Observation of site-selective chemical bond changes via ultrafast chemical shifts.

The concomitant motion of electrons and nuclei on the femtosecond time scale marks the fate of chemical and biological processes. Here we demonstrate the ability to initiate and track the ultrafast electron rearrangement and chemical bond breaking site-specifically in real time for the carbon monoxide diatomic molecule. We employ a local resonant x-ray pump at the oxygen atom and probe the chemical shifts of the carbon core-electron binding energy. We observe charge redistribution accompanying core-excitation followed by Auger decay, eventually leading to dissociation and hole trapping at one site of the molecule. The presented technique is general in nature with sensitivity to chemical environment changes including transient electronic excited state dynamics. This work provides a route to investigate energy and charge transport processes in more complex systems by tracking selective chemical bond changes on their natural timescale.

Time-dependent dynamical Bragg diffraction in deformed crystals by the beam propagation method.

This paper describes how to efficiently solve time-dependent X-ray dynamic diffraction problems in distorted crystals with a fast Fourier transform based beam propagation method. Examples are given of using the technique to simulate the propagation of X-ray beams in deformed crystals in space and time domains relevant to the cavity-based X-ray free-electron lasers and X-ray free-electron laser self-seeding systems.

Temporal X-ray Reconstruction using Temporal and Spectral Measurements at LCLS.

Transverse deflecting structures (TDSs) are widely used in accelerator physics to measure the longitudinal density of particle bunches. When used in combination with a dispersive section, the whole longitudinal phase space density can be imaged. At the Linac Coherent Light Source (LCLS), the installation of such a device downstream of the undulators enables the reconstruction of the X-ray temporal intensity profile by comparing longitudinal phase space distributions with lasing on and lasing off. However, the resolution of this TDS is limited to around 1 fs rms (root mean square), and therefore, it is not possible to resolve single self-amplified spontaneous emission (SASE) spikes within an X-ray photon pulse. By combining the power spectrum from a high resolution photon spectrometer and the temporal structure from the TDS, the overall resolution is enhanced, thus allowing the observation of temporal, single SASE spikes. The combined data from the spectrometer and the TDS is analysed using an iterative algorithm to obtain the actual intensity profile. In this paper, we present some improvements to the reconstruction algorithm as well as real data taken at LCLS.

Laguerre-Gaussian Mode Laser Heater for Microbunching Instability Suppression in Free-Electron Lasers.

Microbunching instability (MBI) driven by beam collective effects is known to be detrimental to high-brightness storage rings, linacs, and free-electron lasers (FELs). One known way to suppress this instability is to induce a small amount of energy spread to an electron beam by a laser heater. The distribution of the induced energy spread greatly affects MBI suppression and can be controlled by shaping the transverse profile of the heater laser. Here, we present the first experimental demonstration of effective MBI suppression using a LG_{01} transverse laser mode and compare the improved results with respect to traditional Gaussian transverse laser mode at the Linac Coherent Light Source. The effects on MBI suppression are characterized by multiple downstream measurements, including longitudinal phase space analysis and coherent radiation spectroscopy. We also discuss the role of LG_{01} shaping in soft x-ray self-seeded FEL emission, one of the most advanced operation modes of a FEL for which controlled suppression of MBI is critical.

Refractive Guide Switching a Regenerative Amplifier Free-Electron Laser for High Peak and Average Power Hard X Rays.

We present an x-ray regenerative amplifier free-electron laser design capable of producing fully coherent hard x-ray pulses across a broad tuning range at a high steady state repetition rate. The scheme leverages a strong undulator taper and an apertured diamond output-coupling cavity crystal to produce both high peak and average spectral brightness radiation that is 2 to 3 orders of magnitude greater than conventional single-pass self-amplified spontaneous emission free-electron laser amplifiers. Refractive guiding in the postsaturation regime is found to play a key role in passively controlling the stored cavity power. The scheme is explored both analytically and numerically in the context of the Linac Coherent Light Source II High Energy upgrade.

Atom-specific activation in CO oxidation.

We report on atom-specific activation of CO oxidation on Ru(0001) via resonant X-ray excitation. We show that resonant 1s core-level excitation of atomically adsorbed oxygen in the co-adsorbed phase of CO and oxygen directly drives CO oxidation. We separate this direct resonant channel from indirectly driven oxidation via X-ray induced substrate heating. Based on density functional theory calculations, we identify the valence-excited state created by the Auger decay as the driving electronic state for direct CO oxidation. We utilized the fresh-slice multi-pulse mode at the Linac Coherent Light Source that provided time-overlapped and 30 fs delayed pairs of soft X-ray pulses and discuss the prospects of femtosecond X-ray pump X-ray spectroscopy probe, as well as X-ray two-pulse correlation measurements for fundamental investigations of chemical reactions via selective X-ray excitation.

Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging.

Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.

High-Power Femtosecond Soft X Rays from Fresh-Slice Multistage Free-Electron Lasers.

