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Modelling regularity of Si/Al distributions in disordered tectosilicates - application to zeolites with the GIS framework type. 无序构造硅酸盐中Si/Al分布规律的建模——基于GIS框架型的沸石应用。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2025-09-01 Epub Date: 2025-08-15 DOI: 10.1107/S2053273325006217
Montauban Moreira de Oliveira, Jean Guillaume Eon
{"title":"Modelling regularity of Si/Al distributions in disordered tectosilicates - application to zeolites with the GIS framework type.","authors":"Montauban Moreira de Oliveira, Jean Guillaume Eon","doi":"10.1107/S2053273325006217","DOIUrl":"10.1107/S2053273325006217","url":null,"abstract":"<p><p>As an extension of a previous work, we analyse ordered and disordered Si/Al distributions in a few tectosilicates. The method is based on an analysis of the inter-relations between maximal independent sets in a labelled quotient graph of the net. The analysis suggests the presence of specific disordered substructures, called here alveoli, coexisting with fully ordered parts, defining partial order in submicroscopic domains. The method is first illustrated with bikitaite, chabazite and analcime and fully developed for natural zeolites with the GIS framework type. We show that the principle of maximal independence applied to the labelled quotient graph of the net gis can be used to justify composition and order/disorder of the two ordered phases gismondine and amicite and of the disordered phases garronite and gobbinsite. To this list of natural zeolites, we add the disordered, synthetic Na-P2 phase. The results are in good agreement with published <sup>29</sup>Si magic-angle spinning NMR data for bikitaite, chabazite and analcime.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"353-370"},"PeriodicalIF":1.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144854058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Temporal ghost imaging for pump-probe X-ray solution scattering. 泵浦探针x射线溶液散射的时间鬼影成像。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2025-09-01 Epub Date: 2025-07-07 DOI: 10.1107/S2053273325004243
B R Mobley, Kevin E Schmidt, R A Kirian
{"title":"Temporal ghost imaging for pump-probe X-ray solution scattering.","authors":"B R Mobley, Kevin E Schmidt, R A Kirian","doi":"10.1107/S2053273325004243","DOIUrl":"10.1107/S2053273325004243","url":null,"abstract":"<p><p>Time-resolved small- and wide-angle X-ray scattering is a valuable tool for investigating biomolecular dynamics on a wide variety of timescales, without cryo-freezing or crystallization. However, some systems, such as the initial excitation of photo-active proteins, evolve dynamically on timescales that may be faster than the duration of the pump and probe beams. Data from a single pump-probe pulse pair therefore contain information from a mixture of time points. In this work, a simple algorithm is developed to recover the dynamics of solution scattering profiles. It leverages information about the pump and probe pulse beams' temporal profiles by using the same mathematical framework as ghost imaging [Pittman et al. (1995). Phys. Rev. A 52, R3429-R3432; Bennink et al. (2002). Phys. Rev. Lett. 89, 113601; Gatti et al. (2004). Phys. Rev. Lett. 93, 093602]. Results from several simulated data sets are presented.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"371-380"},"PeriodicalIF":1.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12415634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144574522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Machine learning for the classification of serial electron diffraction patterns: synthetic data. 用于连续电子衍射图分类的机器学习：合成数据。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2025-09-01 Epub Date: 2025-07-07 DOI: 10.1107/S2053273325005327
Tatiana E Gorelik, Evgeny Gorelik
{"title":"Machine learning for the classification of serial electron diffraction patterns: synthetic data.","authors":"Tatiana E Gorelik, Evgeny Gorelik","doi":"10.1107/S2053273325005327","DOIUrl":"10.1107/S2053273325005327","url":null,"abstract":"<p><p>Serial electron crystallography faces a fundamental challenge due to the flat Ewald sphere resulting from the short electron wavelength, leading to limited 3D information in individual patterns. Recently, an algorithm for unit-cell determination from zonal electron diffraction patterns (GM algorithm) [Miehe (1997). Ber. Dtsch. Miner. Ges. Beih. z. Eur. J. Miner. 9, 250; Gorelik et al. (2025). Acta Cryst. A81, 124-136] was introduced in the context of serial electron crystallography. This algorithm requires the extraction of 2D zonal patterns from the complete serial dataset. Here, we present a machine learning approach for pattern sorting and apply it initially to simulated electron diffraction patterns.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"397-400"},"PeriodicalIF":1.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12415633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144574521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Updating direct methods IV. Reduction of the structural complexity when quartet invariant phases are estimated by using the Patterson map as prior information. IV.利用Patterson映射作为先验信息估计四重奏不变相时，降低了结构复杂性。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2025-09-01 Epub Date: 2025-07-10 DOI: 10.1107/S2053273325004735
Carmelo Giacovazzo
