Journal of Applied Crystallography最新文献

A machine learning inversion method is developed for analyzing scattering functions of mechanically driven polymers and extracting the corresponding feature parameters, which include energy parameters and conformation variables. The polymer is modeled as a chain of fixed-length bonds constrained by bending energy, and it is subject to external forces such as stretching and shear. We generate a data set consisting of random combinations of energy parameters, including bending modulus, stretching and shear force, along with Monte Carlo-calculated scattering functions and conformation variables such as end-to-end distance, radius of gyration and off-diagonal component of the gyration tensor. The effects of the energy parameters on the polymer are captured by the scattering function, and principal component analysis ensures the feasibility of the machine learning inversion. Finally, we train a Gaussian process regressor using part of the data set as a training set and validate the trained regressor for inversion using the rest of the data. The regressor successfully extracts the feature parameters.

CrimsonCalc is open-source software for processing ruby fluorescence spectra and calculating pressure from the shift of the R ₁ peak. It supports processing and plotting of an individual spectrum as well as batch processing of spectra from data in text or Bruker OPUS binary format. Core features include baseline correction, pseudo-Voigt peak fitting, automated detection of detector saturation, and pressure calculation using user-defined or automatically detected reference spectra. The software provides batch output in both human-readable and machine-readable formats. With an intuitive graphical user interface, CrimsonCalc is designed as a high-pressure research aid and includes additional tools such as a diamond Raman edge pressure calculator, an interferometry-based gasket thickness calculator and an estimator for the upper pressure limit based on diamond anvil culet diameter. The program can be easily adopted in high-pressure research laboratories to facilitate pressure readings directly from simple text data, and to generate the images and result files that enable straightforward report preparation.

The sensitivity towards Bragg peak parameters constitutes a crucial performance attribute of X-ray diffraction experiments. Diffraction peaks are frequently characterized by model-free angular moment analysis, which offers greater versatility compared with traditional model-based peak fitting. Here, we have theoretically determined the ultimate limit of the sensitivities of angular moments imposed by photon shot noise. These predictions have been validated by experimental data provided by three different setups. We have observed experimentally achieved sensitivities of the first moment below 1/1000th of a detector pixel and below 1 µrad. The formulae provided for the uncertainties of angular moments can now be used to rapidly determine experimentally achieved sensitivities from a single diffraction frame. Corresponding limitations (i.e. ultra-low photon counts and exceedingly high photon count rates) are identified and discussed.

The small-angle neutron scattering (SANS) diffractometer KWS-2 of the Jülich Centre for Neutron Science at the Heinz Maier-Leibnitz Zentrum, Garching, Germany, is a high-flux instrument based on the combination of a specially developed neutron guide system, which allows delivery of a high neutron intensity for a wide wavelength range λ between 2.8 and 20 Å to the instrument, and a versatile velocity selector, which allows an easy choice of wavelength spread Δλ/λ depending on whether the specific scientific goal is either improved resolution, i.e. Δλ/λ = 10%, or high intensity, i.e. Δλ/λ = 20%. Here we report an evaluation of KWS-2 performance by measurements and McStas simulations under the condition that only the thermal neutron source (TNS) is available at the FRM II reactor. According to the simulations, a flux decrease by a factor of 2.5 for λ = 2.8-3 Å and by a factor of 10 for λ ≥ 4.5 Å is expected if the reactor is operated only with the TNS compared with the established performance with cold neutrons provided by the cold neutron source. The flux decrease in TNS operation can be mitigated for λ ≥ 4.5 Å by using a low-resolution velocity selector which provides Δλ/λ = 20% for standard positioning and Δλ/λ = 35% when tilted at an angle ξ_i = -10° to the beam axis. According to measurements, this degradation of resolution for increasing intensity does not seem to be critical for the structural characterization of small biological morphologies, which would be one of the most investigated topics if only thermal neutrons were available at the FRM II. However, ordering effects in the scattering characteristics of lamellar soft or biophysical systems are barely observable when the resolution is relaxed to Δλ/λ ≥ 20%, which defines the performance limits of the experimental approach. Furthermore, by using MgF₂ focusing lenses when working with large samples, an intensity gain on the sample of up to 12-fold is achieved while keeping the same Q _min resolution as with the standard pinhole mode, restoring the flux loss expected with thermal neutrons for λ ≥ 7 Å.

The Patterson function, P(u), is useful in many crystallographic applications, including experimental phasing, molecular replacement and the exploration of non-crystallographic symmetries. P(u) is defined as the autocorrelation of the electron density. Autocorrelation is often an unfamiliar concept for students of biological or biomedical fields of study. I present a freely available animated PowerPoint slide deck featuring 1D electron density plots and the corresponding autocorrelation resulting in the Patterson function that is readily interpretable as an interatomic distance map. The animation makes it easy to grasp the concept of autocorrelation in an intuitive manner.

