Open-access and free articles in Journal of Applied Crystallography
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Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.en-gbCopyright (c) 2024 International Union of CrystallographyInternational Union of CrystallographyInternational Union of CrystallographytextJournal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.Open-access and free articles in Journal of Applied Crystallographyurn:issn:0021-8898https://journals.iucr.orgtext/html62002-02-01T00:00+00:00yearlyurn:issn:0021-8898Journal of Applied Crystallographymed@iucr.orgCopyright (c) 2024 International Union of CrystallographyOpen-access and free articles in Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
https://journals.iucr.org/j/journalhomepage.html
Still imageCrystals in the community and the classroom
http://scripts.iucr.org/cgi-bin/paper?gj5303
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. Though it has a simple basis, this activity can be extended in numerous ways to reflect the aims of the demonstrator, and a few of these are described.International Union of CrystallographytextThe 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. Though it has a simple basis, this activity can be extended in numerous ways to reflect the aims of the demonstrator, and a few of these are described.enMurray, C.Maynard-Casely, H.E.Harrington, R.McCready, S.Sneddon, D.J.Thomas, L.Warren, A.J.Crystals in the community and the classroom2024-02-01CRYSTALLOGRAPHY; EDUCATION; OUTREACHdoi:10.1107/S1600576724000207urn:issn:1600-5767Most introductions to the topic of crystallography only occur during tertiary education, which presents a challenge to communicating it to wider groups. This work describes a simple activity targeted at classroom and community audiences to demonstrate crystal structure(s) and the wider impact of crystallography.https://creativecommons.org/licenses/by/4.0/text/html1862024-02-0157teaching and educationFebruary 2024Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1med@iucr.org1600-57671600-5767181Time-resolved AUSAXS at BL28XU at SPring-8
http://scripts.iucr.org/cgi-bin/paper?jl5077
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 change in energy dependence of the scattered intensity with time was found during vulcanization, suggesting the transformation of zinc in the reaction.International Union of CrystallographytextAn 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 change in energy dependence of the scattered intensity with time was found during vulcanization, suggesting the transformation of zinc in the reaction.enNakanishi, Y.Fujinami, S.Shibata, M.Miyazaki, T.Yamamoto, K.Takenaka, M.Time-resolved AUSAXS at BL28XU at SPring-82024-02-01ANOMALOUS ULTRA-SMALL-ANGLE X-RAY SCATTERING; TIME-RESOLVED MEASUREMENTS; CHANNEL-CUT COMPACT MONOCHROMATORSdoi:10.1107/S1600576723011135urn:issn:1600-5767This work reports the successful construction of an anomalous ultra-small-angle X-ray scattering (AUSAXS) measurement system at the BL28XU beamline at SPring-8. A minimum of q = 0.0069 nm−1 was attained and time-resolved measurements were carried out by performing scattering measurements at 17 different energies in 30 s.https://creativecommons.org/licenses/by/4.0/text/html2192024-02-01laboratory notes57February 2024https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1med@iucr.org1600-57671600-5767215A simple solution to the Rietveld refinement recipe problem
http://scripts.iucr.org/cgi-bin/paper?fc5075
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. This provides the partial derivatives with respect to each parameter, along with information to discriminate meaningful values from numerical computational errors. The implementation of this mechanism in the open-source GSAS-II program is discussed. This new method is discussed as an important step towards the development of automated Rietveld refinement technology.International Union of CrystallographytextRietveld 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. This provides the partial derivatives with respect to each parameter, along with information to discriminate meaningful values from numerical computational errors. The implementation of this mechanism in the open-source GSAS-II program is discussed. This new method is discussed as an important step towards the development of automated Rietveld refinement technology.enToby, B.H.A simple solution to the Rietveld refinement recipe problem2024-02-01RIETVELD ANALYSIS; POWDER DIFFRACTION; PARAMETER SELECTION; GSAS-IIdoi:10.1107/S1600576723011032urn:issn:1600-5767A method to determine the order in which parameters should be added to a Rietveld refinement is presented.https://creativecommons.org/licenses/by/4.0/text/htmlFebruary 202457research papers2024-02-011801751600-57671600-5767med@iucr.org1https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyBioXTAS RAW 2: new developments for a free open-source program for small-angle scattering data reduction and analysis
http://scripts.iucr.org/cgi-bin/paper?jl5075
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 Dmax 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. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.International Union of CrystallographytextBioXTAS 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 Dmax 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. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.enHopkins, J.B.BioXTAS RAW 2: new developments for a free open-source program for small-angle scattering data reduction and analysis2024-02-01SMALL-ANGLE SCATTERING; DATA ANALYSIS; BIOLOGICAL MACROMOLECULES; BIOXTAS RAW 2; COMPUTER PROGRAMSdoi:10.1107/S1600576723011019urn:issn:1600-5767BioXTAS RAW is a free open-source program for reduction, analysis and modelling of small-angle scattering data. This article describes the new and improved features in RAW version 2, including new tools for liquid-chromatography coupled data processing, advanced reporting capabilities and a new API.https://creativecommons.org/licenses/by/4.0/text/html1https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767194med@iucr.org1600-576757computer programs2082024-02-01February 2024Refinement of X-ray and electron diffraction crystal structures using analytical Fourier transforms of Slater-type atomic wavefunctions in Olex2
http://scripts.iucr.org/cgi-bin/paper?nb5360
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. Atomic wavefunctions for singly charged ions are implemented and made accessible, and these show drastic changes in electron diffraction scattering factors compared with the neutral atom. A comparison between the two different spherical models of neutral atoms is presented as an example for four different kinds of X-ray and two electron diffraction structures, and comparisons of refinement results using the existing diffraction data are discussed. A systematic but slight improvement in R values and residual densities can be observed when using the new scattering factors, and this is discussed relative to effects on the atomic displacement parameters and atomic positions, which are prominent near the heavier elements in a structure.International Union of CrystallographytextAn 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. Atomic wavefunctions for singly charged ions are implemented and made accessible, and these show drastic changes in electron diffraction scattering factors compared with the neutral atom. A comparison between the two different spherical models of neutral atoms is presented as an example for four different kinds of X-ray and two electron diffraction structures, and comparisons of refinement results using the existing diffraction data are discussed. A systematic but slight improvement in R values and residual densities can be observed when using the new scattering factors, and this is discussed relative to effects on the atomic displacement parameters and atomic positions, which are prominent near the heavier elements in a structure.enKleemiss, F.Peyerimhoff, N.Bodensteiner, M.Refinement of X-ray and electron diffraction crystal structures using analytical Fourier transforms of Slater-type atomic wavefunctions in Olex22024-02-01REFINEMENT; ELECTRON DIFFRACTION; X-RAY DIFFRACTIONdoi:10.1107/S1600576723010981urn:issn:1600-5767Analytical scattering factors for X-ray and electron diffraction from spherical Slater-type orbitals are implemented in Olex2 to overcome shortcomings of interpolation and fitting methods and compare refinement results.https://creativecommons.org/licenses/by/4.0/text/htmlFebruary 202457research papers1742024-02-011600-5767161med@iucr.org1600-57671Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Using XAS to monitor radiation damage in real time and post-analysis, and investigation of systematic errors of fluorescence XAS for Cu-bound amyloid-β
http://scripts.iucr.org/cgi-bin/paper?jo5093
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). A new protocol was developed using extended X-ray absorption fine structure (EXAFS) data analysis for monitoring radiation damage in real time and post-analysis. The reliability of the structural determinations and consistency were validated using the XAS measurement experimental uncertainty. The correction of detector pixel efficiencies improved the fitting χ2 by 12%. An improvement of about 2.5% of the structural fitting was obtained after dead-time corrections. Normalization allowed the elimination of 90% of the monochromator glitches. The remaining glitches were manually removed. The dispersion of spectra due to self-absorption was corrected. Standard errors of experimental measurements were propagated from pointwise variance of the spectra after systematic corrections. Calculated uncertainties were used in structural refinements for obtaining precise and reliable values of structural parameters including atomic bond lengths and thermal parameters. This has permitted hypothesis testing.International Union of CrystallographytextX-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). A new protocol was developed using extended X-ray absorption fine structure (EXAFS) data analysis for monitoring radiation damage in real time and post-analysis. The reliability of the structural determinations and consistency were validated using the XAS measurement experimental uncertainty. The correction of detector pixel efficiencies improved the fitting χ2 by 12%. An improvement of about 2.5% of the structural fitting was obtained after dead-time corrections. Normalization allowed the elimination of 90% of the monochromator glitches. The remaining glitches were manually removed. The dispersion of spectra due to self-absorption was corrected. Standard errors of experimental measurements were propagated from pointwise variance of the spectra after systematic corrections. Calculated uncertainties were used in structural refinements for obtaining precise and reliable values of structural parameters including atomic bond lengths and thermal parameters. This has permitted hypothesis testing.enEkanayake, R.S.K.Streltsov, V.A.Best, S.P.Chantler, C.T.Using XAS to monitor radiation damage in real time and post-analysis, and investigation of systematic errors of fluorescence XAS for Cu-bound amyloid-β2024-02-01X-RAY ABSORPTION SPECTRO-ELECTROCHEMICAL MEASUREMENTS; XAS-EC; RADIATION DAMAGE; DEAD-TIME CORRECTION; N-TRUNCATED AMYLOID PEPIDES; EXAFS; EXTENDED X-RAY ABSORPTION FINE STRUCTUREdoi:10.1107/S1600576723010890urn:issn:1600-5767X-ray absorption spectroscopy (XAS) measurements of N-truncated amyloid-β samples were corrected for systematic effects such as dead time, detector efficiencies, monochromator glitches, self-absorption, radiation damage and noise at higher wavenumbers k, permitting hypothesis testing in structural refinements. A new protocol was developed using extended X-ray absorption fine structure data analysis for monitoring radiation damage in real time and post-analysis.https://creativecommons.org/licenses/by/4.0/text/htmlresearch papers571392024-02-01February 20241https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767125med@iucr.org1600-5767Fast nanoscale imaging of strain in a multi-segment heterostructured nanowire with 2D Bragg ptychography
http://scripts.iucr.org/cgi-bin/paper?xx5037
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 spatial resolution affects the quantitative accuracy of the strain maps, where BPP shows much-improved agreement with an elastic 3D finite element model compared with scanning XRD. The sensitivity of BPP to small deviations from the Bragg condition is systematically investigated. The experimental confirmation of the model suggests that the large lattice mismatch of 1.52% is accommodated without defects.International Union of CrystallographytextDeveloping 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 spatial resolution affects the quantitative accuracy of the strain maps, where BPP shows much-improved agreement with an elastic 3D finite element model compared with scanning XRD. The sensitivity of BPP to small deviations from the Bragg condition is systematically investigated. The experimental confirmation of the model suggests that the large lattice mismatch of 1.52% is accommodated without defects.enHammarberg, S.Dzhigaev, D.Marcal, L.A.B.Dagyte, V.Björling, A.Borgström, M.T.Wallentin, J.Fast nanoscale imaging of strain in a multi-segment heterostructured nanowire with 2D Bragg ptychography2024-02-01BRAGG PROJECTION PTYCHOGRAPHY; III-V MATERIALS; NANOWIRES; X-RAY IMAGINGdoi:10.1107/S1600576723010403urn:issn:1600-5767A strained heterostructured nanowire is investigated using 2D Bragg ptychography and scanning X-ray diffraction.https://creativecommons.org/licenses/by/4.0/text/htmlFebruary 202457research papers702024-02-011600-576760med@iucr.org1600-57671https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyProLEED Studio: software for modeling low-energy electron diffraction patterns
http://scripts.iucr.org/cgi-bin/paper?nb5365
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. The interactive graphical user interface allows real-time modeling of experimental diffraction patterns, change of depicted diffraction spot intensities, visualization of different diffraction domains, and manipulation of any lattice points or diffraction spots. The visualization of unit cells, lattice vectors, grids and scale bars as well as the possibility of exporting ready-to-publish models in bitmap and vector formats significantly simplifies the modeling process and publishing of results.International Union of CrystallographytextLow-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. The interactive graphical user interface allows real-time modeling of experimental diffraction patterns, change of depicted diffraction spot intensities, visualization of different diffraction domains, and manipulation of any lattice points or diffraction spots. The visualization of unit cells, lattice vectors, grids and scale bars as well as the possibility of exporting ready-to-publish models in bitmap and vector formats significantly simplifies the modeling process and publishing of results.enProcházka, P.Čechal, J.ProLEED Studio: software for modeling low-energy electron diffraction patterns2024-02-01LOW-ENERGY ELECTRON DIFFRACTION; LEED; PROLEED STUDIO; RECIPROCAL SPACE; COMPUTER PROGRAMSdoi:10.1107/S1600576723010312urn:issn:1600-5767ProLEED Studio is software designed for simple, intuitive and precise modeling of low-energy electron diffraction patterns.https://creativecommons.org/licenses/by/4.0/text/html1600-5767med@iucr.org1871600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1February 20242024-02-01193computer programs57Operation model of a skew-symmetric split-crystal neutron interferometer
http://scripts.iucr.org/cgi-bin/paper?ei5097
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. It is found that, with a Gaussian Schell model of an incoherent source, the integrated density of the particles leaving the interferometer is the same as that yielded by a coherent Gaussian source having a radius equal to the coherence length.International Union of CrystallographytextThe 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. It is found that, with a Gaussian Schell model of an incoherent source, the integrated density of the particles leaving the interferometer is the same as that yielded by a coherent Gaussian source having a radius equal to the coherence length.enSasso, C.P.Mana, G.Massa, E.Operation model of a skew-symmetric split-crystal neutron interferometer2024-02-01SPLIT-CRYSTAL INTERFEROMETRY; NEUTRON INTERFEROMETRY; X-RAY INTERFEROMETRY; DYNAMICAL THEORY OF X-RAY DIFFRACTION; X-RAY AND NEUTRON COHERENCEdoi:10.1107/S1600576723010245urn:issn:1600-5767The 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. In contrast with previous studies, both incoherent sources and the three-dimensional operation of the interferometer are considered.https://creativecommons.org/licenses/by/4.0/text/html57research papers592024-02-01February 20241https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-576744med@iucr.org1600-5767POMFinder: identifying polyoxometallate cluster structures from pair distribution function data using explainable machine learning
http://scripts.iucr.org/cgi-bin/paper?in5097
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 approach is shown to identify suitable POMs from experimental data, including in situ data collected with fast acquisition times. This automated approach has significant potential for identifying suitable models for structure refinement to extract quantitative structural parameters in materials chemistry research. POMFinder is open source and user friendly, making it accessible to those without prior ML knowledge. It is also demonstrated that POMFinder offers a promising modelling framework for combined modelling of multiple scattering techniques.International Union of CrystallographytextCharacterization 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 approach is shown to identify suitable POMs from experimental data, including in situ data collected with fast acquisition times. This automated approach has significant potential for identifying suitable models for structure refinement to extract quantitative structural parameters in materials chemistry research. POMFinder is open source and user friendly, making it accessible to those without prior ML knowledge. It is also demonstrated that POMFinder offers a promising modelling framework for combined modelling of multiple scattering techniques.enAnker, A.S.Kjær, E.T.S.Juelsholt, M.Jensen, K.M.Ø.POMFinder: identifying polyoxometallate cluster structures from pair distribution function data using explainable machine learning2024-02-01COMPUTATIONAL MODELLING; MACHINE LEARNING; POLYOXOMETALLATE CLUSTERS; POMFINDERdoi:10.1107/S1600576723010014urn:issn:1600-5767Machine learning is used to analyse pair distribution functions obtained from polyoxometallate clusters. The new classifier POMFinder can rapidly screen a database of structures and identify which model is most suitable for describing the experimental data.https://creativecommons.org/licenses/by/4.0/text/html57research papers432024-02-01February 20241https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-576734med@iucr.org1600-5767John W. White (1937–2023)
http://scripts.iucr.org/cgi-bin/paper?in5096
International Union of CrystallographytextenGilbert, E.P.Higgins, J.Lander, G.John W. White (1937–2023)2023-11-24OBITUARIESdoi:10.1107/S1600576723009949urn:issn:1600-5767Obituary for Professor John White.text/html56crystallographers2023-11-241884December 20236Journal of Applied Crystallography18821600-57671600-5767med@iucr.orgVan Vleck analysis of angularly distorted octahedra using VanVleckCalculator
http://scripts.iucr.org/cgi-bin/paper?oc5030
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 (Q2, Q3) along the bond axes of the octahedron, disregarding the angular distortion and losing information on the octahedral shear modes (Q4, Q5 and Q6) in the process. In this paper, the validity of assuming bond lengths to be orthogonal in order to calculate the Van Vleck modes is discussed, and a method is described for calculating Van Vleck modes without disregarding the angular distortion. A Python package for doing this, VanVleckCalculator, is introduced and some examples of its use are given. Finally, it is shown that octahedral shear and angular distortion are often, but not always, correlated, and a parameter η is proposed as the shear fraction. It is demonstrated that η can be used to predict whether the values will be correlated when varying a tuning parameter such as temperature or pressure.International Union of CrystallographytextVan 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 (Q2, Q3) along the bond axes of the octahedron, disregarding the angular distortion and losing information on the octahedral shear modes (Q4, Q5 and Q6) in the process. In this paper, the validity of assuming bond lengths to be orthogonal in order to calculate the Van Vleck modes is discussed, and a method is described for calculating Van Vleck modes without disregarding the angular distortion. A Python package for doing this, VanVleckCalculator, is introduced and some examples of its use are given. Finally, it is shown that octahedral shear and angular distortion are often, but not always, correlated, and a parameter η is proposed as the shear fraction. It is demonstrated that η can be used to predict whether the values will be correlated when varying a tuning parameter such as temperature or pressure.enNagle-Cocco, L.A.V.Dutton, S.E.Van Vleck analysis of angularly distorted octahedra using VanVleckCalculator2024-02-01CRYSTAL STRUCTURE; JAHN-TELLER DISTORTION; OCTAHEDRAL DISTORTION; OCTAHEDRAL TILTING; CRYSTALLOGRAPHIC SOFTWAREdoi:10.1107/S1600576723009925urn:issn:1600-5767A method and associated Python script, VanVleckCalculator, are described for parameterizing octahedral shear and first-order Jahn–Teller distortions in crystal structures.https://creativecommons.org/licenses/by/4.0/text/htmlhttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1med@iucr.org1600-57671600-576720332024-02-0157research papersFebruary 2024An electropneumatic cleaning device for piezo-actuator-driven picolitre-droplet dispensers
http://scripts.iucr.org/cgi-bin/paper?te5126
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.International Union of CrystallographytextRecently, 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.enBerkes, A.Kleine-Doepke, S.Leimkohl, J.-P.Schikora, H.Mehrabi, P.Tellkamp, F.Schulz, E.C.An electropneumatic cleaning device for piezo-actuator-driven picolitre-droplet dispensers2024-02-01DROPLET DEPOSITION; SERIAL CRYSTALLOGRAPHY; PIEZO-ACTUATORS; TIME-RESOLVED CRYSTALLOGRAPHYdoi:10.1107/S1600576723009573urn:issn:1600-5767A device for automated cleaning of piezo-actuator-driven picolitre-droplet dispensers required for the liquid application method for time-resolved analyses is presented.https://creativecommons.org/licenses/by/4.0/text/html57laboratory notes2142024-02-01February 20241Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767209med@iucr.org1600-5767Time-resolved high-energy X-ray diffraction studies of ultrathin Ni ferrite films on MgO(001)
http://scripts.iucr.org/cgi-bin/paper?xx5034
Time-resolved high-energy X-ray diffraction was used during growth of ultrathin NixFe3−xO4 films with varying Ni content (0 ≤ x ≤ 1.5) deposited on MgO(001) substrates by reactive molecular beam epitaxy, providing an insight into the growth dynamics of these films. In order to obtain structural information, reciprocal-space maps were recorded and the temporal evolution of the Bragg peaks specific to the octahedral and tetrahedral lattice sites of the inverse spinel structure of NixFe3−xO4 was observed during growth of the films. A time delay, corresponding to a coverage of 1.2–1.8 nm, between the appearance of the Bragg reflections originating from octahedral sites and reflections originating exclusively from tetrahedral sites indicates that the ferrite films grow in two stages. In the initial growth phase, a rock salt interface layer is formed. Afterwards, a structural transition occurs and the films grow in an inverse spinel structure. The thickness of the initial rock salt phase was found to increase with Ni content and to be responsible for atypical strain in the thin films. Films with Ni contents x > 1 do not show a structural transition. These films remain in a (deficient) rock salt structure consisting of a mixed Ni–Fe oxide and do not form a spinel structure at all. They show an increased number of NiO clusters as detected by X-ray photoelectron spectroscopy of the valence band, accompanied by a significant roughening of the films.International Union of CrystallographytextTime-resolved high-energy X-ray diffraction was used during growth of ultrathin NixFe3−xO4 films with varying Ni content (0 ≤ x ≤ 1.5) deposited on MgO(001) substrates by reactive molecular beam epitaxy, providing an insight into the growth dynamics of these films. In order to obtain structural information, reciprocal-space maps were recorded and the temporal evolution of the Bragg peaks specific to the octahedral and tetrahedral lattice sites of the inverse spinel structure of NixFe3−xO4 was observed during growth of the films. A time delay, corresponding to a coverage of 1.2–1.8 nm, between the appearance of the Bragg reflections originating from octahedral sites and reflections originating exclusively from tetrahedral sites indicates that the ferrite films grow in two stages. In the initial growth phase, a rock salt interface layer is formed. Afterwards, a structural transition occurs and the films grow in an inverse spinel structure. The thickness of the initial rock salt phase was found to increase with Ni content and to be responsible for atypical strain in the thin films. Films with Ni contents x > 1 do not show a structural transition. These films remain in a (deficient) rock salt structure consisting of a mixed Ni–Fe oxide and do not form a spinel structure at all. They show an increased number of NiO clusters as detected by X-ray photoelectron spectroscopy of the valence band, accompanied by a significant roughening of the films.enAlexander, A.Pohlmann, T.Hoppe, M.Röh, J.Gutowski, O.Küpper, K.Bertram, F.Wollschläger, J.Time-resolved high-energy X-ray diffraction studies of ultrathin Ni ferrite films on MgO(001)2023-11-29NICKEL FERRITE; TIME-RESOLVED HIGH-ENERGY X-RAY DIFFRACTION; HEXRD; THIN FILMS; EPITAXYdoi:10.1107/S1600576723009287urn:issn:1600-5767Time-resolved high-energy X-ray diffraction was used during growth of ultrathin NixFe3−xO4 films of varying Ni content (0 ≤ x ≤ 1.5) on MgO(001). For low Ni contents (x ≤ 1), the films grow initially in a rock salt phase followed by an inverse spinel structure, while overstoichiometric films (Ni contents x > 1) grow completely in a rock salt structure.https://creativecommons.org/licenses/by/4.0/text/html2023-11-29179156research papersDecember 2023Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/61600-5767med@iucr.org17841600-5767Texture measurements on quartz single crystals to validate coordinate systems for neutron time-of-flight texture analysis
http://scripts.iucr.org/cgi-bin/paper?xx5024
In crystallographic texture analysis, ensuring that sample directions are preserved from experiment to the resulting orientation distribution is crucial to obtain physical meaning from diffraction data. This work details a procedure to ensure instrument and sample coordinates are consistent when analyzing diffraction data with a Rietveld refinement using the texture analysis software MAUD. A quartz crystal is measured on the HIPPO diffractometer at Los Alamos National Laboratory for this purpose. The methods described here can be applied to any diffraction instrument measuring orientation distributions in polycrystalline materials.International Union of CrystallographytextIn crystallographic texture analysis, ensuring that sample directions are preserved from experiment to the resulting orientation distribution is crucial to obtain physical meaning from diffraction data. This work details a procedure to ensure instrument and sample coordinates are consistent when analyzing diffraction data with a Rietveld refinement using the texture analysis software MAUD. A quartz crystal is measured on the HIPPO diffractometer at Los Alamos National Laboratory for this purpose. The methods described here can be applied to any diffraction instrument measuring orientation distributions in polycrystalline materials.enSchmitt, M.M.Savage, D.J.Yeager, J.D.Wenk, H.-R.Lutterotti, L.Vogel, S.C.Texture measurements on quartz single crystals to validate coordinate systems for neutron time-of-flight texture analysis2023-11-24TEXTURE; NEUTRON DIFFRACTION; COORDINATE SYSTEMSdoi:10.1107/S1600576723009275urn:issn:1600-5767A method for verifying that coordinate systems are conserved while performing texture analysis using MAUD is demonstrated for neutron diffraction data of a quartz single crystal.https://creativecommons.org/licenses/by/4.0/text/htmlDecember 202356research papers2023-11-24177517641600-57671600-5767med@iucr.org6Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/The International Tables Symmetry Database
http://scripts.iucr.org/cgi-bin/paper?dv5006
The International Tables Symmetry Database (https://symmdb.iucr.org/), which is part of International Tables for Crystallography, is a collection of individual databases of crystallographic space-group and point-group information with associated programs. The programs let the user access and in some cases interactively visualize the data, and some also allow new data to be calculated `on the fly'. Together these databases and programs expand upon and complement the symmetry information provided in International Tables for Crystallography Volume A, Space-Group Symmetry, and Volume A1, Symmetry Relations between Space Groups. The Symmetry Database allows users to learn about and explore the space and point groups, and facilitates the study of group–subgroup relations between space groups, with applications in determining crystal-structure relationships, in studying phase transitions and in domain-structure analysis. The use of the International Tables Symmetry Database in all these areas is demonstrated using several examples.International Union of CrystallographytextThe International Tables Symmetry Database (https://symmdb.iucr.org/), which is part of International Tables for Crystallography, is a collection of individual databases of crystallographic space-group and point-group information with associated programs. The programs let the user access and in some cases interactively visualize the data, and some also allow new data to be calculated `on the fly'. Together these databases and programs expand upon and complement the symmetry information provided in International Tables for Crystallography Volume A, Space-Group Symmetry, and Volume A1, Symmetry Relations between Space Groups. The Symmetry Database allows users to learn about and explore the space and point groups, and facilitates the study of group–subgroup relations between space groups, with applications in determining crystal-structure relationships, in studying phase transitions and in domain-structure analysis. The use of the International Tables Symmetry Database in all these areas is demonstrated using several examples.ende la Flor, G.Kroumova, E.Hanson, R.M.Aroyo, M.I.The International Tables Symmetry Database2023-11-29INTERNATIONAL TABLES FOR CRYSTALLOGRAPHY; SYMMETRY DATABASE; SPACE-GROUP SYMMETRY; SYMMETRY RELATIONS BETWEEN SPACE GROUPS; POINT GROUPS; SUBGROUPS; SUPERGROUPSdoi:10.1107/S1600576723009068urn:issn:1600-5767The International Tables Symmetry Database (https://symmdb.iucr.org/), part of International Tables for Crystallography, is a collection of individual databases of crystallographic space-group and point-group information. Programs are provided to access and interactively visualize the data, and also allow new data to be calculated `on the fly', facilitating the in-depth study of group–subgroup relations, domain structures and twinning, families of related crystal structures and phase transitions, and the prediction of new crystal structures.https://creativecommons.org/licenses/by/4.0/text/htmlDecember 2023teaching and education5618402023-11-291600-57671824med@iucr.org1600-57676Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/(U)SAXS characterization of porous microstructure of chert: insights into organic matter preservation
http://scripts.iucr.org/cgi-bin/paper?uu5001
This study characterizes the microstructure and mineralogy of 132 (ODP sample), 1000 and 1880 million-year-old chert samples. By using ultra-small-angle X-ray scattering (USAXS), wide-angle X-ray scattering and other techniques, the preservation of organic matter (OM) in these samples is studied. The scarce microstructural data reported on chert contrast with many studies addressing porosity evolution in other sedimentary rocks. The aim of this work is to solve the distribution of OM and silica in chert by characterizing samples before and after combustion to pinpoint the OM distribution inside the porous silica matrix. The samples are predominantly composed of alpha quartz and show increasing crystallite sizes up to 33 ± 5 nm (1σ standard deviation or SD). In older samples, low water abundances (∼0.03%) suggest progressive dehydration. (U)SAXS data reveal a porous matrix that evolves over geological time, including, from younger to older samples, (1) a decreasing pore volume down to 1%, (2) greater pore sizes hosting OM, (3) decreasing specific surface area values from younger (9.3 ± 0.1 m2 g−1) to older samples (0.63 ± 0.07 m2 g−1, 1σ SD) and (4) a lower background intensity correlated to decreasing hydrogen abundances. The pore-volume distributions (PVDs) show that pores ranging from 4 to 100 nm accumulate the greater volume fraction of OM. Raman data show aromatic organic clusters up to 20 nm in older samples. Raman and PVD data suggest that OM is located mostly in mesopores. Observed structural changes, silica–OM interactions and the hydrophobicity of the OM could explain the OM preservation in chert.International Union of CrystallographytextThis study characterizes the microstructure and mineralogy of 132 (ODP sample), 1000 and 1880 million-year-old chert samples. By using ultra-small-angle X-ray scattering (USAXS), wide-angle X-ray scattering and other techniques, the preservation of organic matter (OM) in these samples is studied. The scarce microstructural data reported on chert contrast with many studies addressing porosity evolution in other sedimentary rocks. The aim of this work is to solve the distribution of OM and silica in chert by characterizing samples before and after combustion to pinpoint the OM distribution inside the porous silica matrix. The samples are predominantly composed of alpha quartz and show increasing crystallite sizes up to 33 ± 5 nm (1σ standard deviation or SD). In older samples, low water abundances (∼0.03%) suggest progressive dehydration. (U)SAXS data reveal a porous matrix that evolves over geological time, including, from younger to older samples, (1) a decreasing pore volume down to 1%, (2) greater pore sizes hosting OM, (3) decreasing specific surface area values from younger (9.3 ± 0.1 m2 g−1) to older samples (0.63 ± 0.07 m2 g−1, 1σ SD) and (4) a lower background intensity correlated to decreasing hydrogen abundances. The pore-volume distributions (PVDs) show that pores ranging from 4 to 100 nm accumulate the greater volume fraction of OM. Raman data show aromatic organic clusters up to 20 nm in older samples. Raman and PVD data suggest that OM is located mostly in mesopores. Observed structural changes, silica–OM interactions and the hydrophobicity of the OM could explain the OM preservation in chert.enMunoz, P.Ilavsky, J.Newville, M.Wetter, N.U.Lourenço, R.A.Barbosa de Andrade, M.Martins, T.S.Dipold, J.Freitas, A.Z.Cides da Silva, L.C.Oliveira, C.L.P.(U)SAXS characterization of porous microstructure of chert: insights into organic matter preservation2023-11-15SILICA-RICH SEDIMENTARY ROCKS; CHERTS; ORGANIC MATTER; ULTRA-SMALL-ANGLE X-RAY SCATTERING; (U)SAXS; WIDE-ANGLE X-RAY SCATTERING; WAXS; MESOPORES; MICROSTRUCTURE; IODPdoi:10.1107/S1600576723008889urn:issn:1600-5767Silica-rich sedimentary rocks (chert) exhibit an evolving microstructure able to preserve organic matter mostly in mesopores during geological timescales. Under compaction, silica porous matrices experience porosity reduction, dehydration of silica and redistribution of organics inside the pore network.https://creativecommons.org/licenses/by/4.0/text/html16921600-57671600-5767med@iucr.org6https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyDecember 202356research papers2023-11-151706Form factor of helical structures and twisted fibres
http://scripts.iucr.org/cgi-bin/paper?fs5223
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.International Union of CrystallographytextA 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.envan der Maarel, J.R.C.Form factor of helical structures and twisted fibres2023-11-07HELICAL FILAMENTS; HELICAL FIBRES; SMALL-ANGLE SCATTERING; FORM FACTORS; TWISTED HEXAGONAL FIBRESdoi:10.1107/S1600576723008671urn:issn:1600-5767A general formalism is presented for the single-chain scattering function of helices and twisted fibres with easy adaptation of number of strands and cross-sectional symmetry.https://creativecommons.org/licenses/by/4.0/text/html17202023-11-0756research papersDecember 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography6med@iucr.org1600-57671600-57671714Polynator: a tool to identify and quantitatively evaluate polyhedra and other shapes in crystal structures
http://scripts.iucr.org/cgi-bin/paper?jl5072