{"title":"Updating direct methods IV. Reduction of the structural complexity when quartet invariant phases are estimated by using the Patterson map as prior information.","authors":"Carmelo Giacovazzo","doi":"10.1107/S2053273325004735","DOIUrl":"10.1107/S2053273325004735","url":null,"abstract":"<p><p>Quartet invariants play a minor role in modern direct methods. In practice, only the quartets whose cosine is estimated to be negative are used, as they have no correlation with the triplet invariants. However, their role remains marginal: in fact, the quartet relations are of order 1/N while the triplet relations are of order 1/√N. The reliability of the quartets is therefore relatively low, in particular for the quartets estimated to be negative. Two papers have recently appeared (Papers I and II of this series) that describe procedures able to exploit the information contained in the Patterson map to estimate the triplet phases. The improvements in estimates are notable, apparently capable of resolving macromolecular structures even at non-atomic resolution. It therefore seems useful to develop a theory of quartet invariants that is able to exploit the Patterson information. This is the main purpose of this article. The method of joint probability distribution functions is used to obtain a von Mises-type distribution which associates a probability with each quartet phase. It is expected that the Patterson map, used as a priori information, can significantly increase the reliabilities of quartet invariants, particularly those whose cosine is estimated to be negative. The quartets may thus be able to play a more prominent role in future.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"389-396"},"PeriodicalIF":1.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144598868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Can Z, the number of formula units per unit cell, be a fraction? A report of the IUCr Commission on Crystallographic Nomenclature. Z，每个单元格的公式单位数，可以是分数吗？国际自然保护联盟晶体学命名委员会的报告。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2025-09-01 Epub Date: 2025-08-15 DOI: 10.1107/S2053273325007053
Carolyn P Brock
{"title":"Can Z, the number of formula units per unit cell, be a fraction? A report of the IUCr Commission on Crystallographic Nomenclature.","authors":"Carolyn P Brock","doi":"10.1107/S2053273325007053","DOIUrl":"10.1107/S2053273325007053","url":null,"abstract":"<p><p>The IUCr Commission on Crystallographic Nomenclature (the CCN) has considered the question of whether fractional values of Z, the number of formula units in the unit cell, can be permitted. The consideration was initiated by a crystallographer who had determined a very unusual molecular structure, but the discussion was later broadened to cover all non-polymeric structures. Reliable structures having a fractional Z were located in the structural databases and in the literature, and were studied carefully. The CCN concluded that in some rare cases the Z value reported for a structure of a stoichiometric compound may be a fraction, but that that choice would have to be justified very carefully and convincingly. For solid solutions Z should be an integer.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"405-408"},"PeriodicalIF":1.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144854057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
3-Periodic weavings: piecewise linear embeddings of symmetric structures. 周期性编织：对称结构的分段线性嵌入。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2025-09-01 Epub Date: 2025-07-07 DOI: 10.1107/S2053273325004802
Michael O'Keeffe, Michael M J Treacy
{"title":"3-Periodic weavings: piecewise linear embeddings of symmetric structures.","authors":"Michael O'Keeffe, Michael M J Treacy","doi":"10.1107/S2053273325004802","DOIUrl":"10.1107/S2053273325004802","url":null,"abstract":"<p><p>We provide a systematic account using symmetry and coordinates to explore symmetric (vertex- and edge-transitive) 3-periodic weavings of piecewise linear threads. The dia-w graph, derived from the diamond structure, generates an infinite family of supersymmetric 3-periodic thread weaves - a unique property shared only with the 2-periodic sql-w family of fabric weaves. Additionally, we describe a selection of symmetric 3-periodic, 3-coordinated weavings related to the srs graph and a supersymmetric Borromean weave of hcb graphs.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"381-388"},"PeriodicalIF":1.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144574520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Artificial intelligence in action: building simulation and analysis tools for powder diffraction. 人工智能在行动：粉末衍射模拟和分析工具的建立。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2025-09-01 Epub Date: 2025-09-04 DOI: 10.1107/S2053273325007508
Paolo Scardi, Marcelo A Malagutti