We propose LaB₆ as a temperature calibration standard for high-temperature (HT) X-ray diffractometry owing to its high temperature stability. Such HT applications require a reliable HT lattice parameter or, equivalently, peak position data, which have not been readily accessible to the diffraction community to date. As such, the thermal expansion behavior of NIST SRM 660a LaB₆ was assessed in the temperature range 298-998 K using HT Bragg-Brentano parafocusing θ:θ X-ray diffractometry in conjunction with Rietveld analysis. Data were collected in the 2θ range 20-150° at a data collection rate of 0.5° θ min^-1 in air and at 1 atm. The temperature was stepped in 50 K increments. The cubic unit-cell lattice parameter [a(T)] of LaB₆ in Å was found to vary as a(T) = 4.15678 (±0.00001) + Ξ(T - 298 K) + Ψ(T - 298 K)², where Ξ = 2.4645 × 10^-5 (±4.8904 × 10^-8) Å K^-1 and Ψ = 1.0325 × 10^-8 (±6.7376 × 10^-11) Å K^-1. The isobaric volume thermal expansion coefficient (TEC) was obtained as α_V ^P  = (5.9291 × 10^-6) + (4.9680 × 10^-9)(T - 298 K) K^-1, from which the corresponding linear TEC was obtained as α_L ^P = (1.9764 × 10^-6) + (1.6560 × 10^-9)(T - 298 K) K^-1. The 3 × 3 matrix representations of the single-crystal isobaric linear TEC and the volume expansivity were obtained for the cubic crystal class to which LaB₆ belongs. Also, the temperature dependence of the lattice parameter data of this study was compared with past landmark studies on LaB₆ by Dutchak et al. [Inorg. Mater. (1972), 8, 1877-1880] and Aivazov et al. [Inorg. Mater. (1979), 15, 1015-1016].

SUNBIM (supramolecular and submolecular nano- and biomaterials X-ray imaging) is a computer suite of integrated programs which, through a user-friendly graphical interface, is able to perform a number of functions for (grazing-incidence) small- and wide-angle X-ray scattering [(GI)SAXS and (GI)WAXS] data analysis. The software combines in the same package both originally developed algorithms and reliable methods documented in the literature. Recently, new tools have been added to the original program that are particularly devoted to data reduction. The release presented in this work, named SUNBIM 4.0, features a new interface to perform deeper data reduction for multi-scan SAXS/WAXS, including dark-current subtraction, background evaluation and subtraction, and normalization of scattering intensity against local sample thickness derived from absorption contrast maps. In SUNBIM 4.0, these functionalities have been made accessible for data sets in .edf, a data format commonly used by many next-generation X-ray detectors, thanks to a new guided procedure for converting entire multi-scan data sets into a format readable by the software. A new functionality in the single data analysis section has been implemented, consisting of a semi-automatic background subtraction from the 1D profile of the azimuthal integration, corrected for a flat-panel detector geometry, to enhance peak visibility at large scattering angles (WAXS/GIWAXS). This new SUNBIM release will include a Microsoft Windows installer, as in the previous version, and will also be available for Mac OSX. We are confident that the new features will enable a more accurate and comprehensive analysis of (GI)SAXS/(GI)WAXS data, addressing the issues and limitations of the previous release while also enhancing the extraction of structural information contained within the data.

XRDlicious is an online computational tool for calculating powder X-ray diffraction and neutron diffraction patterns (diffractograms) and partial and total radial distribution functions [(P)RDFs] from crystal structures. It features a user-friendly browser-based interface that supports widely used structural file formats, such as CIF, POSCAR, XYZ and LMP. The structures can be either uploaded or retrieved directly from the Crystallography Open Database, Materials Project and Automatic FLOW databases via an integrated search interface. Uploaded structures can be modified and exported in CIF, POSCAR, LMP or XYZ formats. The tool also enables the conversion of experimental powder diffraction data between different wavelengths, to d-space or q-space representations, and between fixed or automatic divergence slits. By eliminating the need for software installation, this application ensures accessibility across various devices (including mobile phones and tablets) and different computer operating systems. Its ability to simultaneously plot diffraction patterns from multiple structures is particularly useful for comparing structures obtained from computational simulations. Beyond research applications, its intuitive interface also makes it suitable for educational purposes, allowing students to explore concepts such as diffraction patterns and (P)RDFs in an easily approachable way. XRDlicious is accessible at https://xrdlicious.com.

The quantitative analysis of local ordering principles in disordered crystalline systems has gained much attention over the past few years, as it is often considered crucial for optimizing material functionality. This development has been driven by significant advancements in computational and experimental methods, which have led to the establishment and widespread use of various analytical techniques. In this study, we perform model calculations to compare the effectiveness of atomic resolution holography and three-dimensional difference pair distribution function analysis (3D-ΔPDF). Using Cu₃Au as a model system, we demonstrate an approach to derive local order parameters quantitatively and show that both techniques are well suited to quantifying chemical short-range order correlations and local bond-distance variations. By evaluating the strengths and limitations of both techniques, we advocate for their combined use to solve complex short-range order problems accurately.

The velocity gradient dependent shear-induced structural evolution of wormlike micelles (WLMs) formed by a gemini-type cationic surfactant (12-2-12) in an aqueous solution was investigated using small-angle neutron scattering (SANS). To achieve this, a cell for observation in the velocity-velocity gradient (1-2) shear plane was constructed. SANS measurements were conducted at multiple positions across the gap of this 1-2 shear cell under various shear rates, covering both shear-thickening and shear-thinning regimes. During shear thickening at apparent shear rates of 70-200 s^-1, a clear position-dependent alignment of WLMs was observed, with higher orientation near the rotor. In contrast, the intermicellar distance remained largely uniform across the gap. Neutron transmission measurements indicated no significant macroscopic concentration fluctuations. These results suggest that shear thickening is primarily driven by shear-induced micellar elongation and orientation, rather than the formation of concentration fluctuations. This study indicates the utility of SANS measurements in the 1-2 shear plane in revealing spatially resolved structural details, providing crucial insights into the 3D behavior of complex fluids under shear and complementing previous Rheo-SANS findings.