X-ray Free-electron Laser Sources Research Articles

Tracking structural solvent reorganization and recombination dynamics following e- photoabstraction from aqueous I- with femtosecond x-ray spectroscopy and scattering.

We present a sub-picosecond resolved investigation of the structural solvent reorganization and geminate recombination dynamics following 400nm two-photon excitation and photodetachment of a valence p electron from the aqueous atomic solute, I-(aq). The measurements utilized time-resolved X-ray Absorption Near Edge Structure (TR-XANES) spectroscopy and X-ray Solution Scattering (TR-XSS) at the Linac Coherent Light Source x-ray free electron laser in a laser pump/x-ray probe experiment. The XANES measurements around the L1-edge of the generated nascent iodine atoms (I0) yield an average electron ejection distance from the iodine parent of 7.4 ± 1.5 Å with an excitation yield of about 1/3 of the 0.1M NaI aqueous solution. The kinetic traces of the XANES measurement are in agreement with a purely diffusion-driven geminate iodine-electron recombination model without the need for a long-lived (I0:e-) contact pair. Nonequilibrium classical molecular dynamics simulations indicate a delayed response of the caging H2O solvent shell and this is supported by the structural analysis of the XSS data: We identify a two-step process exhibiting a 0.1ps delayed solvent shell reorganization time within the tight H-bond network and a 0.3ps time constant for the mean iodine-oxygen distance changes. The results indicate that most of the reorganization can be explained classically by a transition from a hydrophilic cavity with a well-ordered first solvation shell (hydrogens pointing toward I-) to an expanded cavity around I0 with a more random orientation of the H2O molecules in a broadened first solvation shell.

14th International Conference on Synchrotron Radiation Instrumentation (SRI 2021), 28 March to 1 April 2022

The International Conference on Synchrotron Radiation Instrumentation (SRI) is a unique and significant international forum held every three years in the community of synchrotron radiation (SR) and free electron lasers (FEL). It is the prime forum for fostering connections between cutting-edge synchrotron radiation instrumentation, science, and the requirements of the user community. The SRI 2021 had originally been scheduled to take place in Hamburg in summer 2021. Due to the COVID-19 pandemic, it was postponed to 2022 and held as an online event.More than 1160 international participants from 25 countries met virtually at the SRI 2021. In nearly 290 talks and 450 posters, latest results were presented. Although it was an online-only conference, lively discussions took place in the nearly 40 parallel sessions, and the eight poster sessions were also very well attended.The main topics of the SRI conference were: new SR and FEL facilities, update plans of these facilities, and recent developments in various instrumentation areas like beamline design, X-ray optics, sample environments, detectors and spectrometers, data acquisition, and data analysis techniques or automation. These innovations contributed to new results for a wide range of experimental techniques and scientific applications such as X-ray scattering and spectroscopy, bio- and scanning imaging, structural biology crystallography, coherent techniques, or in-situ/operando methods. A dedicated session concerned industrial applications of synchrotron radiation.The field of synchrotron radiation instrumentation is currently seeing very active development due to various factors. Firstly, the number of SR sources world-wide is increasing significantly, with new sources in particular in Europe and in Asia. Secondly, a new generation of storage rings with new multi-bend achromat lattices are being implemented at a growing number of existing facilities. These facilities offer a significant increase of brilliance and coherence and thereby lead to new and improved applications of synchrotron radiation, in particular in the areas of imaging and high spatial resolution. Thirdly, the increase of soft and hard X-ray FEL sources worldwide and the maturation of their experimental techniques and scientific applications is the background for a strongly increasing number of developments for ultrafast time-resolved investigations of dynamic behaviour of materials and reactions. Most of the keynote speakers and many invited and contributed talks or posters at the conference showed new results directly related to these three major developments.Lists of International Advisory Committee (listed by facility), Scientific Programme Committee (listed by facility), Local Organising Committee (listed by facility) are available in this PDF.

Wall-free droplet microfluidics for probing biological processes by high-brilliance X-ray scattering techniques.

Here we review probing biological processes initiated by the deposition of droplets on surfaces by micro- and nanobeam X-ray scattering techniques using synchrotron radiation and X-ray free-electron laser sources. We review probing droplet evaporation on superhydrophobic surfaces and reactions with substrates, basics of droplets deposition and flow simulations, droplet deposition techniques and practical experience at a synchrotron beamline. Selected applications with biological relevance will be reviewed and perspectives for the latest generation of high-brilliance X-ray sources discussed.

Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties.

