of Evolution of elliptical SAXS patterns in aligned systems By journals.iucr.org Published On :: 2024-07-11 Small-angle X-ray and neutron scattering (SAXS and SANS) patterns from certain semicrystalline polymers and liquid crystals contain discrete reflections from ordered assemblies and central diffuse scattering (CDS) from uncorrelated structures. Systems with imperfectly ordered lamellar structures aligned by stretching or by a magnetic field produce four distinct SAXS patterns: two-point `banana', four-point pattern, four-point `eyebrow' and four-point `butterfly'. The peak intensities of the reflections lie not on a layer line, or the arc of a circle, but on an elliptical trajectory. Modeling shows that randomly placed lamellar stacks modified by chain slip and stack rotation or interlamellar shear can create these forms. On deformation, the isotropic CDS becomes an equatorial streak with an oval, diamond or two-bladed propeller shape, which can be analyzed by separation into isotropic and oriented components. The streak has elliptical intensity contours, a natural consequence of the imperfect alignment of the elongated scattering objects. Both equatorial streaks and two- and four-point reflections can be fitted in elliptical coordinates with relatively few parameters. Equatorial streaks can be analyzed to obtain the size and orientation of voids, fibrils or surfaces. Analyses of the lamellar reflection yield lamellar spacing, stack orientation (interlamellar shear) angle α and chain slip angle ϕ, as well as the size distribution of the lamellar stacks. Currently available computational tools allow these microstructural parameters to be rapidly refined. Full Article text
of On the analysis of two-time correlation functions: equilibrium versus non-equilibrium systems By journals.iucr.org Published On :: 2024-07-04 X-ray photon correlation spectroscopy (XPCS) is a powerful tool for the investigation of dynamics covering a broad range of timescales and length scales. The two-time correlation function (TTC) is commonly used to track non-equilibrium dynamical evolution in XPCS measurements, with subsequent extraction of one-time correlations. While the theoretical foundation for the quantitative analysis of TTCs is primarily established for equilibrium systems, where key parameters such as the diffusion coefficient remain constant, non-equilibrium systems pose a unique challenge. In such systems, different projections (`cuts') of the TTC may lead to divergent results if the underlying fundamental parameters themselves are subject to temporal variations. This article explores widely used approaches for TTC calculations and common methods for extracting relevant information from correlation functions, particularly in the light of comparing dynamics in equilibrium and non-equilibrium systems. Full Article text
of Quality assessment of the wide-angle detection option planned at the high-intensity/extended Q-range SANS diffractometer KWS-2 combining experiments and McStas simulations By journals.iucr.org Published On :: 2024-06-27 For a reliable characterization of materials and systems featuring multiple structural levels, a broad length scale from a few ångström to hundreds of nanometres must be analyzed and an extended Q range must be covered in X-ray and neutron scattering experiments. For certain samples or effects, it is advantageous to perform such characterization with a single instrument. Neutrons offer the unique advantage of contrast variation and matching by D-labeling, which is of great value in the characterization of natural or synthetic polymers. Some time-of-flight small-angle neutron scattering (TOF-SANS) instruments at neutron spallation sources can cover an extended Q range by using a broad wavelength band and a multitude of detectors. The detectors are arranged to cover a wide range of scattering angles with a resolution that allows both large-scale morphology and crystalline structure to be resolved simultaneously. However, for such analyses, the SANS instruments at steady-state sources operating in conventional monochromatic pinhole mode rely on additional wide-angle neutron scattering (WANS) detectors. The resolution must be tuned via a system of choppers and a TOF data acquisition option to reliably measure the atomic to mesoscale structures. The KWS-2 SANS diffractometer at Jülich Centre for Neutron Science allows the exploration of a wide Q range using conventional pinhole and lens focusing modes and an adjustable resolution Δλ/λ between 2 and 20%. This is achieved through the use of a versatile mechanical velocity selector combined with a variable slit opening and rotation frequency chopper. The installation of WANS detectors planned on the instrument required a detailed analysis of the quality of the data measured over a wide angular range with variable resolution. This article presents an assessment of the WANS performance by comparison with a McStas [Willendrup, Farhi & Lefmann (2004). Physica B, 350, E735–E737] simulation of ideal experimental conditions at the instrument. Full Article text
of On the feasibility of time-resolved X-ray powder diffraction of macromolecules using laser-driven ultrafast X-ray sources By journals.iucr.org Published On :: 2024-07-29 With the emergence of ultrafast X-ray sources, interest in following fast processes in small molecules and macromolecules has increased. Most of the current research into ultrafast structural dynamics of macromolecules uses X-ray free-electron lasers. In parallel, small-scale laboratory-based laser-driven ultrafast X-ray sources are emerging. Continuous development of these sources is underway, and as a result many exciting applications are being reported. However, because of their low flux, such sources are not commonly used to study the structural dynamics of macromolecules. This article examines the feasibility of time-resolved powder diffraction of macromolecular microcrystals using a laboratory-scale laser-driven ultrafast X-ray source. Full Article text
