Related papers: Loops in canonical RNA pseudoknot structures
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
The purpose of this paper is to study the number of limit cycles of canard type in linear regularizations of piecewise linear systems with non-monotonic transition functions. Using the notion of slow divergence integral and elementary…
In this paper, we find and prove that, under some conditions, the embedding distributions of $H$-linear graph families with spiders are asymptotic normal distributions. It can been seen a version of central limit theorem in topological…
In this paper we compute the loop homology of bi-secondary structures. Bi-secondary structures were introduced by Haslinger and Stadler and are pairs of RNA secondary structures, i.e. diagrams having non-crossing arcs in the upper…
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…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
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 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 study the limiting distribution of critical points and extrema of random spherical harmonics, in the high energy limit. In particular, we first derive the density functions of extrema and saddles; we then provide analytic expressions for…
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…
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…
We consider nonintersecting random walks satisfying the condition that the increments have a finite moment generating function. We prove that in a certain limiting regime where the number of walks and the number of time steps grow to…
The representation sets of central loops are investigated and the results obtained are used to construct a finite C-loop. It is shown that for certain types of isotopisms, the central identities are isotopic invariant.
Using transfer matrices up to next-nearest-neighbour (NNN) interactions, we examine the structural correlations of quasi-one-dimensional systems of hard disks confined by two parallel lines and hard spheres confined in cylinders.…
In this paper we compute the sharp lower bounds for the crossing number of $n$-string $k$-loop essential tangles. For essential tangles with only string components, we characterise the ones with the minimum crossing number for a given…
A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a…
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…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
Given a Coxeter system of large type we prove a non--commutative central limit theorem: After normalisation with the square root of n the characteristic function of the set of the first n generators tends in distribution to Wigners…