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Time‐resolved crystallography enables the visualization of protein molecular motion during a reaction. Although light is often used to initiate reactions in time‐resolved crystallography, only a small number of proteins can be activated by light. However, many biological reactions can be triggered by the interaction between proteins and ligands. The sample delivery method presented here uses a mix‐and‐extrude approach based on 3D‐printed microchannels in conjunction with a micronozzle. The diffusive mixing enables the study of the dynamics of samples in viscous media. The device design allows mixing of the ligands and protein crystals in 2 to 20 s. The device characterization using a model system (fluorescence quenching of iq‐mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within lipidic cubic phase, can be mixed efficiently. The potential of this approach for time‐resolved membrane protein crystallography to support the development of new drugs is discussed. [ABSTRACT FROM AUTHOR]

X‐ray crystallography has witnessed a massive development over the past decade, driven by large increases in the intensity and brightness of X‐ray sources and enabled by employing high‐frame‐rate X‐ray detectors. The analysis of large data sets is done via automatic algorithms that are vulnerable to imperfections in the detector and noise inherent with the detection process. By improving the model of the behaviour of the detector, data can be analysed more reliably and data storage costs can be significantly reduced. One major requirement is a software mask that identifies defective pixels in diffraction frames. This paper introduces a methodology and program based upon concepts of machine learning, called robust mask maker (RMM), for the generation of bad‐pixel masks for large‐area X‐ray pixel detectors based on modern robust statistics. It is proposed to discriminate normally behaving pixels from abnormal pixels by analysing routine measurements made with and without X‐ray illumination. Analysis software typically uses a Bragg peak finder to detect Bragg peaks and an indexing method to detect crystal lattices among those peaks. Without proper masking of the bad pixels, peak finding methods often confuse the abnormal values of bad pixels in a pattern with true Bragg peaks and flag such patterns as useful regardless, leading to storage of enormous uninformative data sets. Also, it is computationally very expensive for indexing methods to search for crystal lattices among false peaks and the solution may be biased. This paper shows how RMM vastly improves peak finders and prevents them from labelling bad pixels as Bragg peaks, by demonstrating its effectiveness on several serial crystallography data sets. [ABSTRACT FROM AUTHOR]

Liquid sample delivery systems are used extensively for serial femtosecond crystallography at X‐ray free‐electron lasers (XFELs). However, misalignment of the liquid jet and the XFEL beam leads to the X‐rays either partially or completely missing the sample, resulting in sample wastage and a loss of experiment time. Implemented here is an algorithm to analyse optical images using machine vision to determine whether there is overlap of the X‐ray beam and liquid jet. The long‐term goal is to use the output from this algorithm to implement an automated feedback mechanism to maintain constant alignment of the X‐ray beam and liquid jet. The key elements of this jet alignment algorithm are discussed and its performance is characterized by comparing the results with a manual analysis of the optical image data. The success rate of the algorithm for correctly identifying hits is quantified via a similarity metric, the Dice coefficient. In total four different nozzle designs were used in this study, yielding an overall Dice coefficient of 0.98.A novel strategy is presented for sample jet alignment using machine vision for liquid‐jet‐based sample delivery systems. Feedback using height‐resolution images from an optical microscope positioned perpendicular to the path of the X‐ray beam enables tracking of the relative alignment of the liquid jet and X‐ray beam. [ABSTRACT FROM AUTHOR]

Meteor impacts can induce unique pressure‐dependent structural changes in minerals due to the propagation of shock waves. Plagioclase—ubiquitous throughout the Earth's crust, extraterrestrial bodies, and meteorites—is commonly used for reconstructing the impact history and conditions of the parent bodies. However, there have been unresolved inconsistencies in the interpretation of shock transformations across previous studies: The pressure at which amorphization begins and the process by which it occurs is the subject of ongoing debate. Here, we utilize time‐resolved in situ X‐ray diffraction (XRD) to probe the phase transformation pathway of plagioclase during shock compression at a sub‐nanosecond timescale. Direct amorphization begins at pressures much lower than what was previously assumed, just above the Hugoniot elastic limit of 5 GPa, with full amorphization to a high‐density amorphous phase, observed at 32(10) GPa and 20 ns. Upon release, the material partially recrystallizes back into the original structure, demonstrating a memory effect. [ABSTRACT FROM AUTHOR]