We demonstrate a novel multistage amplification scheme for self-amplified spontaneous-emission free electron lasers for the production of few femtosecond pulses with very high power in the soft x-ray regime. The scheme uses the fresh-slice technique to produce an x-ray pulse on the bunch tail, subsequently amplified in downstream undulator sections by fresh electrons. With three-stages amplification, x-ray pulses with an energy of hundreds of microjoules are produced in few femtoseconds. For single-spike spectra x-ray pulses the pulse power is increased more than an order of magnitude compared to other techniques in the same wavelength range.

Efficiency and coherence preservation studies of Be refractive lenses for XFELO application.

Performance tests of parabolic beryllium refractive lenses, considered as X-ray focusing elements in the future X-ray free-electron laser oscillator (XFELO), are reported. Single and double refractive lenses were subject to X-ray tests, which included: surface profile, transmissivity measurements, imaging capabilities and wavefront distortion with grating interferometry. Optical metrology revealed that surface profiles were close to the design specification in terms of the figure and roughness. The transmissivity of the lenses is >94% at 8 keV and >98% at 14.4 and 18 keV. These values are close to the theoretical values of ideal lenses. Images of the bending-magnet source obtained with the lenses were close to the expected ones and did not show any significant distortion. Grating interferometry revealed that the possible wavefront distortions produced by surface and bulk lens imperfections were on the level of ∼λ/60 for 8 keV photons. Thus the Be lenses can be succesfully used as focusing and beam collimating elements in the XFELO.

Damage thresholds for blaze diffraction gratings and grazing incidence optics at an X-ray free-electron laser.

The Linac Coherent Light Source is upgrading its machine to high repetition rate and to extended ranges. Novel coatings, with limited surface oxidation, which are able to work at the carbon edge, are required. In addition, high-resolution soft X-ray monochromators become necessary. One of the big challenges is to design the mirror geometry and the grating profile to have high reflectivity (or efficiency) and at the same time survive the high peak energy of the free-electron laser pulses. For these reasons the experimental damage threshold, at 900 eV, of two platinum-coated gratings with different blazed angles has been investigated. The gratings were tested at 1° grazing incidence. To validate a model for which the damage threshold on the blaze grating can be estimated by calculating the damage threshold of a mirror with an angle of incidence identical to the angle of incidence on the grating plus the blaze angle, tests on Pt-coated substrates have also been performed. The results confirmed the prediction. Uncoated silicon, platinum and SiB3 (both deposited on a silicon substrate) were also investigated. In general, the measured damage threshold at grazing incidence is higher than that calculated under the assumption that there is no energy transport from the volume where the photons are absorbed. However, it was found that, for the case of the SiB3 coating, the grazing incidence condition did not increase the damage threshold, indicating that the energy transport away from the extinction volume is negligible.

Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers.

X-ray absorption spectroscopy at the L-edge of 3d transition metals provides unique information on the local metal charge and spin states by directly probing 3d-derived molecular orbitals through 2p-3d transitions. However, this soft x-ray technique has been rarely used at synchrotron facilities for mechanistic studies of metalloenzymes due to the difficulties of x-ray-induced sample damage and strong background signals from light elements that can dominate the low metal signal. Here, we combine femtosecond soft x-ray pulses from a free-electron laser with a novel x-ray fluorescence-yield spectrometer to overcome these difficulties. We present L-edge absorption spectra of inorganic high-valent Mn complexes (Mn ∼ 6-15 mmol/l) with no visible effects of radiation damage. We also present the first L-edge absorption spectra of the oxygen evolving complex (Mn4CaO5) in Photosystem II (Mn < 1 mmol/l) at room temperature, measured under similar conditions. Our approach opens new ways to study metalloenzymes under functional conditions.

X-ray absorption spectroscopy using a self-seeded soft X-ray free-electron laser.

X-ray free electron lasers (XFELs) enable unprecedented new ways to study the electronic structure and dynamics of transition metal systems. L-edge absorption spectroscopy is a powerful technique for such studies and the feasibility of this method at XFELs for solutions and solids has been demonstrated. However, the required x-ray bandwidth is an order of magnitude narrower than that of self-amplified spontaneous emission (SASE), and additional monochromatization is needed. Here we compare L-edge x-ray absorption spectroscopy (XAS) of a prototypical transition metal system based on monochromatizing the SASE radiation of the linac coherent light source (LCLS) with a new technique based on self-seeding of LCLS. We demonstrate how L-edge XAS can be performed using the self-seeding scheme without the need of an additional beam line monochromator. We show how the spectral shape and pulse energy depend on the undulator setup and how this affects the x-ray spectroscopy measurements.

Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser.

Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.

Filamentation effect in a gas attenuator for high-repetition-rate X-ray FELs.

A sustained filamentation or density depression phenomenon in an argon gas attenuator servicing a high-repetition femtosecond X-ray free-electron laser has been studied using a finite-difference method applied to the thermal diffusion equation for an ideal gas. A steady-state solution was obtained by assuming continuous-wave input of an equivalent time-averaged beam power and that the pressure of the entire gas volume has reached equilibrium. Both radial and axial temperature/density gradients were found and describable as filamentation or density depression previously reported for a femtosecond optical laser of similar attributes. The effect exhibits complex dependence on the input power, the desired attenuation, and the geometries of the beam and the attenuator. Time-dependent simulations were carried out to further elucidate the evolution of the temperature/density gradients in between pulses, from which the actual attenuation received by any given pulse can be properly calculated.

