Title: Exploring free energy landscapes of RNA folding by all-atom simulations using Replica Exchange Sampling Method

Abstract:

Replica Exchange Method (REM) is a powerful method for speeding up the sampling by using high temperatures to escape kinetic traps. However, even with REM, it is still a difficult task to compute the converged folding free energy landscapes even for small bio-molecules (e.g. small proteins with 20~30 residues) with all-atom simulations in the explicit solvent. In this study, we apply a Serial version of Replica Exchange (SREM) in a distributed computing environment, Folding@home.  We apply SREM on a few small RNA molecules: a RNA kink-turn motif and a RNA tetra-loop motif. A large number of SREM simulations (~2000 100 ns simulations) were performed for each system.  Thermodynamic properties and folding pathways of these two systems were studied. The convergence of the folding free energy landscapes was also discussed.