X-ray Free-electron Laser Experiments Research Articles

Real-time analysis of liquid jet sample delivery stability for an X-ray free-electron laser using machine vision

Automated evaluation of optical microscopy images of liquid jets, commonly used for sample delivery at X-ray free-electron lasers (XFELs), enables real-time tracking of the jet position and liquid jet hit rates, defined here as the proportion of XFEL pulses intersecting with the liquid jet. This method utilizes machine vision for preprocessing, feature extraction, segmentation and jet detection as well as tracking to extract key physical characteristics (such as the jet angle) from optical microscopy images captured during experiments. To determine the effectiveness of these tools in monitoring jet stability and enhancing sample delivery efficiency, we conducted XFEL experiments with various sample compositions (pure water, buffer and buffer with crystals), nozzle designs and jetting conditions. We integrated our real-time analysis algorithm into the Karabo control system at the European XFEL. The results indicate that the algorithm performs well in monitoring the jet angle and provides a quantitative characterization of liquid jet stability through optical image analysis conducted during experiments.

Green upgrading of SPring-8 to produce stable, ultrabrilliant hard X-ray beams.

SPring-8-II is a major upgrade project of SPring-8 that was inaugurated in October 1997 as a third-generation synchrotron radiation light source. This upgrade project aims to achieve three goals simultaneously: achievement of excellent light source performance, refurbishment of aged systems, and significant reduction in power consumption for the entire facility. A small emittance of 50 pm rad will be achieved by (1) replacing the existing double-bend lattice structure with a five-bend achromat one, (2) lowering the stored beam energy from 8 to 6 GeV, (3) increasing the horizontal damping partition number from 1to 1.3, and (4) enhancing horizontal radiation damping by installing damping wigglers in long straight sections. The use of short-period in-vacuum undulators allows ultrabrilliant X-rays to be provided while keeping a high-energy spectral range even at the reduced electron-beam energy of 6 GeV. To reduce power consumption, the dedicated, aged injector system has been shut down and the high-performance linear accelerator of SACLA, a compact X-ray free-electron laser (XFEL) facility, is used as the injector of the ring in a time-shared manner. This allows the simultaneous operation of XFEL experiments at SACLA and full/top-up injection of the electron beam into the ring. This paper overviews the concept of the SPring-8-II project, the system design of the light source and the details of the accelerator component design.

Measurement bias in self-heating x-ray free electron laser experiments from diffraction studies of phase transformation in titanium

X-ray self-heating is a common by-product of X-ray Free Electron Laser (XFEL) techniques that can affect targets, optics, and other irradiated materials. Diagnosis of heating and induced changes in samples may be performed using the x-ray beam itself as a probe. However, the relationship between conditions created by and inferred from x-ray irradiation is unclear and may be highly dependent on the material system under consideration. Here, we report on a simple case study of a titanium foil irradiated, heated, and probed by a MHz XFEL pulse train at 18.1 keV delivered by the European XFEL using measured x-ray diffraction to determine temperature and finite element analysis to interpret the experimental data. We find a complex relationship between apparent temperatures and sample temperature distributions that must be accounted for to adequately interpret the data, including beam averaging effects, multivalued temperatures due to sample phase transitions, and jumps and gaps in the observable temperature near phase transformations. The results have implications for studies employing x-ray probing of systems with large temperature gradients, particularly where these gradients are produced by the beam itself. Finally, this study shows the potential complexity of studying nonlinear sample behavior, such as phase transformations, where biasing effects of temperature gradients can become paramount, precluding clear observation of true transformation conditions.

Acceleration of flow-focused liquid jets in the presence of a strong electric field

This paper investigates the acceleration of flow-focused micro-jets under an applied external electric field. Such thin and fast jets are needed, for example, to deliver protein crystals in X-ray free electron laser experiments. This contribution focuses on analysing the acceleration of liquid jets produced from 50 % vol water and ethanol mixture. Such jets are focused with nitrogen gas and are subjected to 0 - 7 kV electric potential between a submerged electrode and an external electrode downstream of the nozzle. To gain insights into jet geometric properties an automatic image recognition and computer vision algorithm is utilised on already published data. Jet velocities and acceleration calculated for two jetting regimes show that application of external electric field accelerates the jets up to four orders of magnitude larger than the conventional micro-jets.

