Related papers: Motzkin path on RNA abstract shapes
Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…
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 find a bijection between bi-banded paths and peak-counting paths, applying to two classes of lattice paths including Dyck paths. Thus we find a new interpretation of Narayana numbers as coefficients of weight polynomials enumerating…
We relate the combinatorics of periodic generalized Dyck and Motzkin paths to the cluster coefficients of particles obeying generalized exclusion statistics, and obtain explicit expressions for the counting of paths with a fixed number of…
We derive formulae for the number of set-valued standard tableaux of two-rowed shapes, keeping track of the total number of entries, the number of entries in the first row, and the number of entries in the second row. Key in the proofs is a…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
Combinatorial objects such as rooted trees that carry a recursive structure have found important applications recently in both mathematics and physics. We put such structures in an algebraic framework of operated semigroups. This framework…
Motzkin paths with air pockets (MAP) are defined as a generalization of Dyck paths with air pockets by adding some horizontal steps with certain conditions. In this paper, we introduce two generalizations. The first one consists of lattice…
In this paper we present the asymptotic enumeration of RNA structures with pseudoknots. We develop a general framework for the computation of exponential growth rate and the sub exponential factors for $k$-noncrossing RNA structures. Our…
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…
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…
We give two combinatorial interpretations of the Matrix Ansatz of the PASEP in terms of lattice paths and rook placements. This gives two (mostly) combinatorial proofs of a new enumeration formula for the partition function of the PASEP.…
We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common…
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…
Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction…
Paths are important structural elements in complex networks because they are finite (unlike walks), related to effective node coverage (minimum spanning trees), and can be understood as being dual to star connectivity. This article…
A {\em Motzkin path} of length $n$ is a lattice path from $(0,0)$ to $(n,0)$ in the plane integer lattice $\mathbb{Z}\times\mathbb{Z}$ consisting of horizontal-steps $(1, 0)$, up-steps $(1,1)$, and down-steps $(1,-1)$, which never passes…
We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure.
We introduce a computational topology-based approach with unsupervised machine-learning algorithms to estimate the database size and content of RNA-like graph topologies. Specifically, we apply graph theory enumeration to generate all…
In the present paper we find a new interpretation of Narayana polynomials N_n(x) which are the generating polynomials for the Narayana numbers N_{n,k} counting Dyck paths of length n and with exactly k peaks. Strangely enough Narayana…