Journal of Applied Crystallography最新文献

{"title":"Real-time analysis of liquid jet sample delivery stability for an X-ray free-electron laser using machine vision.","authors":"Jaydeep Patel, Adam Round, Raphael de Wijn, Mohammad Vakili, Gabriele Giovanetti, Diogo Filipe Monrroy Vilan E Melo, Juncheng E, Marcin Sikorski, Jayanth Koliyadu, Faisal H M Koua, Tokushi Sato, Adrian Mancuso, Andrew Peele, Brian Abbey","doi":"10.1107/S1600576724009853","DOIUrl":"10.1107/S1600576724009853","url":null,"abstract":"<p><p>Automated evaluation of optical microscopy images of liquid jets, commonly used for sample delivery at X-ray free-electron lasers (XFELs), enables real-time tracking of the jet position and liquid jet hit rates, defined here as the proportion of XFEL pulses intersecting with the liquid jet. This method utilizes machine vision for preprocessing, feature extraction, segmentation and jet detection as well as tracking to extract key physical characteristics (such as the jet angle) from optical microscopy images captured during experiments. To determine the effectiveness of these tools in monitoring jet stability and enhancing sample delivery efficiency, we conducted XFEL experiments with various sample compositions (pure water, buffer and buffer with crystals), nozzle designs and jetting conditions. We integrated our real-time analysis algorithm into the Karabo control system at the European XFEL. The results indicate that the algorithm performs well in monitoring the jet angle and provides a quantitative characterization of liquid jet stability through optical image analysis conducted during experiments.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1859-1870"},"PeriodicalIF":6.1,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploiting Friedel pairs to interpret scanning 3DXRD data from complex geological materials.","authors":"Jean-Baptiste Jacob, Jonathan Wright, Benoît Cordonnier, François Renard","doi":"10.1107/S1600576724009634","DOIUrl":"10.1107/S1600576724009634","url":null,"abstract":"<p><p>The present study introduces a processing strategy for synchrotron scanning 3D X-ray diffraction (s3DXRD) data, aimed at addressing the challenges posed by large, highly deformed, polyphase materials such as crystalline rocks. Leveraging symmetric Bragg reflections known as Friedel pairs, our method enables diffraction events to be precisely located within the sample volume. This method allows for fitting the phase, crystal structure and unit-cell parameters at the intra-grain scale on a voxel grid. The processing workflow incorporates several new modules, designed to (i) efficiently match Friedel pairs in large s3DXRD datasets containing up to 10⁸ diffraction peaks; (ii) assign phases to each pixel or voxel, resolving potential ambiguities arising from overlap in scattering angles between different crystallographic phases; and (iii) fit the crystal orientation and unit cell locally on a point-by-point basis. We demonstrate the effectiveness of our technique on fractured granite samples, highlighting the ability of the method to characterize complex geological materials and show their internal structure and mineral composition. Additionally, we include the characterization of a metal gasket made of a commercial aluminium alloy, which surrounded the granite sample during experiments. The results show the effectiveness of the technique in recovering information about the internal texture and residual strain of materials that have undergone high levels of plastic deformation.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1823-1840"},"PeriodicalIF":6.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611280/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>AnACor2.0</i>: a GPU-accelerated open-source software package for analytical absorption corrections in X-ray crystallography.","authors":"Yishun Lu, Karel Adámek, Tihana Stefanic, Ramona Duman, Armin Wagner, Wesley Armour","doi":"10.1107/S1600576724009506","DOIUrl":"10.1107/S1600576724009506","url":null,"abstract":"<p><p>Analytical absorption corrections are employed in scaling diffraction data for highly absorbing samples, such as those used in long-wavelength crystallography, where empirical corrections pose a challenge. <i>AnACor2.0</i> is an accelerated software package developed to calculate analytical absorption corrections. It accomplishes this by ray-tracing the paths of diffracted X-rays through a voxelized 3D model of the sample. Due to the computationally intensive nature of ray-tracing, the calculation of analytical absorption corrections for a given sample can be time consuming. Three experimental datasets (insulin at λ = 3.10 Å, thermolysin at λ = 3.53 Å and thaumatin at λ = 4.13 Å) were processed to investigate the effectiveness of the accelerated methods in <i>AnACor2.0</i>. These methods demonstrated a maximum reduction in execution time of up to 175× compared with previous methods. As a result, the absorption factor calculation for the insulin dataset can now be completed in less than 10 s. These acceleration methods combine sampling, which evaluates subsets of crystal voxels, with modifications to standard ray-tracing. The bisection method is used to find path lengths, reducing the complexity from <i>O</i>(<i>n</i>) to <i>O</i>(log₂ <i>n</i>). The gridding method involves calculating a regular grid of diffraction paths and using interpolation to find an absorption correction for a specific reflection. Additionally, optimized and specifically designed CUDA implementations for NVIDIA GPUs are utilized to enhance performance. Evaluation of these methods using simulated and real datasets demonstrates that systematic sampling of the 3D model provides consistently accurate results with minimal variance across different sampling ratios. The mean difference of absorption factors from the full calculation (without sampling) is at most 2%. Additionally, the anomalous peak heights of sulfur atoms in the Fourier map show a mean difference of only 1% compared with the full calculation. This research refines and accelerates the process of analytical absorption corrections, introducing innovative sampling and computational techniques that significantly enhance efficiency while maintaining accurate results.