Numerical simulations of temperature loads on multilayer Laue lenses

We present numerical simulations of the heat loads on novel diffractive X-ray optics, known as multilayer Laue lenses, exposed to high-intensity X-ray beams produced by an X-ray free electron laser (XFEL). These lenses can be used to focus XFEL beams to nanometer spots. The temperature distribution within the lens and temperature evolution as a function of incident pulse frequencies were calculated for two different lens geometries and several material pairs and material ratios of the MLLs. Simulations considered the special pulse structure of European XFEL with X-rays being delivered in pulse trains. After defining the geometric model, computational grid, material properties, and boundary conditions, a grid sensitivity study was carried out. We solved the transient heat energy transport equation in solids for mixed boundary conditions. The results of these simulations will help select materials and lens geometry for future XFEL experiments.

Deep residual networks for crystallography trained on synthetic data.

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

Development of spinning-disk solid sample delivery system for high-repetition rate x-ray free electron laser experiments.

X-ray free-electron lasers (XFELs) deliver intense x-ray pulses that destroy the sample in a single shot by a Coulomb explosion. Experiments using XFEL pulse trains or the new generation of high-repetition rate XFELs require rapid sample replacement beyond those provided by the systems now used at low repletion-rate XFELs. We describe the development and characterization of a system based on a spinning disk to continuously deliver a solid sample into an XFEL interaction point at very high speeds. We tested our system at the Linac Coherent Light Source and European XFEL hard x-ray nano-focus instruments, employing it to deliver a 25 μm copper foil sample, which can be used as a gain medium for stimulated x-ray emission for the proposed x-ray laser oscillator.

Target Design for XFEL Experiments

High-energy-density (HED) experiments utilizing X-ray free electron lasers (XFELs) must take a different approach to fielding these experiments than the current methodology used for the large HED facilities in the United States. The XFELs and their associated laser drivers have a much faster repetition rate than do the larger facilities. Experiments must be designed to execute hundreds rather than a few shots per experimental run. The new paradigm requires a different approach to data collection and analysis. It also requires an integrated approach to experiment and target design. In this study, we developed new target designs for a future XFEL experiment that meet both experiment and cost goals.

Relaxation of Ne1+ 1s02s22p6 np produced by resonant excitation of an ultraintense ultrafast x-ray pulse

The creation and relaxation of double K-hole states 1s02s22p6 np (n ≥ 3) of Ne1+ in the interaction with ultraintense ultrafast x-ray pulses are theoretically investigated. The x-ray photon energies are selected so that x-rays first photoionize 1s22s22p6 of a neon atom to create a single K-hole state of 1s2s2p6 of Ne1+, which is further excited resonantly to double K-hole states of 1s02s22p6 np (n ≥ 3). A time-dependent rate equation is used to investigate the creation and relaxation processes of 1s02s22p6 np, where the primary microscopic atomic processes including photoexcitation, spontaneous radiation, photoionization and Auger decay are considered. The calculated Auger electron energy spectra are compared with recent experimental results, which shows good agreement. The relative intensity of Auger electrons is very sensitive to the photon energy and bandwidth of x-ray pulses, which could be used as a diagnostic tool for x-ray free electron laser and atom experiments.

Multiparticle Cumulant Mapping for Coulomb Explosion Imaging.

We extend covariance velocity map ion imaging to four particles, establishing cumulant mapping and allowing for measurements that provide insights usually associated with coincidence detection, but at much higher count rates. Without correction, a fourfold covariance analysis is contaminated by the pairwise correlations of uncorrelated events, but we have addressed this with the calculation of a full cumulant, which subtracts pairwise correlations. We demonstrate the approach on the four-body breakup of formaldehyde following strong field multiple ionization in few-cycle laser pulses. We compare Coulomb explosion imaging for two different pulse durations (30 and 6fs), highlighting the dynamics that can take place on ultrafast timescales. These results have important implications for Coulomb explosion imaging as a tool for studying ultrafast structural changes in molecules, a capability that is especially desirable for high-count-rate x-ray free-electron laser experiments.

