Showing papers in "Journal of Applied Crystallography in 2022"
TL;DR: In this article , a generic framework for parent grain reconstruction from fully or partially transformed child microstructures has been integrated into the open-source crystallographic toolbox MTEX, which can be programmatically modified by users to suit their specific applications.
Abstract: A versatile generic framework for parent grain reconstruction from fully or partially transformed child microstructures has been integrated into the open-source crystallographic toolbox MTEX. The framework extends traditional parent grain reconstruction, phase transformation and variant analysis to all parent-child crystal symmetry combinations. The inherent versatility of the universally applicable parent grain reconstruction methods and the ability to conduct in-depth variant analysis are showcased via example workflows that can be programmatically modified by users to suit their specific applications. This is highlighted by three applications, namely α'-to-γ reconstruction in a lath martensitic steel, α-to-β reconstruction in a Ti alloy, and a two-step reconstruction from α' to ɛ to γ in a twinning and transformation-induced plasticity steel. Advanced orientation relationship discovery and analysis options, including variant analysis, are demonstrated via the add-on function library ORTools.
53 citations
TL;DR: In this article , the ID02 beamline with the Extremely Brilliant Source (EBS) at the ESRF is described, which enables static and kinetic investigations of a broad range of systems from ångström to micrometre size scales by combining different small-angle X-ray scattering techniques in a single instrument.
Abstract: The new technical features and enhanced performance of the ID02 beamline with the Extremely Brilliant Source (EBS) at the ESRF are described. The beamline enables static and kinetic investigations of a broad range of systems from ångström to micrometre size scales and down to the sub-millisecond time range by combining different small-angle X-ray scattering techniques in a single instrument. In addition, a nearly coherent beam obtained in the high-resolution mode allows multispeckle X-ray photon correlation spectroscopy measurements down to the microsecond range over the ultra-small- and small-angle regions. While the scattering vector (of magnitude q) range covered is the same as before, 0.001 ≤ q ≤ 50 nm-1 for an X-ray wavelength of 1 Å, the EBS permits relaxation of the collimation conditions, thereby obtaining a higher flux throughput and lower background. In particular, a coherent photon flux in excess of 1012 photons s-1 can be routinely obtained, allowing dynamic studies of relatively dilute samples. The enhanced beam properties are complemented by advanced pixel-array detectors and high-throughput data reduction pipelines. All these developments together open new opportunities for structural, dynamic and kinetic investigations of out-of-equilibrium soft matter and biophysical systems.
23 citations
TL;DR: MoloVol as discussed by the authors is a free user-parametrizable open-source software, developed for calculating a range of geometric features for both unit-cell and isolated structures, which utilizes up to two spherical probes to define cavities, surfaces and volumes.
Abstract: Cavities are a ubiquitous feature of chemical structures encountered in various fields ranging from supramolecular chemistry to molecular biology. They are involved in the encapsulation, transport and transformation of guest molecules, thus necessitating a precise and accessible tool for estimating and visualizing their size and shape. MoloVol, a free user-parametrizable open-source software, developed for calculating a range of geometric features for both unit-cell and isolated structures, is presented here. MoloVol utilizes up to two spherical probes to define cavities, surfaces and volumes. The program was optimized by combining an octree data structure with voxel-partitioned space, allowing for even high-resolution protein structure calculations on reasonable timescales. MoloVol comes with a user-friendly graphic interface along with a command-line interface for high-throughput calculations. It was written in C++ and is available on Windows, macOS and Linux distributions.
23 citations
TL;DR: ReciPro as mentioned in this paper is a comprehensive multipurpose crystallographic program equipped with an intuitive graphical user interface (GUI), and it can smoothly and quantitatively simulate not only single-crystal and/or polycrystalline (powder) diffraction patterns of X-ray, electron and neutron diffraction of a selected crystal model, based on the kinematic scattering theory, but also various electron diffraction images and high-resolution transmission electron microscopy (TEM) images based on dynamical scattering theory.
