RNA FoldingSimulation RNA FoldingSimulation Giff Ransom Comp 259 UNC Chapel Hill
Scientific Background • RNA molecules are single stranded copies of a segment of a gene in the DNA. • RNA molecules fold back on themselves, and the three-dimensional shape formed by a given strand is important for studying its interaction with other molecules.
Kurt Grunberger, 2002 The molecular model can be simplified while still fairly accurately predicting the RNA tertiary structure
My Model • Molecular Dynamics Simulation • One Particle for the Sugar Backbone • One Rigid Particle for the Nucleotide Base • Velocity Verlet Integration • Constrained Dynamics
Future Work • Use aDNA rather than bDNA configuration for constants • Compare with actual Molecular Dynamics simulations and attempt to reproduce results as accurately as possible • Implement optimizations for non-bonded interactions