Journal of Applied Crystallography最新文献

{"title":"Simulation of bright and dark diffuse multiple scattering lines in high-flux synchrotron X-ray experiments.","authors":"Maurício B Estradiote, A Gareth A Nisbet, Rafaela F S Penacchio, Marcus A R Miranda, Guilherme A Calligaris, Sérgio L Morelhão","doi":"10.1107/S1600576725003553","DOIUrl":"10.1107/S1600576725003553","url":null,"abstract":"<p><p>We present a theoretical framework for understanding diffuse multiple scattering (DMS) in single crystals, focusing on diffuse scattering Bragg channels. These channels, when probed with high-flux low-divergence monochromatic synchrotron X-rays, provide well defined visualizations of Bragg cones. Our main contribution lies in modelling the intensity distribution along these lines by considering diffuse scattering (DS) around individual reciprocal-lattice nodes. The model incorporates contributions from both general DS and mosaicity, elucidating their connection to second-order scattering events. This comprehensive approach advances our understanding of DMS phenomena, enabling their use as probes for complex material behaviour, particularly under extreme conditions.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 3","pages":"859-868"},"PeriodicalIF":6.1,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234182","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":"Machine-learning-informed scattering correlation analysis of sheared colloids.","authors":"Lijie Ding, Yihao Chen, Changwoo Do","doi":"10.1107/S1600576725003280","DOIUrl":"10.1107/S1600576725003280","url":null,"abstract":"<p><p>We have carried out theoretical analysis, Monte Carlo simulations and machine-learning analysis to quantify microscopic rearrangements of dilute dispersions of spherical colloidal particles from coherent scattering intensity. Both monodisperse and polydisperse dispersions of colloids were created and underwent a rearrangement consisting of an affine simple shear and non-affine rearrangement using the Monte Carlo method. We calculated the coherent scattering intensity of the dispersions and the correlation function of intensity before and after the rearrangement and generated a large data set of angular correlation functions for varying system parameters, including number density, polydispersity, shear strain and non-affine rearrangement. Singular value decomposition of the data set shows the feasibility of machine-learning inversion from the correlation function for the polydispersity, shear strain and non-affine rearrangement using only three parameters. A Gaussian process regressor is then trained on the data set and can retrieve the affine shear strain, non-affine rearrangement and polydispersity with relative errors of 3%, 1% and 6%, respectively. Altogether, our model provides a framework for quantitative studies of both steady and non-steady microscopic dynamics of colloidal dispersions using coherent scattering methods.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 3","pages":"992-999"},"PeriodicalIF":6.1,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234175","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":"Classification and statistical analysis of structural disorder in crystalline materials.","authors":"Dmytro Antypov, Chris M Collins, Matthew S Dyer, John B Claridge, Matthew J Rosseinsky","doi":"10.1107/S1600576725003000","DOIUrl":"10.1107/S1600576725003000","url":null,"abstract":"<p><p>Approximately 50% of entries in the Inorganic Crystal Structure Database (ICSD; https://www.fiz-karlsruhe.de/en) exhibit some form of structural disorder. This work aims to provide a thorough analysis of structurally disordered materials within the ICSD, using data extracted from crystallographic information files. To achieve this, we derive a classification of structurally disordered crystalline materials described by their spatially averaged structures and introduce a range of quantitative measures of structural disorder. The overarching aim of this classification and analysis is to facilitate high-throughput and machine learning studies of disordered materials. To demonstrate the application of our approach, we perform statistical analysis of the disordered compounds reported in the ICSD to identify general trends in the distribution of disorder across different chemical elements, structures and classes of materials.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 3","pages":"659-677"},"PeriodicalIF":6.