Development Of X-ray Free Electron Lasers Research Articles

Novel Ultrafast Molecular Imaging Based on the Combination of X-ray and Electron Diffraction

Recent development of X-ray free-electron lasers and megaelectronvolt radio-frequency electron guns have made ultrafast X-ray and electron diffraction measurements possible, thereby capturing chemical dynamics with atomic-spatial and femtosecond-temporal resolutions. We present a unified formulation of standard homodyne-detected and heterodyne-detected signals for both techniques. Noting that X-rays scatter from molecular electrons while electrons scatter from both molecular electrons and nuclei, we show how the two diffraction signals can be combined to reveal novel chemical information that is unavailable by solely using each technique alone. By subtracting the homodyne-detected X-ray and electron diffraction signals, a mixed electronic-nuclear interference in electron diffraction can be identified with a self-heterodyne nature for the direct imaging of attosecond electron dynamics where the scattering off molecular nuclei serves as a local oscillator for the scattering off molecular electrons. By subtracting heterodyne-detected X-ray and electron diffraction, the purely nuclear charge density can be singled out.

Arrival time diagnosis method of high refrequency hard X-ray free electron laser

X-ray free electron laser (XFEL) pulse time diagnosis technology is often used to detect the relative arrival time of XFEL pulse and auxiliary laser near the experimental station. It is an important auxiliary technology and provides a reference signal for the pump-probe pulse in the XFEL laser pump-probe experiment. With the development of XFEL towards high repetition frequency and short pulse, higher requirements are put forward for diagnostic frequency, pump sample and resolution in time diagnosis. The technology is realized by the pump-probe method and optical cross-correlation method. When the XFEL pulse is incident on the high-bandwidth semiconductor solid target instantaneously, the complex refractive index of the solid target will change, then the arrival time of XFEL will be encoded in the mutation space. In thiswork, we design an XFEL pulse arrival time diagnostic device based on two methods: spatial coding and spectral coding. In this framework, the interaction between X-ray and solid target is explored by Beer's absorption theory and atomic scattering theory. Therefore, the response to X-ray absorption and refractive index in this process are investigated, and the solid target selection model is developed. This model is used to analyze the influence of solid target type and thickness in diagnosis, while avoiding situations where the sample is too hot due to a lot X-ray absorption. Moreover, the influence of hard X-ray on sample temperature at high frequency is considered, and the samples suitable for different X-ray bands are given. The chirped pulse modulation in spectral coding is analyzed, and the influence of dispersion medium and pulse parameters on the diagnostic resolution of spectral coding are obtained. Finally, the error effects of X-ray, spatial coding and spectral coding on the results are analyzed, and the analysis methods and consideration factors of the two coding methods are given. This work is of great significance in using the XFEL pulse arrival time diagnostic device.

Speckle contrast of interfering fluorescence X-rays

With the development of X-ray free-electron lasers (XFELs), producing pulses of femtosecond durations comparable with the coherence times of X-ray fluorescence, it has become possible to observe intensity-intensity correlations due to the interference of emission from independent atoms. This has been used to compare durations of X-ray pulses and to measure the size of a focusedX-raybeam, for example. Here it is shown that it is also possible to observe the interference of fluorescence photons through the measurement of the speckle contrast of angle-resolved fluorescence patterns. Speckle contrast is often used as a measure of the degree of coherence of the incident beam or the fluctuations of the illuminated sample as determined from X-ray diffraction patterns formed by elastic scattering, rather than from fluorescence patterns as addressed here. Commonly used approaches to estimate speckle contrast were found to suffer when applied to XFEL-generated fluorescence patterns due to low photon counts and a significant variation of the excitation pulse energy from shot to shot. A new method to reliably estimate speckle contrast under such conditions, using a weighting scheme, is introduced. The method is demonstrated by comparing the speckle contrast of fluorescence observed with pulses of 3 fs to 15 fs duration.

Explanation of the anomalous redshift on a nonlinear X-ray Compton scattering spectrum by a bound electron.

