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The structure and mechanism of the water-oxidation chemistry that occurs in photosystem II have been subjects of great interest. The advent of X-ray free electron lasers allowed the determination of structures of the stable intermediate states and of steps in the transitions between these intermediate states, bringing a new perspective to this field. The room-temperature structures collected as the photosynthetic water oxidation reaction proceeds in real time have provided important novel insights into the structural changes and the mechanism of the water oxidation reaction. The time-resolved measurements have also given us a view of how this reaction-which involves multielectron, multiproton processes-is facilitated by the interaction of the ligands and the protein residues in the oxygen-evolving complex. These structures have also provided a picture of the dynamics occurring in the channels within photosystem II that are involved in the transport of the substrate water to the catalytic center and protons to the bulk.

The thermal conductivity of bridgmanite, the primary constituent of the Earth's lower mantle, has been investigated using diamond anvil cells at pressures up to 85 GPa and temperatures up to 3,100 K. We report the results of time‐domain optical laser flash heating and X‐ray Free Electron Laser heating experiments from a variety of bridgmanite samples with different Al and Fe contents. The results demonstrate that Fe or Fe,Al incorporation in bridgmanite reduces thermal conductivity by about 50% in comparison to end‐member MgSiO3 at the pressure‐temperature conditions of Earth's lower mantle. The effect of temperature on the thermal conductivity at 28–60 GPa is moderate, well described as k=k300(300/T)a ${k={k}_{300}(300/T)}^{a}$, where a is 0.2–0.5. The results yield thermal conductivity of 7.5–15 W/(m × K) in the thermal boundary layer of the lowermost mantle composed of Fe,Al‐bearing bridgmanite. Plain Language Summary: Heat transport from the Earth's core and mantle to the surface drives plate tectonics and is crucial for sustaining the magnetic field which shields the surface from the solar wind. To quantify the heat transport process across the core‐mantle boundary layer, it is important to know thermal conductivity of major constituent minerals of the lower mantle in the region. Bridgmanite, which was called silicate perovskite, is the most abundant mineral in the lower mantle. Here we measured thermal conductivity on lab‐grown bridgmanite with different Fe and Al compositions compressed at the tips of two opposing diamonds to reproduce relevant pressures in the mantle. To obtain thermal conductivity, we applied optical and X‐ray Free Electron Lasers combined with optical spectroscopy and X‐ray diffraction to heat and measure time‐dependent temperature distributions of the sample. Our study provides relevant high pressure‐temperature data sets to better constrain the heat flux across the core‐mantle boundary. Key Points: We measured thermal conductivity of Fe,Al‐bearing bridgmanite, the most abundant mineral in the Earth's lower mantle, up to 85 GPa and 3,100 KFinite‐element calculations to temperatures obtained from laser flash and X‐ray Free Electron Laser heating measurements are fitted to evaluate temperature effect on conductivityWe assessed pressure, temperature, composition effects on thermal conductivity of bridgmanite at the thermal boundary layer of the lowermost mantle [ABSTRACT FROM AUTHOR]

The ultrashort (10s of femtoseconds) X-ray pulses generated by X-ray free electron lasers enable the measurement of X-ray diffraction and spectroscopic data from radiation-sensitive metalloenzymes at room temperature while mostly avoiding the effects of radiation damage usually encountered when performing such experiments at synchrotron sources. Here we discuss an approach to measure both X-ray emission and X-ray crystallographic data at the same time from the same sample volume. The droplet-on-tape setup described allows for efficient sample use and the integration of different reaction triggering options in order to conduct time-resolved studies with limited sample amounts. The approach is illustrated by two examples, photosystem II that catalyzes the light-driven oxidation of water to oxygen, and isopenicillin N synthase, an enzyme that catalyzes the double ring cyclization of a tripeptide precursor into the β-lactam isopenicillin and can be activated by oxygen exposure. We describe the necessary steps to obtain microcrystals of both proteins as well as the operation procedure for the drop-on-tape setup and details of the data acquisition and processing involved in this experiment. At the end, we present how the combination of time-resolved X-ray emission spectra and diffraction data can be used to improve the knowledge about the enzyme reaction mechanism.

