Acta Crystallographica Section A: Foundations and Advances最新文献_第7页

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2023-11-01 Epub Date: 2023-09-25 DOI: 10.1107/S2053273323008094

A M Stanley

引用次数: 0

A novel algorithm for calculation of Fourier and asymmetric units. 一种计算傅立叶和不对称单位的新算法。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2023-11-01 Epub Date: 2023-09-25 DOI: 10.1107/S2053273323007714

Frantisek Pavelcik

引用次数: 0

Site-occupancy factors in the Debye scattering equation. A theoretical discussion on significance and correctness. 德拜散射方程中的场地占用系数。关于意义和正确性的理论讨论。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2023-11-01 Epub Date: 2023-11-02 DOI: 10.1107/S2053273323008446

Fabio Ferri, Maria Chiara Bossuto, Pietro Anzini, Antonio Cervellino, Antonietta Guagliardi, Federica Bertolotti, Norberto Masciocchi

{"title":"Site-occupancy factors in the Debye scattering equation. A theoretical discussion on significance and correctness.","authors":"Fabio Ferri, Maria Chiara Bossuto, Pietro Anzini, Antonio Cervellino, Antonietta Guagliardi, Federica Bertolotti, Norberto Masciocchi","doi":"10.1107/S2053273323008446","DOIUrl":"10.1107/S2053273323008446","url":null,"abstract":"The Debye scattering equation (DSE) [Debye (1915). Ann. Phys. 351, 809-823] is widely used for analyzing total scattering data of nanocrystalline materials in reciprocal space. In its modified form (MDSE) [Cervellino et al. (2010). J. Appl. Cryst. 43, 1543-1547], it includes contributions from uncorrelated thermal agitation terms and, for defective crystalline nanoparticles (NPs), average site-occupancy factors (s.o.f.'s). The s.o.f.'s were introduced heuristically and no theoretical demonstration was provided. This paper presents in detail such a demonstration, corrects a glitch present in the original MDSE, and discusses the s.o.f.'s physical significance. Three new MDSE expressions are given that refer to distinct defective NP ensembles characterized by: (i) vacant sites with uncorrelated constant site-occupancy probability; (ii) vacant sites with a fixed number of randomly distributed atoms; (iii) self-excluding (disordered) positional sites. For all these cases, beneficial aspects and shortcomings of introducing s.o.f.'s as free refinable parameters are demonstrated. The theoretical analysis is supported by numerical simulations performed by comparing the corrected MDSE profiles and the ones based on atomistic modeling of a large number of NPs, satisfying the structural conditions described in (i)-(iii).","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"587-596"},"PeriodicalIF":1.8,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10626651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71418681","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

Chiral spiral cyclic twins. II. A two-parameter family of cyclic twins composed of discrete circle involute spirals. 手性螺旋环状孪晶。二、由离散圆渐开线螺旋组成的双参数循环孪晶族。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2023-11-01 Epub Date: 2023-10-31 DOI: 10.1107/S2053273323008276

Wolfgang Hornfeck

{"title":"Chiral spiral cyclic twins. II. A two-parameter family of cyclic twins composed of discrete circle involute spirals.","authors":"Wolfgang Hornfeck","doi":"10.1107/S2053273323008276","DOIUrl":"10.1107/S2053273323008276","url":null,"abstract":"A mathematical toy model of chiral spiral cyclic twins is presented, describing a family of deterministically generated aperiodic point sets. Its individual members depend solely on a chosen pair of integer parameters, a modulus m and a multiplier μ. By means of their specific parameterization they comprise local features of both periodic and aperiodic crystals. In particular, chiral spiral cyclic twins are composed of discrete variants of continuous curves known as circle involutes, each discrete spiral being generated from an integer inclination sequence. The geometry of circle involutes does not only provide for a constant orthogonal separation distance between adjacent spiral branches but also yields an approximate delineation of the intrinsically periodic twin domains as well as a single aperiodic core domain interconnecting them. Apart from its mathematical description and analysis, e.g. concerning its circle packing densities, the toy model is studied in association with the crystallography and crystal chemistry of α-uranium and CrB-type crystal structures.","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"570-586"},"PeriodicalIF":1.8,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10626652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71409833","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

TERSE/PROLIX (TRPX) - a new algorithm for fast and lossless compression and decompression of diffraction and cryo-EM data. TERSE/PROLIX (TRPX) -一种快速无损压缩和解压衍射和低温电镜数据的新算法。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2023-11-01 Epub Date: 2023-09-25 DOI: 10.1107/S205327332300760X