Abstract:
ReciPro is a comprehensive multipurpose crystallographic program equipped with an intuitive graphical user interface (GUI), and it is completely free and open source. This software has a built-in crystal database consisting of over 20 000 crystal models, and the visualization system can seamlessly display a specified crystal model as an attractive three-dimensional graphic. The comprehensive features are not confined to these crystal model databases and viewers. It can smoothly and quantitatively simulate not only single-crystal and/or polycrystalline (powder) diffraction patterns of X-ray, electron and neutron diffraction of a selected crystal model, based on the kinematic scattering theory, but also various electron diffraction patterns and high-resolution transmission electron microscopy (TEM) images, based on the dynamical scattering theory. The features of stereographic projection of crystal planes/axes to explore crystal orientation relationships and the semi-automatic diffraction spot indexing function for experimental diffraction patterns assist diffraction experiments and analyses. These features are linked through a user-friendly GUI, and the results can be synchronously displayed almost in real time. ReciPro will assist a wide range of crystallographers (including beginners) using X-ray, electron and neutron diffraction crystallography and TEM.
19 citations
TL;DR: A description and the performance of the very small angle neutron scattering diffractometer at the National Institute of Standards and Technology are presented in this paper , where the measurement range of the instrument extends over three decades of momentum transfer q from 2 × 10-4 to 0.7 Å-1.
Abstract: A description and the performance of the very small angle neutron scattering diffractometer at the National Institute of Standards and Technology are presented. The measurement range of the instrument extends over three decades of momentum transfer q from 2 × 10-4 to 0.7 Å-1. The entire scattering angle range from 8 × 10-5 to π/6 rad (30°) can be measured simultaneously using three separate detector carriages on rails holding nine 2D detector arrays. Versatile choices of collimation options and neutron wavelength selection allow the q resolution and beam intensity to be optimized for the needs of the experiment. High q resolution is achieved using multiple converging-beam collimation with circular pinholes combined with refractive lenses and prisms. Relaxed vertical resolution with much higher beam intensity can be achieved with narrow slit collimation and a broad wavelength range chosen by truncating the moderator source distribution below 4 Å with a Be crystalline filter and above 8 Å with a supermirror deflector. Polarized beam measurements with full polarization analysis are also provided by a high-performance supermirror polarizer and spin flipper, capable of producing flipping ratios of over 100, along with a high-efficiency 3He polarization analyzer.
16 citations
TL;DR: GenX as mentioned in this paper is a standard package for analyzing X-ray and neutron reflectometry data, which includes a simplified model builder for beginners, simple samples, additional sample models, statistical error analysis and the use of just-in-time compilation modules for the reflectometry kernel to achieve higher performance.
Abstract: Since its publication more than 15 years ago the GenX software has been continuously developed and has established itself as a standard package for analyzing X-ray and neutron reflectometry data. The evolution of the software during the last two major revisions is reported here. This includes a simplified model builder for beginners, simple samples, additional sample models, statistical error analysis and the use of just-in-time compilation modules for the reflectometry kernel to achieve higher performance. In addition, the influence of experimental errors on the reflectivity curve is discussed, and new features are described that allow the user to include these in the error statistics to improve the fitting and uncertainty estimation.
15 citations
TL;DR: The beamline enables static and time-resolved investigations from ångström to micrometre size scales down to the sub-millisecond time range and coherent scattering studies in the ultra-small-angle region as mentioned in this paper .
Abstract: The new technical features and improved performance of the time-resolved ultra-small-angle X-ray scattering beamline at the ESRF are presented. The beamline enables static and time-resolved investigations from ångström to micrometre size scales down to the sub-millisecond time range and coherent scattering studies in the ultra-small-angle region. Among the main applications are the elucidation of static and transient hierarchical structures in soft matter and biophysical systems, and the dynamics of out-of-equilibrium complex fluids.
14 citations
TL;DR: MoloVol is a free program for calculating volumes and surface areas of molecules and their cavities and its successor, MoloVol2, is available for Windows.
Abstract: MoloVol is a free program for calculating volumes and surface areas of molecules and their cavities.
10 citations
TL;DR: In this article , an immiscible inert oil phase is used to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device, resulting in stable injection conditions for two different resin materials experimentally.
Abstract: Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macro-molecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.