Enzymes populate ensembles of structures with intrinsically different catalytic proficiencies that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL) to observe catalysis in a designed mutant (G150T) isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations and formation of the thioimidate catalytic intermediate selects for catalytically competent substates. A prior proposal for active site cysteine charge-coupled conformational changes in ICH is validated by determining structures of the enzyme over a range of pH values. A combination of large molecular dynamics simulations of the enzyme in crystallo and time-resolved electron density maps shows that ionization of the general acid Asp17 during catalysis causes additional conformational changes that propagate across the dimer interface, connecting the two active sites. These ionization-linked changes in the ICH conformational ensemble permit water to enter the active site in a location that is poised for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

This article explores the challenges and solutions in data reduction at the European XFEL facility, which produces X-ray pulses. The facility generates a large amount of data during experiments, which presents difficulties in storage and interpretation. The article outlines the data infrastructure and various techniques for data reduction, aiming to maximize scientific value while minimizing strain on the infrastructure. The facility has successfully implemented reduction methods to decrease data storage volume and has assessed the risks associated with data reduction. Data reduction is important for scientific research, benefiting users by improving decision-making and simplifying data analysis, as well as having environmental benefits. The article emphasizes the collaboration between facility experts and users to ensure effective data reduction strategies and excellent scientific results. [Extracted from the article]

Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions. In this review, S. Botha and P. Fromme summarize the important milestones of serial femtosecond crystallography including the impact of the COVID-19 pandemic and give a future outlook into the impact of emerging new X-ray free electron laser technology on serial femtosecond crystallography. [ABSTRACT FROM AUTHOR]

The European XFEL is a megahertz repetition-rate facility producing extremely bright and coherent pulses of a few tens of femtoseconds duration. The amount of data generated in the context of user experiments can exceed hundreds of gigabits per second, resulting in tens of petabytes stored every year. These rates and volumes pose significant challenges both for facilities and users thereof. In fact, if unaddressed, extraction and interpretation of scientific content will be hindered, and investment and operational costs will quickly become unsustainable. In this article, we outline challenges and solutions in data reduction.

BackgroundRuthenium (Ru) exhibits outstanding mechanical properties and chemical stability, along with excellent optical properties such as high reflectivity and a larger critical angle. These attributes make it a good candidate coating material for optical components in X-ray free electron laser facilities.PurposeThis study aims to analyze the fundamental thermal evolutions of the Ru electron and lattice subsystems under irradiation of X-ray free electron laser pulses for better understanding of the laser-optics interaction mechanism under operating conditions.MethodsThe numerical method was adopted to solve the two-temperature model (TTM) in terms of simulating the interaction process between X-ray free electron laser pulses and thin ruthenium films. The laser energy incident on the Ru target material was the actual energy absorbed by the material and the pulse laser incidence was in the x-direction with a film thickness of 50 nm, spatial discretization step size of 0.2 nm and the time step size of 0.02 fs. Simutanously, the influence of different laser source parameters, such as pulse width, penetration depth, energy density, etc., on the thermal effects during the interaction between laser and metal Ru was explored, and the temperature evolutions of the Ru electron and lattice subsystems were obtained, as well as the corresponding dependency relationships of the heat transfer processes on source parameters.ResultsNumerical solution of the TTM indicate that the system equilibrium temperature of Ru is identified to be positively correlated with energy density. The peak electron temperature of Ru decreases with the increasing of pulse width. Besides, as penetration depth increases, the equilibrium temperature of Ru will decrease until a stable level. As for the front surface, the time taken to achieve electron-lattice equilibrium decrease with the increasing of electron-phonon coupling coefficient.ConclusionsSimulation data and theoretical analyses presented in this study throw an insight into the thermal response of the optical material (Ru) to laser irradiation.