of Rapid detection of rare events from in situ X-ray diffraction data using machine learning By journals.iucr.org Published On :: 2024-07-17 High-energy X-ray diffraction methods can non-destructively map the 3D microstructure and associated attributes of metallic polycrystalline engineering materials in their bulk form. These methods are often combined with external stimuli such as thermo-mechanical loading to take snapshots of the evolving microstructure and attributes over time. However, the extreme data volumes and the high costs of traditional data acquisition and reduction approaches pose a barrier to quickly extracting actionable insights and improving the temporal resolution of these snapshots. This article presents a fully automated technique capable of rapidly detecting the onset of plasticity in high-energy X-ray microscopy data. The technique is computationally faster by at least 50 times than the traditional approaches and works for data sets that are up to nine times sparser than a full data set. This new technique leverages self-supervised image representation learning and clustering to transform massive data sets into compact, semantic-rich representations of visually salient characteristics (e.g. peak shapes). These characteristics can rapidly indicate anomalous events, such as changes in diffraction peak shapes. It is anticipated that this technique will provide just-in-time actionable information to drive smarter experiments that effectively deploy multi-modal X-ray diffraction methods spanning many decades of length scales. Full Article text
of Operando pair distribution function analysis of nanocrystalline functional materials: the case of TiO2-bronze nanocrystals in Li-ion battery electrodes By journals.iucr.org Published On :: 2024-07-29 Structural modelling of operando pair distribution function (PDF) data of complex functional materials can be highly challenging. To aid the understanding of complex operando PDF data, this article demonstrates a toolbox for PDF analysis. The tools include denoising using principal component analysis together with the structureMining, similarityMapping and nmfMapping apps available through the online service `PDF in the cloud' (PDFitc, https://pdfitc.org/). The toolbox is used for both ex situ and operando PDF data for 3 nm TiO2-bronze nanocrystals, which function as the active electrode material in a Li-ion battery. The tools enable structural modelling of the ex situ and operando PDF data, revealing two pristine TiO2 phases (bronze and anatase) and two lithiated LixTiO2 phases (lithiated versions of bronze and anatase), and the phase evolution during galvanostatic cycling is characterized. Full Article text
of Coherent X-ray diffraction imaging of single particles: background impact on 3D reconstruction By journals.iucr.org Published On :: 2024-08-30 Coherent diffractive imaging with X-ray free-electron lasers could enable structural studies of macromolecules at room temperature. This type of experiment could provide a means to study structural dynamics on the femtosecond timescale. However, the diffraction from a single protein is weak compared with the incoherent scattering from background sources, which negatively affects the reconstruction analysis. This work evaluates the effects of the presence of background on the analysis pipeline. Background measurements from the European X-ray Free-Electron Laser were combined with simulated diffraction patterns and treated by a standard reconstruction procedure, including orientation recovery with the expand, maximize and compress algorithm and 3D phase retrieval. Background scattering did have an adverse effect on the estimated resolution of the reconstructed density maps. Still, the reconstructions generally worked when the signal-to-background ratio was 0.6 or better, in the momentum transfer shell of the highest reconstructed resolution. The results also suggest that the signal-to-background requirement increases at higher resolution. This study gives an indication of what is possible at current setups at X-ray free-electron lasers with regards to expected background strength and establishes a target for experimental optimization of the background. Full Article text
of Flow-Xl: a new facility for the analysis of crystallization in flow systems By journals.iucr.org Published On :: 2024-08-19 Characterization of crystallization processes in situ is of great importance to furthering knowledge of how nucleation and growth processes direct the assembly of organic and inorganic materials in solution and, critically, understanding the influence that these processes have on the final physico-chemical properties of the resulting solid form. With careful specification and design, as demonstrated here, it is now possible to bring combined X-ray diffraction and Raman spectroscopy, coupled to a range of fully integrated segmented and continuous flow platforms, to the laboratory environment for in situ data acquisition for timescales of the order of seconds. The facility used here (Flow-Xl) houses a diffractometer with a micro-focus Cu Kα rotating anode X-ray source and a 2D hybrid photon-counting detector, together with a Raman spectrometer with 532 and 785 nm lasers. An overview of the diffractometer and spectrometer setup is given, and current sample environments for flow crystallization are described. Commissioning experiments highlight the sensitivity of the two instruments for time-resolved in situ data collection of samples in flow. Finally, an example case study to monitor the batch crystallization of sodium sulfate from aqueous solution, by tracking both the solute and solution phase species as a function of time, highlights the applicability of such measurements in determining the kinetics associated with crystallization processes. This work illustrates that the Flow-Xl facility provides high-resolution time-resolved in situ structural phase information through diffraction data together with molecular-scale solution data through spectroscopy, which allows crystallization mechanisms and their associated kinetics to be analysed in a laboratory setting. Full Article text
of Determining pair distribution functions of thin films using laboratory-based X-ray sources By journals.iucr.org Published On :: 2024-08-30 This article demonstrates the feasibility of obtaining accurate pair distribution functions of thin amorphous films down to 80 nm, using modern laboratory-based X-ray sources. The pair distribution functions are obtained using a single diffraction scan without the requirement of additional scans of the substrate or of the air. By using a crystalline substrate combined with an oblique scattering geometry, most of the Bragg scattering of the substrate is avoided, rendering the substrate Compton scattering the primary contribution. By utilizing a discriminating energy filter, available in the latest generation of modern detectors, it is demonstrated that the Compton intensity can further be reduced to negligible levels at higher wavevector values. Scattering from the sample holder and the air is minimized by the systematic selection of pixels in the detector image based on the projected detection footprint of the sample and the use of a 3D-printed sample holder. Finally, X-ray optical effects in the absorption factors and the ratios between the Compton intensity of the substrate and film are taken into account by using a theoretical tool that simulates the electric field inside the film and the substrate, which aids in planning both the sample design and the measurement protocol. Full Article text
