Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.

Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.

Atomic inner-shell X-ray laser at 1.46 nanometres pumped by an X-ray free-electron laser.

Since the invention of the laser more than 50 years ago, scientists have striven to achieve amplification on atomic transitions of increasingly shorter wavelength. The introduction of X-ray free-electron lasers makes it possible to pump new atomic X-ray lasers with ultrashort pulse duration, extreme spectral brightness and full temporal coherence. Here we describe the implementation of an X-ray laser in the kiloelectronvolt energy regime, based on atomic population inversion and driven by rapid K-shell photo-ionization using pulses from an X-ray free-electron laser. We established a population inversion of the Kα transition in singly ionized neon at 1.46 nanometres (corresponding to a photon energy of 849 electronvolts) in an elongated plasma column created by irradiation of a gas medium. We observed strong amplified spontaneous emission from the end of the excited plasma. This resulted in femtosecond-duration, high-intensity X-ray pulses of much shorter wavelength and greater brilliance than achieved with previous atomic X-ray lasers. Moreover, this scheme provides greatly increased wavelength stability, monochromaticity and improved temporal coherence by comparison with present-day X-ray free-electron lasers. The atomic X-ray lasers realized here may be useful for high-resolution spectroscopy and nonlinear X-ray studies.

Numerical simulations of the hard X-ray pulse intensity distribution at the Linac Coherent Light Source.

Numerical simulations of the current and future pulse intensity distributions at selected locations along the Far Experimental Hall, the hard X-ray section of the Linac Coherent Light Source (LCLS), are provided. Estimates are given for the pulse fluence, energy and size in and out of focus, taking into account effects due to the experimentally measured divergence of the X-ray beam, and measured figure errors of all X-ray optics in the beam path. Out-of-focus results are validated by comparison with experimental data. Previous work is expanded on, providing quantitatively correct predictions of the pulse intensity distribution. Numerical estimates in focus are particularly important given that the latter cannot be measured with direct imaging techniques due to detector damage. Finally, novel numerical estimates of improvements to the pulse intensity distribution expected as part of the on-going upgrade of the LCLS X-ray transport system are provided. We suggest how the new generation of X-ray optics to be installed would outperform the old one, satisfying the tight requirements imposed by X-ray free-electron laser facilities.

Single mimivirus particles intercepted and imaged with an X-ray laser.

X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.

Aperiodic Mo/Si multilayers for hard x-rays.

In this work we have developed aperiodic Molybdenum/Silicon (Mo/Si) multilayers (MLs) to reflect 16.25 keV photons at a grazing angle of incidence of 0.6° ± 0.05°. To the best of our knowledge this is the first time this material system has been used to fabricate aperiodic MLs for hard x-rays. At these energies new hurdles arise. First of all a large number of bilayers is required to reach saturation. This poses a challenge from the manufacturing point of view, as thickness control of each ML period becomes paramount. The latter is not well defined a priori, due to the thickness of the interfacial silicide layers which has been observed to vary as a function of Mo and Si thickness. Additionally an amorphous-to-crystalline transition for Mo must be avoided in order maintain reasonably low roughness at the interfaces. This transition is well within the range of thicknesses pertinent to this study. Despite these difficulties our data demonstrates that we achieved reasonably flat ML response across the angular acceptance of ± 0.05°, with an experimentally confirmed average reflectivity of 28%. Such a ML prescription is well suited for applications in the field of hard x-ray imaging of highly diverging sources.

Effect of slope errors on the performance of mirrors for x-ray free electron laser applications.

In this work we point out that slope errors play only a minor role in the performance of a certain class of x-ray optics for X-ray Free Electron Laser (XFEL) applications. Using physical optics propagation simulations and the formalism of Church and Takacs [Opt. Eng. 34, 353 (1995)], we show that diffraction limited optics commonly found at XFEL facilities posses a critical spatial wavelength that makes them less sensitive to slope errors, and more sensitive to height error. Given the number of XFELs currently operating or under construction across the world, we hope that this simple observation will help to correctly define specifications for x-ray optics to be deployed at XFELs, possibly reducing the budget and the timeframe needed to complete the optical manufacturing and metrology.

Femtosecond time-delay X-ray holography.