Senik Matinyan, Jan Pieter Abrahams

{"title":"TERSE/PROLIX (TRPX) - a new algorithm for fast and lossless compression and decompression of diffraction and cryo-EM data.","authors":"Senik Matinyan, Jan Pieter Abrahams","doi":"10.1107/S205327332300760X","DOIUrl":"10.1107/S205327332300760X","url":null,"abstract":"High-throughput data collection in crystallography poses significant challenges in handling massive amounts of data. Here, TERSE/PROLIX (or TRPX for short) is presented, a novel lossless compression algorithm specifically designed for diffraction data. The algorithm is compared with established lossless compression algorithms implemented in gzip, bzip2, CBF (crystallographic binary file), Zstandard(zstd), LZ4 and HDF5 with gzip, LZF and bitshuffle+LZ4 filters, in terms of compression efficiency and speed, using continuous-rotation electron diffraction data of an inorganic compound and raw cryo-EM data. The results show that TRPX significantly outperforms all these algorithms in terms of speed and compression rate. It was 60 times faster than bzip2 (which achieved a similar compression rate), and more than 3 times faster than LZ4, which was the runner-up in terms of speed, but had a much worse compression rate. TRPX files are byte-order independent and upon compilation the algorithm occupies very little memory. It can therefore be readily implemented in hardware. By providing a tailored solution for diffraction and raw cryo-EM data, TRPX facilitates more efficient data analysis and interpretation while mitigating storage and transmission concerns. The C++20 compression/decompression code, custom TIFF library and an ImageJ/Fiji Java plugin for reading TRPX files are open-sourced on GitHub under the permissive MIT license.","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"536-541"},"PeriodicalIF":1.8,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10626653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41090553","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

Ice structures assembled from cubic water clusters of D_2d and S₄ symmetry. 由D2d和S4对称的立方水团组成的冰结构。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2023-11-01 Epub Date: 2023-09-14 DOI: 10.1107/S2053273323007428

Sergey V Gudkovskikh, Mikhail V Kirov

引用次数: 0

Colorings of patterns fixed by an arbitrary finite-index subgroup of the symmetry group. 由对称群的任意有限指数子群固定的图案的着色。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2023-11-01 Epub Date: 2023-10-26 DOI: 10.1107/S2053273323007878

Allan O Junio

引用次数: 0

Molecular replacement for small-molecule crystal structure determination from X-ray and electron diffraction data with reduced resolution. 用分子置换法测定分辨率降低的X射线和电子衍射数据中的小分子晶体结构。

IF 1.9 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2023-11-01 Epub Date: 2023-10-19 DOI: 10.1107/S2053273323008458

Tatiana E Gorelik, Peer Lukat, Christian Kleeberg, Wulf Blankenfeldt, Rolf Mueller

{"title":"Molecular replacement for small-molecule crystal structure determination from X-ray and electron diffraction data with reduced resolution.","authors":"Tatiana E Gorelik, Peer Lukat, Christian Kleeberg, Wulf Blankenfeldt, Rolf Mueller","doi":"10.1107/S2053273323008458","DOIUrl":"10.1107/S2053273323008458","url":null,"abstract":"The resolution of 3D electron diffraction (ED) data of small-molecule crystals is often relatively poor, due to either electron-beam radiation damage during data collection or poor crystallinity of the material. Direct methods, used as standard for crystal structure determination, are not applicable when the data resolution falls below the commonly accepted limit of 1.2 Å. Therefore an evaluation was carried out of the performance of molecular replacement (MR) procedures, regularly used for protein structure determination, for structure analysis of small-molecule crystal structures from 3D ED data. In the course of this study, two crystal structures of Bi-3812, a highly potent inhibitor of the oncogenic transcription factor BCL6, were determined: the structure of α-Bi-3812 was determined from single-crystal X-ray data, the structure of β-Bi-3812 from 3D ED data, using direct methods in both cases. These data were subsequently used for MR with different data types, varying the data resolution limit (1, 1.5 and 2 Å) and by using search models consisting of connected or disconnected fragments of BI-3812. MR was successful with 3D ED data at 2 Å resolution using a search model that represented 74% of the complete molecule.","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"504-514"},"PeriodicalIF":1.9,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10626656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49671904","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

Small-angle scattering tensor tomography algorithm for robust reconstruction of complex textures. 用于复杂纹理鲁棒重建的小角度散射张量层析成像算法。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2023-11-01 Epub Date: 2023-10-19 DOI: 10.1107/S205327332300863X

Leonard C Nielsen, Paul Erhart, Manuel Guizar-Sicairos, Marianne Liebi

{"title":"Small-angle scattering tensor tomography algorithm for robust reconstruction of complex textures.","authors":"Leonard C Nielsen, Paul Erhart, Manuel Guizar-Sicairos, Marianne Liebi","doi":"10.1107/S205327332300863X","DOIUrl":"10.1107/S205327332300863X","url":null,"abstract":"The development of small-angle scattering tensor tomography has enabled the study of anisotropic nanostructures in a volume-resolved manner. It is of great value to have reconstruction methods that can handle many different nanostructural symmetries. For such a method to be employed by researchers from a wide range of backgrounds, it is crucial that its reliance on prior knowledge about the system is minimized, and that it is robust under various conditions. Here, a method is presented that employs band-limited spherical functions to enable the reconstruction of reciprocal-space maps of a wide variety of nanostructures. This method has been thoroughly tested and compared with existing methods in its ability to retrieve known reciprocal-space maps, as well as its robustness to changes in initial conditions, using both simulations and experimental data. It has also been evaluated for its computational performance. The anchoring of this method in a framework of integral geometry and linear algebra highlights its possibilities and limitations.","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"515-526"},"PeriodicalIF":1.8,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10626654/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49671905","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

Predicting chemical shifts with graph neural networks 利用图神经网络预测化学位移

IF 2.29 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2023-09-26 DOI: 10.1107/s2053273323099618

Ziyue Yang, Maghesree Chakraborty, Andrew White

引用次数: 0