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1984-1995"},"PeriodicalIF":6.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving the reliability of small- and wide-angle X-ray scattering measurements of anisotropic precipitates in metallic alloys using sample rotation.","authors":"Thomas Perrin, Gilbert A Chahine, Stéphan Arnaud, Arthur Després, Pierre Heugue, Alexis Deschamps, Frédéric De Geuser","doi":"10.1107/S1600576724009294","DOIUrl":"10.1107/S1600576724009294","url":null,"abstract":"<p><p>Nanometric precipitates in metallic alloys often have highly anisotropic shapes. Given the large grain size and non-random texture typical of these alloys, performing small- and wide-angle X-ray scattering (SAXS/WAXS) measurements on such samples for determining their characteristics (typically size and volume fraction) results in highly anisotropic and irreproducible data. Rotations of flat samples during SAXS/WAXS acquisitions are presented here as a solution to these anisotropy issues. Two aluminium alloys containing anisotropic precipitates are used as examples to validate the approach with a -45°/45° angular range. Clear improvements can be seen on the SAXS <i>I</i>(<i>q</i>) fitting and the consistency between the different SAXS/WAXS measurements. This method-ology results in more reliable measurements of the precipitate's characteristics, and thus allows for time- and space-resolved measurements with higher accuracy.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1800-1814"},"PeriodicalIF":6.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping domain structures near a grain boundary in a lead zirconate titanate ferroelectric film using X-ray nanodiffraction.","authors":"Stanislav Udovenko, Yeongwoo Son, Pannawit Tipsawat, Reilly J Knox, Stephan O Hruszkewycz, Hanfei Yan, Xiaojing Huang, Ajith Pattammattel, Marc Zajac, Wonsuk Cha, Darren C Pagan, Susan Trolier-McKinstry","doi":"10.1107/S1600576724009026","DOIUrl":"10.1107/S1600576724009026","url":null,"abstract":"<p><p>The effect of an electric field on local domain structure near a 24° tilt grain boundary in a 200 nm-thick Pb(Zr_0.2Ti_0.8)O₃ bi-crystal ferroelectric film was probed using synchrotron nanodiffraction. The bi-crystal film was grown epitaxially on SrRuO₃-coated (001) SrTiO₃ 24° tilt bi-crystal substrates. From the nanodiffraction data, real-space maps of the ferroelectric domain structure around the grain boundary prior to and during application of a 200 kV cm^-1 electric field were reconstructed. In the vicinity of the tilt grain boundary, the distributions of densities of <i>c</i>-type tetragonal domains with the <i>c</i> axis aligned with the film normal were calculated on the basis of diffracted intensity ratios of <i>c</i>- and <i>a</i>-type domains and reference powder diffraction data. Diffracted intensity was averaged along the grain boundary, and it was shown that the density of <i>c</i>-type tetragonal domains dropped to ∼50% of that of the bulk of the film over a range ±150 nm from the grain boundary. This work complements previous results acquired by band excitation piezoresponse force microscopy, suggesting that reduced nonlinear piezoelectric response around grain boundaries may be related to the change in domain structure, as well as to the possibility of increased pinning of domain wall motion. The implications of the results and analysis in terms of understanding the role of grain boundaries in affecting the nonlinear piezoelectric and dielectric responses of ferroelectric materials are discussed.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1789-1799"},"PeriodicalIF":6.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating machine learning interatomic potentials with hybrid reverse Monte Carlo structure refinements in <i>RMCProfile</i>.","authors":"Paul Cuillier, Matthew G Tucker, Yuanpeng Zhang","doi":"10.1107/S1600576724009282","DOIUrl":"10.1107/S1600576724009282","url":null,"abstract":"<p><p>Structure refinement with reverse Monte Carlo (RMC) is a powerful tool for interpreting experimental diffraction data. To ensure that the under-constrained RMC algorithm yields reasonable results, the hybrid RMC approach applies interatomic potentials to obtain solutions that are both physically sensible and in agreement with experiment. To expand the range of materials that can be studied with hybrid RMC, we have implemented a new interatomic potential constraint in <i>RMCProfile</i> that grants flexibility to apply potentials supported by the <i>Large-scale Atomic/Molecular Massively Parallel Simulator</i> (<i>LAMMPS</i>) molecular dynamics code. This includes machine learning interatomic potentials, which provide a pathway to applying hybrid RMC to materials without currently available interatomic potentials. To this end, we present a methodology to use RMC to train machine learning interatomic potentials for hybrid RMC applications.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1780-1788"},"PeriodicalIF":6.