Extremely intense and ultrafast X-ray pulses from free-electron lasers offer unique opportunities to study fundamental aspects of complex transient phenomena in materials. Ultrafast time-resolved methods usually require highly synchronized pulses to initiate a transition and then probe it after a precisely defined time delay. In the X-ray regime, these methods are challenging because they require complex optical systems and diagnostics. Here we propose and apply a simple holographic measurement scheme, inspired by Newton's 'dusty mirror' experiment, to monitor the X-ray-induced explosion of microscopic objects. The sample is placed near an X-ray mirror; after the pulse traverses the sample, triggering the reaction, it is reflected back onto the sample by the mirror to probe this reaction. The delay is encoded in the resulting diffraction pattern to an accuracy of one femtosecond, and the structural change is holographically recorded with high resolution. We apply the technique to monitor the dynamics of polystyrene spheres in intense free-electron-laser pulses, and observe an explosion occurring well after the initial pulse. Our results support the notion that X-ray flash imaging can be used to achieve high resolution, beyond radiation damage limits for biological samples. With upcoming ultrafast X-ray sources we will be able to explore the three-dimensional dynamics of materials at the timescale of atomic motion.

Photoelectron dynamics in x-ray free-electron-laser diffractive imaging of biological samples.

X-ray free electron lasers hold the promise of enabling atomic-resolution diffractive imaging of single biological molecules. We develop a hybrid continuum-particle model to describe the x-ray induced damage and find that the photoelectron dynamics and electrostatic confinement strongly affect the time scale of the damage processes. These phenomena are not fully captured in hydrodynamic modeling approaches.

Sacrificial tamper slows down sample explosion in FLASH diffraction experiments.

Intense and ultrashort x-ray pulses from free-electron lasers open up the possibility for near-atomic resolution imaging without the need for crystallization. Such experiments require high photon fluences and pulses shorter than the time to destroy the sample. We describe results with a new femtosecond pump-probe diffraction technique employing coherent 0.1 keV x rays from the FLASH soft x-ray free-electron laser. We show that the lifetime of a nanostructured sample can be extended to several picoseconds by a tamper layer to dampen and quench the sample explosion, making <1 nm resolution imaging feasible.

Near-ultraviolet luminescence of N2 irradiated by short X-ray pulses.

The Linac Coherent Light Source is an x-ray free-electron laser that recently demonstrated lasing in the 1.5-15 Å wavelength range. We report on luminescence measurements of a molecular nitrogen gas irradiated by ∼2 mJ, 80 fs x-ray pulses at energies of 0.83, 2.7, and 8.3 keV. These results provide a direct test of our current understanding of photoabsorption, electron dynamics, and fluorescence processes for such intense, ultrashort x-ray pulses. At 0.83 keV, the duration of the fluorescence signal depends strongly on space-charge effects. At 8.3 keV, space-charge effects are weak, and the signal duration is determined by the Auger electron dynamics.

Effect of the coherence properties of self-amplified-spontaneous-emission x-ray free electron lasers on single-particle diffractive imaging.

The longitudinal coherence properties of self-amplified-spontaneous- emission x-ray free electron lasers limit the resolution of single-particle diffraction imaging. We found that for the Linac Coherent Light Source (LCLS) at a wavelength of 1.5 A the particles have to be smaller than 500 nm in diameter to achieve atomic-resolution imaging with a resolution length of less than 2 A, suggesting that the longitudinal coherence is sufficient for imaging most biomolecular samples of interest.

Modeling of the damage dynamics of nanospheres exposed to x-ray free-electron-laser radiation.

Atomic-resolution diffraction imaging of biological particles using x-ray free-electron lasers (XFELs) at 1 A wavelength requires a detailed understanding of the photon-induced damage processes. We discuss how several aspects of existing continuum damage models can be tested during early operation of XFELs at lower x-ray energies in the range of 0.8-5 keV and low fluences, focusing particularly on macroscopic collective effects such as particle charging, expansion, and average ionization of nanospheres.

Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals.

Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography at X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump-probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.

Soft-x-ray free-electron-laser interaction with materials.

Soft-x-ray free-electron lasers have enabled materials studies in which structural information is obtained faster than the relevant probe-induced damage mechanisms. We present a continuum model to describe the damage process based on hot-dense plasma theory, which includes a description of the energy deposition in the samples, the subsequent dynamics of the sample, and the detector signal. We compared the model predictions with experimental data and mostly found reasonable agreement. In view of future free-electron-laser performance, the model was also used to predict damage dynamics of samples and optical elements at shorter wavelengths and larger photon fluences than currently available.

Reflection of attosecond x-ray free electron laser pulses.