Polynator is a Python program capable of identifying coordination polyhedra, molecules and other shapes in crystal structures and evaluating their distortions. Distortions are quantified by fitting the vertices of a model to a selected set of atoms. In contrast to earlier programs, models can be deformable, which allows them to represent a point group or a range of shapes such as the set of all trigonal prisms, rather than a specific, rigid shape such as the equilateral trigonal prism. The program comes with a graphical user interface and is freely available. This paper discusses its working principle and illustrates a number of applications.International Union of CrystallographytextPolynator is a Python program capable of identifying coordination polyhedra, molecules and other shapes in crystal structures and evaluating their distortions. Distortions are quantified by fitting the vertices of a model to a selected set of atoms. In contrast to earlier programs, models can be deformable, which allows them to represent a point group or a range of shapes such as the set of all trigonal prisms, rather than a specific, rigid shape such as the equilateral trigonal prism. The program comes with a graphical user interface and is freely available. This paper discusses its working principle and illustrates a number of applications.enLink, L.Niewa, R.Polynator: a tool to identify and quantitatively evaluate polyhedra and other shapes in crystal structures2023-10-20DISTORTION; SHAPE; POLYHEDRA; CONTINUOUS SYMMETRYdoi:10.1107/S1600576723008476urn:issn:1600-5767A computer program that implements a new approach to quantifying distortions in coordination polyhedra, molecules and cages by optimizing dynamic model shapes is presented.https://creativecommons.org/licenses/by/4.0/text/htmlDecember 202318642023-10-20computer programs56med@iucr.org1600-57671600-57671855Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/6Absolute scattering length density profile of liposome bilayers obtained by SAXS combined with GIXOS: a tool to determine model biomembrane structure
http://scripts.iucr.org/cgi-bin/paper?fs5220
Lipid membranes play an essential role in biology, acting as host matrices for biomolecules like proteins and facilitating their functions. Their structures and structural responses to physiologically relevant interactions (i.e. with membrane proteins) provide key information for understanding biophysical mechanisms. Hence, there is a crucial need of methods to understand the effects of membrane host molecules on the lipid bilayer structure. Here, a purely experimental method is presented for obtaining the absolute scattering length density profile and the area per lipid of liposomal bilayers, by aiding the analysis of small-angle X-ray scattering (SAXS) data with the volume of bare headgroups obtained from grazing-incidence X-ray off-specular scattering (GIXOS) data of monolayers of the same model membrane lipid composition. The GIXOS data experimentally demonstrate that the variation of the bare headgroup volume upon change in lipid packing density is small enough to allow its usage as a reference value without knowing the lipid packing stage in a bilayer. This approach also has the advantage that the reference volume is obtained in the same aqueous environment as used for the model membrane bilayers. The validity of this method is demonstrated using several typical membrane compositions, as well as one example of a phospholipid membrane with an incorporated transmembrane peptide. This methodology allows us to obtain absolute scale rather than relative scale values using solely X-ray-based instrumentation, retaining a similar resolution to SAXS experiments. The method presented has high potential for understanding the structural effects of membrane proteins on the biomembrane structure.International Union of CrystallographytextLipid membranes play an essential role in biology, acting as host matrices for biomolecules like proteins and facilitating their functions. Their structures and structural responses to physiologically relevant interactions (i.e. with membrane proteins) provide key information for understanding biophysical mechanisms. Hence, there is a crucial need of methods to understand the effects of membrane host molecules on the lipid bilayer structure. Here, a purely experimental method is presented for obtaining the absolute scattering length density profile and the area per lipid of liposomal bilayers, by aiding the analysis of small-angle X-ray scattering (SAXS) data with the volume of bare headgroups obtained from grazing-incidence X-ray off-specular scattering (GIXOS) data of monolayers of the same model membrane lipid composition. The GIXOS data experimentally demonstrate that the variation of the bare headgroup volume upon change in lipid packing density is small enough to allow its usage as a reference value without knowing the lipid packing stage in a bilayer. This approach also has the advantage that the reference volume is obtained in the same aqueous environment as used for the model membrane bilayers. The validity of this method is demonstrated using several typical membrane compositions, as well as one example of a phospholipid membrane with an incorporated transmembrane peptide. This methodology allows us to obtain absolute scale rather than relative scale values using solely X-ray-based instrumentation, retaining a similar resolution to SAXS experiments. The method presented has high potential for understanding the structural effects of membrane proteins on the biomembrane structure.enHarvey, R.D.Bello, G.Kikhney, A.G.Torres, J.Surya, W.Wölk, C.Shen, C.Absolute scattering length density profile of liposome bilayers obtained by SAXS combined with GIXOS: a tool to determine model biomembrane structure2023-10-20SMALL-ANGLE X-RAY SCATTERING; SAXS; GRAZING-INCIDENCE X-RAY OFF-SPECULAR SCATTERING; GIXOS; ASYMMETRIC LIPID BILAYERS; SCATTERING LENGTH DENSITY; ABSOLUTE SLDdoi:10.1107/S1600576723008439urn:issn:1600-5767A purely experimental method to determine absolute scales from small-angle X-ray scattering (SAXS) data of lipid bilayers with the aid of grazing-incidence X-ray off-specular scattering (GIXOS) data from lipid monolayers at the air–water interface is presented.https://creativecommons.org/licenses/by/4.0/text/html16391600-57671600-5767med@iucr.org6https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyDecember 202356research papers2023-10-201649New features of the RootProf program for model-free analysis of unidimensional profiles
http://scripts.iucr.org/cgi-bin/paper?vb5057
The RootProf computer program applies multivariate model-free analysis to crystallographic data and to any x, y experimental data in general. It has been enhanced with several new features, including a graphical user interface, multithreading implementation and additional pre-processing options. The program also includes novel qualitative analysis methods, such as semiquantitative estimates derived from principal component analysis (PCA) and restrained PCA to extract the diffraction signal from active atoms. Additional quantitative analysis methods have been included, involving the combination of different datasets or the application of the standard addition method as well as tools for crystallinity analysis, kinetic analysis and extraction of free crystal cell parameters from a pair distribution function profile. The ROOT data analysis framework supports the program and can be installed on the current major platforms such as Windows, Linux and Mac OSX with detailed user documentation included. Applications of the new developments are presented and discussed in the paper, and related command files are provided as supporting information.International Union of CrystallographytextThe RootProf computer program applies multivariate model-free analysis to crystallographic data and to any x, y experimental data in general. It has been enhanced with several new features, including a graphical user interface, multithreading implementation and additional pre-processing options. The program also includes novel qualitative analysis methods, such as semiquantitative estimates derived from principal component analysis (PCA) and restrained PCA to extract the diffraction signal from active atoms. Additional quantitative analysis methods have been included, involving the combination of different datasets or the application of the standard addition method as well as tools for crystallinity analysis, kinetic analysis and extraction of free crystal cell parameters from a pair distribution function profile. The ROOT data analysis framework supports the program and can be installed on the current major platforms such as Windows, Linux and Mac OSX with detailed user documentation included. Applications of the new developments are presented and discussed in the paper, and related command files are provided as supporting information.enMazzone, A.Lopresti, M.Belviso, B.D.Caliandro, R.New features of the RootProf program for model-free analysis of unidimensional profiles2023-10-20MULTIVARIATE ANALYSIS; DATA ANALYSIS; X-RAY POWDER DIFFRACTION; PAIR DISTRIBUTION FUNCTIONS; IN SITU EXPERIMENTSdoi:10.1107/S1600576723008348urn:issn:1600-5767New features of the RootProf program for model-free analysis of unidimensional profiles are presented and discussed.https://creativecommons.org/licenses/by/4.0/text/htmlhttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography6med@iucr.org1600-57671600-5767184118542023-10-2056computer programsDecember 2023The human factor: results of a small-angle scattering data analysis round robin
http://scripts.iucr.org/cgi-bin/paper?tu5042
A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population mean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed.International Union of CrystallographytextA round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population mean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed.enPauw, B.R.Smales, G.J.Anker, A.S.Annadurai, V.Balazs, D.M.Bienert, R.Bouwman, W.G.Breßler, I.Breternitz, J.Brok, E.S.Bryant, G.Clulow, A.J.Crater, E.R.De Geuser, F.Del Giudice, A.Deumer, J.Disch, S.Dutt, S.Frank, K.Fratini, E.Garcia, P.R.A.F.Gilbert, E.P.Hahn, M.B.Hallett, J.Hohenschutz, M.Hollamby, M.Huband, S.Ilavsky, J.Jochum, J.K.Juelsholt, M.Mansel, B.W.Penttilä, P.Pittkowski, R.K.Portale, G.Pozzo, L.D.Rochels, L.Rosalie, J.M.Saloga, P.E.J.Seibt, S.Smith, A.J.Smith, G.N.Spiering, G.A.Stawski, T.M.Taché, O.Thünemann, A.F.Toth, K.Whitten, A.E.Wuttke, J.The human factor: results of a small-angle scattering data analysis round robin2023-10-31ROUND ROBINS; DATA ANALYSIS; SMALL-ANGLE SCATTERING; NANOMATERIALS; INTERLABORATORY COMPARABILITY; NANOSTRUCTURE QUANTIFICATIONdoi:10.1107/S1600576723008324urn:issn:1600-5767A data-analysis round robin was performed using four real-world datasets to quantify the role of the human factor in analysis; the 46 responses show that the analyses by different researchers and laboratories may not be directly comparable, with large reporting inconsistencies in distribution widths and volume fractions. Several underlying causes for these inconsistencies are highlighted that can be addressed by the community.https://creativecommons.org/licenses/by/4.0/text/htmlDecember 202356research papers16292023-10-311600-57671618med@iucr.org1600-57676https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyTwinning and homoepitaxy cooperation in the already rich growth morphology of CaCO3 polymorphs. I. Aragonite
http://scripts.iucr.org/cgi-bin/paper?gj5306
Calcite and aragonite are the two most abundant among the CaCO3 polymorphs and are also well known for their rich morphology and habit, to which twinning relevantly contributes. Moreover, the calcite → aragonite transformation has been debated for a long time, even though the homo-epitaxies occurring within each polymorph have been overlooked, to date, from both experimental and theoretical points of view. Twinning is common and unfortunately can be deceptive as it can be mistaken for homo-epitaxy, thus leading to confusion regarding the growth mechanisms of many crystal aggregates. Here, experimental and theoretical studies were carried out to investigate the twinning and homo-epitaxy that operate in aragonite: (i) the connection between twinning and homo-epitaxy for contact and penetration aggregates made by the lateral {010} and {110} aragonite forms; (ii) the homo-epitaxial relationships among the {001} pinacoid and both the {010} pinacoid and the prismatic {110} aragonite forms. This work attempts to provide a new approach to monitoring the growth mechanisms of aragonite in cases where it is obtained not as a single crystal but as an aggregate. An analogous problem will be explored in our forthcoming work on calcite.International Union of CrystallographytextCalcite and aragonite are the two most abundant among the CaCO3 polymorphs and are also well known for their rich morphology and habit, to which twinning relevantly contributes. Moreover, the calcite → aragonite transformation has been debated for a long time, even though the homo-epitaxies occurring within each polymorph have been overlooked, to date, from both experimental and theoretical points of view. Twinning is common and unfortunately can be deceptive as it can be mistaken for homo-epitaxy, thus leading to confusion regarding the growth mechanisms of many crystal aggregates. Here, experimental and theoretical studies were carried out to investigate the twinning and homo-epitaxy that operate in aragonite: (i) the connection between twinning and homo-epitaxy for contact and penetration aggregates made by the lateral {010} and {110} aragonite forms; (ii) the homo-epitaxial relationships among the {001} pinacoid and both the {010} pinacoid and the prismatic {110} aragonite forms. This work attempts to provide a new approach to monitoring the growth mechanisms of aragonite in cases where it is obtained not as a single crystal but as an aggregate. An analogous problem will be explored in our forthcoming work on calcite.enAquilano, D.Bruno, M.Ghignone, S.Pastero, L.Twinning and homoepitaxy cooperation in the already rich growth morphology of CaCO3 polymorphs. I. Aragonite2023-10-20ARAGONITE; TWINNING; HOMO-EPITAXY; GROWTH MORPHOLOGYdoi:10.1107/S1600576723008208urn:issn:1600-5767The twinning and homo-epitaxy that operate in aragonite have been investigated by experimental and theoretical studies.https://creativecommons.org/licenses/by/4.0/text/html16301600-57671600-5767med@iucr.org6https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyDecember 202356research papers2023-10-201638Upgraded LauePt4 for rapid recognition and fitting of Laue patterns from crystals with unknown orientations
http://scripts.iucr.org/cgi-bin/paper?iu5045
The LauePt program is a popular and easy-to-use crystallography tool for indexing and simulating X-ray Laue patterns, but its previous versions lack search functions for recognizing Laue patterns taken from crystals with unknown orientations. To overcome this obstacle, a major upgrade of the program, called LauePt4, is presented with three robust search schemes implemented: (i) crystal rotation along a single diffraction vector, (ii) a look-up method to search for reflection pairs matching the interplanar angle of two selected diffraction spots, and (iii) a more efficient look-up scheme to search for reflection triplets matching three interplanar angles. Extensive tests show that all these schemes, together with the convenient graphical user interfaces and highly optimized computing algorithms, are reliable and powerful for recognizing and fitting Laue patterns of any crystal taken under any diffraction geometry.International Union of CrystallographytextThe LauePt program is a popular and easy-to-use crystallography tool for indexing and simulating X-ray Laue patterns, but its previous versions lack search functions for recognizing Laue patterns taken from crystals with unknown orientations. To overcome this obstacle, a major upgrade of the program, called LauePt4, is presented with three robust search schemes implemented: (i) crystal rotation along a single diffraction vector, (ii) a look-up method to search for reflection pairs matching the interplanar angle of two selected diffraction spots, and (iii) a more efficient look-up scheme to search for reflection triplets matching three interplanar angles. Extensive tests show that all these schemes, together with the convenient graphical user interfaces and highly optimized computing algorithms, are reliable and powerful for recognizing and fitting Laue patterns of any crystal taken under any diffraction geometry.enHuang, V.W.Liu, Y.Raghothamachar, B.Dudley, M.Upgraded LauePt4 for rapid recognition and fitting of Laue patterns from crystals with unknown orientations2023-09-27LAUE DIFFRACTION; LAUEPT4; X-RAY CRYSTALLOGRAPHY; INDEXINGdoi:10.1107/S1600576723007926urn:issn:1600-5767An upgrade is presented to the popular LauePt program for indexing and simulating X-ray Laue patterns. The upgraded program allows for recognizing and fitting Laue patterns of any crystal type recorded under any diffraction geometry.https://creativecommons.org/licenses/by/4.0/text/html5https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-57671610med@iucr.org1600-576756computer programs16152023-09-27October 2023Simultaneous SANS/FTIR measurement system incorporating the ATR sampling method
http://scripts.iucr.org/cgi-bin/paper?tu5039
Small-angle neutron scattering (SANS) is widely used as a powerful technique to study the higher-order structure of soft matter. To increase the reliability of SANS profile analysis for complex multi-component systems, combining different types of structural information obtained by other methods is desirable. A simultaneous measurement system combining SANS and Fourier transform infrared (FTIR) spectroscopy meets this objective. It is beneficial for targets where matching the timing of structural changes between experiments is difficult, but the issue is that samples suitable for SANS are too thick for the typical transmission FTIR method. To overcome this problem, a new simultaneous measurement system that employs the attenuated total reflectance (ART) sampling method for FTIR spectroscopy has been developed.International Union of CrystallographytextSmall-angle neutron scattering (SANS) is widely used as a powerful technique to study the higher-order structure of soft matter. To increase the reliability of SANS profile analysis for complex multi-component systems, combining different types of structural information obtained by other methods is desirable. A simultaneous measurement system combining SANS and Fourier transform infrared (FTIR) spectroscopy meets this objective. It is beneficial for targets where matching the timing of structural changes between experiments is difficult, but the issue is that samples suitable for SANS are too thick for the typical transmission FTIR method. To overcome this problem, a new simultaneous measurement system that employs the attenuated total reflectance (ART) sampling method for FTIR spectroscopy has been developed.enKaneko, F.Radulescu, A.Nakagawa, H.Simultaneous SANS/FTIR measurement system incorporating the ATR sampling method2023-09-27SMALL-ANGLE NEUTRON SCATTERING; SANS; FOURIER TRANSFORM INFRARED SPECTROSCOPY; FTIR; SIMULTANEOUS MEASUREMENT; ATTENUATED TOTAL REFLECTANCE; ATRdoi:10.1107/S1600576723007744urn:issn:1600-5767A simultaneous small-angle neutron scattering (SANS) and infrared absorption measurement system using the attenuated total reflection (ATF) sampling method for Fourier transform infrared (FTIR) spectroscopy has been developed to handle samples with large infrared absorption. This system allows each measurement to be performed under appropriate conditions.https://creativecommons.org/licenses/by/4.0/text/html15272023-09-27research papers56October 2023Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/5med@iucr.org1600-57671600-57671522Explainable machine learning for diffraction patterns
http://scripts.iucr.org/cgi-bin/paper?te5112
Serial crystallography experiments at X-ray free-electron laser facilities produce massive amounts of data but only a fraction of these data are useful for downstream analysis. Thus, it is essential to differentiate between acceptable and unacceptable data, generally known as `hit' and `miss', respectively. Image classification methods from artificial intelligence, or more specifically convolutional neural networks (CNNs), classify the data into hit and miss categories in order to achieve data reduction. The quantitative performance established in previous work indicates that CNNs successfully classify serial crystallography data into desired categories [Ke, Brewster, Yu, Ushizima, Yang & Sauter (2018). J. Synchrotron Rad. 25, 655–670], but no qualitative evidence on the internal workings of these networks has been provided. For example, there are no visualization methods that highlight the features contributing to a specific prediction while classifying data in serial crystallography experiments. Therefore, existing deep learning methods, including CNNs classifying serial crystallography data, are like a `black box'. To this end, presented here is a qualitative study to unpack the internal workings of CNNs with the aim of visualizing information in the fundamental blocks of a standard network with serial crystallography data. The region(s) or part(s) of an image that mostly contribute to a hit or miss prediction are visualized.International Union of CrystallographytextSerial crystallography experiments at X-ray free-electron laser facilities produce massive amounts of data but only a fraction of these data are useful for downstream analysis. Thus, it is essential to differentiate between acceptable and unacceptable data, generally known as `hit' and `miss', respectively. Image classification methods from artificial intelligence, or more specifically convolutional neural networks (CNNs), classify the data into hit and miss categories in order to achieve data reduction. The quantitative performance established in previous work indicates that CNNs successfully classify serial crystallography data into desired categories [Ke, Brewster, Yu, Ushizima, Yang & Sauter (2018). J. Synchrotron Rad. 25, 655–670], but no qualitative evidence on the internal workings of these networks has been provided. For example, there are no visualization methods that highlight the features contributing to a specific prediction while classifying data in serial crystallography experiments. Therefore, existing deep learning methods, including CNNs classifying serial crystallography data, are like a `black box'. To this end, presented here is a qualitative study to unpack the internal workings of CNNs with the aim of visualizing information in the fundamental blocks of a standard network with serial crystallography data. The region(s) or part(s) of an image that mostly contribute to a hit or miss prediction are visualized.enNawaz, S.Rahmani, V.Pennicard, D.Setty, S.P.R.Klaudel, B.Graafsma, H.Explainable machine learning for diffraction patterns2023-09-20EXPLAINABLE MACHINE LEARNING; GRADIENT-WEIGHTED CLASS ACTIVATION MAPPING; GRAD-CAM; VISUALIZATION OF REPRESENTATIONSdoi:10.1107/S1600576723007446urn:issn:1600-5767This article describes a qualitative study to unpack the internal workings of convolutional neural networks with the aim of visualizing information in the fundamental blocks of a standard network with serial crystallography data. Moreover, the study highlights region(s) or part(s) of an image that mostly contribute to a hit or miss prediction.https://creativecommons.org/licenses/by/4.0/text/html14941600-57671600-5767med@iucr.org5https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyOctober 202356research papers2023-09-201504Graphical reduction and analysis small-angle neutron scattering program: GRASP
http://scripts.iucr.org/cgi-bin/paper?jl5070
GRASP is a scientific software application designed for the graphical inspection, reduction and analysis of multidetector data produced by the small-angle neutron scattering (SANS) instruments at the Institut Laue–Langevin and other neutron sources around the world. The first developments of GRASP began more than 20 years ago and were written in MATLAB, allowing rapid development of scientific code, with much of the data handling, matrix manipulation, mathematical tools, user interface and graphical tools integrated at a high level in the underlying MATLAB platform. By their very nature, multidimensional data are often best appreciated in graphical form. GRASP deals with many of the diverse requirements for data reduction and analysis of SANS data using a general set of tools and reduction algorithms suited to 2D multidetector data. A further fundamental architectural inclusion is a third dimension of data manipulation, thereby easily allowing parametric analysis and cross referencing of series data such as composition, kinetic measurements, temperature, magnetic field, angle or time of flight, often considered as a single `measurement'. This article serves as a reference document for users of the software, and outlines the architecture and strategy of the program. An overview of some of the features, capabilities, peripheral user modules and neutron scattering tools is presented.International Union of CrystallographytextGRASP is a scientific software application designed for the graphical inspection, reduction and analysis of multidetector data produced by the small-angle neutron scattering (SANS) instruments at the Institut Laue–Langevin and other neutron sources around the world. The first developments of GRASP began more than 20 years ago and were written in MATLAB, allowing rapid development of scientific code, with much of the data handling, matrix manipulation, mathematical tools, user interface and graphical tools integrated at a high level in the underlying MATLAB platform. By their very nature, multidimensional data are often best appreciated in graphical form. GRASP deals with many of the diverse requirements for data reduction and analysis of SANS data using a general set of tools and reduction algorithms suited to 2D multidetector data. A further fundamental architectural inclusion is a third dimension of data manipulation, thereby easily allowing parametric analysis and cross referencing of series data such as composition, kinetic measurements, temperature, magnetic field, angle or time of flight, often considered as a single `measurement'. This article serves as a reference document for users of the software, and outlines the architecture and strategy of the program. An overview of some of the features, capabilities, peripheral user modules and neutron scattering tools is presented.enDewhurst, C.D.Graphical reduction and analysis small-angle neutron scattering program: GRASP2023-09-20SMALL-ANGLE NEUTRON SCATTERING; SOFTWARE; DATA TREATMENT; GRASP; MATLAB; MULTIDETECTOR DATAdoi:10.1107/S1600576723007379urn:issn:1600-5767This article describes the GRASP software package, designed for the graphical inspection, reduction and analysis of multidetector data produced by the small-angle neutron scattering instruments at the Institut Laue–Langevin and other neutron sources.https://creativecommons.org/licenses/by/4.0/text/htmlOctober 202356computer programs16092023-09-201600-57671595med@iucr.org1600-57675Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Indium Kα radiation from a MetalJet X-ray source: comparison of the Eiger2 CdTe and Photon III detectors
http://scripts.iucr.org/cgi-bin/paper?nb5354
The MetalJet source makes available new Kα radiation wavelengths for use in X-ray diffraction experiments. The purpose of this paper is to demonstrate the application of indium Kα radiation in independent-atom model refinement, as well as approaches using aspherical atomic form factors. The results vary greatly depending on the detector employed, as the energy cut-off of the Eiger2 CdTe provides a solution to a unique energy contamination problem of the MetalJet In radiation, which the Photon III detector cannot provide.International Union of CrystallographytextThe MetalJet source makes available new Kα radiation wavelengths for use in X-ray diffraction experiments. The purpose of this paper is to demonstrate the application of indium Kα radiation in independent-atom model refinement, as well as approaches using aspherical atomic form factors. The results vary greatly depending on the detector employed, as the energy cut-off of the Eiger2 CdTe provides a solution to a unique energy contamination problem of the MetalJet In radiation, which the Photon III detector cannot provide.enRuth, P.N.Graw, N.Ernemann, T.Herbst-Irmer, R.Stalke, D.Indium Kα radiation from a MetalJet X-ray source: comparison of the Eiger2 CdTe and Photon III detectors2023-09-05IN RADIATION; INDEPENDENT-ATOM MODEL; MULTIPOLE MODEL; HIRSHFELD ATOM REFINEMENT; METALJET; DETECTORSdoi:10.1107/S1600576723007215urn:issn:1600-5767This paper communicates the first application of MetalJet In Kα radiation to single-crystal X-ray crystallography and evaluates two different detectors, the Bruker Photon III and the Dectris Eiger2 CdTe, for usage in spherical and aspherical structural models.https://creativecommons.org/licenses/by/4.0/text/htmlOctober 202356research papers13292023-09-051600-57671322med@iucr.org1600-57675https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyIndium Kα radiation from a MetalJet X-ray source: the long way to a successful charge-density investigation
http://scripts.iucr.org/cgi-bin/paper?nb5353
The MetalJet X-ray source provides indium Kα radiation with a wavelength even shorter than Ag radiation. This paper reports on problematic spectral impurities and presents possible countermeasures so that collection of data with excellent quality up to a high resolution is possible. It is demonstrated that these data can be used in the refinement of a multipole model, the results of which are used for a topological analysis to assess the bonding situation in a sulfur ylide compound.International Union of CrystallographytextThe MetalJet X-ray source provides indium Kα radiation with a wavelength even shorter than Ag radiation. This paper reports on problematic spectral impurities and presents possible countermeasures so that collection of data with excellent quality up to a high resolution is possible. It is demonstrated that these data can be used in the refinement of a multipole model, the results of which are used for a topological analysis to assess the bonding situation in a sulfur ylide compound.enGraw, N.Ruth, P.N.Ernemann, T.Herbst-Irmer, R.Stalke, D.Indium Kα radiation from a MetalJet X-ray source: the long way to a successful charge-density investigation2023-09-05INDIUM RADIATION; CHARGE DENSITY; MULTIPOLE MODEL; METALJET; YLIDE COMPOUNDSdoi:10.1107/S1600576723007203urn:issn:1600-5767Enabling of an In Kα MetalJet source is described, culminating in the first charge-density investigation.https://creativecommons.org/licenses/by/4.0/text/html1600-57671315med@iucr.org1600-57675https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyOctober 202356research papers13212023-09-05Remote and automated high-throughput powder diffraction measurements enabled by a robotic sample changer at SSRL beamline 2-1
http://scripts.iucr.org/cgi-bin/paper?vb5062
The general-purpose powder diffractometer beamline (BL2-1) at the Stanford Synchrotron Radiation Lightsource (SSRL) is described. The evolution of design and performance of BL2-1 are presented, in addition to current operating specifications, applications and measurement capabilities. Recent developments involve a robotic sample changer enabling high-throughput X-ray diffraction measurements, applicable to mail-in and remote operations. In situ and operando capabilities to measure samples with different form factors (e.g. capillary, flat plate or thin film, and transmission) and under variable experimental conditions are discussed. Several example datasets and accompanying Rietveld refinements are presented.International Union of CrystallographytextThe general-purpose powder diffractometer beamline (BL2-1) at the Stanford Synchrotron Radiation Lightsource (SSRL) is described. The evolution of design and performance of BL2-1 are presented, in addition to current operating specifications, applications and measurement capabilities. Recent developments involve a robotic sample changer enabling high-throughput X-ray diffraction measurements, applicable to mail-in and remote operations. In situ and operando capabilities to measure samples with different form factors (e.g. capillary, flat plate or thin film, and transmission) and under variable experimental conditions are discussed. Several example datasets and accompanying Rietveld refinements are presented.enStone, K.H.Cosby, M.R.Strange, N.A.Thampy, V.Walroth, R.C.Troxel Jr, C.Remote and automated high-throughput powder diffraction measurements enabled by a robotic sample changer at SSRL beamline 2-12023-09-20POWDER DIFFRACTION; SYNCHROTRON BEAMLINES; AUTOMATED MEASUREMENT; ROBOTIC SAMPLE CHANGERSdoi:10.1107/S1600576723007148urn:issn:1600-5767The general-purpose powder diffraction beamline at Stanford Synchrotron Radiation Lightsource (SSRL) is described. The latest developments at the beamline, including the implementation of a robotic sample changer for mail-in operations, are discussed and several datasets measured from this setup are included for reference.https://creativecommons.org/licenses/by/4.0/text/html1600-57671480med@iucr.org1600-57675https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyOctober 202356research papers14842023-09-20XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO
http://scripts.iucr.org/cgi-bin/paper?yr5110
XDSGUI is a lightweight graphical user interface (GUI) for the XDS, SHELX and ARCIMBOLDO program packages that serves both novice and experienced users in obtaining optimal processing and phasing results for X-ray, neutron and electron diffraction data. The design of the program enables data processing and phasing without command line usage, and supports advanced command flows in a simple user-modifiable and user-extensible way. The GUI supplies graphical information based on the tabular log output of the programs, which is more intuitive, comprehensible and efficient than text output can be.International Union of CrystallographytextXDSGUI is a lightweight graphical user interface (GUI) for the XDS, SHELX and ARCIMBOLDO program packages that serves both novice and experienced users in obtaining optimal processing and phasing results for X-ray, neutron and electron diffraction data. The design of the program enables data processing and phasing without command line usage, and supports advanced command flows in a simple user-modifiable and user-extensible way. The GUI supplies graphical information based on the tabular log output of the programs, which is more intuitive, comprehensible and efficient than text output can be.enBrehm, W.Triviño, J.Krahn, J.M.Usón, I.Diederichs, K.XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO2023-09-05X-RAY DIFFRACTION; NEUTRON DIFFRACTION; ELECTRON DIFFRACTION; DATA PROCESSING; GRAPHICAL USER INTERFACES; PHASING; XDS; ARCIMBOLDO; SHELXdoi:10.1107/S1600576723007057urn:issn:1600-5767A customizable stateless graphical user interface simplifies the processing, analysis and phasing of diffraction data.https://creativecommons.org/licenses/by/4.0/text/htmlOctober 202356computer programs15942023-09-051600-57671585med@iucr.org1600-57675https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyRevisiting the structures and phase transitions of Ba2NaNb5O15
http://scripts.iucr.org/cgi-bin/paper?iu5044
The room-temperature and low-temperature structure(s) of Ba2NaNb5O15 (BNN) have been debated since the structure was proposed in the 1960s. This work revisits the structures and phase transitions of BNN, combining high-resolution X-ray and neutron powder diffraction with density functional theory calculations. Temperature-dependent high-resolution X-ray powder diffraction patterns are collected from 4 to 918 K, and sequential batch Rietveld refinement using a symmetry mode approach to describe the structure is used to extract the main structural changes as a function of temperature. The data show that the average structure of BNN is best described by the Ama2 space group, and no other structural phase transitions were observed below the ferroelastic transition. The symmetry mode analysis, combining results from diffraction and density functional theory, shows significant octahedral tilting and corrugations of both the A1 and A2 sites along the c direction. A strong correlation between the spontaneous strain and the octahedral tilting was observed, and a potential connection with emerging microstructure at low temperatures is proposed, all enabled by the symmetry mode approach used in this work.International Union of CrystallographytextThe room-temperature and low-temperature structure(s) of Ba2NaNb5O15 (BNN) have been debated since the structure was proposed in the 1960s. This work revisits the structures and phase transitions of BNN, combining high-resolution X-ray and neutron powder diffraction with density functional theory calculations. Temperature-dependent high-resolution X-ray powder diffraction patterns are collected from 4 to 918 K, and sequential batch Rietveld refinement using a symmetry mode approach to describe the structure is used to extract the main structural changes as a function of temperature. The data show that the average structure of BNN is best described by the Ama2 space group, and no other structural phase transitions were observed below the ferroelastic transition. The symmetry mode analysis, combining results from diffraction and density functional theory, shows significant octahedral tilting and corrugations of both the A1 and A2 sites along the c direction. A strong correlation between the spontaneous strain and the octahedral tilting was observed, and a potential connection with emerging microstructure at low temperatures is proposed, all enabled by the symmetry mode approach used in this work.enGrendal, O.G.Evans, D.M.Aamlid, S.S.Revisiting the structures and phase transitions of Ba2NaNb5O152023-09-05BA2NANB5O15; POWDER DIFFRACTION; DENSITY FUNCTIONAL THEORY; DFT; STRUCTURE DETERMINATIONdoi:10.1107/S1600576723006969urn:issn:1600-5767Structural changes and phase transitions of ferroelectric Ba2NaNb5O15 are studied using high-resolution X-ray powder diffraction combined with neutron powder diffraction and density functional theory calculations.https://creativecommons.org/licenses/by/4.0/text/htmlresearch papers562023-09-051465October 20235Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/14561600-57671600-5767med@iucr.orgRetrieving the size distribution of SBA-15 mesopores from small-angle X-ray scattering data using a Monte Carlo method
http://scripts.iucr.org/cgi-bin/paper?jl5060