9 citations
TL;DR: The magnetic small-angle neutron scattering (SANS) has emerged in recent years as one of the most important methods for magnetic microstructure determination in condensedmatter physics and materials science as mentioned in this paper .
Abstract: With its unique sensitivity to magnetic inhomogeneities on mesoscopic length scales, magnetic small-angle neutron scattering (SANS) has emerged in recent years as one of the most important methods for magnetic microstructure determination in condensedmatter physics and materials science. However, as it is based on the nanoscale variation of both orientation and magnitude of the magnetization vector, the well established theories for nuclear SANS do not go far enough in many cases to describe the magnetic SANS cross section. This is particularly relevant for the diffuse magnetic SANS resulting from the spin misalignment present in inhomogeneous and nonuniformly magnetized materials such as nanostructured bulk ferromagnets, magnetic vortices, nanoparticles and ferrofluids, magnetic steels, spin glasses, and amorphous magnets. This book is therefore a perfect fit to fill the gap in the existing literature and provide a comprehensive overview on the magnetic SANS technique. It uniquely discusses the full theoretical background of polarized SANS and gives extensive examples of diffuse magnetic SANS experiments. The great strength of this book is in its additional focus on the application of numerical micromagnetic simulations to experimental scattering data. This approach has lately seen a massive development and is a very promising means to tackle the resolution of three-dimensional mesoscale spin structures in the near future. The book is organized in seven chapters. The first chapter provides the reader with an introduction to the basic expressions of neutron scattering cross sections and the elastic magnetic SANS cross section. It emphasizes the origins of magnetic SANS and its differences from conventional particle scattering. Chapters 2 and 3 provide the basic concepts of SANS and micromagnetism. Both chapters give a concise overview of the most important aspects needed to follow the discussion of magnetic SANS. Chapter 2, Basics of SANS, starts with general aspects of experimental setups and instrumental resolution. It discusses the influence of inelastic SANS contributions such as phonon and magnon scattering on the energy-integrated SANS signal, highlighting the left–right asymmetry method using polarized neutrons to study helical spin dynamics. After summarizing the basics of nonmagnetic SANS, including the relation of scattering cross sections and correlation functions, the chapter proceeds to the specifics of magnetic SANS. Based on the magnetic scattering vector, the unpolarized and polarized magnetic SANS cross sections are provided for the two most commonly used experimental setups. A discussion of the derived magnetic SANS cross sections at magnetic saturation establishes the connection to the particle–matrix concept. Chapter 3, Basics of Static Micromagnetism, introduces the main micromagnetic energy contributions and the static equations of micromagnetics. For the approach-to-saturation regime, the micromagnetic equations can be linearized and the transverse Fourier components of the magnetization, related to the spin misalignment, are derived. These are directly connected to the magnetic SANS cross section and provide a measure for the autocorrelation function of the magnetization, defining the characteristic length scale of the system. The magnetic SANS is hence intimately linked to fundamental micromagnetic parameters (such as exchange, anisotropy, magnetostatics) and microstructure (e.g. the particle form factor). Chapters 4 and 5 are dedicated to the combination of SANS and micromagnetism and the application of magnetic SANS to the mesoscale magnetism in different ISSN 1600-5767
9 citations
TL;DR: In this article , a description and performance of the very small angle neutron scattering diffractometer at the National Institute of Standards and Technology (NIST) is presented. But the performance of this diffractometry is limited.
Abstract: A description and the performance of the very small angle neutron scattering diffractometer at the National Institute of Standards and Technology are presented.
TL;DR: SGTools as mentioned in this paper is an open-source software suite to perform data processing and analysis for in situ synchrotron small-angle X-ray scattering (SAXS) and GISAXS experiments.
