Journal of Applied Crystallography最新文献

{"title":"Incorporating coherent multiple scattering into modelling of small-<i>q</i> scattering data.","authors":"Henrich Frielinghaus","doi":"10.1107/S1600576726005066","DOIUrl":"10.1107/S1600576726005066","url":null,"abstract":"<p><p>In a recent paper [Frielinghaus & Gommes (2025), <i>J. Appl. Cryst.</i> <b>58</b>, 1553-1570] the appearance of coherent multiple scattering was discussed, whereby surface scattering takes over against the classical bulk scattering. This effect has been overlooked in the past and happens in a transition region between the classical bulk scattering that involves the first-order Born approximation and the quantum mechanical limit where the projected shadow of the structure is observed. This paper discusses a new example emerging from small-angle light scattering and describes it with surface scattering from the Teubner-Strey model that is also used to describe porous materials.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 4","pages":"1327-1331"},"PeriodicalIF":2.8,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678762","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":"Rust-accelerated powder X-ray diffraction simulation for high-throughput and machine-learning-driven materials science.","authors":"Miroslav Lebeda, Jan Drahokoupil, Petr Veřtát, Petr Vlčák","doi":"10.1107/S1600576726005273","DOIUrl":"10.1107/S1600576726005273","url":null,"abstract":"<p><p>High-throughput powder X-ray diffraction (XRD) simulations are a key prerequisite for generating large datasets used in the development of machine-learning models for XRD-based materials analysis. However, the widely used <i>pymatgen</i> powder XRD calculator, implemented entirely in Python, can be computationally inefficient for large-scale workloads, limiting throughput. We present <i>XRD-Rust</i>, a Rust-accelerated implementation of the <i>pymatgen</i> powder XRD calculator that maintains compatibility with the existing Python-based workflows. The method retains <i>pymatgen</i> for crystal structure handling, while reimplementing the computationally intensive parts of the XRD calculation in the Rust language, with optional further acceleration via single instruction, multiple data (SIMD) vectorization and multi-threaded execution across reflections using the <i>Rayon</i> library. Performance benchmarking on two large crystallographic datasets, the Materials Cloud Three-Dimensional Structure Database (MC3D, 33142 structures) and the Crystallography Open Database (COD, 515181 structures), demonstrates substantial speedups. For the MC3D, <i>XRD-Rust</i> achieves a median serial SIMD speedup of 10.8× [median absolute deviation (MAD) of 1.8×], increasing to 15.1× (MAD 3.8×) with eight-thread parallel execution, with a maximum runtime reduction from 40.5 s to 0.9 s. For the COD, the median serial SIMD acceleration reaches 10.7× (MAD 4.2×), while eight-thread parallel execution yields 19.5× (MAD 10.0×), with a maximum reduction from 1437 to 1 min. SIMD vectorization alone provides additional performance gains ranging from a few percent to several tens of percent, depending on the workload and execution mode. Overall, these benchmarks demonstrate that <i>XRD-Rust</i> significantly accelerates powder XRD simulations compared with the original <i>pymatgen</i> implementation, enabling efficient high-throughput dataset generation and improving performance in interactive diffraction analysis applications.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 4","pages":"1344-1350"},"PeriodicalIF":2.8,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678807","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 polarized neutron reflectometry experiments on soft-matter samples: optimization of the solid substrate structure.","authors":"Ivan P Yakimenko, Alessandra Luchini, Joshaniel F K Cooper, Sebastian Köhler, Tommy Nylander, Sean Langridge, Christy J Kinane, Andrew J Caruana, Björgvin Hjörvarsson, Max Wolff, Alexei Vorobiev, Sergiy Valyukh, Fredrik Eriksson, Jens Birch, Kenneth Järrendahl","doi":"10.1107/S160057672600539X","DOIUrl":"10.1107/S160057672600539X","url":null,"abstract":"<p><p>In this study we use Fisher information within the software <i>HOGBEN</i> to optimize the structure of magnetic reference layers to maximize the information gained from polarized neutron reflectometry (PNR) measurements on soft-matter and biological samples. Our approach is based on simulating the reflectivity from an experimentally determined dataset of a supported lipid bilayer. A set of reflectivity curves is calculated by varying parameters associated with the substrate assembly containing a magnetic reference layer. For each of the calculated reflectivity curves, we quantified the sensitivity of the