Related papers: Motzkin path on RNA abstract shapes
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,…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
The Motzkin numbers can be derived as coefficients of hybrid polynomials. Such an identification allows the derivation of new identities for this family of numbers and offers a tool to investigate previously unnoticed links with the theory…
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…
RNA motifs typically consist of short, modular patterns that include base pairs formed within and between modules. Estimating the abundance of these patterns is of fundamental importance for assessing the statistical significance of matches…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…
In the 1980s, Viennot developed a combinatorial approach to studying mixed moments of orthogonal polynomials using Motzkin paths. Recently, an alternative combinatorial model for these mixed moments based on lecture hall paths was…
Myriad viruses use positive-strand RNA molecules as their genomes. Far from being only a repository of genetic material, viral RNA performs numerous other functions mediated by its physical structure and chemical properties. In this…
The prevalent method for RNA secondary structure prediction for a single sequence is free energy minimization based on the nearest neighbor thermodynamic model (NNTM). One of the least well-developed parts of the model is the energy…
Motzkin paths are simple yet important combinatorial objects. In this paper, we consider families of Motzkin paths with restrictions on peak heights, valley heights, upward-run lengths, downward-run lengths, and flat-run lengths. This paper…
Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA…
We review a derivation of the numbers of RNA complexes of an arbitrary topology. These numbers are encoded in the free energy of the hermitian matrix model with potential V(x)=x^2/2-stx/(1-tx), where s and t are respective generating…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
So called $S$-Motzkin paths are combined the concepts `catastrophes' and `air pockets. The enumeration is done by properly set up bivariate generating functions which can be extended using the kernel method.
We derive precise asymptotic expressions for the expectations, variances, covariance, and quite a few further mixed moments for the number of hairpins and the number of basepairs in RNA secondary structures, and give convincing evidence…
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is $1.104366 \cdot n^{-3/2} \cdot 2.618034^n$. Motivated by the kinetics of RNA secondary structure formation, we are interested in…
We prove a conjecture of Drake and Kim: the number of $2$-distant noncrossing partitions of $\{1,2,...,n\}$ is equal to the sum of weights of Motzkin paths of length $n$, where the weight of a Motzkin path is a product of certain fractions…
In this paper we present a novel framework for sequence to shape maps. These combinatorial maps realize exponentially many shapes, and have preimages which contain extended connected subgraphs of diameter n (neutral networks). We prove that…
We show that the spectral curve for Eynard-Orantin topological recursions satisfied by counting Grothendieck's dessins d'enfants are related to Narayana numbers. This suggests a connection of dessins to combinatorics of Coxeter groups,…
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…