Nonlinear Compton scattering is an inelastic scattering process where a photon is emitted due to the interaction between an electron and an intense laser field. With the development of X-ray free-electron lasers, the intensity of X-ray laser is greatly enhanced, and the signal from X-ray nonlinear Compton scattering is no longer weak. Although the nonlinear Compton scattering by an initially free electron has been thoroughly investigated, the mechanism of nonrelativistic nonlinear Compton scattering of X-ray photons by bound electrons is unclear yet. Here, we present a frequency-domain formulation based on the nonperturbative quantum electrodynamics to study nonlinear Compton scattering of two photons by an atom in a strong X-ray laser field. In contrast to previous theoretical works, our results clearly reveal the existence of a redshift phenomenon observed experimentally by Fuchs et al.(Nat. Phys.)11, 964(2015) and suggest its origin as the binding energy of the electron as well as the momentum transfer from incident photons to the electron during the scattering process. Our work builds a bridge between intense-laser atomic physics and Compton scattering processes that can be used to study atomic structure and dynamics at high laser intensities.

Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes.

The metal centres in metalloenzymes and molecular catalysts are responsible for the rearrangement of atoms and electrons during complex chemical reactions, and they enable selective pathways of charge and spin transfer, bond breaking/making and the formation of new molecules. Mapping the electronic structural changes at the metal sites during the reactions gives a unique mechanistic insight that has been difficult to obtain to date. The development of X-ray free-electron lasers (XFELs) enables powerful new probes of electronic structure dynamics to advance our understanding of metalloenzymes. The ultrashort, intense and tunable XFEL pulses enable X-ray spectroscopic studies of metalloenzymes, molecular catalysts and chemical reactions, under functional conditions and in real time. In this Technical Review, we describe the current state of the art of X-ray spectroscopy studies at XFELs and highlight some new techniques currently under development. With more XFEL facilities starting operation and more in the planning or construction phase, new capabilities are expected, including high repetition rate, better XFEL pulse control and advanced instrumentation. For the first time, it will be possible to make real-time molecular movies of metalloenzymes and catalysts in solution, while chemical reactions are taking place.

Classification of diffraction patterns in single particle imaging experiments performed at x-ray free-electron lasers using a convolutional neural network

Single particle imaging (SPI) is a promising method of native structure determination, which has undergone fast progress with the development of x-ray free-electron lasers. Large amounts of data are collected during SPI experiments, driving the need for automated data analysis. The necessary data analysis pipeline has a number of steps including binary object classification (single versus non-single hits). Classification and object detection are areas where deep neural networks currently outperform other approaches. In this work, we use the fast object detector networks YOLOv2 and YOLOv3. By exploiting transfer learning, a moderate amount of data is sufficient to train the neural network. We demonstrate here that a convolutional neural network can be successfully used to classify data from SPI experiments. We compare the results of classification for the two different networks, with different depth and architecture, by applying them to the same SPI data with different data representation. The best results are obtained for diffracted intensity represented by color images on a linear scale using YOLOv2 for classification. It shows an accuracy of about 95% with precision and recall of about 50% and 60%, respectively, in comparison to manual data classification.

The Sensitivity of the Pair-Angle Distribution Function to Protein Structure

The continued development of X-ray free-electron lasers and serial crystallography techniques has opened up new experimental frontiers. Nanoscale dynamical processes such as crystal growth can now be probed at unprecedented time and spatial resolutions. Pair-angle distribution function (PADF) analysis is a correlation-based technique that has the potential to extend the limits of current serial crystallography experiments, by relaxing the requirements for crystal order, size and number density per exposure. However, unlike traditional crystallographic methods, the PADF technique does not recover the electron density directly. Instead it encodes substantial information about local three-dimensional structure in the form of three- and four-body correlations. It is not yet known how protein structure maps into the many-body PADF correlations. In this paper, we explore the relationship between the PADF and protein conformation. We calculate correlations in reciprocal and real space for model systems exhibiting increasing degrees of order and secondary structural complexity, from disordered polypeptides, single alpha helices, helix bundles and finally a folded 100 kilodalton protein. These models systems inform us about the distinctive angular correlations generated by bonding, polypeptide chains, secondary structure and tertiary structure. They further indicate the potential to use angular correlations as a sensitive measure of conformation change that is complementary to existing structural analysis techniques.

The development of XFELs

X-ray free-electron lasers (XFELs) have rapidly developed into unique tools for probing diverse systems of interest to different scientific disciplines with angstrom–femtosecond resolution. Claudio Pellegrini provides an overview of the milestones in the development of XFELs and their unique capabilities.

Is radiation damage the limiting factor in high-resolution single particle imaging with X-ray free-electron lasers?

