Modern Synchrotron Research Articles

Identification of chemical transformations in enamel apatite during the development of fissure caries at the nanoscale by means of synchrotron infrared nanospectroscopy: A pilot study

The spectral data sets obtained in our work using classical micro Fourier transform infrared spectroscopy (μFTIR) and modern broadband synchrotron infrared nanospectroscopy (SINS) methods, as well as their analysis and comparison with the known μFTIR spectroscopic results, provide new fundamental information on the mechanisms of pathological processes development in the carious fissure region of a human tooth at the level of enamel apatite crystallites (nano level). The infrared vibration signatures detected in our nanoscale study allowed us to establish gradient changes in chemical composition (phase transformations) occurring within the enamel roads at the level of apatite nanocrystals forming a prism, also to estimate changes in the crystallinity coefficient and the proportion of acid phosphates, as well as the depth of bacteria metabolism products (acid invasion). The results of the comparative study of this technique demonstrate that the combination of s-SNOM, IR spectroscopy and synchrotron broadband source in the SINS method provides excellent chemical sensitivity, sufficient for the providing of chemical identification of phase transformations with enhanced spatial resolution of ∼25 nm and the depth of useful signal output of several tens of nanometers. These advantages of SINS claim to be an advanced approach for investigations of objects of biological nature at a qualitatively new level.

Site-vibration assessment for the SKIF SYNCHROTRON

The Siberian ring source of photons (SKIF) is a new fourth-generation synchrotron light source currently under construction in Koltsovo city, Russia. The beam stability of modern synchrotron sources, characterized by low emittance, is sensitive to insignificant levels of ground vibrations. We assessed the seismic noise variation from external sources recorded at the construction site of the SKIF. For the frequency range 1–20 Hz, the transmission coefficients for the vertical and horizontal recording components were 0.38 and 0.725, respectively. In the frequency range 20–100 Hz – 0.12 and 0.06, respectively. Analysis of experimental data shows the effectiveness of suppressing high-amplitude external noise in the frequency range of 2-100 Hz when transmitting vibrations from the ground to the SKIF storage ring basement. The coefficients determined for the basement match well with the design model.

A novel approach using nonlinear surfaces for dynamic aperture optimization in MBA synchrotron light sources

MBA cell-based synchrotron light sources have enabled an unprecedented increase in beam coherence and brightness, greatly benefiting the scientific disciplines that rely on X-ray techniques. However, controlling the electron dynamics is a theoretical and technological challenge, due to the large number of parameters to adjust and constraints to satisfy when designing modern synchrotrons. Having versatile tools for the description and manipulation of electron dynamics could favor the design of these accelerators and lead to progress on several fronts in the understanding of matter. In this paper, a formalism based on the use of nonlinear geometric surfaces represented by polynomial quasi-invariants, to analyze and optimize the dynamic aperture of electrons in MBA storage rings, is introduced. The formalism considers on- and off-momentum particle dynamics. Within the optimization scheme, different objective functions defined in terms of the nonlinear surfaces, which are minimized using genetic algorithm methods, are proposed. A remarkable horizontal dynamic aperture exceeding 19 mm is obtained for the design particle of a synchrotron model with 86 pm ·\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\cdot $$\\end{document} rad emittance along with a dynamic aperture above 5 mm for momentum deviations of ± 3%\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\%$$\\end{document}. According to the results presented, this formalism could be greatly useful for manipulating the dynamical properties of electrons in synchrotrons light sources close to the diffraction limit.

Insight into structural biophysics from solution X-ray scattering

The current challenges of structural biophysics include determining the structure of large self-assembled complexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystallography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.

X-ray mirrors with sub-nanometre figure errors obtained by differential deposition of thin WSi2 films.

