Journal of Applied Crystallography最新文献

{"title":"Shot-noise-limited X-ray powder diffraction from organic crystals with laser-driven femtosecond X-ray source.","authors":"Iuliia Baranova, Yelyzaveta Pulnova, Roya Garayeva, Yadu Ram Panthi, Gabriel Žoldák, Jaroslav Nejdl, Borislav Angelov, Filip Leonarski, Jakob Andreasson, Krishna Khakurel","doi":"10.1107/S1600576726009040","DOIUrl":"https://doi.org/10.1107/S1600576726009040","url":null,"abstract":"<p><p>Laser-driven X-ray sources are increasingly used to investigate the transient behaviour of optically excited materials. While their application to thin films and powders of radiation-hard samples has been extensively explored, their use for radiation-sensitive materials such as organic and protein crystals remains limited. A key challenge is the low signal-to-noise (S/N) ratio, caused by the inherently low flux of these sources and additional non-Poissonian noise arising from temporal fluctuations. Improving noise suppression and enhancing the S/N ratio are therefore critical steps toward extending the applicability of these sources to more demanding systems. We demonstrate shot-noise-limited X-ray powder diffraction from 4-phenylazophenol, representing an organic crystal, using a laser-driven plasma X-ray source. These results highlight the potential of such sources for future studies of transient structural dynamics in photo-excited organic crystals.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1707-1713"},"PeriodicalIF":2.8,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109911","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":"Enhancing microstructural fidelity in near-field high-energy diffraction microscopy reconstruction with Noise2Void denoising.","authors":"Xiaoxu Guo, Dishant Beniwal, Derek McLain, Jonathan Almer, Jun-Sang Park, Peter Kenesei, Hemant Sharma","doi":"10.1107/S1600576726007612","DOIUrl":"https://doi.org/10.1107/S1600576726007612","url":null,"abstract":"<p><p>The resolution and fidelity of grain reconstruction from near-field high-energy diffraction microscopy (NF-HEDM) are often limited by poor signal-to-noise ratios, especially for fine microstructural features. Traditional denoising methods require clean ground-truth data, which is physically impossible in these experiments. To overcome this, we introduce a self-supervised deep learning network, Noise2Void (N2V), to denoise NF-HEDM images at the detector level prior to segmentation. By avoiding the requirement for clean ground-truth images or paired noisy data sets, which are typically unavailable in experimental settings, the N2V technique presented here is highly suitable for NF-HEDM and potentially transferable to other diffraction-based microstructure imaging techniques compromised by uncorrelated noise, such as micro Laue diffraction and far-field HEDM. The N2V model is trained solely with noisy images and then applied to those same images to obtain denoised data. The resulting cleaner images allow for the application of a lower segmentation threshold, enabling the capture of very weak signals that were previously lost. This yields a quantifiable improvement in reconstruction confidence by ∼9% on average and, validated grain by grain against an electron backscatter diffraction (EBSD) ground truth, recovers more of the true grain population - concentrated in the small grains and fine microstructural features that conventional thresholding discards - without altering the boundaries of grains already detected.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1531-1543"},"PeriodicalIF":2.8,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109447","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":"Application of electrostatic and multi-layer embedding in Hirshfeld atom refinements: a cost-effective approach for approximating bulk effects in crystalline environments.","authors":"Bruno Landeros-Rivera, Florian Kleemiss","doi":"10.1107/S160057672600717X","DOIUrl":"https://doi.org/10.1107/S160057672600717X","url":null,"abstract":"<p><p>One of the main advantages of Hirshfeld atom refinement (HAR), besides improved refinement statistics and reduced uncertainties of all derived parameters, is the possibility of refining anisotropic hydrogen atoms without any type of restriction to a correct distance. Notwithstanding this, there are still some problems that need attention for an accurate refinement of H atoms. For instance, <i>X</i>-H bond distances (<i>X</i> = N, O) are typically underestimated when they participate in a strong hydrogen bond and the crystallographic environment is not accounted for in the refinement model. In this work, we propose the use of an embedding scheme to model bulk effects approximately, where a molecule or group of molecules is polarized by electrostatic potential (ESP)-derived charges. Quantum mechanics/molecular mechanics methods based on ESP-derived charges have been used successfully to reproduce band gaps or optical and electronic properties of crystalline systems. It is demonstrated that the H-atom refinement parameters obtained with this approach are comparable to those obtained from pure quantum mechanical models, but with a significantly lower computational cost. Thus, this embedded HAR method is suitable for performing refinements in reasonable time frames for large systems in which strong intermolecular interactions, such as hydrogen bonds, exist.