In X-ray crystallography and Coherent Diffraction Imaging, only the diffraction patterns’ light density can be directly measured, not its phase. The process of retrieving the phase is defined as the phase retrieval problem. In this project, I explore a classic iterative approach for phase retrieval to apply to an XFEL simulator real space data. The conventional Gerchberg-Saxton algorithm is modified and simulated. Two figures of merit are developed to quantify the algorithm’s performance. Convergence time, initial phase, and noise sensitivity are evaluated. It is determined that the algorithm can be used to solve the phase problem for XFEL applications. [ABSTRACT FROM AUTHOR]

The dynamics of lattice vibrations govern many material processes, such as acoustic wave propagation, displacive phase transitions, and ballistic thermal transport. The maximum velocity of these processes and their effects is determined by the speed of sound, which therefore defines the temporal resolution (picoseconds) needed to resolve these phenomena on their characteristic length scales (nanometers). Here, we present an X-ray microscope capable of imaging acoustic waves with subpicosecond resolution within mm-sized crystals. We directly visualize the generation, propagation, branching, and energy dissipation of longitudinal and transverse acoustic waves in diamond, demonstrating how mechanical energy thermalizes from picosecond to microsecond timescales. Bulk characterization techniques capable of resolving this level of structural detail have previously been available on millisecond time scales--orders of magnitude too slow to capture these fundamental phenomena in solid-state physics and geoscience. As such, the reported results provide broad insights into the interaction of acoustic waves with the structure of materials, and the availability of ultrafast time-resolved dark-field X-ray microscopy opens a vista of new opportunities for 3D imaging of materials dynamics on their intrinsic submicrosecond time scales. [ABSTRACT FROM AUTHOR]

Serial femtosecond crystallography (SFX) using an X-ray free electron laser (XFEL) enables the determination of room-temperature structures without causing radiation damage. Using an optical pump-probe or mix-and-injection, SFX enables the intermediate state visualization of a molecular reaction. In SFX experiments, serial and stable microcrystal delivery to the X-ray interaction point is vital for reasonable data collection and efficient beam time. The Pohang Accelerator Laboratory X-ray Free Electron Laser (PAL-XFEL) facility established SFX instruments at a nanocrystallography and coherent imaging (NCI) experimental station. Various sample delivery methods, including injection, fixed-target scanning, and hybrid methods, have been developed and applied to collect XFEL diffraction data. Herein, we report the currently available sample delivery methods for SFX at the NCI experimental station at the PAL-XFEL. This article will help PAL-XFEL users access the SFX system for their experiments. [ABSTRACT FROM AUTHOR]

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

We report the start-to-end modeling of our accelerator lattice design employing a laser-assisted bunch compression (LABC) scheme in an X-ray free electron laser (XFEL), using the proposed Matter-Radiation Interactions in Extremes (MaRIE) XFEL parameters. The accelerator lattice utilized a two-stage bunch compression scheme, with the first bunch compressor performing a conventional bulk compression enhancing the beam current from 20 A to 500 A, at 750 MeV. The second bunch compression was achieved by modulating the beam immediately downstream of the first bunch compressor by a laser with 1- μ m wavelength in a laser modulator, accelerating the beam to the final energy of 12 GeV, and compressing the individual 1- μ m periods of the modulated beam into a sequence of microbunches with 3-kA current spikes by the second bunch compressor. The LABC architecture presented had been developed based on the scheme of enhanced self-amplified spontaneous emission (ESASE), but operated in a disparate regime of parameters. Enabled by the novel technology of the cryogenic normal conducting radiofrequency photoinjector, we investigated an electron beam with ultra-low emittance at the starting point of the lattice design. Our work aimed at mitigating the well-known beam instabilities to preserve the beam emittance and suppress the energy spread growth. [ABSTRACT FROM AUTHOR]