A Monte Carlo (MC) method was introduced into a state-of-the-art model used to analyse small-angle X-ray scattering (SAXS) data of SBA-15, an ordered mesoporous material with many applications. With this new procedure, referred to herein as the SBA-15+MC model, it is possible to retrieve the size distribution of the mesopores, D(r), in a free modelling approach. To achieve this, two main points were addressed: (i) based on previous implementations, the method was adapted to work with long core–shell cylinders; (ii) since the MC model requires longer processing times, strategies to speed up the calculations were developed, which included a simplified version of the original model used to analyse SAXS data of SBA-15 (referred to as the SBA-15 model) as well as the determination of several structural features from the SAXS curve prior to the fit. The new model was validated with simulated data and later used to fit experimental SAXS curves of SBA-15. The obtained results show that the SBA-15 model only works well because the mesopore size distribution of SBA-15 is narrow, whereas the new approach can be successfully used in cases where D(r) is wider and/or has a more complex profile, such as SBA-15 with expanded mesopores. Even though a specific SAXS example was chosen to prove the model, the strategies presented herein are general and suitable for inclusion in other models aimed at the analysis of SBA-15 and similar ordered mesoporous materials.International Union of CrystallographytextA Monte Carlo (MC) method was introduced into a state-of-the-art model used to analyse small-angle X-ray scattering (SAXS) data of SBA-15, an ordered mesoporous material with many applications. With this new procedure, referred to herein as the SBA-15+MC model, it is possible to retrieve the size distribution of the mesopores, D(r), in a free modelling approach. To achieve this, two main points were addressed: (i) based on previous implementations, the method was adapted to work with long core–shell cylinders; (ii) since the MC model requires longer processing times, strategies to speed up the calculations were developed, which included a simplified version of the original model used to analyse SAXS data of SBA-15 (referred to as the SBA-15 model) as well as the determination of several structural features from the SAXS curve prior to the fit. The new model was validated with simulated data and later used to fit experimental SAXS curves of SBA-15. The obtained results show that the SBA-15 model only works well because the mesopore size distribution of SBA-15 is narrow, whereas the new approach can be successfully used in cases where D(r) is wider and/or has a more complex profile, such as SBA-15 with expanded mesopores. Even though a specific SAXS example was chosen to prove the model, the strategies presented herein are general and suitable for inclusion in other models aimed at the analysis of SBA-15 and similar ordered mesoporous materials.enTan, X.Gerbelli, B.B.Fantini, M.C.A.Oliveira, C.L.P.Bordallo, H.N.Oseliero Filho, P.L.Retrieving the size distribution of SBA-15 mesopores from small-angle X-ray scattering data using a Monte Carlo method2023-09-01MONTE CARLO METHODS; SAXS; SMALL-ANGLE X-RAY SCATTERING; DATA MODELLING; SBA-15doi:10.1107/S160057672300691Xurn:issn:1600-5767The new model proposed in this work allows retrieval of the mesopore size distribution of SBA-15 (and similar ordered mesoporous materials) from small-angle X-ray scattering data using a free modelling approach. According to the obtained results, even more complex size distributions can be recovered, such as the case of SBA-15 with expanded mesopores.https://creativecommons.org/licenses/by/4.0/text/htmlOctober 202356research papers13912023-09-011600-57671381med@iucr.org1600-57675Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/The dependence of X-ray elastic constants with respect to the penetration depth
http://scripts.iucr.org/cgi-bin/paper?nb5357
X-ray diffraction techniques are widely used to estimate stresses within polycrystalline materials. The application of these techniques requires the knowledge of the X-ray elastic constants relating the lattice strains to the stress state. Different analytical methods have been proposed to evaluate the X-ray elastic constants from the single-crystal elastic constants. For a given material, such methods provide the bulk X-ray elastic constants but they do not consider the role of free surfaces. However, for many practical applications of X-ray diffraction techniques, the penetration depth of X-rays is the same order of magnitude as the grain size, which means that the influence of the free surface on X-ray elastic constants cannot be excluded. In the present work, a numerical procedure is proposed to evaluate the surface and bulk X-ray elastic constants of polycrystalline materials. While the former correspond to the situation where the penetration is infinitely small in comparison with the grain size, the latter are representative of an infinite penetration depth with no free-surface effect. According to numerical results, the difference between surface and bulk X-ray elastic constants is important for strongly anisotropic crystals. Also, it is possible to propose a relation that allows evaluating X-ray elastic constants as a function of the ratio between the penetration depth and the average grain size. The corresponding parameters of such a relation are provided here for many engineering materials.International Union of CrystallographytextX-ray diffraction techniques are widely used to estimate stresses within polycrystalline materials. The application of these techniques requires the knowledge of the X-ray elastic constants relating the lattice strains to the stress state. Different analytical methods have been proposed to evaluate the X-ray elastic constants from the single-crystal elastic constants. For a given material, such methods provide the bulk X-ray elastic constants but they do not consider the role of free surfaces. However, for many practical applications of X-ray diffraction techniques, the penetration depth of X-rays is the same order of magnitude as the grain size, which means that the influence of the free surface on X-ray elastic constants cannot be excluded. In the present work, a numerical procedure is proposed to evaluate the surface and bulk X-ray elastic constants of polycrystalline materials. While the former correspond to the situation where the penetration is infinitely small in comparison with the grain size, the latter are representative of an infinite penetration depth with no free-surface effect. According to numerical results, the difference between surface and bulk X-ray elastic constants is important for strongly anisotropic crystals. Also, it is possible to propose a relation that allows evaluating X-ray elastic constants as a function of the ratio between the penetration depth and the average grain size. The corresponding parameters of such a relation are provided here for many engineering materials.enMareau, C.The dependence of X-ray elastic constants with respect to the penetration depth2023-09-01X-RAY DIFFRACTION; X-RAY ELASTIC CONSTANTS; STRESS ANALYSIS; PENETRATION DEPTHS; ANISOTROPY; POLYCRYSTALLINE MATERIALS; FREE SURFACESdoi:10.1107/S1600576723006878urn:issn:1600-5767A numerical method that provides the surface and bulk X-ray elastic constants of non-textured polycrystalline materials is proposed. The results obtained for engineering materials with such a method indicate that, for crystalline materials with significant elastic anisotropy, the X-ray elastic constants depend on the penetration-depth-to-grain-size ratio.https://creativecommons.org/licenses/by/4.0/text/htmlOctober 202356research papers2023-09-01145514461600-57671600-5767med@iucr.org5Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Remote laboratory training for high school students: grocery store based hands-on project in protein crystallography
http://scripts.iucr.org/cgi-bin/paper?gj5304
The COVID-19 pandemic measures forced students to stay home and confined them to remote learning. This had a large impact on laboratory experiments, which are often impossible to complete from home. This article is a resource for instructors/educators to introduce the topic of structural biology and crystallographic methods. The main focus is to describe a hands-on crystallization laboratory exercise that can be carried out remotely at home with safe household products. X-ray crystallography is a vital technique for determining protein structure and function. This information can be used to understand fundamental biological processes and to help in the design of life-saving medications. Here, a method was developed to teach crystallography using reagents and equipment that can be found in grocery stores. The steps involved in a crystallography experiment are detailed with links and references to additional resources.International Union of CrystallographytextThe COVID-19 pandemic measures forced students to stay home and confined them to remote learning. This had a large impact on laboratory experiments, which are often impossible to complete from home. This article is a resource for instructors/educators to introduce the topic of structural biology and crystallographic methods. The main focus is to describe a hands-on crystallization laboratory exercise that can be carried out remotely at home with safe household products. X-ray crystallography is a vital technique for determining protein structure and function. This information can be used to understand fundamental biological processes and to help in the design of life-saving medications. Here, a method was developed to teach crystallography using reagents and equipment that can be found in grocery stores. The steps involved in a crystallography experiment are detailed with links and references to additional resources.enFox, A.L.Teteris, A.R.Mathews, I.I.Remote laboratory training for high school students: grocery store based hands-on project in protein crystallography2023-08-18REMOTE LEARNING; HIGH SCHOOL PROJECTS; PROTEIN CRYSTALLOGRAPHY; PROTEIN FUNCTION; DRUG DESIGNdoi:10.1107/S1600576723006805urn:issn:1600-5767This paper describes a hands-on crystallization laboratory exercise that can be carried out remotely at home with safe household products. The project meets some of the US Next Generation Science Standards (NGSS) goals for K-12 education, including teaching scientific practices that reflect those used by professional scientists.text/html1600-5767med@iucr.org15571600-5767Journal of Applied Crystallography5October 20232023-08-181568teaching and education56Escape our Lab: creating an escape room game in the field of materials science and crystallography
http://scripts.iucr.org/cgi-bin/paper?dv5005
Although many challenges of the 21st century need solutions which are directly connected with the development of new technologies, the preferences of prospective students in Germany are often far from mathematics, physics and chemistry. Moreover, the acceptance and recognition of new achievements in these disciplines are quite low in society, even if these achievements are the basis for the development of new technologies that positively affect daily life. As a part of a campaign intended to increase the number of students in the fields of materials science and materials technology (and related fields), the authors created an escape room focused on materials science and crystallography, which illustrates the approaches used by materials scientists and the beauty of crystallography. The fundamental features of the escape room, which are presented in this contribution, are its variability and the ability to inspire participants who have different backgrounds in physics, chemistry and/or materials science. By varying the level of difficulty and the game play duration, the escape room structure makes it possible to appeal to a broad audience, offer an authentic escape room experience and impart lasting knowledge through reflection after completion. The authors' experiences with the escape room and the feedback from the attendees are summarized at the end of the contribution.International Union of CrystallographytextAlthough many challenges of the 21st century need solutions which are directly connected with the development of new technologies, the preferences of prospective students in Germany are often far from mathematics, physics and chemistry. Moreover, the acceptance and recognition of new achievements in these disciplines are quite low in society, even if these achievements are the basis for the development of new technologies that positively affect daily life. As a part of a campaign intended to increase the number of students in the fields of materials science and materials technology (and related fields), the authors created an escape room focused on materials science and crystallography, which illustrates the approaches used by materials scientists and the beauty of crystallography. The fundamental features of the escape room, which are presented in this contribution, are its variability and the ability to inspire participants who have different backgrounds in physics, chemistry and/or materials science. By varying the level of difficulty and the game play duration, the escape room structure makes it possible to appeal to a broad audience, offer an authentic escape room experience and impart lasting knowledge through reflection after completion. The authors' experiences with the escape room and the feedback from the attendees are summarized at the end of the contribution.enSchimpf, C.Lachmann, J.Wetzel, M.H.Fischer, P.D.B.Leineweber, A.Rafaja, D.Escape our Lab: creating an escape room game in the field of materials science and crystallography2023-08-18ESCAPE ROOMS; STEM EDUCATIONdoi:10.1107/S1600576723006714urn:issn:1600-5767A variable educational exit game is presented to stimulate interest of young people in STEM-related fields. The game addresses scientific content from crystallography, materials science and related fields and is suitable for a wide range of player groups, such as secondary school pupils, undergraduate students and teachers.https://creativecommons.org/licenses/by/4.0/text/htmlOctober 20232023-08-181556teaching and education561600-5767med@iucr.org15441600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography5Shear influence on colloidal cluster growth: a SANS and USANS study
http://scripts.iucr.org/cgi-bin/paper?uu5009
This study examines the time evolution of silica/water clusters where the formation of a gel network from unitary silica particles is interrupted by a simple Couette shear field. The aim is to enable the general understanding of this simple system by examining the microscopic basis for the changes in viscosity by providing structural inputs from small-angle scattering for a simple theoretical model. The experimental system is an 8.3 nm particle silica solution (Ludox) where the gelation has been initiated by lowering the pH in a Couette cell providing a constant shear rate of 250 s−1. A unified small-angle neutron scattering (SANS) and ultra-small-angle neutron scattering (USANS) procedure is described to measure the scattered intensity in a wavevector range of 3 × 10−4 ≤ q (nm−1) ≤ 3.1 × 10−1, probing structural changes over a broad range of length scales from the nanometre to the micrometre. Scattering data provide a new means of better understanding the behaviour of colloidal clusters when subjected to an external applied shear over a continuous time sequence after gel initiation; a fit of the time-dependent scattered intensity leads to an estimation of the cluster's effective volume fraction and size as a function of time. A reductionist theoretical basis is described to predict the time-dependent viscosity behaviour of the sheared colloidal suspension gel-initiated cluster growth from the volume fraction of the clusters.International Union of CrystallographytextThis study examines the time evolution of silica/water clusters where the formation of a gel network from unitary silica particles is interrupted by a simple Couette shear field. The aim is to enable the general understanding of this simple system by examining the microscopic basis for the changes in viscosity by providing structural inputs from small-angle scattering for a simple theoretical model. The experimental system is an 8.3 nm particle silica solution (Ludox) where the gelation has been initiated by lowering the pH in a Couette cell providing a constant shear rate of 250 s−1. A unified small-angle neutron scattering (SANS) and ultra-small-angle neutron scattering (USANS) procedure is described to measure the scattered intensity in a wavevector range of 3 × 10−4 ≤ q (nm−1) ≤ 3.1 × 10−1, probing structural changes over a broad range of length scales from the nanometre to the micrometre. Scattering data provide a new means of better understanding the behaviour of colloidal clusters when subjected to an external applied shear over a continuous time sequence after gel initiation; a fit of the time-dependent scattered intensity leads to an estimation of the cluster's effective volume fraction and size as a function of time. A reductionist theoretical basis is described to predict the time-dependent viscosity behaviour of the sheared colloidal suspension gel-initiated cluster growth from the volume fraction of the clusters.enMuzny, C.de Campo, L.Sokolova, A.Garvey, C.J.Rehm, C.Hanley, H.Shear influence on colloidal cluster growth: a SANS and USANS study2023-08-25COLLOIDAL SILICA; RETARDED GELATION; APPLIED SHEAR; VISCOSITY; TIME-DEPENDENT PHENOMENA; SMALL-ANGLE NEUTRON SCATTERING; SANS; ULTRA-SMALL-ANGLE NEUTRON SCATTERING; USANS; MICROMETRE SCALE; STRUCTURE FACTOR DERIVATION; VOLUME FRACTIONdoi:10.1107/S1600576723006726urn:issn:1600-5767This study examines the time evolution of microscopic structure in a model industrial process, a sol of gel-initiated silica particles in a simple Couette shear field, using small-angle neutron scattering SANS) and ultra-small-angle neutron scattering (USANS) over a large range of scattering vector magnitudes/length scales. Comparison of the experimentally derived parameters with a simple theoretical model provides additional insight.https://creativecommons.org/licenses/by/4.0/text/htmlmed@iucr.org1600-57671600-57671371Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/5October 202313802023-08-25research papers56Strategy to simulate and fit 2D grazing-incidence small-angle X-ray scattering patterns of nanostructured thin films
http://scripts.iucr.org/cgi-bin/paper?ge5137
Grazing-incidence small-angle X-ray scattering (GISAXS) is a widely used method for the characterization of the nanostructure of supported thin films and enables time-resolved in situ measurements. The 2D scattering patterns contain detailed information about the nanostructures within the film and at its surface. However, this information is distorted not only by the reflection of the X-ray beam at the substrate–film interface and its refraction at the film surface but also by scattering of the substrate, the sample holder and other types of parasitic background scattering. In this work, a new, efficient strategy to simulate and fit 2D GISAXS patterns that explicitly includes these effects is introduced and demonstrated for (i) a model case nanostructured thin film on a substrate and (ii) experimental data from a microphase-separated block copolymer thin film. To make the protocol efficient, characteristic linecuts through the 2D GISAXS patterns, where the different contributions dominate, are analysed. The contributions of the substrate and the parasitic background scattering – which ideally are measured separately – are determined first and are used in the analysis of the 2D GISAXS patterns of the nanostructured, supported film. The nanostructures at the film surface and within the film are added step by step to the real-space model of the simulation, and their structural parameters are determined by minimizing the difference between simulated and experimental scattering patterns in the selected linecuts. Although in the present work the strategy is adapted for and tested with BornAgain, it can be easily used with other types of simulation software. The strategy is also applicable to grazing-incidence small-angle neutron scattering.International Union of CrystallographytextGrazing-incidence small-angle X-ray scattering (GISAXS) is a widely used method for the characterization of the nanostructure of supported thin films and enables time-resolved in situ measurements. The 2D scattering patterns contain detailed information about the nanostructures within the film and at its surface. However, this information is distorted not only by the reflection of the X-ray beam at the substrate–film interface and its refraction at the film surface but also by scattering of the substrate, the sample holder and other types of parasitic background scattering. In this work, a new, efficient strategy to simulate and fit 2D GISAXS patterns that explicitly includes these effects is introduced and demonstrated for (i) a model case nanostructured thin film on a substrate and (ii) experimental data from a microphase-separated block copolymer thin film. To make the protocol efficient, characteristic linecuts through the 2D GISAXS patterns, where the different contributions dominate, are analysed. The contributions of the substrate and the parasitic background scattering – which ideally are measured separately – are determined first and are used in the analysis of the 2D GISAXS patterns of the nanostructured, supported film. The nanostructures at the film surface and within the film are added step by step to the real-space model of the simulation, and their structural parameters are determined by minimizing the difference between simulated and experimental scattering patterns in the selected linecuts. Although in the present work the strategy is adapted for and tested with BornAgain, it can be easily used with other types of simulation software. The strategy is also applicable to grazing-incidence small-angle neutron scattering.enJung, F.A.Papadakis, C.M.Strategy to simulate and fit 2D grazing-incidence small-angle X-ray scattering patterns of nanostructured thin films2023-08-16GRAZING-INCIDENCE SMALL-ANGLE X-RAY SCATTERING; GISAXS; DISTORTED-WAVE BORN APPROXIMATION; NANOSTRUCTURED THIN FILMS; SIMULATIONS; DATA ANALYSISdoi:10.1107/S1600576723006520urn:issn:1600-5767A strategy to simulate and fit 2D grazing-incidence small-angle X-ray scattering patterns of supported, nanostructured soft-matter thin films using the distorted-wave Born approximation is introduced. The different scattering contributions of the nanostructure, surface roughness and background scattering are treated separately and are adjusted step by step. To minimize calculation efforts, 1D line cuts are chosen, in which the scattering is predominantly attributed to one of the contributions, and the parameters found are used in the subsequent steps. Hence, separate measurements of the bare substrate are beneficial.https://creativecommons.org/licenses/by/4.0/text/html1600-57671330med@iucr.org1600-57675https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyOctober 202356research papers13472023-08-16A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography
http://scripts.iucr.org/cgi-bin/paper?jt5069
Serial crystallography has emerged as an important tool for structural studies of integral membrane proteins. The ability to collect data from micrometre-sized weakly diffracting crystals at room temperature with minimal radiation damage has opened many new opportunities in time-resolved studies and drug discovery. However, the production of integral membrane protein microcrystals in lipidic cubic phase at the desired crystal density and quantity is challenging. This paper introduces VIALS (versatile approach to high-density microcrystals in lipidic cubic phase for serial crystallography), a simple, fast and efficient method for preparing hundreds of microlitres of high-density microcrystals suitable for serial X-ray diffraction experiments at both synchrotron and free-electron laser sources. The method is also of great benefit for rational structure-based drug design as it facilitates in situ crystal soaking and rapid determination of many co-crystal structures. Using the VIALS approach, room-temperature structures are reported of (i) the archaerhodopsin-3 protein in its dark-adapted state and 110 ns photocycle intermediate, determined to 2.2 and 1.7 Å, respectively, and (ii) the human A2A adenosine receptor in complex with two different ligands determined to a resolution of 3.5 Å.International Union of CrystallographytextSerial crystallography has emerged as an important tool for structural studies of integral membrane proteins. The ability to collect data from micrometre-sized weakly diffracting crystals at room temperature with minimal radiation damage has opened many new opportunities in time-resolved studies and drug discovery. However, the production of integral membrane protein microcrystals in lipidic cubic phase at the desired crystal density and quantity is challenging. This paper introduces VIALS (versatile approach to high-density microcrystals in lipidic cubic phase for serial crystallography), a simple, fast and efficient method for preparing hundreds of microlitres of high-density microcrystals suitable for serial X-ray diffraction experiments at both synchrotron and free-electron laser sources. The method is also of great benefit for rational structure-based drug design as it facilitates in situ crystal soaking and rapid determination of many co-crystal structures. Using the VIALS approach, room-temperature structures are reported of (i) the archaerhodopsin-3 protein in its dark-adapted state and 110 ns photocycle intermediate, determined to 2.2 and 1.7 Å, respectively, and (ii) the human A2A adenosine receptor in complex with two different ligands determined to a resolution of 3.5 Å.enBirch, J.Kwan, T.O.C.Judge, P.J.Axford, D.Aller, P.Butryn, A.Reis, R.I.Bada Juarez, J.F.Vinals, J.Owen, R.L.Nango, E.Tanaka, R.Tono, K.Joti, Y.Tanaka, T.Owada, S.Sugahara, M.Iwata, S.Orville, A.M.Watts, A.Moraes, I.A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography2023-08-18SERIAL CRYSTALLOGRAPHY; MEMBRANE PROTEINS; LIPIDIC CUBIC PHASE; ARCHAERHODOPSIN-3; A2A ADENOSINE RECEPTOR; STRUCTURE-BASED DRUG DESIGNdoi:10.1107/S1600576723006428urn:issn:1600-5767A versatile approach for the preparation of high-density membrane protein microcrystals in lipidic cubic phase for serial crystallography is described.https://creativecommons.org/licenses/by/4.0/text/htmlOctober 202356research papers13702023-08-181600-57671361med@iucr.org1600-57675Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Small-angle scattering from flat bilayers containing correlated scattering length density inhomogeneities
http://scripts.iucr.org/cgi-bin/paper?ge5136
Model lipid bilayers have been widely employed as a minimal system to investigate the structural properties of biological membranes by small-angle X-ray (SAXS) and neutron scattering (SANS) techniques. These have nanometre resolution and can give information regarding membrane thickness and scattering length densities (SLDs) of polar and apolar regions. However, biological membranes are complex systems containing different lipids and protein species, in which lipid domains can be dynamically assembled and disassembled. Therefore, SLD variations can occur within the biomembrane. In this work, a novel method has been developed to simulate SAXS and SANS profiles obtained from large unilamellar vesicles containing SLD inhomogeneities that are spatially correlated over the membrane surface. Such inhomogeneities are represented by cylindrical entities with equivalent SLDs. Stacking of bilayers is also included in the model, with no correlation between horizontal and vertical order. The model is applied to a lipid bilayer containing SLD inhomogeneities representing pores, lipid domains, and transmembrane, partially immersed and anchored proteins. It is demonstrated that all the structural information from the host lipid bilayer and from the SLD inhomogeneity can be consistently retrieved by a combined analysis of experimental SAXS and SANS data through the methodology proposed here.International Union of CrystallographytextModel lipid bilayers have been widely employed as a minimal system to investigate the structural properties of biological membranes by small-angle X-ray (SAXS) and neutron scattering (SANS) techniques. These have nanometre resolution and can give information regarding membrane thickness and scattering length densities (SLDs) of polar and apolar regions. However, biological membranes are complex systems containing different lipids and protein species, in which lipid domains can be dynamically assembled and disassembled. Therefore, SLD variations can occur within the biomembrane. In this work, a novel method has been developed to simulate SAXS and SANS profiles obtained from large unilamellar vesicles containing SLD inhomogeneities that are spatially correlated over the membrane surface. Such inhomogeneities are represented by cylindrical entities with equivalent SLDs. Stacking of bilayers is also included in the model, with no correlation between horizontal and vertical order. The model is applied to a lipid bilayer containing SLD inhomogeneities representing pores, lipid domains, and transmembrane, partially immersed and anchored proteins. It is demonstrated that all the structural information from the host lipid bilayer and from the SLD inhomogeneity can be consistently retrieved by a combined analysis of experimental SAXS and SANS data through the methodology proposed here.enSpinozzi, F.Barbosa, L.R.S.Corucci, G.Mariani, P.Itri, R.Small-angle scattering from flat bilayers containing correlated scattering length density inhomogeneities2023-08-16SMALL-ANGLE X-RAY SCATTERING; SAXS; SMALL-ANGLE NEUTRON SCATTERING; SANS; DOMAINS; PROTEINS; PORES; LIPID BILAYERS; SCATTERING LENGTH DENSITY INHOMOGENEITIESdoi:10.1107/S1600576723006143urn:issn:1600-5767An approach to simulating small-angle X-ray and neutron scattering curves of planar bilayers with horizontally correlated inhomogeneities representing lipid domains, proteins or pores is presented.https://creativecommons.org/licenses/by/4.0/text/html5https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-57671348med@iucr.org1600-576756research papers13602023-08-16October 2023In situ neutron diffraction for analysing complex coarse-grained functional materials
http://scripts.iucr.org/cgi-bin/paper?vb5054
Complex functional materials play a crucial role in a broad range of energy-related applications and in general for materials science. Revealing the structural mechanisms is challenging due to highly correlated coexisting phases and microstructures, especially for in situ or operando investigations. Since the grain sizes influence the properties, these microstructural features further complicate investigations at synchrotrons due to the limitations of illuminated sample volumes. In this study, it is demonstrated that such complex functional materials with highly correlated coexisting phases can be investigated under in situ conditions with neutron diffraction. For large grain sizes, these experiments are valuable methods to reveal the structural mechanisms. For an example of in situ experiments on barium titanate with an applied electric field, details of the electric-field-induced phase transformation depending on grain size and frequency are revealed. The results uncover the strain mechanisms in barium titanate and elucidate the complex interplay of stresses in relation to grain sizes as well as domain-wall densities and mobilities.International Union of CrystallographytextComplex functional materials play a crucial role in a broad range of energy-related applications and in general for materials science. Revealing the structural mechanisms is challenging due to highly correlated coexisting phases and microstructures, especially for in situ or operando investigations. Since the grain sizes influence the properties, these microstructural features further complicate investigations at synchrotrons due to the limitations of illuminated sample volumes. In this study, it is demonstrated that such complex functional materials with highly correlated coexisting phases can be investigated under in situ conditions with neutron diffraction. For large grain sizes, these experiments are valuable methods to reveal the structural mechanisms. For an example of in situ experiments on barium titanate with an applied electric field, details of the electric-field-induced phase transformation depending on grain size and frequency are revealed. The results uncover the strain mechanisms in barium titanate and elucidate the complex interplay of stresses in relation to grain sizes as well as domain-wall densities and mobilities.enHinterstein, M.Lemos da Silva, L.Knapp, M.Schoekel, A.Etter, M.Studer, A.In situ neutron diffraction for analysing complex coarse-grained functional materials2023-08-01NEUTRON DIFFRACTION; IN SITU; APPLIED ELECTRIC FIELDS; BARIUM TITANATE; STRAIN MECHANISMS; GRAIN SIZES; COMPLEX FUNCTIONAL MATERIALS; MICROSTRUCTURES; COEXISTING PHASESdoi:10.1107/S1600576723005940urn:issn:1600-5767This work reports in situ neutron diffraction experiments on a broad range of grain sizes of barium titanate. The study reveals the grain-size-dependent strain mechanisms and shows the competitiveness of neutron diffraction with high-resolution synchrotron diffraction.https://creativecommons.org/licenses/by/4.0/text/html12512023-08-01research papers56August 2023Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/4med@iucr.org1600-57671600-57671242Towards scanning nanostructure X-ray microscopy
http://scripts.iucr.org/cgi-bin/paper?vb5028
This article demonstrates spatial mapping of the local and nanoscale structure of thin film objects using spatially resolved pair distribution function (PDF) analysis of synchrotron X-ray diffraction data. This is exemplified in a lab-on-chip combinatorial array of sample spots containing catalytically interesting nanoparticles deposited from liquid precursors using an ink-jet liquid-handling system. A software implementation is presented of the whole protocol, including an approach for automated data acquisition and analysis using the atomic PDF method. The protocol software can handle semi-automated data reduction, normalization and modeling, with user-defined recipes generating a comprehensive collection of metadata and analysis results. By slicing the collection using included functions, it is possible to build images of different contrast features chosen by the user, giving insights into different aspects of the local structure.International Union of CrystallographytextThis article demonstrates spatial mapping of the local and nanoscale structure of thin film objects using spatially resolved pair distribution function (PDF) analysis of synchrotron X-ray diffraction data. This is exemplified in a lab-on-chip combinatorial array of sample spots containing catalytically interesting nanoparticles deposited from liquid precursors using an ink-jet liquid-handling system. A software implementation is presented of the whole protocol, including an approach for automated data acquisition and analysis using the atomic PDF method. The protocol software can handle semi-automated data reduction, normalization and modeling, with user-defined recipes generating a comprehensive collection of metadata and analysis results. By slicing the collection using included functions, it is possible to build images of different contrast features chosen by the user, giving insights into different aspects of the local structure.enKovyakh, A.Banerjee, S.Liu, C.-H.Wright, C.J.Li, Y.C.Mallouk, T.E.Feidenhans'l, R.Billinge, S.J.L.Towards scanning nanostructure X-ray microscopy2023-07-28ATOMIC PAIR DISTRIBUTION FUNCTION; NANOPARTICLES; SPATIAL MAPPING; THIN FILMSdoi:10.1107/S1600576723005927urn:issn:1600-5767A semi-automated workflow is described for rapid-scanning powder X-ray diffraction and pair distribution function experiments. The software infrastructure saves metadata and raw and analyzed files into a collection stored on the local hard drive for easier reuse.https://creativecommons.org/licenses/by/4.0/text/html12211600-57671600-5767med@iucr.org4Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/August 202356research papers2023-07-281228Shape2SAS: a web application to simulate small-angle scattering data and pair distance distributions from user-defined shapes
http://scripts.iucr.org/cgi-bin/paper?jl5064
Shape2SAS is a web application that allows researchers and students to build intuition about and understanding of small-angle scattering. It is available at https://somo.chem.utk.edu/shape2sas. The user defines a model of arbitrary shape by combining geometrical subunits, and Shape2SAS then calculates and displays the scattering intensity and the pair distance distribution, as well as a visualization of the user-defined shape. Simulated data with realistic noise are also generated. Here, it is demonstrated how Shape2SAS can calculate and display the different scattering patterns for various geometrical shapes, such as spheres and cylinders. It is also shown how the effect of structure factors can be visualized. Finally, it is indicated how multi-contrast particles can readily be generated, and how the calculated scattering may be used to validate and visualize analytical models generated in analysis software for fitting small-angle scattering data.International Union of CrystallographytextShape2SAS is a web application that allows researchers and students to build intuition about and understanding of small-angle scattering. It is available at https://somo.chem.utk.edu/shape2sas. The user defines a model of arbitrary shape by combining geometrical subunits, and Shape2SAS then calculates and displays the scattering intensity and the pair distance distribution, as well as a visualization of the user-defined shape. Simulated data with realistic noise are also generated. Here, it is demonstrated how Shape2SAS can calculate and display the different scattering patterns for various geometrical shapes, such as spheres and cylinders. It is also shown how the effect of structure factors can be visualized. Finally, it is indicated how multi-contrast particles can readily be generated, and how the calculated scattering may be used to validate and visualize analytical models generated in analysis software for fitting small-angle scattering data.enLarsen, A.H.Brookes, E.Pedersen, M.C.Kirkensgaard, J.J.K.Shape2SAS: a web application to simulate small-angle scattering data and pair distance distributions from user-defined shapes2023-07-28SMALL-ANGLE SCATTERING; SHAPE2SAS; GEOMETRICAL SHAPES; TEACHING; SIMULATION; VIRTUAL EXPERIMENTS; PAIR DISTANCE DISTRIBUTIONS; STRUCTURE FACTORS; FORM FACTORS; MULTI-CONTRAST PARTICLESdoi:10.1107/S1600576723005848urn:issn:1600-5767Shape2SAS allows the user to simulate solution small-angle scattering data and pair distance distributions from user-defined shapes. The program is available as a web application, and is useful for teaching and tutorials, as well as for checking the validity of analytical form factors.https://creativecommons.org/licenses/by/4.0/text/html2023-07-28129456computer programsAugust 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography41600-5767med@iucr.org12871600-5767Introduction to Python Dynamic Diffraction Toolkit (PyDDT): structural refinement of single crystals via X-ray phase measurements
