X-ray Free-electron Laser Beam Research Articles

Bayesian Structure Determination from Ultrafast Single Molecule X-Ray Diffraction

Single molecule X-Ray diffraction experiments are a promising new method for the structure determination of biomolecules. In the experiments, a stream of single molecules enters a femtosecond high-intensity X-Ray free electron laser beam, and for each molecule the scattered photons are recorded as an image. The reconstruction of the structure from this data is quite challenging: The orientations of the molecules during the scattering events are unknown, the signal to noise ratio is very low, and the recorded images are sparse, with typically less than 10-50 photons per image. Previously available analysis methods require at least 100 photons per image, or a very large number (e.g. 10⁹) of images. We present a novel Bayesian approach that requires fewer photons per image and, at the same time, a relatively few images. It is flexible in that many different representations of the electron density can be used, both in Fourier space and directly in real space. Using synthetic data, we demonstrated the method is able to recover the atomic structure of (fictional) 20-atom molecules using only 5000 images with on average 15 photons each. Scaling up to larger molecules is work in progress.

Ultrafast Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser

The development of ultrafast X-ray free-electron lasers (XFELs) gives a new avenue to experimentally investigate protein dynamics in the picosecond and femtosecond time regimes. The XFEL beam of the LCLS has a very high peak X-ray brightness, which is key for probing elusive ultrafast structural changes during the biological function of protein molecules. With XFELs, femtosecond time-resolved small- and wide-angle X-ray scattering (TR-SWAXS) experiments afford unprecedented opportunities in membrane biophysics.

X-ray radiography based on the phase-contrast imaging with using LiF detector

An x-ray radiography technique based upon phase contrast imaging using a lithium fluoride detector has been demonstrated for goals of high energy density physics experiments. Based on the simulation of propagation an x-ray free-electron laser beam through a test-object, the visibility of phase-contrast image depending on an object-detector distance was investigated. Additionally, the metrological capabilities of a lithium fluoride crystal as a detector were demonstrated.

2D monochromatic x-ray imaging for beam monitoring of an x-ray free electron laser and a high-power femtosecond laser.

In pump-probe experiments with an X-ray Free Electron Laser (XFEL) and a high-power optical laser, spatial overlap of the two beams must be ensured to probe a pumped area with the x-ray beam. A beam monitoring diagnostic is particularly important in short-pulse laser experiments where a tightly focused beam is required to achieve a relativistic laser intensity for generation of energetic particles. Here, we report the demonstration of on-shot beam pointing measurements of an XFEL and a terawatt class femtosecond laser using 2D monochromatic Kα imaging at the Matter in Extreme Conditions end-station of the Linac Coherent Light Source. A thin solid titanium foil was irradiated by a 25-TW laser for fast electron isochoric heating, while a 7.0 keV XFEL beam was used to probe the laser-heated region. Using a spherical crystal imager (SCI), the beam overlap was examined by measuring 4.51 keV Kα x rays produced by laser-accelerated fast electrons and the x-ray beam. Measurements were made for XFEL-only at various focus lens positions, laser-only, and two-beam shots. Successful beam overlapping was observed on ∼58% of all two-beam shots for 10 μm thick samples. It is found that large spatial offsets of laser-induced Kα spots are attributed to imprecise target positioning rather than shot-to-shot laser pointing variations. By applying the Kα measurements to x-ray Thomson scattering measurements, we found an optimum x-ray beam spot size that maximizes scattering signals. Monochromatic x-ray imaging with the SCI could be used as an on-shot beam pointing monitor for XFEL-laser or multiple short-pulse laser experiments.

Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase.

Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A2A receptor (A2AAR) at 2.0 Å resolution is determined and compared with previous A2AAR structures determined in vacuum and/or at cryogenic temperatures. Specifically, the capability of utilizing high XFEL beam transmissions is demonstrated, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete dataset. The experimental setup presented herein can be applied to future SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize.

Two-color X-ray free-electron laser consisting of broadband and narrowband beams.

A simple scheme is proposed and experimentally confirmed to generate X-ray free-electron lasers (XFELs) consisting of broadband and narrowband beams with a controllable intensity ratio and a large photon-energy separation. This unique two-color XFEL beam will open new opportunities for investigation of nonlinear interactions between intense X-rays and matter.

Femtosecond electronic structure response to high intensity XFEL pulses probed by iron X-ray emission spectroscopy

We report the time-resolved femtosecond evolution of the K-shell X-ray emission spectra of iron during high intensity illumination of X-rays in a micron-sized focused hard X-ray free electron laser (XFEL) beam. Detailed pulse length dependent measurements revealed that rapid spectral energy shift and broadening started within the first 10 fs of the X-ray illumination at intensity levels between 1017 and 1018 W cm-2. We attribute these spectral changes to the rapid evolution of high-density photoelectron mediated secondary collisional ionization processes upon the absorption of the incident XFEL radiation. These fast electronic processes, occurring at timescales well within the typical XFEL pulse durations (i.e., tens of fs), set the boundary conditions of the pulse intensity and sample parameters where the widely-accepted ‘probe-before-destroy’ measurement strategy can be adopted for electronic-structure related XFEL experiments.

