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An integrated computer software system for macromolecular crystallography (MX) data collection at the BL02U1 and BL10U2 beamlines of the Shanghai Synchrotron Radiation Facility is described. The system, Finback, implements a set of features designed for the automated MX beamlines, and is marked with a user-friendly web-based graphical user interface (GUI) for interactive data collection. The Finback client GUI can run on modern browsers and has been developed using several modern web technologies including WebSocket, WebGL, WebWorker and WebAssembly. Finback supports multiple concurrent sessions, so on-site and remote users can access the beamline simultaneously. Finback also cooperates with the deployed experimental data and information management system, the relevant experimental parameters and results are automatically deposited to a database.
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The infrared beamline at BESSYâ II storage ring was upgraded recently to extend the capabilities of infrared microscopy. The endstations available at the beamline are now facilitating improved characterization of molecules and materials at different length scales and time resolutions. Here, the current outline of the beamline is reported and an overview of the endstations available is given. In particular, the first results obtained by using a new microscope for nano-spectroscopy that was implemented are presented. The capabilities of the scattering-type near-field optical microscope (s-SNOM) are demonstrated by investigating cellulose microfibrils, representing nanoscopic objects of a hierarchical structure. It is shown that the s-SNOM coupled to the beamline allows imaging to be performed with a spatial resolution of less than 30â nm and infrared spectra to be collected from an effective volume of less than 30â nm × 30â nm × 12â nm. Potential steps for further optimization of the beamline performance are discussed.
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The Shanghai Soft X-ray Free-Electron Laser (SXFEL) is the first X-ray free-electron laser facility in China. The SASE beamline, which consists of a pink-beam branch and a mono-beam branch, is one of the two beamlines in the Phase-I construction. The pink-beam branch opened for users in 2023 after successful first-round beamline commissioning. In this paper, the design of the beamline is presented and the performance of the pink-beam branch is reported. The measured energy-resolving power of the online spectrometer is over 6000 @ 400â eV. The focusing spot size of the pink beam is less than 3â µm in both the horizontal and vertical at the endstation.
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To characterize an electron beam, visible synchrotron light is often used and dedicated beamlines at synchrotron sources are becoming a more common feature as instruments and methods for the diagnostics are, along with the accelerators, further developed. At KARA (Karlsruhe Research Accelerator), such a beamline exists and is based on a typical infrared/visible-light configuration. From experience at such beamlines no significant radiation was expected (dose rates larger than 0.5â µSvâ h-1). This was found not to be the case and a higher dose was measured which fortunately could be shielded to an acceptable level with 0.3â mm of aluminium foil or 2.0â mm of Pyrex glass. The presence of this radiation led to further investigation by both experiment and calculation. A custom setup using a silicon drift detector for energy-dispersive spectroscopy (Ketek GmbH) and attenuation experiments showed the radiation to be predominantly copper K-shell fluorescence and is confirmed by calculation. The measurement of secondary radiation from scattering of synchrotron and other radiation, and its calculation, is important for radiation protection, and, although a lot of experience exists and methods for radiation protection are well established, changes in machine, beamlines and experiments mean a constant appraisal is needed.
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Synchrotron light sources can provide the required spatial coherence, stability and control to support the development of advanced lithography at the extreme ultraviolet and soft X-ray wavelengths that are relevant to current and future fabricating technologies. Here an evaluation of the optical performance of the soft X-ray (SXR) beamline of the Australian Synchrotron (AS) and its suitability for developing interference lithography using radiation in the 91.8â eV (13.5â nm) to 300â eV (4.13â nm) range are presented. A comprehensive physical optics model of the APPLE-II undulator source and SXR beamline was constructed to simulate the properties of the illumination at the proposed location of a photomask, as a function of photon energy, collimation and monochromator parameters. The model is validated using a combination of experimental measurements of the photon intensity distribution of the undulator harmonics. It is shown that the undulator harmonics intensity ratio can be accurately measured using an imaging detector and controlled using beamline optics. Finally, the photomask geometric constraints and achievable performance for the limiting case of fully spatially coherent illumination are evaluated.
