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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 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. [ABSTRACT FROM AUTHOR]

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 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]

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]

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]

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]

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]

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]

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]

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]

A focused jet is an axisymmetric jet of liquid surrounded by an outer coaxial gas jet. The gas jet is typically used to compress the liquid jet in the radial direction thereby focusing it. At microscales, it is difficult to manufacture micro-scale delivery nozzles (needles) and to consistently align and axially position the liquid and the gas needles. However, it is very easy, using standard etching technologies to make precise and repeatable rectangular nozzle designs. This work will therefore explore the geometric and fluid dynamics constraints that allow one to design rectangular nozzles that produce round coaxial micro-jets of liquid and gas. Because of the small scales, the fluid dynamics of the focusing jet is unusual, and this work demonstrates that the liquid jet is best focused by shear stretching and not via gas compression. This paper shows that sheet jetting occurs when the Reynolds number of the gas is too high. Dripping occurs when the Weber number of the liquid is too low. The desired round jet occurs by balancing Weber number of the liquid jet and Reynolds number of the gas such that surface tension at the interface holds the water jet round while the acceleration of the water jet due to shear at the interface from fast-moving air causes the liquid jet cross-sectional area to decrease. The goal of this initial paper is to demonstrate that a parameter region exists where this flow behavior is possible. [ABSTRACT FROM AUTHOR]

The development of the X-ray free electron laser (XFEL) as a tool for crystallography started a new era in protein science with the intriguing possibility of determining time-resolved structural changes under physiological conditions. This chapter summarizes the current state of XFEL-based structural research on tetrapyrrole containing proteins including the photosystems of oxygenic photosynthesis, the purple bacterial reaction center, phycobilins, and phytochromes. Besides describing technical developments that were necessary to fully exploit the advantages of the method, emphasis is put on the task of producing suitable protein microcrystals for XFEL experiments. In particular, issues encountered in crystallizing membrane proteins are described with photosystem II as the prime example to underscore the importance of combining physical and biochemical knowledge, but also to point to unsolved problems. Finally, novel structural information obtained by XFEL experiments for the various systems is given with a focus on recent advances in understanding photosynthetic water oxidation. [ABSTRACT FROM AUTHOR]

The evolution of synchrotron radiation (SR) sources and related sciences is discussed to explain the 'generation' of the SR sources. Most of the contemporary SR sources belong to the third generation, where the storage rings are optimized for the use of undulator radiation. The undulator development allowed to reduction of the electron energy of the storage ring necessary for delivering 10 keV X-rays from the initial 6-8 GeV to the current 3Gev. Now is the transitional period from the doublebend- achromat lattice-based storage ring to the multi-bend-achromat lattice to achieve much smaller electron beam emittance. Free electron lasers are the other important accelerator-based light sources which recently reached hard X-ray regime by using self-amplified spontaneous emission scheme. Future accelerator-based X-ray sources should be continuous wave X-ray free electron lasers and pulsed X-ray free electron lasers. Some pathways to reach the future case are discussed. [ABSTRACT FROM AUTHOR]

The ability to produce ultrashort, high-brightness X-ray pulses is revolutionizing the field of ultrafast X-ray spectroscopy. Free-electron laser (FEL) facilities are driving this revolution, but unique aspects of the FEL process make the required characterization and use of the pulses challenging. In this paper, we describe a number of developments in the generation of ultrashort X-ray FEL pulses, and the concomitant progress in the experimental capabilities necessary for their characterization and use at the Linac Coherent Light Source. This includes the development of sub-femtosecond hard and soft X-ray pulses, along with ultrafast characterization techniques for these pulses. We also describe improved techniques for optical cross-correlation as needed to address the persistent challenge of external optical laser synchronization with these ultrashort X-ray pulses. [ABSTRACT FROM AUTHOR]

Many remarkable properties of quantum materials emerge from states with intricate coupling between the charge, spin and orbital degrees of freedom. Ultrafast photo-excitation of these materials holds great promise for understanding and controlling the properties of these states. Here, we introduce time-resolved resonant inelastic X-ray scattering (tr-RIXS) as a means of measuring the charge, spin and orbital excitations out of equilibrium. These excitations encode the correlations and interactions that determine the detailed properties of the states generated. After outlining the basic principles and instrumentations of tr-RIXS, we review our first observations of transient antiferromagnetic correlations in quasi two dimensions in a photoexcited Mott insulator and present possible future routes of this fast-developing technique. The increasing number of X-ray free electron laser facilities not only enables tackling long-standing fundamental scientific problems, but also promises to unleash novel inelastic X-ray scattering spectroscopies. [ABSTRACT FROM AUTHOR]

