Journal of Applied Crystallography最新文献

{"title":"Spin-contrast-variation small-angle neutron scattering study of fully and partially swollen silica-filled rubber.","authors":"Yohei Noda, Satoshi Koizumi, Tomomi Masui, Hiroyuki Kishimoto, Daisuke Yamaguchi, Takayuki Kumada, Shin-Ichi Takata, Kazuki Ohishi, Jun-Ichi Suzuki","doi":"10.1107/S1600576726000361","DOIUrl":"https://doi.org/10.1107/S1600576726000361","url":null,"abstract":"<p><p>We have elucidated the polymer adsorption layer structure in filler-rubber systems by conducting spin-contrast-variation small-angle neutron scattering (SANS) on partially and fully swollen filler-rubber samples with and without a silane coupling agent. In spin-contrast-variation SANS, dynamic nuclear polarization (DNP) was used to polarize protons and change their scattering length with respect to polarized neutron beams significantly. SANS measurements were performed in dynamically polarized states using a DNP cryostat (1.2 K and 3.35 T). From SANS profiles obtained at various proton spin polarizations, partial scattering functions (PSFs) for each component were separated by regarding each sample as a three-component system composed of silica, polymer and deuterated toluene. To analyze the obtained PSFs in detail, we built a structure model for the silica aggregates and the surrounding polymer adsorption layer. Numerical calculation based on this model successfully reproduced the experimentally obtained PSFs, providing the structural parameters of the silica aggregates and polymer adsorption layer. The results showed a considerable difference in structural parameters between the partially and fully swollen states. For the sample with the silane coupling agent, the thickness of the polymer adsorption layer decreased as the solvent fraction increased. The difference in polymer volume fraction between the polymer adsorption layer and the outside matrix was very small in less swollen states but significant in the fully swollen state. Furthermore, the scattering contribution of the polymer chains in the solvent was accurately separated via contrast variation. In the swollen silica-filled rubber without the silane coupling agent, the size of the polymer-dense regions was almost constant, regardless of the swelling ratio. By contrast, in the swollen silica-filled rubber with the silane coupling agent, the size of the polymer-dense regions significantly increased by a factor of 2 with an increase in the swelling ratio.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 2","pages":"492-512"},"PeriodicalIF":2.8,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13060475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645295","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>pyDiSCaMB</i>: enabling the use of multipolar scattering factors in <i>Phenix</i>.","authors":"Viljar J Femoen, Laura Pacoste, Michał Leszek Chodkiewicz, Pavel V Afonine, Billy K Poon, Marta Kulik, Łukasz Golon, Nigel W Moriarty, Paul D Adams, Gerhard Hofer, Paulina Maria Dominiak, Dorothee Liebschner, Xiaodong Zou","doi":"10.1107/S1600576726000828","DOIUrl":"https://doi.org/10.1107/S1600576726000828","url":null,"abstract":"<p><p>Multipolar scattering models, such as the transferable aspherical atom model, account for atomic chemical interactions and provide a more accurate representation of experimental data. However, the simpler independent atom model (IAM), which assumes non-interacting atoms, is the only model available in the most widely used macromolecular refinement programs. This is primarily because IAM offers a hard-to-beat combination of computational efficiency and modelling power at typical macromolecular resolutions. By contrast, more accurate multipolar modelling has historically been limited due to its computational cost and the absence of an interface between software capable of calculating structure factors and gradients based on multipolar models and software designed for macromolecular refinement. This work introduces <i>pyDiSCaMB</i>, a Python software package designed to integrate between the computational crystallography toolbox (<i>cctbx</i>) and the quantum crystallography library <i>DiSCaMB</i> (<i>Densities in Structural Chemistry and Molecular Biology</i>), thus enabling multipolar scattering models in <i>Phenix</i>'s toolkit. The implementation, features and capabilities of <i>pyDiSCaMB</i> are presented, the runtimes for the calculation of structure factor and target gradients with respect to atomic parameters are explored, and Fourier images of electrostatic potential, electron density and deformation maps are computed as illustrative examples. The <i>pyDiSCaMB</i> library will make multipolar modelling widely available to the structural biology community, potentially transforming refinement and model-building for both crystallography and cryogenic electron microscopy (cryoEM).</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 2","pages":"662-672"},"PeriodicalIF":2.8,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13060618/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147644967","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>LaueMatching</i>: an approach for rapid and robust indexing of Laue diffraction patterns.","authors":"Hemant Sharma, Dina Sheyfer, Ross Harder, Jonathan Z Tischler","doi":"10.1107/S1600576726001196","DOIUrl":"https://doi.org/10.1107/S1600576726001196","url":null,"abstract":"<p><p>Traditional Laue diffraction pattern indexing often struggles with noisy data, weak signals, peak overlap and missing reflections, particularly from complex or deformed microstructures. Here, we introduce <i>LaueMatching</i>, a high-throughput indexing algorithm designed to overcome these limitations. <i>LaueMatching</i> utilizes a fundamentally different approach based on direct pattern correlation: experimentally pre-processed images are compared against a comprehensive pre-computed library of simulated diffraction patterns corresponding to a dense grid of possible orientations. This approach bypasses the need for explicit peak identification and fitting, steps that are often a failure point for traditional methods. The algorithm rapidly and robustly indexes multiple crystallographic orientations and crystal systems simultaneously, even from challenging patterns. <i>LaueMatching</i>'s effectiveness and accuracy have been rigorously tested and validated on diverse experimental (Ni, Al, EuAl₂O₄) and simulated diffraction patterns, demonstrating high-fidelity orientation refinement. Code to implement this approach on both CPU and GPU resources can be downloaded from https://github.com/AdvancedPhotonSource/LaueMatching.