Differential deposition by DC magnetron sputtering was applied to correct for figure errors of X-ray mirrors to be deployed on low-emittance synchrotron beamlines. During the deposition process, the mirrors were moved in front of a beam-defining aperture and the required velocity profile was calculated using a deconvolution algorithm. The surface figure was characterized using conventional off-line visible-light metrology instrumentation (long trace profiler and Fizeau interferometer) before and after the deposition. WSi2 was revealed to be a promising candidate material since it conserves the initial substrate surface roughness and limits the film stress to acceptable levels. On a 300 mm-long flat Si mirror the average height errors were reduced by a factor of 20 down to 0.2 nm root mean square. This result shows the suitability of WSi2 for differential deposition. Potential promising applications include the upgrade of affordable, average-quality substrates to the standards of modern synchrotron beamlines.

Cloud–Edge Hybrid Computing Architecture for Large-Scale Scientific Facilities Augmented with an Intelligent Scheduling System

Synchrotron radiation sources are widely used in interdisciplinary research, generating an enormous amount of data while posing serious challenges to the storage, processing, and analysis capabilities of the large-scale scientific facilities worldwide. A flexible and scalable computing architecture, suitable for complex application scenarios, combined with efficient and intelligent scheduling strategies, plays a key role in addressing these issues. In this work, we present a novel cloud–edge hybrid intelligent system (CEHIS), which was architected, developed, and deployed by the Big Data Science Center (BDSC) at the Shanghai Synchrotron Radiation Facility (SSRF) and meets the computational needs of the large-scale scientific facilities. Our methodical simulations demonstrate that the CEHIS is more efficient and performs better than the cloud-based model. Here, we have applied a deep reinforcement learning approach to the task scheduling system, finding that it effectively reduces the total time required for the task completion. Our findings prove that the cloud–edge hybrid intelligent architectures are a viable solution to address the requirements and conditions of the modern synchrotron radiation facilities, further enhancing their data processing and analysis capabilities.

Vacuum chamber conditioning and saturation simulation tool (VacuumCOST): Enabling time-dependent simulations of pressure and NEG sticking in UHV chambers

Modern particle accelerators, synchrotrons, and other machines requiring UHV frequently make use of NEG coatings to achieve low pressures and resulting high beam stability and lifetime. It is the nature of NEG pumps and coatings, that a limited amount of gas can be pumped before saturation is reached, at which point the NEG must be re-activated to pump efficiently again. While the pumping mechanism and absorption limits are well understood and software packages exist for simulating the steady-state vacuum systems, there is a need for simulating the temporal evolution of the pumping capability of NEG coatings in regions of high outgassing rates such as near crotch absorbers. This paper presents a simple framework, written in Python, for running time-dependent simulations of NEG-coated vacuum systems in molecular flow, by making use of the command-line interface of the already widely used MolFlow simulation software. It also compares simulation results with accelerator pressure measurements.

Turning high-throughput structural biology into predictive inhibitor design

A common challenge in drug design pertains to finding chemical modifications to a ligand that increases its affinity to the target protein. An underutilized advance is the increase in structural biology throughput, which has progressed from an artisanal endeavor to a monthly throughput of hundreds of different ligands against a protein in modern synchrotrons. However, the missing piece is a framework that turns high-throughput crystallography data into predictive models for ligand design. Here, we designed a simple machine learning approach that predicts protein-ligand affinity from experimental structures of diverse ligands against a single protein paired with biochemical measurements. Our key insight is using physics-based energy descriptors to represent protein-ligand complexes and a learning-to-rank approach that infers the relevant differences between binding modes. We ran a high-throughput crystallography campaign against the SARS-CoV-2 main protease (MPro), obtaining parallel measurements of over 200 protein-ligand complexes and their binding activities. This allows us to design one-step library syntheses which improved the potency of two distinct micromolar hits by over 10-fold, arriving at a noncovalent and nonpeptidomimetic inhibitor with 120 nM antiviral efficacy. Crucially, our approach successfully extends ligands to unexplored regions of the binding pocket, executing large and fruitful moves in chemical space with simple chemistry.

