Simbios Talk by Samuel Flores, Stanford University, February 6, 2008

Title:  As coarse as it gets: RNA dynamics in six degrees of freedom

Significant advances have been made in the prediction of protein dynamics, but the dynamics of RNA are comparatively less understood.  It is well appreciated that RNA duplexes are stable and therefore solving the structure of junctions connecting those duplexes in many cases effectively solves the structure of the entire molecule.  The Poisson-Boltzmann Equation has been shown to correctly predict the electrostatic interactions of duplexes in solvent with monovalent counterions.  What is not known is whether dynamics of junctions is governed by specific interactions or if it is driven mostly by coarser information such as length of linkers.  In either case it is also unclear whether entropy, electrostatics, Van der Waals, and other interactions are all important or if some subset is sufficient to capture the relevant effects.  We are generating a large number of random junctions consistent with topological and steric constraints.  The entropy will be estimated by counting the conformers in near neighborhoods, and the potential will be evaluated using a physics based force field.  The soon to be released Simbody library will be used as the platform to sample the conformations and evaluate the potentials.  Simbody automates much of the work and in particular allows us to add constraints in ways that traditional MD codes do not.  In addition to the scientific segment I will be giving a technical demonstration of how one goes about doing sampling and dynamics using Simbody, and show a couple of movies.