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 2","pages":"552-563"},"PeriodicalIF":2.8,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13060470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147644920","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":"Erratum: The crystal structure of dypingite: understanding the long-range disorder. Corrigendum.","authors":"Anton Sednev-Lugovets, Yang Lu, Ørnulv Vistad, Patricia Almeida Carvalho, Alexander Missyul, Håkon Austrheim, Henrik Friis, Matylda N Guzik","doi":"10.1107/S1600576726002438","DOIUrl":"https://doi.org/10.1107/S1600576726002438","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1107/S1600576725007915.].</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 2","pages":"705"},"PeriodicalIF":2.8,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13060614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645266","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":"Twin-compartment solid-liquid cells for neutron reflectometry.","authors":"Nicoló Paracini, Hannah Burrall, Thomas Saerbeck, Philipp Gutfreund, Giovanna Fragneto, Luke A Clifton, Thomas Arnold, Marité Cárdenas","doi":"10.1107/S1600576726000919","DOIUrl":"https://doi.org/10.1107/S1600576726000919","url":null,"abstract":"<p><p>We propose a new type of sample environment for neutron reflectometry at solid-liquid interfaces. The twin-compartment solid-liquid cell optimizes several aspects of neutron reflectometry measurements by splitting the surface of substrates currently in use at facilities into two independent samples. This approach increases the capacity of mounted samples on the stage of current neutron reflectometers by a factor of two, shortens alignment times, and enables side-by-side comparison and control experiments on identical substrates. Furthermore, it reduces sample preparation time for a variety of samples prepared by Langmuir monolayer transfer techniques, spin coating, sputter coating, <i>ex situ</i> self-assembly and more. We present results from three cell prototypes tested on vertical and horizontal reflectometers at ISIS and Institut Laue-Langevin.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 2","pages":"369-380"},"PeriodicalIF":2.8,"publicationDate":"2026-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13060453/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645337","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>LamelODF</i>: a MATLAB-based toolbox for orientation distribution analysis and mapping of lamellar minerals for laboratory and synchrotron X-ray diffractometers.","authors":"Baptiste Dazas, Eric Ferrage, Fabien Hubert, Brian Gregoire, Pierre Fertey, Laurent Michot","doi":"10.1107/S1600576726000968","DOIUrl":"https://doi.org/10.1107/S1600576726000968","url":null,"abstract":"<p><p>We present <i>LamelODF</i>, a MATLAB-based software platform for automated extraction and mapping of axisymmetric orientation distribution functions (ODFs) from 2D X-ray diffraction patterns of lamellar minerals. Building on a maximum-entropy-method-derived ODF specifically for clay mineral systems, the software provides a streamlined workflow for texture analysis under the assumption of transverse isotropy. The program features dedicated file converters for both laboratory and synchrotron data formats, batch processing capabilities, and flexible background-correction algorithms. The analytical pipeline performs azimuthal intensity integration with background subtraction, followed by non-linear fitting to extract quantitative orientation parameters including the 〈<i>P</i> ₂〉 order parameter, the deviation angle δ between the main orientation of lamellar particles and the detector reference, and integrated intensities, focusing specifically on basal 001 reflections to enable rapid processing of thousands of diffraction patterns for spatial mapping applications. Mapping of a laboratory-prepared porous clay medium and a natural soil sample demonstrates the software's ability to detect density stratification, sedimentation discontinuities and complex geological structures such as relict topsoil crusts. The software successfully discriminates between different clay mineral phases, providing a practical complementary tool for researchers investigating the organization of lamellar minerals in natural and engineered materials.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 2","pages":"648-661"},"PeriodicalIF":2.8,"publicationDate":"2026-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13060612/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645313","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":"Experimental absorption corrections for highly absorbing europium compounds in powder neutron diffraction.","authors":"A Hoshikawa, K Kuwahara, C Sekine","doi":"10.1107/S1600576726001044","DOIUrl":"https://doi.org/10.1107/S1600576726001044","url":null,"abstract":"<p><p>For materials with strong neutron absorption, such as europium (Eu), the absorption correction method is important but difficult to manage. This is because Eu has a strong isotope dependence. The energy dependence of absorption is also complex, making it even more difficult to handle in a time-of-flight neutron diffractometer, where wavelength varies with the time of flight. Experimental measurement of the transmittance of a sample using a vanadium plate, possibly due to unexpected experimental conditions, allowed more accurate structural analysis than absorption correction based on theoretically calculated absorption cross sections.