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Application of clustering techniques to electron-diffraction data: determination of unit-cell parameters. 聚类技术在电子衍射数据中的应用:单胞参数的测定。
IF 1.8 4区 材料科学
Acta Crystallographica Section A Pub Date : 2012-09-01 Epub Date: 2012-07-20 DOI: 10.1107/S0108767312026438
Sebastian Schlitt, Tatiana E Gorelik, Andrew A Stewart, Elmar Schömer, Thorsten Raasch, Ute Kolb
{"title":"Application of clustering techniques to electron-diffraction data: determination of unit-cell parameters.","authors":"Sebastian Schlitt,&nbsp;Tatiana E Gorelik,&nbsp;Andrew A Stewart,&nbsp;Elmar Schömer,&nbsp;Thorsten Raasch,&nbsp;Ute Kolb","doi":"10.1107/S0108767312026438","DOIUrl":"https://doi.org/10.1107/S0108767312026438","url":null,"abstract":"<p><p>A new approach to determining the unit-cell vectors from single-crystal diffraction data based on clustering analysis is proposed. The method uses the density-based clustering algorithm DBSCAN. Unit-cell determination through the clustering procedure is particularly useful for limited tilt sequences and noisy data, and therefore is optimal for single-crystal electron-diffraction automated diffraction tomography (ADT) data. The unit-cell determination of various materials from ADT data as well as single-crystal X-ray data is demonstrated.</p>","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 5","pages":"536-46"},"PeriodicalIF":1.8,"publicationDate":"2012-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767312026438","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30834703","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: 25
Computation of fluctuation scattering profiles via three-dimensional Zernike polynomials. 基于三维Zernike多项式的波动散射剖面计算。
IF 1.8 4区 材料科学
Acta Crystallographica Section A Pub Date : 2012-09-01 Epub Date: 2012-08-15 DOI: 10.1107/S0108767312029637
Haiguang Liu, Billy K Poon, Augustus J E M Janssen, Peter H Zwart
{"title":"Computation of fluctuation scattering profiles via three-dimensional Zernike polynomials.","authors":"Haiguang Liu,&nbsp;Billy K Poon,&nbsp;Augustus J E M Janssen,&nbsp;Peter H Zwart","doi":"10.1107/S0108767312029637","DOIUrl":"https://doi.org/10.1107/S0108767312029637","url":null,"abstract":"<p><p>Ultrashort X-ray pulses from free-electron laser X-ray sources make it feasible to conduct small- and wide-angle scattering experiments on biomolecular samples in solution at sub-picosecond timescales. During these so-called fluctuation scattering experiments, the absence of rotational averaging, typically induced by Brownian motion in classic solution-scattering experiments, increases the information content of the data. In order to perform shape reconstruction or structure refinement from such data, it is essential to compute the theoretical profiles from three-dimensional models. Based on the three-dimensional Zernike polynomial expansion models, a fast method to compute the theoretical fluctuation scattering profiles has been derived. The theoretical profiles have been validated against simulated results obtained from 300 000 scattering patterns for several representative biomolecular species.</p>","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 5","pages":"561-7"},"PeriodicalIF":1.8,"publicationDate":"2012-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767312029637","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30835233","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: 18
Tilting structures in spinels. 尖晶石中的倾斜结构。
IF 1.8 4区 材料科学
Acta Crystallographica Section A Pub Date : 2012-09-01 Epub Date: 2012-08-15 DOI: 10.1107/S0108767312028991
V M Talanov, V B Shirokov
{"title":"Tilting structures in spinels.","authors":"V M Talanov,&nbsp;V B Shirokov","doi":"10.1107/S0108767312028991","DOIUrl":"https://doi.org/10.1107/S0108767312028991","url":null,"abstract":"<p><p>The possible distortions in the spinel structure resulting from rotation of the tetrahedra and octahedra have been investigated by a group-theoretical method. The possibility of the existence of 28 phases of rotation of the tetrahedra and five phases of rotation of the octahedra has been shown. In all these phases the polyhedra are equivalent, but their orientation can be different. Among the phases of the tetrahedra rotation there is one phase of pure rotation, i.e. not accompanied by additional (not rotation) distortions of the structure. Of the five phases of the rotation of the octahedra three phases can be obtained only by pure rotation of the octahedra.</p>","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 5","pages":"595-606"},"PeriodicalIF":1.8,"publicationDate":"2012-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767312028991","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30835237","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: 20
Radial integrals for the magnetic form factor of the 5d electrons of rare earth elements. 稀土元素5d电子磁性形状因子的径向积分。
IF 1.8 4区 材料科学
Acta Crystallographica Section A Pub Date : 2012-09-01 Epub Date: 2012-07-26 DOI: 10.1107/S0108767312027614
Kohjiro Kobayashi, Tatsuya Nagao, Masahisa Ito
