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Preview: Forthcoming in Journal of Synchrotron Radiation

Forthcoming article in 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



 



Protein crystallography beamline (BL2S1) at the Aichi synchrotron
A protein crystallography beamline, BL2S1, has been constructed on the 5 T superbend port of the AichiSR.



Comparison of helical scan and standard rotation methods in single-crystal X-ray data collection strategies
Helical scans are compared with standard rotation methods in single-crystal X-ray diffraction experiments and, for certain cases, the helical scan methods improve the quality of the diffraction data and the electron density maps.



Uridine as a new scavenger for synchrotron-based structural biology techniques
The protective properties of uridine against radiation damage for small-angle X-ray scattering and macromolecular crystallography experiments at room temperature are shown. The scavenging effect of uridine is similar to, or more pronounced than, the most commonly used scavengers.






AI-BL1.0: a program for automatic on-line beamline optimization using the evolutionary algorithm
An open-source Labview-based program for automatic on-line beamline optimization using an evolutionary algorithm is reported.



Design of a multilayer-based collimated plane-grating monochromator for tender X-ray range
A multilayer-based collimated plane-grating monochromator (cPGM) with efficiency one order of magnitude higher than the traditional cPGM is proposed for the tender X-ray range. The resolving power can also be increased with improved photon flux by using a large blaze angle and working at high diffraction order.



Design of a prototype split-and-delay unit for XFEL pulses, and their evaluation by synchrotron radiation X-rays
A prototype split-and-delay unit (SDU) for XFEL pulses was designed based on the Graeff–Bonse four-Bragg-reflection interferometer by installing 12.5° slopes and evaluated by synchrotron radiation X-rays. The ease of the tunability of the exact delay time across 0 fs by the present SDU was demonstrated.



Automatic processing of multimodal tomography datasets
Multimodal chemical tomography is a technique that has to deal with a variety of big (>100 GB) datasets. Here, a novel method for approaching the analysis of such data using a Python-based big data solution is presented.



Generation of apodized X-ray illumination and its application to scanning and diffraction microscopy
Apodized X-ray illumination generated by a two-stage deformable Kirkpatrick–Baez mirror system was employed to improve the image quality in scanning X-ray fluorescence microscopy. It is also demonstrated that the apodized X-ray illumination enables non-isolated objects to be imaged by coherent X-ray diffractive imaging in a non-scanning mode.



X-ray grating interferometer for in situ and at-wavelength wavefront metrology
An X-ray grating interferometry setup for wavefront metrology measurements at synchrotron and X-ray free-electron laser facilities and exemplary measurements are reported.



Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography
A combination of Bragg coherent diffractive imaging and reciprocal-space mapping results indicate that the global radiation damage behaviour of micro-crystals is different compared with macroscale crystals.



Performance of photoelectron spin polarimeters with continuous and pulsed sources: from storage rings to free electron lasers
The experimental uncertainties concerning electron spin polarization under various realistic measurement conditionse are theoretically derived. Supported by numerical simulations, these results define new mathematical instruments for handling the correct statistics of spin polarization measurements in the presence of source intensity fluctuations and are applied to the characteristics of a wide set of state-of-the-art facilities.



Conformational variation of proteins at room temperature is not dominated by radiation damage
The conformational variation of three different proteins as a function of dose is examined at 278 and 100 K.



Linear parabolic single-crystal diamond refractive lenses for synchrotron X-ray sources
One-dimensional single-crystal diamond refractive lenses of novel design were produced by laser ablation. They were tested using an X-ray focusing mode, Talbot interferometry, X-ray radiography and X-ray topography.












Miniature diamond anvils for X-ray Raman scattering spectroscopy experiments at high pressure
Limitations arise for the pressure range where high quality data can be recorded with X-ray Raman scattering spectroscopy. To overcome such issues, miniature diamond anvils of less than 500 µm thickness that can sustain pressure of 70 GPa with large opening enabling high scattering geometry have been developed. On beamline ID20 at the ESRF, data of unprecedented quality were collected on the silicon L-edge and oxygen K-edge in SiO2 glass up to 47 GPa.



1s2p resonant inelastic X-ray scattering combined dipole and quadrupole analysis method
An investigation into when RIXS measurements bring extra information compared with XAS is presented. Two models are used to analyse the RIXS data: an exciton model and a continuum model, which describe the quadrupole and dipole excitations, respectively.



