Journal of Applied Crystallography最新文献

{"title":"Advanced EXAFS analysis techniques applied to the <i>L</i>-edges of the lanthanide oxides.","authors":"Adam Smerigan, Adam S Hoffman, Lars Ostervold, Jiyun Hong, Jorge Perez-Aguillar, Ash C Caine, Lauren Greenlee, Simon R Bare","doi":"10.1107/S1600576724010240","DOIUrl":"10.1107/S1600576724010240","url":null,"abstract":"<p><p>The unique properties of the lanthanide (Ln) elements make them critical components of modern technologies, such as lasers, anti-corrosive films and catalysts. Thus, there is significant interest in establishing structure-property relationships for Ln-containing materials to advance these technologies. Extended X-ray absorption fine structure (EXAFS) is an excellent technique for this task considering its ability to determine the average local structure around the Ln atoms for both crystalline and amorphous materials. However, the limited availability of EXAFS reference spectra of the Ln oxides and challenges in the EXAFS analysis have hindered the application of this technique to these elements. The challenges include the limited <i>k</i>-range available for the analysis due to the superposition of <i>L</i>-edges on the EXAFS, multielectron excitations (MEEs) creating erroneous peaks in the EXAFS and the presence of inequivalent absorption sites. Herein, we removed MEEs to model the local atomic environment more accurately for light Ln oxides. Further, we investigated the use of cubic and non-cubic lattice expansion to minimize the fitting parameters needed and connect the fitting parameters to physically meaningful crystal parameters. The cubic expansion reduced the number of fitting parameters but resulted in a statistically worse fit. The non-cubic expansion resulted in a similar quality fit and showed non-isotropic expansion in the crystal lattice of Nd₂O₃. In total, the EXAFS spectra and the fits for the entire set of Ln oxides (excluding promethium) are included. The knowledge developed here can assist in the structural determination of a wide variety of Ln compounds and can further studies on their structure-property relationships.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1913-1923"},"PeriodicalIF":6.1,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769041","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>TOMOMAN</i>: a software package for large-scale cryo-electron tomography data preprocessing, community data sharing and collaborative computing.","authors":"Sagar Khavnekar, Philipp S Erdmann, William Wan","doi":"10.1107/S1600576724010264","DOIUrl":"10.1107/S1600576724010264","url":null,"abstract":"<p><p>Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) are becoming the preferred methodologies for investigating subcellular and macromolecular structures in native or near-native environments. Although cryo-ET is amenable to a wide range of biological problems, these problems often have data-processing requirements that need to be individually optimized, precluding the notion of a one-size-fits-all processing pipeline. Cryo-ET data processing is also becoming progressively more complex due to the increasing number of packages for each processing step. Though each package has its strengths and weaknesses, independent development and different data formats make them difficult to interface with one another. <i>TOMOMAN</i> (<i>TOMOgram MANager</i>) is an extensible package for streamlining the interoperability of packages, enabling users to develop project-specific processing workflows. <i>TOMOMAN</i> does this by maintaining an internal metadata format and wrapping external packages to manage and perform preprocessing, from raw tilt-series data to reconstructed tomograms. <i>TOMOMAN</i> can also export these metadata between various STA packages. <i>TOMOMAN</i> includes tools for archiving projects to data repositories, allowing subsequent users to download <i>TOMOMAN</i> projects and directly resume processing. By tracking essential metadata, <i>TOMOMAN</i> streamlines data sharing, which improves the reproducibility of published results, reduces computational costs by minimizing reprocessing, and enables the distribution of cryo-ET projects between multiple groups and institutions. <i>TOMOMAN</i> provides a way for users to test different software packages in order to develop processing workflows that meet the specific needs of their biological questions and to distribute their results to the broader scientific community.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"2010-2016"},"PeriodicalIF":6.1,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142768127","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":"Non-invasive nanoscale imaging of protein micro- and nanocrystals for screening crystallization conditions.","authors":"Krishna Prasad Khakurel, Kei Hosomi, Wataru Inami, Kawata Yoshimasa","doi":"10.1107/S1600576724010124","DOIUrl":"10.1107/S1600576724010124","url":null,"abstract":"<p><p>Crystallography has been the routine technique for studying high-resolution structures of proteins for over five decades. A major bottleneck in structure determination of macromolecules is obtaining crystals of a size and quality suitable for single-crystal X-ray crystallography experiments. Many challenging proteins either fail to grow into crystals or fail to grow into crystals of a size suitable for obtaining high-resolution structures using conventional X-ray crystallography. When it comes to smaller crystals, they can be used either for seeding to get larger crystals or for serial crystallography and electron diffraction for obtaining the structures. For both purposes, a limiting step is to non-invasively image such small crystals of sub-micrometre dimensions and to screen the conditions where such crystals prevail. Here we use cathodoluminescence-based (CL-based) nanoscopy to image protein nanocrystals. We show that crystals of micrometre and submicrometre dimensions can be non-invasively imaged by the CL-based nanoscope. The results presented here demonstrate the feasibility of non-invasive imaging of protein crystals with sub-100 nm resolution.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1907-1912"},"PeriodicalIF":6.1,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769060","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":"Modulating phase segregation during spin-casting of fullerene-based polymer solar-cell thin films upon minor addition of a high-boiling co-solvent.","authors":"Kuan-Hsun Lu, Wei-Ru Wu, Chun-Jen Su, Po-Wei Yang, Norifumi L Yamada, Hong-Jun Zhuo, Show-An Chen, Wei-Tsung Chuang, Yi-Kang Lan, An-Chung Su, U-Ser Jeng","doi":"10.1107/S1600576724010082","DOIUrl":"10.1107/S1600576724010082","url":null,"abstract":"<p><p>The impact of additives on the nanoscale structures of spin-cast polymer composite films, particularly in polymer solar cells, is a topic of significant interest. This study focuses on the blend film comprising poly(thieno[3,4-<i>b</i>]thio-phene-<i>alt</i>-benzodi-thio-phene) (PTB7) and [6,6]-phenyl-C₇₁-butyric acid methyl ester (PC₇₁BM), exploring how additives like 1,8-di-iodo-octane (DIO) influence the film structures spin-cast from chloro-benzene solution. Combined results of specular X-ray and neutron reflectivity, grazing-incidence small- and wide-angle X-ray scattering (GISAXS and GIWAXS), and X-ray photoelectron spectroscopy indicate that DIO could significantly enhance the dispersion of PC₇₁BM and reduce composition inhomogeneity in the film. Time-resolved GISAXS-GIWAXS with 100 ms resolution further captures a rapid spinodal decomposition of the mixture within 1 s in the constant-evaporation stage of spin-casting. Further combined with parallel analysis of time-resolved UV-Vis reflectance, these findings reveal that DIO mitigates the spinodal decomposition process by accelerating solvent evaporation, which, in turn, decelerates phase segregation, leading to a nucleation-driven process. These observations provide mechanistic insights into the role of additives in controlling the nanostructural evolution of spin-cast films by altering the kinetics of solvent evaporation and phase separation during the spin-coating process.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1871-1883"},"PeriodicalIF":6.1,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611283/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769059","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":"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}