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In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…

Given a tame knot K presented in the form of a knot diagram, we show that the problem of determining whether K is knotted is in the complexity class NP, assuming the generalized Riemann hypothesis (GRH). In other words, there exists a…

This paper is centered on covariant dynamics on unimodular random graphs and random networks, namely maps from the set of vertices to itself which are preserved by graph or network isomorphisms. Such dynamics are referred to as…

We construct meta-stable knotted domain strings on the surface of a soliton of the shape of a torus in 3+1 dimensions. We consider the simplest case of Z2 Wess-Zumino-type domain walls for which we can cover the torus with a domain string…

Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…

We study random knotting by considering knot and link diagrams as decorated, (rooted) topological maps on spheres and pulling them uniformly from among sets of a given number of vertices $n$, as first established in recent work with…

Dual graphs have been applied to model RNA secondary structures. The purpose of the paper is two-fold: we present new graph-theoretic properties of dual graphs to validate the further analysis and classification of RNAs using these…

In $2013$ a novel self-assembly strategy for polypeptide nanostructure design which could lead to significant developments in biotechnology was presented in [Design of a single-chain polypeptide tetrahedron assembled from coiled-coil…

Given an integer $c\in \mathbb{N}$, we say a graph $G$ is $c$-pinched if $G$ does not contain an induced subgraph consisting of $c$ cycles, all going through a single common vertex and otherwise pairwise disjoint and with no edges between…

Consider an oriented curve $\Gamma$ in a domain $D$ in the plane $\boldsymbol R^2$. Thinking of $D$ as a piece of paper, one can make a curved folding in the Euclidean space $\boldsymbol R^3$. This can be expressed as the image of an…

We introduce a notion of genus range as a set of values of genera over all surfaces into which a graph is embedded cellularly, and we study the genus ranges of a special family of four-regular graphs with rigid vertices that has been used…

We provide an existence proof for two 1-parameter families of embedded triply periodic minimal surfaces of genus three, namely the tG family with tetragonal symmetry that contains the gyroid, and the rGL family with rhombohedral symmetry…

Self-assembly is a process found everywhere in the Nature. In particular, it is known that DNA self-assembly is Turing universal. Thus one can do arbitrary computations or build nano-structures using DNA self-assembly. In order to…

Given a graph, does there exist an orientation of the edges such that the resulting directed graph is strongly connected? Robbins' theorem [Robbins, Am. Math. Monthly, 1939] states that such an orientation exists if and only if the graph is…

Let $\Lambda(T)$ denote the set of leaves in a tree $T$. One natural problem is to look for a spanning tree $T$ of a given graph $G$ such that $\Lambda(T)$ is as large as possible. This problem is called maximum leaf number, and it is a…

We consider the classical problems (Edge) Steiner Tree and Vertex Steiner Tree after restricting the input to some class of graphs characterized by a small set of forbidden induced subgraphs. We show a dichotomy for the former problem…

Graphene-based nanostructures exhibit a vast range of exciting electronic properties that are absent in extended graphene. For example, quantum confinement in carbon nanotubes and armchair graphene nanoribbons (AGNRs) leads to the opening…

We study edge-maximal, non-complete graphs on surfaces that do not triangulate the surface. We prove that there is no such graph on the projective plane $\mathbb{N}_1$, $K_7-e$ is the unique such graph on the Klein bottle $\mathbb{N}_2$ and…

Knitted and woven textile structures are examples of doubly periodic structures in a thickened plane made out of intertwining strands of yarn. Factoring out the group of translation symmetries of such a structure gives rise to a link…

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…