An analytical model for fluorescent and scattering X-ray beam monitor designing

All the beamlines at modern synchrotron facilities are equipped with X-ray Beam Intensity or Position Monitors. Among those monitors, a relatively simple device is aiming at measuring the X-ray fluorescence and the X-ray scattering (elastic and inelastic) signal emitted from a thin foil with a punctual detector, a combination of several punctual detectors or a 2D detector. To improve the design of this kind of monitor, an analytical simulation has been developed to estimate the recording signal intensity according to the foil, the detector and the beam parameters. The mains X-ray interaction with matter processes involved in these monitors are simulated and several parameters of the incident X-ray beam are taken into account such as its intensity, energy, size and polarization. Furthermore, in contrast to the complex and time-consuming Monte-Carlo method, this analytical simulation is performed in few seconds and is implemented in a user-friendly interface. In order to validate our tool, the simulated results were compared to a series of measurements performed on the METROLOGIE beamline of the SOLEIL synchrotron. The differences with the experimental results are less than 30% by using a metallic foil and less than 50% with a Kapton® foil. The performances of our tool in term of accuracy, computation time and ease of use are perfectly adapted for the design of X-ray monitors based on an X-ray fluorescence and scattering foil.

Использование метода синхротронной компьютерной ламинографии при изучении особенностей строения металлических сплавов (обзор исследований)

The paper contains a review of research related to the use of synchrotron radiation computed laminography in the study of the structure features of metal alloys subjected to various methods of external action. Introduction. The important role of X-rays in the field of materials research is discussed. The capabilities of standard X-ray devices equipped with X-ray tubes and modern synchrotron radiation (SR) sources with unique parameters are compared. Methods for studying flat samples. Tomography and synchrotron laminography. An informative method based on the use of synchrotron X-rays is synchrotron radiation computed tomography (SRCT), which allows obtaining cross-section images of objects by processing multiple absorption radiographs. A brief classification of five generations of tomographs is presented. The problems encountered in obtaining data from non-compact (non-isometric) samples are avoided by using the method of synchrotron radiation computed laminography (SRCL), which combines the principles of laminography with the advantages of synchrotron imaging. Currently the method is used for non-destructive testing of non-isometric objects by a number of synchrotron radiation sources (ESRF, ANKA, Spring-8). Resolution of synchrotron radiation computed laminography. The use of monochromatic radiation in realization of computed laminography method is a factor, which provides high spatial resolution down to micron and submicron scale. An equally important factor is related to the characteristics of the detector. Images with a resolution of ~100 nm were obtained using nanolaminography. Comparison of laminography and tomography methods. Augmented laminography. Augmented laminography allows improving image quality by augmenting the Fourier space analyzed by laminography with information obtained from lower resolution CT. Reconstruction performed using Augmented laminography is characterized by the absence of significant artifacts and high resolution. Implementation of the laminography method. The angle of inclination of the rotary axis θ (SRCL method) is related to the geometry of samples and is determined experimentally in each case. In order to achieve the necessary resolution, the value θ should provide an optimal average value of the intensity of the passed radiation. The energy of X-rays is calculated on the basis of material characteristics. To reconstruct images of the objects, software complexes that implement the filtered back projection method based on the Radon transform are used. Examples of laminography application for analysis of metal alloys samples. The laminography method can be used for in-situ investigations allowing real time monitoring of processes occurring under different conditions of external action, e.g. during plastic deformation of metal plates. Data on formation of pore-type defects in the process of loading of metal workpieces are interesting. Numerous examples of post-mortem studies of metal alloys for various purposes are described in the literature. Important information is obtained in the study of fatigue cracks, as well as defects arising in the process of contact-fatigue loading of materials. Conclusion. The SRCT and SRCL methods are rationally implemented at the generation 4+ synchrotron radiation source “SKIF” under construction in Novosibirsk.

Physical optics simulations for synchrotron radiation sources.

We describe approaches to high-accuracy physical optics calculations used for the development of x-ray beamlines at synchrotron radiation sources, as well as simulation of experiments and processing of experimental data at some of these beamlines. We pay special attention to the treatment of the partial coherence of x rays, a topic of high practical importance for modern low-emittance high-brightness synchrotron radiation facilities. The approaches are based, to a large extent, on the works of Emil Wolf and co-authors, including the basic scalar diffraction theory and the coherent mode decomposition method. The presented simulation examples are related to the case of the novel Coherent Diffractive Imaging beamline that is currently under development at the National Synchrotron Light Source II at the Brookhaven National Laboratory.

