Coarse-grained modelling applied to RNA morphologies and flexibility

Abstract

Traditional methods in Molecular Dynamics are encountering their computational boundaries to simulate long-time periods and large macromolecules, such as RNA. We develop an alternative approach by using: i) an ultra-simplified coarse-grained (CG) representation of the molecule and ii) a flexible non-linear potential intended to represent the accessible conformational space of RNA. This model can reproduce the flexibility observed in force-field simulations and different morphologies can be modelled. These results underscore the necessity of non-linear dynamics and statistical physics in CG to capture the dynamic behaviour of Hydrogen Bonds in RNA.