Related papers: The Expected Order of Saturated RNA Secondary Stru…
We address the expected supremum of a linear combination of shifts of the sinc kernel with random coefficients. When the coefficients are Gaussian, the expected supremum is of order \sqrt{\log n}, where n is the number of shifts. When the…
Consider a random word $X^n=(X_1,\ldots ,X_n)$ in an alphabet consisting of $4$ letters, with the letters viewed either as $A$, $U$, $G$ and $C$ (i.e., nucleotides in an RNA sequence) or $\alpha$, $\bar{\alpha}$, $\beta$ and $\bar{\beta}$…
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…
The analytical study of disordered system is usually difficult due to the necessity to perform a quenched average over the disorder. Thus, one may resort to the easier annealed ensemble as an approximation to the quenched system. In the…
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…
An RNA secondary structure is designable if there is an RNA sequence which can attain its maximum number of base pairs only by adopting that structure. The combinatorial RNA design problem, introduced by Hale\v{s} et al. in 2016, is to…
Let $\pi_n$ be a uniformly chosen random permutation on $[n]$. Using an analysis of the probability that two overlapping consecutive $k$-permutations are order isomorphic, we show that the expected number of distinct consecutive patterns in…
High-order structures have been recognised as suitable models for systems going beyond the binary relationships for which graph models are appropriate. Despite their importance and surge in research on these structures, their random cases…
A simple method to produce a random order type is to take the order type of a random point set. We conjecture that many probability distributions on order types defined in this way are heavily concentrated and therefore sample inefficiently…
An elementary, at the undergraduate level derivation is given of precise upper bounds of the number of various RNA secondary structures. The method works when the generating function has multiple singularities at the circle of convergence,…
Disordered systems like liquids, gels, glasses, or granular materials are not only ubiquitous in daily life and in industrial applications but they are also crucial for the mechanical stability of cells or the transport of chemical and…
We establish a list of characterizations of bounded twin-width for hereditary, totally ordered binary structures. This has several consequences. First, it allows us to show that a (hereditary) class of matrices over a finite alphabet either…
A k-noncrossing RNA pseudoknot structure is a graph over $\{1,...,n\}$ without 1-arcs, i.e. arcs of the form (i,i+1) and in which there exists no k-set of mutually intersecting arcs. In particular, RNA secondary structures are 2-noncrossing…
Let $\pi_n$ be a uniformly chosen random permutation on $[n]$. The authors of [2] showed that the expected number of distinct consecutive patterns of all lengths $k\in\{1,2,\ldots,n\}$ in $\pi_n$ was $\frac{n^2}{2}(1-o(1))$ as $n\to\infty$,…
Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides,…
In this paper we determine the number and typical structure of sets of integers with bounded doubling. In particular, improving recent results of Green and Morris, and of Mazur, we show that the following holds for every fixed $\lambda > 2$…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
A random 2-cell embedding of a given graph $G$ is obtained by choosing a random local rotation around every vertex. We analyze the expected number of faces of such an embedding, which is equivalent to studying its average genus. In 1991,…
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…