of Revealing nanoscale sorption mechanisms of gases in a highly porous silica aerogel By journals.iucr.org Published On :: 2024-08-19 Geological formations provide a promising environment for the long-term and short-term storage of gases, including carbon dioxide, hydrogen and hydrocarbons, controlled by the rock-specific small-scale pore structure. This study investigates the nanoscale structure and gas uptake in a highly porous silica aerogel (a synthetic proxy for natural rocks) using transmission electron microscopy, X-ray diffraction, and small-angle and ultra-small-angle neutron scattering with a tracer of deuterated methane (CD4) at pressures up to 1000 bar. The results show that the adsorption of CD4 in the porous silica matrix is scale dependent. The pore space of the silica aerogel is fully accessible to the invading gas, which quickly equilibrates with the external pressure and shows no condensation on the sub-nanometre scale. In the 2.5–50 nm pore size region a classical two-phase adsorption behaviour is observed. The structure of the aerogel returns to its original state after the CD4 pressure has been released. Full Article text
of Practical courses on advanced methods in macromolecular crystallization: 20 years of history and future perspectives By journals.iucr.org Published On :: 2024-08-30 The first Federation of European Biochemical Societies Advanced Course on macromolecular crystallization was launched in the Czech Republic in October 2004. Over the past two decades, the course has developed into a distinguished event, attracting students, early career postdoctoral researchers and lecturers. The course topics include protein purification, characterization and crystallization, covering the latest advances in the field of structural biology. The many hands-on practical exercises enable a close interaction between students and teachers and offer the opportunity for students to crystallize their own proteins. The course has a broad and lasting impact on the scientific community as participants return to their home laboratories and act as nuclei by communicating and implementing their newly acquired knowledge and skills. Full Article text
of Laboratory-based 3D X-ray standing-wave analysis of nanometre-scale gratings By journals.iucr.org Published On :: 2024-08-19 The increasing structural complexity and downscaling of modern nanodevices require continuous development of structural characterization techniques that support R&D and manufacturing processes. This work explores the capability of laboratory characterization of periodic planar nanostructures using 3D X-ray standing waves as a promising method for reconstructing atomic profiles of planar nanostructures. The non-destructive nature of this metrology technique makes it highly versatile and particularly suitable for studying various types of samples. Moreover, it eliminates the need for additional sample preparation before use and can achieve sub-nanometre reconstruction resolution using widely available laboratory setups, as demonstrated on a diffractometer equipped with a microfocus X-ray tube with a copper anode. Full Article text
of Energy-dispersive Laue diffraction analysis of the influence of statherin and histatin on the crystallographic texture during human dental enamel demineralization By journals.iucr.org Published On :: 2024-09-25 Energy-dispersive Laue diffraction (EDLD) is a powerful method to obtain position-resolved texture information in inhomogeneous biological samples without the need for sample rotation. This study employs EDLD texture scanning to investigate the impact of two salivary peptides, statherin (STN) and histatin-1 (HTN) 21 N-terminal peptides (STN21 and HTN21), on the crystallographic structure of dental enamel. These proteins are known to play crucial roles in dental caries progression. Three healthy incisors were randomly assigned to three groups: artificially demineralized, demineralized after HTN21 peptide pre-treatment and demineralized after STN21 peptide pre-treatment. To understand the micro-scale structure of the enamel, each specimen was scanned from the enamel surface to a depth of 250 µm using microbeam EDLD. Via the use of a white beam and a pixelated detector, where each pixel functions as a spectrometer, pole figures were obtained in a single exposure at each measurement point. The results revealed distinct orientations of hydroxyapatite crystallites and notable texture variation in the peptide-treated demineralized samples compared with the demineralized control. Specifically, the peptide-treated demineralized samples exhibited up to three orientation populations, in contrast to the demineralized control which displayed only a single orientation population. The texture index of the demineralized control (2.00 ± 0.21) was found to be lower than that of either the STN21 (2.32 ± 0.20) or the HTN21 (2.90 ± 0.46) treated samples. Hence, texture scanning with EDLD gives new insights into dental enamel crystallite orientation and links the present understanding of enamel demineralization to the underlying crystalline texture. For the first time, the feasibility of EDLD texture measurements for quantitative texture evaluation in demineralized dental enamel samples is demonstrated. Full Article text
of Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications By journals.iucr.org Published On :: 2024-09-17 X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclodextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0, which is available to download from https://12idb.xray.aps.anl.gov/solx.html. Full Article text
of The promise of GaAs 200 in small-angle neutron scattering for higher resolution By journals.iucr.org Published On :: 2024-08-27 The Q resolution in Bonse–Hart double-crystal diffractometers is determined for a given Bragg angle by the value of the crystallographic structure factor. To date, the reflections Si 220 or Si 111 have been used exclusively in neutron scattering, which provide resolutions for triple-bounce crystals of about 2 × 10−5 Å−1 (FWHM). The Darwin width of the GaAs 200 reflection is about a factor of 10 smaller, offering the possibility of a Q resolution of 2 × 10−6 Å−1 provided crystals of sufficient quality are available. This article reports a feasibility study with single-bounce GaAs 200, yielding a Q resolution of 4.6 × 10−6 Å−1, six times superior in comparison with a Si 220 setup. Full Article text
