Journal of Synchrotron Radiation最新文献

The second phase of the ESRF upgrade program did not only provide a new storage ring (Extremely Brilliant Source, EBS) but also allowed several beamlines to be refurbished. The BioSAXS beamline (located on port BM29) was upgraded with a new wiggler source and a larger detector. All analysis software has been rewritten to cope with the increased data flux and continues to provide beamline users with reduced and pre-processed data in real time. This article describes FreeSAS, an open-source collection of various small-angle scattering analysis algorithms needed to reduce and analyze BioSAXS data, and Dahu, the tool used to interface data analysis with beamline control. It further presents the data-processing pipelines for the different data acquisitions modes of the beamline, using either a sample changer for individual homogeneous samples or an inline size-exclusion chromatography setup.

The acquisition speed and spatial resolution of X-ray nanotomography have continuously improved over the last decades. Coherent diffraction-based techniques breach the 10 nm resolution barrier frequently and thus pose stringent demands on sample positioning accuracy and stability. At the same time there is an increasing desire to accommodate in situ or operando measurements. Here, an environmental control system for X-ray nanotomography is introduced to regulate the temperature of a sample from room temperature up to 850°C in a controlled atmospheric composition. The system allows for a 360° sample rotation, permitting tomographic studies in situ or operando free of missing wedge constraints. The system is implemented and available at the flOMNI microscope at the Swiss Light Source. In addition to the environmental control system itself, the related modifications of flOMNI are described. Tomographic measurements of a nanoporous gold sample at 50°C and 600°C at a resolution of sub-20 nm demonstrate the performance of the device.

The SASE3 soft X-ray beamline at the European XFEL has been designed and built to provide experiments with a pink or monochromatic beam in the photon energy range 250-3000 eV. Here, the focus is monochromatic operation of the SASE3 beamline, and the design and performance of the SASE3 grating monochromator are reported. The unique capability of a free-electron laser source to produce short femtosecond pulses of a high degree of coherence challenges the monochromator design by demanding control of both photon energy and temporal resolution. The aim to transport close to transform-limited pulses poses very high demands on the optics quality, in particular on the grating. The current realization of the SASE3 monochromator is discussed in comparison with optimal design performance. At present, the monochromator operates with two gratings: the low-resolution grating is optimized for time-resolved experiments and allows for moderate resolving power of about 2000-5000 along with pulse stretching of a few to a few tens of femtoseconds RMS, and the high-resolution grating reaches a resolving power of 10 000 at the cost of larger pulse stretching.

Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two β-lactamases: a class D serine β-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-β-lactamase from Stenotrophomonas maltophilia K279a.

High-energy-resolution fluorescence-detected (HERFD) X-ray absorption near-edge spectroscopy (XANES) is a spectroscopic method that allows for increased spectral feature resolution, and greater selectivity to decrease complex matrix effects compared with conventional XANES. XANES is an ideal tool for speciation of elements in solid-phase environmental samples. Accurate speciation of As in mine waste materials is important for understanding the mobility and toxicity of As in near-surface environments. In this study, linear combination fitting (LCF) was performed on synthetic spectra generated from mixtures of eight measured reference compounds for both HERFD-XANES and transmission-detected XANES to evaluate the improvement in quantitative speciation with HERFD-XANES spectra. The reference compounds arsenolite (As₂O₃), orpiment (As₂S₃), getchellite (AsSbS₃), arsenopyrite (FeAsS), kaňkite (FeAsO₄·3.5H₂O), scorodite (FeAsO₄·2H₂O), sodium arsenate (Na₃AsO₄), and realgar (As₄S₄) were selected for their importance in mine waste systems. Statistical methods of principal component analysis and target transformation were employed to determine whether HERFD improves identification of the components in a dataset of mixtures of reference compounds. LCF was performed on HERFD- and total fluorescence yield (TFY)-XANES spectra collected from mine waste samples. Arsenopyrite, arsenolite, orpiment, and sodium arsenate were more accurately identified in the synthetic HERFD-XANES spectra compared with the transmission-XANES spectra. In mine waste samples containing arsenopyrite and either scorodite or kaňkite, LCF with HERFD-XANES measurements resulted in fits with smaller R-factors than concurrently collected TFY measurements. The improved accuracy of HERFD-XANES analysis may provide enhanced delineation of As phases controlling biogeochemical reactions in mine wastes, contaminated soils, and remediation systems.

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).