Simbios Talk by Pengyu Ren, University of Texas at Austin

Title: Coarse-Grained Physical Model for RNA

Abstract: To explore macromolecules such as RNAs at the relevant time-scale, a hierarchical coarse-gained physical model is being developed. Rather than resorting to typical strings-of-beads approaches, we base our coarse-grained model on fundamental physical chemical interactions that arise from van der Waals and electrostatic forces. Not only the explicit treatment of electrostatic interactions is critical for nucleic acids, such a model is also consistent with the current state-of-art all-atom approach. Combining physical potentials at various scales, from atoms to functional groups and to strands of residues, we will be able to address a range of issues central to RNA folding and dynamics via computer simulations. We will discuss the underlying physical model that is based on Gay-Berne and point multipole potentials, as well as the parameterization for RNA. Recent progress and future plan on the development of the coarse-grain simulation program will also be presented.