Stochastic atomic acceleration during the X-ray-induced fluidization of a silica glass.

The X-ray-induced, nonthermal fluidization of the prototypical SiO2 glass is investigated by X-ray photon correlation spectroscopy in the small-angle scattering range. This process is initiated by the absorption of X-rays and leads to overall atomic displacements which reach at least few nanometers at temperatures well below the glass transition. At absorbed doses of ∼5 GGy typical of many modern X-ray-based experiments, the atomic displacements display a hyperdiffusive behavior and are distributed according to a heavy-tailed, Lévy stable distribution. This is attributed to the stochastic generation of X-ray-induced point defects which give rise to a dynamically fluctuating potential landscape, thus providing a microscopic picture of the fluidization process.

Improvement of ultra-small-angle XPCS with the Extremely Brilliant Source.

Recent technical developments and the performance of the X-ray photon correlation spectroscopy (XPCS) method over the ultra-small-angle range with the Extremely Brilliant Source (EBS) at the ESRF are described. With higher monochromatic coherent photon flux (∼1012 photons s-1) provided by the EBS and the availability of a fast pixel array detector (EIGER 500K detector operating at 23000 frames s-1), XPCS has become more competitive for probing faster dynamics in relatively dilute suspensions. One of the goals of the present development is to increase the user-friendliness of the method. This is achieved by means of a Python-based graphical user interface that enables online visualization and analysis of the processed data. The improved performance of XPCS on the Time-Resolved Ultra-Small-Angle X-ray Scattering instrument (ID02 beamline) is demonstrated using dilute model colloidal suspensions in several different applications.

High-pressure X-ray photon correlation spectroscopy at fourth-generation synchrotron sources.

A new experimental setup combining X-ray photon correlation spectroscopy (XPCS) in the hard X-ray regime and a high-pressure sample environment has been developed to monitor the pressure dependence of the internal motion of complex systems down to the atomic scale in the multi-gigapascal range, from room temperature to 600 K. The high flux of coherent high-energy X-rays at fourth-generation synchrotron sources solves the problems caused by the absorption of diamond anvil cells used to generate high pressure, enabling the measurement of the intermediate scattering function over six orders of magnitude in time, from 10-3 s to 103 s. The constraints posed by the high-pressure generation such as the preservation of X-ray coherence, as well as the sample, pressure and temperature stability, are discussed, and the feasibility of high-pressure XPCS is demonstrated through results obtained on metallic glasses.

Speckle contrast of interfering fluorescence X-rays.

With the development of X-ray free-electron lasers (XFELs), producing pulses of femtosecond durations comparable with the coherence times of X-ray fluorescence, it has become possible to observe intensity-intensity correlations due to the interference of emission from independent atoms. This has been used to compare durations of X-ray pulses and to measure the size of a focusedX-ray beam, for example. Here it is shown that it is also possible to observe the interference of fluorescence photons through the measurement of the speckle contrast of angle-resolved fluorescence patterns. Speckle contrast is often used as a measure of the degree of coherence of the incident beam or the fluctuations of the illuminated sample as determined from X-ray diffraction patterns formed by elastic scattering, rather than from fluorescence patterns as addressed here. Commonly used approaches to estimate speckle contrast were found to suffer when applied to XFEL-generated fluorescence patterns due to low photon counts and a significant variation of the excitation pulse energy from shot to shot. A new method to reliably estimate speckle contrast under such conditions, using a weighting scheme, is introduced. The method is demonstrated by comparing the speckle contrast of fluorescence observed with pulses of 3 fs to 15 fs duration.

The PERCIVAL detector: first user experiments.

The PERCIVAL detector is a CMOS imager designed for the soft X-ray regime at photon sources. Although still in its final development phase, it has recently seen its first user experiments: ptychography at a free-electron laser, holographic imaging at a storage ring and preliminary tests on X-ray photon correlation spectroscopy. The detector performed remarkably well in terms of spatial resolution achievable in the sample plane, owing to its small pixel size, large active area and very large dynamic range; but also in terms of its frame rate, which is significantly faster than traditional CCDs. In particular, it is the combination of these features which makes PERCIVAL an attractive option for soft X-ray science.

Direct measurement of Stokes-Einstein diffusion of Cowpea mosaic virus with 19 µs-resolved XPCS.

Brownian motion of Cowpea mosaic virus (CPMV) in water was measured using small-angle X-ray photon correlation spectroscopy (SA-XPCS) at 19.2 µs time resolution. It was found that the decorrelation time τ(Q) = 1/DQ2 up to Q = 0.091 nm-1. The hydrodynamic radius RH determined from XPCS using Stokes-Einstein diffusion D = kT/(6πηRH) is 43% larger than the geometric radius R0 determined from SAXS in the 0.007 M K3PO4 buffer solution, whereas it is 80% larger for CPMV in 0.5 M NaCl and 104% larger in 0.5 M (NH4)2SO4, a possible effect of aggregation as well as slight variation of the structures of the capsid resulting from the salt-protein interactions.

