Conformation Kinetics as a Reduced Model for Transition Pathways

The complexity of molecular kinetics can be reduced significantly by a restriction to metastable conformations which are almost invariant sets of molecular dynamical systems. With the Robust Perron Cluster Analysis PCCA+, developed by Weber and Deuflhard [6], we have a tool available which can be used to identify these conformations from a transition probability matrix. This method can also be applied to the corresponding transition rate matrix which provides important information concerning transition pathways of single molecules. In the present paper, we explain the relationship between these two concepts and the extraction of conformation kinetics from transition rates. Moreover, we show how transition rates can be approximated and conclude with an example.