The prospect of single particle imaging with atomic resolution is one of the scientific drivers for the development of X-ray free-electron lasers. The assumption since the beginning has been that damage to the sample caused by intense X-ray pulses is one of the limiting factors for achieving subnanometer X-ray imaging of single particles and that X-ray pulses need to be as short as possible. Based on the molecular dynamics simulations of proteins in X-ray fields of various durations (5 fs, 25 fs, and 50 fs), we show that the noise in the diffracted signal caused by radiation damage is less than what can be expected from other sources, such as sample inhomogeneity and X-ray shot-to-shot variations. These findings show a different aspect of the feasibility of high-resolution single particle imaging using free-electron lasers, where employing X-ray pulses of longer durations could still provide a useful diffraction signal above the noise due to the Coulomb explosion.

DIY XES - development of an inexpensive, versatile, and easy to fabricate XES analyzer and sample delivery system.

The application of X-ray emission spectroscopy (XES) has grown substantially with the development of X-ray free electron lasers, third and fourth generation synchrotron sources and high-power benchtop sources. By providing the high X-ray flux required for XES, these sources broaden the availability and application of this method of probing electronic structure. As the number of sources increase, so does the demand for X-ray emission detection and sample delivery systems that are cost effective and customizable. Here, we present a detailed fabrication protocol for von Hamos X-ray optics and give details for a 3D-printed spectrometer design. Additionally, we outline an automated, externally triggered liquid sample delivery system that can be used to repeatedly deliver nanoliter droplets onto a plastic substrate for measurement. These systems are both low cost, efficient and easy to recreate or modify depending on the application. A low cost multiple X-ray analyzer system enables measurement of dilute samples, whereas the sample delivery limits sample loss and replaces spent sample with fresh sample in the same position. While both systems can be used in a wide range of applications, the design addresses several challenges associated specifically with time-resolved XES (TRXES). As an example application, we show results from TRXES measurements of photosystem II, a dilute, photoactive protein.

Demonstration of femtosecond X-ray pump X-ray probe diffraction on protein crystals.

The development of X-ray free-electron lasers (XFELs) has opened the possibility to investigate the ultrafast dynamics of biomacromolecules using X-ray diffraction. Whereas an increasing number of structures solved by means of serial femtosecond crystallography at XFELs is available, the effect of radiation damage on protein crystals during ultrafast exposures has remained an open question. We used a split-and-delay line based on diffractive X-ray optics at the Linac Coherent Light Source XFEL to investigate the time dependence of X-ray radiation damage to lysozyme crystals. For these tests, crystals were delivered to the X-ray beam using a fixed-target approach. The presented experiments provide probe signals at eight different delay times between 19 and 213 femtoseconds after a single pump event, thereby covering the time-scales relevant for femtosecond serial crystallography. Even though significant impact on the crystals was observed at long time scales after exposure with a single X-ray pulse, the collected diffraction data did not show significant signal reduction that could be assigned to beam damage on the crystals in the sampled time window and resolution range. This observation is in agreement with estimations of the applied radiation dose, which in our experiment was clearly below the values expected to cause damage on the femtosecond time scale. The experiments presented here demonstrate the feasibility of time-resolved pump-multiprobe X-ray diffraction experiments on protein crystals.

The Linac Coherent Light Source: Recent Developments and Future Plans

The development of X-ray free-electron lasers (XFELs) has launched a new era in X-ray science by providing ultrafast coherent X-ray pulses with a peak brightness that is approximately one billion times higher than previous X-ray sources. The Linac Coherent Light Source (LCLS) facility at the SLAC National Accelerator Laboratory, the world’s first hard X-ray FEL, has already demonstrated a tremendous scientific impact across broad areas of science. Here, a few of the more recent representative highlights from LCLS are presented in the areas of atomic, molecular, and optical science; chemistry; condensed matter physics; matter in extreme conditions; and biology. This paper also outlines the near term upgrade (LCLS-II) and motivating science opportunities for ultrafast X-rays in the 0.25–5 keV range at repetition rates up to 1 MHz. Future plans to extend the X-ray energy reach to beyond 13 keV (<1 Å) at high repetition rate (LCLS-II-HE) are envisioned, motivated by compelling new science of structural dynamics at the atomic scale.