Strong interactions between electrons give rise to the complexity of quantum materials, which exhibit exotic functional properties and extreme susceptibility to external perturbations. A growing research trend involves the study of these materials away from equilibrium, especially in cases in which the stimulation with optical pulses can coherently enhance cooperative orders. Time-resolved X-ray probes are integral to this type of research, as they can be used to track atomic and electronic structures as they evolve on ultrafast timescales. Here, we review a series of recent experiments where femtosecond X-ray diffraction was used to measure dynamics of complex solids. [ABSTRACT FROM AUTHOR]

Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain. [ABSTRACT FROM AUTHOR]

X‐ray optics were implemented for advanced ultrafast X‐ray experiments with different techniques at the hard X‐ray beamline BL3 of SPring‐8 Ångstrom Compact free‐electron LAser. A double channel‐cut crystal monochromator (DCCM) and compound refractive lenses (CRLs) were installed to tailor the beam conditions. These X‐ray optics can work simultaneously with an arrival‐timing monitor that compensates for timing jitter and drift. Inner‐walls of channel‐cut crystals (CCs) in the DCCM were processed by plasma chemical vaporization machining to remove crystallographic damage. Four‐bounced reflection profiles of the CCs were investigated and excellent diffraction qualities were achieved. The use of CRLs enabled two‐dimensional X‐ray focusing with a spot size of ∼1.5 µm × 1.5 µm full width at half‐maximum, while keeping reasonable throughputs for a wide photon energy range of 5−15 keV. A double channel‐cut crystal monochromator and compound refractive lenses were implemented for advanced pump–probe X‐ray experiments at SACLA BL3. [ABSTRACT FROM AUTHOR]

Cytochrome c oxidase (CcO) reduces dioxygen to water and harnesses the chemical energy to drive proton translocation across the inner mitochondrial membrane by an unresolved mechanism. By using time-resolved serial femtosecond crystallography, we identified a key oxygen intermediate of bovine CcO. It is assigned to the PR-intermediate, which is characterized by specific redox states of the metal centers and a distinct protein conformation. The heme a3 iron atom is in a ferryl (Fe4+ = O2-) configuration, and heme a and CuB are oxidized while CuA is reduced. A Helix-X segment is poised in an open conformational state; the heme a farnesyl sidechain is H-bonded to S382, and loop-I-II adopts a distinct structure. These data offer insights into the mechanism by which the oxygen chemistry is coupled to unidirectional proton translocation. [ABSTRACT FROM AUTHOR]

Microbial rhodopsin is a membrane protein with a domain of seven-transmembrane helices and a retinal chromophore. The main function of this protein is to perform light-induced ion transport, either actively or passively, by acting as pumps, channels, and light sensors. It is widely used for optogenetic application to control the activity of specific cells in living tissues by light. Time-resolved serial femtosecond crystallography (TR-SFX) with the use of X-ray free electron lasers is an effective technique for capturing dynamic ion transport and efflux structures across membranes with high spatial and temporal resolutions. Here, we outline recent TR-SFX studies of microbial rhodopsins, including a pump and a channel. We also discuss differences and similarities observed in the structural dynamics derived from the TR-SFX structures. • X-ray free electron lasers allow determination of protein dynamic structure. • Dynamic structures of several microbial rhodopsins were determined recently. • The obtained dynamic structures showed common light-induced conformational changes. [ABSTRACT FROM AUTHOR]

Intense femtosecond lasers as well as X-ray free electron lasers provide new means to produce multiply charged molecular cations. The fragmentation processes that these high energy species undergo, termed Coulomb explosion, are utilized to determine the static molecular structures as well as to trace the molecular dynamics of ultrafast chemical reactions. This review focuses on recent advances made in studies of Coulomb explosion imaging, highlighting the use of this process to determine the static structures of complex molecules, geometric isomers, chiral molecules and molecular complexes. Briefly, we summarize the recent time-resolved studies of surface electric fields and the controversy pertaining to the contribution of Coulomb explosion to the mechanism for ablation of solid surfaces. [ABSTRACT FROM AUTHOR]

