Journal of Applied Crystallography

Dark-field X-ray microscopy (DFXM) is a full-field imaging technique that non-destructively maps the structure and local strain inside deeply embedded crystalline elements in three dimensions. In DFXM, an objective lens is placed along the diffracted beam to generate a magnified projection image of the local diffracted volume. This work explores contrast methods and optimizes the DFXM setup specifically for the case of mapping dislocations. Forward projections of detector images are generated using two complementary simulation tools based on geometrical optics and wavefront propagation, respectively...

Analysis of small-angle scattering (SAS) data requires intensive modeling to infer and characterize the structures present in a sample. This iterative improvement of models is a time-consuming process. Presented here is Scattering Equation Builder ( SEB ), a C++ library that derives exact analytic expressions for the form factors of complex composite structures. The user writes a small program that specifies how the sub-units should be linked to form a composite structure and calls SEB to obtain an expression for the form factor...

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...

This article describes a correction procedure for the removal of indirect background contributions to measured small-angle X-ray scattering patterns. The high scattering power of a sample in the ultra-small-angle region may serve as a secondary source for a window placed in front of the detector. The resulting secondary scattering appears as a sample-dependent background in the measured pattern that cannot be directly subtracted. This is an intricate problem in measurements at ultra-low angles, which can significantly reduce the useful dynamic range of detection...

Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining structure-factor amplitudes for serial crystallography or single-particle imaging experiments. Here, a new data-classification tool is reported that offers a variety of machine-learning algorithms to sort data trained either on manual data sorting by the user or by profile fitting the intensity distribution on the detector based on the experiment...

X-ray absorption spectroscopy (XAS) is a promising technique for determining structural information from sensitive biological samples, but high-accuracy X-ray absorption fine structure (XAFS) requires corrections of systematic errors in experimental data. Low-temperature XAS and room-temperature X-ray absorption spectro-electrochemical (XAS-EC) measurements of N-truncated amyloid-β samples were collected and corrected for systematic effects such as dead time, detector efficiencies, monochromator glitches, self-absorption, radiation damage and noise at higher wavenumber ( k )...

An implementation of Slater-type spherical scattering factors for X-ray and electron diffraction for elements in the range Z = 1-103 is presented within the software Olex2 . Both high- and low-angle Fourier behaviour of atomic electron density and electrostatic potential can thus be addressed, in contrast to the limited flexibility of the four Gaussian plus constant descriptions which are currently the most widely used method for calculating atomic scattering factors during refinement. The implementation presented here accommodates the increasing complexity of the electronic structure of heavier elements by using complete atomic wavefunctions without any interpolation between precalculated tables or intermediate fitting functions...

Recently, we introduced the liquid application method for time-resolved analyses (LAMA). The time-consuming cleaning cycles required for the substrate solution exchange and storage of the sensitive droplet-dispenser nozzles present practical challenges. In this work, a dispenser cleaning system for the semi-automated cleaning of the piezo-actuator-driven picolitre-droplet dispensers required for LAMA is introduced to streamline typical workflows.

Low-energy electron diffraction patterns contain precise information about the structure of the surface studied. However, retrieving the real space lattice periodicity from complex diffraction patterns is challenging, especially when the modeled patterns originate from superlattices with large unit cells composed of several symmetry-equivalent domains without a simple relation to the substrate. This work presents ProLEED Studio software, built to provide simple, intuitive and precise modeling of low-energy electron diffraction patterns...

Characterization of a material structure with pair distribution function (PDF) analysis typically involves refining a structure model against an experimental data set, but finding or constructing a suitable atomic model for PDF modelling can be an extremely labour-intensive task, requiring carefully browsing through large numbers of possible models. Presented here is POMFinder , a machine learning (ML) classifier that rapidly screens a database of structures, here polyoxometallate (POM) clusters, to identify candidate structures for PDF data modelling...