Measurement of the coherent beam properties at the CoSAXS beamline.

The CoSAXS beamline at the MAX IV Laboratory is a modern multi-purpose (coherent) small-angle X-ray scattering (CoSAXS) instrument, designed to provide intense and optionally coherent illumination at the sample position, enabling coherent imaging and speckle contrast techniques. X-ray tracing simulations used to design the beamline optics have predicted a total photon flux of 1012-1013 photons s-1 and a degree of coherence of up to 10% at 7.1 keV. The normalized degree of coherence and the coherent flux of this instrument were experimentally determined using the separability of a ptychographic reconstruction into multiple mutually incoherent modes and thus the Coherence in the name CoSAXS was verified. How the beamline can be used both for coherent imaging and XPCS measurements, which both heavily rely on the degree of coherence of the beam, was demonstrated. These results are the first experimental quantification of coherence properties in a SAXS instrument at a fourth-generation synchrotron light source.

Use of continuous sample translation to reduce radiation damage for XPCS studies of protein diffusion.

An experimental setup to measure X-ray photon correlation spectroscopy during continuous sample translation is presented and its effectiveness as a means to avoid sample damage in dynamics studies of protein diffusion is evaluated. X-ray damage from focused coherent synchrotron radiation remains below tolerable levels as long as the sample is translated through the beam sufficiently quickly. Here it is shown that it is possible to separate sample dynamics from the effects associated with the transit of the sample through the beam. By varying the sample translation rate, the damage threshold level, Dthresh = 1.8 kGy, for when beam damage begins to modify the dynamics under the conditions used, is also determined. Signal-to-noise ratios, Rsn ≥ 20, are obtained down to the shortest delay times of 20 µs. The applicability of this method of data collection to the next generation of multi-bend achromat synchrotron sources is discussed and it is shown that sub-microsecond dynamics should be obtainable on protein samples.

20†µs-resolved high-throughput X-ray photon correlation spectroscopy on a 500k pixel detector enabled by data-management workflow.

The performance of the new 52 kHz frame rate Rigaku XSPA-500k detector was characterized on beamline 8-ID-I at the Advanced Photon Source at Argonne for X-ray photon correlation spectroscopy (XPCS) applications. Due to the large data flow produced by this detector (0.2 PB of data per 24 h of continuous operation), a workflow system was deployed that uses the Advanced Photon Source data-management (DM) system and high-performance software to rapidly reduce area-detector data to multi-tau and two-time correlation functions in near real time, providing human-in-the-loop feedback to experimenters. The utility and performance of the workflow system are demonstrated via its application to a variety of small-angle XPCS measurements acquired from different detectors in different XPCS measurement modalities. The XSPA-500k detector, the software and the DM workflow system allow for the efficient acquisition and reduction of up to ∼109 area-detector data frames per day, facilitating the application of XPCS to measuring samples with weak scattering and fast dynamics.

Spatially-resolved nanometer-scale measurement of cartilage extracellular matrix mobility.

OBJECTIVE: Tissues have complex structures, comprised of solid and fluid phases. Improved understanding of interactions between joint fluid and extracellular matrix (ECM) is required in models of cartilage mechanics. X-ray photon correlation spectroscopy (XPCS) directly measures nanometer-scale dynamics and can provide insight into biofluid-biosolid interactions in cartilage. This study applies XPCS to evaluate dynamic interactions between intact cartilage and biofluids. DESIGN: Cartilage biopsies were collected from bovine femoral condyles. During XPCS measurements, cartilage samples were exposed to different fluids: deionized water, PBS, synovial fluid, or sonicated synovial fluid. ECM-biofluid interactions were also assessed at different length scales and different depths from the cartilage surface. RESULTS: Using XPCS, cartilage ECM mobility was detected at length scales from 50 to 207 nm. As length scale decreased, time scale for autocorrelation decay decreased, suggesting smaller ECM components are more mobile. ECM dynamics were slowed by dehydrating the sample, demonstrating XPCS assesses matrix mobility in hydrated environments. At all length scales, the matrix was more mobile in deionized water and slowest in synovial fluid. Using the 207 nm length scale assessment, ECM dynamics in synovial fluid were fastest at the cartilage surface and progressively slowed as depth into the sample increased, demonstrating XPCS can assess spatial distribution of ECM dynamics. Finally, ECM mobility increased for degraded synovial fluid. CONCLUSIONS: This study demonstrates the potential of XPCS to provide unique insights into nanometer-scale cartilage ECM mobility in a spatially resolved manner and illustrates the importance of biosolid-biofluid interactions in dictating ECM dynamics.