For the LCLS-II X-ray instruments, laser power meters are being developed as compact X-ray power diagnostics to operate at soft and tender X-ray photon energies. These diagnostics can be installed at various locations along an X-ray free-electron laser (FEL) beamline in order to monitor the transmission of X-ray optics along the beam path. In addition, the power meters will be used to determine the absolute X-ray power at the endstations. Here, thermopile power meters, which measure average power, and have been chosen primarily for their compatibility with the high repetition rates at LCLS-II, are evaluated. A number of characteristics in the soft X-ray range are presented including linearity, calibrations conducted with a photodiode and a gas monitor detector as well as ultra-high-vacuum compatibility tests using residual gas analysis. The application of these power meters for LCLS-II and other X-ray FEL sources is discussed. [ABSTRACT FROM AUTHOR]

At SACLA, we are developing a data collection system focusing on dynamic crystallography putting a particular effort on membrane proteins. An experimental system for pump-probe experiments based on serial femtosecond crystallography using a viscous material injector has been developed. We used time-resolved serial femtosecond crystallography to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. The cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons. We have also applied this system to study the light-induced structural changes and the site of O=O bond formation in photosystem II. [ABSTRACT FROM AUTHOR]

X-ray free electron lasers (XFELs) have the potential to revolutionize macromolecular structural biology due to the unique combination of spatial coherence, extreme peak brilliance, and short duration of X-ray pulses. A recently emerged serial femtosecond (fs) crystallography (SFX) approach using XFEL radiation overcomes some of the biggest hurdles of traditional crystallography related to radiation damage through the diffraction-before-destruction principle. Intense fs XFEL pulses enable high-resolution room-temperature structure determination of difficult-to-crystallize biological macromolecules, while simultaneously opening a new era of time-resolved structural studies. Here, we review the latest developments in instrumentation, sample delivery, data analysis, crystallization methods, and applications of SFX to important biological questions, and conclude with brief insights into the bright future of structural biology using XFELs. [ABSTRACT FROM AUTHOR]

Cytochrome c oxidase (CcO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine CcO (bCcO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a3 iron atom, with a bent Fe-C-O angle of ~142°. In contrast, in the synchrotron structure, the Fe-CO bond is cleaved; CO relocates to a new site near CuB, which, in turn, moves closer to the heme a3 iron by ~0.38 Å. Structural comparison reveals that ligand binding to the heme a3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a3, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry. [ABSTRACT FROM AUTHOR]

The propagation within a one-dimensional photonic crystal of a single ultra-short and ultra-intense pulse delivered by an X-ray free-electron laser is analysed with the framework of the time-dependent coupled-wave theory in non-linear media. It is shown that the reflection and the transmission of an ultra-short pulse present a transient period conditioned by the extinction length and also the thickness of the structure for transmission. For ultra-intense pulses, non-linear effects are expected: they could give rise to numerous phenomena, bi-stability, self-induced transparency, gap solitons, switching, etc., which have been previously shown in the optical domain. [ABSTRACT FROM AUTHOR]

Hybrid approaches combine computational modeling techniques with low-resolution structural data. Such approaches have proven to be powerful tools to obtain new 3D structural and dynamical information on biological systems. Currently, major applications focus on cryo-EM data. Methods and some applications to construct atomic structural models of new functional states will be reviewed. In addition, possible extension to data from X-ray free electron laser, which currently provides low-resolution data, will be discussed. [ABSTRACT FROM AUTHOR]

ABC exporters are highly dynamic membrane proteins that span a huge spectrum of different conformations. A detailed integrated approach of cellular, biochemical and biophysical characterization of these 'open', 'closed' and other intermediate states is central to understanding their function. Almost 40 years after the discovery of the first ABC transporter, thanks to the enormous development in methodologies, a picture is slowly emerging to visualize how these fascinating molecules transport their substrates. This mini review summarizes some of the biophysical tools that have made a major impact in understanding the function of the ABC exporters. [ABSTRACT FROM AUTHOR]

