X-ray Free-electron Laser Radiation Research Articles

Comparing the spatial coherence of the natural and focused X-rays from a free electron laser.

The degree of spatial coherence, as basic characteristics of the radiation, becomes an important guide to evaluate the performance of X-rays from newly introduced advanced light sources including the X-ray free electron laser (XFEL). Often the modification of the X-ray wavefronts to fulfill various applications is necessary, but also there is the need to preserve its coherence property. However, experimental investigation directly comparing the coherence property of focused X-ray radiations with the unmodified ones has not been available. We have performed Young's double-slit experiments by recording diffraction patterns both from slit apertures for unfocused XFEL radiation and from pairs of Au nanoparticles for one-micron focused XFEL radiations. The results confirm that the degree of spatial coherence is preserved for well-built K-B focusing mirrors.

Diffraction properties of a strongly bent diamond crystal used as a dispersive spectrometer for XFEL pulses

Self-amplified spontaneous emission (SASE) enables X-ray free-electron lasers (XFELs) to generate hard X-ray pulses of sub-100fs duration. However, due to the stochastic nature of SASE, the energy spectrum fluctuates from pulse to pulse. Many experiments that employ XFEL radiation require the resolution of the spectrum of each pulse. The work presented here investigates the capacity of a thin strongly bent diamond crystal to resolve the energy spectra of hard X-ray SASE pulses by studying its diffraction properties. Rocking curves of the symmetric C*(440) reflection have been measured for different bending radii. The experimental data match the theoretical modelling based on the Takagi-Taupin equations of dynamical diffraction. A uniform strain gradient has proven to be a valid model of strain deformations in the crystal.

ClickX: a visualization-based program for preprocessing of serial crystallography data.

Serial crystallography is a powerful technique in structure determination using many small crystals at X-ray free-electron laser or synchrotron radiation facilities. The large diffraction data volumes require high-throughput software to preprocess the raw images for subsequent analysis. ClickX is a program designated for serial crystallography data preprocessing, capable of rapid data sorting for online feedback and peak-finding refinement by parameter optimization. The graphical user interface (GUI) provides convenient access to various operations such as pattern visualization, statistics plotting and parameter tuning. A batch job module is implemented to facilitate large-data-volume processing. A two-step geometry calibration for single-panel detectors is also integrated into the GUI, where the beam center and detector tilting angles are optimized using an ellipse center shifting method first, then all six parameters, including the photon energy and detector distance, are refined together using a residual minimization method. Implemented in Python, ClickX has good portability and extensibility, so that it can be installed, configured and used on any computing platform that provides a Python interface or common data file format. ClickX has been tested in online analysis at the Pohang Accelerator Laboratory X-ray Free-Electron Laser, Korea, and the Linac Coherent Light Source, USA. It has also been applied in post-experimental data analysis. The source code is available via https://github.com/LiuLab-CSRC/ClickX under a GNU General Public License.

Radiation damage in protein crystallography at X-ray free-electron lasers.

Radiation damage is still the most limiting factor in obtaining high-resolution structures of macromolecules in crystallographic experiments at synchrotrons. With the advent of X-ray free-electron lasers (XFELs) that produce ultrashort and highly intense X-ray pulses, it became possible to outrun most of the radiation-damage processes occurring in the sample during exposure to XFEL radiation. Although this is generally the case, several experimental and theoretical studies have indicated that structures from XFELs may not always be radiation-damage free. This is especially true when higher intensity pulses are used and protein molecules that contain heavy elements in their structures are studied. Here, the radiation-damage mechanisms that occur in samples exposed to XFEL pulses are summarized, results that show indications of radiation damage are reviewed and methods that can partially overcome it are discussed.

Ultrafast Self-Induced X-Ray Transparency and Loss of Magnetic Diffraction.

Using ultrafast ≃2.5 fs and ≃25 fs self-amplified spontaneous emission pulses of increasing intensity and a novel experimental scheme, we report the concurrent increase of stimulated emission in the forward direction and loss of out-of-beam diffraction contrast for a Co/Pd multilayer sample. The experimental results are quantitatively accounted for by a statistical description of the pulses in conjunction with the optical Bloch equations. The dependence of the stimulated sample response on the incident intensity, coherence time, and energy jitter of the employed pulses reveals the importance of increased control of x-ray free electron laser radiation.

Two-photon absorption of soft X-ray free electron laser radiation by graphite near the carbon K-absorption edge

We have examined the transmission of soft X-ray pulses from the FERMI free electron laser through carbon films of varying thickness, quantifying nonlinear effects of pulses above and below the carbon K-edge. At typical of soft X-ray free electron laser intensities, pulses exhibit linear absorption at photon energies above and below the K-edge, ∼308 and ∼260 eV, respectively; whereas two-photon absorption becomes significant slightly below the K-edge, ∼284.2 eV. The measured two-photon absorption cross section at 284.18 eV (∼6 × 10−48 cm4 s) is 7 orders of magnitude above what is expected from a simple theory based on hydrogen-like atoms – a result of resonance effects.