In order to utilize hard x-ray free electron lasers (XFEL's) when they are extended to attosecond pulse lengths, it is necessary to choose optical elements with minimal response time. Specular grazing-incidence optics made of low-Z materials are popular candidates for reflectors since they are likely to withstand x-ray damage and provide sufficiently large reflectivities. Using linear-optics reflection theory, we calculated the transient reflectivity of a delta-function electric pulse from a homogenous semi-infinite medium as a function of angle of incidence for s- and p-polarized light. We specifically considered the pulse response of beryllium, diamond, silicon carbide, and silicon, all of which are of relevance to the XFEL's that are currently being built. We found that the media emit energy in a damped oscillatory way, and that the impulse-response times are shorter than 0.3 fs for normal incidence. For grazing incidence, the impulse-response time is substantially shorter, making grazing-incidence mirrors a good choice for deep subfemtosecond reflective optics.

Microfield dynamics in dense hydrogen plasmas with high-Z impurities.

We use large-scale classical molecular dynamics to determine microfield properties for several dense plasma mixtures. By employing quantum statistical potentials (QSPs) to regularize the Coulomb interaction, our simulations follow motions of electrons as well as ions for times long enough to track relaxation phenomena involving both types of particles. Coulomb coupling, relative to temperature, of different pairs of species in the hot, dense matter being simulated ranges from weak to strong. We first study the effect of such coupling differences, along with composition and QSP differences, on the roles of electrons and various mixture components in determining probability distributions of instantaneous, total microfields experienced by the ions. Then, we address two important dynamical questions: (1) How is the quasistatic part of the total field to be extracted from the time-dependent simulation data? (2) Under what conditions does the commonly used approximation of ions with fixed Yukawa-like screening by free electrons accurately describe quasistatic fields? We identify a running, short-time average of the total field at each ion as its slowly evolving, quasistatic part. We consider several ways to specify the averaging interval, and note the influence of ion dynamics in this issue. When all species are weakly coupled, the quasistatic fields have probability distributions agreeing well with those we obtain from simulations of Yukawa-screened ions. However, agreement deteriorates as the coupling between high-Z ions increases well beyond unity, principally because the Yukawa model tends to underestimate the true screening of close high-Z pairs. Examples of this fact are given, and some consequences for the high-field portions of probability distributions are discussed.

Pulse requirements for x-ray diffraction imaging of single biological molecules.

In this paper we estimate the required pulse parameters for the future application of x-ray free electron lasers to imaging single biological molecules. The parameters are determined by a tradeoff between minimizing image degradation due to damage and maximizing the image signal-to-noise ratio. We discuss several means to alleviate the pulse requirements, and compare the requirements with parameters of two planned x-ray lasers.

Reproducible radiation-damage processes in proteins irradiated by intense x-ray pulses.

X-ray free-electron lasers have enabled femtosecond protein nanocrystallography, a novel method to determine the structure of proteins. It allows time-resolved imaging of nanocrystals that are too small for conventional crystallography. The short pulse duration helps in overcoming the detrimental effects of radiation damage because x rays are scattered before the sample has been significantly altered. It has been suggested that, fortuitously, the diffraction process self-terminates abruptly once radiation damage destroys the crystalline order. Our calculations show that high-intensity x-ray pulses indeed trigger a cascade of damage processes in ferredoxin crystals, a particular metalloprotein of interest. However, we found that the damage process is initially not completely random. Correlations exist among the protein monomers, so that Bragg diffraction still occurs in the damaged crystals, despite significant atomic displacements. Our results show that the damage process is reproducible to a certain degree, which is potentially beneficial for the orientation step in single-molecule imaging.

SPEDEN: reconstructing single particles from their diffraction patterns.

SPEDEN is a computer program that reconstructs the electron density of single particles from their X-ray diffraction patterns, using a single-particle adaptation of the holographic method in crystallography [Szöke, Szöke & Somoza (1997). Acta Cryst. A53, 291-313]. The method, like its parent, is unique because it does not rely on 'back' transformation from the diffraction pattern into real space and on interpolation within measured data. It is designed to deal successfully with sparse, irregular, incomplete and noisy data. It is also designed to use prior information for ensuring sensible results and for reliable convergence. This article describes the theoretical basis for the reconstruction algorithm, its implementation, and quantitative results of tests on synthetic and experimentally obtained data. The program could be used for determining the structures of radiation-tolerant samples and, eventually, of large biological molecular structures without the need for crystallization.

Dynamics of biological molecules irradiated by short x-ray pulses.

Very short and intense x-ray pulses can be used for diffraction imaging of single biological molecules. Inevitably, x-ray absorption initiates damage that degrades the molecule's image. This paper presents a continuum model of the physics that leads to damage when a small particle absorbs a large x-ray dose. The main processes are found to be ionization and Coulomb-force driven atomic motion. Trapping of electrons, Debye shielding, and nonuniform collisional ionization all have a significant effect on the overall damage kinetics.