Ultrafast X-ray crystallography of the photoactive yellow protein with femtosecond delays using an X-ray free electron laser has successfully probed the dynamics of an early Franck-Condon species. The femtosecond pump-probe application of protein crystallography represents a new experimental regime that provides an X-ray structural probe for coherent processes that were previously accessible primarily using ultrafast spectroscopy. We address how the optical regime of the visible pump, that is necessary to successfully resolve ultrafast structural differences, affects the motions that are measured using the technique. The sub-picosecond photochemical dynamics in PYP involves evolution of a mixture of electronic ground and excited state populations. Additional to photoisomerisation that is considered to proceed through activated barrier crossing, within the dephasing time structural motion include vibrational coherence arising from excited states, the ground state and a ground state intermediate under experimental conditions used for ultrafast crystallography. Intense optical pulses are required to convert population levels in PYP crystals that allow detection by X-ray crystallography, but the compromise currently needed for the optical bandwidth and power has consequences with regard to the contributions to the motions that are experimentally measured with femtosecond delays. We briefly review the ultrafast spectroscopy literature of the primary photoreactions of PYP and discuss relevant physical models taken from coherent control and femtosecond coherence spectroscopy literature that address both the population transfer as well as the vibrational coherences. We apply linear response theory, with the additional use of a high power approximation, of on-resonance impulsive vibrational coherence in the ground state and the non-impulsive coherence in the excited state and discuss experimental approaches to manipulate the coherence contributions. The results are generalised and extended to discuss the future capabilities of high repetition rate X-ray free electron laser instruments providing enhanced sensitivity to perform the crystallographic equivalent of an impulsive Raman measurement of vibrational coherence. [ABSTRACT FROM PUBLISHER]

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. [ABSTRACT FROM AUTHOR]

Basic features of the ultra-short Ti:sapphire laser for driving compact X-ray free electron laser (XFEL) seeded by laser-driven high harmonic generation (HHG) at SIOM (Shanghai, China) is presented. The laser system consists of four-stage Ti:sapphire amplifiers and can produce 8 J energy at 1 Hz repetition rate after the final power amplifier. The best shot-to-shot energy fluctuation is as low as 0.54% in rms value, which is a desirable characteristic for driving stable electron acceleration and HHG seed. After compression, maximal pulse energy of 5.6 J and pulse duration of 27 fs can be obtained, the corresponding pulse peak power is above 200 TW. To achieve full coherent XFEL, the amplified chirped laser beam is split into two beams after the final power amplifier. After compression in two independent compressors, the two laser beams can be used to drive laser wakefield acceleration (LWFA) and HHG respectively. The benefit of such a scheme is to improve the timing jitter and achieve all-optical synchronization between the electron beam and HHG seed in the near future. [ABSTRACT FROM AUTHOR]

The Pohang Accelerator Laboratory X-ray Free Electron Laser project, a new worldwide-user facility to deliver ultrashort, laser-like x-ray photon pulses, will begin user operation in 2017 after one year of commissioning. Initially, it will provide two beamlines for hard and soft x-rays, respectively, and two experimental end-stations for the hard x-ray beamline will be constructed by the end of 2015. This article introduces one of the two hard x-ray end-stations, which is for hard x-ray pump-probe experiments, and primarily outlines the overall design of this end-station and its critical components. The content of this article will provide useful guidelines for the planning of experiments conducted at the new facility. [ABSTRACT FROM AUTHOR]

The silicon sample irradiated with femtosecond soft X-ray pulses at the Linac Coherent Light Source has been studied with several synchrotron X-ray diffraction topographic methods at HASYLAB. The irradiations were performed for two different wavelengths combined with various impact energy controlled by means of the gas attenuator. The topographic investigation revealed characteristic images of the created craters included the inner region reflecting the X-rays at lower angle, coming most probably from part of the silicon melted during the irradiation. The melted region was surrounded by strained outer region, similar to those observed in the case of rod-like inclusion but less regular in view of some irregularity of the beam used for generation of the craters. It was observed that the higher impact energy higher dose of the irradiating pulses resulted in increasing diameter of the melted area of the crater and the range of the strained region around it. Some features of the monochromatic and white beam back reflection section images of the craters were reproduced in numerically simulated images approximating the strain field in the crater by a droplet containing uniformly distributed point inclusions. [ABSTRACT FROM AUTHOR]