of Determination of the average crystallite size and the crystallite size distribution: the envelope function approach EnvACS By journals.iucr.org Published On :: 2024-09-17 A procedure is presented to exactly obtain the apparent average crystallite size (ACS) of powder samples using standard in-house powder diffraction experiments without any restriction originating from the Scherrer equation. Additionally, the crystallite size distribution within the sample can be evaluated. To achieve this, powder diffractograms are background corrected and long-range radial distribution functions G(r) up to 300 nm are calculated from the diffraction data. The envelope function fenv of G(r) is approximated by a procedure determining the absolute maxima of G(r) in a certain interval (r range). Fitting of an ACS distribution envelope function to this approximation gives the ACS and its distribution. The method is tested on diffractograms of LaB6 standard reference materials measured with different wavelengths to demonstrate the validity of the approach and to clarify the influence of the wavelength used. The latter results in a general description of the maximum observable average crystallite size, which depends on the instrument and wavelength used. The crystallite site distribution is compared with particle size distributions based on transmission electron microscopy investigations, providing an approximation of the average number of crystallites per particle. Full Article text
of Pushing the limits of accessible length scales via a modified Porod analysis in small-angle neutron scattering on ordered systems By journals.iucr.org Published On :: 2024-08-27 Small-angle neutron scattering is a widely used technique to study large-scale structures in bulk samples. The largest accessible length scale in conventional Bragg scattering is determined by the combination of the longest available neutron wavelength and smallest resolvable scattering angle. A method is presented that circumvents this limitation and is able to extract larger length scales from the low-q power-law scattering using a modification of the well known Porod law connecting the scattered intensity of randomly distributed objects to their specific surface area. It is shown that in the special case of a highly aligned domain structure the specific surface area extracted from the modified Porod law can be used to determine specific length scales of the domain structure. The analysis method is applied to study the micrometre-sized domain structure found in the intermediate mixed state of the superconductor niobium. The analysis approach allows the range of accessible length scales to be extended from 1 µm to up to 40 µm using a conventional small-angle neutron scattering setup. Full Article text
of In situ counter-diffusion crystallization and long-term crystal preservation in microfluidic fixed targets for serial crystallography By journals.iucr.org Published On :: 2024-09-25 Compared with batch and vapor diffusion methods, counter diffusion can generate larger and higher-quality protein crystals yielding improved diffraction data and higher-resolution structures. Typically, counter-diffusion experiments are conducted in elongated chambers, such as glass capillaries, and the crystals are either directly measured in the capillary or extracted and mounted at the X-ray beamline. Despite the advantages of counter-diffusion protein crystallization, there are few fixed-target devices that utilize counter diffusion for crystallization. In this article, different designs of user-friendly counter-diffusion chambers are presented which can be used to grow large protein crystals in a 2D polymer microfluidic fixed-target chip. Methods for rapid chip fabrication using commercially available thin-film materials such as Mylar, propylene and Kapton are also detailed. Rules of thumb are provided to tune the nucleation and crystal growth to meet users' needs while minimizing sample consumption. These designs provide a reliable approach to forming large crystals and maintaining their hydration for weeks and even months. This allows ample time to grow, select and preserve the best crystal batches before X-ray beam time. Importantly, the fixed-target microfluidic chip has a low background scatter and can be directly used at beamlines without any crystal handling, enabling crystal quality to be preserved. The approach is demonstrated with serial diffraction of photoactive yellow protein, yielding 1.32 Å resolution at room temperature. Fabrication of this standard microfluidic chip with commercially available thin films greatly simplifies fabrication and provides enhanced stability under vacuum. These advances will further broaden microfluidic fixed-target utilization by crystallographers. Full Article text
of Multidimensional Rietveld refinement of high-pressure neutron diffraction data of PbNCN By journals.iucr.org Published On :: 2024-09-05 High-pressure neutron powder diffraction data from PbNCN were collected on the high-pressure diffraction beamline SNAP located at the Spallation Neutron Source (SNS) of Oak Ridge National Laboratory (Tennessee, USA). The diffraction data were analyzed using the novel method of multidimensional (two dimensions for now, potentially more in the future) Rietveld refinement and, for comparison, employing the conventional Rietveld method. To achieve two-dimensional analysis, a detailed description of the SNAP instrument characteristics was created, serving as an instrument parameter file, and then yielding both cell and spatial parameters as refined under pressure for the first time for solid-state cyanamides/carbodiimides. The bulk modulus B0 = 25.1 (15) GPa and its derivative B'0 = 11.1 (8) were extracted for PbNCN following the Vinet equation of state. Surprisingly, an internal transition was observed beyond 2.0 (2) GPa, resulting from switching the bond multiplicities (and bending direction) of the NCN2− complex anion. The results were corroborated using electronic structure calculation from first principles, highlighting both local structural and chemical bonding details. Full Article text
of Use of a confocal optical device for centring a diamond anvil cell in single-crystal X-ray diffraction experiments By journals.iucr.org Published On :: 2024-09-20 High-pressure crystallographic data can be measured using a diamond anvil cell (DAC), which allows the sample to be viewed only along a cell vector which runs perpendicular to the diamond anvils. Although centring a sample perpendicular to this direction is straightforward, methods for centring along this direction often rely on sample focusing, measurements of the direct beam or short data collections followed by refinement of the crystal offsets. These methods may be inaccurate, difficult to apply or slow. Described here is a method based on precise measurement of the offset in this direction using a confocal optical device, whereby the cell centre is located at the mid-point of two measurements of the distance between a light source and the external faces of the diamond anvils viewed along the forward and reverse directions of the cell vector. It is shown that the method enables a DAC to be centred to within a few micrometres reproducibly and quickly. Full Article text