Although beam emittance is critical for the performance of high-brightness accelerators, optimization is often time limited as emittance calculations, commonly done via quadrupole scans, are typically slow. Such calculations are a type of multipoint query , i.e. each query requires multiple secondary measurements. Traditional black-box optimizers such as Bayesian optimization are slow and inefficient when dealing with such objectives as they must acquire the full series of measurements, but return only the emittance, with each query. We propose a new information-theoretic algorithm, Multipoint-BAX , for black-box optimization on multipoint queries, which queries and models individual beam-size measurements using techniques from Bayesian Algorithm Execution (BAX). Our method avoids the slow multipoint query on the accelerator by acquiring points through a virtual objective , i.e. calculating the emittance objective from a fast learned model rather than directly from the accelerator. We use Multipoint-BAX to minimize emittance at the Linac Coherent Light Source (LCLS) and the Facility for Advanced Accelerator Experimental Tests II (FACET-II). In simulation, our method is 20× faster and more robust to noise compared to existing methods. In live tests, it matched the hand-tuned emittance at FACET-II and achieved a 24% lower emittance than hand-tuning at LCLS. Our method represents a conceptual shift for optimizing multipoint queries, and we anticipate that it can be readily adapted to similar problems in particle accelerators and other scientific instruments.

In this paper, a computational-theoretical analysis of the possibilities of using the method of phase-contrast X-ray radiography for the study of low-contrast turbulent flows in laser plasma in experiments with astrophysical similarity is carried out. By modeling the passage of hard coherent X-ray radiation through test objects, we studied the parameters of a laboratory experiment that affect the contrast and resolution of the resulting phase-contrast images. The limiting scale for measuring the frequency-spatial spectrum of image power was determined, on which the manifestation of artifacts from the superimposition of diffraction effects from neighboring objects is not yet critical for the correct interpretation of the results. Optimal object-detector distances are found that provide resolution of the power spectrum of a turbulent flow on micron scales. These results are relevant for future laboratory experiments on the development of instabilities in plasma with astrophysical similarity up to the stage of energy dissipation. [ABSTRACT FROM AUTHOR]

The emergence of novel computational hardware is enabling a new paradigm for rapid machine learning model training. For the Department of Energy’s major research facilities, this developing technology will enable a highly adaptive approach to experimental sciences. In this manuscript we present the per-epoch and end-to-end training times for an example of a streaming diagnostic that is planned for the upcoming high-repetition rate x-ray Free Electron Laser, the Linac Coherent Light Source-II. We explore the parameter space of batch size and data parallel training across multiple Graphics Processing Units and Reconfigurable Dataflow Units. We show the landscape of training times with a goal of full model retraining in under 15 min. Although a full from scratch retraining of a model may not be required in all cases, we nevertheless present an example of the application of emerging computational hardware for adapting machine learning models to changing environments in real-time, during streaming data acquisition, at the rates expected for the data fire hoses of accelerator-based user facilities.

Serial femtosecond crystallography (SFX) using an X-ray free electron laser (XFEL) enables the determination of room-temperature structures without causing radiation damage. Using an optical pump-probe or mix-and-injection, SFX enables the intermediate state visualization of a molecular reaction. In SFX experiments, serial and stable microcrystal delivery to the X-ray interaction point is vital for reasonable data collection and efficient beam time. The Pohang Accelerator Laboratory X-ray Free Electron Laser (PAL-XFEL) facility established SFX instruments at a nanocrystallography and coherent imaging (NCI) experimental station. Various sample delivery methods, including injection, fixed-target scanning, and hybrid methods, have been developed and applied to collect XFEL diffraction data. Herein, we report the currently available sample delivery methods for SFX at the NCI experimental station at the PAL-XFEL. This article will help PAL-XFEL users access the SFX system for their experiments.