The unprecedented intensity of x-ray free-electron laser sources has enabled single-particle x-ray diffraction imaging (SPI) of various biological specimens in both two-dimensional projection and three dimensions (3D). The potential of studying protein dynamics in their native conditions, without crystallization or chemical staining, has encouraged researchers to aim for increasingly higher resolutions with this technique. The currently achievable resolution of SPI is limited to the sub-10 nanometer range, mainly due to background effects, such as instrumental noise and parasitic scattering from the carrier gas used for sample delivery. Recent theoretical studies have quantified the effects of x-ray pulse parameters, as well as the required number of diffraction patterns to achieve a certain resolution, in a 3D reconstruction, although the effects of detector noise and the random particle orientation in each diffraction snapshot were not taken into account. In this work, we show these shortcomings and address limitations on achievable image resolution imposed by the adaptive gain integrating pixel detector noise.

Fast wavefront sensing for X-ray optics with an alternating speckle tracking technique.

Advances in accelerator technologies have enabled the continuous development of synchrotron radiation and X-ray free electron laser (XFEL) sources. At the same time, it has been critical to perform in-situ wavefront sensing to aid delivery of high-quality X-ray beams to the end users of these facilities. The speckle-based scanning technique has obtained popularity due to its high spatial resolution and superior sensitivity compared to other wavefront sensing methods. However, these advantages often come at the expense of longer data acquisition times since multiple images have to be collected to derive the necessary wavefront information. Whereas initial speckle tracking techniques could obtain wavefront information relatively quickly, the installation of additional hardware was routinely required to do so. Here, we propose a novel speckle-based approach, termed Alternating Speckle Tracking (AST), to perform fast wavefront sensing within a conventional beamline setup. The wavefront information derived from the new technique has proven to be valuable for many applications that require temporal resolution. Importantly, both horizontal and vertical wavefront information can be simultaneously derived by moving the speckle generator along the diagonal direction. We expect this method will be widely used by the synchrotron radiation and XFEL community in the future.

Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers

The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX.

Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning

Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II (PSII). However, due to the incoherent transition of the S-states, the resolved structures are a convolution from different catalytic states. Here, we train Decision Tree Classifier and K-means clustering models on Mn compounds obtained from the Cambridge Crystallographic Database to predict the S-state of the X-ray, XFEL, and CryoEM structures by predicting the Mn’s oxidation states in the oxygen-evolving complex. The model agrees mostly with the XFEL structures in the dark S1 state. However, significant discrepancies are observed for the excited XFEL states (S2, S3, and S0) and the dark states of the X-ray and CryoEM structures. Furthermore, there is a mismatch between the predicted S-states within the two monomers of the same dimer, mainly in the excited states. We validated our model against other metalloenzymes, the valence bond model and the Mn spin densities calculated using density functional theory for two of the mismatched predictions of PSII. The model suggests designing a more optimized sample delivery and illumiation systems are crucial to precisely resolve the geometry of the advanced S-states to overcome the noncoherent S-state transition. In addition, significant radiation damage is observed in X-ray and CryoEM structures, particularly at the dangler Mn center (Mn4). Our model represents a valuable tool for investigating the electronic structure of the catalytic metal cluster of PSII to understand the water splitting mechanism.

Automated matching of two-time X-ray photon correlation maps from phase-separating proteins with Cahn-Hilliard-type simulations using auto-encoder networks.

Machine learning methods are used for an automated classification of experimental two-time X-ray photon correlation maps from an arrested liquid-liquid phase separation of a protein solution. The correlation maps are matched with correlation maps generated with Cahn-Hilliard-type simulations of liquid-liquid phase separations according to two simulation parameters and in the last step interpreted in the framework of the simulation. The matching routine employs an auto-encoder network and a differential evolution based algorithm. The method presented here is a first step towards handling large amounts of dynamic data measured at high-brilliance synchrotron and X-ray free-electron laser sources, facilitating fast comparison with phase field models of phase separation.

Shot-to-shot two-dimensional photon intensity diagnostics within megahertz pulse-trains at the European XFEL.

Characterizing the properties of X-ray free-electron laser (XFEL) sources is a critical step for optimization of performance and experiment planning. The recent availability of MHz XFELs has opened up a range of new opportunities for novel experiments but also highlighted the need for systematic measurements of the source properties. Here, MHz-enabled beam imaging diagnostics developed for the SPB/SFX instrument at the European XFEL are exploited to measure the shot-to-shot intensity statistics of X-ray pulses. The ability to record pulse-integrated two-dimensional transverse intensity measurements at multiple planes along an XFEL beamline at MHz rates yields an improved understanding of the shot-to-shot photon beam intensity variations. These variations can play a critical role, for example, in determining the outcome of single-particle imaging experiments and other experiments that are sensitive to the transverse profile of the incident beam. It is observed that shot-to-shot variations in the statistical properties of a recorded ensemble of radiant intensity distributions are sensitive to changes in electron beam current density. These changes typically occur during pulse-distribution to the instrument and are currently not accounted for by the existing suite of imaging diagnostics. Modulations of the electron beam orbit in the accelerator are observed to induce a time-dependence in the statistics of individual pulses - this is demonstrated by applying radio-frequency trajectory tilts to electron bunch-trains delivered to the instrument. We discuss how these modifications of the beam trajectory might be used to modify the statistical properties of the source and potential future applications.