of Measurable structure factors of dense dispersions containing polydisperse optically inhomogeneous particles By journals.iucr.org Published On :: 2024-09-25 Here, it is investigated how optical properties of single scatterers in interacting multi-particle systems influence measurable structure factors. Both particles with linear gradients of their scattering length density and core–shell structures evoke characteristic deviations between the weighted sum 〈S(Q)〉 of partial structure factors in a multi-component system and experimentally accessible measurable structure factors SM(Q). While 〈S(Q)〉 contains only the structural information of self-organizing systems, SM(Q) is additionally influenced by the optical properties of their constituents, resulting in features such as changing amplitudes, additional peaks in the low-wavevector region or splitting of higher-order maxima, which are not related to structural reasons. It is shown that these effects can be systematically categorized according to the qualitative behaviour of the form factor in the Guinier region, which enables assessing the suitability of experimentally obtained structure factors to genuinely represent the microstructure of complex systems free from any particular model assumption. Hence, a careful data analysis regarding size distribution and optical properties of single scatterers is mandatory to avoid a misinterpretation of measurable structure factors. Full Article text
of SUBGROUPS: a computer tool at the Bilbao Crystallographic Server for the study of pseudo-symmetric or distorted structures By journals.iucr.org Published On :: 2024-10-01 SUBGROUPS is a free online program at the Bilbao Crystallographic Server (https://www.cryst.ehu.es/). It permits the exploration of all possible symmetries resulting from the distortion of a higher-symmetry parent structure, provided that the relation between the lattices of the distorted and parent structures is known. The program calculates all the subgroups of the parent space group which comply with this relation. The required minimal input is the space-group information of the parent structure and the relation of the unit cell of the distorted or pseudo-symmetric structure with that of the parent structure. Alternatively, the wavevector(s) observed in the diffraction data characterizing the distortion can be introduced. Additional conditions can be added, including filters related to space-group representations. The program provides very detailed information on all the subgroups, including group–subgroup hierarchy graphs. If a Crystallographic Information Framework (CIF) file of the parent high-symmetry structure is uploaded, the program generates CIF files of the parent structure described under each of the chosen lower symmetries. These CIF files may then be used as starting points for the refinement of the distorted structure under these possible symmetries. They can also be used for density functional theory calculations or for any other type of analysis. The power and efficiency of the program are illustrated with a few examples. Full Article text
of Twinning and homo-epitaxy cooperation in the already rich growth morphology of CaCO3 polymorphs. II. Calcite By journals.iucr.org Published On :: 2024-09-20 The two most abundant CaCO3 polymorphs, calcite and aragonite, are universally recognized for the richness of their morphology to which different twins make relevant contributions. The epitaxial transformation calcite ↔ aragonite has long been debated. While the twinning has been thoroughly treated, the homo-epitaxy occurring within each of these minerals has, inexplicably, been overlooked to date, both experimentally and theoretically. Twinning can be deceptive to the point where it can be mistaken for homo-epitaxy, thus making the proposed growth mechanism in the crystal aggregate wrong. Within the present work, the first aim is a theoretical investigation of the homo-epitaxies among the three {10.4}-cleavage, {01.2}-steep and {01.8}-flat rhombohedra of calcite. Accordingly, the specific adhesion energies were calculated between facing crystal forms, unequivocally showing that the {01.2}/{01.8} homo-epitaxy competes with the generation of both {01.2} and {01.8} contact twins. Secondly, the calculation of the specific adhesion energy was extended to consider homo-epitaxy for the {10.4} rhombohedron. The two-dimensional geometric lattice coincidence has been tried for the {00.1} pinacoidal form as well. Full Article text
of Deconstructing 3D growth rates from transmission microscopy images of facetted crystals as captured in situ within supersaturated aqueous solutions By journals.iucr.org Published On :: 2024-09-25 Here, a morphologically based approach is used for the in situ characterization of 3D growth rates of facetted crystals from the solution phase. Crystal images of single crystals of the β-form of l-glutamic acid are captured in situ during their growth at a relative supersaturation of 1.05 using transmission optical microscopy. The crystal growth rates estimated for both the {101} capping and {021} prismatic faces through image processing are consistent with those determined using reflection light mode [Jiang, Ma, Hazlehurst, Ilett, Jackson, Hogg & Roberts (2024). Cryst. Growth Des. 24, 3277–3288]. The growth rate in the {010} face is, for the first time, estimated from the shadow widths of the {021} prismatic faces and found to be typically about half that of the {021} prismatic faces. Analysis of the 3D shape during growth reveals that the initial needle-like crystal morphology develops during the growth process to become more tabular, associated with the Zingg factor evolving from 2.9 to 1.7 (>1). The change in relative solution supersaturation during the growth process is estimated from calculations of the crystal volume, offering an alternative approach to determine this dynamically from visual observations. Full Article text
of Electronic angle focusing for neutron time-of-flight powder diffractometers By journals.iucr.org Published On :: 2024-10-01 A neutron time-of-flight (TOF) powder diffractometer with a continuous wide-angle array of detectors can be electronically focused to make a single pseudo-constant wavelength diffraction pattern, thus facilitating angle-dependent intensity corrections. The resulting powder diffraction peak profiles are affected by the neutron source emission profile and resemble the function currently used for TOF diffraction. Full Article text