Abstract: In situ synchrotron small-angle X-ray scattering (SAXS) is a powerful tool for studying dynamic processes during material preparation and application. The processing and analysis of large data sets generated from in situ X-ray scattering experiments are often tedious and time consuming. However, data processing software for in situ experiments is relatively rare, especially for grazing-incidence small-angle X-ray scattering (GISAXS). This article presents an open-source software suite ( SGTools ) to perform data processing and analysis for SAXS and GISAXS experiments. The processing modules in this software include (i) raw data calibration and background correction; (ii) data reduction by multiple methods; (iii) animation generation and intensity mapping for in situ X-ray scattering experiments; and (iv) further data analysis for the sample with an order degree and interface correlation. This article provides the main features and framework of SGTools . The workflow of the software is also elucidated to allow users to develop new features. Three examples are demonstrated to illustrate the use of SGTools for dealing with SAXS and GISAXS data. Finally, the limitations and future features of the software are also discussed.
TL;DR: In this paper , a combined inject-and-transfer system (BITS) method for sample delivery in serial femtosecond crystallography (SFX) experiments is presented.
Abstract: Serial femtosecond crystallography (SFX) enables the determination of room-temperature crystal structures of macromolecules with minimized radiation damage and provides time-resolved molecular dynamics by pump–probe or mix-and-inject experiments. In SFX, a variety of sample delivery methods with unique advantages have been developed and applied. The combination of existing sample delivery methods can enable a new approach to SFX data collection that combines the advantages of the individual methods. This study introduces a combined inject-and-transfer system (BITS) method for sample delivery in SFX experiments: a hybrid injection and fixed-target scanning method. BITS allows for solution samples to be reliably deposited on ultraviolet ozone (UVO)-treated polyimide films, at a minimum flow rate of 0.5 nl min −1 , in both vertical and horizontal scanning modes. To utilize BITS in SFX experiments, lysozyme crystal samples were embedded in a viscous lard medium and injected at flow rates of 50–100 nl min −1 through a syringe needle onto a UVO-treated polyimide film, which was mounted on a fixed-target scan stage. The crystal samples deposited on the film were raster scanned with an X-ray free electron laser using a motion stage in both horizontal and vertical directions. Using the BITS method, the room-temperature structure of lysozyme was successfully determined at a resolution of 2.1 Å, and thus BITS could be utilized in future SFX experiments.
TL;DR: In this article , a global uniaxial magnetic anisotropy (texture) of the material, in addition to the already included random zero-average local anisotropic local a priori properties, is derived for spin-misalignment response functions.
Abstract: Micromagnetic small-angle neutron scattering theory is well established for analyzing spin-misalignment scattering data of bulk ferromagnets. Here, this theory is extended to allow for a global uniaxial magnetic anisotropy (texture) of the material, in addition to the already included random zero-average local anisotropy. Macroscopic cross sections and spin-misalignment response functions are computed analytically for several practically relevant mutual anisotropy and external magnetic field orientations in both parallel and perpendicular scattering geometries for field magnitudes both above and below the rotational saturation. Some of these expressions are tested on published experimental data of magnetic-field-annealed Vitroperm and plastically deformed Ni, allowing determination of the corresponding global uniaxial anisotropy quality factors.
TL;DR: The mlreflect as discussed by the authors package implements an optimized pipeline for the automated analysis of reflectometry data using machine learning, which combines several training and data treatment techniques discussed in previous publications, and the predictions made by the neural network are accurate and robust enough to serve as good starting parameters for an optional subsequent least-mean-squares fit of the data.
Abstract: The Python package mlreflect is demonstrated, which implements an optimized pipeline for the automated analysis of reflectometry data using machine learning. The package combines several training and data treatment techniques discussed in previous publications. The predictions made by the neural network are accurate and robust enough to serve as good starting parameters for an optional subsequent least-mean-squares (LMS) fit of the data. For a large data set of 242 reflectivity curves of various thin films on silicon substrates, the pipeline reliably finds an LMS minimum very close to a fit produced by a human researcher with the application of physical knowledge and carefully chosen boundary conditions. The differences between simulated and experimental data and their implications for the training and performance of neural networks are discussed. The experimental test set is used to determine the optimal noise level during training. The extremely fast prediction times of the neural network are leveraged to compensate for systematic errors by sampling slight variations in the data.
TL;DR: SAXSDOG as discussed by the authors is a Python-based environment for real-time azimuthal integration of large-area scattering images, which is primarily designed for dedicated data pipelines: once a scattering image is transferred from the detector onto the storage unit, it is automatically integrated and pre-evaluated using integral parameters within milliseconds.
