The Extremely Brilliant Source storage ring of the European Synchrotron Radiation Facility

Texture tomography, a versatile framework to study crystalline texture in 3D

Crystallographic texture is a key organization feature of many technical and biological materials. In these materials, especially hierarchically structured ones, the preferential alignment of the nano constituents heavily influences the macroscopic behavior of the material. To study local crystallographic texture with both high spatial and angular resolution, we developed Texture Tomography (TexTOM). This approach allows the user to model the diffraction data of polycrystalline materials using the full reciprocal space of the crystal ensemble and describe the texture in each voxel via an orientation distribution function, hence it provides 3D reconstructions of the local texture by measuring the probabilities of all crystal orientations. The TexTOM approach addresses limitations associated with existing models: it correlates the intensities from several Bragg reflections, thus reducing ambiguities resulting from symmetry. Further, it yields quantitative probability distributions of local real space crystal orientations without further assumptions about the sample structure. Finally, its efficient mathematical formulation enables reconstructions faster than the time scale of the experiment. This manuscript presents the mathematical model, the inversion strategy and its current experimental implementation. We show characterizations of simulated data as well as experimental data obtained from a synthetic, inorganic model sample: the silica-witherite biomorph. TexTOM provides a versatile framework to reconstruct 3D quantitative texture information for polycrystalline samples; it opens the door for unprecedented insights into the nanostructural makeup of natural and technical materials.

Crossing length scales: X-ray approaches to studying the structure of biological materials

Biological materials have outstanding properties. With ease, challenging mechanical, optical or electrical properties are realised from comparatively `humble' building blocks. The key strategy to realise these properties is through extensive hierarchical structuring of the material from the millimetre to the nanometre scale in 3D. Though hierarchical structuring in biological materials has long been recognized, the 3D characterization of such structures remains a challenge. To understand the behaviour of materials, multimodal and multi-scale characterization approaches are needed. In this review, we outline current X-ray analysis approaches using the structures of bone and shells as examples. We show how recent advances have aided our understanding of hierarchical structures and their functions, and how these could be exploited for future research directions. We also discuss current roadblocks including radiation damage, data quantity and sample preparation, as well as strategies to address them.

In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry

The advent of serial crystallography has rejuvenated and popularized room-temperature X-ray crystal structure determination. Structures determined at physiological temperature reveal protein flexibility and dynamics. In addition, challenging samples (e.g. large complexes, membrane proteins and viruses) form fragile crystals that are often difficult to harvest for cryo-crystallography. Moreover, a typical serial crystallography experiment requires a large number of microcrystals, mainly achievable through batch crystallization. Many medically relevant samples are expressed in mammalian cell lines, producing a meager quantity of protein that is incompatible with batch crystallization. This can limit the scope of serial crystallography approaches. Direct in situ data collection from a 96-well crystallization plate enables not only the identification of the best diffracting crystallization condition but also the possibility for structure determination under ambient conditions. Here, we describe an in situ serial crystallography (iSX) approach, facilitating direct measurement from crystallization plates mounted on a rapidly exchangeable universal plate holder deployed at a microfocus beamline, ID23-2, at the European Synchrotron Radiation Facility. We applied our iSX approach on a challenging project, autotaxin, a therapeutic target expressed in a stable human cell line, to determine the structure in the lowest-symmetry P1 space group at 3.0 Å resolution. Our in situ data collection strategy provided a complete dataset for structure determination while screening various crystallization conditions. Our data analysis reveals that the iSX approach is highly efficient at a microfocus beamline, improving throughput and demonstrating how crystallization plates can be routinely used as an alternative method of presenting samples for serial crystallography experiments at synchrotrons.

Spontaneous Supercrystal Formation During a Strain-Engineered Metal-Insulator Transition

Mott metal-insulator transitions possess electronic, magnetic, and structural degrees of freedom promising next-generation energy-efficient electronics. A previously unknown, hierarchically ordered, and anisotropic supercrystal state is reported and its intrinsic formation characterized in-situ during a Mott transition in a Ca2RuO4 thin film. Machine learning-assisted X-ray nanodiffraction together with cryogenic electron microscopy reveal multi-scale periodic domain formation at and below the film transition temperature (TFilm ≈ 200-250 K) and a separate anisotropic spatial structure at and above TFilm. Local resistivity measurements imply an intrinsic coupling of the supercrystal orientation to the material's anisotropic conductivity. These findings add a new degree of complexity to the physical understanding of Mott transitions, opening opportunities for designing materials with tunable electronic properties.