Capturing the evolving geometric and electronic structure in the course of a chemical reaction or biological process is the principal aim of time-resolved X-ray spectroscopies. Recent technological and methodological improvements, such as high repetition rate lasers and femtosecond laser-electron slicing have made this a reality. The advent of X-ray free electron lasers introduces a paradigm shift in terms of the temporal resolution of X-ray spectroscopies, and offer exciting possibilities for time-resolved second-order X-ray spectroscopies and non-linear X-ray experiments. In parallel, the improved data quality is making it increasingly important to accurately simulate the fine spectroscopic details. This has been the driving force for new theoretical methods permitting a detailed interpretation of the spectra in terms of the geometrical and electronic properties of the system. In this contribution, we discuss recent experimental and theoretical developments in ultrafast X-ray absorption spectroscopies (XAS) and explore the new opportunities they offer. [ABSTRACT FROM AUTHOR]

Saturable absorption was recently observed in transmission measurements above the L II , III edge of pure Al thin films using ultra short X-ray pulses at a free-electron-laser (FEL) facility. The high fluence reachable by FEL pulses, the shortness of the pulse duration, and the typical lifetime of the excited state are all important factors enabling observation of the phenomenon. We devised a simplified theoretical approach describing the saturation phenomenon using a three-channel model containing ground, excited and relaxed states. This phenomenological model explicitly includes the interaction between the solid and photon field in a semi-classical way, and the resulting non-linear coupled equation is solved numerically. We successfully applied this model to recent experimental results obtained using FEL radiation. [ABSTRACT FROM AUTHOR]

We study a nonlinear Schrödinger equation which arises as an effective single particle model in X-ray free electron lasers (XFEL). This equation appears as a first principles model for the beam-matter interactions that would take place in an XFEL molecular imaging experiment in [A. Fratalocchi and G. Ruocco, Phys. Rev. Lett., 106 (2011), 105504]. Since XFEL are more powerful by several orders of magnitude than more conventional lasers, the systematic investigation of many of the standard assumptions and approximations has attracted increased attention. In this model the electrons move under a rapidly oscillating electromagnetic field, and the convergence of the problem to an effective time-averaged one is examined. We use an operator splitting pseudospectral method to investigate numerically the behavior of the model versus that of its time-averaged version in complex situations, namely the energy subcritical/mass supercritical case and in the presence of a periodic lattice. We find the time-averaged model to be an effective approximation, even close to blowup, for fast enough oscillations of the external field. This work extends previous analytical results for simpler cases [P. Antonelli, A. Athanassoulis, H. Hajaiej, and P. Markowich, Arch. Ration. Mech. Anal., 211 (2014), pp. 711-732]. [ABSTRACT FROM AUTHOR]

Highlights: [•] Time-resolved spectroscopy of fluoride crystals are carried out by EUV-FEL excitation. [•] Fluorescence at 160nm that is not reported in previous paper was observed from BaLiF. [•] Fluoride composition can be engineered to develop LED in the VUV region. [ABSTRACT FROM AUTHOR]

Abstract: Beamline mirrors and a monochromator were developed as key optical devices for the Japanese XFEL facility, SPring-8 Ångstrom Compact Free Electron Laser (SACLA). The optics were designed for transporting extremely intense, transversely coherent XFEL light to the experimental stations. The mirror system delivers a pink beam with high intensity and an energy range below 15keV, while the monochromator with Si (111) covers wider energy range of 4–30keV with 0.01% bandwidth. For realizing high stability and contamination-free environment, the mechanics of these optical components were designed to have high stiffness with ultra-high vacuum (UHV) compatibility. After 100 days of operation, no radiation damage was observed on the mirror surfaces. [Copyright &y& Elsevier]