simulated data to the sample structure. Our Fisher information analysis predicts that decreasing the thickness of the capping layer combined with increasing the magnetic scattering length density of the magnetic reference layer will reduce measurement time of similar PNR experiments by up to a factor of 5.6 or, equivalently, reduce parameter uncertainties at fixed beam time by the same factor relative to the reference experiment. Within a practically realizable SiO₂ capping layer window of 200-400 Å, the predicted gain remains substantial (<i>G</i> ≈ 2.7). Because the parameters determining reflectivity curves are often correlated, such information is difficult to obtain in any other way. Experimental validation of these predictions on substrate assemblies synthesized according to the proposed designs is the natural next step. We established a theoretical method that can also be implemented within the context of other neutron reflectometry experiment. The approach allows the optimization of PNR experiments and will enable more straightforward and robust extraction of relevant parameters as well as more efficient use of neutron beam time.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 4","pages":"1192-1199"},"PeriodicalIF":2.8,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678814","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":"Convergent-beam X-ray crystallography.","authors":"Chufeng Li, Margarita Zakharova, Mauro Prasciolu, Jia Chyi Wong, Holger Fleckenstein, Nikolay Ivanov, Wenhui Zhang, Mansi Butola, J Lukas Dresselhaus, Ivan De Gennaro Aquino, Dmitry Egorov, Philipp Middendorf, Alessa Henkel, Bjarne Klopprogge, Lars Klemeyer, Tobias Beck, Oleksandr Yefanov, Miriam Barthelmess, Janina Sprenger, Dominik Oberthuer, Saša Bajt, Henry N Chapman","doi":"10.1107/S1600576726005236","DOIUrl":"10.1107/S1600576726005236","url":null,"abstract":"<p><p>Molecular and polymeric crystals show a wide range of functional properties that arise from the interplay between the atomic-scale structure of their constituent molecules and the organization of these molecules within the crystal at macroscopic length scales. X-ray diffraction can provide structural information at these disparate length scales, but usually only through experiments that address one or the other of molecular (or unit-cell) structure versus crystal structure. Consequently, the accuracy of determined molecular or polymer structures may be limited by unaccounted for crystal inhomogeneities and the characterization of crystalline materials might not reveal the underlying causes of crystal morphology. Here we introduce X-ray convergent-beam diffraction to obtain spatially resolved structural information from crystals by projection topographic imaging. Using highly focusing X-ray multilayer Laue lenses, we show that Bragg reflections can be mapped into tomographic images of the crystal, for the characterization of strain and defects at high resolution. We demonstrate how the crystal morphology obtained this way can be accounted for when determining structure factors as a function of position in the crystal. The approach may assist in studies such as diffusion and binding in metal-organic framework structures, protein-drug binding, crystal growth, and the mechanical responses of photo-reactive or thermally driven dynamic crystals.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 4","pages":"1200-1218"},"PeriodicalIF":2.8,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440054/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678776","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":"Shannon sampling based approach for the structural solution of nano-objects by laboratory and synchrotron SAXS data.","authors":"Liberato De Caro, Domenico Alberga, Francesco Scattarella, Teresa Sibillano, Vincenzo Mangini, Boyang Zhou, Thibaud Stoll, Cinzia Giannini","doi":"10.1107/S1600576726004358","DOIUrl":"10.1107/S1600576726004358","url":null,"abstract":"<p><p>We propose a Shannon sampling based approach for the analysis of laboratory and synchrotron small-angle X-ray scattering (SAXS) data. This method avoids calculation of the pair distance distribution function <i>P</i>(<i>r</i>), which is typically used as an alternative to the model-dependent fitting of SAXS data for determining the size and shape of the scattering object. Using this new approach it is also possible to skip any model-dependent fit of the SAXS data. The method has been tested on SAXS data collected from Polysorbate 20, d-α-tocopheryl polyethyl-ene glycol 1000 succinate spheroidal core-shell micelles and relevant well known proteins (lysozyme, apoferritin, carbonic anhydrase 2) of different molecular weights. The results confirm the potential of the approach, even for laboratory scattering data and in the presence of polydispersity. The method allows the reliable derivation of maximum size, mass, volume, polar/equatorial asymmetry, hydration fraction, shell thickness and core/shell electron-density differences for core-shell structures, directly in the <i>q</i> domain, working on SAXS data measured from dilute samples for which interparticle structure factors are negligible.