Calculations of Activated Trajectories with Boundary Value Formulation

Monday, April 11, 2005 - 11:15am - 12:15pm
EE/CS 3-180
Ron Elber (Cornell University)
Activated trajectories are paths that pass over a significant energy barrier between two (or more) stable states. A typical activated trajectory incubates in one of the wells for a significant time period, but once the process is initiated the transition time can be extremely short. A boundary value formulation is proposed that computes efficiently rare and activated trajectories. A large integration step is used in two examples: the Mueller potential, and a conformational transition in alanine dipeptide, a model for protein backbone.