Beamline-implemented stretching devices for in situ X-ray scattering experiments

Two recently developed experimental devices for investigating soft matter deformation are presented. Both devices exploit the capabilities of a modern synchrotron beamline to enable advanced and highly precise materials-science experiments in which X-ray scattering is registered. The devices can be operated both in monotonic as well as cyclic mode and are implemented into a beamline at DESY, Hamburg (Germany). Hence, relevant experimental parameters, such as displacement, force and temperature, are recorded synchronously with the individual X-ray scattering patterns. In addition, spatial variation of materials deformation can be monitored and recorded with optical microscopy. This unique sample environment enables in situ X-ray experiments in transmission, i.e. small- or wide-angle X-ray scattering (SAXS or WAXS), and in grazing-incidence geometry, i.e. grazing-incidence (GI-) SAXS or WAXS. One device with stepper motors is designed for studies of slow, (quasi-) static deformation and the other one with pneumatic actuators can be used for fast, impact deformation. Both devices are available to external beamline users, too.

Time-Delayed Magnetic Control of X-ray Spectral Enhancement in Two-Target Nuclear Forward Scattering

Controlling and narrowing x-ray frequency spectra in magnetically perturbed two-target nuclear forward scattering is theoretically studied. We show that different hard-x-ray spectral redistributions can be achieved by single or multiple switching of magnetic field in nuclear targets. Our scheme can generate x-ray spectral lines with tenfold intensity enhancement and spectral width narrower than four times the nuclear natural linewidth. The present results pave the way towards a brighter and flexible x-ray source for precision spectroscopy of nuclear resonances using modern synchrotron radiation.

Measuring Magnetic Excitation Spectra Using Resonant Inelastic X-ray Scattering

The advent of modern synchrotron radiation facilities providing extremely intense x-rays has enabled measuring momentum-resolved spin excitation spectra of magnetic materials, which have long been exclusively accessible through inelastic neutron scattering. In this article, we briefly review the recent development of hard x-ray resonant inelastic x-ray scattering (RIXS) and discuss few examples of RIXS measurements on iridium oxides.

Broad band waveguide to coaxial transition for HOM suppression in RF cavities for future synchrotron light sources

In the modern storage ring light sources, exploiting multi-bunch beams, the longitudinal and transverse coupled bunch instabilities are predominantly driven by higher order modes (HOM) of the accelerator RF cavities. In order to suppress the HOM to a harmless level, we propose using a modified broadband waveguide to coaxial line transitions placed on the cavity body, similar to those used for the DAΦNE collider RF cavities. Such a solution has a simple design that avoids the application of the ferrite materials under the ultra-high vacuum and dissipates the HOM power on the external loadings. Different from DAΦNE with a single cavity per ring, where the damping waveguides are placed laterally on the cavity body, we consider the possibility of allocating the waveguides vertically. Since the modern synchrotron light sources require using more RF cavities to compensate for the synchrotron radiation losses, such a solution helps to save the occupied space when placing the cavities in a row next to each other. This paper describes the design optimization process and discusses the obtained results concerning the effectiveness of the HOM suppression and minimization of the impact of the transitions on the fundamental mode parameters.

TimeMaxyne: A Shot-Noise Limited, Time-Resolved Pump-and-Probe Acquisition System Capable of 50 GHz Frequencies for Synchrotron-Based X-ray Microscopy

With the advent of modern synchrotron sources, X-ray microscopy was developed as a vigorous tool for imaging material structures with element-specific, structural, chemical and magnetic sensitivity at resolutions down to 25 nm and below. Moreover, the X-ray time structure emitted from the synchrotron source (short bunches of less than 100 ps width) provides a unique possibility to combine high spatial resolution with high temporal resolution for periodic processes by means of pump-and-probe measurements. To that end, TimeMaxyne was developed as a time-resolved acquisition setup for the scanning X-ray microscope MAXYMUS at the BESSY II synchrotron in order to perform high precision, high throughput pump-and-probe imaging. The setup combines a highly sensitive single photon detector, a real time photon sorting system and a dedicated synchronization scheme for aligning various types of sample excitations of up to 50 GHz bandwidth to the photon probe. Hence, TimeMaxyne has been demonstrated to be capable of shot-noise limited, time-resolved imaging, at time resolutions of 50 ps and below, only limited by the X-ray pulse widths of the synchrotron.

