Related papers: The Expected Order of Saturated RNA Secondary Stru…
Given an RNA sequence a, consider the network G = (V;E), where the set V of nodes consists of all secondary structures of a, and whose edge set E consists of all edges connecting two secondary structures whose base pair distance is 1.…
Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of…
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…
A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed…
The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on…
In post-transcriptional regulation, an mRNA molecule is bound by many proteins and/or miRNAs to modulate its function. To enable combinatorial gene regulation, these binding partners of an RNA must communicate with each other, exhibiting…
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…
In this article we consider the cycle structure of compositions of pairs of involutions in the symmetric group S_n chosen uniformly at random. These can be modeled as modified 2-regular graphs, giving rise to exponential generating…
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…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
Let M=M(n,q) be the average of the orders of the elements in the finite unitary group U(n,q). The asymptotic estimate log(M)=nlog(q)-log(n) +o(log n) is proved.
We establish the following two main results on order types of points in general position in the plane (realizable simple planar order types, realizable uniform acyclic oriented matroids of rank $3$): (a) The number of extreme points in an…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
In the preprint arxiv:1703.03425 "strong evidence" for the normal neutrino mass ordering is claimed. The authors obtain Bayesian odds of 42:1 in favour of the normal ordering. Their conclusion is based on adopting a flat logarithmic prior…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
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…
We generalize the notion of saturated order to infinite partial orders and give both a set-theoretic and an algebraic characterization of such orders. We then study the proof theoretic strength of the equivalence of these characterizations…
An old problem of Erd\H{o}s, Fajtlowicz and Staton asks for the order of a largest induced regular subgraph that can be found in every graph on n vertices. Motivated by this problem, we consider the order of such a subgraph in a typical…
We consider saturated fusion systems $\mathcal F$ on a Sylow $2$-subgroup of $\Omega^+_8(2)$ with $O_2(\mathcal F) = 1$. Examples for this are the $2$-fusion systems of $\Omega^+_8(2)$, $\Omega^+_8(2):3$, $P\Omega^+_8(3)$ and…
We study three different poset structures on the set of all compositions. In the first case, the covering relation consists of inserting a part of size one to the left or to the right, or increasing the size of some part by one. The…