X-ray free-electron laser based dark-field X-ray microscopy: a simulation-based study

Dark-field X-ray microscopy (DFXM) is a nondestructive full-field imaging technique providing three-dimensional mapping of microstructure and local strain fields in deeply embedded crystalline elements. This is achieved by placing an objective lens in the diffracted beam, giving a magnified projection image. So far, the method has been applied with a time resolution of milliseconds to hours. In this work, the feasibility of DFXM at the picosecond time scale using an X-ray free-electron laser source and a pump–probe scheme is considered. Thermomechanical strain-wave simulations are combined with geometrical optics and wavefront propagation optics to simulate DFXM images of phonon dynamics in a diamond single crystal. Using the specifications of the XCS instrument at the Linac Coherent Light Source as an example results in simulated DFXM images clearly showing the propagation of a strain wave.

Capturing Atom-Specific Electronic Structural Dynamics of Transition-Metal Complexes with Ultrafast Soft X-Ray Spectroscopy.

The atomic specificity of X-ray spectroscopies provides a distinct perspective on molecular electronic structure. For 3d metal coordination and organometallic complexes, the combination of metal- and ligand-specific X-ray spectroscopies directly interrogates metal-ligand covalency-the hybridization of metal and ligand electronic states. Resonant inelastic X-ray scattering (RIXS), the X-ray analog of resonance Raman scattering, provides access to all classes of valence excited states in transition-metal complexes, making it a particularly powerful means of characterizing the valence electronic structure of 3d metal complexes. Recent advances in X-ray free-electron laser sources have enabled RIXS to be extended to the ultrafast time domain. We review RIXS studies of two archetypical photochemical processes: charge-transfer excitation in ferricyanide and ligand photodissociation in iron pentacarbonyl. These studies demonstratefemtosecond-resolution RIXS can directly characterize the time-evolving electronic structure, including the evolution of the metal-ligand covalency.

Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light.

Directly observing enzyme catalysis in real time at the molecular level has been a long-standing goal of structural enzymology. Time-resolved serial crystallography methods at synchrotron and X-ray free electron laser (XFEL) sources have enabled researchers to follow enzyme catalysis and other nonequilibrium events at ambient conditions with unprecedented time resolution. X-ray crystallography provides detailed information about conformational heterogeneity and protein dynamics, which is enhanced when time-resolved approaches are used. This review outlines the ways in which information about the underlying energy landscape of a protein can be extracted from X-ray crystallographic data, with an emphasis on new developments in XFEL and synchrotron time-resolved crystallography. The emerging view of enzyme catalysis afforded by these techniques can be interpreted as enzymes moving on a time-dependent energy landscape. Some consequences of this view are discussed, including the proposal that irreversible enzymes or enzymes that use covalent catalytic mechanisms may commonly exhibit catalysis-activated motions.

Inner shell excitation by strong field laser rescattering: optimal laser conditions for high energy recollision

We address the challenge of finding the optimal laser intensity and wavelength to drive high-energy, strong field rescattering and report the maximum yields of K-shell and L I -shell hole creation. Surprisingly, our results show laser-driven rescattering is able to create inner shell holes in all atoms from lithium to uranium with the interaction spanning from the deep IR to x-ray free electron laser sources. The calculated peak rescattering follows a simple scaling with the atomic number and laser wavelength. The results show it is possible to describe the ideal laser intensity and wavelength for general high-energy laser rescattering processes.

Generation of highly mutually coherent hard-x-ray pulse pairs with an amplitude-splitting delay line

Beam splitters and delay lines are among the key building blocks of modern-day optical laser technologies. Progress in x-ray free electron laser source development and applications over the past decade is calling for their counter part operating in the Angstrom wavelength regime. Recent efforts in x-ray optics development have demonstrated relatively stable delay lines that most often adopted the division of wavefront approach for the beam splitting and recombination configuration. However, the two recombined beams have yet to achieve sufficient mutual coherence to enable applications such as interferometry, correlation spectroscopy, and nonlinear spectroscopy. We present the first experimental realization of the generation of highly mutually coherent pulse pairs using an amplitude-split delay line design based on transmission grating beam splitters and channel-cut crystal optic delay lines. The performance of the prototype system was analyzed in the context of x-ray coherent scattering and correlation spectroscopy, where we obtained nearly identical high-contrast speckle patterns from both branches. We show in addition the high level of dynamical stability during continuous delay scans, a capability essential for high sensitivity ultra-fast measurements.

