2,105 research outputs found
Circuits in graphs embedded on the torus
AbstractWe give a survey of some recent results on circuits in graphs embedded on the torus. Especially we focus on methods relating graphs embedded on the torus to integer polygons in the Euclidean plane
Networks, (K)nots, Nucleotides, and Nanostructures
Designing self-assembling DNA nanostructures often requires the identification of a route for a scaffolding strand of DNA through the target structure. When the target structure is modeled as a graph, these scaffolding routes correspond to Eulerian circuits subject to turning restrictions imposed by physical constraints on the strands of DNA. Existence of such Eulerian circuits is an NP-hard problem, which can be approached by adapting solutions to a version of the Traveling Salesperson Problem. However, the author and collaborators have demonstrated that even Eulerian circuits obeying these turning restrictions are not necessarily feasible as scaffolding routes by giving examples of nontrivially knotted circuits which cannot be traced by the unknotted scaffolding strand.
Often, targets of DNA nanostructure self-assembly are modeled as graphs embedded on surfaces in space. In this case, Eulerian circuits obeying the turning restrictions correspond to A-trails, circuits which turn immediately left or right at each vertex. In any graph embedded on the sphere, all A-trails are unknotted regardless of the embedding of the sphere in space. We show that this does not hold in general for graphs on the torus. However, we show this property does hold for checkerboard-colorable graphs on the torus, that is, those graphs whose faces can be properly 2-colored, and provide a partial converse to this result. As a consequence, we characterize (with one exceptional family) regular triangulations of the torus containing unknotted A-trails. By developing a theory of sums of A-trails, we lift constructions from the torus to arbitrary n-tori, and by generalizing our work on A-trails to smooth circuit decompositions, we construct all torus links and certain sums of torus links from circuit decompositions of rectangular torus grids.
Graphs embedded on surfaces are equivalent to ribbon graphs, which are particularly well-suited to modeling DNA nanostructures, as their boundary components correspond to strands of DNA and their twisted ribbons correspond to double-helices. Every ribbon graph has a corresponding delta-matroid, a combinatorial object encoding the structure of the ribbon-graph\u27s spanning quasi-trees (substructures having exactly one boundary component). We show that interlacement with respect to quasi-trees can be generalized to delta-matroids, and use the resulting structure on delta-matroids to provide feasible-set expansions for a family of delta-matroid polynomials, both recovering well-known expansions of this type (such as the spanning-tree expansion of the Tutte polynnomial) as well as providing several previously unknown expansions. Among these are expansions for the transition polynomial, a version of which has been used to study DNA nanostructure self-assembly, and the interlace polynomial, which solves a problem in DNA recombination
The Topology of Scaffold Routings on Non-Spherical Mesh Wireframes
The routing of a DNA-origami scaffold strand is often modelled as an Eulerian circuit of an Eulerian graph in combinatorial models of DNA origami design. The knot type of the scaffold strand dictates the feasibility of an Eulerian circuit to be used as the scaffold route in the design. Motivated by the topology of scaffold routings in 3D DNA origami, we investigate the knottedness of Eulerian circuits on surface-embedded graphs. We show that certain graph embeddings, checkerboard colorable, always admit unknotted Eulerian circuits. On the other hand, we prove that if a graph admits an embedding in a torus that is not checkerboard colorable, then it can be re-embedded so that all its non-intersecting Eulerian circuits are knotted. For surfaces of genus greater than one, we present an infinite family of checkerboard-colorable graph embeddings where there exist knotted Eulerian circuits
Developing a Mathematical Model for Bobbin Lace
Bobbin lace is a fibre art form in which intricate and delicate patterns are
created by braiding together many threads. An overview of how bobbin lace is
made is presented and illustrated with a simple, traditional bookmark design.
Research on the topology of textiles and braid theory form a base for the
current work and is briefly summarized. We define a new mathematical model that
supports the enumeration and generation of bobbin lace patterns using an
intelligent combinatorial search. Results of this new approach are presented
and, by comparison to existing bobbin lace patterns, it is demonstrated that
this model reveals new patterns that have never been seen before. Finally, we
apply our new patterns to an original bookmark design and propose future areas
for exploration.Comment: 20 pages, 18 figures, intended audience includes Artists as well as
Computer Scientists and Mathematician
One brick at a time: a survey of inductive constructions in rigidity theory
We present a survey of results concerning the use of inductive constructions
to study the rigidity of frameworks. By inductive constructions we mean simple
graph moves which can be shown to preserve the rigidity of the corresponding
framework. We describe a number of cases in which characterisations of rigidity
were proved by inductive constructions. That is, by identifying recursive
operations that preserved rigidity and proving that these operations were
sufficient to generate all such frameworks. We also outline the use of
inductive constructions in some recent areas of particularly active interest,
namely symmetric and periodic frameworks, frameworks on surfaces, and body-bar
frameworks. We summarize the key outstanding open problems related to
inductions.Comment: 24 pages, 12 figures, final versio
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