XFEL beamline design for vacuum birefringence experiment

The station of extreme light (SEL) at Shanghai High repetition rate XFEL and Extreme light facility (SHINE) combines 100 PW laser pulse and an X-ray free electron laser (XFEL) beam, which provides possible experimental conditions for observing the effect of vacuum birefringence. We have designed the XFEL beamline of SEL with X-ray energy of 12.914 keV aiming for vacuum birefringence experiment. Ultra-high polarization purity of the X-ray beam at the level of 10−10 is required before colliding with a 100 PW laser pulse. An X-ray polarizer is set at the end of the designed beamline to avoid the potential risk of depolarization induced by any other X-ray component. The designed beamline provides a focal X-ray beam FWHM size of 6.35μm and total transmission of 3.5%. Further calculation indicates that 333 shots are needed to reach 5σ confidence level for the vacuum birefringence experiment under optimal conditions with present design parameters of 100 PW laser pulse and XFEL beam in SEL. Moreover, potential radiation damage, and proposed engineering stability requirements and system’s adjustment capabilities of X-ray beamline have been discussed.

Focus characterization of an X-ray free-electron laser by intensity correlation measurement of X-ray fluorescence.

This paper proposes and demonstrates a simple method using the intensity correlation of X-ray fluorescence to evaluate the focused beam size of an X-ray free-electron laser (XFEL). This method was applied to the sub-micrometre focused XFEL beam at the SPring-8 Angstrom Compact Free Electron Laser, and the beam size evaluated using the proposed method was consistent with that measured using the knife-edge scan method. The proposed method is readily applicable to extremely small X-ray spots and can be applied for the precise diagnostics of sub-10 nm focused X-ray beams which have recently emerged.

Generation of an X-ray nanobeam of a free-electron laser using reflective optics with speckle interferometry.

Ultimate focusing of an X-ray free-electron laser (XFEL) enables the generation of ultrahigh-intensity X-ray pulses. Although sub-10 nm focusing has already been achieved using synchrotron light sources, the sub-10 nm focusing of XFEL beams remains difficult mainly because the insufficient stability of the light source hinders the evaluation of a focused beam profile. This problem is specifically disadvantageous for the Kirkpatrick-Baez (KB) mirror focusing system, in which a slight misalignment of ∼300 nrad can degrade thefocused beam. In this work, an X-ray nanobeam of a free-electron laser wasgenerated using reflective KB focusing optics combined with speckle interferometry. The speckle profiles generated by 2 nm platinum particles were systematically investigated on a single-shot basis by changing the alignment of the multilayer KB mirror system installed at the SPring-8 Angstrom Compact Free-Electron Laser, in combination with computer simulations. It was verified that the KB mirror alignments were optimized with the required accuracy, and a focused vertical beam of 5.8 nm (±1.2 nm) was achieved after optimization. The speckle interferometry reported in this study is expected to be an effective tool for optimizing the alignment of nano-focusing systems and for generating an unprecedented intensity of up to 1022 W cm-2 using XFEL sources.

Double grating shearing interferometry for X-ray free-electron laser beams

The advancements in bright and coherent X-ray free-electron lasers (XFEL) have in the last decade revolutionized diverse fields of study, leading to an ever-increasing demand in more intense X-ray pulses. The accurate knowledge of the wavefront and the focal profile of such pulses ultimately dictates much of the experimental outcome. Here we present a single-shot shearing interferometry method to measure the wavefront of a focused hard XFEL pulse. Two identical transmission gratings are placed near the focus, and the interference pattern of overlapping diffraction orders is analyzed, resulting in a two-dimensional reconstruction of the X-ray wavefront. The spatial resolution and wavefront sensitivity can be tuned in-situ during the measurement. The method is non-invasive (i.e., the zeroth order or transmitted pulse is not modified in intensity or profile), allowing for either a simultaneous intensity measurement at high resolution or a fully characterized transmitted pulse for general experimental use.

Wavefront preserving and high efficiency diamond grating beam splitter for x-ray free electron laser.