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1467-1477"},"PeriodicalIF":2.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109961","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>AES-Debye</i>: an accurate, efficient and scalable engine for Debye scattering calculations.","authors":"Navid Panchi, Sebastian Kuckuk, Markus Wittmann, Michael Engel, Alberto Leonardi","doi":"10.1107/S1600576726007429","DOIUrl":"https://doi.org/10.1107/S1600576726007429","url":null,"abstract":"<p><p>Total scattering models are essential for characterizing the structure and disorder of nanoscale materials. The Debye scattering equation (DSE) provides a rigorous route to elastic total scattering, but its direct evaluation is computationally demanding because pairwise contributions must be accumulated at every scattering vector, whereas common acceleration strategies based on binned pair-distance distributions or gridded fast Fourier transforms can introduce discretization and aliasing artifacts that compromise diffuse-scattering accuracy. Here, we present <i>AES-Debye</i>, an accuracy-preserving DSE framework that aggregates pair distances into a pair distribution function (PDF) using corrected bin centers and numerically robust accumulation to suppress discretization and summation errors. A data-locality-aware parallel design enables efficient execution on CPUs and GPUs. We demonstrate strong scalability by computing a high-resolution total scattering profile for a system of 90 million atoms, (0.1 µm)³, in minutes on a distributed-memory CPU platform. These capabilities extend accurate elastic total scattering calculations to large complex systems while simultaneously providing high-resolution PDFs for downstream structural analysis.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1478-1490"},"PeriodicalIF":2.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109925","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 low-cost, portable polarizing digital light microscope for monitoring crystal growth and for crystal harvesting.","authors":"Sarah Kennedy, Ryan H Huang, Wojciech Witek, Pawel Krawinski, Coilín Boland, Linjie Yang, Neal Leddy, Martin Caffrey","doi":"10.1107/S1600576726007880","DOIUrl":"https://doi.org/10.1107/S1600576726007880","url":null,"abstract":"<p><p>Motivated by the need for a convenient way to demonstrate the growth of crystals in glass plates by the lipid cubic phase method at crystallization workshops and courses, we developed a lightweight, portable, compact and inexpensive digital microscope device. The device is built around hand-held Wi-Fi and hardwired digital microscopes that are available commercially at low cost and that can use cell phones and personal computers for imaging without the need for unwieldy eyepieces. The device provides illumination from above and below the crystallization plate over a range of brightness levels. It can be used with regular white light and with polarized light to detect birefringent crystals. While not the focus of this study, the new device has been shown to also work with batch and vapour-diffusion plates. Remote monitoring of crystallization plates in a cold cabinet or walk-in refrigerator at 4 °C is possible with the Wi-Fi microscope. Crystals grown in lipid cubic phase and vapour-diffusion crystallization plates were harvested with the aid of the new device and used for diffraction data collection, leading to structure determination at high resolution. Most parts of the device were 3D printed in polylactic acid plastic. The corresponding STL files, included as part of this publication, can be used to make replicates of the current microscope and to produce bespoke devices suited to the specific needs of the user. We envision using the new device for outreach activities at primary, secondary and third-level schools, and at science fairs in support of the citizen scientist. Relatedly, in this study examples are included of recorded images of plant and animal tissue sections. One reveals birefringent materials in a tomato leaf. Another shows optically active crystals of calcium oxalate in onion tunic tissue.