Title: Estimation of the infinitesimal generator by square-root approximation,
Abstract: For the analysis of molecular processes, the estimation of time-scales, i.e.,
transition rates, is very important. Estimating the transition rates between
molecular conformations is -- from a mathematical point of view -- an invariant
subspace projection problem. A certain infinitesimal generator acting on
function space is projected to a low-dimensional rate matrix. This projection
can be performed in two steps. First, the infinitesimal generator is
discretized, then the invariant subspace is approxi-mated and used for the
subspace projection. In our approach, the discretization will be based on a
Voronoi tessellation of the conformational space. We will show that the
discretized infinitesimal generator can simply be approximated by the geometric
average of the Boltzmann weights of the Voronoi cells. Thus, there is a direct
correla-tion between the potential energy surface of molecular structures and
the transition rates of conformational changes. We present results for a
2d-diffusion process and Alanine dipeptide.