determined to be dissimilar is defined as the radiation damage onset threshold (RDOT). Analysis of RDOTs has been used to compare the efficacy of radioprotectant compounds to extend the useful lifetime of SAXS samples. Comparison of the RDOTs shows that, for radioprotectant compounds at 5 and 10 mM concentration, glucose is the most effective compound. However, at 1 and 2 mM concentrations, dithiothreitol (DTT) appears to be most effective. Our newly developed visualization library contains methods that highlight the unusual radiation damage results given by SAXS data collected using higher concentrations of DTT: these observations should pave the way to the development of more sophisticated frame merging strategies.

Identification of the point of diminishing returns in high-multiplicity data collection for sulfur SAD phasing


High-quality high-multiplicity X-ray diffraction data were collected on five different crystals of thaumatin using a homogeneous-profile X-ray beam at E = 8 keV to investigate the counteracting effects of increased multiplicity and increased radiation damage on the quality of anomalous diffraction data collected on macromolecular crystals. By comparing sulfur substructures obtained from subsets of the data selected as a function of absorbed X-ray dose with sulfur positions in the respective refined reference structures, the doses at which the highest quality of anomalous differences could be obtained were identified for the five crystals. A statistic σ{ΔF}D, calculated as the width σ of the normalized distribution of a set {ΔF} of anomalous differences collected at a dose D, is suggested as a measure of anomalous data quality as a function of dose. An empirical rule is proposed to identify the dose at which the gains in data quality due to increased multiplicity are outbalanced by the losses due to decreases in signal-to-noise as a consequence of radiation damage. Identifying this point of diminishing returns allows the optimization of the choice of data collection parameters and the selection of data to be used in subsequent crystal structure determination steps.

Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography


Serial crystallography, in which single-shot diffraction images are collected, has great potential for protein microcrystallography. Although serial femtosecond crystallography (SFX) has been successfully demonstrated, limited beam time prevents its routine use. Inspired by SFX, serial synchrotron crystallography (SSX) has been investigated at synchrotron macromolecular crystallography beamlines. Unlike SFX, the longer exposure time of milliseconds to seconds commonly used in SSX causes radiation damage. However, in SSX, crystals can be rotated during the exposure, which can achieve efficient coverage of the reciprocal space. In this study, mercury single-wavelength anomalous diffraction (Hg-SAD) phasing of the luciferin regenerating enzyme (LRE) was performed using serial synchrotron rotation crystallography. The advantages of rotation and influence of dose on the data collected were evaluated. The results showed that sample rotation was effective for accurate data collection, and the optimum helical rotation step depended on multiple factors such as multiplicity and partiality of reflections, exposure time per rotation angle and the contribution from background scattering. For the LRE microcrystals, 0.25° was the best rotation step for the achievable resolution limit, whereas a rotation step larger than or equal to 1° was favorable for Hg-SAD phasing. Although an accumulated dose beyond 1.1 MGy caused specific damage at the Hg site, increases in resolution and anomalous signal were observed up to 3.4 MGy because of a higher signal-to-noise ratio.

Fast iterative reconstruction of data in full interior tomography


This paper introduces two novel strategies for iterative reconstruction of full interior tomography (FINT) data, i.e. when the field of view is entirely inside the object support and knowledge of the object support itself or the attenuation coefficients inside specific regions of interest are not available. The first approach is based on data edge-padding. The second technique creates an intermediate virtual sinogram, which is, then, reconstructed by a standard iterative algorithm. Both strategies are validated in the framework of the alternate direction method of multipliers plug-and-play with gridding projectors that provide a speed-up of three orders of magnitude with respect to standard operators implemented in real space. The proposed methods are benchmarked on synchrotron-based X-ray tomographic microscopy datasets of mouse lung alveoli. Compared with analytical techniques, the proposed methods substantially improve the reconstruction quality for FINT underconstrained datasets, facilitating subsequent post-processing steps.

Determination of copper nanoparticle size distributions with total reflection X-ray fluorescence spectroscopy


Total reflection X-ray fluorescence (TXRF) analysis is extensively used by the semiconductor industry for measuring trace metal contamination on silicon surfaces. In addition to determining the quantity of impurities on a surface, TXRF can reveal information about the vertical distribution of contaminants by measuring the fluorescence signal as a function of the angle of incidence. In this study, two samples were intentionally contaminated with copper in non-deoxygenated and deoxygenated ultrapure water (UPW) resulting in impurity profiles that were either atomically dispersed in a thin film or particle-like, respectively. The concentration profile of the samples immersed into deoxygenated UPW was calculated using a theoretical concentration profile representative of particles, yielding a mean particle height of 16.1 nm. However, the resulting theoretical profile suggested that a distribution of particle heights exists on the surface. The fit of the angular distribution data was further refined by minimizing the residual error of a least-squares fit employing a model with a Gaussian distribution of particle heights about the mean height. The presence of a height distribution was also confirmed with atomic force microscopy measurements.

On the use of flat-fields for tomographic reconstruction


Seeking for quantitative tomographic images, it is of utmost importance to limit reconstruction artifacts. Detector imperfections, inhomogeneity of the incident beam, as classically observed in synchrotron beamlines, and their variations in time are a major cause of reconstruction bias such as `ring artifacts'. The present study aims at proposing a faithful estimate of the incident beam local intensity for each acquired projection during a scan, without revisiting the process of data acquisition itself. Actual flat-fields (acquired without specimen in the beam) and sinogram borders (when the specimen is present), which are not masked during the scan, are exploited to construct a suited instantaneous detector-wide flat-field. The proposed treatment is fast and simple. Its performance is assessed on a real scan acquired at ESRF ID19 beamline. Different criteria are used including residuals, i.e. difference between projections of reconstruction and actual projections. All confirm the benefit of the proposed procedure.

