Related papers: Stacks in canonical RNA pseudoknot structures
The topological filtration of interacting RNA complexes is studied and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that for two interacting…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
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.
The manuscript studies configurations of non-overlapping non-bonding dominoes on finite rectangular boards of unit squares characterized by row and column number. The non-bonding dominoes are defined here by the requirement that any domino…
A set of \( k \) spanning trees in a graph \( G \) is called a set of \textit{completely independent spanning trees (CISTs)} if, for every pair of vertices \( x \) and \( y \), the paths connecting \( x \) and \( y \) across different trees…
A growing family of random graphs is called robust if it retains a giant component after percolation with arbitrary positive retention probability. We study robustness for graphs, in which new vertices are given a spatial position on the…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
We study the triangular array defined by the Graham--Knuth--Patashnik recurrence $T(n,k) = (\alpha n + \beta k + \gamma)\, T(n-1,k)+(\alpha' n + \beta' k + \gamma') \, T(n-1,k-1)$ with initial condition $T(0,k) = \delta_{k0}$ and parameters…
Graph spanners are sparse subgraphs that faithfully preserve the distances in the original graph up to small stretch. Spanner have been studied extensively as they have a wide range of applications ranging from distance oracles, labeling…
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…
We study more than $10^4$ random aggregates of $10^6$ monodisperse sticky hard spheres each, generated by various static algorithms. Their packing fraction varies from 0.370 up to 0.593. These aggregates are shown to be based on two types…
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two…
The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…
Non-coding RNA are functional molecules that are not translated into proteins. Their function comes as important regulators of biological function. Because they are not translated, they need not be as stable as other types of RNA. The TKF91…
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of…
When modeling microstructures, the computational resource requirements increase rapidly as the simulation domain becomes larger. As a result, simulating a small representative fraction under periodic boundary conditions is often a necessary…
A linear system is a pair $(P,\mathcal{L})$ where $\mathcal{L}$ is a family of subsets on a ground finite set $P$ such that $|l\cap l^\prime|\leq 1$, for every $l,l^\prime \in \mathcal{L}$. If all elements of $\mathcal{L}$ of a linear…
The well-known Erd\H{o}s--Ko--Rado theorem states that for $n> 2k$, every intersecting family of $k$-sets of $[n]:=\{1,\ldots ,n\}$ has at most $ {n-1 \choose k-1}$ sets, and the extremal family consists of all $k$-sets containing a fixed…
In this series of three papers we start to investigate the rational Chow ring of the stack consisting of nodal curves of genus 0, in particular we determine completely the rational Chow ring of the substack consisting of curves with at most…
A linear external perturbation is introduced in the action of the partition function of the random matrix model of RNA [G. Vernizzi, H. Orland and A. Zee, Phys. Rev. Lett. 94, 168103 (2005)]. It is seen that (i). the perturbation…