Related papers: DNA Origami and Unknotted A-trails in Torus Graphs
Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
If a graph $G$ can be embedded on the torus, and be embedded linklessly in $\mathbb{R}^3$, it's not known whether or not we can always find a linkless embedding of $G$ contained in the standard (unknotted) torus; We show that, for orders 9…
In Theorem 1.2 of the paper math.GT/0002110 the author claimed to have proved that all transversal knots whose topological knot type is that of an iterated torus knot (we call them cable knots) are transversally simple. That theorem is…
Knots are commonly represented and manipulated via diagrams, which are decorated planar graphs. When such a knot diagram has low treewidth, parameterized graph algorithms can be leveraged to ensure the fast computation of many invariants…
In this paper, we discuss optimal $1$-toroidal graphs (abbreviated as O1TG), which are drawn on the torus so that every edge crosses another edge at most once, and has $n$ vertices and exactly $4n$ edges. We first consider connectivity of…
Simple closed curves in the plane can be mapped to nontrivial knots under the action of origami foldings that allow the paper to self-intersect. We show all tame knot types may be produced in this manner, motivating the development of a new…
We prove that every cyclically 4-edge-connected cubic graph that can be embedded in the torus, with the exceptional graph class called "Petersen-like", is 3-edge-colorable. This means every (non-trivial) toroidal snark can be obtained from…
A Schnyder wood is an orientation and coloring of the edges of a planar map satisfying a simple local property. We propose a generalization of Schnyder woods to graphs embedded on the torus with application to graph drawing. We prove…
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origamis, focussing on archetypal 2D and 3D origamis. The model reproduces well the characteristic pattern of helix…
We show how coarse-grained modelling combined with umbrella sampling using distance-based order parameters can be applied to compute the free-energy landscapes associated with mechanical deformations of large DNA nanostructures. We…
A rectangular dual of a plane graph $G$ is a contact representation of $G$ by interior-disjoint rectangles such that (i) no four rectangles share a point, and (ii) the union of all rectangles is a rectangle. In this paper, we study…
Knots are fascinating topological structures that have been observed in various contexts, ranging from micro-worlds to macro-systems, and are conjectured to play a fundamental role in their respective fields. In order to characterize their…
We discuss differences between genera of smooth and locally-flat non-orientable surfaces in the 4-ball with boundary a given torus knot or 2-bridge knot. In particular, we establish that a result by Batson on the smooth non-orientable…
The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…
Through computer-assisted enumeration, we list minimal obstructions for 5-choosability of graphs on the torus with the following additional property: There exists a cyclic system of non-contractible triangles around the torus where the…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
Consider a graph drawn on a surface (for example, the plane minus a finite set of obstacle points), possibly with crossings. We provide an algorithm to decide whether such a drawing can be untangled, namely, if one can slide the vertices…
We show that all nontrivial embeddings of planar graphs on the torus contain a nontrivial knot or a nonsplit link. This is equivalent to showing that no minimally knotted planar spatial graphs on the torus exist that contain neither a…
The A-polynomial of a knot is defined in terms of SL(2,C) representations of the knot group, and encodes information about essential surfaces in the knot complement. In 2005, Dunfield-Garoufalidis and Boyer-Zhang proved that it detects the…