{"title":"Radial integrals for the magnetic form factor of the 5d electrons of rare earth elements.","authors":"Kohjiro Kobayashi,&nbsp;Tatsuya Nagao,&nbsp;Masahisa Ito","doi":"10.1107/S0108767312027614","DOIUrl":"https://doi.org/10.1107/S0108767312027614","url":null,"abstract":"The radial integrals , where L = 0, 2, 4, for several electronic configurations of the 5d electrons of rare earth elements are calculated using radial wavefunctions from the Hartree-Fock relativistic method in the Cowan program. Gaussian analytical expressions with four exponential terms are fitted to the values for rare earth elements and the fitted coefficients are tabulated. The tables can be used to interpret the form factor measurements for rare earth metals. Using the radial integrals of Ce 4f and 5d electrons, the experimental measurement of the magnetic form factor of CePd(3) is investigated.","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 5","pages":"589-94"},"PeriodicalIF":1.8,"publicationDate":"2012-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767312027614","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30835236","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
Rod groups and their settings as special geometric realisations of line groups. 杆群及其设置作为线群的特殊几何实现。
IF 1.8 4区 材料科学
Acta Crystallographica Section A Pub Date : 2012-09-01 Epub Date: 2012-07-20 DOI: 10.1107/S0108767312026670
R A Evarestov, A I Panin
{"title":"Rod groups and their settings as special geometric realisations of line groups.","authors":"R A Evarestov,&nbsp;A I Panin","doi":"10.1107/S0108767312026670","DOIUrl":"https://doi.org/10.1107/S0108767312026670","url":null,"abstract":"<p><p>Rod groups (monoperiodic subgroups of the 3-periodic space groups) are considered as a special case of the commensurate line groups (discrete symmetry groups of the three-dimensional objects translationally periodic along a line). Two different factorizations of line groups are considered: (1) The standard L = T(a)F used in crystallography for rod groups; F is a finite system of representatives of line-group decomposition in cosets of 1-periodic translation group T(a); (2) L = ZP used in the theory of line groups; Z is a cyclic generalized translation group and P is a finite point group. For symmorphic line groups (five line-group families of 13 families) the two factorizations are equivalent: the cyclic group Z is a monoperiodic translation group and P is the point group defining the crystal class. For each of the remaining eight families of non-symmorphic line groups the explicit correspondence between rod groups and relevant geometric realisations of the corresponding line groups is established. The settings of rod groups and line groups are taken into account. The results are presented in a table of 75 rod groups listed (in international and factorized notation) by families of the line groups according to the order of the principal axis q (q = 1, 2, 3, 4, 6) of the corresponding isogonal point group.</p>","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 5","pages":"582-8"},"PeriodicalIF":1.8,"publicationDate":"2012-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767312026670","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30835235","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: 4
Enhanced rigid-bond restraints 增强刚性约束
IF 1.8 4区 材料科学
Acta Crystallographica Section A Pub Date : 2012-05-01 DOI: 10.1107/S0108767312014535
A. Thorn, B. Dittrich, G. Sheldrick
{"title":"Enhanced rigid-bond restraints","authors":"A. Thorn, B. Dittrich, G. Sheldrick","doi":"10.1107/S0108767312014535","DOIUrl":"https://doi.org/10.1107/S0108767312014535","url":null,"abstract":"An extension is proposed to the rigid-bond description of atomic thermal motion in crystals.","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"6 1","pages":"448 - 451"},"PeriodicalIF":1.8,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87381540","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: 134
Refining structures against reflection rank: an alternative metric for electron crystallography. 根据反射等级提炼结构:电子晶体学的另一种度量。
IF 1.8 4区 材料科学
Acta Crystallographica Section A Pub Date : 2012-05-01 Epub Date: 2012-03-13 DOI: 10.1107/S0108767312007234
Alexander S Eggeman, Paul A Midgley
{"title":"Refining structures against reflection rank: an alternative metric for electron crystallography.","authors":"Alexander S Eggeman,&nbsp;Paul A Midgley","doi":"10.1107/S0108767312007234","DOIUrl":"https://doi.org/10.1107/S0108767312007234","url":null,"abstract":"<p><p>A new metric is proposed to improve the fidelity of structures refined against precession electron diffraction data. The inherent dynamical nature of electron diffraction ensures that direct refinement of recorded intensities against structure-factor amplitudes can be prone to systematic errors. Here it is shown that the relative intensity of precessed reflections, their rank, can be used as an alternative metric for refinement. Experimental data from erbium pyrogermanate show that applying precession reduces the dynamical transfer of intensity between reflections and hence stabilizes their rank, enabling accurate and reliable structural refinements. This approach is then applied successfully to an unknown structure of an oxygen-deficient bismuth manganite resulting in a refined structural model that is similar to a calcium analogue.</p>","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 3","pages":"352-8"},"PeriodicalIF":1.8,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767312007234","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30582903","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: 31