of Characterization of sub-micrometre-sized voids in fixed human brain tissue using scanning X-ray microdiffraction By journals.iucr.org Published On :: 2024-10-01 Using a 5 µm-diameter X-ray beam, we collected scanning X-ray microdiffraction in both the small-angle (SAXS) and the wide-angle (WAXS) regimes from thin sections of fixed human brain tissue from Alzheimer's subjects. The intensity of scattering in the SAXS regime of these patterns exhibits essentially no correlation with the observed intensity in the WAXS regime, indicating that the structures responsible for these two portions of the diffraction patterns, which reflect different length scales, are distinct. SAXS scattering exhibits a power-law behavior in which the log of intensity decreases linearly with the log of the scattering angle. The slope of the log–log curve is roughly proportional to the intensity in the SAXS regime and, surprisingly, inversely proportional to the intensity in the WAXS regime. We interpret these observations as being due to the presence of sub-micrometre-sized voids formed during dehydration of the fixed tissue. The SAXS intensity is due largely to scattering from these voids, while the WAXS intensity derives from the secondary structures of macromolecular material surrounding the voids. The ability to detect and map the presence of voids within thin sections of fixed tissue has the potential to provide novel information on the degradation of human brain tissue in neurodegenerative diseases. Full Article text
of Thermal analysis of a reflection mirror by fluid and solid heat transfer method By journals.iucr.org Published On :: 2024-10-15 High-repetition-rate free-electron lasers impose stringent requirements on the thermal deformation of beamline optics. The Shanghai HIgh-repetition-rate XFEL aNd Extreme light facility (SHINE) experiences high average thermal power and demands wavefront preservation. To deeply study the thermal field of the first reflection mirror M1 at the FEL-II beamline of SHINE, thermal analysis under a photon energy of 400 eV was executed by fluid and solid heat transfer method. According to the thermal analysis results and the reference cooling water temperature of 30 °C, the temperature of the cooling water at the flow outlet is raised by 0.15 °C, and the wall temperature of the cooling tube increases by a maximum of 0.5 °C. The maximum temperature position of the footprint centerline in the meridian direction deviates away from the central position, and this asymmetrical temperature distribution will directly affect the thermal deformation of the mirror and indirectly affect the focus spot of the beam at the sample. Full Article text
of In situ/operando method for energy stability measurement of synchrotron radiation By journals.iucr.org Published On :: 2024-10-15 A novel in situ/operando method is introduced to measure the photon beam stability of synchrotron radiation based on orthogonal diffraction imaging of a Laue crystal/analyzer, which can decouple the energy/wavelength and Bragg angle of the photon beam using the dispersion effect in the diffraction process. The method was used to measure the energy jitter and drift of the photon beam on BL09B and BL16U at the Shanghai Synchrotron Radiation Facility. The experimental results show that this method can provide a fast way to measure the beam stability of different light sources including bending magnet and undulator with meV-level energy resolution and ms-level time response. Full Article text
of Mitigation of DMM-induced stripe patterns in synchrotron X-ray radiography through dynamic tilting By journals.iucr.org Published On :: 2024-10-25 In synchrotron X-ray radiography, achieving high image resolution and an optimal signal-to-noise ratio (SNR) is crucial for the subsequent accurate image analysis. Traditional methods often struggle to balance these two parameters, especially in situ applications where rapid data acquisition is essential to capture specific dynamic processes. For quantitative image data analysis, using monochromatic X-rays is essential. A double multilayer monochromator (DMM) is successfully used for this aim at the BAMline, BESSY II (Helmholtz Zentrum Berlin, Germany). However, such DMMs are prone to producing an unstable horizontal stripe pattern. Such an unstable pattern renders proper signal normalization difficult and thereby causes a reduction of the SNR. We introduce a novel approach to enhance SNR while preserving resolution: dynamic tilting of the DMM. By adjusting the orientation of the DMM during the acquisition of radiographic projections, we optimize the X-ray imaging quality, thereby enhancing the SNR. The corresponding shift of the projection during this movement is corrected in post-processing. The latter correction allows a good resolution to be preserved. This dynamic tilting technique enables the homogenization of the beam profile and thereby effectively reduces noise while maintaining high resolution. We demonstrate that data captured using this proposed technique can be seamlessly integrated into the existing radiographic data workflow, as it does not need hardware modifications to classical X-ray imaging beamline setups. This facilitates further image analysis and processing using established methods. Full Article text
of Development of crystal optics for X-ray multi-projection imaging for synchrotron and XFEL sources By journals.iucr.org Published On :: 2024-10-21 X-ray multi-projection imaging (XMPI) is an emerging experimental technique for the acquisition of rotation-free, time-resolved, volumetric information on stochastic processes. The technique is developed for high-brilliance light-source facilities, aiming to address known limitations of state-of-the-art imaging methods in the acquisition of 4D sample information, linked to their need for sample rotation. XMPI relies on a beam-splitting scheme, that illuminates a sample from multiple, angularly spaced viewpoints, and employs fast, indirect, X-ray imaging detectors for the collection of the data. This approach enables studies of previously inaccessible phenomena of industrial and societal relevance such as fractures in solids, propagation of shock waves, laser-based 3D printing, or even fast processes in the biological domain. In this work, we discuss in detail the beam-splitting scheme of XMPI. More specifically, we explore the relevant properties of X-ray splitter optics for their use in XMPI schemes, both at synchrotron insertion devices and XFEL facilities. Furthermore, we describe two distinct XMPI schemes, designed to faciliate large samples and complex sample environments. Finally, we present experimental proof of the feasibility of MHz-rate XMPI at the European XFEL. This detailed overview aims to state the challenges and the potential of XMPI and act as a stepping stone for future development of the technique. Full Article text