X‐ray free‐electron lasers provide intense pulses of coherent X‐rays with a short pulse duration. These sources are chaotic by nature and therefore, to be used at their full potential, require that every X‐ray pulse is characterized in terms of various relevant properties such as intensity, photon energy, position and timing. Diagnostics are for example installed on an X‐ray beamline to specifically monitor the intensity of individual X‐ray pulses. To date, these can however only provide a single‐shot value of the relative number of photons per shot. Here are reported measurements made in January 2015 of the absolute number of photons in the hard X‐ray regime at LCLS which is typically 3.5 × 1011 photons shot−1 between 6 and 9.5 keV at the X‐ray Pump–Probe instrument. Moreover, an average transmission of ≈62% of the hard X‐ray beamline over this energy range is measured and the third‐harmonic content of ≈0.47% below 9 keV is characterized. Measurement of the absolute number of photons per pulse as a function of X‐ray photon energy at the hard X‐ray beamline of LCLS is presented. It is estimated by two different detectors and is used to characterize the hard X‐ray beamline optics transmission as well as the third‐harmonic content of the LCLS radiation. [ABSTRACT FROM AUTHOR]

A prototype ePix100 detector was used in small-angle scattering geometry to capture speckle patterns from a static sample using the Linac Coherent Light Source (LCLS) hard X-ray free-electron laser at 8.34 keV. The average number of detected photons per pixel per pulse was varied over three orders of magnitude from about 23 down to 0.01 to test the detector performance. At high average photon count rates, the speckle contrast was evaluated by analyzing the probability distribution of the pixel counts at a constant scattering vector for single frames. For very low average photon counts of less than 0.2 per pixel, the `droplet algorithm' was first applied to the patterns for correcting the effect of charge sharing, and then the pixel count statistics of multiple frames were analyzed collectively to extract the speckle contrast. Results obtained using both methods agree within the uncertainty intervals, providing strong experimental evidence for the validity of the statistical analysis. More importantly it confirms the suitability of the ePix100 detector for X-ray coherent scattering experiments, especially at very low count rates with performances surpassing those of previously available LCLS detectors. [ABSTRACT FROM AUTHOR]

X-ray focus optimization and characterization based on coherent scattering and quantitative speckle size measurements was demonstrated at the Linac Coherent Light Source. Its performance as a single-pulse free-electron laser beam diagnostic was tested for two typical focusing configurations. The results derived from the speckle size/shape analysis show the effectiveness of this technique in finding the focus' location, size and shape. In addition, its single-pulse compatibility enables users to capture pulse-to-pulse fluctuations in focus properties compared with other techniques that require scanning and averaging. [ABSTRACT FROM AUTHOR]

The X-ray Pump-Probe instrument achieves femtosecond time-resolution with hard X-ray methods using a free-electron laser source. It covers a photon energy range of 4-24 keV. A femtosecond optical laser system is available across a broad spectrum of wavelengths for generating transient states of matter. The instrument is designed to emphasize versatility and the scientific goals encompass ultrafast physical, chemical and biological processes involved in the transformation of matter and transfer of energy at the atomic scale. [ABSTRACT FROM AUTHOR]

The X-ray Correlation Spectroscopy instrument is dedicated to the study of dynamics in condensed matter systems using the unique coherence properties of free-electron lasers. It covers a photon energy range of 4-25 keV. The intrinsic temporal characteristics of the Linac Coherent Light Source, in particular the 120 Hz repetition rate, allow for the investigation of slow dynamics (milliseconds) by means of X-ray photon correlation spectroscopy. Double-pulse schemes could probe dynamics on the picosecond timescale. A description of the instrument capabilities and recent achievements is presented. [ABSTRACT FROM AUTHOR]

X-ray free-electron lasers (FELs) have opened unprecedented possibilities to study the structure and dynamics of matter at an atomic level and ultra-fast timescale. Many of the techniques routinely used at storage ring facilities are being adapted for experiments conducted at FELs. In order to take full advantage of these new sources several challenges have to be overcome. They are related to the very different source characteristics and its resulting impact on sample delivery, X-ray optics, X-ray detection and data acquisition. Here it is described how photon-in photon-out hard X-ray spectroscopy techniques can be applied to study the electronic structure and its dynamics of transition metal systems with ultra-bright and ultra-short FEL X-ray pulses. In particular, some of the experimental details that are different compared with synchrotron-based setups are discussed and illustrated by recent measurements performed at the Linac Coherent Light Source. [ABSTRACT FROM AUTHOR]

We have explored the feasibility of X-ray fluorescence correlation spectroscopy for studying the dynamics of colloidal particles in solution. We measured suspensions of Au nanoparticles from 5 to 150 nm diameter in water/glycerol mixtures of various compositions. Time-averaged sample properties were traced via small-angle X-ray scattering. The contrast of the measured time-correlation functions scales as expected with the particle concentration in the sample. The time constants for translational diffusion and sedimentation in water/glycerol mixtures follow only qualitatively the expected behaviour. [ABSTRACT FROM AUTHOR]