Related papers: Asymptotic connectivity for the network of RNA sec…
Consider the network of all secondary structures of a given RNA sequence, where nodes are connected when the corresponding structures have base pair distance one. The expected degree of the network is the average number of neighbors, where…
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…
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…
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is $1.104366 n^{-3/2} 2.618034^n$. In this paper, we study combinatorial asymptotics for two special subclasses of RNA secondary…
The measurement of the similarity of RNA secondary structures, and in general of contact structures, of a fixed length has several specific applications. For instance, it is used in the analysis of the ensemble of suboptimal secondary…
This paper discusses the enumeration of two-terminal series-parallel networks, i.e. the number of electrical networks built with n identical elements connected in series or parallel with two-terminal nodes. They frequently occur in applied…
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…
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…
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-…
In this paper, we propose a network whose nodes are labeled by the composite numbers and two nodes are connected by an undirected link if they are relatively prime to each other. As the size of the network increases, the network will be…
We prove asymptotic equipartition properties for simple hierarchical structures (modelled as multitype Galton-Watson trees) and networked structures (modelled as randomly coloured random graphs). For example, for large $n$, a networked data…
A network is scale-free if its connectivity density function is proportional to a power-law distribution. Scale-free networks may provide an explanation for the robustness observed in certain physical and biological phenomena, since the…
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 properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
Recently Yoffe {\it et al.} observed that the average distances between $5'-3'$ ends of RNA molecules are very small and largely independent of sequence length. This observation is based on numerical computations as well as theoretical…
The eccentric connectivity index of a connected graph $G$ is the sum over all vertices $v$ of the product $d_{G}(v) e_{G}(v)$, where $d_{G}(v)$ is the degree of $v$ in $G$ and $e_{G}(v)$ is the maximum distance between $v$ and any other…
We study the richness of the ensemble of graphical structures (i.e., unlabeled graphs) of the one-dimensional random geometric graph model defined by $n$ nodes randomly scattered in $[0,1]$ that connect if they are within the connection…
We find conditions for the connectivity of inhomogeneous random graphs with intermediate density. Our results generalize the classical result for G(n, p), when p = c log n/n. We draw n independent points X_i from a general distribution on a…
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…
In this paper, we analyze the exact asymptotic behavior of the connectivity probability in a random binomial bipartite graph $G(n,m,p)$ under various regimes of the edge probability $p=p(n)$. To determine this probability, a method based on…