Abstract: In situ small- and wide-angle scattering experiments at synchrotrons often result in massive quantities of data within just seconds. Especially during such beamtimes, processing of the acquired data online, without appreciable delay, is key to obtaining feedback on the failure or success of the experiment. This had led to the development of SAXSDOG, a Python-based environment for real-time azimuthal integration of large-area scattering images. The software is primarily designed for dedicated data pipelines: once a scattering image is transferred from the detector onto the storage unit, it is automatically integrated and pre-evaluated using integral parameters within milliseconds. The control and configuration of the underlying server-based processes is achieved via a graphical user interface, SAXSLEASH, which visualizes the resulting 1D data together with integral classifiers in real time. SAXSDOG further includes a portable 'take-home' version for users that runs on standalone computers, enabling its use in laboratories or at the preferred workspace.
TL;DR: In this paper , improvements to the GenX program are discussed, including performance, model building and error analysis, as well as performance, error analysis and model building improvements, including model building.
Abstract: Improvements to the GenX program are discussed, including performance, model building and error analysis.
TL;DR: In this article , a standard Bruker D8 QUEST single-crystal X-ray diffractometer equipped with a micro-focus Mo tube and CMOS Photon III detector was adapted to measure pair distribution function (PDF) analysis.
Abstract: Self-assembled polynuclear lanthanide hydroxo complexes are important objects in the reticular chemistry approach to the design of various functional materials. Revealing their structure in the solid state and understanding the molecular mechanism of self-assembly in solution require a universal and reliable structural method. Pair distribution function (PDF) analysis is a powerful technique which enables structural insight for a wide range of crystalline and amorphous materials on the nanoscale, but commonly measurements are performed at synchrotron X-ray sources or on specially designed laboratory diffractometers. In the present paper, a standard Bruker D8 QUEST single-crystal X-ray diffractometer equipped with a micro-focus Mo tube and CMOS Photon III detector was adapted to measure PDF data of high quality with Q
max = 16.97 Å–1 for solid and liquid samples. An improved data collection strategy and the original data reduction software FormagiX enable calibration and azimuthal full-frame integration of 2D frames, delivering reliable PDFs up to 80 Å with instrumental parameters Q
damp = 0.018 Å−1 and Q
broad = 0.010 Å−1. The effectiveness of the developed approach was demonstrated with reference samples and real-case studies of tetranuclear lanthanide hydroxocarboxylates in solid form and in solution.
TL;DR: In this article , a multipurpose computer software package for orbital-free quantum crystallography has been developed based on multipole experimental electron density parameters, which allows users to extract the chemical-bonding information that was previously unavailable for X-ray single-crystal diffraction analysis.
Abstract: A multipurpose computer software package for orbital-free quantum crystallography has been developed. Based on multipole experimental electron-density parameters, this software allows users to extract the chemical-bonding information that was previously unavailable for X-ray single-crystal diffraction analysis.
TL;DR: A program is described for visualizing powder diffraction data and models published in powder CIF format.
Abstract: A program is described for visualizing powder diffraction data and models published in powder CIF format.
TL;DR: The Domain Auto Finder (DAFi) as mentioned in this paper was designed for the analysis of single-crystal X-ray diffraction (SC-XRD) data from multiphase mixtures of microcrystalline solids and powders.
Abstract: This paper presents the Domain Auto Finder (DAFi) program and its application to the analysis of single-crystal X-ray diffraction (SC-XRD) data from multiphase mixtures of microcrystalline solids and powders. The DAFi algorithm is designed to quickly find subsets of reflections from individual domains in a whole set of SC-XRD data and neither requires a priori crystallographic information nor is limited by the number of phases or individual domains.
TL;DR: PyScatman as discussed by the authors is an approximate and fast numerical tool for the simulation and iterative fitting of wide-angle scattering images of isolated samples, which adopts the multi-slice Fourier transform method.