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 4","pages":"1170-1183"},"PeriodicalIF":2.8,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440053/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678784","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":"Quantifying resolution in pink-beam dark-field X-ray microscopy: experiments and simulations.","authors":"M La Bella, H F Poulsen, S Staeck, N A Henningsson, M P Kabukcuoglu, C Detlefs, C Yildirim","doi":"10.1107/S1600576726005200","DOIUrl":"10.1107/S1600576726005200","url":null,"abstract":"<p><p>Pink-beam dark-field X-ray microscopy (pDFXM) is a powerful emerging technique for time-resolved studies of microstructure and strain evolution in bulk crystalline materials. In this work, we systematically assess the performance of pDFXM relative to monochromatic DFXM when using a compound refractive lens as the objective. Analytical expressions for the spatial and angular resolution are derived and compared with numerical simulations based on geometrical optics and experimental data. The pink-beam configuration provides an increased diffraction intensity depending on the deformation state of the sample, accompanied by a general tenfold degradation in angular resolution along the rocking and axial strain (longitudinal) directions. This trade-off is disadvantageous for axial strain mapping but can be advantageous in cases where integrated intensities are needed. For a perfect crystal under parallel illumination with a pink beam, our results show that chromatic aberration is absent, whereas under condensed illumination it becomes significant. The aberration is shown to depend strongly on the local distortion of the crystal. Weak-beam imaging conditions, such as those required for resolving dislocations, are shown to remain feasible under pink-beam operation and may even provide an improved signal-to-noise ratio. The higher incident flux, enhanced by nearly two orders of magnitude, results in a ∼30× increase in diffracted intensity; beam heating effects are quantified and implications for optimized scanning protocols are discussed.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 4","pages":"1139-1152"},"PeriodicalIF":2.8,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440070/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678781","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":"Physical interpretation of Stephens' phenomenological parameters for anisotropic microstrain broadening in cubic systems.","authors":"Ashok Bhakar, Pooja Gupta, Mahesh Kumar Swami, Sanjay Kumar Rai","doi":"10.1107/S1600576726004176","DOIUrl":"10.1107/S1600576726004176","url":null,"abstract":"<p><p>Both the Stephens phenomenological model and the modified Williamson-Hall (mWH) plot analysis address the microstrain-dependent anisotropic peak broadening observed in diffraction patterns. The data analysis strategies of both methods rely on the anisotropic nature of crystalline materials and the quartic form of reflection indices (<i>hkl</i>). Despite these similarities, the results of the two methods are not directly comparable: the Stephens approach is phenomenological, whereas the mWH method is based on the characteristic dislocation parameters for determining microstructural features (size-strain). This study aims to bridge that gap. A simple procedure is proposed to extract microstructural quantities - equivalent to those obtained by the mWH method - using the Stephens phenomenological approach. Furthermore, a microscopic interpretation of Stephens' phenomenological parameters is presented in terms of the nature of dislocations in cubic symmetry. The applicability of this procedure is demonstrated for cubic systems and illustrated with examples.