{"title":"Artificial intelligence in action: building simulation and analysis tools for powder diffraction.","authors":"Paolo Scardi, Marcelo A Malagutti","doi":"10.1107/S2053273325007508","DOIUrl":"10.1107/S2053273325007508","url":null,"abstract":"<p><p>This paper explores the application of generative pre-trained transformer (GPT)-based large language models (LLMs) in the development of simulation and analysis tools for X-ray powder diffraction. We demonstrate how these models enable users with minimal programming experience to generate functional and efficient code through natural language prompts. The discussion highlights both the capabilities and limitations of LLM-assisted coding, offering insights into the practical integration of artificial intelligence for simulating and analysing simple X-ray powder diffraction patterns.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"401-404"},"PeriodicalIF":1.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12415632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144990958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phase seeding may provide a gateway to structure solution by deep learning. 阶段播种可以通过深度学习为结构解决方案提供一个入口。
IF 1.9 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2025-07-01 Epub Date: 2025-06-10 DOI: 10.1107/S2053273325004814
Anders Østergaard Madsen
{"title":"Phase seeding may provide a gateway to structure solution by deep learning.","authors":"Anders Østergaard Madsen","doi":"10.1107/S2053273325004814","DOIUrl":"10.1107/S2053273325004814","url":null,"abstract":"<p><p>The phase-seeding method proposed by Carrozzini et al. [(2025), Acta Cryst. A81, 188-201] introduces a strategy for integrating artificial intelligence (AI) with established ab initio phasing techniques. Rather than presenting an AI-based phasing solution itself, the authors demonstrate how traditional crystallographic methods can be significantly enhanced if provided with a small subset of approximate phase values - a `phase seed' - that could, in principle, be generated by a machine learning model. By discretizing phase values into a few angular bins, the method transforms the continuous phase problem into a classification task, thereby reducing the computational burden on AI training. This hybrid approach shows promise for improving structure solution, particularly for large and complex non-centrosymmetric crystals, and opens a pathway for future AI-assisted crystallographic workflows.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"251-253"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144256873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Symmetries of all lines in monolayer crystals. 单层晶体中所有线的对称性。
IF 1.9 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2025-07-01 Epub Date: 2025-06-13 DOI: 10.1107/S205327332500422X
Bernard Field, Sinéad M Griffin
{"title":"Symmetries of all lines in monolayer crystals.","authors":"Bernard Field, Sinéad M Griffin","doi":"10.1107/S205327332500422X","DOIUrl":"10.1107/S205327332500422X","url":null,"abstract":"<p><p>As `2D' materials (i.e. materials just a few atoms thick) continue to gain prominence, understanding their symmetries is critical for unlocking their full potential. In this work, we present comprehensive tables that tabulate the rod group symmetries of all crystallographic lines in all 80 layer groups, which describe the symmetries of 2D materials. These tables are analogous to the scanning tables for space groups found in Volume E of the International Tables for Crystallography, but are specifically tailored for layer groups and their applications to 2D materials. This resource will aid in the analysis of line defects, such as domain walls, which play a crucial role in determining the properties and functionality of 2D materials.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"339-349"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Updating direct methods III. Reduction of structural complexity when first-rank semi-invariants are estimated via the Patterson map. 更新直接方法利用Patterson映射估计一阶半不变量时结构复杂性的降低。
IF 1.9 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2025-07-01 Epub Date: 2025-05-22 DOI: 10.1107/S2053273325003274
Carmelo Giacovazzo
{"title":"Updating direct methods III. Reduction of structural complexity when first-rank semi-invariants are estimated via the Patterson map.","authors":"Carmelo Giacovazzo","doi":"10.1107/S2053273325003274","DOIUrl":"10.1107/S2053273325003274","url":null,"abstract":"<p><p>A new theory for the probabilistic estimation of first-rank one-phase semi-invariants is presented. In this approach, atomic positions are treated as primitive random variables but are constrained by the a priori knowledge of interatomic vectors. This information is always available, thus allowing the new technique to be considered an ab initio probabilistic method conditioned by the knowledge of the Patterson map. The theoretical foundation for the estimation of triplet invariants was outlined in the first paper of this series [Giacovazzo (2019). Acta Cryst. A75, 142-157]. Subsequent experimental tests, shown in the second paper of this series [Burla et al. (2024). J. Appl. Cryst. 57, 1011-1022], have demonstrated the significant superiority of this new approach over existing methods. The improvements were so notable that it has been suggested this technique could be valuable for the ab initio solution of macromolecular structures. This work expands the probabilistic approach to include the estimation of first-rank one-phase semi-invariants, The hope is that they can contribute to the ab initio solution of macromolecular structures. Only in this way can one-phase semi-invariants go from being a historical curiosity to an effective tool for solving macromolecular structures.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"269-278"},"PeriodicalIF":1.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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