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. [ABSTRACT FROM AUTHOR]

We report the start-to-end modeling of our accelerator lattice design employing a laser-assisted bunch compression (LABC) scheme in an X-ray free electron laser (XFEL), using the proposed Matter-Radiation Interactions in Extremes (MaRIE) XFEL parameters. The accelerator lattice utilized a two-stage bunch compression scheme, with the first bunch compressor performing a conventional bulk compression enhancing the beam current from 20 A to 500 A, at 750 MeV. The second bunch compression was achieved by modulating the beam immediately downstream of the first bunch compressor by a laser with 1-μm wavelength in a laser modulator, accelerating the beam to the final energy of 12 GeV, and compressing the individual 1-μm periods of the modulated beam into a sequence of microbunches with 3-kA current spikes by the second bunch compressor. The LABC architecture presented had been developed based on the scheme of enhanced self-amplified spontaneous emission (ESASE), but operated in a disparate regime of parameters. Enabled by the novel technology of the cryogenic normal conducting radiofrequency photoinjector, we investigated an electron beam with ultra-low emittance at the starting point of the lattice design. Our work aimed at mitigating the well-known beam instabilities to preserve the beam emittance and suppress the energy spread growth.

The X-ray free-electron laser of the Pohang Accelerator Laboratory (PAL-XFEL) was opened to users in 2017. Since then, significant progress has been made in PAL-XFEL operation and beamline experiments. This includes increasing the FEL pulse energy, increasing the FEL photon energy, generating self-seeding FEL, and trials of two-color operation. In the beamline, new instruments or endstations have been added or are being prepared. Overall, beamline operation has been stabilized since its initiation, which has enabled excellent scientific results through efficient user experiments. In this paper, we describe details of the recent progress of the PAL-XFEL. [ABSTRACT FROM AUTHOR]

Serial femtosecond crystallography (SFX) employing high-intensity X-ray free-electron laser (XFEL) sources has enabled structural studies on microcrystalline protein samples at non-cryogenic temperatures. However, the identification and optimization of conditions that produce well diffracting microcrystals remains an experimental challenge. Here, we report parallel SFX and transmission electron microscopy (TEM) experiments using fragmented microcrystals of wild type (WT) homoprotocatechuate 2,3-dioxygenase (HPCD) and an active site variant (H200Q). Despite identical crystallization conditions and morphology, as well as similar crystal size and density, the indexing efficiency of the diffraction data collected using the H200Q variant sample was over 7-fold higher compared to the diffraction results obtained using the WT sample. TEM analysis revealed an abundance of protein aggregates, crystal conglomerates and a smaller population of highly ordered lattices in the WT sample as compared to the H200Q variant sample. While not reported herein, the 1.75 Å resolution structure of the H200Q variant was determined from ∼16 min of beam time, demonstrating the utility of TEM analysis in evaluating sample monodispersity and lattice quality, parameters critical to the efficiency of SFX experiments.

Twelve years ago, the first free electron laser for hard X-rays (XFEL), the Linac Coherent Light Source (LCLS), came online. Due to the extreme brilliance and the ultrashort pulse duration of their X-ray radiation, XFELs are exceptionally well positioned to conduct time-resolved studies on biological macromolecules. Here, some of the pioneering experiments and recent results are summarized. [ABSTRACT FROM AUTHOR]

We present an approach that combines photon spectrum correlation analysis with the reconstruction of three-dimensional momentum distribution from velocity map images in an efficient, single-step procedure. We demonstrate its efficacy with the results from the photoionization of the 2 p -shell of argon using the Free-electron LASer in Hamburg free-electron laser (FEL). Distinct spectral features due to the spin-orbit splitting of Ar $^+(2p^{-1})$ are resolved, despite the large average bandwidth of the ionizing pulses from the FEL. This demonstrates a clear advantage over the conventional analysis method, and it will be broadly beneficial for velocity map imaging experiments with FEL sources. The retrieved linewidth of the binding energy spectrum approaches the resolution limitation prescribed by the spectrometers used to collect the data. Our approach presents a path to extend spectral-domain ghost imaging to the case where the photoproduct observable is high-dimensional.

Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging to structurally characterize using traditional crystallographic approaches. This review describes the use and promise of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the main (Mpro) and papain-like (PLpro) cysteine proteases of SARS-CoV-2, as well as on other examples. We review features of cysteine chemistry that are relevant for the design and execution of time-resolved serial crystallography experiments. In addition, we discuss emerging X-ray techniques, such as time-resolved sulfur X-ray spectroscopy, that may be able to detect changes in sulfur charge states and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes have features that make them especially attractive targets for new time-resolved serial crystallography approaches, which can reveal both changes to enzyme structures and dynamics during catalysis in crystalline samples.

