Georgia Institute of Technology College of Sciences

A discussion of the Ding, Chan, and Lawrence paper (2005) "RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble."

A discussion of the Chan & Ding (2008) paper "Boltzmann ensemble features of RNA secondary structures: a comparative analysis of biological RNA sequences and random shuffles."

The main focus of this working seminar for this semester will be the mathematics of RNA folding, beginning with some historical context. See www.math.gatech.edu/~heitsch/dmbws.html for further information on possible topics and papers. No meeting this week; regular meetings will start on August 29. If interested please email the organizer.

We analyze the mixing time of a natural local Markov Chain (Gibbs sampler) for twocommonly studied models of random surfaces: (i) discrete monotone surfaces in Z3 with ``almostplanar" boundary conditions and (ii) the one-dimensional discrete Solid-on-Solid (SOS) model.In both cases we prove the first almost optimal bounds O(L^2 polylog(L)) where L is the natural size of the system. Our proof is inspired by the so-called ``mean curvature" heuristic: on a large scale, the dynamics should approximate a deterministic motion in which each point of the surface moves according to a drift proportional to the local inverse mean curvature radius. Key technical ingredients are monotonicity, coupling and an argument due to D.Wilson in the framework of lozenge tiling Markov Chains together with Kenyon's results on the free Gaussian field approximation of monotone surfaces. The novelty of our approach with respect to previous results consists in proving that, with high probability, the dynamics is dominated by a deterministic evolution which, apart from polylog(L) corrections, follows the mean curvature prescription. Our method works equally well for both models despite the fact that their equilibrium maximal deviations from the average height profile occur on very different scales (log(L) for monotone surfaces and L^{1/2} for the SOS model).This is work in collaboration with PIETRO CAPUTO and FABIO LUCIO TONINELLI