Temperature diffuse scattering of nanocrystals. 纳米晶体的温度扩散散射。
IF 1.8 4区 材料科学
Acta Crystallographica Section A Pub Date : 2012-05-01 Epub Date: 2012-03-29 DOI: 10.1107/S0108767312009853
K R Beyerlein, M Leoni, P Scardi
{"title":"Temperature diffuse scattering of nanocrystals.","authors":"K R Beyerlein,&nbsp;M Leoni,&nbsp;P Scardi","doi":"10.1107/S0108767312009853","DOIUrl":"https://doi.org/10.1107/S0108767312009853","url":null,"abstract":"<p><p>The effects of thermal vibrations on X-ray powder diffraction patterns are discussed. Special considerations for extremely small crystallites are described, including the occurrence of surface and edge vibrational modes, and a restriction on the maximum phonon wavelength. In doing so, a complete temperature diffuse scattering (TDS) model is presented, which includes the influence of these features on: the Debye-Waller parameter; first-order TDS; and higher-order TDS terms. The importance of using an accurate TDS representation is studied as a function of temperature and crystallite size. It is found that a misrepresentation of the TDS for small crystallites can lead to an error in the determined Debye-Waller parameter on the order of 20-40% and a slight overestimation of the peak broadening. While the presented theory is primarily developed considering X-ray scattering, the same expressions are expected to describe the TDS in faster-than-sound neutron powder diffraction measurements.</p>","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 3","pages":"382-92"},"PeriodicalIF":1.8,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767312009853","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30582906","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: 14
Bayesian analysis of the evidence for minor components in crystallographic models: an alternative to the Hamilton R test. 贝叶斯分析的证据为微小成分的晶体模型:替代汉密尔顿R检验。
IF 1.8 4区 材料科学
Acta Crystallographica Section A Pub Date : 2012-05-01 Epub Date: 2012-04-05 DOI: 10.1107/S0108767312010094
Anthony E Phillips, Jacqueline M Cole
{"title":"Bayesian analysis of the evidence for minor components in crystallographic models: an alternative to the Hamilton R test.","authors":"Anthony E Phillips,&nbsp;Jacqueline M Cole","doi":"10.1107/S0108767312010094","DOIUrl":"https://doi.org/10.1107/S0108767312010094","url":null,"abstract":"<p><p>A simple test based on Bayesian statistics for the presence of minority populations in single-crystal structure refinement is presented. The test is illustrated by analysis of photocrystallographic experiments on single crystals of ruthenium-sulfur-dioxide-based complexes. In data sets collected after irradiation with light, conventional refinements of the populations of different metastable states to values below 4% are shown to be statistically significant. The results also confirm that the photo-induced states are absent from data collected in the dark.</p>","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 3","pages":"324-30"},"PeriodicalIF":1.8,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767312010094","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30583486","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: 3
Parameters for temperature dependence of mean-square displacements for B-, Bi- and Tl-containing binary III-V compounds. 含B-、Bi-和tl二元III-V化合物均方位移的温度依赖性参数。
IF 1.8 4区 材料科学
Acta Crystallographica Section A Pub Date : 2012-05-01 Epub Date: 2012-03-06 DOI: 10.1107/S0108767312002681
Marco Schowalter, Andreas Rosenauer, Kerstin Volz
{"title":"Parameters for temperature dependence of mean-square displacements for B-, Bi- and Tl-containing binary III-V compounds.","authors":"Marco Schowalter,&nbsp;Andreas Rosenauer,&nbsp;Kerstin Volz","doi":"10.1107/S0108767312002681","DOIUrl":"https://doi.org/10.1107/S0108767312002681","url":null,"abstract":"<p><p>Mean-square displacements were computed within the harmonic approximation from ab initio force constants for binary B-, Tl- and Bi-containing III-V compounds in sphalerite crystal structures in the temperature range from 0 to 1000 K in steps of 1 K. An Einstein model with a temperature-dependent characteristic frequency was used to model the temperature dependence of the mean-square displacements. A Gaussian was fitted to the temperature dependence of the characteristic frequency and parameters of the Gaussian are given. Phonon dispersion relations and densities of states derived during the computation of the mean-square displacements are also shown.</p>","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 3","pages":"319-23"},"PeriodicalIF":1.8,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767312002681","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30583485","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: 2
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