http://scripts.iucr.org/cgi-bin/paper?iu5039
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. Key points behind structure refinement using the current approach are presented, and the main features of PyDDT are illustrated for amino acid and filled skutterudite single crystals.International Union of CrystallographytextPyDDT 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. Key points behind structure refinement using the current approach are presented, and the main features of PyDDT are illustrated for amino acid and filled skutterudite single crystals.enPenacchio, R.F.S.Estradiote, M.B.Remédios, C.M.R.Calligaris, G.A.Torikachvili, M.S.Kycia, S.W.Morelhão, S.L.Introduction to Python Dynamic Diffraction Toolkit (PyDDT): structural refinement of single crystals via X-ray phase measurements2023-08-16X-RAY DYNAMIC DIFFRACTION; SINGLE CRYSTALS; TRIPLET PHASE DETERMINATION; PYTHON CODEdoi:10.1107/S1600576723005800urn:issn:1600-5767Computer simulation tools are presented for the easy exploration of dynamic diffraction in refining structural details of known materials. Here several practical examples illustrate their usage, covering all steps from designing of experiments to data analysis.https://creativecommons.org/licenses/by/4.0/text/htmlhttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography51600-5767med@iucr.org15741600-57672023-08-16158456computer programsOctober 2023Alterations promoted by acid straightening and/or bleaching in hair microstructures
http://scripts.iucr.org/cgi-bin/paper?tj5033
Human hair is a biopolymer constituted mainly of keratin intermediate filaments, lipids, pigments and water. Cosmetic treatments usually interact with the hair at the molecular level, inducing changes in its components and modifying the physicochemical and mechanical properties of the fibers. Here, the effect of acid straightening on the morphology and ultrastructure of Caucasian hair was investigated by a group of complementary experimental methods: wide-, small- and ultra-small-angle X-ray scattering; high-resolution 3D X-ray microscopy; quasi-elastic neutron scattering and inelastic neutron scattering; thermogravimetry–mass spectrometry; and differential scanning calorimetry (DSC). X-ray diffraction patterns showed that acid straightening associated with a flat iron (∼180°C) changed the cortex of the fiber, shown by denaturation of the intermediate filaments (measured by DSC). The increase in the spacing of the lipid layers and the observation of the dehydration behavior of the fiber provided indications that water may be confined between these layers, while neutron spectroscopy showed alterations in the vibration mode of the CH2 groups of the lipids and an increase of the proton (H+) mobility in the hair structure. The latter may be associated with the extremely low pH of the formulation (pH ≃ 1). Additionally, this investigation showed that bleached hair (one-time bleached) is more damaged by the action of acid straightening than virgin hair, which was shown by a threefold increase in the percentage of total porosity of the tresses. The obtained results demonstrate that the investigation approach proposed here can provide very important thermodynamic and structural information on induced changes of hair structure, and certainly can be applied for the evaluation of the action mode and efficiency of cosmetic treatments.International Union of CrystallographytextHuman hair is a biopolymer constituted mainly of keratin intermediate filaments, lipids, pigments and water. Cosmetic treatments usually interact with the hair at the molecular level, inducing changes in its components and modifying the physicochemical and mechanical properties of the fibers. Here, the effect of acid straightening on the morphology and ultrastructure of Caucasian hair was investigated by a group of complementary experimental methods: wide-, small- and ultra-small-angle X-ray scattering; high-resolution 3D X-ray microscopy; quasi-elastic neutron scattering and inelastic neutron scattering; thermogravimetry–mass spectrometry; and differential scanning calorimetry (DSC). X-ray diffraction patterns showed that acid straightening associated with a flat iron (∼180°C) changed the cortex of the fiber, shown by denaturation of the intermediate filaments (measured by DSC). The increase in the spacing of the lipid layers and the observation of the dehydration behavior of the fiber provided indications that water may be confined between these layers, while neutron spectroscopy showed alterations in the vibration mode of the CH2 groups of the lipids and an increase of the proton (H+) mobility in the hair structure. The latter may be associated with the extremely low pH of the formulation (pH ≃ 1). Additionally, this investigation showed that bleached hair (one-time bleached) is more damaged by the action of acid straightening than virgin hair, which was shown by a threefold increase in the percentage of total porosity of the tresses. The obtained results demonstrate that the investigation approach proposed here can provide very important thermodynamic and structural information on induced changes of hair structure, and certainly can be applied for the evaluation of the action mode and efficiency of cosmetic treatments.enLima, C.R.R.C.Lima, R.J.S.Bandeira, A.C.C.Couto, R.A.A.Velasco, M.V.R.Bordallo, H.N.Oliveira, C.L.P.Alterations promoted by acid straightening and/or bleaching in hair microstructures2023-08-01HAIR; ACID STRAIGHTENING; BLEACHING; DAMAGE; X-RAY SCATTERING; MICROSTRUCTURE; COSMETIC TREATMENTS; NEUTRON SPECTROSCOPY; BIOPOLYMERSdoi:10.1107/S1600576723005599urn:issn:1600-5767A systematic investigation on alterations promoted by acid straightening and/or bleaching in hair microstructures is presented. By combining X-ray scattering methods and microcomputed tomography, among several other methods, innovative results were obtained on the structure and thermodynamics of human hair subjected to cosmetic procedures.https://creativecommons.org/licenses/by/4.0/text/htmlAugust 202310142023-08-0156research papersmed@iucr.org1600-57671600-57671002https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography4MILK: a Python scripting interface to MAUD for automation of Rietveld analysis
http://scripts.iucr.org/cgi-bin/paper?nb5355
Modern diffraction experiments (e.g. in situ parametric studies) present scientists with many diffraction patterns to analyze. Interactive analyses via graphical user interfaces tend to slow down obtaining quantitative results such as lattice parameters and phase fractions. Furthermore, Rietveld refinement strategies (i.e. the parameter turn-on-off sequences) tend to be instrument specific or even specific to a given dataset, such that selection of strategies can become a bottleneck for efficient data analysis. Managing multi-histogram datasets such as from multi-bank neutron diffractometers or caked 2D synchrotron data presents additional challenges due to the large number of histogram-specific parameters. To overcome these challenges in the Rietveld software Material Analysis Using Diffraction (MAUD), the MAUD Interface Language Kit (MILK) is developed along with an updated text batch interface for MAUD. The open-source software MILK is computer-platform independent and is packaged as a Python library that interfaces with MAUD. Using MILK, model selection (e.g. various texture or peak-broadening models), Rietveld parameter manipulation and distributed parallel batch computing can be performed through a high-level Python interface. A high-level interface enables analysis workflows to be easily programmed, shared and applied to large datasets, and external tools to be integrated with MAUD. Through modification to the MAUD batch interface, plot and data exports have been improved. The resulting hierarchical folders from Rietveld refinements with MILK are compatible with Cinema: Debye–Scherrer, a tool for visualizing and inspecting the results of multi-parameter analyses of large quantities of diffraction data. In this manuscript, the combined Python scripting and visualization capability of MILK is demonstrated with a quantitative texture and phase analysis of data collected at the HIPPO neutron diffractometer.International Union of CrystallographytextModern diffraction experiments (e.g. in situ parametric studies) present scientists with many diffraction patterns to analyze. Interactive analyses via graphical user interfaces tend to slow down obtaining quantitative results such as lattice parameters and phase fractions. Furthermore, Rietveld refinement strategies (i.e. the parameter turn-on-off sequences) tend to be instrument specific or even specific to a given dataset, such that selection of strategies can become a bottleneck for efficient data analysis. Managing multi-histogram datasets such as from multi-bank neutron diffractometers or caked 2D synchrotron data presents additional challenges due to the large number of histogram-specific parameters. To overcome these challenges in the Rietveld software Material Analysis Using Diffraction (MAUD), the MAUD Interface Language Kit (MILK) is developed along with an updated text batch interface for MAUD. The open-source software MILK is computer-platform independent and is packaged as a Python library that interfaces with MAUD. Using MILK, model selection (e.g. various texture or peak-broadening models), Rietveld parameter manipulation and distributed parallel batch computing can be performed through a high-level Python interface. A high-level interface enables analysis workflows to be easily programmed, shared and applied to large datasets, and external tools to be integrated with MAUD. Through modification to the MAUD batch interface, plot and data exports have been improved. The resulting hierarchical folders from Rietveld refinements with MILK are compatible with Cinema: Debye–Scherrer, a tool for visualizing and inspecting the results of multi-parameter analyses of large quantities of diffraction data. In this manuscript, the combined Python scripting and visualization capability of MILK is demonstrated with a quantitative texture and phase analysis of data collected at the HIPPO neutron diffractometer.enSavage, D.J.Lutterotti, L.Biwer, C.M.McKerns, M.Bolme, C.Knezevic, M.Vogel, S.C.MILK: a Python scripting interface to MAUD for automation of Rietveld analysis2023-07-20MILK; MAUD; RIETVELD REFINEMENT; DIFFRACTION SOFTWAREdoi:10.1107/S1600576723005472urn:issn:1600-5767The MAUD Interface Language Kit (MILK) provides a Python interface to the Rietveld software MAUD, enabling scriptable refinements. The MILK framework includes parallel computing and folder management which enable high-throughput Rietveld analysis, visualization and validation.https://creativecommons.org/licenses/by/4.0/text/htmlcomputer programs562023-07-201286August 20234Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/12771600-57671600-5767med@iucr.orgExtended Q-range small-angle neutron scattering to understand the morphology of proton-exchange membranes: the case of the functionalized syndiotactic-polystyrene model system
http://scripts.iucr.org/cgi-bin/paper?jl5067
Semi-crystalline polymers exhibit microphase separation into crystalline and amorphous domains characterized by multiple structural levels with sizes ranging from ångströms to hundreds of nanometres. The combination of small-angle (SANS) and wide-angle (WANS) neutron scattering on the same beamline enables reliable in situ characterization of such materials under application-relevant conditions, with the unique advantage of contrast variation by controlled labelling, allowing the structure of such multi-component systems to be resolved in detail. This paper reports a structural analysis performed on deuterated polymer membranes based on syndiotactic polystyrene (sPS) using an extended Q-range SANS and WANS combination, always with the same neutron scattering instrument, either a pinhole SANS diffractometer installed at a research reactor or a `small- and wide-angle' time-of-flight diffractometer installed at a neutron spallation source. sPS is a semi-crystalline material that becomes hydrophilic and proton conducting when suitable functionalization is achieved by thin film sulfonation, and can form various co-crystalline complexes (clathrates) with small organic molecules stored in the crystalline phase as guests in the vacancies between the polymer helices. Therefore, this material is interesting not only for its conducting properties but also for its versatility as a model system to evaluate the usefulness of extended Q-range neutron scattering in such studies. Variation of neutron contrast was achieved in the amorphous hydrophilic phase by using H2O or D2O to hydrate the membranes and in the crystalline phase by loading the clathrates with deuterated or protonated guest molecules. The experimental approach, the advantages and limitations of the two types of instrumentation used in such analyses, and the main results obtained with respect to the structural characterization of sulfonated sPS membranes under different hydration and temperature conditions are reported, and the potential of this method for similar structural studies on other semi-crystalline polymeric materials is discussed.International Union of CrystallographytextSemi-crystalline polymers exhibit microphase separation into crystalline and amorphous domains characterized by multiple structural levels with sizes ranging from ångströms to hundreds of nanometres. The combination of small-angle (SANS) and wide-angle (WANS) neutron scattering on the same beamline enables reliable in situ characterization of such materials under application-relevant conditions, with the unique advantage of contrast variation by controlled labelling, allowing the structure of such multi-component systems to be resolved in detail. This paper reports a structural analysis performed on deuterated polymer membranes based on syndiotactic polystyrene (sPS) using an extended Q-range SANS and WANS combination, always with the same neutron scattering instrument, either a pinhole SANS diffractometer installed at a research reactor or a `small- and wide-angle' time-of-flight diffractometer installed at a neutron spallation source. sPS is a semi-crystalline material that becomes hydrophilic and proton conducting when suitable functionalization is achieved by thin film sulfonation, and can form various co-crystalline complexes (clathrates) with small organic molecules stored in the crystalline phase as guests in the vacancies between the polymer helices. Therefore, this material is interesting not only for its conducting properties but also for its versatility as a model system to evaluate the usefulness of extended Q-range neutron scattering in such studies. Variation of neutron contrast was achieved in the amorphous hydrophilic phase by using H2O or D2O to hydrate the membranes and in the crystalline phase by loading the clathrates with deuterated or protonated guest molecules. The experimental approach, the advantages and limitations of the two types of instrumentation used in such analyses, and the main results obtained with respect to the structural characterization of sulfonated sPS membranes under different hydration and temperature conditions are reported, and the potential of this method for similar structural studies on other semi-crystalline polymeric materials is discussed.enSchiavone, M.-M.Lamparelli, D.H.Daniel, C.Golla, M.Zhao, Y.Iwase, H.Arima-Osonoi, H.Takata, S.Szentmiklosi, L.Maroti, B.Allgaier, J.Radulescu, A.Extended Q-range small-angle neutron scattering to understand the morphology of proton-exchange membranes: the case of the functionalized syndiotactic-polystyrene model system2023-07-25PINHOLE SANS; SMALL-ANGLE NEUTRON SCATTERING; TOF SANS; TIME OF FLIGHT; WANS; WIDE-ANGLE NEUTRON SCATTERING; ION-CONDUCTING POLYMER MEMBRANESdoi:10.1107/S1600576723005496urn:issn:1600-5767Semi-crystalline polymers present a hierarchical organization of structural levels from ångströms to hundreds of nanometres. By combining small- and wide-angle neutron scattering at the same instrument, such complex morphologies can be resolved under application of relevant humidity and temperature conditions.https://creativecommons.org/licenses/by/4.0/text/html1600-5767med@iucr.org9471600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/4August 20232023-07-2596056research papersRevealing cholesterol effects on PEGylated HSPC liposomes using AF4–MALS and simultaneous small- and wide-angle X-ray scattering
http://scripts.iucr.org/cgi-bin/paper?tj5034
Liposome development is of great interest owing to increasing requirements for efficient drug carriers. The structural features and thermal stability of such liposomes are crucial in drug transport and delivery. Reported here are the results of the structural characterization of PEGylated liposomes via small- and wide-angle X-ray scattering and an asymmetric flow field-flow fractionation (AF4) system coupled with differential refractive-index detection, multi-angle light scattering (MALS) and dynamic light scattering. This integrated analysis of the exemplar PEGylated liposome formed from hydrogenated soy phosphatidylcholine (HSPC) with the addition of cholesterol reveals an average hydrodynamic radius (Rh) of 52 nm with 10% polydispersity, a comparable radius of gyration (Rg) and a major liposome particle mass of 118 kDa. The local bilayer structure of the liposome is found to have asymmetric electronic density profiles in the inner and outer leaflets, sandwiched by two PEGylated outer layers ca 5 nm thick. Cholesterol was found to effectively intervene in lipid chain packing, resulting in the thickening of the liposome bilayer, an increase in the area per lipid and an increase in liposome size, especially in the fluid phase of the liposome. These cholesterol effects show signs of saturation at cholesterol concentrations above ca 1:5 cholesterol:lipid molar ratio.International Union of CrystallographytextLiposome development is of great interest owing to increasing requirements for efficient drug carriers. The structural features and thermal stability of such liposomes are crucial in drug transport and delivery. Reported here are the results of the structural characterization of PEGylated liposomes via small- and wide-angle X-ray scattering and an asymmetric flow field-flow fractionation (AF4) system coupled with differential refractive-index detection, multi-angle light scattering (MALS) and dynamic light scattering. This integrated analysis of the exemplar PEGylated liposome formed from hydrogenated soy phosphatidylcholine (HSPC) with the addition of cholesterol reveals an average hydrodynamic radius (Rh) of 52 nm with 10% polydispersity, a comparable radius of gyration (Rg) and a major liposome particle mass of 118 kDa. The local bilayer structure of the liposome is found to have asymmetric electronic density profiles in the inner and outer leaflets, sandwiched by two PEGylated outer layers ca 5 nm thick. Cholesterol was found to effectively intervene in lipid chain packing, resulting in the thickening of the liposome bilayer, an increase in the area per lipid and an increase in liposome size, especially in the fluid phase of the liposome. These cholesterol effects show signs of saturation at cholesterol concentrations above ca 1:5 cholesterol:lipid molar ratio.enHsu, T.-W.Yang, C.-H.Su, C.-J.Huang, Y.-T.Yeh, Y.-Q.Liao, K.-F.Lin, T.-C.Shih, O.Lee, M.-T.Su, A.-C.Jeng, U.-S.Revealing cholesterol effects on PEGylated HSPC liposomes using AF4–MALS and simultaneous small- and wide-angle X-ray scattering2023-07-25DRUG-CARRYING LIPOSOMES; PHOSPHOLIPID MEMBRANES; CHOLESTEROL EFFECTS; ASYMMETRIC FLOW FIELD-FLOW FRACTIONATION; MULTI-ANGLE LIGHT SCATTERING; AF4-MALS; SMALL-ANGLE X-RAY SCATTERING; WIDE-ANGLE X-RAY SCATTERING; SAXS-WAXSdoi:10.1107/S1600576723005393urn:issn:1600-5767Small- and wide-angle X-ray scattering and asymmetric flow field-flow fractionation integrated with multi-angle light scattering (AF4–MALS) are used to characterize PEGylated liposomes of hydrogenated soy phosphatidylcholine (HSPC) that have potential for drug delivery. Observed local and global structural changes of the phospholipid bilayers reveal the effects of cholesterol on PEGylated HSPC liposomes.https://creativecommons.org/licenses/by/4.0/text/html1600-5767med@iucr.org9881600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography4August 20232023-07-25993research papers56Insights into the precipitation kinetics of CaCO3 particles in the presence of polystyrene sulfonate using in situ small-angle X-ray scattering
http://scripts.iucr.org/cgi-bin/paper?ge5135
The formation of calcium carbonate (CaCO3) nanoparticles (NPs) in the presence of polystyrene sulfonate (PSS) as an additive was examined by time-resolved small-angle X-ray scattering (SAXS) in a flow system that mimics experimental conditions used at home facilities where the precipitation can be achieved in a beaker. The experiments were carried out at low concentrations to remain in the dilute regime. A model-independent analysis was performed using the Porod invariant which defines the scale factor, leaving only the distribution of radii as the adjustable parameter. The presence of the PSS additive strongly retards the precipitation of CaCO3 NPs. The formation of NPs reaches a state of equilibrium after a few minutes. Here, it is shown that the concentration of precursors at a fixed PSS concentration plays a key role in determining the size of the NPs obtained. A full analysis of the SAXS patterns was carried out using the Hurd–Flower model to account for the weaker intensity decay than the classical Porod behaviour. The temporal evolution of the particle radii was determined. Wide-angle X-ray scattering experiments carried out simultaneously show that the particles formed have the structure of vaterite with growth consistent with the evolution of the Porod invariant.International Union of CrystallographytextThe formation of calcium carbonate (CaCO3) nanoparticles (NPs) in the presence of polystyrene sulfonate (PSS) as an additive was examined by time-resolved small-angle X-ray scattering (SAXS) in a flow system that mimics experimental conditions used at home facilities where the precipitation can be achieved in a beaker. The experiments were carried out at low concentrations to remain in the dilute regime. A model-independent analysis was performed using the Porod invariant which defines the scale factor, leaving only the distribution of radii as the adjustable parameter. The presence of the PSS additive strongly retards the precipitation of CaCO3 NPs. The formation of NPs reaches a state of equilibrium after a few minutes. Here, it is shown that the concentration of precursors at a fixed PSS concentration plays a key role in determining the size of the NPs obtained. A full analysis of the SAXS patterns was carried out using the Hurd–Flower model to account for the weaker intensity decay than the classical Porod behaviour. The temporal evolution of the particle radii was determined. Wide-angle X-ray scattering experiments carried out simultaneously show that the particles formed have the structure of vaterite with growth consistent with the evolution of the Porod invariant.enGibaud, A.Younas, D.Matthews, L.Narayanan, T.Longkaew, K.Hageberg, I.U.Chushkin, Y.Breiby, D.W.Chattopadhyay, B.Insights into the precipitation kinetics of CaCO3 particles in the presence of polystyrene sulfonate using in situ small-angle X-ray scattering2023-07-14SMALL-ANGLE X-RAY SCATTERING; SAXS; POROD CONSTANT; TIME-RESOLVED STUDIES; CALCIUM CARBONATE PRECIPITATION; POLYSTYRENE SULFONATE; BIOMINERALIZATIONdoi:10.1107/S1600576723005356urn:issn:1600-5767The kinetics of precipitation of CaCO3 particles in the presence of polystyrene sulfonate was studied by small- and wide-angle X-ray scattering. Employment of the Porod invariant and the Hurd–Flower model provides essential information on the kinetics.https://creativecommons.org/licenses/by/4.0/text/html2023-07-141124research papers56August 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography41600-5767med@iucr.org11141600-5767AlphaFold-predicted protein structures and small-angle X-ray scattering: insights from an extended examination of selected data in the Small-Angle Scattering Biological Data Bank
http://scripts.iucr.org/cgi-bin/paper?uu5005
By providing predicted protein structures from nearly all known protein sequences, the artificial intelligence program AlphaFold (AF) is having a major impact on structural biology. While a stunning accuracy has been achieved for many folding units, predicted unstructured regions and the arrangement of potentially flexible linkers connecting structured domains present challenges. Focusing on single-chain structures without prosthetic groups, an earlier comparison of features derived from small-angle X-ray scattering (SAXS) data taken from the Small-Angle Scattering Biological Data Bank (SASBDB) is extended to those calculated using the corresponding AF-predicted structures. Selected SASBDB entries were carefully examined to ensure that they represented data from monodisperse protein solutions and had sufficient statistical precision and q resolution for reliable structural evaluation. Three examples were identified where there is clear evidence that the single AF-predicted structure cannot account for the experimental SAXS data. Instead, excellent agreement is found with ensemble models generated by allowing for flexible linkers between high-confidence predicted structured domains. A pool of representative structures was generated using a Monte Carlo method that adjusts backbone dihedral allowed angles along potentially flexible regions. A fast ensemble modelling method was employed that optimizes the fit of pair distance distribution functions [P(r) versus r] and intensity profiles [I(q) versus q] computed from the pool to their experimental counterparts. These results highlight the complementarity between AF prediction, solution SAXS and molecular dynamics/conformational sampling for structural modelling of proteins having both structured and flexible regions.International Union of CrystallographytextBy providing predicted protein structures from nearly all known protein sequences, the artificial intelligence program AlphaFold (AF) is having a major impact on structural biology. While a stunning accuracy has been achieved for many folding units, predicted unstructured regions and the arrangement of potentially flexible linkers connecting structured domains present challenges. Focusing on single-chain structures without prosthetic groups, an earlier comparison of features derived from small-angle X-ray scattering (SAXS) data taken from the Small-Angle Scattering Biological Data Bank (SASBDB) is extended to those calculated using the corresponding AF-predicted structures. Selected SASBDB entries were carefully examined to ensure that they represented data from monodisperse protein solutions and had sufficient statistical precision and q resolution for reliable structural evaluation. Three examples were identified where there is clear evidence that the single AF-predicted structure cannot account for the experimental SAXS data. Instead, excellent agreement is found with ensemble models generated by allowing for flexible linkers between high-confidence predicted structured domains. A pool of representative structures was generated using a Monte Carlo method that adjusts backbone dihedral allowed angles along potentially flexible regions. A fast ensemble modelling method was employed that optimizes the fit of pair distance distribution functions [P(r) versus r] and intensity profiles [I(q) versus q] computed from the pool to their experimental counterparts. These results highlight the complementarity between AF prediction, solution SAXS and molecular dynamics/conformational sampling for structural modelling of proteins having both structured and flexible regions.enBrookes, E.Rocco, M.Vachette, P.Trewhella, J.AlphaFold-predicted protein structures and small-angle X-ray scattering: insights from an extended examination of selected data in the Small-Angle Scattering Biological Data Bank2023-07-20SMALL-ANGLE X-RAY SCATTERING; SAXS; ALPHAFOLD; ENSEMBLE MODELLING; STRUCTURAL FLEXIBILITYdoi:10.1107/S1600576723005344urn:issn:1600-5767A rapid ensemble modelling method that optimizes the fit to the small-angle X-ray scattering (SAXS)-derived pair-wise distance distribution function [P(r) versus r] and the measured intensity profile [I(q) versus q] has been used to account for differences between AlphaFold-predicted and experimental SAXS profiles. By considering the confidence levels that come with the predicted structures, a conformational ensemble with potentially flexible linkers between stable folded domains can be optimized to provide representative structures.https://creativecommons.org/licenses/by/4.0/text/html2023-07-2092656research papersAugust 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography41600-5767med@iucr.org9101600-5767Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations
http://scripts.iucr.org/cgi-bin/paper?jl5065
This article presents an upgrade of the D+ software [Ginsburg et al. (2019). J. Appl. Cryst. 52, 219–242], expanding its hierarchical solution X-ray scattering modeling capabilities for fiber diffraction and single crystallographic orientations. This upgrade was carried out using the reciprocal grid algorithm [Ginsburg et al. (2016). J. Chem. Inf. Model. 56, 1518–1527], providing D+ its computational strength. Furthermore, the extensive modifications made to the Python API of D+ are described, broadening the X-ray analysis performed with D+ to account for the effects of the instrument-resolution function and polydispersity. In addition, structure-factor and radial-distribution-function modules were added, taking into account the effects of thermal fluctuations and intermolecular interactions. Finally, numerical examples demonstrate the usage and potential of the added features.International Union of CrystallographytextThis article presents an upgrade of the D+ software [Ginsburg et al. (2019). J. Appl. Cryst. 52, 219–242], expanding its hierarchical solution X-ray scattering modeling capabilities for fiber diffraction and single crystallographic orientations. This upgrade was carried out using the reciprocal grid algorithm [Ginsburg et al. (2016). J. Chem. Inf. Model. 56, 1518–1527], providing D+ its computational strength. Furthermore, the extensive modifications made to the Python API of D+ are described, broadening the X-ray analysis performed with D+ to account for the effects of the instrument-resolution function and polydispersity. In addition, structure-factor and radial-distribution-function modules were added, taking into account the effects of thermal fluctuations and intermolecular interactions. Finally, numerical examples demonstrate the usage and potential of the added features.enBalken, E.Ben-Nun, I.Fellig, A.Khaykelson, D.Raviv, U.Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations2023-07-28X-RAY SCATTERING; FIBER DIFFRACTION; HIERARCHICAL MODELING; D+ SOFTWARE; STRUCTURE FACTORS; POLYDISPERSITY; ORIENTATIONSdoi:10.1107/S1600576723005319urn:issn:1600-5767An upgrade to the D+ software is presented, simulating the 2D scattering pattern from structures with a single orientation or fibers. An upgraded independent D+ Python API is described, including structure factor, polydispersity and several other features.https://creativecommons.org/licenses/by/4.0/text/htmlAugust 2023computer programs562023-07-28130312951600-57671600-5767med@iucr.org4Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Combining synchrotron X-ray diffraction, mechanistic modeling and machine learning for in situ subsurface temperature quantification during laser melting
http://scripts.iucr.org/cgi-bin/paper?xx5027
Laser melting, such as that encountered during additive manufacturing, produces extreme gradients of temperature in both space and time, which in turn influence microstructural development in the material. Qualification and model validation of the process itself and the resulting material necessitate the ability to characterize these temperature fields. However, well established means to directly probe the material temperature below the surface of an alloy while it is being processed are limited. To address this gap in characterization capabilities, a novel means is presented to extract subsurface temperature-distribution metrics, with uncertainty, from in situ synchrotron X-ray diffraction measurements to provide quantitative temperature evolution data during laser melting. Temperature-distribution metrics are determined using Gaussian process regression supervised machine-learning surrogate models trained with a combination of mechanistic modeling (heat transfer and fluid flow) and X-ray diffraction simulation. The trained surrogate model uncertainties are found to range from 5 to 15% depending on the metric and current temperature. The surrogate models are then applied to experimental data to extract temperature metrics from an Inconel 625 nickel superalloy wall specimen during laser melting. The maximum temperatures of the solid phase in the diffraction volume through melting and cooling are found to reach the solidus temperature as expected, with the mean and minimum temperatures found to be several hundred degrees less. The extracted temperature metrics near melting are determined to be more accurate because of the lower relative levels of mechanical elastic strains. However, uncertainties for temperature metrics during cooling are increased due to the effects of thermomechanical stress.International Union of CrystallographytextLaser melting, such as that encountered during additive manufacturing, produces extreme gradients of temperature in both space and time, which in turn influence microstructural development in the material. Qualification and model validation of the process itself and the resulting material necessitate the ability to characterize these temperature fields. However, well established means to directly probe the material temperature below the surface of an alloy while it is being processed are limited. To address this gap in characterization capabilities, a novel means is presented to extract subsurface temperature-distribution metrics, with uncertainty, from in situ synchrotron X-ray diffraction measurements to provide quantitative temperature evolution data during laser melting. Temperature-distribution metrics are determined using Gaussian process regression supervised machine-learning surrogate models trained with a combination of mechanistic modeling (heat transfer and fluid flow) and X-ray diffraction simulation. The trained surrogate model uncertainties are found to range from 5 to 15% depending on the metric and current temperature. The surrogate models are then applied to experimental data to extract temperature metrics from an Inconel 625 nickel superalloy wall specimen during laser melting. The maximum temperatures of the solid phase in the diffraction volume through melting and cooling are found to reach the solidus temperature as expected, with the mean and minimum temperatures found to be several hundred degrees less. The extracted temperature metrics near melting are determined to be more accurate because of the lower relative levels of mechanical elastic strains. However, uncertainties for temperature metrics during cooling are increased due to the effects of thermomechanical stress.enLim, R.E.Mukherjee, T.Chuang, C.Phan, T.Q.DebRoy, T.Pagan, D.C.Combining synchrotron X-ray diffraction, mechanistic modeling and machine learning for in situ subsurface temperature quantification during laser melting2023-07-20SYNCHROTRON X-RAY DIFFRACTION; ADDITIVE MANUFACTURING; SUPERALLOYS; LASER MELTING; MACHINE LEARNING; HEAT-TRANSFER AND FLUID-FLOW MODELING; GAUSSIAN PROCESS REGRESSION; TEMPERATURE-DISTRIBUTION METRICS; THERMOMECHANICAL STRESS; ELASTIC STRAINSdoi:10.1107/S1600576723005198urn:issn:1600-5767A new methodology is demonstrated for analyzing spatial temperature distributions using modeling and machine learning. The method is applied to X-ray data gathered during in situ laser melting.https://creativecommons.org/licenses/by/4.0/text/htmlJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/4med@iucr.org1600-57671600-5767113111432023-07-20research papers56August 2023TEMGYM Basic: transmission electron microscopy simulation software for teaching and training of microscope operation
http://scripts.iucr.org/cgi-bin/paper?yr5104
An interactive simulation of a transmission electron microscope (TEM) called TEMGYM Basic is developed here, which enables users to understand how to operate and control an electron beam without the need to access an instrument. TEMGYM Basic allows users to familiarize themselves with alignment procedures offline, reducing the time and money required to become a proficient TEM operator. In addition to teaching the basics of electron beam alignments, the software enables users to create bespoke microscope configurations and develop an understanding of how to operate the configurations without sitting at a microscope. TEMGYM Basic also creates static ray diagram figures for a given lens configuration. The available components include apertures, lenses, quadrupoles, deflectors and biprisms. The software design uses first-order ray transfer matrices to calculate ray paths through each electron microscope component, and the program is developed entirely in Python to facilitate compatibility with machine-learning packages for future exploration of automated control.International Union of CrystallographytextAn interactive simulation of a transmission electron microscope (TEM) called TEMGYM Basic is developed here, which enables users to understand how to operate and control an electron beam without the need to access an instrument. TEMGYM Basic allows users to familiarize themselves with alignment procedures offline, reducing the time and money required to become a proficient TEM operator. In addition to teaching the basics of electron beam alignments, the software enables users to create bespoke microscope configurations and develop an understanding of how to operate the configurations without sitting at a microscope. TEMGYM Basic also creates static ray diagram figures for a given lens configuration. The available components include apertures, lenses, quadrupoles, deflectors and biprisms. The software design uses first-order ray transfer matrices to calculate ray paths through each electron microscope component, and the program is developed entirely in Python to facilitate compatibility with machine-learning packages for future exploration of automated control.enLanders, D.Clancy, I.Weber, D.Dunin-Borkowski, R.E.Stewart, A.TEMGYM Basic: transmission electron microscopy simulation software for teaching and training of microscope operation2023-07-14PYTHON; COMPUTER PROGRAMS; SIMULATION; VIRTUAL MICROSCOPES; TRANSMISSION ELECTRON MICROSCOPY; ALIGNMENTS; INTERACTIVE SOFTWARE; RAY TRACING; TEMGYM BASICdoi:10.1107/S1600576723005174urn:issn:1600-5767TEMGYM Basic is a Python-based ray-tracing tool for novel experiment visualization and an interactive learning environment for using transmission electron microscopes.https://creativecommons.org/licenses/by/4.0/text/htmlcomputer programs562023-07-141276August 20234https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography12671600-57671600-5767med@iucr.orgIn situ biaxial loading and multi-scale deformation measurements of nanostructured materials at the CoSAXS beamline at MAX IV Laboratory