Deciphering the intrinsic dynamics from the beam-induced atomic motions in oxide glasses.

Probing the microscopic slow structural relaxation in oxide glasses by X-ray photon correlation spectroscopy (XPCS) revealed faster than expected dynamics induced by the X-ray illumination. The fast beam-induced dynamics mask true slow structural relaxation in glasses and challenges application of XPCS to probe the atomic dynamics in oxide glasses. Here an approach that allows estimation of the true relaxation time of the sample in the presence of beam-induced dynamics is presented. The method requires two measurements either with different X-ray beam intensities or at different temperatures. Using numerical simulations it is shown that the slowest estimated true relaxation time is limited by the accuracy of the measured relaxation times of the sample. By analyzing the reported microscopic dynamics in SiO2, GeO2 and B2O3 glasses, it is concluded that the beam-induced dynamics show rich behavior depending on the sample.

Accurate contrast determination for X-ray speckle visibility spectroscopy.

X-ray speckle visibility spectroscopy using X-ray free-electron lasers has long been proposed as a probe of fast dynamics in noncrystalline materials. In this paper, numerical modeling is presented to show how the data interpretation of visibility spectroscopy can be impacted by the nonidealities of real-life X-ray detectors. Using simulated detector data, this work provides a detailed analysis of the systematic errors of several contrast extraction algorithms in the context of low-count-rate X-ray speckle visibility spectroscopy and their origins are discussed. Here, it was found that the finite detector charge cloud and pixel size lead to an unavoidable `degeneracy' in photon position determination, and that the contrasts extracted using different algorithms can all be corrected by a simple linear model. The results suggest that experimental calibration of the correction coefficient at the count rate of interest is possible and essential. This allows computationally lightweight algorithms to be implemented for on-the-fly analysis.

Early-onset nucleotide excision repair disorders with neurological impairment: Clues for early diagnosis and prognostic counseling.

Nucleotide excision repair associated diseases comprise overlapping phenotypes and a wide range of outcomes. The early stages still remain under-investigated and underdiagnosed, even although an early recognition of the first symptoms is of utmost importance for appropriate care and genetic counseling. We systematically collected clinical and molecular data from the literature and from newly diagnosed NER patients with neurological impairment, presenting clinical symptoms before the age of 12 months, including foetal cases. One hundred and eighty-five patients were included, 13 with specific symptoms during foetal life. Arthrogryposis, microcephaly, cataracts, and skin anomalies are the most frequently reported signs in early subtypes. Non ERCC6/CSB or ERCC8/CSA genes are overrepresented compared to later onset cohorts: 19% patients of this cohort presented variants in ERCC1, ERCC2/XPD, ERCC3/XPB or ERCC5/XPG. ERCC5/XPG is even the most frequently involved gene in foetal cases (10/13 cases, [4/7 families]). In this cohort, the mutated gene, the age of onset, the type of disease, severe global developmental delay, IUGR and skin anomalies were associated with earlier death. This large survey focuses on specific symptoms that should attract the attention of clinicians towards early-onset NER diagnosis in foetal and neonatal period, without waiting for the completeness of classical criteria.

Compact hard X-ray split-and-delay line for studying ultrafast dynamics at free-electron laser sources.

A compact hard X-ray split-and-delay line for studying ultrafast dynamics at free-electron laser sources is presented. The device is capable of splitting a single X-ray pulse into two fractions to introduce time delays from -5 to 815 ps with femtosecond resolution. The split-and-delay line can operate in a wide and continuous energy range between 7 and 16 keV. Compact dimensions of 60 × 60 × 30 cm with a total weight of about 60 kg make it portable and suitable for direct installation in an experimental hutch. The concept of the device is based on crystal diffraction. The piezo-driven stages utilized in the device give nanometre positioning accuracy. On-line monitoring systems based on X-ray cameras and intensity monitors are implemented to provide active alignment feedback. Performance estimates of the system are also presented.

Implications of disturbed photon-counting statistics of Eiger detectors for X-ray speckle visibility experiments.

This paper reports on coherent scattering experiments in the low-count regime with less than one photon per pixel per acquisition on average, conducted with two detectors based on the Eiger single-photon-counting chip. The obtained photon-count distributions show systematic deviations from the expected Poisson-gamma distribution, which result in a strong overestimation of the measured speckle contrast. It is shown that these deviations originate from an artificial increase of double-photon events, which is proportional to the detected intensity and inversely proportional to the exposure time. The observed miscounting effect may have important implications for new coherent scattering experiments emerging with the advent of high-brilliance X-ray sources. Different correction schemes are discussed in order to obtain the correct photon distributions from the data. A successful correction is demonstrated with the measurement of Brownian motion from colloidal particles using X-ray speckle visibility spectroscopy.

