Related papers: Pseudoknot RNA structures with arc-length $\ge 4$
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
In this paper we study canonical $\gamma$-structures, a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A $\gamma$-structure is composed by specific building…
For a knot K, let b_n(K) be the minimum length of an n-stranded braid representative of K. Examples of knots exist for which b_n(K) is a non-increasing function. We investigate the behavior of b_n(K). We develop bounds on the function in…
We give recurrence relations for the enumeration of symmetric elements within four classes of arc diagrams corresponding to certain involutions and set partitions whose blocks contain no consecutive integers. These arc diagrams are…
The contact map of a protein fold is a graph that represents the patterns of contacts in the fold. It is known that the contact map can be decomposed into stacks and queues. RNA secondary structures are special stacks in which the degree of…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both…
RNA molecules are single-stranded analogues of DNA that can fold into various structures which influence their biological function within the cell. RNA structures can be modelled combinatorially in terms of a certain type of graph called an…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
The non-orientable 4-genus of a knot $K$ in $S^{3}$, denoted $\gamma_4(K)$, measures the minimum genus of a non-orientable surface in $B^{4}$ bounded by $K$. We compute bounds for the non-orientable 4-genus of knots $T_{5, q}$ and $T_{6,…
In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various…
We determine a lower gap property for the growth of an unbounded \(\mathbb{Z}\)-valued \(k\)-regular sequence. In particular, if \(f:\mathbb{N}\to\mathbb{Z}\) is an unbounded \(k\)-regular sequence, we show that there is a constant \(c>0\)…
We construct an intersecting $k$-family of transversal size $\lceil \frac{k+1}{2} \rceil$ and length $k+1$ and study some of its properties. We use this family to prove that $q(4) = 9$. We also construct a $k$-family for $k = 2^m - 1$ of…
In previous work, we gave asymptotic counting results for the number of tree-child and normal networks with $k$ reticulation vertices and explicit exponential generating functions of the counting sequences for $k=1,2,3$. The purpose of this…
Let $A_k$ be the set of permutations in the symmetric group $S_k$ with prefix 12. This paper concerns the enumeration of involutions which avoid the set of patterns $A_k$. We present a bijection between symmetric Schroder paths of length…
Kostochka and Yancey resolved a famous conjecture of Ore on the asymptotic density of $k$-critical graphs by proving that every $k$-critical graph $G$ satisfies $|E(G)| \geq (\frac{k}{2} - \frac{1}{k-1})|V(G)| - \frac{k(k-3)}{2(k-1)}$. The…
Let Sn denote the network of all RNA secondary structures of length n, in which undirected edges exist between structures s, t such that t is obtained from s by the addition, removal or shift of a single base pair. Using context-free…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
In this paper we study $\gamma$-structures filtered by topological genus. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A…