Related papers: DNA Origami and Unknotted A-trails in Torus Graphs
We extend the Penrose polynomial, originally defined only for plane graphs, to graphs embedded in arbitrary surfaces. Considering this Penrose polynomial of embedded graphs leads to new identities and relations for the Penrose polynomial…
This project mathematically models the self-assembly of DNA nanostructures in the shape of select Archimedean graphs using the flexible tile model. Under three different sets of restrictions called scenarios, we employ principles of linear…
A triangulation of a surface is irreducible if there is no edge whose contraction produces another triangulation of the surface. In this work we propose an algorithm that constructs the set of irreducible triangulations of any surface with…
There is no 5,7-triangulation of the torus, that is, no triangulation with exactly two exceptional vertices, of degree 5 and 7. Similarly, there is no 3,5-quadrangulation. The vertices of a 2,4-hexangulation of the torus cannot be…
Tilings are around us everywhere, and our curiosity draws us to study their properties. A tiling is a way of arranging pieces on a board, such that there is no space left uncovered, nor any space covered by more than one tile. In…
We construct a new gauge theory on a pair of d-dimensional noncommutative tori. The latter comes from an intimate relationship between the noncommutative geometry associated with a lattice vertex operator algebra A and the noncommutative…
A graph is called intrinsically knotted if every embedding of the graph contains a knotted cycle. Johnson, Kidwell and Michael, and, independently, Mattman showed that intrinsically knotted graphs have at least 21 edges. Recently Lee, Kim,…
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…
The checkerboard coloring of knot diagrams offers a graph-theoretical approach to address topological questions. Champanerkar and Kofman defined a complex generated by the spanning trees of a graph obtained from the checkerboard coloring…
The Cartesian product of two cycles (of length m and length n) has a natural embedding on the torus, such that each face of the embedding is a 4-cycle. The toroidal grid Qd(m,n,r) is a generalization of this in which there is a shift by r…
In this note, we investigate genera for the slopes of a knotted torus in the 4-sphere analogous to the genus of a classical knot. We compare various formulations of this notion, and use this notion to study the extendable subgroup of the…
The amount and type of self-entanglement of DNA filaments is significantly affected by spatial confinement, which is ubiquitous in biological systems. Motivated by recent advancements in single DNA molecule experiments based on nanofluidic…
This dissertation explores applications of discrete geometry in mathematical neuroscience. We begin with convex neural codes, which model the activity of hippocampal place cells and other neurons with convex receptive fields. In Chapter 4,…
For integers $n\ge 0$, an iterated triangulation $Tr(n)$ is defined recursively as follows: $Tr(0)$ is the plane triangulation on three vertices and, for $n\ge 1$, $Tr(n)$ is the plane triangulation obtained from the plane triangulation…
The geometric dual of a cellularly embedded graph is a fundamental concept in graph theory and also appears in many other branches of mathematics. The partial dual is an essential generalization which can be obtained by forming the…
In a region R consisting of unit squares, a (domino) tiling is a collection of dominoes (the union of two adjacent squares) which pave fully the region. The flip graph of R is defined on the set of all tilings of R where two tilings are…
We define an elementary relatively $\mathbb Z/4$ graded Lagrangian-Floer chain complex for restricted immersions of compact 1-manifolds into the pillowcase, and apply it to the intersection diagram obtained by taking traceless $SU(2)$…
The number of graph neural network (GNN) architectures has increased rapidly due to the growing adoption of graph analysis. Although we use GNNs in wide application scenarios, it is a laborious task to design/select optimal GNN…
Graph Neural Networks (GNNs) have emerged as a flexible and powerful approach for learning over graphs. Despite this success, existing GNNs are constrained by their local message-passing architecture and are provably limited in their…
A theta is a graph consisting of two non-adjacent vertices and three internally disjoint paths between them, each of length at least two. For a family $\mathcal{H}$ of graphs, we say a graph $G$ is $\mathcal{H}$-free if no induced subgraph…