Ron Elber

Cornell University

Conformational transitions of biological macromolecules are essential to life. They control the initiation of biochemical and biophysical processes, switching from active to non-active conformations, performing numerous biochemical functions, and playing an important role in converting biological to mechanical energy. The rate of these transitions determines the system response time and also helps select specific channels (by making them faster). Understanding the mechanisms and time evolution of these systems and their computational modeling is therefore of great importance. The broad range of relevant time scales and the mechanical characteristics of some of these motions (like in motor proteins) suggest that at least some of the degrees of freedom are not in thermal equilibrium and that the kinetics are not necessarily exponential nor Markovian.

I will present a new theory and an algorithm (Milestoning) that allows for atomically detailed simulations and computation of rates for non-equilibrium (partially), non-Markovian processes in molecular systems. I shall then discuss a few "toy" problems and will continue to a conformational transition in solvated alanine dipeptide. Preliminary results for the R to T transition in scapharca hemoglobin, and the power stroke in myosin will be discussed as well.