Binary matroids and local complementation

We introduce a binary matroid M(IAS(G)) associated with a looped simple graph G. M(IAS(G)) classifies G up to local equivalence, and determines the delta-matroid and isotropic system associated with G. Moreover, a parametrized form of its Tutte polynomial yields the interlace polynomials of G.Comment: This article supersedes arXiv:1301.0293. v2: 26 pages, 2 figures. v3 - v5: 31 pages, 2 figures v6: Final prepublication versio

Interlace Polynomials for Multimatroids and Delta-Matroids

We provide a unified framework in which the interlace polynomial and several related graph polynomials are defined more generally for multimatroids and delta-matroids. Using combinatorial properties of multimatroids rather than graph-theoretical arguments, we find that various known results about these polynomials, including their recursive relations, are both more efficiently and more generally obtained. In addition, we obtain several interrelationships and results for polynomials on multimatroids and delta-matroids that correspond to new interrelationships and results for the corresponding graphs polynomials. As a tool we prove the equivalence of tight 3-matroids and delta-matroids closed under the operations of twist and loop complementation, called vf-safe delta-matroids. This result is of independent interest and related to the equivalence between tight 2-matroids and even delta-matroids observed by Bouchet.Comment: 35 pages, 3 figure

On the colored Tutte polynomial of a graph of bounded treewidth

AbstractWe observe that a formula given by Negami [Polynomial invariants of graphs, Trans. Amer. Math. Soc. 299 (1987) 601–622] for the Tutte polynomial of a k-sum of two graphs generalizes to a colored Tutte polynomial. Consequently, an algorithm of Andrzejak [An algorithm for the Tutte polynomials of graphs of bounded treewidth, Discrete Math. 190 (1998) 39–54] may be directly adapted to compute the colored Tutte polynomial of a graph of bounded treewidth in polynomial time. This result has also been proven by Makowsky [Colored Tutte polynomials and Kauffman brackets for graphs of bounded tree width, Discrete Appl. Math. 145 (2005) 276–290], using a different algorithm based on logical techniques

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