Femtosecond x-ray diffraction reveals a liquid-liquid phase transition in phase-change materials.

In phase-change memory devices, a material is cycled between glassy and crystalline states. The highly temperature-dependent kinetics of its crystallization process enables application in memory technology, but the transition has not been resolved on an atomic scale. Using femtosecond x-ray diffraction and ab initio computer simulations, we determined the time-dependent pair-correlation function of phase-change materials throughout the melt-quenching and crystallization process. We found a liquid-liquid phase transition in the phase-change materials Ag4In3Sb67Te26 and Ge15Sb85 at 660 and 610 kelvin, respectively. The transition is predominantly caused by the onset of Peierls distortions, the amplitude of which correlates with an increase of the apparent activation energy of diffusivity. This reveals a relationship between atomic structure and kinetics, enabling a systematic optimization of the memory-switching kinetics.

Ultrafast nonthermal heating of water initiated by an X-ray Free-Electron Laser.

The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 106 J/cm2 These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.

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.

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.

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.

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.

Electric microfields in dense carbon-hydrogen plasmas.

Classical molecular dynamics is used to investigate stationary and time-dependent properties of microfields in hot, solid density, electron-ion plasmas. Even at the high temperatures considered here, such simulations require quantum statistical potentials (QSPs) to mimic the essential effects of diffraction and exchange symmetry for electrons. Fortunately, key results relevant to microfield distributions are found to be insensitive to different, plausible QSP choices. Atomic processes in plasmas will depend on the time average of the microfields. It is not clear, a priori, what the time duration of this average should be. The question of how best to extract the quasistatic (low-frequency) microfield from a classical molecular dynamics simulation is explored in some detail, and the time-averaging approach we adopt involves both plasma and atomic time scale constraints. One of the major findings described in the paper is that for a large time interval, the time-averaged microfield does not significantly change. Our discussion of this suite of large simulations for plasma mixtures focuses on understanding various features and trends revealed by data for C-H plasmas having carbon fractions ranging from 0.01 to 1, and different temperatures well above TFermi.

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.

Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams.

Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe-4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe-4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.

Fixed-target protein serial microcrystallography with an x-ray free electron laser.

We present results from experiments at the Linac Coherent Light Source (LCLS) demonstrating that serial femtosecond crystallography (SFX) can be performed to high resolution (~2.5 Å) using protein microcrystals deposited on an ultra-thin silicon nitride membrane and embedded in a preservation medium at room temperature. Data can be acquired at a high acquisition rate using x-ray free electron laser sources to overcome radiation damage, while sample consumption is dramatically reduced compared to flowing jet methods. We achieved a peak data acquisition rate of 10 Hz with a hit rate of ~38%, indicating that a complete data set could be acquired in about one 12-hour LCLS shift using the setup described here, or in even less time using hardware optimized for fixed target SFX. This demonstration opens the door to ultra low sample consumption SFX using the technique of diffraction-before-destruction on proteins that exist in only small quantities and/or do not produce the copious quantities of microcrystals required for flowing jet methods.

Femtosecond X-ray diffraction from two-dimensional protein crystals.

X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Šresolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

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.

7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source.

Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump-probe experiments at subpicosecond time resolution.

Sensing the wavefront of x-ray free-electron lasers using aerosol spheres.

Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 10(21) W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.

Nonequilibrium electron dynamics in materials driven by high-intensity x-ray pulses.

We calculated the evolution of the electron system in solid-density matter irradiated by high-intensity x-ray pulses between 2 and 8 keV using molecular dynamics. For pulses shorter than 40 fs, the kinetic energy distribution of the electrons is highly nonthermal during and right after the pulse, and a large fraction of the absorbed x-ray energy resides with the fast photoelectrons which equilibrate on the timescale of the pulse length. The average ionization and electron temperature of the bulk of the electrons are significantly lower than their equilibrium values.

Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers.

Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.

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.

Time-resolved protein nanocrystallography using an X-ray free-electron laser.

We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.

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.