Synchrotron-based phase-sensitive imaging of leaves grown from magneto-primed seeds of soybean


Experiments were conducted to study the effects of static magnetic fields (SMFs) on the venation network of soybean leaves using the synchrotron-based X-ray micro-imaging technique. The seeds of soybean (Glycine max, variety JS-335) were pretreated with different SMFs from 50 to 300 mT in steps of 50 mT for 1 h. The phase-contrast images obtained showed that, as the strength of the SMF increased, the area, width of the midrib, area of the midrib and minor vein of the middle leaflets of third trifoliate leaves also increased up to the SMF strength of 200 mT (1 h) and decreased thereafter. Quantification of the major conducting vein also showed the differences in the major and minor vein structures of the soybean leaves as compared with control leaves. Further, the phase-retrieval technique has been applied to make the segmentation process easy and to quantify the major and minor veins in the venation network. The width and area of midrib enhancement by pre-treatment with SMF implies an enhancement in the uptake of water, which in turn causes an increased rate of photosynthesis and stomatal conductance.

Dynamic X-ray diffraction sampling for protein crystal positioning


A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by limiting the dose and area exposed for image reconstruction and crystal positioning using data collection hardware present in most macromolecular crystallography end-stations.

1s2p resonant inelastic X-ray scattering combined dipole and quadrupole analysis method


In this study an analysis strategy towards using the resonant inelastic X-ray scattering (RIXS) technique more effectively compared with X-ray absorption spectroscopy (XAS) is presented. In particular, the question of when RIXS brings extra information compared with XAS is addressed. To answer this question the RIXS plane is analysed using two models: (i) an exciton model and (ii) a continuum model. The continuum model describes the dipole pre-edge excitations while the exciton model describes the quadrupole excitations. Applying our approach to the experimental 1s2p RIXS planes of VO2 and TiO2, it is shown that only in the case of quadrupole excitations being present is additional information gained by RIXS compared with XAS. Combining this knowledge with methods to calculate the dipole contribution in XAS measurements gives scientists the opportunity to plan more effective experiments.

An endstation for resonant inelastic X-ray scattering studies of solid and liquid samples


A novel experimental setup is presented for resonant inelastic X-ray scattering investigations of solid and liquid samples in the soft X-ray region for studying the complex electronic configuration of (bio)chemical systems. The uniqueness of the apparatus is its high flexibility combined with optimal energy resolution and energy range ratio. The apparatus enables investigation of chemical analyses, which reflects the chemical imprints. The endstation is composed of a main sample chamber, a sample holder for either solid or liquid jet delivery system, and a soft X-ray grating spectrometer for 210–1250 eV with a resolving power of ∼1000. It combines for the first time liquid jet technology with a soft X-ray spectrometer based on the variable line spacing principle. This setup was commissioned at the soft X-ray beamline P04 at PETRA III of the Deutsches Elektronen-Synchrotron in Hamburg which is currently the most brilliant storage-ring-based X-ray radiation source in the world. The first results of liquid and solid samples show that this setup allows the detection of photons across an energy range of ∼300 eV. This covers simultaneously the emission lines of life-important elements like carbon, nitrogen and oxygen in a shot-based procedure.

Coherent X-ray beam metrology using 2D high-resolution Fresnel-diffraction analysis


Direct metrology of coherent short-wavelength beamlines is important for obtaining operational beam characteristics at the experimental site. However, since beam-time limitation imposes fast metrology procedures, a multi-parametric metrology from as low as a single shot is desirable. Here a two-dimensional (2D) procedure based on high-resolution Fresnel diffraction analysis is discussed and applied, which allowed an efficient and detailed beamline characterization at the SACLA XFEL. So far, the potential of Fresnel diffraction for beamline metrology has not been fully exploited because its high-frequency fringes could be only partly resolved with ordinary pixel-limited detectors. Using the high-spatial-frequency imaging capability of an irradiated LiF crystal, 2D information of the coherence degree, beam divergence and beam quality factor M2 were retrieved from simple diffraction patterns. The developed beam metrology was validated with a laboratory reference laser, and then successfully applied at a beamline facility, in agreement with the source specifications.

X-ray fluorescence at nanoscale resolution for multicomponent layered structures: a solar cell case study


The study of a multilayered and multicomponent system by spatially resolved X-ray fluorescence microscopy poses unique challenges in achieving accurate quantification of elemental distributions. This is particularly true for the quantification of materials with high X-ray attenuation coefficients, depth-dependent composition variations and thickness variations. A widely applicable procedure for use after spectrum fitting and quantification is described. This procedure corrects the elemental distribution from the measured fluorescence signal, taking into account attenuation of the incident beam and generated fluorescence from multiple layers, and accounts for sample thickness variations. Deriving from Beer–Lambert's law, formulae are presented in a general integral form and numerically applicable framework. The procedure is applied using experimental data from a solar cell with a Cu(In,Ga)Se2 absorber layer, measured at two separate synchrotron beamlines with varied measurement geometries. This example shows the importance of these corrections in real material systems, which can change the interpretation of the measured distributions dramatically.