Structure determination of proteins and enzymes by X-ray crystallography remains the most widely used approach to complement functional and mechanistic studies. Capturing the structures of intact redox states in metalloenzymes is critical for assigning the chemistry carried out by the metal in the catalytic cycle. Unfortunately, X-rays interact with protein crystals to generate solvated photoelectrons that can reduce redox active metals and hence change the coordination geometry and the coupled protein structure. Approaches to mitigate such site-specific radiation damage continue to be developed, but nevertheless application of such approaches to metalloenzymes in combination with mechanistic studies are often overlooked. In this review, we summarize our recent structural and kinetic studies on a set of three heme peroxidases found in the bacterium Streptomyces lividans that each belong to the dye decolourizing peroxidase (DyP) superfamily. Kinetically, each of these DyPs has a distinct reactivity with hydrogen peroxide. Through a combination of low dose synchrotron X-ray crystallography and zero dose serial femtosecond X-ray crystallography using an X-ray free electron laser (XFEL), high-resolution structures with unambiguous redox state assignment of the ferric and ferryl (FeIV = O) heme species have been obtained. Experiments using stopped-flow kinetics, solvent-isotope exchange and site-directed mutagenesis with this set of redox state validated DyP structures have provided the first comprehensive kinetic and structural framework for how DyPs can modulate their distal heme pocket Asp/Arg dyad to use either the Asp or the Arg to facilitate proton transfer and rate enhancement of peroxide heterolysis. [ABSTRACT FROM AUTHOR]

We developed a single-shot coherent X-ray imaging instrument at the hard X-ray beamline of the Pohang Accelerator Laboratory X-ray Free Electron Laser (PAL-XFEL). This experimental platform was established to conduct a variety of XFEL experiments, including coherent diffraction imaging (CDI), X-ray photon correlation spectroscopy (XPCS), and coherent X-ray scattering (CXS). Based on the forward-scattering geometry, this instrument utilizes a fixed-target method for sample delivery. It is well optimized for single-shot-based experiments in which one expects to observe the ultrafast phenomena of nanoparticles at picosecond temporal and nanometer spatial resolutions. In this paper, we introduce a single-shot coherent X-ray imaging instrument and report pump–probe coherent diffraction imaging (PPCDI) of Ag nanoparticles as an example of its applications. [ABSTRACT FROM AUTHOR]

Experiments creating extreme states of matter almost invariably create non-equilibrium states. These are very interesting in their own right but need to be understood even if the ultimate goal is to probe high-pressure or high-temperature equilibrium properties like the equation of state. Here, we report on the capabilities of the newly developed imaginary time correlation function (ITCF) technique [1] to detect and quantify non-equilibrium in pump-probe experiments fielding time resolved x-ray scattering diagnostics. We find a high sensitivity of the ITCF even to a small fraction of non-equilibrium electrons in the Wigner distribution. The behavior of the ITCF technique is such that modern lasers and detectors should be able to trace the non-equilibrium relaxation from tens of femto-seconds to several 10s of picoseconds without the need for a model. • The newly developed imaginary time correlation function technique can detect and quantify non-equilibrium in pump-probe experiments. • Time resolved x-ray Thomson scattering is sensitive to a small fraction of non-equilibrium electrons in the Wigner distribution. • Modern setups will allow to trace the relaxation from tens of femto-seconds to several 10s of picoseconds without a model. [ABSTRACT FROM AUTHOR]