X-ray free electron lasers (XFELs) provide femtosecond high-power x-ray beams with high spatial coherence, resulting in numerous influential discoveries. Diffractive optics allow for the easy manipulation and measurement of an x-ray beam's wavefront and enable the realization of complex designed properties and specifications. For example, phase gratings can be used as x-ray beam splitters to enable beam sharing by multiple end stations or in-situ beam monitoring, including spectrum and wavefront measurements. Wavefront preservation and high efficiency and survivability under high power are requirements for such beam splitters. Diamond is the most suitable choice for phase grating fabrication, due to its high thermal conductivity that enables it to survive high average power XFEL beams. We have fabricated a large area (2×2 mm2) high aspect ratio (13:1) diamond grating on a diamond plate. Testing was performed at 9.5 keV and resulted in a high splitting efficiency (30%). Tunable efficiency was obtained via tilting the grating with respect to the x-ray beam. Wavefront fidelity of the split beams were measured to less than λ/100 using a Talbot wavefront sensor.

Double-pulse speckle contrast correlations with near Fourier transform limited free-electron laser light using hard X-ray split-and-delay

The ability to deliver two coherent X-ray pulses with precise time-delays ranging from a few femtoseconds to nanoseconds enables critical capabilities of probing ultra-fast phenomena in condensed matter systems at X-ray free electron laser (FEL) sources. Recent progress made in the hard X-ray split-and-delay optics developments now brings a very promising prospect for resolving atomic-scale motions that were not accessible by previous time-resolved techniques. Here, we report on characterizing the spatial and temporal coherence properties of the hard X-ray FEL beam after propagating through split-and-delay optics. Speckle contrast analysis of small-angle scattering measurements from nanoparticles reveals well-preserved transverse coherence of the beam. Measuring intensity fluctuations from successive X-ray pulses also reveals that only single or double temporal modes remain in the transmitted beam, corresponding to nearly Fourier transform limited pulses.

Design of a liquid cell toward three-dimensional imaging of unidirectionally-aligned particles in solution using X-ray free-electron lasers.

X-ray free-electron lasers (XFELs) opened up a possibility for molecular-scale single particle imaging (SPI) without the need for crystallization. In SPI experiments, the orientation of each particle has to be determined from the measured diffraction pattern. Preparing unidirectionally-aligned particles can facilitate the determination of the sample orientation. Here, we show the design principles of a liquid cell for three-dimensional imaging of unidirectionally-aligned particles in solution with XFELs. The liquid cell was designed so that neither incident X-rays nor diffracted X-rays are blocked by the substrate of the liquid cell even at high tilt angles. As a feasibility evaluation, we performed coherent diffraction measurements using the cells with a 1 μm focused XFEL beam. We successfully measured coherent diffraction patterns of a nano-fabricated metal pattern at 70° tilt angle and obtained the reconstructed image by applying iterative phase retrieval. The liquid cell will be usefully applied to molecular-scale SPI by using more tightly focused XFELs. In particular, imaging of membrane proteins embedded in lipid membranes is expected to have an enormous impact on life science and medicine.

Coherent diffractive imaging of microtubules using an X-ray laser

X-ray free electron lasers (XFELs) create new possibilities for structural studies of biological objects that extend beyond what is possible with synchrotron radiation. Serial femtosecond crystallography has allowed high-resolution structures to be determined from micro-meter sized crystals, whereas single particle coherent X-ray imaging requires development to extend the resolution beyond a few tens of nanometers. Here we describe an intermediate approach: the XFEL imaging of biological assemblies with helical symmetry. We collected X-ray scattering images from samples of microtubules injected across an XFEL beam using a liquid microjet, sorted these images into class averages, merged these data into a diffraction pattern extending to 2 nm resolution, and reconstructed these data into a projection image of the microtubule. Details such as the 4 nm tubulin monomer became visible in this reconstruction. These results illustrate the potential of single-molecule X-ray imaging of biological assembles with helical symmetry at room temperature.

Xcalib: a focal spot calibrator for intense X-ray free-electron laser pulses based on the charge state distributions of light atoms.

The xcalib toolkit has been developed to calibrate the beam profile of an X-ray free-electron laser (XFEL) at the focal spot based on the experimental charge state distributions (CSDs) of light atoms. Characterization of the fluence distribution at the focal spot is essential to perform the volume integrations of physical quantities for a quantitative comparison between theoretical and experimental results, especially for fluence-dependent quantities. The use of the CSDs of light atoms is advantageous because CSDs directly reflect experimental conditions at the focal spot, and the properties of light atoms have been well established in both theory and experiment. Theoretical CSDs are obtained using xatom, a toolkit to calculate atomic electronic structure and to simulate ionization dynamics of atoms exposed to intense XFEL pulses, which involves highly excited multiple core-hole states. Employing a simple function with a few parameters, the spatial profile of an XFEL beam is determined by minimizing the difference between theoretical and experimental results. The optimization procedure employing the reinforcement learning technique can automatize and organize calibration procedures which, before, had been performed manually. xcalib has high flexibility, simultaneously combining different optimization methods, sets of charge states, and a wide range of parameter space. Hence, in combination with xatom, xcalib serves as a comprehensive tool to calibrate the fluence profile of a tightly focused XFEL beam in the interaction region.