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 4","pages":"1121-1128"},"PeriodicalIF":2.8,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678769","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":"Microsecond X-ray reflectometry.","authors":"Michael Haberl, Maximilian Eder, Erwin Pfeiler, David Schumi-Mareček, Florian Bertram, Petr Mikulík, Stefan Kowarik","doi":"10.1107/S1600576726004449","DOIUrl":"10.1107/S1600576726004449","url":null,"abstract":"<p><p>We accelerate synchrotron X-ray reflectometry (XRR) by more than an order of magnitude and demonstrate the acquisition of full reflectivity curves within 213 µs over a <i>q</i> _<i>z</i> range of 0.05 to 0.35 Å^-1 at 0.001 Å^-1 resolution. This is achieved by rapidly sweeping the incidence angle with a high-speed galvanometer and recording the reflected beam on an area detector. The method preserves a monochromatic parallel-beam geometry, requires only straightforward geometric and exposure time corrections, and yields quantitative agreement with standard XRR in thickness, density and roughness. At the shortest acquisition times, the photon statistics enter the low-count Poisson regime, where conventional least-squares fitting becomes biased. We show that applying an Anscombe variance-stabilizing transform restores near-Gaussian error behavior and significantly improves fitting robustness. Our approach benefits not only ultrafast XRR but reflectometry data in general at large <i>q</i> _<i>z</i> , where count rates are intrinsically low. This advance enables time-resolved studies of thin-film growth, diffusion, photoswitching and other rapid kinetic processes.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 4","pages":"1112-1120"},"PeriodicalIF":2.8,"publicationDate":"2026-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678779","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":"NeuDiff Agent: a governed AI workflow for single-crystal neutron crystallography.","authors":"Zhongcan Xiao, Leyi Zhang, Guannan Zhang, Xiaoping Wang","doi":"10.1107/S1600576726004474","DOIUrl":"10.1107/S1600576726004474","url":null,"abstract":"<p><p>Large-scale facilities increasingly face analysis and reporting latency as a limiting step in scientific throughput, particularly for structural studies that require iterative reduction, integration, refinement and validation. To improve the time to result and analysis efficiency, NeuDiff Agent is introduced as a governed, tool-using AI workflow for TOPAZ at the Spallation Neutron Source. NeuDiff Agent takes instrument data through reduction, integration, refinement and validation to a validated crystal structure and a publication-ready CIF. NeuDiff Agent coordinates established crystallographic tools under explicit governance by restricting actions to allowlisted tools, enforcing fail-closed verification gates at key workflow boundaries, and capturing complete provenance for inspection, auditing and controlled replay. The present benchmark is limited to structural crystallography for periodic structures; magnetic structure analysis and incommensurate or superspace refinement are outside the scope of the current workflow. Performance is assessed using a fixed prompt protocol and repeated end-to-end runs with two large language model backends, with user and machine time partitioned and intervention burden and recovery behaviors quantified under gating. In a reference-case benchmark, NeuDiff Agent reduces wall time from 435 min (manual) to 86.5 ± 4.7 to 94.4 ± 3.5 min (4.6-5.0× faster) while producing a validated CIF with no <i>checkCIF</i> level A or B alerts. These results establish a practical route to deploy agentic AI in facility crystallography while preserving traceability and publication-facing validation requirements.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 4","pages":"1102-1111"},"PeriodicalIF":2.8,"publicationDate":"2026-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678736","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":"X-ray-induced hydride formation in palladium nanowires in a gaseous hydrogen environment.","authors":"Hanna Sjö, Huaiyu Chen, Giuseppe Abbondanza, Dmitry Dzhigaev, Megan O Hill Landberg, Jesper Wallentin, Johan Gustafson","doi":"10.1107/S1600576726004620","DOIUrl":"10.1107/S1600576726004620","url":null,"abstract":"<p><p>Palladium hydrides are promising systems for hydrogen sensors and hydrogen storage, making the study of hydride formation in nanoparticles highly relevant. Lately, such studies have often been performed <i>in situ</i> or <i>operando</i> using synchrotron radiation of increasingly high intensity and brilliance. While beam-induced effects are well documented in liquid environments, they are rarely considered in the gaseous phase. Here, X-ray diffraction is used to investigate hydride formation in palladium nanowires, comparing hydrogen-induced transitions with transitions triggered by varying X-ray exposure rates. Although hydrogen exposure naturally drives hydride formation, we observe a clear additional contribution from beam-induced effects. These findings highlight the need to account for such effects when studying gas-solid reactions with X-rays.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 4","pages":"1005-1012"},"PeriodicalIF":2.8,"publicationDate":"2026-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678754","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}