Acta Crystallographica Section A: Foundations and Advances最新文献

{"title":"A physical optics formulation of Bloch waves and its application to 4D STEM, 3D ED and inelastic scattering simulations.","authors":"Budhika G Mendis","doi":"10.1107/S2053273325000142","DOIUrl":"10.1107/S2053273325000142","url":null,"abstract":"<p><p>Bloch waves are often used in dynamical diffraction calculations, such as simulating electron diffraction intensities for crystal structure refinement. However, this approach relies on matrix diagonalization and is therefore computationally expensive for large unit cell crystals. Here Bloch wave theory is re-formulated using the physical optics concepts underpinning the multislice method. In particular, the multislice phase grating and propagator functions are expressed in matrix form using elements of the Bloch wave structure matrix. The specimen is divided into thin slices, and the evolution of the electron wavefunction through the specimen calculated using the Bloch phase grating and propagator matrices. By decoupling specimen scattering from free space propagation of the electron beam, many computationally demanding simulations, such as 4D STEM imaging modes, 3D ED precession and rotation electron diffraction, phonon and plasmon inelastic scattering, are considerably simplified. The computational cost scales as {cal O}({N^2} ) per slice, compared with {cal O}({N^3} ) for a standard Bloch wave calculation, where N is the number of diffracted beams. For perfect crystals the performance can at times be better than multislice, since only the important Bragg reflections in the otherwise sparse diffraction plane are calculated. The physical optics formulation of Bloch waves is therefore an important step towards more routine dynamical diffraction simulation of large data sets.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"113-123"},"PeriodicalIF":1.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11873815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062165","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}

{"title":"Honeycombs - their variety, topology and symmetry.","authors":"Zbigniew Dauter, Mariusz Jaskolski","doi":"10.1107/S2053273325000889","DOIUrl":"10.1107/S2053273325000889","url":null,"abstract":"<p><p>The double-layer honeycomb with hexagonal cells, three rhombic faces between the two layers and p3m1 layer space-group symmetry, used universally by honeybees, is often considered to be the most efficient (from the point of view of wax economy) and the only honeycomb manufactured by bees. However, another variant of a symmetric and periodic double-layer hexagonal honeycomb with two hexagons and two rhombi between the two layers and slightly better wax economy was discovered theoretically in 1964 by Fejes Tóth and found in nature some years later. The present work shows that there is yet another possibility, with the interface formed by one hexagon and two quadrangles, in addition to the trivial case with flat hexagonal cell bottoms and very poor wax economy. Moreover, we demonstrate that the geometry of the Fejes Tóth honeycomb can be optimized for even better wax economy. All the theoretical honeycomb types are derived using the principle of Dirichlet-domain construction and shown to have more and less symmetric variants. Wax economy is calculated for each case, confirming that indeed the modified Fejes Tóth honeycomb is the most efficient, while the trivial flat-bottom case is the least.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"159-166"},"PeriodicalIF":1.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11873813/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412457","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}

{"title":"Isogonal 1-periodic polycatenanes (chains). Transitivity and intransitivity of links.","authors":"Michael O'Keeffe, Michael M J Treacy","doi":"10.1107/S2053273325001044","DOIUrl":"10.1107/S2053273325001044","url":null,"abstract":"<p><p>A systematic description of 1-periodic polycatenanes is given. The description uses piecewise-linear embeddings (straight edges) and is limited to structures with symmetry-related vertices (isogonal). Components linked are polygons, including knotted polygons and polyhedra. The structures described are generally those with the order of rotational symmetry up to 10. An account is given of transitivity and intransitivity in patterns of links.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"151-158"},"PeriodicalIF":1.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412458","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}

{"title":"Symmetric 3-periodic polycatenanes: catenated rings, polyhedra and rods.","authors":"Michael O'Keeffe, Michael M J Treacy","doi":"10.1107/S2053273324012129","DOIUrl":"10.1107/S2053273324012129","url":null,"abstract":"<p><p>We report symmetric (vertex- and arc-transitive) embeddings of catenated rings, polyhedra and rods. Linked triangles form infinite families of structures, and we limit this report to only structures with each ring linked to three or six others. For linked squares, hexagons, tetrahedra, octahedra, cubes and rods, only a small number of symmetric structures were found, and all are reported.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"107-112"},"PeriodicalIF":1.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941513","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}

{"title":"Crystallography of quasiperiodic moiré patterns in homophase twisted bilayers.","authors":"Marianne Quiquandon, Denis Gratias","doi":"10.1107/S2053273324012087","DOIUrl":"10.1107/S2053273324012087","url":null,"abstract":"<p><p>This paper discusses the geometric properties and symmetries of general moiré patterns generated by homophase bilayers twisted by rotation 2δ. These patterns are generically quasiperiodic of rank 4 and result from the interferences between two basic periodicities incommensurate to each other, defined by the sites in the layers that are kept invariant through the symmetry operations of the structure. These invariant sites are distributed on the nodes of a set of lattices called Φ-lattices - where Φ runs on the rotation operations of the symmetry group of the monolayers - which are the centers of rotation 2δ + Φ transforming a lattice node of the first layer into a node of the second. It is demonstrated that when a coincidence lattice exists, it is the intersection of all the Φ-lattices of the structure.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"94-106"},"PeriodicalIF":1.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11873816/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062183","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}

