Journal of Synchrotron Radiation最新文献

Amyloidosis is known to be caused by the deposition of amyloid fibrils into various biological tissues; effective treatments for the disease are little established today. An infrared free-electron laser (IR-FEL) is an accelerator-based picosecond-pulse laser having tunable infrared wavelengths. In the current study, the irradiation effect of an IR-FEL was tested on an 11-residue peptide (NFLNCYVSGFH) fibril from β2-microglobulin (β2M) with the aim of applying IR-FELs to amyloidosis therapy. Infrared microspectroscopy (IRM) and scanning electron microscopy showed that a fibril of β2M peptide was clearly dissociated by IR-FEL at 6.1 µm (amide I) accompanied by a decrease of the β-sheet and an increase of the α-helix. No dissociative process was recognized at 6.5 µm (amide II) as well as at 5.0 µm (non-specific wavelength). Equilibrium molecular dynamics simulations indicated that the α-helix can exist stably and the probability of forming interchain hydrogen bonds associated with the internal asparagine residue (N4) is notably reduced compared with other amino acids after the β-sheet is dissociated by amide I specific irradiation. This result implies that N4 plays a key role for recombination of hydrogen bonds in the dissociation of the β2M fibril. In addition, the β-sheet was disrupted at temperatures higher than 340 K while the α-helix did not appear even though the fibril was heated up to 363 K as revealed by IRM. The current study gives solid evidence for the laser-mediated conversion from β-sheet to α-helix in amyloid fibrils at the molecular level.

Monochromators for synchrotron radiation beamlines typically use perfect crystals for the hard X-ray regime and gratings for soft X-rays. There is an intermediate range, typically 1-3 keV (tender X-rays), which common perfect crystals have difficulties covering and gratings have low efficiency, although some less common crystals with high d-spacing could be suitable. To evaluate the suitability of these crystals for a particular beamline, it is useful to evaluate the crystals' performance using tools such as ray-tracing. However, simulations for double-crystal monochromators are only available for the most used crystals such as Si, Ge or diamond. Here, an upgrade of the SHADOW ray-tracing code and complementary tools in the OASYS suite are presented to simulate high d-spacing crystals with arbitrary, and sometimes complex, structures such as beryl, YB₆₆, muscovite, etc. Isotropic and anisotropic temperature factors are also considered. The YB₆₆ crystal with 1936 atomic sites in the unit cell is simulated, and its applicability for tender X-ray monochromators is discussed in the context of new low-emittance storage rings.

The present work demonstrates the performance of a von Hámos high-energy-resolution X-ray spectrometer based on a non-conventional conical Si single-crystal analyzer. The analyzer is tested with different primary and secondary X-ray sources as well as a hard X-ray sensitive CCD camera. The spectrometer setup is also characterized with ray-tracing simulations. Both experimental and simulated results affirm that the conical spectrometer can efficiently detect and resolve the two pairs of two elements (Ni and Cu) Kα X-ray emission spectroscopy (XES) peaks simultaneously, requiring a less than 2 cm-wide array on a single position-sensitive detector. The possible applications of this simple yet broad-energy-spectrum crystal spectrometer range from quickly adapting it as another probe for complex experiments at synchrotron beamlines to analyzing X-ray emission from plasma generated by ultrashort laser pulses at modern laser facilities.

The Argonne X-ray Emission Analysis Package (AXEAP) has been developed to calibrate and process X-ray emission spectroscopy (XES) data collected with a two-dimensional (2D) position-sensitive detector. AXEAP is designed to convert a 2D XES image into an XES spectrum in real time using both calculations and unsupervised machine learning. AXEAP is capable of making this transformation at a rate similar to data collection, allowing real-time comparisons during data collection, reducing the amount of data stored from gigabyte-sized image files to kilobyte-sized text files. With a user-friendly interface, AXEAP includes data processing for non-resonant and resonant XES images from multiple edges and elements. AXEAP is written in MATLAB and can run on common operating systems, including Linux, Windows, and MacOS.

