Processing Of Diffraction Data Research Articles

Possibilities of the X-ray diffraction data processing method for detecting reflections with intensity below the background noise component

The values of the signal-to-noise ratio are determined, at which the method of processing X-ray diffraction data reveals reflections with intensity less than the noise component of the background. The possibilities of the method are demonstrated on weak reflections of α-quartz. The method of processing X-ray diffraction data makes it possible to increase the possibilities of X-ray phase analysis in determining the qualitative phase composition of multiphase materials with a small (down to 0.1 wt.%) content of several (up to eight) phases.

Residual Stress Evaluation in L-PBF-Produced SS 316L Specimens.

The identification of residual stresses (RS) in components made by selective laser melting (SLM) is necessary for subsequent technological optimization. The presented research is devoted to evaluating the influence of the combination of laser power (P), scanning velocity (v) and the rarely considered number of layers (nL) on surface residual stresses in SLM stainless steel SS 316L. Experimental parameters were set based on the Design of Experiment (DoE) method, with follow-up X-ray diffraction (XRD) measurements and data processing using analysis of variance (ANOVA) and regression analysis. The obtained data are a valuable stepping-stone for the subsequent design of research focused on the application of sustainable eco-friendly Abrasive Water Jet (AWJ) peening for RS modification in the evaluated material.

Breaking barriers: Innovative methods for 4DSTEM diffraction data acquisition and processing in SEM

Breaking barriers: Innovative methods for 4DSTEM diffraction data acquisition and processing in SEM

Image segmentation and advanced processing of 2D diffraction data

Image segmentation and advanced processing of 2D diffraction data

Per-pixel XFEL diffraction data processing for wavelength deconvolution

Per-pixel XFEL diffraction data processing for wavelength deconvolution

Reciprocalspaceship: a Python library for crystallographic data analysis.

Crystallography uses the diffraction of X-rays, electrons or neutrons by crystals to provide invaluable data on the atomic structure of matter, from single atoms to ribosomes. Much of crystallography's success is due to the software packages developed to enable automated processing of diffraction data. However, the analysis of unconventional diffraction experiments can still pose significant challenges - many existing programs are closed source, sparsely documented, or challenging to integrate with modern libraries for scientific computing and machine learning. Described here is reciprocalspaceship, a Python library for exploring reciprocal space. It provides a tabular representation for reflection data from diffraction experiments that extends the widely used pandas library with built-in methods for handling space groups, unit cells and symmetry-based operations. As is illustrated, this library facilitates new modes of exploratory data analysis while supporting the prototyping, development and release of new methods.

Serial Electron Diffraction Data Processing With diffractem and CrystFEL.

Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D Electron Diffraction), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.

Multi-crystal data collection using synchrotron radiation as exemplified with low-symmetry crystals of Dps.

Multi-crystal data collection using synchrotron radiation was successfully applied to determine the three-dimensional structure of a triclinic crystal form of Dps from Escherichia coli at 2.0 Å resolution. The final data set was obtained by combining 261 partial diffraction data sets measured from crystals with an average size of approximately 5 µm. The most important features of diffraction data measurement and processing for low-symmetry crystals are discussed.

Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron.

The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.

Method of X-Ray Diffraction Data Processing for Multiphase Materials with Low Phase Contents

Amorphous, glass, and glass-ceramic materials practically always include a significant number (more than eight) of crystalline phases, with the contents of the latter ranging from a few wt.% to several hundredths or tenths of wt.%. The study of such materials using the method of X-ray phase analysis faces difficulties, when determining the phase structure. In this work, we will develop a method for the analysis of the diffraction patterns of such materials, when diffraction patterns include X-ray lines, whose intensities are at the noise level. The identification of lines is based on the search for correlations between the experimental and test lines and the verification of the coincidence making use of statistical methods (computer statistics). The method is tested on the specimens of a-quartz, which are often used as standard ones, and applied to analyze lava-like fuel-containing materials from the destroyed Chornobyl NPP Unit 4. It is shown that the developed technique allows X-ray lines to be identified, if the contents of separate phases is not less than 0.1 wt.%. The method also significantly enhances a capability to determine the phase contents quantitatively on the basis of lines with low intensities.

The development and exploitation of synchrotron single-crystal diffraction for chemistry and materials.