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135987/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234167","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 multiscale <i>in situ</i> time-resolved study of the nano- to millisecond structural dynamics during protein crystallization.","authors":"Christian Beck, Ilaria Mosca, Laura M Miñarro, Benedikt Sohmen, Cara Buchholz, Ralph Maier, Lara Franziska Reichart, Anna Carlotta Grundel, Famke Bäuerle, Roody Nasro, Hadra Banks, Simon Christmann, Kai-Florian Pastryk, Bela Farago, Orsolya Czakkel, Sylvain Prévost, Alexander Gerlach, Marco Grimaldo, Felix Roosen-Runge, Olga Matsarskaia, Frank Schreiber, Tilo Seydel","doi":"10.1107/S160057672500353X","DOIUrl":"10.1107/S160057672500353X","url":null,"abstract":"<p><p>Protein crystallization is key to determining the structure of proteins at atomic resolution. It can occur naturally, including in pathological pathways, for instance with aquaporin and γ-crystallin proteins. A fundamental understanding of the underlying crystallization process is both technologically and biologically relevant. A multitechnique approach is employed here to investigate protein crystallization <i>in situ</i>, allowing us to assess the evolution of the liquid suspension and crystallite structure as well as protein diffusion during the crystallization process. The wide range of methods probe the sample on ångström to millimetre length scales, accessing nanosecond to millisecond dynamics information while acquiring data with minute-timescale kinetic resolution during crystallization. This process takes several hours from an initial state of monomers or small clusters until the presence of large crystallites. Employing neutron spectroscopy allows us to distinguish different crystallization pathways and to reveal the presence of coexisting clusters during the entire crystallization process. We demonstrate the multitechnique approach on human serum albumin (HSA) proteins crystallized from aqueous solution in the presence of LaCl₃. For this system, the crystallization kinetics can be consistently described by a sigmoid function across all methods, and the kinetics can be controlled by the salt concentration. Moreover, we compare the HSA-LaCl₃ model system with the crystallization behavior of β-lactoglobulin-CdCl₂, which includes a metastable intermediate state.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 3","pages":"845-858"},"PeriodicalIF":6.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135975/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234162","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":"Changes of the lipid membrane structures caused by chain-length-dependent doxorubicin embedment in PEGylated liposomes.","authors":"Jia-Jhen Kang, Zhih-Chen Huang, Li-Wen Tang, Chun-Jen Su, Hua-De Gao, Hsien-Ming Lee, U-Ser Jeng","doi":"10.1107/S1600576725003577","DOIUrl":"10.1107/S1600576725003577","url":null,"abstract":"<p><p>Poly(ethyl-ene glycol)-grafted (PEGylated) liposomes receive increasingly more attention due to their practical applications in delivering vaccines, nutrients and drug molecules such as doxorubicin (DOX). PEGylated liposomes have been well documented for their capability in carrying DOX as rod-like crystallites enclosed inside the unilamellar vesicles. This study addresses the previously unresolved question of whether DOX intercalates into liposome bilayers by employing simultaneous small- and wide-angle X-ray scattering (SWAXS), complemented by an integrated asymmetric flow field-flow fractionation system coupled with multi-angle light scattering, dynamic light scattering and refractive index detection. The DOX-loaded PEGylated liposomes used are composed of phosphatidylcholine (<i>N</i>:0 PC) lipids, with different lipid chain lengths <i>N</i> = 18, 20 and 22, and a fixed molar ratio of lipid:cholesterol:DSPE-PEG2000 of 45:50:5. SWAXS analysis reveals that rod-like DOX nanocrystallites-approximately 70-95 nm in length and 14 nm in diameter-are encapsulated within the PEGylated liposomes across all three lipid types, with each exhibiting distinct membrane structural responses to DOX incorporation. Notably, 22:0 PC liposomes demonstrate significant DOX-induced disruption of lipid chain packing, accompanied by enhanced alignment of phosphate headgroups in the outer leaflet. Consistently, cryo-EM imaging reveals pronounced faceted membrane morphologies in DOX-loaded 22:0 PC liposomes. This faceting phenomenon is attributed to the accumulation of DOX within the excess hydro-phobic core regions created by the extended aliphatic chains beyond the cholesterol saturation limit. These DOX-enriched domains locally stiffen the membrane, promoting the formation of rigid, faceted structures.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 3","pages":"897-908"},"PeriodicalIF":6.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135973/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234166","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>SAXS-A-FOLD</i>: a website for fast ensemble modeling optimizing the fit of <i>AlphaFold</i> or user-supplied protein structures with flexible regions to SAXS data.","authors":"Emre Brookes, Joseph E Curtis, Aaron Householder, Mattia Rocco","doi":"10.1107/S1600576725003590","DOIUrl":"10.1107/S1600576725003590","url":null,"abstract":"<p><p>AI programs such as <i>AlphaFold</i> (<i>AF</i>) are having a major impact on structural biology. However, predicted unstructured regions, the arrangement of linker-connected domains and their conformational changes in response to environmental variables present challenges that are not easily dealt with on purely computational grounds. An approach that uses predicted (or solved) protein modules/domains linked by potentially unstructured regions and that generates ensembles of models optimized against small-angle X-ray scattering (SAXS) data has been recently described [Brookes <i>et al.