The growing pressure on school curricula has meant crystals and the science of crystallography have been cut from or made optional for many educational programs. This omission is a serious disservice to the history and understanding of modern sciences, given that crystallography underpins many of the greatest advancements in science over the past century, is a critical component of many modern research papers and patents, and has 29 Nobel Prizes awarded in the field. This contribution describes a simple activity to target classroom and public engagement with crystallography, using marshmallows or equivalent sweets/candy to represent atoms and cocktail sticks to represent bonds, together with examples of how crystals are studied and how they are useful...

Artificial intelligence is more present than ever, both in our society in general and in science. At the center of this development has been the concept of deep learning, the use of artificial neural networks that are many layers deep and can often reproduce human-like behavior much better than other machine-learning techniques. The articles in this collection are some recent examples of its application for X-ray photon science and crystallography that have been published in Journal of Applied Crystallography ...

Rietveld refinements are widely used for many purposes in the physical sciences. Conducting a Rietveld refinement typically requires expert input because correct results may require that parameters be added to the fit in the proper order. This order will depend on the nature of the data and the initial parameter values. A mechanism for computing the next parameter to add to the refinement is shown. The fitting function is evaluated with the current parameter value set and each parameter incremented and decremented by a small offset...

BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI ; updated automated Guinier fitting and D max finding algorithms; automated series ( e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares ( REGALS ); creation of electron-density reconstructions using electron density via solution scattering ( DENSS ); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis...

Van Vleck modes describe all possible displacements of octahedrally coordinated ligands about a core atom. They are a useful analytical tool for analysing the distortion of octahedra, particularly for first-order Jahn-Teller distortions, but determination of the Van Vleck modes of an octahedron is complicated by the presence of angular distortion of the octahedron. This problem is most commonly resolved by calculating the bond distortion modes ( Q 2 , Q 3 ) along the bond axes of the octahedron, disregarding the angular distortion and losing information on the octahedral shear modes ( Q 4 , Q 5 and Q 6 ) in the process...

Developing semiconductor devices requires a fast and reliable source of strain information with high spatial resolution and strain sensitivity. This work investigates the strain in an axially heterostructured 180 nm-diameter GaInP nanowire with InP segments of varying lengths down to 9 nm, simultaneously probing both materials. Scanning X-ray diffraction (XRD) is compared with Bragg projection ptychography (BPP), a fast single-projection method. BPP offers a sufficient spatial resolution to reveal fine details within the largest segments, unlike scanning XRD...

The observation of neutron interference using a triple Laue interferometer formed by two separate crystals opens the way to the construction and operation of skew-symmetric interferometers with extended arm separation and length. The specifications necessary for their successful operation are investigated here: most importantly, how the manufacturing tolerance and crystal alignments impact the interference visibility. In contrast with previous studies, both incoherent sources and the three-dimensional operation of the interferometer are considered...

An anomalous ultra-small-angle X-ray scattering (AUSAXS) system has been constructed at BL28XU at SPring-8 for time-resolved AUSAXS experiments. The path length was extended to 9.1 m and a minimum of q = 0.0069 nm-1 was attained. Scattering profiles at 0.0069 to 0.3 nm-1 were successfully obtained at 17 different X-ray energies in 30 s using the BL28XU optical setup, which enables adjustment of the energy of the incident X-rays quickly without the beam position drifting. Time-resolved measurements were conducted to investigate changes in the structure of zinc compounds in poly(styrene- ran -butadiene) rubber during vulcanization...

A general formalism is presented for the isotropically averaged single-chain scattering function (form factor) of single, double, triple and higher-order helices, as well as twisted fibres consisting of concentric layers of strands. Form factors for double and triple helices with differently sized grooves have also been derived. The formulas include the longitudinal and transverse interference over the pitch and radius of the helices, respectively. The results may be useful for the analysis of small-angle scattering data of (bio)macromolecules or molecular assemblies exhibiting a helical arrangement...

PyDDT is a free Python package of computer codes for exploiting X-ray dynamic multiple diffraction in single crystals. A wide range of tools are available for evaluating the usefulness of the method, planning feasible experiments, extracting phase information from experimental data and further improving model structures of known materials. Graphical tools are also useful in analytical methodologies related to the three-dimensional aspect of multiple diffraction. For general X-ray users, the PyDDT tutorials provide the insight needed to understand the principles of phase measurements and other related methodologies...