Acta Crystallographica Section A: Foundations and Advances最新文献_第8页

Modelling dynamical 3D electron diffraction intensities. II. The role of inelastic scattering. 动态三维电子衍射强度建模。二. 非弹性散射的作用非弹性散射的作用

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-03-01 Epub Date: 2024-01-25 DOI: 10.1107/S2053273323010690

Budhika Mendis

{"title":"Modelling dynamical 3D electron diffraction intensities. II. The role of inelastic scattering.","authors":"Budhika Mendis","doi":"10.1107/S2053273323010690","DOIUrl":"10.1107/S2053273323010690","url":null,"abstract":"The strong interaction of high-energy electrons with a crystal results in both dynamical elastic scattering and inelastic events, particularly phonon and plasmon excitation, which have relatively large cross sections. For accurate crystal structure refinement it is therefore important to uncover the impact of inelastic scattering on the Bragg beam intensities. Here a combined Bloch wave-Monte Carlo method is used to simulate phonon and plasmon scattering in crystals. The simulated thermal and plasmon diffuse scattering are consistent with experimental results. The simulations also confirm the empirical observation of a weaker unscattered beam intensity with increasing energy loss in the low-loss regime, while the Bragg-diffracted beam intensities do not change significantly. The beam intensities include the diffuse scattered background and have been normalized to adjust for the inelastic scattering cross section. It is speculated that the random azimuthal scattering angle during inelastic events transfers part of the unscattered beam intensity to the inner Bragg reflections. Inelastic scattering should not significantly influence crystal structure refinement, provided there are no artefacts from any background subtraction, since the relative intensity of the diffracted beams (which includes the diffuse scattering) remains approximately constant in the low energy loss regime.","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"178-188"},"PeriodicalIF":1.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10913673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139544989","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

Double-slit asymmetrical dynamical diffraction of X-rays in ideal crystals. 理想晶体中 X 射线的双缝非对称动态衍射。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-03-01 Epub Date: 2024-01-23 DOI: 10.1107/S2053273323010331

Minas Balyan

{"title":"Double-slit asymmetrical dynamical diffraction of X-rays in ideal crystals.","authors":"Minas Balyan","doi":"10.1107/S2053273323010331","DOIUrl":"10.1107/S2053273323010331","url":null,"abstract":"The theoretical investigation of double-slit asymmetrical dynamical diffraction of X-rays in perfect crystals establishes that Young's interference fringes on the exit surface are formed. The position of the fringes in the cross section of the beam depends on deviation from the Bragg exact orientation and asymmetry angle. An equation for the period of the fringes is presented, according to which the period is polarization sensitive. The period increases with increasing the absolute value of the asymmetry angle. In its turn, the size of the interference region also increases with increasing the absolute value of the asymmetry angle. However, the ratio of interference region size to period, i.e. the number of observed fringes, decreases with increasing the absolute value of the asymmetry angle. The size of the interference region can be of the order of a few tens of mm, which can be used for obtaining Fourier dynamical diffraction holograms of a large size. This type of diffraction can also be used for obtaining double-slit dynamical diffraction contrast of defects and deformations. Due to the phase difference information, in comparison with single-slit diffraction, double-slit diffraction is more sensitive to the existence of objects and deformations in the path of the wave.","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"161-166"},"PeriodicalIF":1.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139519271","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

Automated selection of nanoparticle models for small-angle X-ray scattering data analysis using machine learning. 利用机器学习自动选择用于小角 X 射线散射数据分析的纳米粒子模型。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-03-01 Epub Date: 2024-02-29 DOI: 10.1107/S2053273324000950

Nicolas Monge, Alexis Deschamps, Massih Reza Amini

{"title":"Automated selection of nanoparticle models for small-angle X-ray scattering data analysis using machine learning.","authors":"Nicolas Monge, Alexis Deschamps, Massih Reza Amini","doi":"10.1107/S2053273324000950","DOIUrl":"10.1107/S2053273324000950","url":null,"abstract":"Small-angle X-ray scattering (SAXS) is widely used to analyze the shape and size of nanoparticles in solution. A multitude of models, describing the SAXS intensity resulting from nanoparticles of various shapes, have been developed by the scientific community and are used for data analysis. Choosing the optimal model is a crucial step in data analysis, which can be difficult and time-consuming, especially for non-expert users. An algorithm is proposed, based on machine learning, representation learning and SAXS-specific preprocessing methods, which instantly selects the nanoparticle model best suited to describe SAXS data. The different algorithms compared are trained and evaluated on a simulated database. This database includes 75 000 scattering spectra from nine nanoparticle models, and realistically simulates two distinct device configurations. It will be made freely available to serve as a basis of comparison for future work. Deploying a universal solution for automatic nanoparticle model selection is a challenge made more difficult by the diversity of SAXS instruments and their flexible settings. The poor transferability of classification rules learned on one device configuration to another is highlighted. It is shown that training on several device configurations enables the algorithm to be generalized, without degrading performance compared with configuration-specific training. Finally, the classification algorithm is evaluated on a real data set obtained by performing SAXS experiments on nanoparticles for each of the instrumental configurations, which have been characterized by transmission electron microscopy. This data set, although very limited, allows estimation of the transferability of the classification rules learned on simulated data to real data.","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"202-212"},"PeriodicalIF":1.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10913671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139988763","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 in crystallography and structural science. 晶体学和结构科学中的机器学习。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-03-01 Epub Date: 2024-01-26 DOI: 10.1107/S2053273324000172

