Related papers: Stacks in canonical RNA pseudoknot structures
Let $U$ be a Haar distributed matrix in $\mathbb U(n)$ or $\mathbb O (n)$. In a previous paper, we proved that after centering, the two-parameter process \[T^{(n)} (s,t) = \sum_{i \leq \lfloor ns \rfloor, j \leq \lfloor nt\rfloor}…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
In this paper we study $k$-noncrossing matchings. A $k$-noncrossing matching is a labeled graph with vertex set $\{1,...,2n\}$ arranged in increasing order in a horizontal line and vertex-degree 1. The $n$ arcs are drawn in the upper…
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…
In this paper the Turing pattern formation mechanism of a two component reaction-diffusion system modeling the Schnakenberg chemical reaction coupled to linear cross-diffusion terms is studied. The linear cross-diffusion terms favors the…
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…
We construct 1-parameter families of non-periodic embedded minimal surfaces of infinite genus in $T \times \mathbb{R}$, where $T$ denotes a flat 2-tori. Each of our families converges to a foliation of $T \times \mathbb{R}$ by $T$. These…
In this paper we present a sampling framework for RNA structures of fixed topological genus. We introduce a novel, linear time, uniform sampling algorithm for RNA structures of fixed topological genus $g$, for arbitrary $g>0$. Furthermore…
In this paper we analyze the length-spectrum of rainbows in RNA secondary structures. A rainbow in a secondary structure is a maximal arc with respect to the partial order induced by nesting. We show that there is a significant gap in this…
We present a new stochastic particle system on networks which describes the flocking behavior and pattern formation. More precisely, we consider Cucker-Smale particles with decentralized formation control and multiplicative noises on…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
Chen, Deng, Du, Stanley, and Yan introduced the notion of $k$-crossings and $k$-nestings for set partitions, and proved that the sizes of the largest $k$-crossings and $k$-nestings in the partitions of an $n$-set possess a symmetric joint…
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
An activator-inhibitor-substrate model of side-branching used in the context of pulmonary vascular and lung development is considered on the supposition that spatially localized concentrations of the activator trigger local side-branching.…
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…
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
A set partition is said to be $(k,d)$-noncrossing if it avoids the pattern $12... k12... d$. We find an explicit formula for the ordinary generating function of the number of $(k,d)$-noncrossing partitions of $\{1,2,...,n\}$ when $d=1,2$.