http://scripts.iucr.org/cgi-bin/paper?uu5003
Characterization of the mechanical response of polymers and composite materials relies heavily on the macroscopic stress–strain response in uniaxial tensile configurations. To provide representative information, the deformation process must be homogeneous within the gauge length, which is a condition that is rarely achieved due to stress concentration or inhomogeneities within the specimen. In this work, the development of a biaxial mechanical testing device at the CoSAXS beamline at MAX IV Laboratory is presented. The design facilitates simultaneous measurement of small- and wide-angle X-ray scattering (SAXS/WAXS), allowing assessment of the microstructural configuration before, after and during the continuous deformation process at multiple length scales. The construction also supports multiple deformation conditions, while guaranteeing stability even at high loads. Furthermore, the mechanical experiments can be complemented with spatially resolved mesoscopic surface deformation measurements using 3D-surface digital image correlation (DIC). Polycarbonate (PC) was used to demonstrate the varied material response to multi-axial deformation, as PC is isotropic with a high glass transition temperature (∼150°) and high strength. As a result, a clear correlation between full-field methods and the microstructural information determined from WAXS measurements is demonstrated. When a uniaxial load is applied, homogeneous strain regions could be observed extending perpendicular to the applied load. When a secondary axial load was added (biaxial mode), it was observed that high strain domains were created near the centre of the sample and at the boundaries after yield. With increased strain, the deformation in the main deformation direction also increases. Mechanical reliability was demonstrated by carrying out static loading of polyacrylonitrile-based carbon fibre (CF) bundles. As a result, the nonlinear stiffening behaviour typically observed in CFs was seen, while no evidence of the creation of new voids during loading was observed. The results support the reliability and broad applicability of the developed technique.International Union of CrystallographytextCharacterization of the mechanical response of polymers and composite materials relies heavily on the macroscopic stress–strain response in uniaxial tensile configurations. To provide representative information, the deformation process must be homogeneous within the gauge length, which is a condition that is rarely achieved due to stress concentration or inhomogeneities within the specimen. In this work, the development of a biaxial mechanical testing device at the CoSAXS beamline at MAX IV Laboratory is presented. The design facilitates simultaneous measurement of small- and wide-angle X-ray scattering (SAXS/WAXS), allowing assessment of the microstructural configuration before, after and during the continuous deformation process at multiple length scales. The construction also supports multiple deformation conditions, while guaranteeing stability even at high loads. Furthermore, the mechanical experiments can be complemented with spatially resolved mesoscopic surface deformation measurements using 3D-surface digital image correlation (DIC). Polycarbonate (PC) was used to demonstrate the varied material response to multi-axial deformation, as PC is isotropic with a high glass transition temperature (∼150°) and high strength. As a result, a clear correlation between full-field methods and the microstructural information determined from WAXS measurements is demonstrated. When a uniaxial load is applied, homogeneous strain regions could be observed extending perpendicular to the applied load. When a secondary axial load was added (biaxial mode), it was observed that high strain domains were created near the centre of the sample and at the boundaries after yield. With increased strain, the deformation in the main deformation direction also increases. Mechanical reliability was demonstrated by carrying out static loading of polyacrylonitrile-based carbon fibre (CF) bundles. As a result, the nonlinear stiffening behaviour typically observed in CFs was seen, while no evidence of the creation of new voids during loading was observed. The results support the reliability and broad applicability of the developed technique.enMota-Santiago, P.Engqvist, J.Hall, S.Appio, R.Maghe, M.Sathikumar, G.Ristinmaa, M.Plivelic, T.S.In situ biaxial loading and multi-scale deformation measurements of nanostructured materials at the CoSAXS beamline at MAX IV Laboratory2023-06-30BIAXIAL MECHANICAL TESTING; SOFT MATTER; SMALL-ANGLE X-RAY SCATTERING; SAXS; WIDE-ANGLE X-RAY SCATTERING; WAXSdoi:10.1107/S1600576723005034urn:issn:1600-5767A novel biaxial tensile tester designed to work in combination with 2D synchrotron-based scanning small- and wide-angle X-ray scattering and digital image correlation is described. The available biaxial modes and a proposed sample geometry are discussed.https://creativecommons.org/licenses/by/4.0/text/htmlmed@iucr.org1600-57671600-5767967https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography4August 20239752023-06-3056research papersIn situ neutron diffraction to investigate the solid-state synthesis of Ni-rich cathode materials
http://scripts.iucr.org/cgi-bin/paper?jo5081
Studying chemical reactions in real time can provide unparalleled insight into the evolution of intermediate species and can provide guidance to optimize the reaction conditions. For solid-state synthesis reactions, powder diffraction has been demonstrated as an effective tool for resolving the structural evolution taking place upon heating. The synthesis of layered Ni-rich transition-metal oxides at a large scale (grams to kilograms) is highly relevant as these materials are commonly employed as cathodes for Li-ion batteries. In this work, in situ neutron diffraction was used to monitor the reaction mechanism during the high-temperature synthesis of Ni-rich cathode materials with a varying ratio of Ni:Mn from industrially relevant hydroxide precursors. Rietveld refinement was further used to model the observed phase evolution during synthesis and compare the behaviour of the materials as a function of temperature. The results presented herein confirm the suitability of in situ neutron diffraction to investigate the synthesis of batches of several grams of electrode materials with well-controlled stoichiometry. Furthermore, monitoring the structural evolution of the mixtures with varying Ni:Mn content in real time reveals a delayed onset of lithiation as the Mn content is increased, necessitating the use of higher annealing temperatures to achieve layering.International Union of CrystallographytextStudying chemical reactions in real time can provide unparalleled insight into the evolution of intermediate species and can provide guidance to optimize the reaction conditions. For solid-state synthesis reactions, powder diffraction has been demonstrated as an effective tool for resolving the structural evolution taking place upon heating. The synthesis of layered Ni-rich transition-metal oxides at a large scale (grams to kilograms) is highly relevant as these materials are commonly employed as cathodes for Li-ion batteries. In this work, in situ neutron diffraction was used to monitor the reaction mechanism during the high-temperature synthesis of Ni-rich cathode materials with a varying ratio of Ni:Mn from industrially relevant hydroxide precursors. Rietveld refinement was further used to model the observed phase evolution during synthesis and compare the behaviour of the materials as a function of temperature. The results presented herein confirm the suitability of in situ neutron diffraction to investigate the synthesis of batches of several grams of electrode materials with well-controlled stoichiometry. Furthermore, monitoring the structural evolution of the mixtures with varying Ni:Mn content in real time reveals a delayed onset of lithiation as the Mn content is increased, necessitating the use of higher annealing temperatures to achieve layering.enGoonetilleke, D.Suard, E.Bergner, B.Janek, J.Brezesinski, T.Bianchini, M.In situ neutron diffraction to investigate the solid-state synthesis of Ni-rich cathode materials2023-06-23IN SITU NEUTRON DIFFRACTION; SYNTHESIS; CATHODES; NI RICH; SOLID STATE; HIGH ANNEALING TEMPERATURES; RIETVELD REFINEMENT; LITHIATIONdoi:10.1107/S1600576723004909urn:issn:1600-5767In situ neutron diffraction is demonstrated as a suitable technique to track phase evolution during synthesis of layered oxide compounds. The synthesis of a series of cathode materials for Li-ion batteries with different Ni/Mn ratio is investigated, in batches comparable to standard laboratory conditions, demonstrating the delayed onset of lithiation with increasing Mn content.https://creativecommons.org/licenses/by/4.0/text/htmlresearch papers562023-06-231075August 20234https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography10661600-57671600-5767med@iucr.orgEquilibration of precipitants in a counter-diffusion apparatus for protein crystallization
http://scripts.iucr.org/cgi-bin/paper?ei5096
A cost-effective capillary dialysis apparatus (Toledo Capillary Box, TCB) developed for biomacromolecule crystal growth in microgravity and unit gravity environments can provide slow equilibration between the precipitant reservoir and capillary solutions, nurturing growth of neutron-diffraction-quality crystals. Under microgravity conditions, mass transfer of precipitants and biomacromolecules occurs under diffusion-controlled conditions, promoting slow growth and suppressing defect formation. The equilibration of common precipitants (polyethylene glycol and salts such as ammonium sulfate) between capillary and reservoir solutions was measured for capillaries oriented horizontally or vertically with respect to the gravitational field at unit gravity. Precipitants equilibrated less rapidly in the vertical orientation when capillary solution densities were lower than those of the reservoir solutions. A plug filled with agarose gel was introduced in the TCB apparatus for salt precipitants since salts often exhibit relatively high free diffusion. Equilibration of the capillaries with reservoir solutions was significantly delayed for many of the salt precipitants tested. Analytical and semi-analytical models allow the prediction of precipitant equilibration of capillary and reservoir solutions under diffusion-controlled transport and show good agreement with experimental results.International Union of CrystallographytextA cost-effective capillary dialysis apparatus (Toledo Capillary Box, TCB) developed for biomacromolecule crystal growth in microgravity and unit gravity environments can provide slow equilibration between the precipitant reservoir and capillary solutions, nurturing growth of neutron-diffraction-quality crystals. Under microgravity conditions, mass transfer of precipitants and biomacromolecules occurs under diffusion-controlled conditions, promoting slow growth and suppressing defect formation. The equilibration of common precipitants (polyethylene glycol and salts such as ammonium sulfate) between capillary and reservoir solutions was measured for capillaries oriented horizontally or vertically with respect to the gravitational field at unit gravity. Precipitants equilibrated less rapidly in the vertical orientation when capillary solution densities were lower than those of the reservoir solutions. A plug filled with agarose gel was introduced in the TCB apparatus for salt precipitants since salts often exhibit relatively high free diffusion. Equilibration of the capillaries with reservoir solutions was significantly delayed for many of the salt precipitants tested. Analytical and semi-analytical models allow the prediction of precipitant equilibration of capillary and reservoir solutions under diffusion-controlled transport and show good agreement with experimental results.enKober, U.A.Ogbuoji, E.A.Hutchinson, J.A.Mueser, T.C.Schall, C.A.Equilibration of precipitants in a counter-diffusion apparatus for protein crystallization2023-06-23MICROGRAVITY; DIFFUSION; LARGE-VOLUME CRYSTALS; PROTEIN CRYSTALLIZATIONdoi:10.1107/S1600576723004958urn:issn:1600-5767A cost-effective capillary dialysis apparatus (Toledo Capillary Box) was developed for biomacromolecule crystal growth in microgravity and unit gravity environments to provide slow equilibration between the precipitant reservoir and capillary solutions. Analytical and semi-analytical models allow the prediction of precipitant equilibration of capillary and reservoir solutions under diffusion-controlled transport and show good agreement with experimental results.https://creativecommons.org/licenses/by/4.0/text/html10652023-06-23research papers56August 2023Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/4med@iucr.org1600-57671600-57671057Small-angle X-ray scattering in the era of fourth-generation light sources
http://scripts.iucr.org/cgi-bin/paper?uu5008
Recently, fourth-generation synchrotron sources with several orders of magnitude higher brightness and higher degree of coherence compared with third-generation sources have come into operation. These new X-ray sources offer exciting opportunities for the investigation of soft matter and biological specimens by small-angle X-ray scattering (SAXS) and related scattering methods. The improved beam properties together with the advanced pixel array detectors readily enhance the angular resolution of SAXS and ultra-small-angle X-ray scattering in the pinhole collimation. The high degree of coherence is a major boost for the X-ray photon correlation spectroscopy (XPCS) technique, enabling the equilibrium dynamics to be probed over broader time and length scales. This article presents some representative examples illustrating the performance of SAXS and XPCS with the Extremely Brilliant Source at the European Synchrotron Radiation Facility. The rapid onset of radiation damage is a significant challenge with the vast majority of samples, and appropriate protocols need to be adopted for circumventing this problem.International Union of CrystallographytextRecently, fourth-generation synchrotron sources with several orders of magnitude higher brightness and higher degree of coherence compared with third-generation sources have come into operation. These new X-ray sources offer exciting opportunities for the investigation of soft matter and biological specimens by small-angle X-ray scattering (SAXS) and related scattering methods. The improved beam properties together with the advanced pixel array detectors readily enhance the angular resolution of SAXS and ultra-small-angle X-ray scattering in the pinhole collimation. The high degree of coherence is a major boost for the X-ray photon correlation spectroscopy (XPCS) technique, enabling the equilibrium dynamics to be probed over broader time and length scales. This article presents some representative examples illustrating the performance of SAXS and XPCS with the Extremely Brilliant Source at the European Synchrotron Radiation Facility. The rapid onset of radiation damage is a significant challenge with the vast majority of samples, and appropriate protocols need to be adopted for circumventing this problem.enNarayanan, T.Chèvremont, W.Zinn, T.Small-angle X-ray scattering in the era of fourth-generation light sources2023-06-23SMALL-ANGLE X-RAY SCATTERING; ULTRA-SMALL-ANGLE X-RAY SCATTERING; X-RAY PHOTON CORRELATION SPECTROSCOPY; FOURTH-GENERATION SYNCHROTRONS; ACTIVE COLLOIDS; SOFT MATTER SYSTEMS; RADIATION DAMAGEdoi:10.1107/S1600576723004971urn:issn:1600-5767This article presents some representative examples illustrating the performance of small-angle X-ray scattering and X-ray photon correlation spectroscopy methods with the Extremely Brilliant Source at the European Synchrotron Radiation Facility.https://creativecommons.org/licenses/by/4.0/text/htmlresearch papers569462023-06-23August 20234https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767939med@iucr.org1600-5767Texture-based residual stress analysis of laser powder bed fused Inconel 718 parts
http://scripts.iucr.org/cgi-bin/paper?xx5022
Although layer-based additive manufacturing methods such as laser powder bed fusion (PBF-LB) offer an immense geometrical freedom in design, they are typically subject to a build-up of internal stress (i.e. thermal stress) during manufacturing. As a consequence, significant residual stress (RS) is retained in the final part as a footprint of these internal stresses. Furthermore, localized melting and solidification inherently induce columnar-type grain growth accompanied by crystallographic texture. Although diffraction-based methods are commonly used to determine the RS distribution in PBF-LB parts, such features pose metrological challenges in their application. In theory, preferred grain orientation invalidates the hypothesis of isotropic material behavior underlying the common methods to determine RS. In this work, more refined methods are employed to determine RS in PBF-LB/M/IN718 prisms, based on crystallographic texture data. In fact, the employment of direction-dependent elastic constants (i.e. stress factors) for the calculation of RS results in insignificant differences from conventional approaches based on the hypothesis of isotropic mechanical properties. It can be concluded that this result is directly linked to the fact that the {311} lattice planes typically used for RS analysis in nickel-based alloys have high multiplicity and less strong texture intensities compared with other lattice planes. It is also found that the length of the laser scan vectors determines the surface RS distribution in prisms prior to their removal from the baseplate. On removal from the baseplate the surface RS considerably relaxes and/or redistributes; a combination of the geometry and the scanning strategy dictates the sub-surface RS distribution.International Union of CrystallographytextAlthough layer-based additive manufacturing methods such as laser powder bed fusion (PBF-LB) offer an immense geometrical freedom in design, they are typically subject to a build-up of internal stress (i.e. thermal stress) during manufacturing. As a consequence, significant residual stress (RS) is retained in the final part as a footprint of these internal stresses. Furthermore, localized melting and solidification inherently induce columnar-type grain growth accompanied by crystallographic texture. Although diffraction-based methods are commonly used to determine the RS distribution in PBF-LB parts, such features pose metrological challenges in their application. In theory, preferred grain orientation invalidates the hypothesis of isotropic material behavior underlying the common methods to determine RS. In this work, more refined methods are employed to determine RS in PBF-LB/M/IN718 prisms, based on crystallographic texture data. In fact, the employment of direction-dependent elastic constants (i.e. stress factors) for the calculation of RS results in insignificant differences from conventional approaches based on the hypothesis of isotropic mechanical properties. It can be concluded that this result is directly linked to the fact that the {311} lattice planes typically used for RS analysis in nickel-based alloys have high multiplicity and less strong texture intensities compared with other lattice planes. It is also found that the length of the laser scan vectors determines the surface RS distribution in prisms prior to their removal from the baseplate. On removal from the baseplate the surface RS considerably relaxes and/or redistributes; a combination of the geometry and the scanning strategy dictates the sub-surface RS distribution.enSchröder, J.Evans, A.Luzin, V.Abreu Faria, G.Degener, S.Polatidis, E.Čapek, J.Kromm, A.Dovzhenko, G.Bruno, G.Texture-based residual stress analysis of laser powder bed fused Inconel 718 parts2023-06-30ADDITIVE MANUFACTURING; ELECTRON BACKSCATTERED DIFFRACTION; PRINCIPAL STRESS; RESIDUAL STRESSdoi:10.1107/S1600576723004855urn:issn:1600-5767In this article, a texture-based characterization of surface, sub-surface and bulk residual stress in laser powder bed fused Inconel 718 alloy is carried out. It is shown that, in the case of this nickel-based superalloy, the texture affects the residual stress determination only when it has sufficient strength.https://creativecommons.org/licenses/by/4.0/text/html4https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography10761600-57671600-5767med@iucr.orgresearch papers562023-06-301090August 2023Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10
http://scripts.iucr.org/cgi-bin/paper?ap5049
Binder H33 is a small protein binder engineered by ribosome display to bind human interleukin 10. Crystals of binder H33 display severe diffraction anisotropy. A set of data files with correction for diffraction anisotropy based on different local signal-to-noise ratios was prepared. Paired refinement was used to find the optimal anisotropic high-resolution diffraction limit of the data: 3.13–2.47 Å. The structure of binder H33 belongs to the 2% of crystal structures with the highest solvent content in the Protein Data Bank.International Union of CrystallographytextBinder H33 is a small protein binder engineered by ribosome display to bind human interleukin 10. Crystals of binder H33 display severe diffraction anisotropy. A set of data files with correction for diffraction anisotropy based on different local signal-to-noise ratios was prepared. Paired refinement was used to find the optimal anisotropic high-resolution diffraction limit of the data: 3.13–2.47 Å. The structure of binder H33 belongs to the 2% of crystal structures with the highest solvent content in the Protein Data Bank.enKolenko, P.Mikulecký, P.Pham, P.N.Malý, M.Schneider, B.Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 102023-06-16ANISOTROPY; PAIRED REFINEMENT; BINDER H33doi:10.1107/S160057672300479Xurn:issn:1600-5767The paired refinement procedure was applied on diffraction data from binder H33 corrected for strong diffraction anisotropy.https://creativecommons.org/licenses/by/4.0/text/htmlAugust 202356short communications2023-06-16126612611600-57671600-5767med@iucr.org4Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Progress in detection of and correction for low-energy contamination
http://scripts.iucr.org/cgi-bin/paper?oc5025
Contamination with low-energy radiation leads to an increased number of weighted residuals being larger in absolute terms than three standard uncertainties. For a Gaussian distribution, these rare events occur only in 0.27% of all cases, which is a small number for small- to medium-sized data sets. The correct detection of rare events – and an adequate correction procedure – thus relies crucially on correct standard uncertainties, which are often not available [Henn (2019), Crystallogr. Rev. 25, 83–156]. It is therefore advisable to use additional, more robust, metrics to complement the established ones. These metrics are developed here and applied to reference data sets from two different publications about low-energy contamination. Other systematic errors were found in the reference data sets. These errors compromise the correction procedures and may lead to under- or overcompensation. This can be demonstrated clearly with the new metrics. Empirical correction procedures generally may be compromised or bound to fail in the presence of other systematic errors. The following systematic errors, which were found in the reference data sets, need to be corrected for prior to application of the low-energy contamination correction procedure: signals of 2λ contamination, extinction, disorder, twinning, and too-large or too-low standard uncertainties (this list may not be complete). All five reference data sets of one publication show a common resolution-dependent systematic error of unknown origin. How this affects the correction procedure can be stated only after elimination of this error. The methodological improvements are verified with data published by other authors.International Union of CrystallographytextContamination with low-energy radiation leads to an increased number of weighted residuals being larger in absolute terms than three standard uncertainties. For a Gaussian distribution, these rare events occur only in 0.27% of all cases, which is a small number for small- to medium-sized data sets. The correct detection of rare events – and an adequate correction procedure – thus relies crucially on correct standard uncertainties, which are often not available [Henn (2019), Crystallogr. Rev. 25, 83–156]. It is therefore advisable to use additional, more robust, metrics to complement the established ones. These metrics are developed here and applied to reference data sets from two different publications about low-energy contamination. Other systematic errors were found in the reference data sets. These errors compromise the correction procedures and may lead to under- or overcompensation. This can be demonstrated clearly with the new metrics. Empirical correction procedures generally may be compromised or bound to fail in the presence of other systematic errors. The following systematic errors, which were found in the reference data sets, need to be corrected for prior to application of the low-energy contamination correction procedure: signals of 2λ contamination, extinction, disorder, twinning, and too-large or too-low standard uncertainties (this list may not be complete). All five reference data sets of one publication show a common resolution-dependent systematic error of unknown origin. How this affects the correction procedure can be stated only after elimination of this error. The methodological improvements are verified with data published by other authors.enDomagala, S.Nourd, P.Diederichs, K.Henn, J.Progress in detection of and correction for low-energy contamination2023-07-25DATA QUALITY METRICS; SYSTEMATIC ERRORS; FLAWED STANDARD UNCERTAINTIES; ROBUST METRICS; LOW-ENERGY CONTAMINATIONdoi:10.1107/S1600576723004764urn:issn:1600-5767A new robust indicator for low-energy contamination is presented and applied to experimental data. The standard correction procedure for low-energy contamination is improved.https://creativecommons.org/licenses/by/4.0/text/htmlAugust 20232023-07-25122056research papers1600-5767med@iucr.org12001600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography4Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography
http://scripts.iucr.org/cgi-bin/paper?jo5080
Time-resolved crystallography enables the visualization of protein molecular motion during a reaction. Although light is often used to initiate reactions in time-resolved crystallography, only a small number of proteins can be activated by light. However, many biological reactions can be triggered by the interaction between proteins and ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D-printed microchannels in conjunction with a micronozzle. The diffusive mixing enables the study of the dynamics of samples in viscous media. The device design allows mixing of the ligands and protein crystals in 2 to 20 s. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within lipidic cubic phase, can be mixed efficiently. The potential of this approach for time-resolved membrane protein crystallography to support the development of new drugs is discussed.International Union of CrystallographytextTime-resolved crystallography enables the visualization of protein molecular motion during a reaction. Although light is often used to initiate reactions in time-resolved crystallography, only a small number of proteins can be activated by light. However, many biological reactions can be triggered by the interaction between proteins and ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D-printed microchannels in conjunction with a micronozzle. The diffusive mixing enables the study of the dynamics of samples in viscous media. The device design allows mixing of the ligands and protein crystals in 2 to 20 s. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within lipidic cubic phase, can be mixed efficiently. The potential of this approach for time-resolved membrane protein crystallography to support the development of new drugs is discussed.enVakili, M.Han, H.Schmidt, C.Wrona, A.Kloos, M.de Diego, I.Dörner, K.Geng, T.Kim, C.Koua, F.H.M.Melo, D.V.M.Rappas, M.Round, A.Round, E.Sikorski, M.Valerio, J.Zhou, T.Lorenzen, K.Schulz, J.Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography2023-06-12TIME-RESOLVED SERIAL CRYSTALLOGRAPHY; MIX-AND-EXTRUDE; 3D-PRINTED NOZZLES; MEMBRANE PROTEINS; X-RAY FREE-ELECTRON LASERSdoi:10.1107/S1600576723004405urn:issn:1600-57673D-printed mixing high-viscosity extruder devices address time-resolved membrane protein crystallography challenges via compact dual-flow lipidic cubic phase injection.https://creativecommons.org/licenses/by/4.0/text/html10381600-57671600-5767med@iucr.org4Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/August 2023research papers562023-06-121045Representative volume elements of strain/stress fields measured by diffraction techniques
http://scripts.iucr.org/cgi-bin/paper?xx5016
Finite-element modelling has been used to simulate local strains and stresses within free-standing polycrystalline slabs of W, Cu and W–Cu, heated with free or constrained boundaries. The elastic strain values in crystallites that satisfied the diffraction condition were used to simulate the lattice strain data that would be obtained from diffraction analysis, from which the average stresses within diffracting domains were computed. Comparison of direct-space stresses in the model with the average stresses determined from diffraction analysis shows that the representative volume elements (RVEs) required to obtain equivalent stress/strain values depend on the deformation mode suffered by the material. Further, the direct-space and diffraction stress values agree only under strict sampling and strain/stress uniformity conditions. Consequently, in samples where measurements are conducted in volumes smaller than the RVE, or where the uniformity conditions are not satisfied, further experimental and numerical techniques might be needed for the accurate determination of applied or residual stress distributions.International Union of CrystallographytextFinite-element modelling has been used to simulate local strains and stresses within free-standing polycrystalline slabs of W, Cu and W–Cu, heated with free or constrained boundaries. The elastic strain values in crystallites that satisfied the diffraction condition were used to simulate the lattice strain data that would be obtained from diffraction analysis, from which the average stresses within diffracting domains were computed. Comparison of direct-space stresses in the model with the average stresses determined from diffraction analysis shows that the representative volume elements (RVEs) required to obtain equivalent stress/strain values depend on the deformation mode suffered by the material. Further, the direct-space and diffraction stress values agree only under strict sampling and strain/stress uniformity conditions. Consequently, in samples where measurements are conducted in volumes smaller than the RVE, or where the uniformity conditions are not satisfied, further experimental and numerical techniques might be needed for the accurate determination of applied or residual stress distributions.enŞeren, M.H.Pagan, D.C.Noyan, I.C.Representative volume elements of strain/stress fields measured by diffraction techniques2023-07-20DIFFRACTION ANALYSIS; STRESS; STRAIN; POLYCRYSTALLINE SOLIDSdoi:10.1107/S1600576723004351urn:issn:1600-5767Representative volume elements for diffraction-based stress/strain distributions in polycrystalline materials are compared with direct-space values of these quantities using numerical modelling. The results indicate that these volumes and their stress states are equivalent under very specific conditions.https://creativecommons.org/licenses/by/4.0/text/html11672023-07-20research papers56August 2023Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/4med@iucr.org1600-57671600-57671144Bragg coherent diffraction imaging with the CITIUS charge-integrating detector
http://scripts.iucr.org/cgi-bin/paper?te5114
The CITIUS detector is a next-generation high-speed X-ray imaging detector. It has integrating-type pixels and is designed to show a consistent linear response at a frame rate of 17.4 kHz, which results in a saturation count rate of over 30 Mcps pixel−1 when operating at an acquisition duty cycle close to 100%, and up to 20 times higher with special extended acquisition modes. Here, its application for Bragg coherent diffraction imaging is demonstrated by taking advantage of the fourth-generation Extremely Brilliant Source of the European Synchrotron (ESRF-EBS, Grenoble, France). The CITIUS detector outperformed a photon-counting detector, similar spatial resolution being achieved (20 ± 6 nm versus 22 ± 9 nm) with greatly reduced acquisition times (23 s versus 200 s). It is also shown how the CITIUS detector can be expected to perform during dynamic Bragg coherent diffraction imaging measurements. Finally, the current limitations of the CITIUS detector and further optimizations for coherent imaging techniques are discussed.International Union of CrystallographytextThe CITIUS detector is a next-generation high-speed X-ray imaging detector. It has integrating-type pixels and is designed to show a consistent linear response at a frame rate of 17.4 kHz, which results in a saturation count rate of over 30 Mcps pixel−1 when operating at an acquisition duty cycle close to 100%, and up to 20 times higher with special extended acquisition modes. Here, its application for Bragg coherent diffraction imaging is demonstrated by taking advantage of the fourth-generation Extremely Brilliant Source of the European Synchrotron (ESRF-EBS, Grenoble, France). The CITIUS detector outperformed a photon-counting detector, similar spatial resolution being achieved (20 ± 6 nm versus 22 ± 9 nm) with greatly reduced acquisition times (23 s versus 200 s). It is also shown how the CITIUS detector can be expected to perform during dynamic Bragg coherent diffraction imaging measurements. Finally, the current limitations of the CITIUS detector and further optimizations for coherent imaging techniques are discussed.enGrimes, M.Pauwels, K.Schülli, T.U.Martin, T.Fajardo, P.Douissard, P.-A.Kocsis, M.Nishino, H.Ozaki, K.Honjo, Y.Nishiyama Hiraki, T.Joti, Y.Hatsui, T.Levi, M.Rabkin, E.Leake, S.J.Richard, M.-I.Bragg coherent diffraction imaging with the CITIUS charge-integrating detector2023-06-12CHARGE-INTEGRATING DETECTORS; BRAGG COHERENT DIFFRACTION IMAGING; FOURTH-GENERATION SYNCHROTRONS; PHOTON-COUNTING DETECTORS; DYNAMIC RANGEdoi:10.1107/S1600576723004314urn:issn:1600-5767Three-dimensional Bragg coherent diffraction imaging with the CITIUS charge-integrating detector is demonstrated.https://creativecommons.org/licenses/by/4.0/text/htmlAugust 202356research papers2023-06-12103710321600-57671600-5767med@iucr.org4https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyImplication of the double-gating mode in a hybrid photon counting detector for measurements of transient heat conduction in GaAs/AlAs superlattice structures
http://scripts.iucr.org/cgi-bin/paper?jl5061
Understanding and control of thermal transport in solids at the nanoscale are crucial in engineering and enhance the properties of a new generation of optoelectronic, thermoelectric and photonic devices. In this regard, semiconductor superlattice structures provide a unique platform to study phenomena associated with phonon propagations in solids such as heat conduction. Transient X-ray diffraction can directly probe atomic motions and therefore is among the rare techniques sensitive to phonon dynamics in condensed matter. Here, optically induced transient heat conduction in GaAs/AlAs superlattice structures is studied using the EIGER2 detector. Benchmark experiments have been performed at the Austrian SAXS beamline at Elettra–Sincrotrone Trieste operated in the hybrid filling mode. This work demonstrates that drifts of experimental conditions, such as synchrotron beam fluctuations, become less essential when utilizing the EIGER2 double-gating mode which results in a faster acquisition of high-quality data and facilitates data analysis and data interpretation.International Union of CrystallographytextUnderstanding and control of thermal transport in solids at the nanoscale are crucial in engineering and enhance the properties of a new generation of optoelectronic, thermoelectric and photonic devices. In this regard, semiconductor superlattice structures provide a unique platform to study phenomena associated with phonon propagations in solids such as heat conduction. Transient X-ray diffraction can directly probe atomic motions and therefore is among the rare techniques sensitive to phonon dynamics in condensed matter. Here, optically induced transient heat conduction in GaAs/AlAs superlattice structures is studied using the EIGER2 detector. Benchmark experiments have been performed at the Austrian SAXS beamline at Elettra–Sincrotrone Trieste operated in the hybrid filling mode. This work demonstrates that drifts of experimental conditions, such as synchrotron beam fluctuations, become less essential when utilizing the EIGER2 double-gating mode which results in a faster acquisition of high-quality data and facilitates data analysis and data interpretation.enNaumenko, D.Burian, M.Marmiroli, B.Haider, R.Radeticchio, A.Wagner, L.Piazza, L.Glatt, L.Brandstetter, S.Dal Zilio, S.Biasiol, G.Amenitsch, H.Implication of the double-gating mode in a hybrid photon counting detector for measurements of transient heat conduction in GaAs/AlAs superlattice structures2023-06-16PUMP-PROBE X-RAY DIFFRACTION; NON-FOURIER HEAT TRANSPORT; GAAS/ALAS SUPERLATTICES; HYBRID PHOTON COUNTING DETECTORSdoi:10.1107/S1600576723004302urn:issn:1600-5767Use of the double-gating mode implemented on the modern hybrid photon counting system EIGER2 helps to suppress the influence of beam fluctuations in pump–probe experiments at synchrotron radiation facilities and provides better data quality.https://creativecommons.org/licenses/by/4.0/text/html2023-06-1696656research papersAugust 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography41600-5767med@iucr.org9611600-5767Robust phase determination in complex solid solutions using diffuse multiple scattering