</i> (2023). <i>J. Appl. Cryst.</i> <b>56</b>, 910-926]. Its implementation on a public-domain website, <i>SAXS-A-FOLD</i> (https://saxsafold.genapp.rocks), is presented here. User-supplied SAXS experimental intensity <i>I</i>(<i>q</i>) versus scattering vector magnitude <i>q</i> and the derived pair-wise distance distribution function <i>P</i>(<i>r</i>) versus <i>r</i> are first uploaded. An <i>AF</i> or user-supplied structure (currently only single chains without prosthetic groups) is then uploaded and displayed, and its SAXS <i>I</i>(<i>q</i>) and <i>P</i>(<i>r</i>) profiles are computed and compared with the experimental data. If uploaded from <i>AF</i>, the structure is color-coded by the associated confidence level: on this basis, the website automatically proposes potential flexible regions that can be user modified. For user-supplied structures, these regions have to be directly entered. A starting pool of typically 10-50 × 10³ conformations is generated using a Monte Carlo method that samples backbone dihedral angles along the chosen segments of potential flexibility in the protein structures. The initial pool is reduced to obtain a tractable set of models, for which <i>P</i>(<i>r</i>) and <i>I</i>(<i>q</i>) are computed with fast established methods. A global fit is performed using non-negatively constrained least-squares (NNLS) versus original data. The <i>P</i>(<i>r</i>) and <i>I</i>(<i>q</i>) NNLS results are then displayed, showing both the reconstructed curves and the contributing model curves, with their percentage contributions. A <i>WAXSiS</i> (https://waxsis.uni-saarland.de) implementation is utilized to calculate an <i>I</i>(<i>q</i>) for each selected model. These sets can be enhanced by adding a user-defined number of models generated before and after each selected model in the original Monte Carlo pool, ensuring the inclusion of nearby models that might better fit the data. Finally, NNLS is used on the <i>WAXSiS</i>-generated <i>I</i>(<i>q</i>) set versus the original <i>I</i>(<i>q</i>) data, with the results displaying the contributing models and their <i>I</i>(<i>q</i>). Aside from being representative of contributing conformations, the models selected by <i>SAXS-A-FOLD</i> could constitute a set of starting structures for more advanced MD simulations.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 3","pages":"1034-1049"},"PeriodicalIF":6.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234160","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":"Linearization routines for the parameter space concept to determine crystal structures without Fourier inversion.","authors":"Muthu Vallinayagam, Melanie Nentwich, Dirk C Meyer, Matthias Zschornak","doi":"10.1107/S1600576725001955","DOIUrl":"10.1107/S1600576725001955","url":null,"abstract":"<p><p>We present the elaboration and first generally applicable linearization routines of the parameter space concept (PSC) for determining one-dimensionally projected structures of <i>m</i> independent scatterers. This crystal determination approach does not rely on Fourier inversion but rather considers all structure parameter combinations consistent with available diffraction data in a parameter space of dimension <i>m</i>. The method utilizes <i>m</i> structure-factor amplitudes or intensities represented by piecewise analytic hyper-surfaces to define the acceptable parameter regions. The coordinates of the point scatterers are obtained through the intersection of multiple isosurfaces. This approach allows for the detection of all possible solutions for the given structure-factor amplitudes in a single derivation. Taking the resonant contrast into account, the spatial resolution achieved by the presented method may exceed that of traditional Fourier inversion, and the algorithms can be significantly optimized by exploiting the symmetry properties of the isosurfaces. The applied one-dimensional projection demonstrates the efficiency of the PSC linearization approach based on fewer reflections than Fourier sums. Monte Carlo simulations, using the projections of various random two- and three-atom structure examples, are presented to illustrate the universal applicability of the proposed method. Furthermore, ongoing efforts aim to enhance the efficiency of data handling and to overcome current constraints, promising further advancements in the capabilities and accuracy of the PSC framework.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 3","pages":"768-788"},"PeriodicalIF":6.