Damage-Free Femtosecond X-Ray Laser Snapshot Imaging of Catalyst Layer Nano-Structures of Polymer Electrolyte Fuel Cells

The realization of the hydrogen society, where hydrogen is used as clean and renewable energy, is desired to reduce carbon dioxide emissions and achieve sustainable development. The polymer electrolyte fuel cell (PEFC) is a key technology for automobiles in the hydrogen society as an alternative to conventional internal combustion engines. However, further improvements in PEFC performances are required for the full-scale spread of fuel cell vehicles. This study aims to image the nanostructures of the catalyst layer, which is particularly important in determining the performance of PEFCs, and correlate the observed structures with mass transfer in the catalyst layer. The catalyst layer contains catalyst-loaded carbon supports thinly covered with an ionomer responsible for proton conduction. We are especially interested in observing the support structure and ionomer coverage.We performed coherent X-ray imaging studies on the catalyst particles of PEFCs using an X-ray free-electron laser (XFEL) facility: SACLA (SPring-8 Angstrom Compact free electron LAser). Femtosecond XFEL allows us to capture radiation-damage-free snapshot images by outrunning major radiation damage processes. Damage-free imaging is of great value because radiation damage often causes a problem in high-resolution electron microscopy observation of ionomers. We used the coherent diffractive imaging (CDI) technique to observe catalyst particles of PEFCs. In CDI, sample images are reconstructed from measured coherent diffraction patterns using phase-retrieval calculation instead of objective lenses. CDI enables quantitative phase imaging and allows high-contrast imaging of the catalyst particles, which are almost transparent to X-rays.The measurement was carried out for catalyst particles in the dried condition and in solution. Our study showed that the image contrast can be adjusted by changing the electron density of the volume surrounding the sample1). The dried sample was prepared by dropping catalyst ink onto a silicon nitride membrane and air-dried. The solution sample was enclosed in micro-liquid enclosure arrays2,3) developed at Hokkaido University. The coherent diffraction patterns were measured by irradiating the sample catalyst particles with the 100-nm-focused XFEL beam with a photon energy of 4 keV using MAXIC-S (Multiple Application X-ray Imaging Chamber-S)4). The phase-retrieval calculation reconstructed the sample images. Fig. 1 shows a reconstructed image of a catalyst particle in water. The reconstructed image shows many white spots, which can be interpreted as platinum-cobalt catalysts. The pixel size of the reconstructed image is 1.3 nm, demonstrating among the highest spatial resolution in X-ray imaging. We will continue our study to observe the support structures and their ionomer coverage to understand the mass transfer in the catalyst layer.This work was supported by the FC-Platform of NEDO (New Energy and Industrial Technology Development Organization). The XFEL experiments were performed at SACLA with the approval of the Japan Synchrotron Radiation Research Institute (JASRI) (Proposal Nos. 2020A8106, 2021A8010, and 2021B8019).

Megahertz-rate ultrafast X-ray scattering and holographic imaging at the European XFEL.

The advent of X-ray free-electron lasers (XFELs) has revolutionized fundamental science, from atomic to condensed matter physics, from chemistry to biology, giving researchers access to X-rays with unprecedented brightness, coherence and pulse duration. All XFEL facilities built until recently provided X-ray pulses at a relatively low repetition rate, with limited data statistics. Here, results from the first megahertz-repetition-rate X-ray scattering experiments at the Spectroscopy and Coherent Scattering (SCS) instrument of the European XFEL are presented. The experimental capabilities that the SCS instrument offers, resulting from the operation at megahertz repetition rates and the availability of the novel DSSC 2D imaging detector, are illustrated. Time-resolved magnetic X-ray scattering and holographic imaging experiments in solid state samples were chosen as representative, providing an ideal test-bed for operation at megahertz rates. Our results are relevant and applicable to any other non-destructive XFEL experiments in the soft X-ray range.

A machine learning photon detection algorithm for coherent x-ray ultrafast fluctuation analysis.

X-ray free electron laser experiments have brought unique capabilities and opened new directions in research, such as creating new states of matter or directly measuring atomic motion. One such area is the ability to use finely spaced sets of coherent x-ray pulses to be compared after scattering from a dynamic system at different times. This enables the study of fluctuations in many-body quantum systems at the level of the ultrafast pulse durations, but this method has been limited to a select number of examples and required complex and advanced analytical tools. By applying a new methodology to this problem, we have made qualitative advances in three separate areas that will likely also find application to new fields. As compared to the “droplet-type” models, which typically are used to estimate the photon distributions on pixelated detectors to obtain the coherent x-ray speckle patterns, our algorithm achieves an order of magnitude speedup on CPU hardware and two orders of magnitude improvement on GPU hardware. We also find that it retains accuracy in low-contrast conditions, which is the typical regime for many experiments in structural dynamics. Finally, it can predict photon distributions in high average-intensity applications, a regime which up until now has not been accessible. Our artificial intelligence-assisted algorithm will enable a wider adoption of x-ray coherence spectroscopies, by both automating previously challenging analyses and enabling new experiments that were not otherwise feasible without the developments described in this work.

