Self-Assembly of DNA Graphs and Postman Tours

DNA graph structures can self-assemble from branched junction molecules to yield solutions to computational problems. Self-assembly of graphs have previously been shown to give polynomial time solutions to hard computational problems such as 3-SAT and k-colorability problems. Jonoska et al. have proposed studying self-assembly of graphs topologically, considering the boundary components of their thickened graphs, which allows for reading the solutions to computational problems through reporter strands. We discuss weighting algorithms and consider applications of self-assembly of graphs and the boundary components of their thickened graphs to problems involving minimal weight Eulerian walks such as the Chinese Postman Problem and the Windy Postman Problem

Genus Ranges of Chord Diagrams

A chord diagram consists of a circle, called the backbone, with line segments, called chords, whose endpoints are attached to distinct points on the circle. The genus of a chord diagram is the genus of the orientable surface obtained by thickening the backbone to an annulus and attaching bands to the inner boundary circle at the ends of each chord. Variations of this construction are considered here, where bands are possibly attached to the outer boundary circle of the annulus. The genus range of a chord diagram is the genus values over all such variations of surfaces thus obtained from a given chord diagram. Genus ranges of chord diagrams for a fixed number of chords are studied. Integer intervals that can, and cannot, be realized as genus ranges are investigated. Computer calculations are presented, and play a key role in discovering and proving the properties of genus ranges.Comment: 12 pages, 8 figure

Unsigned state models for the Jones polynomial

It is well a known and fundamental result that the Jones polynomial can be expressed as Potts and vertex partition functions of signed plane graphs. Here we consider constructions of the Jones polynomial as state models of unsigned graphs and show that the Jones polynomial of any link can be expressed as a vertex model of an unsigned embedded graph. In the process of deriving this result, we show that for every diagram of a link in the 3-sphere there exists a diagram of an alternating link in a thickened surface (and an alternating virtual link) with the same Kauffman bracket. We also recover two recent results in the literature relating the Jones and Bollobas-Riordan polynomials and show they arise from two different interpretations of the same embedded graph.Comment: Minor corrections. To appear in Annals of Combinatoric

Twisty itsy bitsy topological field theory

We extend the topological field theory (``itsy bitsy topological field theory"') of our previous work from mod-2 to twisted coefficients. This topological field theory is derived from sutured Floer homology but described purely in terms of surfaces with signed points on their boundary (occupied surfaces) and curves on those surfaces respecting signs (sutures). It has information-theoretic (``itsy'') and quantum-field-theoretic (``bitsy'') aspects. In the process we extend some results of sutured Floer homology, consider associated ribbon graph structures, and construct explicit admissible Heegaard decompositions.Comment: 52 pages, 26 figure

What is a virtual link?

Several authors have recently studied virtual knots and links because they admit invariants arising from R-matrices. We prove that every virtual link is uniquely represented by a link L in S X I, a thickened, compact, oriented surface S, such that the link complement (S X I) - L has no essential vertical cylinder.Comment: Published by Algebraic and Geometric Topology at http://www.maths.warwick.ac.uk/agt/AGTVol3/agt-3-20.abs.htm