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Near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy is a powerful tool for identifying chemical bonding states at synchrotron radiation facilities. Advances in new materials require researchers in both academia and industry to measure tens to hundreds of samples during the available beam time on a synchrotron beamline, which is typically allocated to users. Automated measurement methods, along with analysis software, have been developed for beamlines. Automated measurements facilitate high-throughput experiments and accumulate vast amounts of measured spectral data. The analysis software supports various functions for analyzing the experimental data; however, these analysis methods are complicated, and learning them can be time-consuming. To process large amounts of spectral data, a new analysis software, dedicated to NEXAFS spectroscopy, that is easy to use and can provide results in a short time is desired. Herein, the development of Beagle is described, software calculating molecular orientation from NEXAFS spectroscopy data that can report results in a short time comparable with that required to measure one sample at the beamline. It was designed to progress in a single sequence from data loading to the printing of the results with a `click of a button'. The functions of the software include recognizing the dataset, correcting the background, normalizing the plot, calculating the electron yield and determining the molecular orientation. The analysis results can be saved as {\tt{.txt}} files (spectral data), {\tt{.pdf}} files (graphic images) and Origin files (spectral data and graphic images).
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The SIRIUS beamline of Synchrotron SOLEIL is dedicated to X-ray scattering and spectroscopy of surfaces and interfaces, covering the tender to mid-hard X-ray range (1.1-13â keV). The beamline has hosted a wide range of experiments in the field of soft interfaces and beyond, providing various grazing-incidence techniques such as diffraction and wide-angle scattering (GIXD/GIWAXS), small-angle scattering (GISAXS) and X-ray fluorescence in total reflection (TXRF). SIRIUS also offers specific sample environments tailored for in situ complementary experiments on solid and liquid surfaces. Recently, the beamline has added compound refractive lenses associated with a transfocator, allowing for the X-ray beam to be focused down to 10â µm × 10â µm while maintaining a reasonable flux on the sample. This new feature opens up new possibilities for faster GIXD measurements at the liquid-air interface and for measurements on samples with narrow geometries.
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The damage threshold of an Au-coated flat mirror, one of the reflective optics installed on the FEL-2 beamline of the Dalian Coherent Light Source, China, upon far-UV free-electron laser irradiation is evaluated. The surface of the coating is characterized by profilometer and optical microscope. A theoretical approach of the phenomenon is also presented, by application of conventional single-pulse damage threshold calculations, a one-dimensional thermal diffusion model, as well as finite-element analysis with ANSYS.
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The advent of diffraction-limited storage rings (DLSRs) has boosted the brilliance or coherent flux by one to two orders of magnitude with respect to the previous generation. One consequence of this brilliance enhancement is an increase in the flux density or number of photons per unit of area and time, which opens new possibilities for the spatiotemporal resolution of X-ray imaging techniques. This paper studies the time-resolved microscopy capabilities of such facilities by benchmarking the ForMAX beamline at the MAX IV storage ring. It is demonstrated that this enhanced flux density using a single harmonic of the source allows micrometre-resolution time-resolved imaging at 2000 tomograms per second and 1.1â MHz 2D acquisition rates using the full dynamic range of the detector system.
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A broadband online X-ray spectrometer has been designed and commissioned at the SUD beamline of the Shanghai Soft X-ray Free-Electron Laser Facility, which can deliver both SASE and seeded FEL pulses to user experiments, spanning the photon energy range of 50-620â eV. The resolving powers of the spectrometer calibrated via online measurement at 92â eV and 249â eV are â¼20000 and â¼15000, respectively, and the absolute photon energy is characterized by an electron time-of-flight spectrometer. The high energy resolution provided by the spectrometer can differentiate the fine structure in the FEL spectrum, to determine its pulse length.
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Viruses are obligate intracellular pathogens that depend on their host cell machinery and metabolism for their replicative life cycle. Virus entry, replication, and assembly are dynamic processes that lead to the reorganisation of host cell components. Therefore, a complete understanding of the viral processes requires their study in the cellular context where advanced imaging has been proven valuable in providing the necessary information. Among the available imaging techniques, soft X-ray tomography (SXT) at cryogenic temperatures can provide three-dimensional mapping to 25 nm resolution and is ideally suited to visualise the internal organisation of virus-infected cells. In this chapter, the principles and practices of synchrotron-based cryo-soft X-ray tomography (cryo-SXT) in virus research are presented. The potential of the cryo-SXT in correlative microscopy platforms is also demonstrated through working examples of reovirus and hepatitis research at Beamline B24 (Diamond Light Source Synchrotron, UK) and BL09-Mistral beamline (ALBA Synchrotron, Spain), respectively.