Data reduction for serial crystallography using a robust peak finder.

A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of 'robust statistics' has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or 'vetoing' of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.

Advances and challenges in time-resolved macromolecular crystallography.

Conformational changes within biological macromolecules control a vast array of chemical reactions in living cells. Time-resolved crystallography can reveal time-dependent structural changes that occur within protein crystals, yielding chemical insights in unparalleled detail. Serial crystallography approaches developed at x-ray free-electron lasers are now routinely used for time-resolved diffraction studies of macromolecules. These techniques are increasingly being applied at synchrotron radiation sources and to a growing diversity of macromolecules. Here, we review recent progress in the field, including visualizing ultrafast structural changes that guide the initial trajectories of light-driven reactions as well as capturing biologically important conformational changes on slower time scales, for which bacteriorhodopsin and photosystem II are presented as illustrative case studies.

Bright future ahead for crystallography

Structural Biology Macromolecular x-ray crystallography typically provides static snapshots of systems at equilibrium. Advances in time-resolved crystallography have made it possible to capture dynamics in biomolecules: large and small, fast and slow. Brändén and Neutze review techniques and concepts that have emerged from recent work at x-ray free electron laser sources and are now being applied in other settings and to a growing number of biological systems. Despite challenges in analyzing and relating these data to a biological context, experiments in this field have opened new frontiers in temporal and spatial resolution and yielded many new insights into nonequilibrium chemistry and conformational changes in biology. Science , aba0954, this issue p. [eaba0954][1] [1]: /lookup/doi/10.1126/science.aba0954

Medium-temperature furnace baking of 1.3 GHz 9-cell superconducting cavities at IHEP

Recently, heat treatment in the range of 250 °C–500 °C has been attempted with the aim of improving the quality factor (Q) of superconducting radio-frequency (SRF) cavities worldwide. Herein, medium-temperature (mid-T) furnace baking experiments were conducted at the Institute of High Energy Physics to obtain higher Q values. First, 1.3 GHz 1-cell cavities received mid-T furnace baking at different temperatures, resulting in not only the improvement of Q but also an anti-Q-slope behavior. Furthermore, mid-T furnace baking was applied to six 1.3 GHz 9-cell cavities, all of which indicated higher Q and anti-Q-slope behavior. The average Q was 3.8 × 1010 at 16 MV m−1. The maximum gradients of the 9-cell cavities were 22.7–26.5 MV m−1. Finally, the mid-T furnace baked 1.3 GHz 9-cell cavities were welded with helium vessel, with no degradation in the vertical tests. In addition, the mid-T furnace baking process was simplified in comparison with European X-ray Free Electron Laser and Linear Coherent Light Source because of the cancellation of light electro-polishing. This simplification is beneficial in the mass production of SRF cavities with high Q, which are widely adopted in free electron lasers and high-energy colliders.

Nonuniform Flow Dynamics Probed by Nanosecond X-Ray Speckle Visibility Spectroscopy.

We report observations of nanosecond nonuniform colloidal dynamics in a free flowing liquid jet using ultrafast x-ray speckle visibility spectroscopy. Utilizing a nanosecond double-bunch mode, the Linac Coherent Light Source free electron laser produced pairs of femtosecond coherent hard x-ray pulses. By exploring anisotropy in the visibility of summed speckle patterns which relates to the correlation functions, we evaluate not only the average particle flow rate in a colloidal nanoparticle jet, but also the nonuniform flow field within. The methodology presented here establishes the foundation for the study of nano- and atomic-scale inhomogeneous fluctuations in complex matter using x-ray free electron laser sources.

Approach of Serial Crystallography II

Serial crystallography (SX) is an emerging X-ray crystallographic method for determining macromolecule structures. It can address concerns regarding the limitations of data collected by conventional crystallography techniques, which require cryogenic-temperature environments and allow crystals to accumulate radiation damage. Time-resolved SX studies using the pump-probe methodology provide useful information for understanding macromolecular mechanisms and structure fluctuation dynamics. This Special Issue deals with the serial crystallography approach using an X-ray free electron laser (XFEL) and synchrotron X-ray source, and reviews recent SX research involving synchrotron use. These reports provide insights into future serial crystallography research trends and approaches.