http://scripts.iucr.org/cgi-bin/paper?iu5035
A novel methodology is presented for identifying and distinguishing between structural phases in multi-phasic systems, such as piezoelectric materials like PMN–PT [Pb(Mg1/3Nb2/3)O3–PbTiO3], PIN–PMN–PT [Pb(In1/2Nb1/2)O3–Pb(Mg1/3Nb2/3)O3–PbTiO3] and PZT [Pb(Zr,Ti)O3], using diffuse multiple scattering and Kossel line diffraction techniques. The method exploits the splitting of triple line intersections from special coplanar reflections combined with logical constraints to generate a splitting fingerprint for robust crystallographic phase determination and discrimination.International Union of CrystallographytextA novel methodology is presented for identifying and distinguishing between structural phases in multi-phasic systems, such as piezoelectric materials like PMN–PT [Pb(Mg1/3Nb2/3)O3–PbTiO3], PIN–PMN–PT [Pb(In1/2Nb1/2)O3–Pb(Mg1/3Nb2/3)O3–PbTiO3] and PZT [Pb(Zr,Ti)O3], using diffuse multiple scattering and Kossel line diffraction techniques. The method exploits the splitting of triple line intersections from special coplanar reflections combined with logical constraints to generate a splitting fingerprint for robust crystallographic phase determination and discrimination.enNisbet, A.G.A.Cain, M.G.Hase, T.Finkel, P.Robust phase determination in complex solid solutions using diffuse multiple scattering2023-06-12MORPHOTROPIC; PIEZOELECTRIC; DIFFUSE MULTIPLE SCATTERING; PHASE DETERMINATION; COMPLEX SOLID SOLUTIONS; FINGERPRINTING; KOSSEL LINESdoi:10.1107/S1600576723004120urn:issn:1600-5767A new fingerprinting methodology is presented for phase discrimination in complex solid solutions near the morphotropic phase boundary.https://creativecommons.org/licenses/by/4.0/text/html1600-57671046med@iucr.org1600-57674https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyAugust 202356research papers10502023-06-12Upgraded D22 SEC–SANS setup dedicated to the biology community
http://scripts.iucr.org/cgi-bin/paper?tj5032
Described here is the current status of the upgraded in situ size-exclusion chromatography (SEC) system implemented with the D22 small-angle neutron scattering (SANS) instrument at the Institut Laue–Langevin. Since its initial proof of principle in 2016, this SEC–SANS arrangement has been continuously requested by the user community, leading to the design of an upgraded version. A detailed description of the setup and its control is provided, and a few examples of protein structural investigations are presented, which will highlight the various possibilities and limitations of the setup to optimize experimental success.International Union of CrystallographytextDescribed here is the current status of the upgraded in situ size-exclusion chromatography (SEC) system implemented with the D22 small-angle neutron scattering (SANS) instrument at the Institut Laue–Langevin. Since its initial proof of principle in 2016, this SEC–SANS arrangement has been continuously requested by the user community, leading to the design of an upgraded version. A detailed description of the setup and its control is provided, and a few examples of protein structural investigations are presented, which will highlight the various possibilities and limitations of the setup to optimize experimental success.enMartel, A.Cocho, C.Caporaletti, F.Jacques, M.El Aazzouzi, A.Lapeyre, F.Porcar, L.Upgraded D22 SEC–SANS setup dedicated to the biology community2023-06-12SIZE-EXCLUSION CHROMATOGRAPHY; SEC; SMALL-ANGLE NEUTRON SCATTERING; SANS; SEC-SANSdoi:10.1107/S1600576723004119urn:issn:1600-5767This publication describes the stable version of a liquid chromatography system combined with the small-angle neutron scattering (SANS) instrument D22 at Institut Laue–Langevin to run size-exclusion chromatography (SEC) immediately before SANS measurement.https://creativecommons.org/licenses/by/4.0/text/html1600-5767med@iucr.org9941600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/4August 20232023-06-12100156research papersEDP2PDF: a computer program for extracting a pair distribution function from an electron diffraction pattern for the structural analysis of materials
http://scripts.iucr.org/cgi-bin/paper?te5109
Pair distribution function (PDF) analysis is a powerful technique to understand atomic scale structure in materials science. Unlike X-ray diffraction (XRD)-based PDF analysis, the PDF calculated from electron diffraction patterns (EDPs) using transmission electron microscopy can provide structural information from specific locations with high spatial resolution. The present work describes a new software tool for both periodic and amorphous structures that addresses several practical challenges in calculating the PDF from EDPs. The key features of this program include accurate background subtraction using a nonlinear iterative peak-clipping algorithm and automatic conversion of various types of diffraction intensity profiles into a PDF without requiring external software. The present study also evaluates the effect of background subtraction and the elliptical distortion of EDPs on PDF profiles. The EDP2PDF software is offered as a reliable tool to analyse the atomic structure of crystalline and non-crystalline materials.International Union of CrystallographytextPair distribution function (PDF) analysis is a powerful technique to understand atomic scale structure in materials science. Unlike X-ray diffraction (XRD)-based PDF analysis, the PDF calculated from electron diffraction patterns (EDPs) using transmission electron microscopy can provide structural information from specific locations with high spatial resolution. The present work describes a new software tool for both periodic and amorphous structures that addresses several practical challenges in calculating the PDF from EDPs. The key features of this program include accurate background subtraction using a nonlinear iterative peak-clipping algorithm and automatic conversion of various types of diffraction intensity profiles into a PDF without requiring external software. The present study also evaluates the effect of background subtraction and the elliptical distortion of EDPs on PDF profiles. The EDP2PDF software is offered as a reliable tool to analyse the atomic structure of crystalline and non-crystalline materials.enLiu, H.Nomoto, K.Ceguerra, A.V.Kruzic, J.J.Cairney, J.Ringer, S.P.EDP2PDF: a computer program for extracting a pair distribution function from an electron diffraction pattern for the structural analysis of materials2023-05-31ELECTRON DIFFRACTION PATTERNS; PAIR DISTRIBUTION FUNCTIONS; COMPUTER PROGRAMSdoi:10.1107/S1600576723004053urn:issn:1600-5767A new program named EDP2PDF is developed for the conversion of an electron diffraction pattern into a pair distribution function for materials structure analysis.https://creativecommons.org/licenses/by/4.0/text/htmlJune 20232023-05-31902computer programs561600-5767med@iucr.org8891600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/3Sub-second pair distribution function using a broad bandwidth monochromator
http://scripts.iucr.org/cgi-bin/paper?vb5050
Here the use of a broad energy bandwidth monochromator, i.e. a pair of B4C/W multilayer mirrors (MLMs), is demonstrated for X-ray total scattering (TS) measurements and pair distribution function (PDF) analysis. Data are collected both on powder samples and from metal oxo clusters in aqueous solution at various concentrations. A comparison between the MLM PDFs and those obtained using a standard Si(111) double-crystal monochromator shows that the measurements yield MLM PDFs of high quality which are suitable for structure refinement. Moreover, the effects of time resolution and concentration on the quality of the resulting PDFs of the metal oxo clusters are investigated. PDFs of heptamolybdate clusters and tungsten α-Keggin clusters from X-ray TS data were obtained with a time resolution down to 3 ms and still showed a similar level of Fourier ripples to PDFs obtained from 1 s measurements. This type of measurement could thus open up faster time-resolved TS and PDF studies.International Union of CrystallographytextHere the use of a broad energy bandwidth monochromator, i.e. a pair of B4C/W multilayer mirrors (MLMs), is demonstrated for X-ray total scattering (TS) measurements and pair distribution function (PDF) analysis. Data are collected both on powder samples and from metal oxo clusters in aqueous solution at various concentrations. A comparison between the MLM PDFs and those obtained using a standard Si(111) double-crystal monochromator shows that the measurements yield MLM PDFs of high quality which are suitable for structure refinement. Moreover, the effects of time resolution and concentration on the quality of the resulting PDFs of the metal oxo clusters are investigated. PDFs of heptamolybdate clusters and tungsten α-Keggin clusters from X-ray TS data were obtained with a time resolution down to 3 ms and still showed a similar level of Fourier ripples to PDFs obtained from 1 s measurements. This type of measurement could thus open up faster time-resolved TS and PDF studies.enMagnard, N.P.L.Sørensen, D.R.Kantor, I.Jensen, K.M.Ø.Jørgensen, M.R.V.Sub-second pair distribution function using a broad bandwidth monochromator2023-05-31TOTAL SCATTERING; PAIR DISTRIBUTION FUNCTION; METAL OXO CLUSTERS; SYNCHROTRON RADIATIONdoi:10.1107/S1600576723004016urn:issn:1600-5767This work demonstrates the use of a broad energy bandwidth multilayer mirror monochromator for X-ray total scattering (TS) measurements and pair distribution function (PDF) analysis. This type of measurement could facilitate faster time-resolved TS and PDF studies.https://creativecommons.org/licenses/by/4.0/text/html56research papers8332023-05-31June 20233https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767825med@iucr.org1600-5767Optimizing surfactant removal from a soft-templated ordered mesoporous carbon precursor: an in situ SAXS study
http://scripts.iucr.org/cgi-bin/paper?uu5006
In situ small-angle X-ray scattering (SAXS) was employed to identify critical parameters during thermal treatment for template removal of an ordered mesoporous carbon precursor synthesized via a direct soft-templating route. The structural parameters obtained from the SAXS data as a function of time were the lattice parameter of the 2D hexagonal structure, the diameter of the cylindrical mesostructures and a power-law exponent characterizing the interface roughness. Moreover, detailed information on contrast changes and pore lattice order was obtained from analysis of the integrated SAXS intensity of the Bragg and diffuse scattering separately. Five characteristic regions during heat treatment were identified and discussed regarding the underlying dominant processes. The influence of temperature and O2/N2 ratio on the final structure was analyzed, and parameter ranges were identified for an optimized template removal without strongly affecting the matrix. The results indicate that the final structure and controllability of the process are optimum for temperatures between 260 and 300°C with a gas flow containing 2 mol% of O2.International Union of CrystallographytextIn situ small-angle X-ray scattering (SAXS) was employed to identify critical parameters during thermal treatment for template removal of an ordered mesoporous carbon precursor synthesized via a direct soft-templating route. The structural parameters obtained from the SAXS data as a function of time were the lattice parameter of the 2D hexagonal structure, the diameter of the cylindrical mesostructures and a power-law exponent characterizing the interface roughness. Moreover, detailed information on contrast changes and pore lattice order was obtained from analysis of the integrated SAXS intensity of the Bragg and diffuse scattering separately. Five characteristic regions during heat treatment were identified and discussed regarding the underlying dominant processes. The influence of temperature and O2/N2 ratio on the final structure was analyzed, and parameter ranges were identified for an optimized template removal without strongly affecting the matrix. The results indicate that the final structure and controllability of the process are optimum for temperatures between 260 and 300°C with a gas flow containing 2 mol% of O2.enRauscher, M.V.Seyffertitz, M.Kohns, R.Stock, S.Amenitsch, H.Huesing, N.Paris, O.Optimizing surfactant removal from a soft-templated ordered mesoporous carbon precursor: an in situ SAXS study2023-05-29IN SITU SMALL-ANGLE X-RAY SCATTERING; SOFT-TEMPLATED CARBONS; ORDERED MESOPOROUS CARBONS; CALCINATIONdoi:10.1107/S1600576723003886urn:issn:1600-5767In situ small-angle X-ray scattering was used to identify structural changes during thermal treatment of an ordered mesoporous carbon precursor material, synthesized via direct soft templating, to remove Pluronic F127 surfactant from a resorcinol–formaldehyde frame.https://creativecommons.org/licenses/by/4.0/text/html56research papers8092023-05-29June 20233Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767801med@iucr.org1600-5767Selected advances in small-angle scattering and applications they serve in manufacturing, energy and climate change
http://scripts.iucr.org/cgi-bin/paper?uu5002
Innovations in small-angle X-ray and neutron scattering (SAXS and SANS) at major X-ray and neutron facilities offer new characterization tools for researching materials phenomena relevant to advanced applications. For SAXS, the new generation of diffraction-limited storage rings, incorporating multi-bend achromat concepts, dramatically decrease electron beam emittance and significantly increase X-ray brilliance over previous third-generation sources. This results in intense X-ray incident beams that are more compact in the horizontal plane, allowing significantly improved spatial resolution, better time resolution, and a new era for coherent-beam SAXS methods such as X-ray photon correlation spectroscopy. Elsewhere, X-ray free-electron laser sources provide extremely bright, fully coherent, X-ray pulses of <100 fs and can support SAXS studies of material processes where entire SAXS data sets are collected in a single pulse train. Meanwhile, SANS at both steady-state reactor and pulsed spallation neutron sources has significantly evolved. Developments in neutron optics and multiple detector carriages now enable data collection in a few minutes for materials characterization over nanometre-to-micrometre scale ranges, opening up real-time studies of multi-scale materials phenomena. SANS at pulsed neutron sources is becoming more integrated with neutron diffraction methods for simultaneous structure characterization of complex materials. In this paper, selected developments are highlighted and some recent state-of-the-art studies discussed, relevant to hard matter applications in advanced manufacturing, energy and climate change.International Union of CrystallographytextInnovations in small-angle X-ray and neutron scattering (SAXS and SANS) at major X-ray and neutron facilities offer new characterization tools for researching materials phenomena relevant to advanced applications. For SAXS, the new generation of diffraction-limited storage rings, incorporating multi-bend achromat concepts, dramatically decrease electron beam emittance and significantly increase X-ray brilliance over previous third-generation sources. This results in intense X-ray incident beams that are more compact in the horizontal plane, allowing significantly improved spatial resolution, better time resolution, and a new era for coherent-beam SAXS methods such as X-ray photon correlation spectroscopy. Elsewhere, X-ray free-electron laser sources provide extremely bright, fully coherent, X-ray pulses of <100 fs and can support SAXS studies of material processes where entire SAXS data sets are collected in a single pulse train. Meanwhile, SANS at both steady-state reactor and pulsed spallation neutron sources has significantly evolved. Developments in neutron optics and multiple detector carriages now enable data collection in a few minutes for materials characterization over nanometre-to-micrometre scale ranges, opening up real-time studies of multi-scale materials phenomena. SANS at pulsed neutron sources is becoming more integrated with neutron diffraction methods for simultaneous structure characterization of complex materials. In this paper, selected developments are highlighted and some recent state-of-the-art studies discussed, relevant to hard matter applications in advanced manufacturing, energy and climate change.enAllen, A.J.Selected advances in small-angle scattering and applications they serve in manufacturing, energy and climate change2023-05-29SMALL-ANGLE X-RAY SCATTERING; SMALL-ANGLE NEUTRON SCATTERING; MICROSTRUCTURE CHARACTERIZATION; ADVANCED MANUFACTURING; ENERGY APPLICATIONS; CARBON DIOXIDE REDUCTIONdoi:10.1107/S1600576723003898urn:issn:1600-5767Selected recent advances in small-angle X-ray and neutron scattering are highlighted, together with some of the hard material applications they serve in the areas of manufacturing, energy and climate change. This paper is associated with work presented at the 18th International Conference on Small-Angle Scattering, Campinas, Brazil, September 2022 (SAS 2022).https://creativecommons.org/licenses/by/4.0/text/htmlJune 202356research papers8002023-05-291600-5767787med@iucr.org1600-57673Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Tool for automatic macrozone characterization from EBSD data sets of titanium alloys
http://scripts.iucr.org/cgi-bin/paper?nb5349
Microtexture heterogeneities are commonly found in titanium forgings because of the thermomechanical processing. Also known as macrozones, these regions can reach millimetres in length, with grains sharing a similar crystallographic orientation leading to less resistance to crack propagation. Since the link between macrozones and the reduction of cold-dwell-fatigue performance on rotative components in gas turbine engines was established, efforts have been put into macrozone definition and characterization. The electron backscatter diffraction (EBSD) technique, widely used for texture analysis, allows for a qualitative macrozone characterization; however, further processing is required to define the boundaries and disorientation spread of each macrozone. Current approaches often use c-axis misorientation criteria, but this can sometimes lead to a large disorientation spread within a macrozone. This article describes the development and application of a computational tool implemented in MATLAB for automatic macrozone identification from EBSD data sets on the basis of a more conservative approach where both the c-axis tilting and rotation are considered. The tool allows for detection of macrozones according to the disorientation angle and density-fraction criteria. The clustering efficiency is validated by pole-figure plots, and the effects of the key parameters defining the macrozone clustering (disorientation and fraction) are discussed. In addition, this tool was successfully applied to both fully equiaxed and bimodal microstructures of titanium forgings.International Union of CrystallographytextMicrotexture heterogeneities are commonly found in titanium forgings because of the thermomechanical processing. Also known as macrozones, these regions can reach millimetres in length, with grains sharing a similar crystallographic orientation leading to less resistance to crack propagation. Since the link between macrozones and the reduction of cold-dwell-fatigue performance on rotative components in gas turbine engines was established, efforts have been put into macrozone definition and characterization. The electron backscatter diffraction (EBSD) technique, widely used for texture analysis, allows for a qualitative macrozone characterization; however, further processing is required to define the boundaries and disorientation spread of each macrozone. Current approaches often use c-axis misorientation criteria, but this can sometimes lead to a large disorientation spread within a macrozone. This article describes the development and application of a computational tool implemented in MATLAB for automatic macrozone identification from EBSD data sets on the basis of a more conservative approach where both the c-axis tilting and rotation are considered. The tool allows for detection of macrozones according to the disorientation angle and density-fraction criteria. The clustering efficiency is validated by pole-figure plots, and the effects of the key parameters defining the macrozone clustering (disorientation and fraction) are discussed. In addition, this tool was successfully applied to both fully equiaxed and bimodal microstructures of titanium forgings.enFernández Silva, B.Jackson, M.Fox, K.Wynne, B.P.Tool for automatic macrozone characterization from EBSD data sets of titanium alloys2023-05-23MACROZONES; ELECTRON BACKSCATTER DIFFRACTION; TITANIUM ALLOYS; TEXTURE; CHARACTERIZATION; CRYSTAL MISORIENTATION CRITERIAdoi:10.1107/S1600576723003862urn:issn:1600-5767An algorithm for macrozone characterization in titanium alloys based on crystal misorientation criteria is presented and applied to electron backscatter diffraction (EBSD) data sets of titanium forgings.https://creativecommons.org/licenses/by/4.0/text/htmlJune 20237492023-05-2356research papersmed@iucr.org1600-57671600-5767737Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/3Implementation of grain mapping by diffraction contrast tomography on a conventional laboratory tomography setup with various detectors
http://scripts.iucr.org/cgi-bin/paper?nb5348
Laboratory-based diffraction contrast tomography (LabDCT) is a novel technique used to resolve grain orientations and shapes in three dimensions at the micrometre scale using laboratory X-ray sources, allowing the user to overcome the constraint of limited access to synchrotron facilities. To foster the development of this technique, the implementation of LabDCT is illustrated in detail using a conventional laboratory-based X-ray tomography setup, and it is shown that such implementation is possible with the two most common types of detectors: CCD and flat panel. As a benchmark, LabDCT projections were acquired on an AlCu alloy sample using the two types of detectors at different exposure times. Grain maps were subsequently reconstructed using the open-source grain reconstruction method reported in the authors' previous work. To characterize the detection limit and the spatial resolution for the current implementation, the reconstructed LabDCT grain maps were compared with the map obtained from a synchrotron measurement, which is considered as ground truth. The results show that the final grain maps from measurements by the CCD and flat panel detector are similar and show comparable quality, while the CCD gives a much better contrast-to-noise ratio than the flat panel. The analysis of the grain maps reconstructed from measurements with different exposure times suggests that a grain map of comparable quality could be obtained in less than 1 h total acquisition time without a significant loss of grain reconstruction quality and indicates a clear potential for time-lapse LabDCT experiments. The current implementation is suggested to promote the generic use of the LabDCT technique for grain mapping on conventional tomography setups.International Union of CrystallographytextLaboratory-based diffraction contrast tomography (LabDCT) is a novel technique used to resolve grain orientations and shapes in three dimensions at the micrometre scale using laboratory X-ray sources, allowing the user to overcome the constraint of limited access to synchrotron facilities. To foster the development of this technique, the implementation of LabDCT is illustrated in detail using a conventional laboratory-based X-ray tomography setup, and it is shown that such implementation is possible with the two most common types of detectors: CCD and flat panel. As a benchmark, LabDCT projections were acquired on an AlCu alloy sample using the two types of detectors at different exposure times. Grain maps were subsequently reconstructed using the open-source grain reconstruction method reported in the authors' previous work. To characterize the detection limit and the spatial resolution for the current implementation, the reconstructed LabDCT grain maps were compared with the map obtained from a synchrotron measurement, which is considered as ground truth. The results show that the final grain maps from measurements by the CCD and flat panel detector are similar and show comparable quality, while the CCD gives a much better contrast-to-noise ratio than the flat panel. The analysis of the grain maps reconstructed from measurements with different exposure times suggests that a grain map of comparable quality could be obtained in less than 1 h total acquisition time without a significant loss of grain reconstruction quality and indicates a clear potential for time-lapse LabDCT experiments. The current implementation is suggested to promote the generic use of the LabDCT technique for grain mapping on conventional tomography setups.enFang, H.Ludwig, W.Lhuissier, P.Implementation of grain mapping by diffraction contrast tomography on a conventional laboratory tomography setup with various detectors2023-05-31DIFFRACTION CONTRAST TOMOGRAPHY; GRAIN RECONSTRUCTION; CCD DETECTORS; FLAT PANEL DETECTORS; SYNCHROTRON X-RAY DIFFRACTIONdoi:10.1107/S1600576723003874urn:issn:1600-5767Implementation of grain mapping by diffraction contrast tomography has been demonstrated on a conventional tomography setup with two common detectors (CCD and flat panel). Typical grain mapping performance has been characterized for the related experimental conditions and setup, and grain reconstructions from diffraction images acquired with different exposure times demonstrate the possibility of fast grain mapping with laboratory-based X-rays.https://creativecommons.org/licenses/by/4.0/text/htmlJune 202356research papers2023-05-318248101600-57671600-5767med@iucr.org3Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Dynamic catcher for stabilization of high-viscosity extrusion jets
http://scripts.iucr.org/cgi-bin/paper?te5116
A `catcher' based on a revolving cylindrical collector is described. The simple and inexpensive device reduces free-jet instabilities inherent to high-viscosity extrusion injection, facilitating delivery of microcrystals for serial diffraction X-ray crystallography.International Union of CrystallographytextA `catcher' based on a revolving cylindrical collector is described. The simple and inexpensive device reduces free-jet instabilities inherent to high-viscosity extrusion injection, facilitating delivery of microcrystals for serial diffraction X-ray crystallography.enDoak, R.B.Shoeman, R.L.Gorel, A.Barends, T.R.M.Marekha, B.Haacke, S.Nizinski, S.Schlichting, I.Dynamic catcher for stabilization of high-viscosity extrusion jets2023-05-29SERIAL CRYSTALLOGRAPHY; INJECTION; HIGH-VISCOSITY EXTRUSION; CATCHERdoi:10.1107/S1600576723003795urn:issn:1600-5767A `catcher' based on a revolving cylindrical collector is described.https://creativecommons.org/licenses/by/4.0/text/html56laboratory notes9072023-05-29June 20233Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767903med@iucr.org1600-5767On the dependence of creep-induced dislocation configurations on crystallographic orientation in pure Al and Al–Mg
http://scripts.iucr.org/cgi-bin/paper?te5108
The peak broadening in neutron diffraction experiments on tensile specimens of pure Al (99.8%) and an Al–Mg alloy pre-deformed at different creep strains is analysed. These results are combined with the kernel angular misorientation of electron backscatter diffraction data from the creep-deformed microstructures. It is found that differently oriented grains possess different microstrains. These microstrains vary with creep strain in pure Al, but not in the Al–Mg alloy. It is proposed that this behaviour can explain the power-law breakdown in pure Al and the large creep strain observed in Al–Mg. The present findings further corroborate a description of the creep-induced dislocation structure as a fractal, predicated on previous work.International Union of CrystallographytextThe peak broadening in neutron diffraction experiments on tensile specimens of pure Al (99.8%) and an Al–Mg alloy pre-deformed at different creep strains is analysed. These results are combined with the kernel angular misorientation of electron backscatter diffraction data from the creep-deformed microstructures. It is found that differently oriented grains possess different microstrains. These microstrains vary with creep strain in pure Al, but not in the Al–Mg alloy. It is proposed that this behaviour can explain the power-law breakdown in pure Al and the large creep strain observed in Al–Mg. The present findings further corroborate a description of the creep-induced dislocation structure as a fractal, predicated on previous work.enFernández, R.Bokuchava, G.Bruno, G.Serrano-Muñoz, I.González-Doncel, G.On the dependence of creep-induced dislocation configurations on crystallographic orientation in pure Al and Al–Mg2023-05-29CREEP; ALUMINIUM ALLOYS; DISLOCATIONS; FRACTALS; DIFFRACTION PEAK WIDTHdoi:10.1107/S1600576723003771urn:issn:1600-5767This work describes the influence of crystallographic orientation on dislocation arrangements during primary and secondary creep of polycrystalline Al and Al–Mg.https://creativecommons.org/licenses/by/4.0/text/html2023-05-2977556research papersJune 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography31600-5767med@iucr.org7641600-5767Three-phase material mapping with incomplete X-ray diffraction spectral information
http://scripts.iucr.org/cgi-bin/paper?tu5026
An equiatomic nickel–titanium shape-memory alloy specimen subjected to a uniaxial tensile load undergoes a two-step phase transformation under stress, from austenite (A) to a rhombohedral phase (R) and further to martensite (M) variants. The pseudo-elasticity that goes accompanies the phase transformation induces spatial inhomogeneity. To unravel the spatial distribution of the phases, in situ X-ray diffraction analyses are performed while the sample is under tensile load. However, the diffraction spectra of the R phase, as well as the extent of potential martensite detwinning, are not known. A novel algorithm, based on a proper orthogonal decomposition and incorporating inequality constraints, is proposed in order to map out the different phases and simultaneously yield the missing diffraction spectral information. An experimental case study illustrates the methodology.International Union of CrystallographytextAn equiatomic nickel–titanium shape-memory alloy specimen subjected to a uniaxial tensile load undergoes a two-step phase transformation under stress, from austenite (A) to a rhombohedral phase (R) and further to martensite (M) variants. The pseudo-elasticity that goes accompanies the phase transformation induces spatial inhomogeneity. To unravel the spatial distribution of the phases, in situ X-ray diffraction analyses are performed while the sample is under tensile load. However, the diffraction spectra of the R phase, as well as the extent of potential martensite detwinning, are not known. A novel algorithm, based on a proper orthogonal decomposition and incorporating inequality constraints, is proposed in order to map out the different phases and simultaneously yield the missing diffraction spectral information. An experimental case study illustrates the methodology.enChang, X.Lavernhe-Taillard, K.Roux, S.Hubert, O.Three-phase material mapping with incomplete X-ray diffraction spectral information2023-05-23X-RAY DIFFRACTION; SHAPE-MEMORY ALLOYS; PROPER ORTHOGONAL DECOMPOSITIONdoi:10.1107/S160057672300331Xurn:issn:1600-5767A novel algorithm, based on a proper orthogonal decomposition and incorporating inequality constraints, is proposed to map out the different phases of a heterogenous material and simultaneously yield missing diffraction spectral information. An experimental case study of a three-phase NiTi shape-memory alloy under tensile loading illustrates the presented methodology.https://creativecommons.org/licenses/by/4.0/text/htmlJune 202356research papers7632023-05-231600-5767750med@iucr.org1600-57673https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyDislocation arrangements in 4H-SiC and their influence on the local crystal lattice properties
http://scripts.iucr.org/cgi-bin/paper?iu5032
Two wafers of one 4H-silicon carbide (4H-SiC) bulk crystal, one cut from a longitudinal position close to the crystal's seed and the other close to the cap, were characterized with synchrotron white-beam X-ray topography (SWXRT) in back-reflection and transmission geometry to investigate the dislocation formation and propagation during growth. For the first time, full wafer mappings were recorded in 00012 back-reflection geometry with a CCD camera system, providing an overview of the dislocation arrangement in terms of dislocation type, density and homogeneous distribution. Furthermore, by having similar resolution to conventional SWXRT photographic film, the method enables identification of individual dislocations, even single threading screw dislocations, which appear as white spots with a diameter in the range of 10 to 30 µm. Both investigated wafers showed a similar dislocation arrangement, suggesting a constant propagation of dislocations during crystal growth. A systematic investigation of crystal lattice strain and tilt at selected wafer areas with different dislocation arrangements was achieved with high-resolution X-ray diffractometry reciprocal-space map (RSM) measurements in the symmetric 0004 reflection. It was shown that the diffracted intensity distribution of the RSM for different dislocation arrangements depends on the locally predominant dislocation type and density. Moreover, the orientation of specific dislocation types along the RSM scanning direction has a strong influence on the local crystal lattice properties.International Union of CrystallographytextTwo wafers of one 4H-silicon carbide (4H-SiC) bulk crystal, one cut from a longitudinal position close to the crystal's seed and the other close to the cap, were characterized with synchrotron white-beam X-ray topography (SWXRT) in back-reflection and transmission geometry to investigate the dislocation formation and propagation during growth. For the first time, full wafer mappings were recorded in 00012 back-reflection geometry with a CCD camera system, providing an overview of the dislocation arrangement in terms of dislocation type, density and homogeneous distribution. Furthermore, by having similar resolution to conventional SWXRT photographic film, the method enables identification of individual dislocations, even single threading screw dislocations, which appear as white spots with a diameter in the range of 10 to 30 µm. Both investigated wafers showed a similar dislocation arrangement, suggesting a constant propagation of dislocations during crystal growth. A systematic investigation of crystal lattice strain and tilt at selected wafer areas with different dislocation arrangements was achieved with high-resolution X-ray diffractometry reciprocal-space map (RSM) measurements in the symmetric 0004 reflection. It was shown that the diffracted intensity distribution of the RSM for different dislocation arrangements depends on the locally predominant dislocation type and density. Moreover, the orientation of specific dislocation types along the RSM scanning direction has a strong influence on the local crystal lattice properties.enRoder, M.Steiner, J.Wellmann, P.Kabukcuoglu, M.Hamann, E.Haaga, S.Hänschke, D.Danilewsky, A.Dislocation arrangements in 4H-SiC and their influence on the local crystal lattice properties2023-05-294H-SIC; DISLOCATIONS; SYNCHROTRON WHITE-BEAM X-RAY TOPOGRAPHY; HIGH-RESOLUTION X-RAY DIFFRACTOMETRY; CRYSTAL GROWTH; RECIPROCAL-SPACE MAPSdoi:10.1107/S1600576723003291urn:issn:1600-5767In this work, the determination of dislocation arrangements in 4H-silicon carbide (4H-SiC), their evolution in the growth direction and their influence on the crystal lattice properties are presented.https://creativecommons.org/licenses/by/4.0/text/html1600-5767776med@iucr.org1600-57673Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/June 2023research papers567862023-05-29Orientation relationships, orientational variants and the embedding approach
http://scripts.iucr.org/cgi-bin/paper?ap5046
For phase transformations within polycrystalline materials, the connection between the crystal orientations of parent grains and those of child grains is usually expressed in terms of (theoretical or measured) orientation relationships. This paper introduces a new approach to various problems associated with orientation relationships: (i) estimation, (ii) whether or not a single orientation relationship fits the data adequately, (iii) whether or not a set of children comes from a common parent, and (iv) reconstruction of a parent or of grain boundaries. The approach is an extension to the crystallographic context of the well established embedding approach to directional statistics. It is inherently statistical, producing precise probabilistic statements. Explicit coordinate systems are not used and arbitrary thresholds are avoided.International Union of CrystallographytextFor phase transformations within polycrystalline materials, the connection between the crystal orientations of parent grains and those of child grains is usually expressed in terms of (theoretical or measured) orientation relationships. This paper introduces a new approach to various problems associated with orientation relationships: (i) estimation, (ii) whether or not a single orientation relationship fits the data adequately, (iii) whether or not a set of children comes from a common parent, and (iv) reconstruction of a parent or of grain boundaries. The approach is an extension to the crystallographic context of the well established embedding approach to directional statistics. It is inherently statistical, producing precise probabilistic statements. Explicit coordinate systems are not used and arbitrary thresholds are avoided.enArnold, R.Jupp, P.Schaeben, H.Orientation relationships, orientational variants and the embedding approach2023-05-12ORIENTATION RELATIONSHIPS; VARIANTS; DETERMINATION; RECONSTRUCTION; DIRECTIONAL STATISTICSdoi:10.1107/S1600576723003187urn:issn:1600-5767A statistical approach is developed for handling some standard problems involving orientation relationships. The approach is based on directional statistics.https://creativecommons.org/licenses/by/4.0/text/htmlJune 202356research papers2023-05-127367251600-57671600-5767med@iucr.org3https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyPolychromatic neutron phase-contrast imaging of weakly absorbing samples enabled by phase retrieval