Understanding the enzyme reaction mechanism is important for identifying fundamental biochemical processes and for providing invaluable information for enzyme engineering for industrial applications. Serial femtosecond crystallography (SFX) enables determination structure of enzymes without radiation damage at room temperature. Time-resolved SFX with ligand mixing provides a molecular movie of enzyme reactions, including the transition states. This structural information provides insight into previously undiscovered molecular dynamics over various time periods. To observe enzyme reactions with SFX, it is essential to comprehend the device used for mixing the protein crystals and reaction solutions, as well as the mixing efficiency and available time delay provided by this equipment. In this review, we summarize the current mixing techniques for time-resolved SFX. We describe the configuration and experimental setup of the SFX sample environment unique to each experimental technique and discuss the technical possibilities and limitations of these techniques for performing time-resolved crystallography. • Time-resolved mixing SFX experiments for enzyme reactions are explained. • Mixing devices and time-resolved mixing SFX results are summarized. • Potential available mixing devices for time-resolved SFX are discussed. • The possibilities and limitations of time-resolved mixing SFX are discussed. [ABSTRACT FROM AUTHOR]

Understanding interfacial charge-transfer processes on the atomic level is crucial to support the rational design of energy-challenge relevant systems such as solar cells, batteries, and photocatalysts. A femtosecond time-resolved core-level photoelectron spectroscopy study is performed that probes the electronic structure of the interface between ruthenium-based N3 dye molecules and ZnO nanocrystals within the first picosecond after photoexcitation and from the unique perspective of the Ru reporter atom at the center of the dye. A transient chemical shift of the Ru 3d inner-shell photolines by (2.3 ± 0.2) eV to higher binding energies is observed 500 fs after photoexcitation of the dye. The experimental results are interpreted with the aid of ab initio calculations using constrained density functional theory. Strong indications for the formation of an interfacial charge-transfer state are presented, providing direct insight into a transient electronic configuration that may limit the efficiency of photoinduced free charge-carrier generation.

High-energy and high-intensity lasers are essential for pushing the boundaries of science. Their development has allowed leaps forward in basic research areas, including laser–plasma interaction, high-energy density science, metrology, biology and medical technology. The Helmholtz International Beamline for Extreme Fields user consortium contributes and operates two high-peak-power optical lasers using the high energy density instrument at the European X-ray free electron laser (EuXFEL) facility. These lasers will be used to generate transient extreme states of density and temperature to be probed by the X-ray beam. This paper introduces the ReLaX laser, a short-pulse high-intensity Ti:Sa laser system, and discusses its characteristics as available for user experiments. It will also present the first experimental commissioning results validating its successful integration into the EuXFEL infrastructure and viability as a relativistic-intensity laser driver. [ABSTRACT FROM AUTHOR]

The X-ray free-electron laser of the Pohang Accelerator Laboratory (PAL-XFEL) was opened to users in 2017. Since then, significant progress has been made in PAL-XFEL operation and beamline experiments. This includes increasing the FEL pulse energy, increasing the FEL photon energy, generating self-seeding FEL, and trials of two-color operation. In the beamline, new instruments or endstations have been added or are being prepared. Overall, beamline operation has been stabilized since its initiation, which has enabled excellent scientific results through efficient user experiments. In this paper, we describe details of the recent progress of the PAL-XFEL.

In photon-limited imaging, the pixel intensities are affected by photon count noise. Many applications require an accurate estimation of the covariance of the underlying 2-D clean images. For example, in X-ray free electron laser (XFEL) single molecule imaging, the covariance matrix of 2-D diffraction images is used to reconstruct the 3-D molecular structure. Accurate estimation of the covariance from low-photon-count images must take into account that pixel intensities are Poisson distributed, hence the classical sample covariance estimator is highly biased. Moreover, in single molecule imaging, including in-plane rotated copies of all images could further improve the accuracy of covariance estimation. In this paper we introduce an efficient and accurate algorithm for covariance matrix estimation of count noise 2-D images, including their uniform planar rotations and possibly reflections. Our procedure, steerable $e$ PCA, combines in a novel way two recently introduced innovations. The first is a methodology for principal component analysis (PCA) for Poisson distributions, and more generally, exponential family distributions, called $e$ PCA. The second is steerable PCA, a fast and accurate procedure for including all planar rotations when performing PCA. The resulting principal components are invariant to the rotation and reflection of the input images. We demonstrate the efficiency and accuracy of steerable $e$ PCA in numerical experiments involving simulated XFEL datasets and rotated face images from Yale Face Database B. [ABSTRACT FROM AUTHOR]

