Graduate Student Mentor

Knowledge of the energy landscape of an RNA molecule is necessary to understand its folding kinetics and nal structure. To eciently analyze the energy landscape of RNA folding with-out enumeration, we apply the probabilistic roadmap (prm) motion planning method which has been successfully applied to the study of protein folding landscapes. In addition, our model deals with secondary structure and connects conformations using methods involving the base-pair distance measurement. The prm-based algorithms for roadmap construction using conformation generation and connection strategies are discussed in this paper. We determine the population kinetics using a statistical mechanical model and predict the fold-ing rates, intermediate states, and folding pathways. Preliminary results are given in this paper.