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Tomografía por Rayos X , Virus , Tomografía por Rayos X/métodos , BiologíaRESUMEN
Mirror-centered, closed-form expressions for hyperbolic surfaces used in X-ray beamlines have been derived. Hyperbolic mirrors create a virtual focus or source point and can be used to lengthen or shorten the effective focal distance of a compound optical system. The derivations here express off-axis segments of a hyperbolic surface in terms of the real and virtual focal distances and the incident glancing angle at the center of the mirror. Conventional mathematical expressions of hyperbolic shapes describe the surfaces in Cartesian or polar coordinates centered on an axis of symmetry, necessitating cumbersome rotation and translation to mirror-centered coordinates. The representation presented here, with zero slope and the origin at the central point, is most convenient for modeling, metrology, aberration correction, and general surface analysis of off-axis configurations. The direct derivation avoids the need for nested coordinate transforms. A series expansion provides a helpful approximation; the coefficients of the implicit equation are also provided.
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The unique diffraction geometry of ESRF beamline ID06-LVP offers continuous static 2D or azimuthally resolving data collections over all accessible solid angles available to the tooling geometry. The system is built around a rotating custom-built Pilatus3 CdTe 900k-W detector from Dectris, in a configuration equivalent to three butted 300k devices. As a non-standard geometry, here the method of alignment, correction and subsequent integration for any data collected over all solid angles accessible, or over any azimuthal range contained therein, are provided and illustrated by parameterizing and extending existing pyFAI routines. At 1° integrated intervals, and typical distances (2.0â m), the system covers an area of near 2.5â m2 (100â Mpx square equivalent), to 0.65â Å resolution, at 53â keV from a total dataset of some 312â Mpx. Standard FWHMs of SRM660a LaB6 vary from 0.005° to 0.01°, depending on beam size, energy and sample dimensions, and are sampled at an elevated rate. The azimuthal range per static frame ranges from <20° to â¼1° over the full range of the detector surface. A full 2θ-intensity data collection at static azimuth takes 1-3â s typically, and can be reduced to ms-1 rates for measurements requiring time-rate determination. A full solid-angle collection can be completed in a minute. Sample detector distances are accessible from 1.6â m to 4.0â m.
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In beamline design, there are many floating parameters that need to be tuned; manual optimization is time-consuming and laborious work, and it is also difficult to obtain well optimized results. Moreover, there are always several objectives that need to be considered and optimized at the same time, making the problem more complicated. For example, asking for both the flux and energy to be as large as possible is a usual requirement, but the changing trends of these two variables are often contradictory. In this study, a novel optimization method based on a multi-objective genetic algorithm is introduced, the first attempt to optimize a beamline with multiple objectives. In order to verify this method, beamline ID17 of the European Synchrotron Radiation Facility (ESRF) is taken as an example for simulation, with energy and dose rate as objectives. The result shows that this method can be effective for beamline optimization, and an optimal solution set can be obtained within 30 generations. For the solutions whose objectives are both improved compared with those of ESRF beamline ID17, the maximums of energy and dose rate increase by around 7% and 20%, respectively.
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Algoritmos , Sincrotrones , Simulación por ComputadorRESUMEN
The mutual optical intensity (MOI) model is a partially coherent radiation propagation tool that can sequentially simulate beamline optics and provide beam intensity, local degree of coherence and phase distribution at any location along a beamline. This paper extends the MOI model to non-ideal two-dimensional (2D) optical systems, such as ellipsoidal and toroidal mirrors with 2D figure errors. Simulation results show that one can tune the trade-off between calculation efficiency and accuracy by varying the number of wavefront elements. The focal spot size of an ellipsoidal mirror calculated with 100â ×â 100 elements gives less than 0.4% deviation from that with 250â ×â 250 elements, and the computation speed is nearly two orders of magnitude faster. Effects of figure errors on 2D focusing are also demonstrated for a non-ideal ellipsoidal mirror and by comparing the toroidal and ellipsoidal mirrors. Finally, the MOI model is benchmarked against the multi-electron Synchrotron Radiation Workshop (SRW) code showing the model's high accuracy.