Undulators and generation of X-ray pulses in free-electron lasers with self-amplified spontaneous emission

The results of theoretical examination and comparative analysis of synchrotron radiation sources (specifically, undulators and X-ray free-electron lasers (FELs)) are presented. The problem of generation of shorter radiation pulses is prioritized; undulator systems and their corresponding FELs, which are considered to be the most promising in terms of generation of high-frequency ultrashort pulses of such radiation (in particular, in the X-ray range) are studied. The possibility of generation of higher harmonics is explored. The advantages and disadvantages of single-pass (with no reflecting elements) and multi-pass (with mirrors) FEL lasing schemes are revealed. The potential to reduce the duration of laser pulses produced by undulators and FELs and use them as sources of femtosecond pulses is investigated. The prospects for further development of X-ray free-electron lasers and the ways to improve the quality of their radiation with the given parameters are discussed.

XMDYNandXATOM: versatile simulation tools for quantitative modeling of X-ray free-electron laser induced dynamics of matter

Rapid development of X-ray free-electron laser (XFEL) science has taken place in recent years owing to the consecutive launch of large-scale XFEL instruments around the world. Research areas such as warm dense matter physics and coherent X-ray imaging take advantage of the unprecedentedly high intensities of XFELs. A single XFEL pulse can induce very complex dynamics within matter initiated by core-hole photoionization. Owing to this complexity, theoretical modeling revealing details of the excitation and relaxation of irradiated matter is important for the correct interpretation of the measurements and for proposing new experiments.XMDYNis a computer simulation tool developed for modeling dynamics of matter induced by high-intensity X-rays. It utilizes atomic data calculated by theab initio XATOMtoolkit. Here these tools are discussed in detail.

A multiple-common-lines method to determine the orientation of snapshot diffraction patterns from single particles.

With the development of X-ray free-electron lasers (XFELs), it is possible to determine the three-dimensional structures of noncrystalline objects with coherent X-ray diffraction imaging. In this diffract-and-destroy mode, many snapshot diffraction patterns are obtained from the identical objects which are presented one by one in random orientations to the XFEL beam. Determination of the orientation of an individual object is essential for reconstruction of a three-dimensional structure. Here a new method, called the multiple-common-lines method, has been proposed to determine the orientations of high- and low-signal snapshot diffraction patterns. The mean errors of recovered orientations (α, β, γ) of high- and low-signal patterns are about 0.14, 0.06, 0.12 and 0.77, 0.31, 0.60°, respectively; both sets of errors can meet the requirements of the reconstruction of a three-dimensional structure.

Crystallography on a chip

A new chip-based crystal-mounting approach for rapid room-temperature data collection from numerous crystals is described. This work was motivated by the recent development of X-ray free-electron lasers. These novel sources deliver very intense femtosecond X-ray pulses that promise to yield high-resolution diffraction data of nanocrystals before their destruction by radiation damage. Thus, the concept of `diffraction before destruction' requires rapid replenishment of the sample for each exposure. The chip promotes the self-assembly of an array of protein crystals on a surface. Rough features on the surface cause the crystals to adopt random orientations, allowing efficient sampling of reciprocal space.

Development of X-ray Free-Electron Lasers

Development of X-ray Free-Electron Lasers

Three-dimensional mapping of a deformation field inside a nanocrystal

Coherent X-ray diffraction imaging is a rapidly advancing form of microscopy: diffraction patterns, measured using the latest third-generation synchrotron radiation sources, can be inverted to obtain full three-dimensional images of the interior density within nanocrystals. Diffraction from an ideal crystal lattice results in an identical copy of this continuous diffraction pattern at every Bragg peak. This symmetry is broken by the presence of strain fields, which arise from the epitaxial contact forces that are inevitable whenever nanocrystals are prepared on a substrate. When strain is present, the diffraction copies at different Bragg peaks are no longer identical and contain additional information, appearing as broken local inversion symmetry about each Bragg point. Here we show that one such pattern can nevertheless be inverted to obtain a 'complex' crystal density, whose phase encodes a projection of the lattice deformation. A lead nanocrystal was crystallized in ultrahigh vacuum from a droplet on a silica substrate and equilibrated close to its melting point. A three-dimensional image of the density, obtained by inversion of the coherent X-ray diffraction, shows the expected facetted morphology, but in addition reveals a real-space phase that is consistent with the three-dimensional evolution of a deformation field arising from interfacial contact forces. Quantitative three-dimensional imaging of lattice strain on the nanometre scale will have profound consequences for our fundamental understanding of grain interactions and defects in crystalline materials. Our method of measuring and inverting diffraction patterns from nanocrystals represents a vital step towards the ultimate goal of atomic resolution single-molecule imaging that is a prominent justification for development of X-ray free-electron lasers.