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1693-1706"},"PeriodicalIF":2.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109944","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>DISCO</i>: a general software tool for dislocation contrast factor calculations in diffraction analysis.","authors":"Marcelo Augusto Malagutti, Mirco D'Incau, Paolo Scardi","doi":"10.1107/S1600576726007053","DOIUrl":"https://doi.org/10.1107/S1600576726007053","url":null,"abstract":"<p><p>Dislocation contrast factors (CFs) play a central role in diffraction-based analyses of plastic deformation, linking the elastic strain fields generated by dislocations to diffraction line broadening. Despite their importance, the calculation of CFs remains a non-trivial task for low-symmetry crystal structures or arbitrary slip systems and is often limited to pre-tabulated solutions for selected lattice types. In this work we present <i>DISCO</i>, a software package for the real-time computation of dislocation contrast factors for any crystal structure and slip system. <i>DISCO</i> supports all space groups, from cubic to triclinic, and allows the calculation of CFs for individual crystallographic directions, as well as orientation-averaged CFs suitable for randomly oriented powder and polycrystalline diffraction analyses. The design principles, computational workflow and input/output structure of <i>DISCO</i> are described in detail, and its capabilities are illustrated through application examples on (cubic) SrTiO₃, (hexagonal) 4H-SiC and (monoclinic) β-Ga₂O₃.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1720-1729"},"PeriodicalIF":2.8,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109948","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":"Probing local atomic structure in thin films by grazing-incidence total X-ray scattering with a convergent X-ray beam.","authors":"Masatsugu Yoshimoto, Kazuki Ito, Kazuhiko Omote","doi":"10.1107/S1600576726007181","DOIUrl":"https://doi.org/10.1107/S1600576726007181","url":null,"abstract":"<p><p>Grazing-incidence total X-ray scattering (GI-TXS) is an important technique for evaluating the short-range order and medium-range order structures of thin films. A high-quality pair distribution function requires high-intensity total scattering data over a wide scattering vector magnitude (<i>Q</i>) range, which necessitates the use of high-energy X-rays. However, a lower incident angle leads to a wider footprint at the sample position, resulting in a trade-off between achieving high-intensity total scattering and using high-energy X-rays in conventional laboratory setups. In this study, we performed GI-TXS measurements on an indium tin oxide (ITO) thin film using a convergent incident X-ray beam to maximize the X-ray flux at the sample position. By incorporating the convergence angle distribution and thin film absorption parameters, the substrate contribution to the observed total scattering intensity was quantitatively estimated and corrected. As a result, the total scattering profile of the ITO thin film was successfully obtained up to <i>Q</i> = 21 Å^-1 using a laboratory X-ray diffractometer.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1420-1425"},"PeriodicalIF":2.8,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109900","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":"Depth-resolved X-ray residual stress analysis on samples with cylindrically shaped surface topography.","authors":"Manuela Klaus, Daniel Apel, Mirko Boin, Robert Wimpory, Christoph Genzel","doi":"10.1107/S1600576726007302","DOIUrl":"https://doi.org/10.1107/S1600576726007302","url":null,"abstract":"<p><p>Angle- and energy-dispersive diffraction are applied to investigate the influence of the X-ray beam diameter on the results of residual stress analysis on a sample with an inhomogeneous surface topography. For sin²ψ measurements on parts of the surface featuring a cylindrical topography, modifications of the fundamental equation of X-ray stress analysis are proposed to correct the experimentally determined residual stresses for the rotational effect caused by the different orientation of the local principal stress coordinate system within the irradiated part of the sample. It is shown that the hoop and longitudinal stress components require different treatments in this respect. For the hoop stress component a correction factor is proposed which considers the variation in the illuminated surface area during the ψ tilt of the sample. Correction of the longitudinal stress component requires knowledge of the hoop stress component, which affects the slope of the sin²ψ regression line and thus partially acts as a normal stress component. For cases in which ψ tilting is not possible for geometric reasons, the applicability of the transverse contraction method is discussed. Experimental verification is carried out on a ferritic steel sample into which grooves of the same diameter were milled to different depths, resulting in different central angles.