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Recently, there has been significant interest in applying machine-learning (ML) techniques to the automated analysis of X-ray scattering experiments, due to the increasing speed and size at which datasets are generated. ML-based analysis presents an important opportunity to establish a closed-loop feedback system, enabling monitoring and real-time decision-making based on online data analysis. In this study, the incorporation of a combined one-dimensional convolutional neural network (CNN) and multilayer perceptron that is trained to extract physical thin-film parameters (thickness, density, roughness) and capable of taking into account prior knowledge is described. ML-based online analysis results are processed in a closed-loop workflow for X-ray reflectometry (XRR), using the growth of organic thin films as an example. Our focus lies on the beamline integration of ML-based online data analysis and closed-loop feedback. Our data demonstrate the accuracy and robustness of ML methods for analyzing XRR curves and Bragg reflections and its autonomous control over a vacuum deposition setup.
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High-data-throughput and multimodal-acquisition experiments will prevail in next-generation synchrotron beamlines. Orchestrating dataflow pipelines connecting the data acquisition, processing, visualization and storage ends are becoming increasingly complex and essential for enhancing beamline performance. Mamba Data Worker (MDW) has been developed to address the data challenges for the forthcoming High Energy Photon Source (HEPS). It is an important component of the Mamba experimental control and data acquisition software ecosystem, which enables fast data acquisition and transmission, dynamic configuration of data processing pipelines, data multiplex in streaming, and customized data and metadata assembly. This paper presents the architecture and development plan of MDW, outlines the essential technologies involved, and illustrates its current application at the Beijing Synchrotron Radiation Facility (BSRF).
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Recent advances in automation have fostered the development of unattended data collection services at a handful of synchrotron facilities worldwide. At the Swiss Light Source, the installation of new high-throughput sample changers at all three macromolecular crystallography beamlines and the commissioning of the Fast Fragment and Compound Screening pipeline created a unique opportunity to automate data acquisition. Here, the DA+ microservice software stack upgrades, implementation of an automatic loop-centering service and deployment of the Smart Digital User (SDU) software for unattended data collection are reported. The SDU software is the decision-making software responsible for communications between services, sample and device safety, sample centering, sample alignment with grid based X-ray diffraction and, finally, data collection.
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Combining wave optics propagation and geometric ray tracing, the mutual optical intensity (MOI) model is extended to quantitatively simulate the propagation of partially coherent light through a kinoform lens at high speed. The MOI model can provide both a high accuracy and a high efficiency simulation. The intensity and coherence degree distributions at the focal plane are calculated using the MOI model. It is beneficial to improve the focusing capability of the kinoform lens by reducing the coherence or increasing the number of lens steps. In addition, increasing the number of steps is also beneficial to increase the photon flux and reduce the depth of focus.
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In August 2021, the SOLEIL storage ring was restarted after the summer shutdown with a new bending magnet made entirely of permanent magnets. Producing a magnetic field of 2.8â T, it replaced one of the 32 electromagnetic dipoles (magnetic field of 1.7â T) of the ring to allow the ROCK beamline to exploit more intense photon fluxes in the hard X-ray range, thus improving the time resolution performances of the beamline for experiments carried out above 20â keV. The reduction of the new dipole magnetic gap required to produce the higher field has led to the construction and installation of a new vacuum vessel. The realization of the new dipole with permanent magnets was a technological feat due to the very strong magnetic forces. The permanent-magnet assembly required dedicated tools to be designed and constructed. Thanks to accurate magnetic measurements, a precise modelization of the new dipole was performed to identify its effects on the electron beam dynamics. The first measurements carried out on the ROCK beamline have highlighted the expected increase in photon flux, and the operation performances remain unchanged for the other beamlines. Here, the major developments and results of this innovative project are described in terms of technology, electron beam dynamics and photon beam performance on the ROCK beamline.