A hybrid approach to study large conformational transitions of biomolecules from single particle XFEL diffraction data.

X-ray free-electron laser (XFEL) is the latest generation of the X-ray source that could become an invaluable technique in structural biology. XFEL has ultrashort pulse duration, extreme peak brilliance, and high spatial coherence, which could enable the observation of the biological molecules in near nature state at room temperature without crystallization. However, for biological systems, due to their low diffraction power and complexity of sample delivery, experiments and data analysis are not straightforward, making it extremely challenging to reconstruct three-dimensional (3D) structures from single particle XFEL data. Given the current limitations to the amount and resolution of the data from such XFEL experiments, we propose a new hybrid approach for characterizing biomolecular conformational transitions by using a single 2D low-resolution XFEL diffraction pattern in combination with another known conformation. In our method, we represent the molecular structure with a coarse-grained model, the Gaussian mixture model, to describe large conformational transitions from low-resolution XFEL data. We obtain plausible 3D structural models that are consistent with the XFEL diffraction pattern by deforming an initial structural model to maximize the similarity between the target pattern and the simulated diffraction patterns from the candidate models. We tested the proposed algorithm on two biomolecules of different sizes with different complexities of conformational transitions, adenylate kinase, and elongation factor 2, using synthetic XFEL data. The results show that, with the proposed algorithm, we can successfully describe the conformational transitions by flexibly fitting the coarse-grained model of one conformation to become consistent with an XFEL diffraction pattern simulated from another conformation. In addition, we showed that the incident beam orientation has some effect on the accuracy of the 3D structure modeling and discussed the reasons for the inaccuracies for certain orientations. The proposed method could serve as an alternative approach for retrieving information on 3D conformational transitions from the XFEL diffraction patterns to interpret experimental data. Since the molecules are represented by Gaussian kernels and no atomic structure is needed in principle, such a method could also be used as a tool to seek initial models for 3D reconstruction algorithms.

Nonsequential two-photon absorption in solid Ge irradiated by an intense x-ray free-electron-laser pulse

We theoretically investigate the formation of highly charged ions in a germanium (Ge) solid driven by intense, ultrashort x-ray pulses and its effect on the cross sections for nonsequential two-photon absorption from the $K$ shell. Our investigation is related to an experiment conducted at the Linac Coherent Light Source, in which $K\ensuremath{\alpha}$ fluorescence was measured to identify nonsequential two-photon ionization. When a solid Ge target is irradiated by an intense x-ray free-electron-laser (XFEL) pulse, it undergoes severe ionization and turns into a plasma state. We employ a Monte Carlo molecular-dynamics approach to simulate the time evolution of Ge plasma formation, and the time-dependent configuration-interaction-singles method for cross-section calculations, taking into account various experimental x-ray beam parameters and Ge charge states created during the plasma formation dynamics. We find that under the given experimental condition at a photon energy of 7200 eV, charged ions are formed quickly (the average charge is $\ensuremath{\approx}+6$ at the peak of the pulse and $\ensuremath{\approx}+10$ at the end of the pulse). The cross sections of Ge for nonsequential two-photon absorption, however, turn out to be insensitive to different charge states, and the average value over all computed data is $(2.61\ifmmode\pm\else\textpm\fi{}0.05)\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}59}\phantom{\rule{4pt}{0ex}}{\mathrm{cm}}^{4}\phantom{\rule{0.16em}{0ex}}\mathrm{s}$. Our paper proposes a theoretical framework of photoabsorption cross-section calculations under the influence of plasma formation, when a solid target is employed in XFEL experiments.

Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules.

X-ray free-electron lasers (XFELs) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges in terms of both experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classifiers using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. Skopi is a resource to aid feasibility studies and advance the development of algorithms for noncrystalline experiments at XFEL facilities.

