Related papers: Pseudoknot RNA structures with arc-length $\ge 4$

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…

Let $K$ be a knot with an unknotting tunnel $\gamma$ and suppose that $K$ is not a 2-bridge knot. There is an invariant $\rho = p/q \in \mathbb{Q}/2 \mathbb{Z}$, $p$ odd, defined for the pair $(K, \gamma)$. The invariant $\rho$ has…

Phylogenetic networks provide a general framework for modeling reticulate evolutionary processes such as hybridization, recombination, and horizontal gene transfer. In this paper, we study the asymptotic counting of binary phylogenetic…

We study the geometry of a class of group extensions, containing permutational wreath products, which we call "permutational extensions". We construct for all natural number k a torsion group with growth function asymptotically…

We present a variety of numerical data related to the growth of terms in aliquot sequences, iterations of the function $s(n) = \sigma(n) - n$. First, we compute the geometric mean of the ratio $s_k(n)/s_{k-1}(n)$ of $k$th iterates for $n…

Two subsets $A$ and $B$ of a ground set $X$ are \emph{crossing} if none of the four sets $A\setminus B,B\setminus A,A\cap B, X\setminus (A\cup B)$ are empty. Almost fifty years ago, Karzanov and Lomonosov conjectured that every family of…

We construct (k+-1)-regular graphs which provide sequences of expanders by adding or substracting appropriate 1-factors from given sequences of k-regular graphs. We compute numerical examples in a few cases for which the given sequences are…

Given a knot $K$ in a closed orientable manifold $M$ we define the growth rate of the tunnel number of $K$ to be $gr_t(K) = \limsup_{n \to \infty} \frac{t(nK) - n t(K)}{n-1}$. As our main result we prove that the Heegaard genus of $M$ is…

Twisting a given knot $K$ about an unknotted circle $c$ a full $n \in \mathbb{N}$ times, we obtain a "twist family" of knots $\{ K_n \}$. Work of Kouno-Motegi-Shibuya implies that for a non-trivial twist family the crossing numbers…

Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…

Let $\crs(K_n)$ be the minimum number of crossings over all rectilinear drawings of the complete graph on $n$ vertices on the plane. In this paper we prove that $\crs(K_n) < 0.380473\binom{n}{4}+\Theta(n^3)$; improving thus on the previous…

The transient number of a knot K, denoted tr(K), is the minimal number of simple arcs that have to be attached to K, in order that K can be homotoped to a trivial knot in a regular neighborhood of the union of K and the arcs. We give a…

The multiplicative structure of the trivial symplectic groupoid over $\mathbb R^d$ associated to the zero Poisson structure can be expressed in terms of a generating function. We address the problem of deforming such a generating function…

The topological filtration of interacting RNA complexes is studied and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that for two interacting…

We investigate $k$-nets with $k\geq 4$ embedded in the projective plane $PG(2,\mathbb{K})$ defined over a field $\mathbb{K}$; they are line configurations in $PG(2,\mathbb{K})$ consisting of $k$ pairwise disjoint line-sets, called…

We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number,…

We prove that, for every positive integer k, there is an integer N such that every 4-connected non-planar graph with at least N vertices has a minor isomorphic to K_{4,k}, the graph obtained from a cycle of length 2k+1 by adding an edge…

We study the impact of forbidding short cycles to the edge density of $k$-planar graphs; a $k$-planar graph is one that can be drawn in the plane with at most $k$ crossings per edge. Specifically, we consider three settings, according to…

Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…

RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two…