Ultrafast isomerization initiated by X-ray core ionization.

Rapid proton migration is a key process in hydrocarbon photochemistry. Charge migration and subsequent proton motion can mitigate radiation damage when heavier atoms absorb X-rays. If rapid enough, this can improve the fidelity of diffract-before-destroy measurements of biomolecular structure at X-ray-free electron lasers. Here we study X-ray-initiated isomerization of acetylene, a model for proton dynamics in hydrocarbons. Our time-resolved measurements capture the transient motion of protons following X-ray ionization of carbon K-shell electrons. We Coulomb-explode the molecule with a second precisely delayed X-ray pulse and then record all the fragment momenta. These snapshots at different delays are combined into a 'molecular movie' of the evolving molecule, which shows substantial proton redistribution within the first 12 fs. We conclude that significant proton motion occurs on a timescale comparable to the Auger relaxation that refills the K-shell vacancy.

High numerical aperture multilayer Laue lenses.

The ever-increasing brightness of synchrotron radiation sources demands improved X-ray optics to utilise their capability for imaging and probing biological cells, nanodevices, and functional matter on the nanometer scale with chemical sensitivity. Here we demonstrate focusing a hard X-ray beam to an 8 nm focus using a volume zone plate (also referred to as a wedged multilayer Laue lens). This lens was constructed using a new deposition technique that enabled the independent control of the angle and thickness of diffracting layers to microradian and nanometer precision, respectively. This ensured that the Bragg condition is satisfied at each point along the lens, leading to a high numerical aperture that is limited only by its extent. We developed a phase-shifting interferometric method based on ptychography to characterise the lens focus. The precision of the fabrication and characterisation demonstrated here provides the path to efficient X-ray optics for imaging at 1 nm resolution.

The Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source.

The Atomic, Molecular and Optical Science (AMO) instrument at the Linac Coherent Light Source (LCLS) provides a tight soft X-ray focus into one of three experimental endstations. The flexible instrument design is optimized for studying a wide variety of phenomena requiring peak intensity. There is a suite of spectrometers and two photon area detectors available. An optional mirror-based split-and-delay unit can be used for X-ray pump-probe experiments. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument.

Damage threshold of platinum coating used for optics for self-seeding of soft X-ray free electron laser.

We investigated the experimental damage threshold of platinum coating on a silicon substrate illuminated by soft x-ray radiation at grazing incidence angle of 2 degrees. The coating was the same as the blazed grating used for the soft X-ray self-seeding optics of the Linac Coherent Light Source free electron laser. The irradiation condition was chosen such that the absorbed dose was similar to the maximum dose expected for the grating. The expected dose was simulated by solving the Helmholtz equation in non-homogenous media. The experiment was performed at 900 eV photon energy for both single pulse and multi-shot conditions. We have not observed single shot damage. This corresponds to a single shot damage threshold being higher than 3 J/cm(2). The multiple shot damage threshold measured for 10 shots and about 600 shots was determined to be 0.95 J/cm(2) and 0.75 J/cm(2) respectively. The damage threshold occurred at an instantaneous dose which is higher that the melt dose of platinum.

Three-dimensional reconstruction of the giant mimivirus particle with an x-ray free-electron laser.

We present a proof-of-concept three-dimensional reconstruction of the giant mimivirus particle from experimentally measured diffraction patterns from an x-ray free-electron laser. Three-dimensional imaging requires the assembly of many two-dimensional patterns into an internally consistent Fourier volume. Since each particle is randomly oriented when exposed to the x-ray pulse, relative orientations have to be retrieved from the diffraction data alone. We achieve this with a modified version of the expand, maximize and compress algorithm and validate our result using new methods.

Fluence scan: an unexplored property of a laser beam.

We present an extended theoretical background of so-called fluence scan (f-scan or F-scan) method, which is frequently being used for offline characterization of focused short-wavelength (EUV, soft X-ray, and hard X-ray) laser beams [J. Chalupský et al., Opt. Express 18, 27836 (2010)]. The method exploits ablative imprints in various solids to visualize iso-fluence beam contours at different fluence and/or clip levels. An f-scan curve (clip level as a function of the corresponding iso-fluence contour area) can be generated for a general non-Gaussian beam. As shown in this paper, fluence scan encompasses important information about energy distribution within the beam profile, which may play an essential role in laser-matter interaction research employing intense non-ideal beams. Here we for the first time discuss fundamental properties of the f-scan function and its inverse counterpart (if-scan). Furthermore, we extensively elucidate how it is related to the effective beam area, energy distribution, and to the so called Liu's dependence [J. M. Liu, Opt. Lett. 7, 196 (1982)]. A new method of the effective area evaluation based on weighted inverse f-scan fit is introduced and applied to real data obtained at the SCSS (SPring-8 Compact SASE Source) facility.