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ~350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated. [ABSTRACT FROM AUTHOR]

X-ray pump/X-ray probe applications are made possible at X-ray Free Electron Laser (XFEL) facilities by generating two X-ray pulses with different wavelengths and controllable temporal delay. In order to enable this capability at the European XFEL, an upgrade project to equip the soft X-ray SASE3 beamline with a magnetic chicane is underway. In the present paper we describe the status of the project, its scientific focus and expected performance, including start-to-end simulations of the photon beam transport up to the sample, as well as recent experimental results demonstrating two-color lasing at photon energies of 805 eV + 835 eV and 910 eV + 950 eV. Additionally, we discuss methods to analyze the spectral properties and the intensity of the generated radiation to provide on-line diagnostics for future user experiments. [ABSTRACT FROM AUTHOR]

Microscopic imaging techniques have been developed to visualize events occurring in biological cells. Coherent X-ray diffraction imaging is one of the techniques applicable to structural analyses of cells and organelles, which have never been crystallized. In the experiment, a single noncrystalline particle is illuminated by an X-ray beam with almost complete spatial coherence. The structure of the particle projected along the direction of the beam is, in principle, retrieved from a finely recorded diffraction pattern alone by using iterative phase-retrieval algorithms. Here, we describe fundamental theory and experimental methods of coherent X-ray diffraction imaging and the recent application in structural studies of noncrystalline specimens by using X-rays available at Super Photon Ring of 8-Gev and SPring-8 Angstrom Compact Free Electron Laser in Japan. [ABSTRACT FROM AUTHOR]

In the probe-before-destroy methodology, developed with the advent of X-ray free-electron lasers, the investigated system is probed with an ultra-short (femtosecond) X-ray pulse within time shorter than that the X-ray-induced damage needs to propagate. Radiation damage is typically considered in terms of the Coulomb explosion which needs about 50 fs to induce observable effects in the material structure. It has been, however, shown that the much faster electronic structure change has also a significant influence on the X-ray emission spectroscopy data and may alter the X-ray diffraction patterns. This work reports on energy and time distribution of photo-electrons induced in water by an X-ray pulse with properties typical for an X-ray free-electron laser operated in the intensity regime below the sequential photoionization regime. The electron flux was simulated on the basis of a kinetic model and was found to be significant over the course of the X-ray pulse duration. The presented findings call for consideration of the X-ray-induced electrons in studies on solutions and samples embedded in matrices. [ABSTRACT FROM AUTHOR]

The recent progress in the development of X-ray free electron lasers (XFELs) allows for the delivery of over 1011 high-energy photons to solid-density samples in a femtosecond time scale. The corresponding peak brightness of XFEL induces a nonlinear response of matter in a short-wavelength regime. The absorption of an XFEL pulse in a solid also results in the creation of high energy density (HED) matter. The electronic structure and related fundamental properties of such HED matter can be investigated with the control of XFEL and various X-ray spectroscopic techniques. These experimental data provide unique opportunities to benchmark theories and models for extreme conditions and to guide further advances. In this article, the current progress in spectroscopic studies on intense XFEL–matter interactions and HED matter are reviewed, and future research opportunities are discussed. [ABSTRACT FROM AUTHOR]

Innovations are expanding the capabilities of experimental investigations of the structural properties of membrane proteins. Traditionally, three-dimensional structures have been determined by measuring x-ray diffraction using protein crystals with a size of least 100 μm. For membrane proteins, achieving crystals suitable for these measurements has been a significant challenge. The availabilities of micro-focus x-ray beams and the new instrumentation of x-ray free-electron lasers have opened up the possibility of using submicrometer-sized crystals. In addition, advances in cryo-electron microscopy have expanded the use of this technique for studies of protein crystals as well as studies of individual proteins as single particles. Together, these approaches provide unprecedented opportunities for the exploration of structural properties of membrane proteins, including dynamical changes during protein function.