Full Picture of Lattice Deformation in a Ge1 - xSnx Micro-Disk by 5D X-ray Diffraction Microscopy

Lattice strain in crystals can be exploited to effectively tune their physical properties. In microscopic structures, experimental access to the full strain tensor with spatial resolution at the (sub-)micrometer scale is at the same time very interesting and challenging. In this work, how scanning X-ray diffraction microscopy, an emerging model-free method based on synchrotron radiation, can shed light on the complex, anisotropic deformation landscape within three dimensional (3D) microstructures is shown. This technique allows the reconstruction of all lattice parameters within any type of crystal with submicron spatial resolution and requires no sample preparation. Consequently, the local state of deformation can be fully quantified. Exploiting this capability, all components of the strain tensor in a suspended, strained Ge1 - xSnx /Ge microdisk are mapped. Subtle elastic deformations are unambiguously correlated with structural defects, 3D microstructure geometry, and chemical variations, as verified by comparison with complementary electron microscopy and finite element simulations. The methodology described here is applicable to a wide range of fields, from bioengineering to metallurgy and semiconductor research.

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.

Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations

The human NQO1 (hNQO1) is a flavin adenine nucleotide (FAD)-dependent oxidoreductase that catalyzes the two-electron reduction of quinones to hydroquinones, being essential for the antioxidant defense system, stabilization of tumor suppressors, and activation of quinone-based chemotherapeutics. Moreover, it is overexpressed in several tumors, which makes it an attractive cancer drug target. To decipher new structural insights into the flavin reductive half-reaction of the catalytic mechanism of hNQO1, we have carried serial crystallography experiments at new ID29 beamline of the ESRF to determine, to the best of our knowledge, the first structure of the hNQO1 in complex with NADH. We have also performed molecular dynamics simulations of free hNQO1 and in complex with NADH. This is the first structural evidence that the hNQO1 functional cooperativity is driven by structural communication between the active sites through long-range propagation of cooperative effects across the hNQO1 structure. Both structural results and MD simulations have supported that the binding of NADH significantly decreases protein dynamics and stabilizes hNQO1 especially at the dimer core and interface. Altogether, these results pave the way for future time-resolved studies, both at x-ray free-electron lasers and synchrotrons, of the dynamics of hNQO1 upon binding to NADH as well as during the FAD cofactor reductive half-reaction. This knowledge will allow us to reveal unprecedented structural information of the relevance of the dynamics during the catalytic function of hNQO1.

INSIGHT: in situ heuristic tool for the efficient reduction of grazing-incidence X-ray scattering data

INSIGHT is a Python-based software tool for processing and reducing 2D grazing-incidence wide- and small-angle X-ray scattering (GIWAXS/GISAXS) data. It offers the geometric transformation of the 2D GIWAXS/GISAXS detector image to reciprocal space, including vectorized and parallelized pixel-wise intensity correction calculations. An explicit focus on efficient data management and batch processing enables full control of large time-resolved synchrotron and laboratory data sets for a detailed analysis of kinetic GIWAXS/GISAXS studies of thin films. It processes data acquired with arbitrarily rotated detectors and performs vertical, horizontal, azimuthal and radial cuts in reciprocal space. It further allows crystallographic indexing and GIWAXS pattern simulation, and provides various plotting and export functionalities. Customized scripting offers a one-step solution to reduce, process, analyze and export findings of large in situ and operando data sets.

Development towards high-resolution kHz-speed rotation-free volumetric imaging

X-ray multi-projection imaging (XMPI) has the potential to provide rotation-free 3D movies of optically opaque samples. The absence of rotation enables superior imaging speed and preserves fragile sample dynamics by avoiding the centrifugal forces introduced by conventional rotary tomography. Here, we present our XMPI observations at the ID19 beamline (ESRF, France) of 3D dynamics in melted aluminum with 1000 frames per second and 8 µm resolution per projection using the full dynamical range of our detectors. Since XMPI is a method under development, we also provide different tests for the instrumentation of up to 3000 frames per second. As the high-brilliance of 4th generation light-sources becomes more available, XMPI is a promising technique for current and future X-ray imaging instruments.

High-precision finishing method for narrow-groove channel-cut crystal x-ray monochromator using plasma chemical vaporization machining with wire electrode

A channel-cut crystal monochromator (CCM) is a popular and powerful device for producing monochromatic x-ray beams with extreme angular stability at a nano-radian level. Narrowing the groove width of CCMs has various benefits; for example, it is made possible to design more compact CCMs with an equivalent working energy range and to reduce the optical delay and the amount of beam shift, enhancing compatibility with various experimental techniques. An obstacle to the use of narrow-groove CCMs is the lack of a high-precision finishing method for the inner-wall reflecting surfaces, which imposes the distortion of x-ray wavefronts and spectral purity. We propose a new, damage-free surface-finishing method for silicon CCMs with a narrow groove of 1 mm or less with a localized etching technique using plasma generated with a wire electrode of 50 µm diameter under atmospheric pressure. Repeating plasma-on and plasma-off periods with a pulsed power supply, we reduce the concentration of reaction products through self-diffusion during the plasma-off periods and minimize the redeposition of the products on the processed surface that deteriorates the surface roughness. Under optimized conditions, we processed a CCM with a groove width of 1.2 mm, which has uniform reflection profiles and a nearly ideal reflectivity behavior for coherent monochromatic x rays.