A historical account is given of the 25-year development of dedicated synchrotron beamlines for single-crystal diffraction as applied to the so-called small-molecule fields of chemistry and materials science. Designs have drawn on previous successful models in macromolecular crystallography, with appropriate modifications in view of the different properties and behaviour of the respective sample types. Key factors in making these facilities attractive and productive for users include familiarity of operational procedures and the availability of experimental techniques and features normally found in local chemical crystallography laboratories, especially for the handling of samples and processing of diffraction data. Beamlines dedicated to single-crystal diffraction rather than shared with other techniques can be optimized for effective and efficient use. The experience gained from the original design, development and exploitation of stations 9.8 and 16.2SMX at the Daresbury Laboratory Synchrotron Radiation Source and beamline 11.3.1 at the Advanced Light Source have led to highly productive current facilities at ALS beamline 12.2.1 and Diamond Light Source beamline I19, including the recent introduction of remote-access operation. Such facilities have generated and continue to provide major impact in academic and commercial research that could otherwise not be achieved, including patents and applications in pharmaceuticals, energy and gas storage systems, and government policy. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.

D2Dplot: 2D X-ray diffraction data processing and analysis for through-the-substrate microdiffraction

The d2Dplot computer program provides a set of tools for the visualization, processing and analysis of 2D X-ray diffraction (2DXRD) data. Among the operations available there are the sum/subtraction of 2DXRD images, conversion to 1D data (powder pattern), azimuthal plotting, calibration of instrumental parameters, background subtraction and a command-line mode to run operations inside data processing pipelines. The graphical user interface allows easy use of the program. It also includes two main features: (i) the possibility of creating a user compound database to help in the fast phase identification of similar samples, and (ii) a detailed peak analysis routine for the application of the through-the-substrate microdiffraction methodology.

Influence of strain conditions on the grain sub-structuration in crept uranium dioxide pellets

Stoichiometric uranium dioxide (UO2) pellets were deformed by uniaxial compression creep tests at 1500 °C. Strains comprised between 3% and 11% were applied at strain rates ranging from ∼ 5 × 10−6 s−1 to 70 × 10−6 s−1 to deform pellets in the dislocational creep regime. An optimized protocol for Electron BackScattered Diffraction (EBSD) data acquisition and processing was applied to detect and quantify low and very low angle sub-boundaries disoriented down to 0.25° inside the prior UO2 grains. Three EBSD based parameters were calculated and are efficient to quantify the evolution of the deformed microstructure with the deformation conditions: the linear fraction of the sub-boundaries, the corresponding Geometrically Necessary Dislocations (GNDs) density and the resulting mean sub-grain size. The linear fraction of sub-boundaries (and their transcription in GNDs) increased significantly with the strain level and rate. New very low angle boundaries disoriented by less than 1° were continuously created whereas already existing sub-boundaries increased continuously their disorientation. This microstructural evolution can be described as a dynamic recovery mechanism by progressive increase of sub-boundaries disorientation angle.

Expression, purification and crystallization of the complex of RNA polymerase II carboxyl-terminal repeat domain kinase subunits CTK2-CTK3 from Saccharomyces cerevisiae

Carboxyl-terminal repeat domain (CTD) of the largest subunit Rpb1 of RNA polymerace II is essential for transcription regulation. Heptapeptide repeat of CTD of Rpb1 is phosphorylated by carboxyl-terminal repeat domain kinase (CTDK-I), composed of CTK1, CTK2 and CTK3, in order to regulate transcription and transcription associated processes. The yeast specific protein CTK3 binds to cyclin CTK2 to form a heterodimer serving as a regulational factor to control CTK1 activity by binding to CTK1. Structural information of CTK2-CTK3 complex is yet to be elucidated. Here, we report the co-expression of CTK2-CTK3 complex from Saccharomyces cerevisiae with N-terminal His6-tag in CTK3 in Escherichia coli (E. coli), purification of the complex by four chromatographic steps and crystallization of the complex as well as the diffraction data collection and processing. This study provides some essential information and a guide for structural and functional study of CTK2-CTK3 complex and CTDK-I in the future.

Riding the camel: the double-peaked rocking curve and its use in the processing of precession electron diffraction data

Riding the camel: the double-peaked rocking curve and its use in the processing of precession electron diffraction data

Electron diffraction data processing with DIALS.

Electron diffraction is a relatively novel alternative to X-ray crystallography for the structure determination of macromolecules from three-dimensional nanometre-sized crystals. The continuous-rotation method of data collection has been adapted for the electron microscope. However, there are important differences in geometry that must be considered for successful data integration. The wavelength of electrons in a TEM is typically around 40 times shorter than that of X-rays, implying a nearly flat Ewald sphere, and consequently low diffraction angles and a high effective sample-to-detector distance. Nevertheless, the DIALS software package can, with specific adaptations, successfully process continuous-rotation electron diffraction data. Pathologies encountered specifically in electron diffraction make data integration more challenging. Errors can arise from instrumentation, such as beam drift or distorted diffraction patterns from lens imperfections. The diffraction geometry brings additional challenges such as strong correlation between lattice parameters and detector distance. These issues are compounded if calibration is incomplete, leading to uncertainty in experimental geometry, such as the effective detector distance and the rotation rate or direction. Dynamic scattering, absorption, radiation damage and incomplete wedges of data are additional factors that complicate data processing. Here, recent features of DIALS as adapted to electron diffraction processing are shown, including diagnostics for problematic diffraction geometry refinement, refinement of a smoothly varying beam model and corrections for distorted diffraction images. These novel features, combined with the existing tools in DIALS, make data integration and refinement feasible for electron crystallography, even in difficult cases.