ANALYSIS OF A TWO-CRYSTAL DELAY LINE FOR FEMTOSECOND PULSES OF THE X-RAY FREE ELECTRON LASER

Using the methods of statistical optics the formation of delayed X-ray pulses in the diffraction reflection of an incident pulse with an arbitrary degree of temporal coherence from a system of parallel crystals with different lattice periods is considered. The results are of interest for constructing delay lines in experiments with a time resolution of the pump-and-probe type and realizing of the self-seeding mode to increase the degree of temporal coherence of the X-ray free-electron laser radiation.
 A rigorous theory of dynamic diffraction in Bragg geometry is applied to the diffraction reflection of short X-ray pulses from a system of two parallel crystals with arbitrary thicknesses, and also, for a system of two pairs of parallel crystals. The dependence of the delay time and the intensity of the delayed pulses on the thickness of the crystals and the distances between them are analyzed. Since the pulses from the X-ray free electron laser have high spatial coherence, i.e. a small angular divergence, but very poor temporal coherence, special attention is paid to the effect of the degree of temporal coherence on the width of the energy spectrum of the incident pulses and on the influence of this width on the intensity of the delayed pulses.

ANALYSIS OF A TWO-CRYSTAL DELAY LINE FOR FEMTOSECOND PULSES OF THE X-RAY FREE ELECTRON LASER

Using the methods of statistical optics the formation of delayed X-ray pulses in the diffraction reflection of an incident pulse with an arbitrary degree of temporal coherence from a system of parallel crystals with different lattice periods is considered. The results are of interest for constructing delay lines in experiments with a time resolution of the pump-and-probe type and realizing of the self-seeding mode to increase the degree of temporal coherence of the X-ray free-electron laser radiation.
 A rigorous theory of dynamic diffraction in Bragg geometry is applied to the diffraction reflection of short X-ray pulses from a system of two parallel crystals with arbitrary thicknesses, and also, for a system of two pairs of parallel crystals. The dependence of the delay time and the intensity of the delayed pulses on the thickness of the crystals and the distances between them are analyzed. Since the pulses from the X-ray free electron laser have high spatial coherence, i.e. a small angular divergence, but very poor temporal coherence, special attention is paid to the effect of the degree of temporal coherence on the width of the energy spectrum of the incident pulses and on the influence of this width on the intensity of the delayed pulses.

Contrasting behavior of covalent and molecular carbon allotropes exposed to extreme ultraviolet and soft x-ray free-electron laser radiation

All carbon materials, e.g., amorphous carbon (a-C) coatings and C60 fullerene thin films, play an important role in short-wavelength free-electron laser (FEL) research motivated by FEL optics development and prospective nanotechnology applications. Responses of a-C and C60 layers to the extreme ultraviolet (SPring-8 Compact SASE Source in Japan) and soft x-ray (free-electron laser in Hamburg) free-electron laser radiation are investigated by Raman spectroscopy, differential interference contrast, and atomic force microscopy. A remarkable difference in the behavior of covalent (a-C) and molecular (C60) carbonaceous solids is demonstrated under these irradiation conditions. Low thresholds for ablation of a fullerene crystal (estimated to be around 0.15 eV/atom for C60 vs 0.9 eV/atom for a-C in terms of the absorbed dose) are caused by a low cohesive energy of fullerene crystals. An efficient mechanism of the removal of intact C60 molecules from the irradiated crystal due to Coulomb repulsion of fullerene-cage cation radicals formed by the ionizing radiation is revealed by a detailed modeling.

Radiation damage in protein crystallography at X-ray free-electron lasers

Radiation damage is still the most limiting factor in obtaining high-resolution structures of macromolecules in crystallographic experiments at synchrotrons. With the advent of X-ray free-electron lasers (XFELs) that produce ultrashort and highly intense X-ray pulses, it became possible to outrun most of the radiation-damage processes occurring in the sample during exposure to XFEL radiation. Although this is generally the case, several experimental and theoretical studies have indicated that structures from XFELs may not always be radiation-damage free. This is especially true when higher intensity pulses are used and protein molecules that contain heavy elements in their structures are studied. Here, the radiation-damage mechanisms that occur in samples exposed to XFEL pulses are summarized, results that show indications of radiation damage are reviewed and methods that can partially overcome it are discussed.