The Linac Coherent Light Source (LCLS) is the first X-ray free electron laser to achieve lasing at subnanometer wavelengths (6 Å). LCLS is poised to reach even shorter wavelengths (1.5 Å) and thus holds the promise of single molecular imaging at atomic resolution. The initial operation at a photon energy of 2 keV provides the possibility to perform the first experiments on damage to biological particles, and to assess the limitations to coherent imaging of biological samples, which are directly relevant at atomic resolution. In this paper we theoretically investigate the damage formation and detection possibilities for a biological crystal, by employing and comparing two different damage models with complementary strengths. Molecular dynamics provides a discrete approach which investigates structural details at the atomic level by tracking all atoms in the real space. Our continuum model is based on a non-local thermodynamics equilibrium code with atomic kinetics and radiation transfer and can treat hydrodynamic expansion of the entire system. The latter approach captures the essential features of atomic displacements, without taking into account structural information and intrinsic atomic movements. This proves to be a powerful computational tool for many samples, including biological crystals, which will be studied with X-ray free electron lasers. [ABSTRACT FROM AUTHOR]

Abstract: Adaptive Gain Integrating Pixel Detector (AGIPD) is currently under development for the European X-ray Free Electron Laser (XFEL). It is a hybrid pixel detector with a specifically developed readout chip bump bonded to a silicon sensor. The chip is being designed in IBM CMOS technology. This paper is focused on the readout chip design. The main challenges for this chip are: the high dynamic range with single photon sensitivity, the long storage chain with a long hold time (99ms), and the high radiation dose (up to 100MGy). A charge integrating amplifier with a gain adaptive to the number of incoming photons is combined with a correlated double sampling (CDS) buffer to achieve the required dynamic range and single photon sensitivity. Several techniques are implemented in the storage cell design in order to reduce leakage current and signal-dependent charge injection. Four prototype chips have been designed for testing the performance of the implemented switches, capacitors, amplifiers, storage cells and periphery circuitry. The recently submitted test chip has a 16×16 pixel matrix, 100 storage cells in each pixel and a periphery circuitry for accessing and controlling the pixels and storage cells. [ABSTRACT FROM AUTHOR]

Abstract: An iron doped, hydrothermal method-grown, zinc oxide (ZnO) scintillator was demonstrated to exhibit an over 10 times faster response time of its excitonic fluorescence compared with an undoped-ZnO crystal. For X-ray free electron laser (XFEL) excitation, the fluorescence rise and decay time constants were measured to be 2.1ps and 70ps, respectively. Accurate timing control of extreme ultraviolet (EUV) femtosecond pulses necessitate temporal jitters to be evaluated. Results suggest that this scintillator’s response time is sufficient to allow the evaluation of sub 100-ps jitter in XFEL measurement systems and will be crucial in pump and probe experiments in the future. [ABSTRACT FROM AUTHOR]

Abstract: The Paul Scherrer Institute is planning the construction of an X-ray free electron laser (SwissFEL), which will produce 20-fs pulses of coherent X-rays in the wavelength range 0.1–7nm, with peak brightness approximately 1010 times that of a third-generation synchrotron beamline. The brightness, the coherence and the short pulses will provide opportunities for performing novel science in the fields of chemistry, biochemistry, solid-state physics and materials science. It is planned that the SwissFEL will be operational by the end of 2016. The present article focuses on promising SwissFEL applications in the field of time-resolved X-ray scattering from chemical systems. [Copyright &y& Elsevier]

Abstract: In segmented undulator systems with adjustable gaps, phase shifters are needed to exactly control the phase retardation between electrons and the radiation field over the entire length. A phase shifter based on permanent magnet technology for the use in the European X-ray free electron laser (XFEL) has been developed and tested. Its magnetic design is explained in detail. Requirements and specifications are discussed with special considerations of the boundary conditions set by the XFEL. Magnetic test results are presented and are thoroughly discussed. Special attention is given to the future operation in the XFEL. [Copyright &y& Elsevier]

Abstract: The Linac Coherent Light Source (LCLS) at SLAC will be the world''s first X-ray free electron laser when it becomes operational in 2009. Pulses of X-ray laser light from LCLS will be many orders of magnitude brighter and several orders of magnitude shorter than what can be produced by other X-ray sources available in the world. These characteristics will enable frontier new science in many areas. This paper describes the LCLS beam parameters and its lay-out. Results of the Monte Carlo calculations for the shielding design of the electron dump line, radiation damage to undulator, the residual radiation and the soil activation around the electron dump are presented. [Copyright &y& Elsevier]