Abstract: Single-shot coherent diffraction imaging (CDI) is a powerful approach to characterize the structure and dynamics of isolated nanoscale objects such as single viruses, aerosols, nanocrystals and droplets. Using X-ray wavelengths, the diffraction images in CDI experiments usually cover only small scattering angles of a few degrees. These small-angle patterns represent the magnitude of the Fourier transform of the 2D projection of the sample's electron density, which can be reconstructed efficiently but lacks any depth information. In cases where the diffracted signal can be measured up to scattering angles exceeding ∼10°, i.e. in the wide-angle regime, some 3D morphological information of the target is contained in a single-shot diffraction pattern. However, the extraction of the 3D structural information is no longer straightforward and defines the key challenge in wide-angle CDI. So far, the most convenient approach relies on iterative forward fitting of the scattering pattern using scattering simulations. Here the Scatman is presented, an approximate and fast numerical tool for the simulation and iterative fitting of wide-angle scattering images of isolated samples. Furthermore, the open-source software implementation of the Scatman algorithm, PyScatman, is published and described in detail. The Scatman approach, which has already been applied in previous work for forward-fitting-based shape retrieval, adopts the multi-slice Fourier transform method. The effects of optical properties are partially included, yielding quantitative results for small, isolated and weakly interacting samples. PyScatman is capable of computing wide-angle scattering patterns in a few milliseconds even on consumer-level computing hardware, potentially enabling new data analysis schemes for wide-angle coherent diffraction experiments.
TL;DR: A detailed description of 2D and 3D epitaxies of the main {010, {001} and {100} forms of deposited bassanite (CaSO4·0.5H2O) on {10.4} calcite is reported in this article .
Abstract: A detailed description of 2D and 3D epitaxies of the main {010}, {001} and {100} forms of deposited bassanite (CaSO4·0.5H2O) on {10.4} calcite (CaCO3) is reported.
TL;DR: Domain Auto Finder (DAFi) as discussed by the authors is a software for the analysis of single-crystal X-ray diffraction (SC-XRD) data from multiphase mixtures of microcrystalline solids and powders.
Abstract: This paper presents the Domain Auto Finder ( DAFi ) program and its application to the analysis of single-crystal X-ray diffraction (SC-XRD) data from multiphase mixtures of microcrystalline solids and powders. Superposition of numerous reflections originating from a large number of single-crystal domains of the same and/or different (especially unknown) phases usually precludes the sorting of reflections coming from individual domains, making their automatic indexing impossible. The DAFi algorithm is designed to quickly find subsets of reflections from individual domains in a whole set of SC-XRD data. Further indexing of all found subsets can be easily performed using widely accessible crystallographic packages. As the algorithm neither requires a priori crystallographic information nor is limited by the number of phases or individual domains, DAFi is powerful software to be used for studies of multiphase polycrystalline and microcrystalline (powder) materials. The algorithm is validated by testing on X-ray diffraction data sets obtained from real samples: a multi-mineral basalt rock at ambient conditions and products of the chemical reaction of yttrium and nitrogen in a laser-heated diamond anvil cell at 50 GPa. The high performance of the DAFi algorithm means it can be used for processing SC-XRD data online during experiments at synchrotron facilities.
TL;DR: In this paper , a fast method for wide-angle coherent scattering simulations of weakly absorbing isolated samples, called the Scatman, is presented and its quantitative agreement with exact solutions and the low simulation time of its software implementation PyScatman open new perspectives for single-shot 3D coherent diffraction imaging.
Abstract: A fast method for wide-angle coherent scattering simulations of weakly absorbing isolated samples, called the Scatman, is presented. Its quantitative agreement with exact solutions and the low simulation time of its software implementation PyScatman open new perspectives for single-shot 3D coherent diffraction imaging.
TL;DR: In this article , electron backscatter diffraction was used to determine the microscopic dislocation structures generated during creep (with tests interrupted at the steady state) in pure 99.8% aluminium.