A novel approach using nonlinear surfaces for dynamic aperture optimization in MBA synchrotron light sources

MBA cell-based synchrotron light sources have enabled an unprecedented increase in beam coherence and brightness, greatly benefiting the scientific disciplines that rely on X-ray techniques. However, controlling the electron dynamics is a theoretical and technological challenge, due to the large number of parameters to adjust and constraints to satisfy when designing modern synchrotrons. Having versatile tools for the description and manipulation of electron dynamics could favor the design of these accelerators and lead to progress on several fronts in the understanding of matter. In this paper, a formalism based on the use of nonlinear geometric surfaces represented by polynomial quasi-invariants, to analyze and optimize the dynamic aperture of electrons in MBA storage rings, is introduced. The formalism considers on- and off-momentum particle dynamics. Within the optimization scheme, different objective functions defined in terms of the nonlinear surfaces, which are minimized using genetic algorithm methods, are proposed. A remarkable horizontal dynamic aperture exceeding 19 mm is obtained for the design particle of a synchrotron model with 86 pm [Formula: see text] rad emittance along with a dynamic aperture above 5 mm for momentum deviations of ± 3[Formula: see text]. According to the results presented, this formalism could be greatly useful for manipulating the dynamical properties of electrons in synchrotrons light sources close to the diffraction limit.

Lipid vesicle pools studied by passive X-ray microrheology

Vesicle pools can form by attractive interaction in a solution, mediated by proteins or divalent ions such as calcium. The pools, which are alternatively also denoted as vesicle clusters, form by liquid-liquid phase separation (LLPS) from an initially homogeneous solution. Due to the short range liquid-like order of vesicles in the pool or cluster, the vesicle-rich phase can also be regarded as a condensate, and one would like to better understand not only the structure of these systems, but also their dynamics. The diffusion of vesicles, in particular, is expected to change when vesicles are arrested in a pool. Here we investigate whether passive microrheology based on X-ray photon correlation spectroscopy (XPCS) is a suitable tool to study model systems of artificial lipid vesicles exhibiting LLPS, and more generally also other heterogeneous biomolecular fluids. We show that by adding highly scattering tracer particles to the solution, valuable information on the single vesicle as well as collective dynamics can be inferred. While the correlation functions reveal freely diffusing tracer particles in solutions at low CaCl[Formula: see text] concentrations, the relaxation rate [Formula: see text] shows a nonlinear dependence on [Formula: see text] at a higher concentration of around 8 mM CaCl[Formula: see text], characterised by two linear regimes with a broad cross-over. We explain this finding based on arrested diffusion in percolating vesicle clusters.

ID22 - the high-resolution powder-diffraction beamline at ESRF

Following Phase 2 of the upgrade of the ESRF in which the storage ring was replaced by a new low-emittance ring along with many other facility upgrades, the status of ID22, the high-resolution powder-diffraction beamline, is described. The beamline has an in-vacuum undulator as source providing X-rays in the range 6-75 keV. ID22's principle characteristics include very high angular resolution as a result of the highly collimated and monochromatic beam, coupled with a 13-channel Si 111 multi-analyser stage between the sample and a Dectris Eiger2 X 2M-W CdTe pixel detector. The detector's axial resolution allows recorded 2θ values to be automatically corrected for the effects of axial divergence, resulting in narrower and more-symmetric peaks compared with the previous fixed-axial-slit arrangement. The axial acceptance can also be increased with increasing diffraction angle, thus simultaneously improving the statistical quality of high-angle data. A complementary Perkin Elmer XRD1611 medical-imaging detector is available for faster, lower-resolution data, often used at photon energies of 60-70 keV for pair-distribution function analysis, although this is also possible in high-resolution mode by scanning up to 120° 2θ at 35 keV. There are various sample environments, allowing sample temperatures from 4 K to 1600°C, a capillary cell for non-corrosive gas atmospheres in the range 0-100 bar, and a sample-changing robot that can accommodate 75 capillary samples compatible with the temperature range 80 K to 950°C.

Fourth-generation light sources

New fourth-generation synchrotron radiation facilities bring large gains in X-ray source brightness, but also challenges in making full use of their potentials. Some of these challenges have been faced at X-ray free-electron laser facilities.