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1407-1419"},"PeriodicalIF":2.8,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109937","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":"The BioSAXS laboratory of the ITACA.SB Research Infrastructure.","authors":"Francesco Scattarella, Davide Altamura, Vincenzo Mangini, Teresa Sibillano, Erika Manicone, Rocco Lassandro, Liberato De Caro, Gemma Newby, Cinzia Giannini","doi":"10.1107/S1600576726007132","DOIUrl":"https://doi.org/10.1107/S1600576726007132","url":null,"abstract":"<p><p>We describe a state-of-the-art X-ray scattering laboratory, within the Research Infrastructure ITACA.SB (Potentiating the Italian Capacity for Structural Biology Services in Instruct-ERIC), designed for multi-scale structural characterization of biological specimens and advanced materials with small- and wide-angle X-ray scattering (SAXS/WAXS) techniques: WAXS to probe atomic and molecular organization, and SAXS to characterize morphological and structural features at the nanoscale. The system enables (i) the concurrent acquisition of SAXS/WAXS data, (ii) the execution of scanning SAXS/WAXS microscopy, and (iii) the collection of ultra-small-angle X-ray scattering, batch BioSAXS and size-exclusion chromatography SAXS data. To demonstrate the system's versatility, we investigated the hierarchical complexity of both biological specimens and synthetic/natural fibers. We also report on analysis of well known proteins and micelles.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1757-1768"},"PeriodicalIF":2.8,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109862","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":"Angle-dependent X-ray absorption correction in small- and wide-angle X-ray scattering: accounting for constrained scattering volume, beam profiles and capillary wall attenuation.","authors":"Jure Kovač, Andrej Jamnik, István Szilágyi, Matija Tomšič","doi":"10.1107/S1600576726006837","DOIUrl":"https://doi.org/10.1107/S1600576726006837","url":null,"abstract":"<p><p>A GPU-accelerated numerical method has been developed to calculate angle-dependent transmission factors <i>A</i>(2θ) for small- and wide-angle X-ray scattering (SWAXS) data collected with a Kratky-type camera using a line-collimated beam and a horizontal cylindrical capillary with a vertically oriented detector. The procedure extends path-length-based absorption correction to the Kratky-type geometry by averaging Beer-Lambert attenuation over the constrained illuminated scattering volume and by including experimentally measured primary beam profiles and capillary-wall absorption. Sensitivity analysis shows that the vertical illumination geometry dominates the calculated angle-dependent transmission factor, whereas the horizontal beam-width effect is negligible. Using measured beam profiles makes the correction instrument specific and avoids introducing an effective uniform beam height as an approximation. For strongly absorbing nona-fluoro-<i>tert</i>-butanol, the conventional scalar primary beam transmission correction fails after subtraction of empty-capillary scattering, while the numerical correction enables physically meaningful absolute-scale data reduction. Comparisons between independently calculated theoretical SWAXS intensities and the two reduced experimental datasets obtained sequentially using two different detectors in the same experiment on the same Kratky-type SWAXS camera provide a direct experimental cross check for the data-reduction workflow based on calculated transmission factors. They indicate that the observed limitation is associated with transmission measurement of a spectrally modified primary beam, rather than with the Kratky-type geometry itself. Importantly, the results show that the limitations of conventional scalar transmission corrections are not confined to extreme cases but may also affect routine water-based absolute-scale SWAXS calibration. A simple Beer-Lambert-type numerical scalar correction can still provide a useful qualitative approximation, whereas reliable quantitative analysis requires the full angle-dependent <i>A</i>(2θ) correction.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1374-1383"},"PeriodicalIF":2.8,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109953","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}