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A micro-beamstop with transmission detection by fluorescence for scanning-beam synchrotron scattering beamlines.","authors":"Henrik Birkedal, Michael Sztucki, Moritz Stammer, Anastasiia Sadetskaia, Manfred C Burghammer, Tilman A Grünewald","doi":"10.1107/S1600576724009129","DOIUrl":"10.1107/S1600576724009129","url":null,"abstract":"<p><p>Quantitative X-ray diffraction approaches require careful correction for sample transmission. Though this is a routine task at state-of-the-art small-angle X-ray scattering (SAXS), wide-angle X-ray scattering (WAXS) or diffraction beamlines at synchrotron facilities, the transmission signal cannot be recorded concurrently with SAXS/WAXS when using the small, sub-millimetre beamstops at many X-ray nanoprobes during SAXS/WAXS experiments due to the divergence-limited size of the beamstop and the generally tight geometry. This is detrimental to the data quality and often the only solution is to re-scan the sample with a PIN photodiode as a detector to obtain transmission values. In this manuscript, we present a simple yet effective solution to this problem in the form of a small beamstop with an inlaid metal target for optimal fluorescence yield. This fluorescence can be detected with a high-sensitivity avalanche photodiode and provides a linear counter to determine the sample transmission.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"2043-2047"},"PeriodicalIF":6.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142768984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Animations, videos and 3D models for teaching space-group symmetry.","authors":"Lauro Bucio, Rosario Moreno-Tovar, Edilberto Hernández-Juárez, Andrea S Sandoval-Santiago, Nerith R Elejalde-Cadena, Andrés Bucio, Moises Falcón-Moreno, Ivonne Rosales-Chávez","doi":"10.1107/S1600576724008872","DOIUrl":"10.1107/S1600576724008872","url":null,"abstract":"<p><p>A series of animations, videos and 3D models that were developed, filmed or built to teach the symmetry properties of crystals are described. At first, these resources were designed for graduate students taking a basic crystallography course, coming from different careers, at the National Autonomous University of Mexico. However, the COVID-19 pandemic had the effect of accelerating the generation of didactic material. Besides our experience with postgraduate students, we have noted that 3D models attract the attention of children, and therefore we believe that these models are particularly useful for teaching children about the assembled arrangements of crystal structures.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1966-1977"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sheet-on-sheet fixed target data collection devices for serial crystallography at synchrotron and XFEL sources.","authors":"R Bruce Doak, Robert L Shoeman, Alexander Gorel, Stanisław Niziński, Thomas R M Barends, Ilme Schlichting","doi":"10.1107/S1600576724008914","DOIUrl":"10.1107/S1600576724008914","url":null,"abstract":"<p><p>Serial crystallography (SX) efficiently distributes over many crystals the radiation dose absorbed during diffraction data acquisition, enabling structure determination of samples at ambient temperature. SX relies on the rapid and reliable replacement of X-ray-exposed crystals with fresh crystals at a rate commensurate with the data acquisition rate. 'Solid supports', also known as 'fixed targets' or 'chips', offer one approach. These are microscopically thin solid panes into or onto which crystals are deposited to be individually interrogated by an X-ray beam. Solid supports are generally patterned using photolithography methods to produce a regular array of features that trap single crystals. A simpler and less expensive alternative is to merely sandwich the microcrystals between two unpatterned X-ray-transparent polymer sheets. Known as sheet-on-sheet (SOS) chips, these offer significantly more versatility. SOS chips place no constraint on the size or size distribution of the microcrystals or their growth conditions. Crystals ranging from true nanocrystals up to microcrystals can be investigated, as can crystals grown in media ranging from low viscosity (aqueous solution) up to high viscosity (such as lipidic cubic phase). Here, we describe our two SOS devices. The first is a compact and lightweight version designed specifically for synchrotron use. It incorporates a standard SPINE-type magnetic base for mounting on a conventional macromolecular crystallography goniometer. The second and larger chip is intended for both X-ray free-electron laser and synchrotron use and is fully compatible with the fast-scanning <i>XY</i>-raster stages developed for data collection with patterned chips.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1725-1732"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electronic angle focusing for neutron time-of-flight powder diffractometers.","authors":"Robert B Von Dreele","doi":"10.1107/S1600576724008756","DOIUrl":"10.1107/S1600576724008756","url":null,"abstract":"<p><p>A neutron time-of-flight (TOF) powder diffractometer with a continuous wide-angle array of detectors can be electronically focused to make a single pseudo-constant wavelength diffraction pattern, thus facilitating angle-dependent intensity corrections. The resulting powder diffraction peak profiles are affected by the neutron source emission profile and resemble the function currently used for TOF diffraction.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1588-1597"},"PeriodicalIF":6.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}