Development of slurry targets for high repetition-rate x-ray free electron laser experiments

Combining an x-ray free electron laser with a high-power laser driver enables the study of equations-of-state, high strain-rate deformation processes, structural phase transitions, and transformation pathways as a function of pressure to hundreds of GPa along different thermodynamic compression paths. Future high repetition-rate laser operation will enable data to be accumulated at >1 Hz, which poses a number of experimental challenges, including the need to rapidly replenish the target. Here, we present a combined shock compression and an x-ray diffraction study on epoxy (50% vol.)-crystalline grains (50% vol.) slurry targets, which can be fashioned into extruded ribbons for high repetition-rate operation. For shock-loaded NaCl-slurry samples, we observe pressure, density, and temperature states within the embedded NaCl grains consistent with observations from shock-compressed single-crystal NaCl.

Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases.

Enoyl-CoA carboxylases/reductases (ECRs) are some of the most efficient CO2-fixing enzymes described to date. However, the molecular mechanisms underlying the extraordinary catalytic activity of ECRs on the level of the protein assembly remain elusive. Here we used a combination of ambient-temperature X-ray free electron laser (XFEL) and cryogenic synchrotron experiments to study the structural organization of the ECR from Kitasatospora setae. The K. setae ECR is a homotetramer that differentiates into a pair of dimers of open- and closed-form subunits in the catalytically active state. Using molecular dynamics simulations and structure-based mutagenesis, we show that catalysis is synchronized in the K. setae ECR across the pair of dimers. This conformational coupling of catalytic domains is conferred by individual amino acids to achieve high CO2-fixation rates. Our results provide unprecedented insights into the dynamic organization and synchronized inter- and intrasubunit communications of this remarkably efficient CO2-fixing enzyme during catalysis.

Molecular Principles of Redox-Coupled Protonation Dynamics in Photosystem II.

Photosystem II (PSII) catalyzes light-driven water oxidization, releasing O2 into the atmosphere and transferring the electrons for the synthesis of biomass. However, despite decades of structural and functional studies, the water oxidation mechanism of PSII has remained puzzling and a major challenge for modern chemical research. Here, we show that PSII catalyzes redox-triggered proton transfer between its oxygen-evolving Mn4O5Ca cluster and a nearby cluster of conserved buried ion-pairs, which are connected to the bulk solvent via a proton pathway. By using multi-scale quantum and classical simulations, we find that oxidation of a redox-active Tyrz (Tyr161) lowers the reaction barrier for the water-mediated proton transfer from a Ca2+-bound water molecule (W3) to Asp61 via conformational changes in a nearby ion-pair (Asp61/Lys317). Deprotonation of this W3 substrate water triggers its migration toward Mn1 to a position identified in recent X-ray free-electron laser (XFEL) experiments [Ibrahim et al. Proc. Natl. Acad. Sci. USA 2020, 117, 12,624–12,635]. Further oxidation of the Mn4O5Ca cluster lowers the proton transfer barrier through the water ligand sphere of the Mn4O5Ca cluster to Asp61 via a similar ion-pair dissociation process, while the resulting Mn-bound oxo/oxyl species leads to O2 formation by a radical coupling mechanism. The proposed redox-coupled protonation mechanism shows a striking resemblance to functional motifs in other enzymes involved in biological energy conversion, with an interplay between hydration changes, ion-pair dynamics, and electric fields that modulate the catalytic barriers.

X-ray free-electron laser heating of water at picosecond time scale

Split-pulse x-ray photon correlation spectroscopy using x-ray free-electron laser is a promising tool to probe atomic dynamics in liquid and soft-matter in picosecond time scale, which has been accessible only by spectroscopy. However, sample heating by x-ray beam is a major obstacle for this technique. Using molecular dynamics and the two-temperature model we examine the atomic level response of water to x-ray laser pulse at picosecond time scale and compare with observations from recent x-ray free-electron laser experiments. We investigate the effects of the heating due to x-ray laser pulses of different energies and the effects of the heat dissipation on the structure and dynamics of water through the atomic density correlation and the dynamic structure factor. Our results indicate, in agreement with experiment that in addition to the beam energy the time delay between the two pulses is a critical factor for obtaining reliable information on the atomic level dynamics of water.