of Development of hard X-ray photoelectron spectroscopy in liquid cells using optimized microfabricated silicon nitride membranes By journals.iucr.org Published On :: 2024-10-15 We present first hard X-ray photoelectron spectroscopy (HAXPES) results of aqueous salt solutions and dispersions of gold nanoparticles in liquid cells equipped with specially designed microfabricated thin silicon nitride membranes, with thickness in the 15–25 nm range, mounted in a high-vacuum-compatible environment. The experiments have been performed at the HAXPES endstation of the GALAXIES beamline at the SOLEIL synchrotron radiation facility. The low-stress membranes are fabricated from 100 mm silicon wafers using standard lithography techniques. Platinum alignment marks are added to the chips hosting the membranes to facilitate the positioning of the X-ray beam on the membrane by detecting the corresponding photoemission lines. Two types of liquid cells have been used, a static one built on an Omicron-type sample holder with the liquid confined in the cell container, and a circulating liquid cell, in which the liquid can flow in order to mitigate the effects due to beam damage. We demonstrate that the membranes are mechanically robust and able to withstand 1 bar pressure difference between the liquid inside the cell and vacuum, and the intense synchrotron radiation beam during data acquisition. This opens up new opportunities for spectroscopic studies of liquids. Full Article text
of Coprecipitation of Ce(III) oxide with UO2 By journals.iucr.org Published On :: 2024-09-30 The neutralization of acidic solutions containing U (IV) and Ce (III) at room temperature in glove box atmosphere and in the presence of dithionite results in coprecipitation of these elements as amorphous solid solutions CexU1–xO2±y. The solubilities of the precipitates with different mole fractions (x) of Ce(OH)3 (x = 0.01 or 0.1) were determined in 1 M NaClO4 solutions between pH 2.2 and 12.8 under reducing conditions. The solids were investigated by a variety of methods (chemical analysis, SEM-EDX, XRD, XPS, XAS) to determine the nature of the solid solutions formed, their composition and the valence state of Ce and U. X-ray photoelectron spectroscopy confirmed the oxidation states of the solids both before and after the equilibration as Ce (III) and U (IV). The amorphous coprecipitates reached equilibrium relatively fast (∼1 week). The release of Ce from the coprecipitates was totally dominated by the release of uranium over the whole pH range. The Ce concentrations decrease slightly with the decrease of Ce content in the solid, suggesting that CexU1–xO2±y solids behave thermodynamically as solid solutions. The concentrations of U in equilibrium with the coprecipitate were in excellent agreement with the solubility of UO2(s) under reducing conditions reported in the literature. The conditional solubility product of Ce(OH)3 from the coprecipitate was several orders of magnitude (∼4 in the near neutral pH range and ∼18 in the acidic range) lower than that of pure Ce(OH)3(s). The activities and activity coefficients of Ce(OH)3(s) in the coprecipitate were also estimated. Activity coefficients are much less than 1, indicating that the mixing of Ce(OH)3 with UO2 is highly favorable. Full Article text
of High-transmission spectrometer for rapid resonant inelastic soft X-ray scattering (rRIXS) maps By journals.iucr.org Published On :: 2024-09-30 The design and first results of a high-transmission soft X-ray spectrometer operated at the X-SPEC double-undulator beamline of the KIT Light Source are presented. As a unique feature, particular emphasis was placed on optimizing the spectrometer transmission by maximizing the solid angle and the efficiencies of spectrometer gratings and detector. A CMOS detector, optimized for soft X-rays, allows for quantum efficiencies of 90% or above over the full energy range of the spectrometer, while simultaneously offering short readout times. Combining an optimized control system at the X-SPEC beamline with continuous energy scans (as opposed to step scans), the high transmission of the spectrometer, and the fast readout of the CMOS camera, enable the collection of entire rapid resonant inelastic soft X-ray scattering maps in less than 1 min. Series of spectra at a fixed energy can be taken with a frequency of up to 5 Hz. Furthermore, the use of higher-order reflections allows a very wide energy range (45 to 2000 eV) to be covered with only two blazed gratings, while keeping the efficiency high and the resolving power E/ΔE above 1500 and 3000 with low- and high-energy gratings, respectively. Full Article text
of Formulation of perfect-crystal diffraction from Takagi–Taupin equations: numerical implementation in the crystalpy library By journals.iucr.org Published On :: 2024-10-29 The Takagi–Taupin equations are solved in their simplest form (zero deformation) to obtain the Bragg-diffracted and transmitted complex amplitudes. The case of plane-parallel crystal plates is discussed using a matrix model. The equations are implemented in an open-source Python library crystalpy adapted for numerical applications such as crystal reflectivity calculations and ray tracing. Full Article text
of Mirror-centered representation of a focusing hyperbolic mirror for X-ray beamlines By journals.iucr.org Published On :: 2024-10-29 Conic sections are commonly used in reflective X-ray optics. Hyperbolic mirrors can focus a converging light source and are frequently paired with elliptical or parabolic mirrors in Wolter type configurations. This paper derives the closed-form expression for a mirror-centered hyperbolic shape, with zero-slope at the origin. Combined with the slope and curvature, such an expression facilitates metrology, manufacturing and mirror-bending calculations. Previous works consider ellipses, parabolas, magnifying hyperbolas or employ lengthy approximations. Here, the exact shape function is given in terms of the mirror incidence angle and the source and image distances. Full Article text