Abstract: In the present work, electron backscatter diffraction was used to determine the microscopic dislocation structures generated during creep (with tests interrupted at the steady state) in pure 99.8% aluminium. This material was investigated at two different stress levels, corresponding to the power-law and power-law breakdown regimes. The results show that the formation of subgrain cellular structures occurs independently of the crystallographic orientation. However, the density of these cellular structures strongly depends on the grain crystallographic orientation with respect to the tensile axis direction, with 〈111〉 grains exhibiting the highest densities at both stress levels. It is proposed that this behaviour is due to the influence of intergranular stresses, which is different in 〈111〉 and 〈001〉 grains.
TL;DR: In this paper , an advanced endstation developed at beamline 13A of the 3.0 GeV Taiwan Photon Source for biological small and wide-angle X-ray scattering (SAXS-WAXS) or SWAXS was presented.
Abstract: Recent developments in the instrumentation and data analysis of synchrotron small-angle X-ray scattering (SAXS) on biomolecules in solution have made biological SAXS (BioSAXS) a mature and popular tool in structural biology. This article reports on an advanced endstation developed at beamline 13A of the 3.0 GeV Taiwan Photon Source for biological small- and wide-angle X-ray scattering (SAXS-WAXS or SWAXS). The endstation features an in-vacuum SWAXS detection system comprising two mobile area detectors (Eiger X 9M/1M) and an online size-exclusion chromatography system incorporating several optical probes including a UV-Vis absorption spectrometer and refractometer. The instrumentation and automation allow simultaneous SAXS-WAXS data collection and data reduction for high-throughput biomolecular conformation and composition determinations. The performance of the endstation is illustrated with the SWAXS data collected for several model proteins in solution, covering a scattering vector magnitude q across three orders of magnitude. The crystal-model fittings to the data in the q range ∼0.005-2.0 Å-1 indicate high similarity of the solution structures of the proteins to their crystalline forms, except for some subtle hydration-dependent local details. These results open up new horizons of SWAXS in studying correlated local and global structures of biomolecules in solution.
TL;DR: In this paper , two CNN configurations are developed: one that maximizes the F1 score and one that emphasizes high recall, and they are also combined with expectation-maximization (EM) selection as well as size filtering.
Abstract: Single particle imaging (SPI) at X-ray free-electron lasers is particularly well suited to determining the 3D structure of particles at room temperature. For a successful reconstruction, diffraction patterns originating from a single hit must be isolated from a large number of acquired patterns. It is proposed that this task could be formulated as an image-classification problem and solved using convolutional neural network (CNN) architectures. Two CNN configurations are developed: one that maximizes the F1 score and one that emphasizes high recall. The CNNs are also combined with expectation-maximization (EM) selection as well as size filtering. It is observed that the CNN selections have lower contrast in power spectral density functions relative to the EM selection used in previous work. However, the reconstruction of the CNN-based selections gives similar results. Introducing CNNs into SPI experiments allows the reconstruction pipeline to be streamlined, enables researchers to classify patterns on the fly, and, as a consequence, enables them to tightly control the duration of their experiments. Incorporating non-standard artificial-intelligence-based solutions into an existing SPI analysis workflow may be beneficial for the future development of SPI experiments.
TL;DR: In this paper , the authors describe the data acquisition, correction and reduction approach developed at the PSICHE beamline of the SOLEIL synchrotron, which is particularly suited to experiments at high pressures in large volume presses, and to the study of liquid or amorphous systems.
Abstract: Combined angular and energy dispersive diffraction is particularly well suited to experiments at high pressures in large-volume presses, and to the study of liquid or amorphous systems. This work describes the data acquisition, correction and reduction approach developed at the PSICHE beamline of the SOLEIL synchrotron. The measured data were normalized for both the scattering volume and the effective incident energy spectrum. By optimizing the acquisition strategy, the measurement time and radiation dose are greatly reduced. The correction and reduction protocol outputs normalized scattering profiles that are suitable for pair distribution function or liquid structure analysis. These processes are demostrated with examples from a number of real experimental data sets.
TL;DR: In this paper , a new endstation for biological small and wide-angle X-ray scattering is detailed, which provides development opportunities for studying correlated local and global structures of biomolecules in solution.
Abstract: A new endstation for biological small- and wide-angle X-ray scattering is detailed, which provides development opportunities for studying correlated local and global structures of biomolecules in solution.