{"title":"Homophase bilayers: more than just the sum of their monolayers.","authors":"M Feuerbacher","doi":"10.1107/S2053273325001573","DOIUrl":"10.1107/S2053273325001573","url":null,"abstract":"<p><p>Twisted homophase bilayers, stacks of two rotated monolayers such as graphene, exhibit remarkable physical properties absent in their constituent monolayers. The structure of bilayer systems is dominated by a moiré effect and critically depends on the twist angle. Quiquandon & Gratias [Acta Cryst. (2025), A81, 94-106] develop a crystallographic framework for rigorous description of the structure of bilayers, including systems without a coincidence lattice. They offer a set of tools that can describe the structure of any arbitrary bilayer system and enable the connection with its physical properties.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"91-93"},"PeriodicalIF":1.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490187","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}

{"title":"Small-angle rigid-unit modes requiring linear strain compensation.","authors":"Bryce T Eggers, Harold T Stokes, Branton J Campbell","doi":"10.1107/S205327332401163X","DOIUrl":"10.1107/S205327332401163X","url":null,"abstract":"<p><p>Group-theoretical and linear-algebraic methods and tools have recently been developed that aim to exhaustively identify the small-angle rotational rigid-unit modes (RUMs) of a given framework material. But in their current form, they fail to detect RUMs that require a compensating lattice strain which grows linearly with the amplitude of the rigid-unit rotations. Here, we present a systematic approach to including linear strain compensation within the linear-algebraic RUM-search method, so that any geometrically possible small-angle RUM can be detected.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"26-35"},"PeriodicalIF":1.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833220","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}

{"title":"Growth functions of periodic space tessellations.","authors":"Bartosz Naskręcki, Jakub Malinowski, Zbigniew Dauter, Mariusz Jaskolski","doi":"10.1107/S2053273324010763","DOIUrl":"10.1107/S2053273324010763","url":null,"abstract":"<p><p>This work analyzes the rules governing the growth of the numbers of vertices, edges and faces in all possible periodic tessellations of the 2D Euclidean space, and encodes those rules in several types of polynomial growth functions. These encodings map the geometric, combinatorial and topological properties of the tessellations into sets of integer coefficients. Several general statements about these encodings are given with rigorous mathematical proof. The variation of the growth functions is represented graphically and analyzed in orphic diagrams, so named because of their similarity to orphic art. Several examples of 3D space groups are included, to emphasize the complexity of the growth functions in higher dimensions. A freely available Python library is presented to facilitate the discovery of the growth functions and the generation of orphic diagrams.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"64-81"},"PeriodicalIF":1.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142778999","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}

{"title":"Periodic graphs with coincident edges: folding-ladder and related graphs.","authors":"Olaf Delgado-Friedrichs, Michael O'Keeffe, Michael M J Treacy","doi":"10.1107/S2053273324009562","DOIUrl":"10.1107/S2053273324009562","url":null,"abstract":"<p><p>Ladder graphs admit a maximum-symmetry embedding in which edges coincide. In folding ladders, there are no zero-length edges. We give examples of high-symmetry 3-periodic ladders, particularly emphasizing the structures of 3-periodic vertex- and edge-transitive folding ladders. For these, the coincident-edge configuration is one of maximum volume for fixed edge length and has the same coordinates as (is isomeghethic to) a higher-symmetry 3-periodic graph.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"49-56"},"PeriodicalIF":1.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666749","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}

{"title":"The general equation of δ direct methods and the novel SMAR algorithm residuals using the absolute value of ρ and the zero conversion of negative ripples.","authors":"Jordi Rius","doi":"10.1107/S2053273324009628","DOIUrl":"10.1107/S2053273324009628","url":null,"abstract":"<p><p>The general equation δ_M(r) = ρ(r) + g(r) of the δ direct methods (δ-GEQ) is established which, when expressed in the form δ_M(r) - ρ(r) = g(r), is used in the SMAR phasing algorithm [Rius (2020). Acta Cryst A76, 489-493]. It is shown that SMAR is based on the alternating minimization of the two residuals R_ρ(χ) = ∫_V [ρ(χ) - ρ(Φ)s_ρ]² dV and R_δ(Φ) = ∫_V m_ρ[δ_M(χ) - ρ(Φ)s_ρ]² dV in each iteration of the algorithm by maximizing the respective S_ρ(Φ) and S_δ(Φ) sum functions. While R_ρ(χ) converges to zero, R_δ(Φ) converges, as predicted by the theory, to a positive quantity. These two independent residuals combine δ_M and ρ each with |ρ| while keeping the same unknowns, leading to overdetermination for diffraction data extending to atomic resolution. At the beginning of a SMAR phase refinement, the zero part of the m_ρ mask [resulting from the zero conversion of the slightly negative ρ(Φ) values] occupies ∼50% of the unit-cell volume and increases by ∼5% when convergence is reached. The effects on the residuals of the two SMAR phase refinement modes, i.e. only using density functions (slow mode) supplemented by atomic constraints (fast mode), are discussed in detail. Due to its architecture, the SMAR algorithm is particularly well suited for Deep Learning. Another way of using δ-GEQ is by solving it in the form ρ(r) = δ_M(r) - g(r), which provides a simple new derivation of the already known δ_M tangent formula, the core of the δ recycling phasing algorithm [Rius (2012). Acta Cryst. A68, 399-400]. The nomenclature used here is: (i) Φ is the set of φ structure factor phases of ρ to be refined; (ii) δ_M(χ) = FT^-1{c(|E| - 〈|E|〉)×exp(iα)} with χ = {α}, the set of phases of |ρ| and c = scaling constant; (iii) m_ρ = mask, being either 0 or 1; s_ρ is 1 or -1 depending on whether ρ(Φ) is positive or negative.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"16-25"},"PeriodicalIF":1.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666723","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}