of A study of structural effects on the focusing and imaging performance of hard X-rays with 20–30 nm zone plates By journals.iucr.org Published On :: 2024-10-28 Hard X-ray microscopes with 20–30 nm spatial resolution ranges are an advanced tool for the inspection of materials at the nanoscale. However, the limited efficiency of the focusing optics, for example, a Fresnel zone plate (ZP) lens, can significantly reduce the power of a nanoprobe. Despite several reports on ZP lenses that focus hard X-rays with 20 nm resolution – mainly constructed by zone-doubling techniques – a systematic investigation into the limiting factors has not been reported. We report the structural effects on the focusing and imaging efficiency of 20–30 nm-resolution ZPs, employing a modified beam-propagation method. The zone width and the duty cycle (zone width/ring pitch) were optimized to achieve maximum efficiency, and a comparative analysis of the zone materials was conducted. The optimized zone structures were used in the fabrication of Pt-hydrogen silsesquioxane (HSQ) ZPs. The highest focusing efficiency of the Pt-HSQ-ZP with a resolution of 30 nm was 10% at 7 keV and >5% in the range 6–10 keV, whereas the highest efficiency of the Pt-HSQ-ZP with a resolution of 20 nm was realized at 7 keV with an efficiency of 7.6%. Optical characterization conducted at X-ray beamlines demonstrated significant enhancement of the focusing and imaging efficiency in a broader range of hard X-rays from 5 keV to 10 keV, demonstrating the potential application in hard X-ray focusing and imaging. Full Article text
of A general Bayesian algorithm for the autonomous alignment of beamlines By journals.iucr.org Published On :: 2024-10-28 Autonomous methods to align beamlines can decrease the amount of time spent on diagnostics, and also uncover better global optima leading to better beam quality. The alignment of these beamlines is a high-dimensional expensive-to-sample optimization problem involving the simultaneous treatment of many optical elements with correlated and nonlinear dynamics. Bayesian optimization is a strategy of efficient global optimization that has proved successful in similar regimes in a wide variety of beamline alignment applications, though it has typically been implemented for particular beamlines and optimization tasks. In this paper, we present a basic formulation of Bayesian inference and Gaussian process models as they relate to multi-objective Bayesian optimization, as well as the practical challenges presented by beamline alignment. We show that the same general implementation of Bayesian optimization with special consideration for beamline alignment can quickly learn the dynamics of particular beamlines in an online fashion through hyperparameter fitting with no prior information. We present the implementation of a concise software framework for beamline alignment and test it on four different optimization problems for experiments on X-ray beamlines at the National Synchrotron Light Source II and the Advanced Light Source, and an electron beam at the Accelerator Test Facility, along with benchmarking on a simulated digital twin. We discuss new applications of the framework, and the potential for a unified approach to beamline alignment at synchrotron facilities. Full Article text
of Green upgrading of SPring-8 to produce stable, ultrabrilliant hard X-ray beams By journals.iucr.org Published On :: 2024-10-24 SPring-8-II is a major upgrade project of SPring-8 that was inaugurated in October 1997 as a third-generation synchrotron radiation light source. This upgrade project aims to achieve three goals simultaneously: achievement of excellent light source performance, refurbishment of aged systems, and significant reduction in power consumption for the entire facility. A small emittance of 50 pm rad will be achieved by (1) replacing the existing double-bend lattice structure with a five-bend achromat one, (2) lowering the stored beam energy from 8 to 6 GeV, (3) increasing the horizontal damping partition number from 1 to 1.3, and (4) enhancing horizontal radiation damping by installing damping wigglers in long straight sections. The use of short-period in-vacuum undulators allows ultrabrilliant X-rays to be provided while keeping a high-energy spectral range even at the reduced electron-beam energy of 6 GeV. To reduce power consumption, the dedicated, aged injector system has been shut down and the high-performance linear accelerator of SACLA, a compact X-ray free-electron laser (XFEL) facility, is used as the injector of the ring in a time-shared manner. This allows the simultaneous operation of XFEL experiments at SACLA and full/top-up injection of the electron beam into the ring. This paper overviews the concept of the SPring-8-II project, the system design of the light source and the details of the accelerator component design. Full Article text
of Foreword to the special virtual issue dedicated to the proceedings of the PhotonMEADOW2023 Joint Workshop By journals.iucr.org Published On :: 2024-10-11 Full Article text
of Celebrating JSR's 30th anniversary: reminiscences of a Main Editor By journals.iucr.org Published On :: 2024-10-01 Full Article text
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of FilmWeek: ‘The Courier,’ ‘Zack Snyder’s Justice League,’ ‘City Of Lies’ And More By www.scpr.org Published On :: Fri, 19 Mar 2021 09:28:00 -0700 Benedict Cumberbatch in “The Courier”; Credit: LIAM DANIEL / LIONSGATE / ROADSIDE ATTRACTIONS FilmWeek MarqueeLarry Mantle and KPCC film critics Tim Cogshell, Lael Loewenstein and Andy Klein review this weekend’s new movie releases.This content is from Southern California Public Radio. View the original story at SCPR.org. Full Article
of FilmWeek: ‘Wrath Of Man,’ ‘Here Today,’ ‘The Paper Tigers’ And More By www.scpr.org Published On :: Fri, 07 May 2021 09:30:00 -0700 Jason Statham's character H in the film "Wrath of Man"; Credit: Metro Goldwyn Mayer Pictures FilmWeek MarqueeLarry Mantle and KPCC film critics Christy Lemire and Tim Cogshell review this weekend’s new movie releases.This content is from Southern California Public Radio. View the original story at SCPR.org. Full Article
of FilmWeek: ‘Spiral,’ ‘The Woman In The Window,’ ‘Profile,’ And More By www.scpr.org Published On :: Fri, 14 May 2021 14:33:00 -0700 Chris Rock as Detective Zeke Banks in the film "Spiral."; Credit: Lionsgate FilmWeek MarqueeGuest host John Horn and KPCC film critics Claudia Puig, Amy Nicholson and Andy Klein review this weekend’s new movie releases.This content is from Southern California Public Radio. View the original story at SCPR.org. Full Article
of FilmWeek: ‘The Conjuring: The Devil Made Me Do It,’ ‘Spirit Untamed,’ ‘Edge Of The World’ And More By www.scpr.org Published On :: Fri, 04 Jun 2021 09:33:00 -0700 Vera Farmiga and Patrick Wilson in "The Conjuring: The Devil Made Me Do It"; Credit: Warner Bros. Pictures FilmWeek MarqueeLarry Mantle and KPCC film critics Amy Nicholson, Wade Major and Charles Solomon review this weekend’s new movie releases on streaming and on demand platforms.This content is from Southern California Public Radio. View the original story at SCPR.org. Full Article