Anomalous Dynamics of Magnetic Anisotropic Colloids Studied by XPCS.

The influence of an applied magnetic field on the collective dynamics of novel anisotropic colloidal particles whose shape resembles peanuts is reported. Being made up of hematite cores and silica shells, these micrometer-sized particles align in a direction perpendicular to the applied external magnetic field, and assemble into chains along the field direction. The anisotropic dynamics of these particles is investigated using multispeckle ultrasmall-angle X-ray photon correlation spectroscopy (USA-XPCS). The results indicate that along the direction of the magnetic field, the particle dynamics strongly depends on the length scale probed. Here, the relaxation of the intermediate scattering function follows a compressed exponential behavior at large distances, while it appears diffusive at distances comparable or smaller than the particle size. Perpendicular to the applied field (and along the direction of gravity), the experimental data can be quantitatively reproduced by a combination of an advective term originating from sedimentation and a purely diffusive one that describes the thermal diffusion of the assembled chains and individual particles.

Pulse intensity characterization of the LCLS nanosecond double-bunch mode of operation.

The recent demonstration of the `nanosecond double-bunch' operation mode, i.e. two X-ray pulses separated in time between 0.35 and hundreds of nanoseconds and by increments of 0.35 ns, offers new opportunities to investigate ultrafast dynamics in diverse systems of interest. However, in order to reach its full potential, this mode of operation requires the precise characterization of the intensity of each X-ray pulse within each pulse pair for any time separation. Here, a transmissive single-shot diagnostic that achieves this goal for time separations larger than 0.7 ns with a precision better than 5% is presented. It also provides real-time monitoring feedback to help tune the accelerator parameters to deliver double pulse intensity distributions optimized for specific experimental goals.

Sub-microsecond-resolved multi-speckle X-ray photon correlation spectroscopy with a pixel array detector.

Small-angle X-ray photon correlation spectroscopy (XPCS) measurements spanning delay times from 826 ns to 52.8 s were performed using a photon-counting pixel array detector with a dynamic range of 0-3 (2 bits). Fine resolution and a wide dynamic range of time scales was achieved by combining two modes of operation of the detector: (i) continuous mode, where data acquisition and data readout are performed in parallel with a frame acquisition time of 19.36 µs, and (ii) burst mode, where 12 frames are acquired with frame integration times of either 2.56 µs frame-1 or 826 ns frame-1 followed by 3.49 ms or 1.16 ms, respectively, for readout. The applicability of the detector for performing multi-speckle XPCS was demonstrated by measuring the Brownian dynamics of 10 nm-radius gold and 57 nm-radius silica colloids in water at room temperature. In addition, the capability of the detector to faithfully record one- and two-photon counts was examined by comparing the statistical distribution of photon counts with expected probabilities from the negative binomial distribution. It was found that in burst mode the ratio of 2 s to 1 s is markedly smaller than predicted and that this is attributable to pixel-response dead-time.

Ultra-small-angle X-ray photon correlation spectroscopy using the Eiger detector.

Successful implementation of the single-photon-counting Eiger 500k pixel array detector for sub-millisecond X-ray photon correlation spectroscopy (XPCS) measurements in the ultra-small-angle scattering region is reported. The performance is demonstrated by measuring the dynamics of dilute silica colloids in aqueous solvents when the detector is operated at different counter depths, 4, 8 and 12 bit. In the fastest mode involving 4 bit parallel readout, a stable frame rate of 22 kHz is obtained that enabled measurement of intensity-intensity autocorrelation functions with good statistics down to the 50 µs range for a sample with sufficient scattering power. The high frame rate and spatial resolution together with large number of pixels of the detector facilitate the investigation of sub-millisecond dynamics over a broad length scale by multispeckle XPCS. This is illustrated by an example involving phoretic motion of colloids during the phase separation of the solvent.

Distributed X-ray photon correlation spectroscopy data reduction using Hadoop MapReduce.

Multi-speckle X-ray photon correlation spectroscopy (XPCS) is a powerful technique for characterizing the dynamic nature of complex materials over a range of time scales. XPCS has been successfully applied to study a wide range of systems. Recent developments in higher-frame-rate detectors, while aiding in the study of faster dynamical processes, creates large amounts of data that require parallel computational techniques to process in near real-time. Here, an implementation of the multi-tau and two-time autocorrelation algorithms using the Hadoop MapReduce framework for distributed computing is presented. The system scales well with regard to the increase in the data size, and has been serving the users of beamline 8-ID-I at the Advanced Photon Source for near real-time autocorrelations for the past five years.