Secondary Structure Models of Nucleic Acid Folding Kinetics

This thesis examines nucleic acid folding processes using secondary structure models, which have the advantage that they may simulate behavior at long timescales. First, it verifies that Kinetic Monte Carlo can reproduce known behavior of biological riboswitches. Motivated by the results of that study, a new and general method for determining the effective barrier between local free energy minima is introduced. Finally, a general rate model is developed that greatly improves simulated agreement with measured dynamic properties by considering the energy of intermediates outside the state space of secondary structure.