High-harmonic x-ray undulator radiation for nanoscale-wavelength free-electron lasers

We explore the undulator radiation (UR) from relativistic electrons in two-frequency undulators intended for use in x-ray free-electron lasers (FELs). We use an exact analytical account for the major sources of spectral line broadening of the spontaneous UR to describe the UR spectrum, intensity and emission line shape. We also show possible partial compensation of the off-axis divergence by ad hoc imposed weak transverse constant magnetic components. The harmonic radiation of the two-frequency undulator is studied. High-harmonics amplification in the two-frequency undulator is underlined for possible use in x-ray FELs and the generation of powerful x-ray radiation is demonstrated. The evolution of high harmonic power is studied with the help of the developed phenomenological self-amplified spontaneous emission FEL model. The performance of a high-gain harmonic generation FEL with a two-frequency undulator–prebuncher is explored. Harmonic multiplication cascades are introduced in FELs to obtain nanometer x-ray FEL radiation in reduced size FELs at ~30 m with seed from commercially available excimer laser and ~0.5 GeV electrons.

High resolution beam profiling of X-ray free electron laser radiation by polymer imprint development

High resolution metrology of beam profiles is presently a major challenge at X-ray free electron lasers. We demonstrate a characterization method based on beam imprints in poly (methyl methacrylate). By immersing the imprints formed at 47.8 eV into organic solvents, the regions exposed to the beam are removed similar to resist development in grayscale lithography. This allows for extending the sensitivity of the method by more than an order of magnitude compared to the established analysis of imprints created solely by ablation. Applying the Beer-Lambert law for absorption, the intensity distribution in a micron-sized focus can be reconstructed from one single shot with a high dynamic range, exceeding 103. The procedure described here allows for beam characterization at free electron lasers revealing even faint beam tails, which are not accessible when using ablation imprint methods. We demonstrate the greatly extended dynamic range on developed imprints taken in focus of conventional Fresnel zone plates and spiral zone plates producing beams with a topological charge.

X-ray Free Electron Laser Radiation Damage through the S-State Cycle of the Oxygen-Evolving Complex of Photosystem II.

The oxygen-evolving complex (OEC) catalyzes water-splitting through a reaction mechanism that cycles the OEC through the "S-state" intermediates. Understanding structure/function relationsships of the S-states is crucial for elucidating the water-oxidation mechanism. Serial femtosecond X-ray crystallography has been used to obtain radiation damage-free structures. However, it remains to be established whether "diffraction-before-destruction" is actually accomplished or if significant changes are produced by the high-intensity X-ray pulses during the femtosecond scattering measurement. Here, we use ab initio molecular dynamics simulations to estimate the extent of structural changes induced on the femtosecond time scale. We found that the radiation damage is dependent on the bonding and charge of each atom in the OEC, in a manner that may provide lessons for XFEL studies of other metalloproteins. The maximum displacement of Mn and oxygen centers is 0.25 and 0.39 Å, respectively, during the 50 fs pulse, which is significantly smaller than the uncertainty given the 1.9 Å resolution of the current PSII crystal structures. However, these structural changes might be detectable when comparing isomorphous Fourier differences of electron density maps of the different S-states. One conclusion is that pulses shorter than 15 fs should be used to avoid significant radiation damage.

Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser.

A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked β-strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual α-synuclein amyloids.

Photon Beam Transport and Scientific Instruments at the European XFEL

European XFEL is a free-electron laser (FEL) user facility providing soft and hard X-ray FEL radiation to initially six scientific instruments. Starting user operation in fall 2017 European XFEL will provide new research opportunities to users from science domains as diverse as physics, chemistry, geo- and planetary sciences, materials sciences or biology. The unique feature of European XFEL is the provision of high average brilliance in the soft and hard X-ray regime, combined with the pulse properties of FEL radiation of extreme peak intensities, femtosecond pulse duration and high degree of coherence. The high average brilliance is achieved through acceleration of up to 27,000 electron bunches per second by the super-conducting electron accelerator. Enabling the usage of this high average brilliance in user experiments is one of the major instrumentation drivers for European XFEL. The radiation generated by three FEL sources is distributed via long beam transport systems to the experiment hall where the scientific instruments are located side-by-side. The X-ray beam transport systems have been optimized to maintain the unique features of the FEL radiation which will be monitored using build-in photon diagnostics. The six scientific instruments are optimized for specific applications using soft or hard X-ray techniques and include integrated lasers, dedicated sample environment, large area high frame rate detector(s) and computing systems capable of processing large quantities of data.

Kinetic modeling of x-ray laser-driven solid Al plasmas via particle-in-cell simulation.