http://scripts.iucr.org/cgi-bin/paper?in5077
The use of a phase-retrieval technique for propagation-based phase-contrast neutron imaging with a polychromatic beam is demonstrated. This enables imaging of samples with low absorption contrast and/or improving the signal-to-noise ratio to facilitate e.g. time-resolved measurements. A metal sample, designed to be close to a phase pure object, and a bone sample with canals partially filled with D2O were used for demonstrating the technique. These samples were imaged with a polychromatic neutron beam followed by phase retrieval. For both samples the signal-to-noise ratios were significantly improved and, in the case of the bone sample, the phase retrieval allowed for separation of bone and D2O, which is important for example for in situ flow experiments. The use of deuteration contrast avoids the use of chemical contrast enhancement and makes neutron imaging an interesting complementary method to X-ray imaging of bone.International Union of CrystallographytextThe use of a phase-retrieval technique for propagation-based phase-contrast neutron imaging with a polychromatic beam is demonstrated. This enables imaging of samples with low absorption contrast and/or improving the signal-to-noise ratio to facilitate e.g. time-resolved measurements. A metal sample, designed to be close to a phase pure object, and a bone sample with canals partially filled with D2O were used for demonstrating the technique. These samples were imaged with a polychromatic neutron beam followed by phase retrieval. For both samples the signal-to-noise ratios were significantly improved and, in the case of the bone sample, the phase retrieval allowed for separation of bone and D2O, which is important for example for in situ flow experiments. The use of deuteration contrast avoids the use of chemical contrast enhancement and makes neutron imaging an interesting complementary method to X-ray imaging of bone.enØstergaard, M.Naver, E.B.Kaestner, A.Willendrup, P.K.Brüel, A.Sørensen, H.O.Thomsen, J.S.Schmidt, S.Poulsen, H.F.Theil Kuhn, L.Birkedal, H.Polychromatic neutron phase-contrast imaging of weakly absorbing samples enabled by phase retrieval2023-05-09PHASE-CONTRAST IMAGING; NEUTRON IMAGING; BONE; TOMOGRAPHY; PHASE RETRIEVAL; POLYCHROMATIC NEUTRONSdoi:10.1107/S1600576723003011urn:issn:1600-5767Neutron imaging enhanced by the retrieval of propagation-based phase contrast is described.https://creativecommons.org/licenses/by/4.0/text/html6822023-05-0956research papersJune 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography3med@iucr.org1600-57671600-5767673Hierarchical synchrotron diffraction and imaging study of the calcium sulfate hemihydrate–gypsum transformation
http://scripts.iucr.org/cgi-bin/paper?vb5051
The mechanism of hydration of calcium sulfate hemihydrate (CaSO4·0.5H2O) to form gypsum (CaSO4·2H2O) was studied by combining scanning 3D X-ray diffraction (s3DXRD) and phase contrast tomography (PCT) to determine in situ the spatial and crystallographic relationship between these two phases. From s3DXRD measurements, the crystallographic structure, orientation and position of the crystalline grains in the sample during the hydration reaction were obtained, while the PCT reconstructions allowed visualization of the 3D shapes of the crystals during the reaction. This multi-scale study unfolds structural and morphological evidence of the dissolution–precipitation process of the gypsum plaster system, providing insights into the reactivity of specific crystallographic facets of the hemihydrate. In this work, epitaxial growth of gypsum crystals on the hemihydrate grains was not observed.International Union of CrystallographytextThe mechanism of hydration of calcium sulfate hemihydrate (CaSO4·0.5H2O) to form gypsum (CaSO4·2H2O) was studied by combining scanning 3D X-ray diffraction (s3DXRD) and phase contrast tomography (PCT) to determine in situ the spatial and crystallographic relationship between these two phases. From s3DXRD measurements, the crystallographic structure, orientation and position of the crystalline grains in the sample during the hydration reaction were obtained, while the PCT reconstructions allowed visualization of the 3D shapes of the crystals during the reaction. This multi-scale study unfolds structural and morphological evidence of the dissolution–precipitation process of the gypsum plaster system, providing insights into the reactivity of specific crystallographic facets of the hemihydrate. In this work, epitaxial growth of gypsum crystals on the hemihydrate grains was not observed.enLa Bella, M.Besselink, R.Wright, J.P.Van Driessche, A.E.S.Fernandez-Martinez, A.Giacobbe, C.Hierarchical synchrotron diffraction and imaging study of the calcium sulfate hemihydrate–gypsum transformation2023-05-09SCANNING 3D X-RAY DIFFRACTION; S3DXRD; PHASE CONTRAST TOMOGRAPHY; GYPSUM HEMIHYDRATEdoi:10.1107/S1600576723002881urn:issn:1600-5767A combined approach of scanning 3D X-ray diffraction and phase contrast tomography has been used to study the hydration of calcium sulfate hemihydrate to form gypsum. This approach was found to be a powerful tool that permitted – for the first time – coupling of detailed crystallographic and morphological information on the hemihydrate–gypsum transition observed in situ.https://creativecommons.org/licenses/by/4.0/text/html2023-05-0967256research papersJune 2023Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/31600-5767med@iucr.org6601600-5767Study of GaN coalescence by dark-field X-ray microscopy at the nanoscale
http://scripts.iucr.org/cgi-bin/paper?xx5023
This work illustrates the potential of dark-field X-ray microscopy (DFXM), a 3D imaging technique of nanostructures, in characterizing novel epitaxial structures of gallium nitride (GaN) on top of GaN/AlN/Si/SiO2 nano-pillars for optoelectronic applications. The nano-pillars are intended to allow independent GaN nanostructures to coalesce into a highly oriented film due to the SiO2 layer becoming soft at the GaN growth temperature. DFXM is demonstrated on different types of samples at the nanoscale and the results show that extremely well oriented lines of GaN (standard deviation of 0.04°) as well as highly oriented material for zones up to 10 × 10 µm2 in area are achieved with this growth approach. At a macroscale, high-intensity X-ray diffraction is used to show that the coalescence of GaN pyramids causes misorientation of the silicon in the nano-pillars, implying that the growth occurs as intended (i.e. that pillars rotate during coalescence). These two diffraction methods demonstrate the great promise of this growth approach for micro-displays and micro-LEDs, which require small islands of high-quality GaN material, and offer a new way to enrich the fundamental understanding of optoelectronically relevant materials at the highest spatial resolution.International Union of CrystallographytextThis work illustrates the potential of dark-field X-ray microscopy (DFXM), a 3D imaging technique of nanostructures, in characterizing novel epitaxial structures of gallium nitride (GaN) on top of GaN/AlN/Si/SiO2 nano-pillars for optoelectronic applications. The nano-pillars are intended to allow independent GaN nanostructures to coalesce into a highly oriented film due to the SiO2 layer becoming soft at the GaN growth temperature. DFXM is demonstrated on different types of samples at the nanoscale and the results show that extremely well oriented lines of GaN (standard deviation of 0.04°) as well as highly oriented material for zones up to 10 × 10 µm2 in area are achieved with this growth approach. At a macroscale, high-intensity X-ray diffraction is used to show that the coalescence of GaN pyramids causes misorientation of the silicon in the nano-pillars, implying that the growth occurs as intended (i.e. that pillars rotate during coalescence). These two diffraction methods demonstrate the great promise of this growth approach for micro-displays and micro-LEDs, which require small islands of high-quality GaN material, and offer a new way to enrich the fundamental understanding of optoelectronically relevant materials at the highest spatial resolution.enWehbe, M.Charles, M.Baril, K.Alloing, B.Pino Munoz, D.Labchir, N.Zuniga-Perez, J.Detlefs, C.Yildirim, C.Gergaud, P.Study of GaN coalescence by dark-field X-ray microscopy at the nanoscale2023-04-25DARK-FIELD X-RAY MICROSCOPY; SYNCHROTRON RADIATION; CHARACTERIZATION; GALLIUM NITRIDE; COALESCENCE; DIFFRACTION IMAGING; NANO-PILLARSdoi:10.1107/S160057672300287Xurn:issn:1600-5767In this article, highly oriented small structures of gallium nitride grown on top of silicon nano-pillars are characterized by dark-field X-ray microscopy for optoelectronic applications such as micro-LEDs.https://creativecommons.org/licenses/by/4.0/text/html6492023-04-2556research papersJune 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography3med@iucr.org1600-57671600-5767643CyRSoXS: a GPU-accelerated virtual instrument for polarized resonant soft X-ray scattering
http://scripts.iucr.org/cgi-bin/paper?jl5058
Polarized resonant soft X-ray scattering (P-RSoXS) has emerged as a powerful synchrotron-based tool that combines the principles of X-ray scattering and X-ray spectroscopy. P-RSoXS provides unique sensitivity to molecular orientation and chemical heterogeneity in soft materials such as polymers and biomaterials. Quantitative extraction of orientation information from P-RSoXS pattern data is challenging, however, because the scattering processes originate from sample properties that must be represented as energy-dependent three-dimensional tensors with heterogeneities at nanometre to sub-nanometre length scales. This challenge is overcome here by developing an open-source virtual instrument that uses graphical processing units (GPUs) to simulate P-RSoXS patterns from real-space material representations with nanoscale resolution. This computational framework – called CyRSoXS (https://github.com/usnistgov/cyrsoxs) – is designed to maximize GPU performance, including algorithms that minimize both communication and memory footprints. The accuracy and robustness of the approach are demonstrated by validating against an extensive set of test cases, which include both analytical solutions and numerical comparisons, demonstrating an acceleration of over three orders of magnitude relative to the current state-of-the-art P-RSoXS simulation software. Such fast simulations open up a variety of applications that were previously computationally unfeasible, including pattern fitting, co-simulation with the physical instrument for operando analytics, data exploration and decision support, data creation and integration into machine learning workflows, and utilization in multi-modal data assimilation approaches. Finally, the complexity of the computational framework is abstracted away from the end user by exposing CyRSoXS to Python using Pybind. This eliminates input/output requirements for large-scale parameter exploration and inverse design, and democratizes usage by enabling seamless integration with a Python ecosystem (https://github.com/usnistgov/nrss) that can include parametric morphology generation, simulation result reduction, comparison with experiment and data fitting approaches.International Union of CrystallographytextPolarized resonant soft X-ray scattering (P-RSoXS) has emerged as a powerful synchrotron-based tool that combines the principles of X-ray scattering and X-ray spectroscopy. P-RSoXS provides unique sensitivity to molecular orientation and chemical heterogeneity in soft materials such as polymers and biomaterials. Quantitative extraction of orientation information from P-RSoXS pattern data is challenging, however, because the scattering processes originate from sample properties that must be represented as energy-dependent three-dimensional tensors with heterogeneities at nanometre to sub-nanometre length scales. This challenge is overcome here by developing an open-source virtual instrument that uses graphical processing units (GPUs) to simulate P-RSoXS patterns from real-space material representations with nanoscale resolution. This computational framework – called CyRSoXS (https://github.com/usnistgov/cyrsoxs) – is designed to maximize GPU performance, including algorithms that minimize both communication and memory footprints. The accuracy and robustness of the approach are demonstrated by validating against an extensive set of test cases, which include both analytical solutions and numerical comparisons, demonstrating an acceleration of over three orders of magnitude relative to the current state-of-the-art P-RSoXS simulation software. Such fast simulations open up a variety of applications that were previously computationally unfeasible, including pattern fitting, co-simulation with the physical instrument for operando analytics, data exploration and decision support, data creation and integration into machine learning workflows, and utilization in multi-modal data assimilation approaches. Finally, the complexity of the computational framework is abstracted away from the end user by exposing CyRSoXS to Python using Pybind. This eliminates input/output requirements for large-scale parameter exploration and inverse design, and democratizes usage by enabling seamless integration with a Python ecosystem (https://github.com/usnistgov/nrss) that can include parametric morphology generation, simulation result reduction, comparison with experiment and data fitting approaches.enSaurabh, K.Dudenas, P.J.Gann, E.Reynolds, V.G.Mukherjee, S.Sunday, D.Martin, T.B.Beaucage, P.A.Chabinyc, M.L.DeLongchamp, D.M.Krishnamurthy, A.Ganapathysubramanian, B.CyRSoXS: a GPU-accelerated virtual instrument for polarized resonant soft X-ray scattering2023-05-23CYRSOXS; VIRTUAL INSTRUMENTS; POLARIZED RESONANT SOFT X-RAY SCATTERING; P-RSOXSdoi:10.1107/S1600576723002790urn:issn:1600-5767This article presents CyRSoXS – an open-source virtual instrument that uses GPUs to simulate polarized resonant soft X-ray scattering (P-RSoXS) patterns from real-space material representations. It is significantly faster than the current state-of-the-art software, and it enables quantitative extraction of orientation information from P-RSoXS data. This enables a wide range of applications, including pattern fitting, co-simulation, data exploration, machine learning workflows and multi-modal data assimilation approaches.https://creativecommons.org/licenses/by/4.0/text/htmlJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/3med@iucr.org1600-57671600-57678688832023-05-23computer programs56June 2023Crystal bending in triple-Laue X-ray interferometry. Part II. Phase-contrast topography
http://scripts.iucr.org/cgi-bin/paper?ei5094
In a previous paper [Sasso et al. (2023). J. Appl. Cryst. 56, 707–715], the operation of a triple-Laue X-ray interferometer having the splitting or recombining crystal cylindrically bent was studied. It was predicted that the phase-contrast topography of the interferometer detects the displacement field of the inner crystal surfaces. Therefore, opposite bendings result in the observation of opposite (compressive or tensile) strains. This paper reports on the experimental confirmation of this prediction, where opposite bendings were obtained by copper deposition on one or the other of the crystal sides.International Union of CrystallographytextIn a previous paper [Sasso et al. (2023). J. Appl. Cryst. 56, 707–715], the operation of a triple-Laue X-ray interferometer having the splitting or recombining crystal cylindrically bent was studied. It was predicted that the phase-contrast topography of the interferometer detects the displacement field of the inner crystal surfaces. Therefore, opposite bendings result in the observation of opposite (compressive or tensile) strains. This paper reports on the experimental confirmation of this prediction, where opposite bendings were obtained by copper deposition on one or the other of the crystal sides.enMassa, E.Mana, G.Sasso, C.P.Crystal bending in triple-Laue X-ray interferometry. Part II. Phase-contrast topography2023-05-12CRYSTAL X-RAY INTERFEROMETRY; PHASE-CONTRAST TOPOGRAPHY; BENT CRYSTALS; MOIRE IMAGES; THIN FILMS; CRYSTAL STRAINSdoi:10.1107/S1600576723002832urn:issn:1600-5767The operation model of a triple-Laue interferometer having one of the splitting and recombining crystals bent predicts that the phase-contrast topography detects the displacement field of the inner crystal surfaces. Therefore, it predicts that opposite bendings must result in the observation of opposite strains. This paper reports on the experimental confirmation of this prediction.https://creativecommons.org/licenses/by/4.0/text/htmlJune 2023research papers567242023-05-121600-5767716med@iucr.org1600-57673https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyCrystal bending in triple-Laue X-ray interferometry. Part I. Theory
http://scripts.iucr.org/cgi-bin/paper?ei5093
The measured value of the (220) lattice-plane spacing of silicon 28 using scanning X-ray interferometry is essential to realize the kilogram by counting 28Si atoms. An assumption made is that the measured lattice spacing is the bulk value of an unstrained crystal forming the analyser of the interferometer. However, analytical and numerical studies of the X-ray propagation in bent crystals suggest that the measured lattice spacing might refer to the analyser surface. To confirm the result of these studies and to support experimental investigations of the matter by phase-contrast topography, a comprehensive analytical model is given of the operation of a triple-Laue interferometer having the splitting or recombining crystal bent.International Union of CrystallographytextThe measured value of the (220) lattice-plane spacing of silicon 28 using scanning X-ray interferometry is essential to realize the kilogram by counting 28Si atoms. An assumption made is that the measured lattice spacing is the bulk value of an unstrained crystal forming the analyser of the interferometer. However, analytical and numerical studies of the X-ray propagation in bent crystals suggest that the measured lattice spacing might refer to the analyser surface. To confirm the result of these studies and to support experimental investigations of the matter by phase-contrast topography, a comprehensive analytical model is given of the operation of a triple-Laue interferometer having the splitting or recombining crystal bent.enSasso, C.P.Mana, G.Massa, E.Crystal bending in triple-Laue X-ray interferometry. Part I. Theory2023-05-12CRYSTAL X-RAY INTERFEROMETRY; DYNAMICAL THEORY OF X-RAY DIFFRACTION; LAUE DIFFRACTION; BENT CRYSTALSdoi:10.1107/S1600576723002844urn:issn:1600-5767Previous studies suggested that the silicon lattice spacing measured by X-ray interferometry might refer to the crystal surface. To confirm this result and to support experimental investigations of the matter, this paper gives a comprehensive analytical model of the operation of a triple-Laue interferometer having one of the splitting and recombining crystals bent.https://creativecommons.org/licenses/by/4.0/text/html2023-05-1271556research papersJune 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography31600-5767med@iucr.org7071600-5767POWTEX visits POWGEN
http://scripts.iucr.org/cgi-bin/paper?tu5033
The high-intensity time-of-flight (TOF) neutron diffractometer POWTEX for powder and texture analysis is currently being built prior to operation in the eastern guide hall of the research reactor FRM II at Garching close to Munich, Germany. Because of the world-wide 3He crisis in 2009, the authors promptly initiated the development of 3He-free detector alternatives that are tailor-made for the requirements of large-area diffractometers. Herein is reported the 2017 enterprise to operate one mounting unit of the final POWTEX detector on the neutron powder diffractometer POWGEN at the Spallation Neutron Source located at Oak Ridge National Laboratory, USA. As a result, presented here are the first angular- and wavelength-dependent data from the POWTEX detector, unfortunately damaged by a 50g shock but still operating, as well as the efforts made both to characterize the transport damage and to successfully recalibrate the voxel positions in order to yield nonetheless reliable measurements. Also described is the current data reduction process using the PowderReduceP2D algorithm implemented in Mantid [Arnold et al. (2014). Nucl. Instrum. Methods Phys. Res. A, 764, 156–166]. The final part of the data treatment chain, namely a novel multi-dimensional refinement using a modified version of the GSAS-II software suite [Toby & Von Dreele (2013). J. Appl. Cryst. 46, 544–549], is compared with a standard data treatment of the same event data conventionally reduced as TOF diffraction patterns and refined with the unmodified version of GSAS-II. This involves both determining the instrumental resolution parameters using POWGEN's powdered diamond standard sample and the refinement of a friendly-user sample, BaZn(NCN)2. Although each structural parameter on its own looks similar upon comparing the conventional (1D) and multi-dimensional (2D) treatments, also in terms of precision, a closer view shows small but possibly significant differences. For example, the somewhat suspicious proximity of the a and b lattice parameters of BaZn(NCN)2 crystallizing in Pbca as resulting from the 1D refinement (0.008 Å) is five times less pronounced in the 2D refinement (0.038 Å). Similar features are found when comparing bond lengths and bond angles, e.g. the two N—C—N units are less differently bent in the 1D results (173 and 175°) than in the 2D results (167 and 173°). The results are of importance not only for POWTEX but also for other neutron TOF diffractometers with large-area detectors, like POWGEN at the SNS or the future DREAM beamline at the European Spallation Source.International Union of CrystallographytextThe high-intensity time-of-flight (TOF) neutron diffractometer POWTEX for powder and texture analysis is currently being built prior to operation in the eastern guide hall of the research reactor FRM II at Garching close to Munich, Germany. Because of the world-wide 3He crisis in 2009, the authors promptly initiated the development of 3He-free detector alternatives that are tailor-made for the requirements of large-area diffractometers. Herein is reported the 2017 enterprise to operate one mounting unit of the final POWTEX detector on the neutron powder diffractometer POWGEN at the Spallation Neutron Source located at Oak Ridge National Laboratory, USA. As a result, presented here are the first angular- and wavelength-dependent data from the POWTEX detector, unfortunately damaged by a 50g shock but still operating, as well as the efforts made both to characterize the transport damage and to successfully recalibrate the voxel positions in order to yield nonetheless reliable measurements. Also described is the current data reduction process using the PowderReduceP2D algorithm implemented in Mantid [Arnold et al. (2014). Nucl. Instrum. Methods Phys. Res. A, 764, 156–166]. The final part of the data treatment chain, namely a novel multi-dimensional refinement using a modified version of the GSAS-II software suite [Toby & Von Dreele (2013). J. Appl. Cryst. 46, 544–549], is compared with a standard data treatment of the same event data conventionally reduced as TOF diffraction patterns and refined with the unmodified version of GSAS-II. This involves both determining the instrumental resolution parameters using POWGEN's powdered diamond standard sample and the refinement of a friendly-user sample, BaZn(NCN)2. Although each structural parameter on its own looks similar upon comparing the conventional (1D) and multi-dimensional (2D) treatments, also in terms of precision, a closer view shows small but possibly significant differences. For example, the somewhat suspicious proximity of the a and b lattice parameters of BaZn(NCN)2 crystallizing in Pbca as resulting from the 1D refinement (0.008 Å) is five times less pronounced in the 2D refinement (0.038 Å). Similar features are found when comparing bond lengths and bond angles, e.g. the two N—C—N units are less differently bent in the 1D results (173 and 175°) than in the 2D results (167 and 173°). The results are of importance not only for POWTEX but also for other neutron TOF diffractometers with large-area detectors, like POWGEN at the SNS or the future DREAM beamline at the European Spallation Source.enHouben, A.Meinerzhagen, Y.Nachtigall, N.Jacobs, P.Dronskowski, R.POWTEX visits POWGEN2023-04-25NEUTRON DETECTORS; POWGEN BEAMLINE; POWTEX DETECTOR; DREAM BEAMLINE; TIME-OF-FLIGHT DIFFRACTION; ANGULAR-DISPERSIVE REFINEMENT; WAVELENGTH-DISPERSIVE REFINEMENT; POWDER DIFFRACTION; RIETVELD REFINEMENT; MULTI-DIMENSIONAL REFINEMENTdoi:10.1107/S1600576723002819urn:issn:1600-5767The first real-world neutron diffraction data have been collected with one of the POWTEX detectors (FRM II, Garching, Germany) mounted for testing at the Spallation Neutron Source (Oak Ridge National Laboratory, USA). They allow for angular- and wavelength-dispersive Rietveld refinement using a modified version of GSAS-II.https://creativecommons.org/licenses/by/4.0/text/html6331600-57671600-5767med@iucr.org3Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/June 2023research papers562023-04-25642101 contact twins in gypsum experimentally obtained from calcium carbonate enriched solutions: mineralogical implications for natural gypsum deposits
http://scripts.iucr.org/cgi-bin/paper?ei5095
Gypsum twins are frequently observed in nature, triggered by a wide array of impurities that are present in their depositional environments and that may exert a critical role in the selection of different twin laws. Identifying the impurities able to promote the selection of specific twin laws has relevance for geological studies aimed at interpreting the gypsum depositional environments in ancient and modern deposits. Here, the effect of calcium carbonate (CaCO3) on gypsum (CaSO4·2H2O) growth morphology has been investigated by performing temperature-controlled laboratory experiments with and without the addition of carbonate ions. The precipitation of twinned gypsum crystals has been achieved experimentally (101 contact twin law) by adding carbonate to the solution, and the involvement of rapidcreekite (Ca2SO4CO3·4H2O) in selecting the 101 gypsum contact twin law was supported, suggesting an epitaxial mechanism. Moreover, the occurrence of 101 gypsum contact twins in nature has been suggested by comparing the natural gypsum twin morphologies observed in evaporitic environments with those obtained in experiments. Finally, both orientations of the primary fluid inclusions (of the negative crystal shape) with respect to the twin plane and the main elongation of sub-crystals that form the twin are proposed as a fast and useful method (especially in geological samples) to distinguish between the 100 and 101 twin laws. The results of this study provide new insights into the mineralogical implications of twinned gypsum crystals and their potential as a tool to better understand natural gypsum deposits.International Union of CrystallographytextGypsum twins are frequently observed in nature, triggered by a wide array of impurities that are present in their depositional environments and that may exert a critical role in the selection of different twin laws. Identifying the impurities able to promote the selection of specific twin laws has relevance for geological studies aimed at interpreting the gypsum depositional environments in ancient and modern deposits. Here, the effect of calcium carbonate (CaCO3) on gypsum (CaSO4·2H2O) growth morphology has been investigated by performing temperature-controlled laboratory experiments with and without the addition of carbonate ions. The precipitation of twinned gypsum crystals has been achieved experimentally (101 contact twin law) by adding carbonate to the solution, and the involvement of rapidcreekite (Ca2SO4CO3·4H2O) in selecting the 101 gypsum contact twin law was supported, suggesting an epitaxial mechanism. Moreover, the occurrence of 101 gypsum contact twins in nature has been suggested by comparing the natural gypsum twin morphologies observed in evaporitic environments with those obtained in experiments. Finally, both orientations of the primary fluid inclusions (of the negative crystal shape) with respect to the twin plane and the main elongation of sub-crystals that form the twin are proposed as a fast and useful method (especially in geological samples) to distinguish between the 100 and 101 twin laws. The results of this study provide new insights into the mineralogical implications of twinned gypsum crystals and their potential as a tool to better understand natural gypsum deposits.enCotellucci, A.Otálora, F.Canals, À.Criado-Reyes, J.Pellegrino, L.Bruno, M.Aquilano, D.Garcia-Ruiz, J.M.Dela Pierre, F.Pastero, L.101 contact twins in gypsum experimentally obtained from calcium carbonate enriched solutions: mineralogical implications for natural gypsum deposits2023-04-13GYPSUM; TWINS; FLUID INCLUSIONS; EVAPORITES; SWALLOWTAILdoi:10.1107/S1600576723002674urn:issn:1600-5767Identifying the impurities that are able to promote the selection of specific gypsum twin laws has relevance for geological studies aimed at interpreting the gypsum depositional environments in ancient and modern deposits. The results of this study provide new insights into the mineralogical implications of twinned gypsum crystals and should help future research to make a better use of the twin laws observed in gypsum in ancient sedimentary successions as a proxy for the chemistry of the original brine.https://creativecommons.org/licenses/by/4.0/text/htmlJune 2023research papers562023-04-136106031600-57671600-5767med@iucr.org3https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyStructural, elastic, electronic, optical and vibrational properties of single-layered, bilayered and bulk molybdenite MoS2-2H
http://scripts.iucr.org/cgi-bin/paper?vb5049
In recent years, transition metal dichalcogenides have received great attention since they can be prepared as two-dimensional semiconductors, presenting heterodesmic structures incorporating strong in-plane covalent bonds and weak out-of-plane interactions, with an easy cleavage/exfoliation in single or multiple layers. In this context, molybdenite, the mineralogical name of molybdenum disulfide, MoS2, has drawn much attention because of its very promising physical properties for optoelectronic applications, in particular a band gap that can be tailored with the material's thickness, optical absorption in the visible region and strong light–matter interactions due to the planar exciton confinement effect. Despite this wide interest and the numerous experimental and theoretical articles in the literature, these report on just one or two specific features of bulk and layered MoS2 and sometimes provide conflicting results. For these reasons, presented here is a thorough theoretical analysis of the different aspects of bulk, monolayer and bilayer MoS2 within the density functional theory (DFT) framework and with the DFT-D3 correction to account for long-range interactions. The crystal chemistry, stiffness, and electronic, dielectric/optical and phonon properties of single-layered, bilayered and bulk molybdenite have been investigated, to obtain a consistent and detailed set of data and to assess the variations and cross correlation from the bulk to single- and double-layer units. The simulations show the indirect–direct transition of the band gap (K–K′ in the first Brillouin zone) from the bulk to the single-layer structure, which however reverts to an indirect transition when a bilayer is considered. In general, the optical properties are in good agreement with previous experimental measurements using spectroscopic ellipsometry and reflectivity, and with preliminary theoretical simulations.International Union of CrystallographytextIn recent years, transition metal dichalcogenides have received great attention since they can be prepared as two-dimensional semiconductors, presenting heterodesmic structures incorporating strong in-plane covalent bonds and weak out-of-plane interactions, with an easy cleavage/exfoliation in single or multiple layers. In this context, molybdenite, the mineralogical name of molybdenum disulfide, MoS2, has drawn much attention because of its very promising physical properties for optoelectronic applications, in particular a band gap that can be tailored with the material's thickness, optical absorption in the visible region and strong light–matter interactions due to the planar exciton confinement effect. Despite this wide interest and the numerous experimental and theoretical articles in the literature, these report on just one or two specific features of bulk and layered MoS2 and sometimes provide conflicting results. For these reasons, presented here is a thorough theoretical analysis of the different aspects of bulk, monolayer and bilayer MoS2 within the density functional theory (DFT) framework and with the DFT-D3 correction to account for long-range interactions. The crystal chemistry, stiffness, and electronic, dielectric/optical and phonon properties of single-layered, bilayered and bulk molybdenite have been investigated, to obtain a consistent and detailed set of data and to assess the variations and cross correlation from the bulk to single- and double-layer units. The simulations show the indirect–direct transition of the band gap (K–K′ in the first Brillouin zone) from the bulk to the single-layer structure, which however reverts to an indirect transition when a bilayer is considered. In general, the optical properties are in good agreement with previous experimental measurements using spectroscopic ellipsometry and reflectivity, and with preliminary theoretical simulations.enUlian, G.Valdrè, G.Structural, elastic, electronic, optical and vibrational properties of single-layered, bilayered and bulk molybdenite MoS2-2H2023-04-25MOLYBDENITE MOS2-2H; MONOLAYERED MOS2; BILAYERED MOS2; CRYSTAL CHEMISTRY; ELECTRONIC PROPERTIES; DIELECTRIC PROPERTIESdoi:10.1107/S1600576723002571urn:issn:1600-5767An extensive density functional theory analysis is reported of the crystal-chemical properties, electronic band structure, and optical (absorption and electron energy-loss spectra) and phonon properties of bulk and mono- and bilayer molybdenite, a transition metal dichalcogenide with important applications in semiconductor technology. This mineral is characterized by virtually infinite bidimensional layers of MoS2 (with covalent Mo—S bonds) held together by weak dispersive forces, explaining the easy cleavage of the (001) surfaces.https://creativecommons.org/licenses/by/4.0/text/htmlJune 2023research papers562023-04-256236111600-57671600-5767med@iucr.org3https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyDerivation of the small-angle scattering profile of a target biomacromolecule from a profile deteriorated by aggregates. AUC–SAS
http://scripts.iucr.org/cgi-bin/paper?ge5127
Aggregates cause a fatal problem in the structural analysis of a biomacromolecule in solution using small-angle X-ray or neutron scattering (SAS): they deteriorate the scattering profile of the target molecule and lead to an incorrect structure. Recently, an integrated method of analytical ultracentrifugation (AUC) and SAS, abbreviated AUC–SAS, was developed as a new approach to overcome this problem. However, the original version of AUC–SAS does not offer a correct scattering profile of the target molecule when the weight fraction of aggregates is higher than ca 10%. In this study, the obstacle point in the original AUC–SAS approach is identified. The improved AUC–SAS method is then applicable to a solution with a relatively larger weight fraction of aggregates (≤20%).International Union of CrystallographytextAggregates cause a fatal problem in the structural analysis of a biomacromolecule in solution using small-angle X-ray or neutron scattering (SAS): they deteriorate the scattering profile of the target molecule and lead to an incorrect structure. Recently, an integrated method of analytical ultracentrifugation (AUC) and SAS, abbreviated AUC–SAS, was developed as a new approach to overcome this problem. However, the original version of AUC–SAS does not offer a correct scattering profile of the target molecule when the weight fraction of aggregates is higher than ca 10%. In this study, the obstacle point in the original AUC–SAS approach is identified. The improved AUC–SAS method is then applicable to a solution with a relatively larger weight fraction of aggregates (≤20%).enMorishima, K.Inoue, R.Sugiyama, M.Derivation of the small-angle scattering profile of a target biomacromolecule from a profile deteriorated by aggregates. AUC–SAS2023-04-25SMALL-ANGLE X-RAY SCATTERING; SMALL-ANGLE NEUTRON SCATTERING; ANALYTICAL ULTRACENTRIFUGATION; PROTEIN SOLUTIONS; AGGREGATES; BIOMACROMOLECULESdoi:10.1107/S1600576723002406urn:issn:1600-5767An integrated method using analytical ultracentrifugation (AUC) and small-angle scattering (SAS), AUC–SAS, has been developed for the structural analysis of a biomacromolecule in solution. In this study, the first version of AUC–SAS is improved upon so as to be applicable to a solution with a large number of aggregates.https://creativecommons.org/licenses/by/4.0/text/htmlresearch papers562023-04-25632June 20233Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/6241600-57671600-5767med@iucr.orgA reactor for time-resolved X-ray studies of nucleation and growth during solvothermal synthesis
http://scripts.iucr.org/cgi-bin/paper?gj5297