Simon J L Billinge, Thomas Proffen

引用次数: 0

Universal parameters of bulk-solvent masks. 块状溶剂掩膜的通用参数。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-03-01 Epub Date: 2024-02-09 DOI: 10.1107/S2053273324000299

Alexandre Urzhumtsev, Paul Adams, Pavel Afonine

{"title":"Universal parameters of bulk-solvent masks.","authors":"Alexandre Urzhumtsev, Paul Adams, Pavel Afonine","doi":"10.1107/S2053273324000299","DOIUrl":"10.1107/S2053273324000299","url":null,"abstract":"The bulk solvent is a major component of biomacromolecular crystals that contributes significantly to the observed diffraction intensities. Accurate modelling of the bulk solvent has been recognized as important for many crystallographic calculations. Owing to its simplicity and modelling power, the flat (mask-based) bulk-solvent model is used by most modern crystallographic software packages to account for disordered solvent. In this model, the bulk-solvent contribution is defined by a binary mask and a scale (scattering) function. The mask is calculated on a regular grid using the atomic model coordinates and their chemical types. The grid step and two radii, solvent and shrinkage, are the three parameters that govern the mask calculation. They are highly correlated and their choice is a compromise between the computer time needed to calculate the mask and the accuracy of the mask. It is demonstrated here that this choice can be optimized using a unique value of 0.6 Å for the grid step irrespective of the data resolution, and the radii values adjusted correspondingly. The improved values were tested on a large sample of Protein Data Bank entries derived from X-ray diffraction data and are now used in the computational crystallography toolbox (CCTBX) and in Phenix as the default choice.","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"194-201"},"PeriodicalIF":1.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10913670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139705389","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

Report of the Executive Committee for 2022. 2022 年执行委员会报告。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-03-01 Epub Date: 2024-02-22 DOI: 10.1107/S2053273323008197

引用次数: 0

Modelling dynamical 3D electron diffraction intensities. I. A scattering cluster algorithm. 动态三维电子衍射强度建模。I. 散射群算法。

IF 1.9 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-03-01 Epub Date: 2024-01-25 DOI: 10.1107/S2053273323010689

Budhika Mendis

{"title":"Modelling dynamical 3D electron diffraction intensities. I. A scattering cluster algorithm.","authors":"Budhika Mendis","doi":"10.1107/S2053273323010689","DOIUrl":"10.1107/S2053273323010689","url":null,"abstract":"Three-dimensional electron diffraction (3D-ED) is a powerful technique for crystallographic characterization of nanometre-sized crystals that are too small for X-ray diffraction. For accurate crystal structure refinement, however, it is important that the Bragg diffracted intensities are treated dynamically. Bloch wave simulations are often used in 3D-ED, but can be computationally expensive for large unit cell crystals due to the large number of diffracted beams. Proposed here is an alternative method, the `scattering cluster algorithm' (SCA), that replaces the eigen-decomposition operation in Bloch waves with a simpler matrix multiplication. The underlying principle of SCA is that the intensity of a given Bragg reflection is largely determined by intensity transfer (i.e. `scattering') from a cluster of neighbouring diffracted beams. However, the penalty for using matrix multiplication is that the sample must be divided into a series of thin slices and the diffracted beams calculated iteratively, similar to the multislice approach. Therefore, SCA is more suitable for thin specimens. The accuracy and speed of SCA are demonstrated on tri-isopropyl silane (TIPS) pentacene and rubrene, two exemplar organic materials with large unit cells.","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"167-177"},"PeriodicalIF":1.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10913674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139544987","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

Analytical models representing X-ray form factors of ions. 代表离子 X 射线形式因子的分析模型。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-01-01 DOI: 10.1107/S2053273323010550

Gunnar Thorkildsen

引用次数: 0

Symmetry groups of two-way twofold and three-way threefold fabrics. 双向两折和三向三折织物的对称群。

IF 1.8 4区材料科学

Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-01-01 DOI: 10.1107/S2053273323008938

Ma Louise Antonette De Las Peñas, Mark Tomenes, Kristan Liza

引用次数: 0

Maximal independence and symmetry in crystal chemistry of natural tectosilicates. 天然构造硅酸盐晶体化学的最大独立性和对称性。