Ultrafast anisotropic disordering in graphite driven by intense hard X-ray pulses

We present results from the SPring-8 Angstrom Compact free electron LAser (SACLA) X-ray free electron laser (XFEL) facility, using an X-ray pump, X-ray probe scheme to observe ultrafast changes in the structure of heated graphite. The 9.8 keV XFEL beam was focused to give an intensity on the order of ∼ 1019 W/cm2, and the evolution of the diffraction pattern observed up to delays of 300 fs. The interplanar diffraction peaks weaken significantly within 10s of femtoseconds, but in-plane diffraction orders i.e. those with Miller Index (hk0), persist up to 300 fs, with the observed signal increasing. We interpret this as nonthermal damage through the breaking of interplanar bonds, which at longer timescales leads to ablation by removal of intact graphite sheets. Post-experiment examination of the graphite samples shows damage which is comparable in size to the range of the excited photoelectrons. These results highlight the challenges of accurately modelling X-ray driven heating, as it becomes a routine approach to generating high energy density states.

On-line monitoring of the spatial properties of hard X-ray free-electron lasers based on a grating splitter.

X-ray free-electron lasers (XFELs) play an increasingly important role in addressing the new scientific challenges relating to their high brightness, high coherence and femtosecond time structure. As a result of pulse-by-pulse fluctuations, the pulses of an XFEL beam may demonstrate subtle differences in intensity, energy spectrum, coherence, wavefront, etc., and thus on-line monitoring and diagnosis of a single pulse are required for many XFEL experiments. Here a new method is presented, based on a grating splitter and bending-crystal analyser, for single-pulse on-line monitoring of the spatial characteristics including the intensity profile, coherence and wavefront, which was suggested and applied experimentally to the temporal diagnosis of an XFEL single pulse. This simulation testifies that the intensity distribution, coherence and wavefront of the first-order diffracted beam of a grating preserve the properties of the incident beam, by using the coherent mode decomposition of the Gaussian-Schell model and Fourier optics. Indicatively, the first-order diffraction of appropriate gratings can be used as an alternative for on-line monitoring of the spatial properties of a single pulse without any characteristic deformation of the principal diffracted beam. However, an interesting simulation result suggests that the surface roughness of gratings will degrade the spatial characteristics in the case of a partially coherent incident beam. So, there exists a suitable roughness value for non-destructive monitoring of the spatial properties of the downstream beam, which depends on the specific optical path. Here, experiments based on synchrotron radiation X-rays are carried out in order to verify this method in principle. The experimental results are consistent with the theoretical calculations.

Generation of narrow-band X-ray free-electron laser via reflection self-seeding

X-ray free-electron lasers (XFELs)1,2 are widely operated on the basis of self-amplified spontaneous emission (SASE)3,4, where spontaneous radiation from the electron beam is amplified along the magnetic field in undulators. Despite their high intensities, SASE-XFELs have a broad spectrum due to the stochastic starting-up process5. To narrow the bandwidth, self-seeding has been proposed6,7 and recently demonstrated8,9, where the seed pulse produced by monochromatizing the SASE-XFELs from the first section of undulators using a thin crystal in transmission geometry is amplified in the remaining undulators. Here, we present an efficient self-seeding scheme using the Bragg reflection to produce a seed pulse. We applied this scheme to SPring-8 Angstrom Compact free-electron LAser (SACLA)10, and produced nearly Fourier-transform-limited XFEL pulses that correspond to an increase in spectral brightness by a factor of six compared with SASE-XFELs. This achievement will not only enhance the throughput of present XFEL experiments but also should open new opportunities for X-ray science. A nearly Fourier-limited X-ray free-electron laser beam is generated by a self-seeding scheme. The beam in the first half of the undulators is monochromatized via Bragg reflection, and is subsequently amplified in the remaining undulators.

Liquid Structure of Shock-Compressed Hydrocarbons at Megabar Pressures.

We present results for the ionic structure in hydrocarbons (polystyrene, polyethylene) that were shock compressed to pressures of up to 190GPa, inducing rapid melting of the samples. The structure of the resulting liquid is then probed using insitu diffraction by an x-ray free electron laser beam, demonstrating the capability to obtain reliable diffraction data in a single shot, even for low-Z samples without long range order. The data agree well with abinitio simulations, validating the ability of such approaches to model mixed samples in states where complex interparticle bonds remain, and showing that simpler models are not necessarily valid. While the results clearly exclude the possibility of complete carbon-hydrogen demixing at the conditions probed, they also, in contrast to previous predictions, indicate that diffraction is not always a sufficient diagnostic for this phenomenon.