OH cleavage from tyrosine: debunking a myth
A systematic macromolecular crystallography investigation into the observed electron density loss around the –OH group of tyrosines, as a function of dose at 100 K, is reported. It is concluded that a probable explanation is aromatic ring disordering as opposed to –OH cleavage; occurrence of the latter mechanism is a misconception perpetuated in radiation damage literature, and is unsupported by any observations in radiation chemistry.



Development of synchrotron X-ray micro-tomography under extreme conditions of pressure and temperature
The development of new sets-ups for tomography measurements under extreme conditions of pressure and temperature at synchrotron sources is reported.



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.



A practical local tomography reconstruction algorithm based on a known sub-region
A method for reducing the cupping effect in local tomography based on a known region is proposed.



Coherent X-ray beam metrology using 2D high-resolution Fresnel-diffraction analysis
Online metrology of beamline specifications is important but often sacrificed for reasons of time constraints. A technique that permits a reliable metrology without interruption of the measurement workflow is presented.



P13, the EMBL macromolecular crystallography beamline at the low-emittance PETRA III ring for high- and low-energy phasing with variable beam focusing
The P13 macromolecular crystallography beamline, based on the low-emittance source PETRA III, enables X-ray diffraction experiments on macromolecular crystals over a wide wavelength range (0.7–3.1 Å). The beam has a variable focus size and a small divergence enabling data collection on micrometre-sized crystals.



Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
The best practice for dose-limiting serial synchrotron rotation crystallography was examined through anomalous signal and single-wavelength anomalous diffraction phasing of mercury-bound luciferin regenerating enzyme. Sample rotation enabled accurate data collection with fewer diffraction images than without rotation, and an increase in resolution and anomalous signal was observed up to 3.4 MGy even though specific damage occurred after an accumulated dose of 1.1 MGy.



Dynamic X-ray diffraction sampling for protein crystal positioning
A supervised learning approach for dynamic sampling was found to enable reconstruction of protein crystal position with a significant reduction in both the total X-ray exposure of the sample and to the exposure to the interior of the crystal.



On the use of flat-fields for tomographic reconstruction
A flat-field correction method is proposed for X-ray computed tomography using the edges of the sinogram (not shadowed by the sample) to adjust the best suited combination of flat-fields.



X-ray fluorescence at nanoscale resolution for multicomponent layered structures: a solar cell case study
The study of multilayer stacks (e.g. thin-film solar cells) by X-ray fluorescence requires a thorough account of the depth-dependent attenuation of incident and excident X-ray beam intensity, as well as spatial thickness variations to achieve an accurate interpretation of the data. A procedure is presented that allows for the assessment of stoichiometric composition variations in high spatial resolution imaging by correcting for multiple effects.



Fast iterative reconstruction of data in full interior tomography
Efficient strategies to perform iterative reconstruction of underconstrained datasets in full interior tomography are presented.



Synchrotron-based phase-sensitive imaging of leaves grown from magneto-primed seeds of soybean
Synchrotron-radiation-based phase-contrast imaging of soybean leaves grown from magneto-primed seeds is presented.



Quantitative characterization of the X-ray beam at the Australian Synchrotron Imaging and Medical Beamline (IMBL)
A comprehensive model of the Imaging and Medical Beamline at the Australian Synchrotron has been developed, validated against a variety of experimental measurements, and its versatility, reliability and robustness demonstrated. The results presented are of particular relevance in X-ray imaging, tomography, radiotherapy and dosimetry.



Determination of copper nanoparticle size distributions with total reflection X-ray fluorescence spectroscopy
The angular distribution of the total reflection X-ray fluorescence signal can suggest a distribution of particle heights deposited on a surface. This height distribution can be deduced by fitting theoretical concentration profiles representative of particles.



Development of tools to automate quantitative analysis of radiation damage in SAXS experiments
Radiation damage analysis with experimental SAXS data allows for the quantitative comparison of the efficacy of various additive radioprotectant compounds. Relevant extensions to RADDOSE-3D and the creation of a new visualization library to enable this study are presented.



Identification of the point of diminishing returns in high-multiplicity data collection for sulfur SAD phasing
A statistic based on the distribution of sets of signed anomalous differences is evaluated as a possible metric for defining the point at which the inclusion of additional data from a progressively more damaged crystal into a S-SAD phasing process will reduce the probability of successful phasing.