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135979/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234173","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":"Forward-model-based grain reconstruction to improve the tolerance of diffraction contrast tomography for increased sample deformation.","authors":"Haixing Fang, Wolfgang Ludwig","doi":"10.1107/S160057672500250X","DOIUrl":"10.1107/S160057672500250X","url":null,"abstract":"<p><p>To extend the applicability of synchrotron diffraction contrast tomography (DCT) towards more plastically deformed materials, we have developed a forward-model-based reconstruction method. This allows us to reconstruct grain shapes and local orientations in materials exhibiting levels of intragranular orientation spread that can no longer be handled with the conventional Friedel-pair-based indexing and tomographic reconstruction approach. This method consists of seed and regional indexing, in which an exhaustive searching and fitting of orientations is first performed to index the seed orientation, and then a regional indexing by testing a list of local orientations around the seed orientation is carried out to maximize the completeness. The capability of this novel method was benchmarked and compared with reconstructions based on the conventional Friedel-pair-matching and tomographic reconstruction method using samples made from fully recrystallized Al-Cu alloy, moderately deformed α-Ti alloy and 10% creep-ruptured Fe-Au alloy. The results show that this method has the potential to overcome the deformation constraint and can reconstruct reasonably well the intragranular orientations. It is also suitable for multi-phase reconstruction and both box-beam and line-beam acquisition geometries. The implementation has been made flexible to support the use of single or multiple GPU machines. The strengths and weaknesses of the current forward-model-based reconstruction are discussed in detail with respect to the conventional Friedel-pair-matching method. To fully exploit and complement the strengths of the two methods, the code to implement the current forward-model-based reconstruction has been fully integrated with the existing DCT code and is open source for beamline data processing.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 3","pages":"796-812"},"PeriodicalIF":6.1,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234170","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":"Phase behavior of silica-PNIPAm nanogels under high hydrostatic pressure.","authors":"Nele N Striker, Christina Krywka, Claudia Goy, Svenja C Hövelmann, Niels C Giesselmann, Florian Schulz, Irina Lokteva, Fabian Westermeier, Frederic Caupin, Michael Paulus, Felix Lehmkühler","doi":"10.1107/S1600576725003188","DOIUrl":"10.1107/S1600576725003188","url":null,"abstract":"<p><p>The structure and dynamics of concentrated silica-PNIPAm (poly-<i>N</i>-iso-prop-yl-acrylamide) nanogels are studied as a function of hydrostatic pressure up to 3500 bar. A combination of X-ray photon correlation spectroscopy and small-angle X-ray scattering shows similar characteristics of the dynamics for both temperature- and pressure-induced volume phase transitions of PNIPAm nanogels. Upon increasing the pressure and depending on the initial particle volume fraction, a transition from a liquid or glass state to a colloidal gel is observed for pressures <i>p</i> ≃ 1500 bar at a temperature of 293 K. Time-dependent analysis of the dynamics shows aging in glass and gel samples which is absent in the liquid state. This indicates stress-dominated dynamics upon pressure changes that equilibrate after a few hundred seconds.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 3","pages":"919-926"},"PeriodicalIF":6.1,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234178","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 machine-learning-driven data labeling pipeline for scientific analysis in <i>MLExchange</i>.","authors":"Tanny Chavez, Zhuowen Zhao, Runbo Jiang, Wiebke Koepp, Dylan McReynolds, Petrus H Zwart, Daniel B Allan, Eliot H Gann, Nicholas Schwarz, Daniela Ushizima, Edward S Barnard, Apurva Mehta, Subramanian Sankaranarayanan, Alexander Hexemer","doi":"10.1107/S1600576725002328","DOIUrl":"10.1107/S1600576725002328","url":null,"abstract":"<p><p>This study introduces a novel labeling pipeline to accelerate the labeling process of scientific data sets by using artificial intelligence (AI)-guided tagging techniques. This pipeline includes a set of interconnected web-based graphical user interfaces (GUIs), where <i>Data Clinic</i> and <i>MLCoach</i> enable the preparation of machine learning (ML) models for data reduction and classification, respectively, while <i>Label Maker</i> is used for label assignment. Throughout this pipeline, data can be accessed through a direct connection to a file system or through <i>Tiled</i> for access through Hypertext Transfer Protocol (HTTP). Our experimental results present three use cases where this labeling pipeline has been instrumental for the study of large X-ray scattering data sets in the area of pattern recognition, the remote analysis of resonant soft X-ray scattering data and the fine-tuning process of foundation models. These use cases highlight the labeling capabilities of this pipeline, including the ability to label large data sets in a short period of time, to perform remote data analysis while minimizing data movement and to enhance the fine-tuning process of complex ML models with human involvement.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 3","pages":"731-745"},"PeriodicalIF":6.1,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135984/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234161","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}