New developments at synchrotron beamlines and the ongoing upgrades of synchrotron facilities allow the possibility to study complex structures with a much better spatial and temporal resolution than ever before. However, the downside is that the data collected are also significantly larger (more than several terabytes) than ever before, and post-processing and analyzing these data is very challenging to perform manually. This issue can be solved by employing automated methods such as machine learning, which show significantly improved performance in data processing and image segmentation than manual methods. In this work, a 3D U-net deep convolutional neural network (DCNN) model with four layers and base-8 characteristic features has been developed to segment precipitates and porosities in synchrotron transmission X-ray micrograms. Transmission X-ray microscopy experiments were conducted on micropillars prepared from additively manufactured 316L steel to evaluate precipitate information. After training the 3D U-net DCNN model, it was used on unseen data and the prediction was compared with manual segmentation. A good agreement was found between both segmentations. An ablation study was performed and revealed that the proposed model showed better statistics than other models with lower numbers of layers and/or characteristic features. The proposed model is able to segment several hundreds of gigabytes of data in a few minutes and could be applied to other materials and tomography techniques. The code and the fitted weights are made available with this paper for any interested researcher to use for their needs (https://github.com/manasvupadhyay/erc-gamma-3D-DCNN).

A method to optimize the notches of water-cooled white-beam mirrors over the entire photon energy range is proposed. A theoretical method is used to quantitatively evaluate the influence of the thermal load on the thermal deformation of a mirror. The result of theoretical calculations and finite-element analysis are consistent, which proves the feasibility of the method. The root mean square of the curvatures of the thermal deformation of the white-beam mirror over the entire photon energy range can be minimized. This method greatly simplifies the design work of water-cooled white-beam mirrors.

A newly designed setup to perform steady-state X-ray excited optical luminescence (XEOL) spectroscopy and simultaneous XEOL and X-ray absorption spectroscopy characterization at beamline P65 of PETRA III is described. The XEOL setup is equipped with a He-flow cryostat and state-of-the-art optical detection system, which covers a wide wavelength range of 300-1700 nm with a high spectral resolution of 0.4 nm. To demonstrate the setup functioning, low-temperature XEOL studies on polycrystalline CuInSe₂ thin film, single-crystalline GaN thin film and single-crystalline ZnO bulk semiconductor samples are performed.

Pump-probe experiments at X-ray free-electron laser (XFEL) facilities are a powerful tool for studying dynamics at ultrafast and longer timescales. Observing the dynamics in diverse scientific cases requires optical laser systems with a wide range of wavelength, flexible pulse sequences and different pulse durations, especially in the pump source. Here, the pump-probe instrumentation available for measurements at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL is reported. The temporal and spatial stability of this instrumentation is also presented.

The development, construction, and first commissioning results of a new scanning microscope installed at the 5-ID Submicron Resolution X-ray Spectroscopy (SRX) beamline at NSLS-II are reported. The developed system utilizes Kirkpatrick-Baez mirrors for X-ray focusing. The instrument is designed to enable spectromicroscopy measurements in 2D and 3D with sub-200 nm spatial resolution. The present paper focuses on the design aspects, optical considerations, and specifics of the sample scanning stage, summarizing some of the initial commissioning results.

A gasket is an important constituent of a diamond anvil cell (DAC) assembly, responsible for the sample chamber stability at extreme conditions for X-ray diffraction studies. In this work, we studied the performance of gaskets made of metallic glass Fe_0.79Si_0.07B_0.14 in a number of high-pressure X-ray diffraction (XRD) experiments in DACs equipped with conventional and toroidal-shape diamond anvils. The experiments were conducted in either axial or radial geometry with X-ray beams of micrometre to sub-micrometre size. We report that Fe_0.79Si_0.07B_0.14 metallic glass gaskets offer a stable sample environment under compression exceeding 1 Mbar in all XRD experiments described here, even in those involving small-molecule gases (e.g. Ne, H₂) used as pressure-transmitting media or in those with laser heating in a DAC. Our results emphasize the material's importance for a great number of delicate experiments conducted under extreme conditions. They indicate that the application of Fe_0.79Si_0.07B_0.14 metallic glass gaskets in XRD experiments for both axial and radial geometries substantially improves various aspects of megabar experiments and, in particular, the signal-to-noise ratio in comparison to that with conventional gaskets made of Re, W, steel or other crystalline metals.