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 2","pages":"472-476"},"PeriodicalIF":2.8,"publicationDate":"2026-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13060451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645274","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":"Automatic calculation of symmetry-adapted tensors under spin-group symmetry: <i>STENSOR</i>, a new tool of the Bilbao Crystallographic Server.","authors":"Luis Elcoro, Jesus Etxebarria, J Manuel Perez-Mato, Emre S Tasci","doi":"10.1107/S1600576726000944","DOIUrl":"https://doi.org/10.1107/S1600576726000944","url":null,"abstract":"<p><p>We present <i>STENSOR</i>, a new computational tool integrated into the Bilbao Crystallographic Server, designed for the automatic calculation of symmetry-adapted tensors under spin-group symmetry. The program requires either a file containing the structural data of the magnetic compound or the generators of the oriented spin point group, together with the generalized Jahn symbol associated with the tensor of interest. The user can propose any arbitrary tensor type or select a particular one from a predefined list. The program output returns the symmetry-adapted tensor under the spin point group and under the magnetic point group, which is also calculated. The comparison of these two tensor forms allows the coefficients due to spin-orbit coupling effects to be distinguished from those that have a non-relativistic origin and thus are usually more important. Two examples are given to illustrate the operation of the program.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 2","pages":"640-647"},"PeriodicalIF":2.8,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13060620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645172","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":"Structure and composition of supported lipid bilayers: a comparison between solvent-assisted lipid bilayer and vesicle fusion methods.","authors":"Birgit Felderer, Claire Buchanan, Shuhong Wang, Hsin-Hui Shen, Andrew Nelson, Stephen C L Hall, Marité Cárdenas","doi":"10.1107/S1600576726000312","DOIUrl":"https://doi.org/10.1107/S1600576726000312","url":null,"abstract":"<p><p>Supported lipid bilayers (SLBs) are crucial model membrane platforms to study the structure and dynamics of cellular membranes. Vesicle fusion (VF) is one of the most widely used approaches to forming SLBs, though it suffers from compositional limitations and substrate compatibility constraints. The solvent-assisted lipid bilayer (SALB) technique enables the possibility of forming SLBs using a wider range of membrane compositions and substrate platforms through organic-solvent-mediated bilayer assembly, yet questions remain regarding structural equivalence and potential organic solvent incorporation effects. Using neutron reflectometry (NR), we systematically compare the structure and composition of phosphatidylcholine-based SLBs formed by either VF or SALB methodologies. SALB conditions were optimized for NR solid/liquid cells, and structural characterization revealed comparable bilayer architectures between the two formation methods, although some changes in the lipid acyl chain thickness were observed. SALBs showed up to 99.2 ± 0.9% surface coverage using ultrapure water for solvent exchange, but the reproducibility of the method was poor. Enhanced-contrast NR using either deuterated lipids or solvents allowed for the quantitative detection of residual organic solvent incorporation of the SALBs, which was up to 3.3 ± 0.9 vol.% in the tail regions. Making use of 1 m<i>M</i> CaCl₂ during solvent exchange substantially improved SALB reproducibility, reducing coverage variability from 21-30 to 2  vol.%. Validation studies using the antimicrobial peptide melittin demonstrated that membrane-peptide interactions proceeded according to established mechanisms, with peptide incorporation of 18 vol.% for the low-coverage (69.7 ± 0.8%) SALB. The quantified solvent incorporation levels and small changes in acyl chain layer thickness in the SALBs must be considered when interpreting protein-membrane interaction studies, which suggests that validation of the SALB methodology for membrane research applications requires assessment on a case by case basis.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 2","pages":"343-356"},"PeriodicalIF":2.8,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13060456/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645305","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>AstroECP</i>: towards more practical electron channeling contrast imaging.","authors":"M Haroon Qaiser, Lukas Berners, Robin J Scales, Tianbi Zhang, Martin Heller, Jiří Dluhoš, Sandra Korte-Kerzel, T Ben Britton","doi":"10.1107/S1600576726000567","DOIUrl":"https://doi.org/10.1107/S1600576726000567","url":null,"abstract":"<p><p>Electron channeling contrast imaging (ECCI) is a scanning electron microscope based technique which enables bulk-sample characterization of crystallographic defects (<i>e.g.</i> dislocations, stacking faults, low-angle boundaries). Despite its potential, ECCI remains underused for quantitative defect analysis as compared with transmission electron microscope based methods. Here, we overcome barriers that limit the use of ECCI by optimizing signal-to-noise contrast and precise determination of the incident beam vector using calibrated, easy-to-use simulations and experimental selected-area electron channeling patterns (SA-ECPs). We introduce a systematic ECCI workflow, alongside a new open-source software tool (<i>AstroECP</i>), which includes calibration of stage tilting, SA-ECP field of view and the energy that forms the ECP/ECCI contrast using dynamical simulations. The functionality of this workflow is demonstrated with case studies that include threading dislocations in GaAs and the cross-validation of precession-based ECCI contrast, which is otherwise known as electron channeling orientation determination. To assist the reader, we also provide best-practice guidelines for ECCI implementation to promote high-resolution defect imaging in the scanning electron microscope.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 2","pages":"530-551"},"PeriodicalIF":2.8,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13060471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645316","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}