Understanding rare transitions occurring in complex systems, for instance c
hemical reactions in solution, poses the problem of finding and analysing t
he trajectories that move from one basin of attraction to another on a comp
licated potential energy surface. We have developed a systematic approach f
or Ending these trajectories using computer simulations without preconceive
d knowledge of transition states. The approach follows from a novel statist
ical mechanics and thermodynamics of trajectories and has been demonstrated
with several applications.