Tangled (up in) cubes

The Symmetry and Topology of Finite and Periodic Graphs and Their Embeddings in Three-Dimensional Euclidean Space

We make the case for the universal use of the Hermann-Mauguin (international) notation for the description of rigid-body symmetries in Euclidean space. We emphasize the importance of distinguishing between graphs and their embeddings and provide examples of 0-, 1-, 2-, and 3-periodic structures. Embeddings of graphs are given as piecewise linear with finite, non-intersecting edges. We call attention to problems of conflicting terminology when disciplines such as materials chemistry and mathematics collide.

Tangled piecewise-linear embeddings of trivalent graphs

A method is described for generating and exploring tangled piecewise-linear embeddings of trivalent graphs under the constraints of point-group symmetry. It is shown that the possible vertex-transitive tangles are either graphs of vertex-transitive polyhedra or bipartite vertex-transitive nonplanar graphs. One tangle is found for 6 vertices, three for 8 vertices (tangled cubes), seven for 10 vertices, and 21 for 12 vertices. Also described are four isogonal embeddings of pairs of cubes and 12 triplets of tangled cubes (16 and 24 vertices, respectively). Vertex 2-transitive embeddings are obtained for tangled trivalent graphs with 6 vertices (two found) and 8 vertices (45 found). Symmetrical tangles of the 10-vertex Petersen graph and the 20-vertex Desargues graph are also described. Extensions to periodic tangles are indicated. These are all interesting and viable targets for molecular synthesis.

Symmetric tangled Platonic polyhedra

Tangled tetrahedra, octahedra, cubes, icosahedra, and dodecahedra are generalizations of classical—untangled—Platonic polyhedra. Like the Platonic polyhedra, all vertices, edges, and faces are symmetrically equivalent. However, the edges of tangled polyhedra are curvilinear, or kinked, to allow entanglement, much like warps and wefts in woven fabrics. We construct the most symmetric entanglements of these polyhedra via assemblies of multistrand helices wound around edges of the conventional polyhedra; they are all necessarily chiral. The construction gives self-entangled chiral polyhedra and compound polyhedra containing catenated multiple tetrahedra or “generalized θ-polyhedra.” An unlimited variety of tangling is possible for any given topology. Related structures have been observed in synthetic materials and clathrin assemblies within cells.

Conventional embeddings of the edge-graphs of Platonic polyhedra, {f, z}, where f, z denote the number of edges in each face and the edge-valence at each vertex, respectively, are untangled in that they can be placed on a sphere (S2) such that distinct edges do not intersect, analogous to unknotted loops, which allow crossing-free drawings of S1 on the sphere. The most symmetric (flag-transitive) realizations of those polyhedral graphs are those of the classical Platonic polyhedra, whose symmetries are *2fz, according to Conway’s two-dimensional (2D) orbifold notation (equivalent to Schönflies symbols I_h, O_h, and T_d). Tangled Platonic {f, z} polyhedra—which cannot lie on the sphere without edge-crossings—are constructed as windings of helices with three, five, seven,… strands on multigenus surfaces formed by tubifying the edges of conventional Platonic polyhedra, have (chiral) symmetries 2fz (I, O, and T), whose vertices, edges, and faces are symmetrically identical, realized with two flags. The analysis extends to the “θ_z” polyhedra, {2,z}. The vertices of these symmetric tangled polyhedra overlap with those of the Platonic polyhedra; however, their helicity requires curvilinear (or kinked) edges in all but one case. We show that these 2fz polyhedral tangles are maximally symmetric; more symmetric embeddings are necessarily untangled. On one hand, their topologies are very constrained: They are either self-entangled graphs (analogous to knots) or mutually catenated entangled compound polyhedra (analogous to links). On the other hand, an endless variety of entanglements can be realized for each topology. Simpler examples resemble patterns observed in synthetic organometallic materials and clathrin coats in vivo.

Isogonal weavings on the sphere: knots, links, polycatenanes

Mathematical knots and links are described as piecewise linear - straight, non-intersecting sticks meeting at corners. Isogonal structures have all corners related by symmetry (`vertex'-transitive). Corner- and stick-transitive structures are termed regular. No regular knots are found. Regular links are cubic or icosahedral and a complete account of these (36 in number) is given, including optimal (thickest-stick) embeddings. Stick 2-transitive isogonal structures are again cubic and icosahedral and also encompass the infinite family of torus knots and links. The major types of these structures are identified and reported with optimal embeddings. The relevance of this work to materials chemistry and biochemistry is noted.

Ideal geometry of periodic entanglements

Three-dimensional entanglements, including knots, knotted graphs, periodic arrays of woven filaments and interpenetrating nets, form an integral part of structure analysis because they influence various physical properties. Ideal embeddings of these entanglements give insight into identification and classification of the geometry and physically relevant configurations in vivo . This paper introduces an algorithm for the tightening of finite, periodic and branched entanglements to a least energy form. Our algorithm draws inspiration from the Shrink-On-No-Overlaps (SONO) (Pieranski 1998 In Ideal knots (eds A Stasiak, V Katritch, LH Kauffman), vol. 19, pp. 20–41.) algorithm for the tightening of knots and links: we call it Periodic-Branched Shrink-On-No-Overlaps (PB-SONO). We reproduce published results for ideal configurations of knots using PB-SONO. We then examine ideal geometry for finite entangled graphs, including θ -graphs and entangled tetrahedron- and cube-graphs. Finally, we compute ideal conformations of periodic weavings and entangled nets. The resulting ideal geometry is intriguing: we see spontaneous symmetrisation in some cases, breaking of symmetry in others, as well as configurations reminiscent of biological and chemical structures in nature.

Trading spaces: building three-dimensional nets from two-dimensional tilings

We construct some examples of finite and infinite crystalline three-dimensional nets derived from symmetric reticulations of homogeneous two-dimensional spaces: elliptic (S (2)), Euclidean (E (2)) and hyperbolic (H (2)) space. Those reticulations are edges and vertices of simple spherical, planar and hyperbolic tilings. We show that various projections of the simplest symmetric tilings of those spaces into three-dimensional Euclidean space lead to topologically and geometrically complex patterns, including multiple interwoven nets and tangled nets that are otherwise difficult to generate ab initio in three dimensions.

A new Euler's formula for DNA polyhedra

DNA polyhedra are cage-like architectures based on interlocked and interlinked DNA strands. We propose a formula which unites the basic features of these entangled structures. It is based on the transformation of the DNA polyhedral links into Seifert surfaces, which removes all knots. The numbers of components , of crossings , and of Seifert circles are related by a simple and elegant formula: . This formula connects the topological aspects of the DNA cage to the Euler characteristic of the underlying polyhedron. It implies that Seifert circles can be used as effective topological indices to describe polyhedral links. Our study demonstrates that, the new Euler's formula provides a theoretical framework for the stereo-chemistry of DNA polyhedra, which can characterize enzymatic transformations of DNA and be used to characterize and design novel cages with higher genus.