Stroboscopic time-of-flight neutron diffraction during cyclic testing using the event data recording system at J-PARC

A time-resolved time-of-flight neutron diffraction technique to characterize the structural properties of materials during cyclic tests has been developed for the neutron diffractometers at J-PARC. Using this technique, diffracted neutrons and the applied cyclic conditions are recorded as event data together with time information. The amplitude and phase of the conditions of all recorded neutron signals can be specified by using the characteristics of the event data. By adopting the developed technique, the behaviors of the crystal lattice and domains of the piezoelectric material in a multilayer-type piezoelectric actuator driven by a cyclic electric field were evaluated. The developed technique enabled the collection and processing of diffraction data for all levels of the applied electric field, as opposed to only the highest and lowest levels. The variation in diffraction intensity during the application of a cyclic electric field was obtained successfully, and the hysteresis-like behaviors of both the lattice strain and the 90° domain switching were revealed.

Processing and analysis of X-ray photoelectron diffraction data using IGOR Pro

A software package is presented for nearly real-time display of diffractograms during X-ray photoelectron diffraction (XPD) data acquisition and for processing and analysis after an experiment. During the experiment, the package is able to automatically read X-ray photoelectron spectroscopy (XPS) data, perform initial data processing and project intensity values as XPD diffractograms. Four display modes are supported. After the experiment, the package is able to open, process and analyze XPD patterns. The processing functions include rotation, cropping, creating a full 2π pattern using symmetry operations, smoothing and converting a pattern to an image suitable for publication. The analysis functions include displaying polar angles, azimuthal angles, intensity, the core level spectrum at a selected angular data point, and azimuthal and radial profiles. The package also integrates fitting functions for core level spectra. The package is developed using the IGOR Pro scripting language. A graphical user interface has been developed to allow all the operations just by mouse clicking. The package is designed to interface directly with an XPD system at the Saclay center of the French Atomic Energy and Alternative Energies Authority, but the algorithms are generally applicable and can be readily adapted to other XPD systems.

Internal rotation and equilibrium structure of the 2-methyl-2-nitropropane molecule from joint processing of gas phase electron diffraction data, vibrational and microwave spectroscopy data, and quantum chemical calculation results

The structure and internal rotation of the 2-methyl-2-nitropropane molecule is studied by electron diffraction and quantum chemical calculations with the use of microwave and vibrational spectroscopy data. The electron diffraction data are analyzed within the general intramolecular anharmonic force field model and the quantum chemical pseudoconformer model, considering the adiabatic separation of the degree of freedom of large amplitude motion, i.e., the internal rotation of the NO2 group. The equilibrium eclipsed configuration of the C s symmetry molecule has the following experimental bond lengths and valence angles: r e(N=O) = 1.226//1.226(8) A, r e(C–N)//r e(C–C) = 1.520//1.515/1,521(4) A, ∠еC–C–N = = 109.1/106,1(8)°, ∠еO=N=O = 124.2(6)°, ∠eC–C–Havg = 110(3)°. The equilibrium geometry parameters are well consistent with MP2/cc-pVTZ quantum chemical calculations and microwave spectroscopy data. The thermally average parameters previously obtained within the small vibration model show a satisfactory agreement with the new results. The electron diffraction data used in this work do not allow a reliable determination of the barrier to internal rotation. However, at a barrier of 203(2) cal/mol, which is derived from the microwave study, it follows from the electron diffraction data that the equilibrium configuration must correspond to an eclipsed arrangement of C–C and N=O bonds, which is also consistent with the results of quantum chemical calculations of various levels.

Effect of Base Material on Microstructure and Texture Evolution of a Ti–6Al–4V Electron-Beam Welded Joint

The effect of base material (BM) on microstructure and crystallographic orientation evolution of a Ti–6Al–4V electron-beam welded joint was investigated. Meanwhile, the crystallographic orientation of prior β grains was studied by advanced electron backscattered diffraction data processing. The inhomogeneity of microstructure within welded joint was formed due to the different microstructures of BM. By comparing microstructure details of the welded joint, including microstructure morphology and crystallographic orientation with those of the base material, it can be found that both the microstructure morphology and crystallographic orientation of the EBW joint would be controlled by BM.