Solid-density plasmas driven by intense x-ray free-electron laser (XFEL) radiation are seeded by sources of nonthermal photoelectrons and Auger electrons that ionize and heat the target via collisions. Simulation codes that are commonly used to model such plasmas, such as collisional-radiative (CR) codes, typically assume a Maxwellian distribution and thus instantaneous thermalization of the source electrons. In this study, we present a detailed description and initial applications of a collisional particle-in-cell code, picls, that has been extended with a self-consistent radiation transport model and Monte Carlo models for photoionization and KLL Auger ionization, enabling the fully kinetic simulation of XFEL-driven plasmas. The code is used to simulate two experiments previously performed at the Linac Coherent Light Source investigating XFEL-driven solid-density Al plasmas. It is shown that picls-simulated pulse transmissions using the Ecker-Kröll continuum-lowering model agree much better with measurements than do simulations using the Stewart-Pyatt model. Good quantitative agreement is also found between the time-dependent picls results and those of analogous simulations by the CR code scfly, which was used in the analysis of the experiments to accurately reproduce the observed Kα emissions and pulse transmissions. Finally, it is shown that the effects of the nonthermal electrons are negligible for the conditions of the particular experiments under investigation.

Asymmetry in serial femtosecond crystallography data.

Serial crystallography is an increasingly important approach to protein crystallography that exploits both X-ray free-electron laser (XFEL) and synchrotron radiation. Serial crystallography recovers complete X-ray diffraction data by processing and merging diffraction images from thousands of randomly oriented non-uniform microcrystals, of which all observations are partial Bragg reflections. Random fluctuations in the XFEL pulse energy spectrum, variations in the size and shape of microcrystals, integrating over millions of weak partial observations and instabilities in the XFEL beam position lead to new types of experimental errors. The quality of Bragg intensity estimates deriving from serial crystallography is therefore contingent upon assumptions made while modeling these data. Here it is observed that serial femtosecond crystallography (SFX) Bragg reflections do not follow a unimodal Gaussian distribution and it is recommended that an idealized assumption of single Gaussian peak profiles be relaxed to incorporate apparent asymmetries when processing SFX data. The phenomenon is illustrated by re-analyzing data collected from microcrystals of the Blastochloris viridis photosynthetic reaction center and comparing these intensity observations with conventional synchrotron data. The results show that skewness in the SFX observations captures the essence of the Wilson plot and an empirical treatment is suggested that can help to separate the diffraction Bragg intensity from the background.

Generation of large-bandwidth x-ray free-electron-laser pulses

X-ray free-electron lasers (XFELs) are modern research tools in disciplines such as biology, material science, chemistry, and physics. Besides the standard operation that aims at minimizing the bandwidth of the produced XFEL radiation, there is a strong scientific demand to produce large-bandwidth XFEL pulses for several applications such as nanocrystallography, stimulated Raman spectroscopy, and multiwavelength anomalous diffraction. We present a self-consistent method that maximizes the XFEL pulse bandwidth by systematically maximizing the energy chirp of the electron beam at the undulator entrance. This is achieved by optimizing the compression scheme and the electron distribution at the source in an iterative back-and-forward tracking. Start-to-end numerical simulations show that a relative bandwidth of 3.25% full-width can be achieved for the hard x-ray pulses in the SwissFEL case.

Single-pulse enhanced coherent diffraction imaging of bacteria with an X-ray free-electron laser.

High-resolution imaging offers one of the most promising approaches for exploring and understanding the structure and function of biomaterials and biological systems. X-ray free-electron lasers (XFELs) combined with coherent diffraction imaging can theoretically provide high-resolution spatial information regarding biological materials using a single XFEL pulse. Currently, the application of this method suffers from the low scattering cross-section of biomaterials and X-ray damage to the sample. However, XFELs can provide pulses of such short duration that the data can be collected using the “diffract and destroy” approach before the effects of radiation damage on the data become significant. These experiments combine the use of enhanced coherent diffraction imaging with single-shot XFEL radiation to investigate the cellular architecture of Staphylococcus aureus with and without labeling by gold (Au) nanoclusters. The resolution of the images reconstructed from these diffraction patterns were twice as high or more for gold-labeled samples, demonstrating that this enhancement method provides a promising approach for the high-resolution imaging of biomaterials and biological systems.

Calculation of x-ray scattering patterns from nanocrystals at high x-ray intensity.

We present a generalized method to describe the x-ray scattering intensity of the Bragg spots in a diffraction pattern from nanocrystals exposed to intense x-ray pulses. Our method involves the subdivision of a crystal into smaller units. In order to calculate the dynamics within every unit, we employ a Monte-Carlo-molecular dynamics-ab-initio hybrid framework using real space periodic boundary conditions. By combining all the units, we simulate the diffraction pattern of a crystal larger than the transverse x-ray beam profile, a situation commonly encountered in femtosecond nanocrystallography experiments with focused x-ray free-electron laser radiation. Radiation damage is not spatially uniform and depends on the fluence associated with each specific region inside the crystal. To investigate the effects of uniform and non-uniform fluence distribution, we have used two different spatial beam profiles, Gaussian and flattop.