Revealing dynamic processes in laser powder bed fusion with in situ X-ray diffraction at PETRA III.

The high flux combined with the high energy of the monochromatic synchrotron radiation available at modern synchrotron facilities offers vast possibilities for fundamental research on metal processing technologies. Especially in the case of laser powder bed fusion (LPBF), an additive manufacturing technology for the manufacturing of complex-shaped metallic parts, in situ methods are necessary to understand the highly dynamic thermal, mechanical, and metallurgical processes involved in the creation of the parts. At PETRA III, Deutsches Elektronen-Synchrotron, a customized LPBF system featuring all essential functions of an industrial LPBF system, is used for in situ x-ray diffraction research. Three use cases with different experimental setups and research questions are presented to demonstrate research opportunities. First, the influence of substrate pre-heating and a complex scan pattern on the strain and internal stress progression during the manufacturing of Inconel 625 parts is investigated. Second, a study on the nickel-base superalloy CMSX-4 reveals the formation and dissolution of γ' precipitates depending on the scan pattern in different part locations. Third, phase transitions during melting and solidification of an intermetallic γ-TiAl based alloy are examined, and the advantages of using thin platelet-shaped specimens to resolve the phase components are discussed. The presented cases give an overview of in situ x-ray diffraction experiments at PETRA III for research on the LPBF technology and provide information on specific experimental procedures.

X-ray beam monitoring and wavelength calibration using four-beam diffraction.

Rigorous dynamical theory calculations show that four-beam diffraction (4BD) can be activated only by a unique photon energy and a unique incidence direction. Thus, 4BD may be used to precisely calibrate X-ray photon energies and beam positions. Based on the principles that the forbidden-reflection 4BD pattern, which is typically an X-shaped cross, can be generated by instant imaging using the divergent beam from a point source without rocking the crystal, a detailed real-time high-resolution beam (and source) position monitoring scheme is illustrated for monitoring two-dimensional beam positions and directions of modern synchrotron light sources, X-ray free-electron lasers and nano-focused X-ray sources.

Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking.

In recent years, crystallographic fragment screening has matured into an almost routine experiment at several modern synchrotron sites. The hits of the screening experiment, i.e. small molecules or fragments binding to the target protein, are revealed along with their 3D structural information. Therefore, they can serve as useful starting points for further structure-based hit-to-lead development. However, the progression of fragment hits to tool compounds or even leads is often hampered by a lack of chemical feasibility. As an attractive alternative, compound analogs that embed the fragment hit structurally may be obtained from commercial catalogs. Here, a workflow is reported based on filtering and assessing such potential follow-up compounds by template docking. This means that the crystallographic binding pose was integrated into the docking calculations as a central starting parameter. Subsequently, the candidates are scored on their interactions within the binding pocket. In an initial proof-of-concept study using five starting fragments known to bind to the aspartic protease endothiapepsin, 28 follow-up compounds were selected using the designed workflow and their binding was assessed by crystallography. Ten of these compounds bound to the active site and five of them showed significantly increased affinity in isothermal titration calorimetry of up to single-digit micromolar affinity. Taken together, this strategy is capable of efficiently evolving the initial fragment hits without major synthesis efforts and with full control by X-ray crystallography.

On-axis sample viewer with flexible working distance for an X-ray spectroscopy beamline.

Conducting research using micrometer-sized X-ray beams with small samples is common at modern synchrotron X-ray sources. Often, the relative alignment between the X-ray beam and sample is time consuming. An on-axis or coaxial camera system with a view of the sample in a direction along the path of the X-ray beam with its depth of field set to coincide with the location of the focal spot of the X-ray beam is preferred. Besides the use of a drilled mirror, I propose the use of a Pellicle mirror to create an on-axis viewer that allows various sample environments and X-ray beam sizes.