Understanding the nucleation and growth mechanisms of nanocrystals under hydro- and solvothermal conditions is key to tailoring functional nanomaterials. High-energy and high-flux synchrotron radiation is ideal for characterization by powder X-ray diffraction and X-ray total scattering in real time. Different versions of batch-type cell reactors have been employed in this work, exploiting the robustness of polyimide-coated fused quartz tubes with an inner diameter of 0.7 mm, as they can withstand pressures up to 250 bar and temperatures up to 723 K for several hours. Reported here are recent developments of the in situ setups available for general users on the P21.1 beamline at PETRA III and the DanMAX beamline at MAX IV to study nucleation and growth phenomena in solvothermal synthesis. It is shown that data suitable for both reciprocal-space Rietveld refinement and direct-space pair distribution function refinement can be obtained on a timescale of 4 ms.International Union of CrystallographytextUnderstanding the nucleation and growth mechanisms of nanocrystals under hydro- and solvothermal conditions is key to tailoring functional nanomaterials. High-energy and high-flux synchrotron radiation is ideal for characterization by powder X-ray diffraction and X-ray total scattering in real time. Different versions of batch-type cell reactors have been employed in this work, exploiting the robustness of polyimide-coated fused quartz tubes with an inner diameter of 0.7 mm, as they can withstand pressures up to 250 bar and temperatures up to 723 K for several hours. Reported here are recent developments of the in situ setups available for general users on the P21.1 beamline at PETRA III and the DanMAX beamline at MAX IV to study nucleation and growth phenomena in solvothermal synthesis. It is shown that data suitable for both reciprocal-space Rietveld refinement and direct-space pair distribution function refinement can be obtained on a timescale of 4 ms.enRoelsgaard, M.Kløve, M.Christensen, R.Bertelsen, A.D.Broge, N.L.N.Kantor, I.Sørensen, D.R.Dippel, A.-C.Banerjee, S.Zimmermann, M.V.Glaevecke, P.Gutowski, O.Jørgensen, M.R.V.Iversen, B.B.A reactor for time-resolved X-ray studies of nucleation and growth during solvothermal synthesis2023-04-13IN SITU X-RAY SCATTERING; POWDER X-RAY DIFFRACTION; TOTAL SCATTERING; SMALL-ANGLE SCATTERING; SOLVOTHERMAL CHEMISTRYdoi:10.1107/S1600576723002339urn:issn:1600-5767A versatile reactor for in situ X-ray scattering studies of solvothermal reactions is presented, capable of providing data with millisecond time resolutionhttps://creativecommons.org/licenses/by/4.0/text/html5882023-04-1356research papersJune 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography3med@iucr.org1600-57671600-5767581SpatDistCalib: a GUI Python software for spatial-distortion correction of 2D detectors using splines
http://scripts.iucr.org/cgi-bin/paper?fs5214
CCD-based X-ray detector systems often suffer from spatial distortions. Reproducible distortions can be quantitatively measured with a calibration grid and described as a displacement matrix or as spline functions. The measured distortion can be used afterwards to undistort raw images or to refine the actual position of each pixel, e.g. for azimuthal integration. This article describes a method using a regular grid, not necessarily orthogonal, to measure the distortions. The graphical user interface (GUI) Python software that is used to implement this method is available under a GPLv3 license on ESRF GitLab, and produces a spline file that is usable with data-reduction software such as FIT2D or pyFAI.International Union of CrystallographytextCCD-based X-ray detector systems often suffer from spatial distortions. Reproducible distortions can be quantitatively measured with a calibration grid and described as a displacement matrix or as spline functions. The measured distortion can be used afterwards to undistort raw images or to refine the actual position of each pixel, e.g. for azimuthal integration. This article describes a method using a regular grid, not necessarily orthogonal, to measure the distortions. The graphical user interface (GUI) Python software that is used to implement this method is available under a GPLv3 license on ESRF GitLab, and produces a spline file that is usable with data-reduction software such as FIT2D or pyFAI.enChèvremont, W.SpatDistCalib: a GUI Python software for spatial-distortion correction of 2D detectors using splines2023-04-252D DETECTOR SYSTEMS; SPATIAL-DISTORTION CORRECTION; REGULAR CALIBRATION GRIDS; GRAPHICAL USER INTERFACE PYTHON SOFTWARE; SPLINESdoi:10.1107/S160057672300225Xurn:issn:1600-5767In this article, Python software with a graphical user interface (GUI) for spatial-distortion correction, using any regular grid as the calibration pattern and producing spline files, is presented.https://creativecommons.org/licenses/by/4.0/text/htmlmed@iucr.org1600-57671600-5767860Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/3June 20238672023-04-25computer programs56inserexs: reflection choice software for resonant elastic X-ray scattering
http://scripts.iucr.org/cgi-bin/paper?nb5346
This paper presents inserexs, an open-source computer program that aims to pre-evaluate the different reflections for resonant elastic X-ray scattering (REXS) diffraction experiments. REXS is an extremely versatile technique that can provide positional and occupational information about the atoms present in a crystal. inserexs was conceived to help REXS experimentalists know beforehand which reflections to choose to determine a parameter of interest. Prior work has already proven this to be useful in the determination of atomic positions in oxide thin films. inserexs allows generalization to any given system and aims to popularize resonant diffraction as an alternative technique to improve the resolution of crystalline structures.International Union of CrystallographytextThis paper presents inserexs, an open-source computer program that aims to pre-evaluate the different reflections for resonant elastic X-ray scattering (REXS) diffraction experiments. REXS is an extremely versatile technique that can provide positional and occupational information about the atoms present in a crystal. inserexs was conceived to help REXS experimentalists know beforehand which reflections to choose to determine a parameter of interest. Prior work has already proven this to be useful in the determination of atomic positions in oxide thin films. inserexs allows generalization to any given system and aims to popularize resonant diffraction as an alternative technique to improve the resolution of crystalline structures.enPeña Corredor, A.Viart, N.Lefevre, C.inserexs: reflection choice software for resonant elastic X-ray scattering2023-04-13INSEREXS; RESONANT ELASTIC X-RAY SCATTERING; REXS; EXAFS; ATOMIC POSITIONS; ATOMIC OCCUPANCIES; THIN FILMSdoi:10.1107/S1600576723002212urn:issn:1600-5767inserexs is an open-source program that allows resonant elastic X-ray scattering users to choose the best conditions to determine any parameter of interest (atomic position, occupancy etc.) before an experiment is carried out.https://creativecommons.org/licenses/by/4.0/text/htmlJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/3med@iucr.org1600-57671600-57678548592023-04-1356computer programsJune 2023Controlling the magnetic structure in W-type hexaferrites
http://scripts.iucr.org/cgi-bin/paper?in5078
W-type hexaferrites with varied Co/Zn ratios were synthesized and the magnetic order was investigated using neutron powder diffraction. In SrCo2Fe16O27 and SrCoZnFe16O27 a planar (Cm′cm′) magnetic ordering was found, rather than the uniaxial ordering (P63/mm′c′) found in SrZn2Fe16O27 which is common in most W-type hexaferrites. In all three studied samples, non-collinear terms were present in the magnetic ordering. One of the non-collinear terms is common to the planar ordering in SrCoZnFe16O27 and uniaxial ordering in SrZn2Fe16O27, which could be a sign of an imminent transition in the magnetic structure. The thermomagnetic measurements revealed magnetic transitions at 520 and 360 K for SrCo2Fe16O27 and SrCoZnFe16O27, and Curie temperatures of 780 and 680 K, respectively, while SrZn2Fe16O27 showed no transition but a Curie temperature at 590 K. This leads to the conclusion that the magnetic transition can be adjusted by fine-tuning the Co/Zn stoichiometry in the sample.International Union of CrystallographytextW-type hexaferrites with varied Co/Zn ratios were synthesized and the magnetic order was investigated using neutron powder diffraction. In SrCo2Fe16O27 and SrCoZnFe16O27 a planar (Cm′cm′) magnetic ordering was found, rather than the uniaxial ordering (P63/mm′c′) found in SrZn2Fe16O27 which is common in most W-type hexaferrites. In all three studied samples, non-collinear terms were present in the magnetic ordering. One of the non-collinear terms is common to the planar ordering in SrCoZnFe16O27 and uniaxial ordering in SrZn2Fe16O27, which could be a sign of an imminent transition in the magnetic structure. The thermomagnetic measurements revealed magnetic transitions at 520 and 360 K for SrCo2Fe16O27 and SrCoZnFe16O27, and Curie temperatures of 780 and 680 K, respectively, while SrZn2Fe16O27 showed no transition but a Curie temperature at 590 K. This leads to the conclusion that the magnetic transition can be adjusted by fine-tuning the Co/Zn stoichiometry in the sample.enMørch, M.I.Christensen, M.Controlling the magnetic structure in W-type hexaferrites2023-04-13HEXAFERRITES; MAGNETIC ORDERING; NEUTRON DIFFRACTION; MULTIFERROICSdoi:10.1107/S1600576723002133urn:issn:1600-5767Using neutron powder diffraction on W-type hexaferrites, planar magnetic ordering described in Cm′cm′ was found for SrCo2Fe16O27 and SrCoZnFe16O27, while SrZn2Fe16O27 had uniaxial ordering described in P63/mm′c′. Thermomagnetic measurements above room temperature also indicated magnetic transitions for SrCo2Fe16O27 and SrCoZnFe16O27.https://creativecommons.org/licenses/by/4.0/text/htmlhttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography31600-5767med@iucr.org5971600-57672023-04-13602research papers56June 2023X-ray powder diffraction in education. Part II. Intensity of a powder pattern
http://scripts.iucr.org/cgi-bin/paper?dv5004
This article is the second part of a series dealing with the description and visualization of mathematical functions used to describe a powder diffraction pattern for teaching and education purposes. The first part dealt with the instrumental and sample contributions to the profile of a Bragg peak [Dinnebier & Scardi (2021). J. Appl. Cryst. 54, 1811–1831]. The second part, here, deals with the mathematics and physics of the intensity in X-ray powder diffraction. Scholarly scripts are again provided using the Wolfram language in Mathematica.International Union of CrystallographytextThis article is the second part of a series dealing with the description and visualization of mathematical functions used to describe a powder diffraction pattern for teaching and education purposes. The first part dealt with the instrumental and sample contributions to the profile of a Bragg peak [Dinnebier & Scardi (2021). J. Appl. Cryst. 54, 1811–1831]. The second part, here, deals with the mathematics and physics of the intensity in X-ray powder diffraction. Scholarly scripts are again provided using the Wolfram language in Mathematica.enDinnebier, R.Scardi, P.X-ray powder diffraction in education. Part II. Intensity of a powder pattern2023-05-09POWDER DIFFRACTION; PEAK INTENSITY; INTENSITY CORRECTIONS; POWDER PATTERNS; MATHEMATICAdoi:10.1107/S1600576723002121urn:issn:1600-5767The most commonly used functions for calculating or correcting step-scan and integrated intensities of a powder diffraction pattern are presented in an educational manner with the support of Mathematica scripts. The scripts can be easily used by interested readers to explore the effects of different instrumental and sample parameters.https://creativecommons.org/licenses/by/4.0/text/htmlJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/31600-5767med@iucr.org8341600-57672023-05-09853teaching and education56June 2023Energy-dispersive X-ray stress analysis under geometric constraints: exploiting the material's inherent anisotropy
http://scripts.iucr.org/cgi-bin/paper?xx5018
Two data evaluation concepts for X-ray stress analysis based on energy-dispersive diffraction on polycrystalline materials with cubic crystal structure, almost random crystallographic texture and strong single-crystal elastic anisotropy are subjected to comparative assessment. The aim is the study of the residual stress state in hard-to-reach measurement points, for which the sin2ψ method is not applicable due to beam shadowing at larger sample tilting. This makes the approaches attractive for stress analysis in engineering parts with complex shapes, for example. Both approaches are based on the assumption of a biaxial stress state within the irradiated sample volume. They exploit in different ways the elastic anisotropy of individual crystallites acting at the microscopic scale and the anisotropy imposed on the material by the near-surface stress state at the macroscopic scale. They therefore complement each other, in terms of both their preconditions and their results. The first approach is based on the evaluation of strain differences, which makes it less sensitive to variations in the strain-free lattice parameter a0. Since it assumes a homogeneous stress state within the irradiated sample volume, it provides an average value of the in-plane stresses. The second approach exploits the sensitivity of the lattice strain to changes in a0. Consequently, it assumes a homogeneous chemical composition but provides a stress profile within the information depth. Experimental examples from different fields in materials science, namely shot peening of austenitic steel and in situ stress analysis during welding, are presented to demonstrate the suitability of the proposed methods.International Union of CrystallographytextTwo data evaluation concepts for X-ray stress analysis based on energy-dispersive diffraction on polycrystalline materials with cubic crystal structure, almost random crystallographic texture and strong single-crystal elastic anisotropy are subjected to comparative assessment. The aim is the study of the residual stress state in hard-to-reach measurement points, for which the sin2ψ method is not applicable due to beam shadowing at larger sample tilting. This makes the approaches attractive for stress analysis in engineering parts with complex shapes, for example. Both approaches are based on the assumption of a biaxial stress state within the irradiated sample volume. They exploit in different ways the elastic anisotropy of individual crystallites acting at the microscopic scale and the anisotropy imposed on the material by the near-surface stress state at the macroscopic scale. They therefore complement each other, in terms of both their preconditions and their results. The first approach is based on the evaluation of strain differences, which makes it less sensitive to variations in the strain-free lattice parameter a0. Since it assumes a homogeneous stress state within the irradiated sample volume, it provides an average value of the in-plane stresses. The second approach exploits the sensitivity of the lattice strain to changes in a0. Consequently, it assumes a homogeneous chemical composition but provides a stress profile within the information depth. Experimental examples from different fields in materials science, namely shot peening of austenitic steel and in situ stress analysis during welding, are presented to demonstrate the suitability of the proposed methods.enGenzel, C.Klaus, M.Hempel, N.Nitschke-Pagel, T.Pantleon, K.Energy-dispersive X-ray stress analysis under geometric constraints: exploiting the material's inherent anisotropy2023-04-01X-RAY STRESS ANALYSIS; ENERGY-DISPERSIVE DIFFRACTION; POLYCRYSTALLINE MATERIALS; SINGLE-CRYSTAL ELASTIC ANISOTROPYdoi:10.1107/S1600576723001759urn:issn:1600-5767The single-crystal elastic anisotropy and the anisotropy of the near-surface (residual) stress state of polycrystalline materials with random texture are exploited in energy-dispersive X-ray stress analysis to study samples under constrained measurement conditions.https://creativecommons.org/licenses/by/4.0/text/html5261600-57671600-5767med@iucr.org2Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/April 202356research papers2023-04-01538An inclined detector geometry for improved X-ray total scattering measurements
http://scripts.iucr.org/cgi-bin/paper?xx5017
X-ray total scattering measurements are implemented using a digital flat-panel area detector in an inclined geometry and compared with the traditional geometry. The traditional geometry is defined here by the incident X-ray beam impinging on and normal to the center-most pixel of a detector. The inclined geometry is defined here by a detector at a pitch angle α, set to 15° in this case, bisected by the vertical scattering plane. The detector is positioned such that the incident X-ray beam strikes the pixels along the bottom edge and 90° scattered X-rays impinge on the pixels along the top edge. The geometric attributes of the inclined geometry translate into multiple benefits, such as an extension of the measurable scattering range to 90°, a 47% increase in the accessible magnitudes of the reciprocal-space vector Q and a leveling of the dynamic range in the measured total scattering pattern. As a result, a sixfold improvement in signal-to-noise ratios is observed at higher scattering angles, enabling up to a 36-fold reduction in acquisition time. Additionally, the extent of applied modification functions is reduced, decreasing the magnitude of termination ripples and improving the real-space resolution of the pair distribution function G(r). Taken all together, these factors indicate that the inclined geometry produces higher quality data than the traditional geometry, usable for simultaneous Rietveld refinement and total scattering studies.International Union of CrystallographytextX-ray total scattering measurements are implemented using a digital flat-panel area detector in an inclined geometry and compared with the traditional geometry. The traditional geometry is defined here by the incident X-ray beam impinging on and normal to the center-most pixel of a detector. The inclined geometry is defined here by a detector at a pitch angle α, set to 15° in this case, bisected by the vertical scattering plane. The detector is positioned such that the incident X-ray beam strikes the pixels along the bottom edge and 90° scattered X-rays impinge on the pixels along the top edge. The geometric attributes of the inclined geometry translate into multiple benefits, such as an extension of the measurable scattering range to 90°, a 47% increase in the accessible magnitudes of the reciprocal-space vector Q and a leveling of the dynamic range in the measured total scattering pattern. As a result, a sixfold improvement in signal-to-noise ratios is observed at higher scattering angles, enabling up to a 36-fold reduction in acquisition time. Additionally, the extent of applied modification functions is reduced, decreasing the magnitude of termination ripples and improving the real-space resolution of the pair distribution function G(r). Taken all together, these factors indicate that the inclined geometry produces higher quality data than the traditional geometry, usable for simultaneous Rietveld refinement and total scattering studies.enBurns, N.Rahemtulla, A.Annett, S.Moreno, B.Kycia, S.An inclined detector geometry for improved X-ray total scattering measurements2023-04-01SYNCHROTRON RADIATION; X-RAY DIFFRACTION; TOTAL SCATTERING; INSTRUMENTATION; AREA DETECTORSdoi:10.1107/S1600576723001747urn:issn:1600-5767An inclined geometry is investigated for X-ray total scattering measurements using a digital flat-panel area detector. The inclined geometry enables acquisition of higher quality data for simultaneous Rietveld refinement and total scattering studies, yielding structural information on the short-, medium- and long-range orders from one single measurement.https://creativecommons.org/licenses/by/4.0/text/htmlApril 20232023-04-0151856research papers1600-5767med@iucr.org5101600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography2Modelling the structural disorder in trigonal-prismatic coordinated transition metal dichalcogenides
http://scripts.iucr.org/cgi-bin/paper?iu5037
Trigonal-prismatic coordinated transition metal dichalcogenides (TMDCs) are formed from stacked (chalcogen)–(transition metal)–(chalcogen) triple layers, where the chemical bond is covalent within the triple layers and van der Waals (vdW) forces are effective between the layers. Bonding is at the origin of the great interest in these compounds, which are used as 2D materials in applications such as catalysis, electronics, photoelectronics, sensors, batteries and thermoelectricity. This paper addresses the issue of modelling the structural disorder in multilayer TMDCs. The structural model takes into account stacking faults, correlated displacement of atoms and average crystallite size/shape, and is assessed by simulation of the X-ray diffraction pattern and fitting to the experimental data relative to a powdered sample of MoS2 exfoliated and restacked via lithiation. From fitting, an average crystallite size of about 50 Å, nearly spherical crystallites and a definite probability of deviation from the fully eclipsed atomic arrangement present in the ordered structure are determined. The increased interlayer distance and correlated intralayer and interlayer atomic displacement are attributed to the presence of lithium intercalated in the vdW gap between triple layers (Li/Mo molar ratio of about 0.06). The model holds for the whole class of trigonal-prismatic coordinated TMDCs, and is suitably flexible to take into account different preparation routes.International Union of CrystallographytextTrigonal-prismatic coordinated transition metal dichalcogenides (TMDCs) are formed from stacked (chalcogen)–(transition metal)–(chalcogen) triple layers, where the chemical bond is covalent within the triple layers and van der Waals (vdW) forces are effective between the layers. Bonding is at the origin of the great interest in these compounds, which are used as 2D materials in applications such as catalysis, electronics, photoelectronics, sensors, batteries and thermoelectricity. This paper addresses the issue of modelling the structural disorder in multilayer TMDCs. The structural model takes into account stacking faults, correlated displacement of atoms and average crystallite size/shape, and is assessed by simulation of the X-ray diffraction pattern and fitting to the experimental data relative to a powdered sample of MoS2 exfoliated and restacked via lithiation. From fitting, an average crystallite size of about 50 Å, nearly spherical crystallites and a definite probability of deviation from the fully eclipsed atomic arrangement present in the ordered structure are determined. The increased interlayer distance and correlated intralayer and interlayer atomic displacement are attributed to the presence of lithium intercalated in the vdW gap between triple layers (Li/Mo molar ratio of about 0.06). The model holds for the whole class of trigonal-prismatic coordinated TMDCs, and is suitably flexible to take into account different preparation routes.enUrsi, F.Virga, S.Pipitone, C.Sanson, A.Longo, A.Giannici, F.Martorana, A.Modelling the structural disorder in trigonal-prismatic coordinated transition metal dichalcogenides2023-03-30CHALCOGENIDES; DISORDER; STOCHASTIC MODELLING; X-RAY DIFFRACTIONdoi:10.1107/S1600576723001589urn:issn:1600-5767The structural disorder in trigonal-prismatic coordinated transition metal layered dichalcogenides is investigated. The structural model taking into account stacking faults, correlated displacement of atoms and average crystallite size is assessed by fitting to the X-ray diffraction pattern of an exfoliated–restacked MoS2 sample.https://creativecommons.org/licenses/by/4.0/text/html56research papers5092023-03-30April 20232https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767502med@iucr.org1600-5767FAIR and scalable management of small-angle X-ray scattering data
http://scripts.iucr.org/cgi-bin/paper?jl5054
A modular research data management toolbox based on the programming language Python, the widely used computing platform Jupyter Notebook, the standardized data exchange format for analytical data (AnIML) and the generic repository Dataverse has been established and applied to analyze small-angle X-ray scattering (SAXS) data according to the FAIR data principles (findable, accessible, interoperable and reusable). The SAS-tools library is a community-driven effort to develop tools for data acquisition, analysis, visualization and publishing of SAXS data. Metadata from the experiment and the results of data analysis are stored as an AnIML document using the novel Python-native pyAnIML API. The AnIML document, measured raw data and plots resulting from the analysis are combined into an archive in OMEX format and uploaded to Dataverse using the novel easyDataverse API, which makes each data set accessible via a unique DOI and searchable via a structured metadata block. SAS-tools is applied to study the effects of alkyl chain length and counterions on the phase diagrams of alkyltrimethylammonium surfactants in order to demonstrate the feasibility and usefulness of a scalable data management workflow for experiments in physical chemistry.International Union of CrystallographytextA modular research data management toolbox based on the programming language Python, the widely used computing platform Jupyter Notebook, the standardized data exchange format for analytical data (AnIML) and the generic repository Dataverse has been established and applied to analyze small-angle X-ray scattering (SAXS) data according to the FAIR data principles (findable, accessible, interoperable and reusable). The SAS-tools library is a community-driven effort to develop tools for data acquisition, analysis, visualization and publishing of SAXS data. Metadata from the experiment and the results of data analysis are stored as an AnIML document using the novel Python-native pyAnIML API. The AnIML document, measured raw data and plots resulting from the analysis are combined into an archive in OMEX format and uploaded to Dataverse using the novel easyDataverse API, which makes each data set accessible via a unique DOI and searchable via a structured metadata block. SAS-tools is applied to study the effects of alkyl chain length and counterions on the phase diagrams of alkyltrimethylammonium surfactants in order to demonstrate the feasibility and usefulness of a scalable data management workflow for experiments in physical chemistry.enGiess, T.Itzigehl, S.Range, J.Schömig, R.Bruckner, J.R.Pleiss, J.FAIR and scalable management of small-angle X-ray scattering data2023-03-21RESEARCH DATA MANAGEMENT; FAIR DATA PRINCIPLES; SMALL-ANGLE X-RAY SCATTERING; SAXS; LYOTROPIC LIQUID CRYSTALS; ALKYLTRIMETHYLAMMONIUM SURFACTANTS; PHASE DIAGRAMSdoi:10.1107/S1600576723001577urn:issn:1600-5767A modular and extensible research data management toolbox based on the programming language Python and the widely used computing platform Jupyter Notebook has been established for the acquisition, visualization, analysis and storage of small-angle X-ray scattering data.https://creativecommons.org/licenses/by/4.0/text/html5752023-03-2156computer programsApril 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography2med@iucr.org1600-57671600-5767565Specimen-displacement correction for powder X-ray diffraction in Debye–Scherrer geometry with a flat area detector. Erratum
http://scripts.iucr.org/cgi-bin/paper?vb5055
An error in Fig. 2(b) in the paper by Hulbert & Kriven [J. Appl. Cryst. (2023), 56, 160–166] is corrected.International Union of CrystallographytextAn error in Fig. 2(b) in the paper by Hulbert & Kriven [J. Appl. Cryst. (2023), 56, 160–166] is corrected.enHulbert, B.S.Kriven, W.M.Specimen-displacement correction for powder X-ray diffraction in Debye–Scherrer geometry with a flat area detector. Erratum2023-03-21DEBYE-SCHERRER; TRANSMISSION; SPECIMEN-TO-DETECTOR DISTANCE; DISPLACEMENT CORRECTION EQUATION; POWDER X-RAY DIFFRACTION; AREA DETECTORSdoi:10.1107/S160057672300153Xurn:issn:1600-5767An error in Fig. 2(b) in the paper by Hulbert & Kriven [J. Appl. Cryst. (2023), 56, 160–166] is corrected.https://creativecommons.org/licenses/by/4.0/text/htmladdenda and errata565762023-03-21April 20232Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767576med@iucr.org1600-5767X-ray scattering study of GaN nanowires grown on Ti/Al2O3 by molecular beam epitaxy
http://scripts.iucr.org/cgi-bin/paper?xx5014
GaN nanowires (NWs) grown by molecular beam epitaxy on Ti films sputtered on Al2O3 are studied by X-ray diffraction (XRD) and grazing-incidence small-angle X-ray scattering (GISAXS). XRD, performed both in symmetric Bragg reflection mode and at grazing incidence, reveals Ti, TiN, Ti3O, Ti3Al and Ga2O3 crystallites with in-plane and out-of-plane lattice parameters intermediate between those of Al2O3 and GaN. These topotaxial crystallites in the Ti film, formed as a result of interfacial reactions and N exposure, possess little misorientation with respect to Al2O3. As a result, GaN NWs grow on the top TiN layer, possessing a high degree of epitaxial orientation with respect to the substrate. The measured GISAXS intensity distributions are modelled by the Monte Carlo method, taking into account the orientational distributions of NWs, the variety of their cross-sectional shapes and sizes, and the roughness of their side facets. The cross-sectional size distributions of the NWs and the relative fractions of the {1100} and {1120} side facets are determined.International Union of CrystallographytextGaN nanowires (NWs) grown by molecular beam epitaxy on Ti films sputtered on Al2O3 are studied by X-ray diffraction (XRD) and grazing-incidence small-angle X-ray scattering (GISAXS). XRD, performed both in symmetric Bragg reflection mode and at grazing incidence, reveals Ti, TiN, Ti3O, Ti3Al and Ga2O3 crystallites with in-plane and out-of-plane lattice parameters intermediate between those of Al2O3 and GaN. These topotaxial crystallites in the Ti film, formed as a result of interfacial reactions and N exposure, possess little misorientation with respect to Al2O3. As a result, GaN NWs grow on the top TiN layer, possessing a high degree of epitaxial orientation with respect to the substrate. The measured GISAXS intensity distributions are modelled by the Monte Carlo method, taking into account the orientational distributions of NWs, the variety of their cross-sectional shapes and sizes, and the roughness of their side facets. The cross-sectional size distributions of the NWs and the relative fractions of the {1100} and {1120} side facets are determined.enKaganer, V.M.Konovalov, O.V.Calabrese, G.van Treeck, D.Kwasniewski, A.Richter, C.Fernández-Garrido, S.Brandt, O.X-ray scattering study of GaN nanowires grown on Ti/Al2O3 by molecular beam epitaxy2023-03-09GAN NANOWIRES; GRAZING-INCIDENCE SMALL-ANGLE X-RAY SCATTERING; GISAXS; MOLECULAR BEAM EPITAXY; TOPOTAXYdoi:10.1107/S1600576723001486urn:issn:1600-5767Monte Carlo modelling of grazing-incidence small-angle X-ray scattering intensity provides detailed information on the cross-sectional size and shape distributions of GaN nanowires, as well as the roughness of their side facets. The cross sections are found to be dodecagons rather than hexagons. A narrow orientational distribution of the nanowires is found using X-ray diffraction. In addition, a variety of different topotaxial crystallites with in-plane and out-of-plane lattice parameters intermediate between those of Al2O3 and GaN are revealed in the sputtered Ti film.https://creativecommons.org/licenses/by/4.0/text/html2023-03-0944856research papersApril 2023https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography21600-5767med@iucr.org4391600-5767A simple goniometer-compatible flow cell for serial synchrotron X-ray crystallography
http://scripts.iucr.org/cgi-bin/paper?ap5048
Serial femtosecond crystallography was initially developed for room-temperature X-ray diffraction studies of macromolecules at X-ray free electron lasers. When combined with tools that initiate biological reactions within microcrystals, time-resolved serial crystallography allows the study of structural changes that occur during an enzyme catalytic reaction. Serial synchrotron X-ray crystallography (SSX), which extends serial crystallography methods to synchrotron radiation sources, is expanding the scientific community using serial diffraction methods. This report presents a simple flow cell that can be used to deliver microcrystals across an X-ray beam during SSX studies. This device consists of an X-ray transparent glass capillary mounted on a goniometer-compatible 3D-printed support and is connected to a syringe pump via lightweight tubing. This flow cell is easily mounted and aligned, and it is disposable so can be rapidly replaced when blocked. This system was demonstrated by collecting SSX data at MAX IV Laboratory from microcrystals of the integral membrane protein cytochrome c oxidase from Thermus thermophilus, from which an X-ray structure was determined to 2.12 Å resolution. This simple SSX platform may help to lower entry barriers for non-expert users of SSX.International Union of CrystallographytextSerial femtosecond crystallography was initially developed for room-temperature X-ray diffraction studies of macromolecules at X-ray free electron lasers. When combined with tools that initiate biological reactions within microcrystals, time-resolved serial crystallography allows the study of structural changes that occur during an enzyme catalytic reaction. Serial synchrotron X-ray crystallography (SSX), which extends serial crystallography methods to synchrotron radiation sources, is expanding the scientific community using serial diffraction methods. This report presents a simple flow cell that can be used to deliver microcrystals across an X-ray beam during SSX studies. This device consists of an X-ray transparent glass capillary mounted on a goniometer-compatible 3D-printed support and is connected to a syringe pump via lightweight tubing. This flow cell is easily mounted and aligned, and it is disposable so can be rapidly replaced when blocked. This system was demonstrated by collecting SSX data at MAX IV Laboratory from microcrystals of the integral membrane protein cytochrome c oxidase from Thermus thermophilus, from which an X-ray structure was determined to 2.12 Å resolution. This simple SSX platform may help to lower entry barriers for non-expert users of SSX.enGhosh, S.Zorić, D.Dahl, P.Bjelčić, M.Johannesson, J.Sandelin, E.Borjesson, P.Björling, A.Banacore, A.Edlund, P.Aurelius, O.Milas, M.Nan, J.Shilova, A.Gonzalez, A.Mueller, U.Brändén, G.Neutze, R.A simple goniometer-compatible flow cell for serial synchrotron X-ray crystallography2023-03-09SERIAL SYNCHROTRON X-RAY CRYSTALLOGRAPHY; MACROMOLECULAR CRYSTALLOGRAPHY; CYTOCHROME C OXIDASE; GONIOMETER-COMPATIBLE FLOW CELLSdoi:10.1107/S1600576723001036urn:issn:1600-5767Serial crystallography, in which X-ray diffraction data are recorded from a sequence of microcrystals in serial fashion, requires a platform for sample delivery. This work describes a simple flow cell device designed to deliver protein microcrystals to an X-ray beam during serial X-ray crystallography studies using synchrotron radiation.https://creativecommons.org/licenses/by/4.0/text/html1600-5767449med@iucr.org1600-57672https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyApril 2023research papers564602023-03-09Use of electron backscatter diffraction patterns to determine the crystal lattice. Part 3. Pseudosymmetry
http://scripts.iucr.org/cgi-bin/paper?nb5341
A pseudosymmetric description of the crystal lattice derived from a single wide-angle Kikuchi pattern can have several causes. The small size (<15%) of the sector covered by an electron backscatter diffraction pattern, the limited precision of the projection centre position and the Kikuchi band definition are crucial. Inherent pseudosymmetries of the crystal lattice and/or structure also pose a challenge in the analysis of Kikuchi patterns. To eliminate experimental errors as much as possible, simulated Kikuchi patterns of 350 phases have been analysed using the software CALM [Nolze et al. (2021). J. Appl. Cryst. 54, 1012–1022] in order to estimate the frequency of and reasons for pseudosymmetric crystal lattice descriptions. Misinterpretations occur in particular when the atomic scattering factors of non-equivalent positions are too similar and reciprocal-lattice points are systematically missing. As an example, a pseudosymmetry prediction depending on the elements involved is discussed for binary AB compounds with B1 and B2 structure types. However, since this is impossible for more complicated phases, this approach cannot be directly applied to compounds of arbitrary composition and structure.International Union of CrystallographytextA pseudosymmetric description of the crystal lattice derived from a single wide-angle Kikuchi pattern can have several causes. The small size (<15%) of the sector covered by an electron backscatter diffraction pattern, the limited precision of the projection centre position and the Kikuchi band definition are crucial. Inherent pseudosymmetries of the crystal lattice and/or structure also pose a challenge in the analysis of Kikuchi patterns. To eliminate experimental errors as much as possible, simulated Kikuchi patterns of 350 phases have been analysed using the software CALM [Nolze et al. (2021). J. Appl. Cryst. 54, 1012–1022] in order to estimate the frequency of and reasons for pseudosymmetric crystal lattice descriptions. Misinterpretations occur in particular when the atomic scattering factors of non-equivalent positions are too similar and reciprocal-lattice points are systematically missing. As an example, a pseudosymmetry prediction depending on the elements involved is discussed for binary AB compounds with B1 and B2 structure types. However, since this is impossible for more complicated phases, this approach cannot be directly applied to compounds of arbitrary composition and structure.enNolze, G.Tokarski, T.Rychłowski, Ł.Use of electron backscatter diffraction patterns to determine the crystal lattice. Part 3. Pseudosymmetry2023-02-24BRAVAIS LATTICES; PSEUDOSYMMETRY; LATTICE POINT DENSITY; ORDERED/DISORDERED STRUCTURES; LATTICE DISTORTION; ELECTRON BACKSCATTER DIFFRACTION; BACKSCATTERED KIKUCHI DIFFRACTION PATTERNS; LATTICE PARAMETERS; FUNK TRANSFORMdoi:10.1107/S1600576723000845urn:issn:1600-5767Distinguishing between actual and apparent pseudosymmetry in electron backscatter diffraction patterns is nearly impossible, even for simulated patterns. However, the resulting lattice is always a superlattice as long as the signal is not a superposition of multiple patterns.https://creativecommons.org/licenses/by/4.0/text/html1600-5767med@iucr.org3671600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography2April 20232023-02-24380research papers56