Related papers: Random $k$-noncrossing RNA Structures

In this paper we present a novel non-parametric method of simplifying piecewise linear curves and we apply this method as a statistical approximation of structure within sequential data in the plane. We consider the problem of minimizing…

In this paper we consider a simple Markov chain for bipartite graphs with given degree sequence on $n$ vertices. We show that the mixing time of this Markov chain is bounded above by a polynomial in $n$ in case of {\em semi-regular} degree…

We consider a natural model of random knotting- choose a knot diagram at random from the finite set of diagrams with n crossings. We tabulate diagrams with 10 and fewer crossings and classify the diagrams by knot type, allowing us to…

Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…

The presence of slipknots in configurations of proteins and DNA has been shown to affect their functionality, or alter it entirely. Historically, polymers are modeled as polygonal chains in space. As an alternative to space curves, we…

Let $\mathcal{P}$ be a graph property which is preserved by removal of edges, and consider the random graph process that starts with the empty $n$-vertex graph and then adds edges one-by-one, each chosen uniformly at random subject to the…

We discuss a non-equilibrium statistical system on a graph or network. Identical particles are injected, interact with each other, traverse, and leave the graph in a stochastic manner described in terms of Poisson rates, possibly dependent…

Using methods from Analytic Combinatorics, we study the families of perfect matchings, partitions, chord diagrams, and hyperchord diagrams on a disk with a prescribed number of crossings. For each family, we express the generating function…

In this paper, we study the combinatorial set of RNA secondary structures of length $n$ with $m$ base-pairs. For a compact representation, we encode an RNA secondary structure by the corresponding Motzkin word. For this combinatorial set,…

Doubly stochastic Poisson processes, also known as the Cox processes, frequently occur in various scientific fields. In this article, motivated primarily by analyzing Cox process data in biophysics, we propose a nonparametric kernel-based…

We propose a new Markov chain Monte Carlo method in which trial configurations are generated by evolving a state, sampled from a prior distribution, using a Markov transition matrix. We present two prototypical algorithms and derive their…

New high-throughput sequencing technologies have made it possible to pursue the advent of genome-wide transcriptomics. That progress combined with the recent discovery of regulatory non-coding RNAs (ncRNAs) has necessitated fast and…

We consider random walks in which the walk originates in one set of nodes and then continues until it reaches one or more nodes in a target set. The time required for the walk to reach the target set is of interest in understanding the…

Let $V(k)$ denote the waiting time, the number of trials needed to get a consecutive $k$ ones. We propose recurrence algorithms for the probability distribution function (pdf) and the probability generating function (pgf) of $V(k)$ in…

In this paper we give a fully polynomial randomized approximation scheme (FPRAS) for the number of matchings in k-uniform hypergraphs whose intersection graphs contain few claws. Our method gives a generalization of the canonical path…

Establishing cutoff, an abrupt transition from "not mixed" to "well mixed", is a classical topic in the theory of mixing times for Markov chains. Interest has grown recently in determining not only the existence of cutoff and the order of…

We present a simple, accurate method for solving consistent, rank-deficient linear systems, with or without addi- tional rank-completing constraints. Such problems arise in a variety of applications, such as the computation of the…

We consider the problem of determining the existence of a sequence of matrices driving a discrete-time consensus system to consensus. We transform this problem into one of the existence of a product of the transition (stochastic) matrices…

We present a new method, Non-Stationary Forward Flux Sampling, that allows efficient simulation of rare events in both stationary and non-stationary stochastic systems. The method uses stochastic branching and pruning to achieve uniform…

We show a generalization of the crossing lemma for multi-graphs drawn on orientable surfaces in which pairs of edges are assumed to be drawn by non-homotopic simple arcs which pairwise cross at most $k$ times.