Divide et impera: the efficient calculation of transition rates in activated processes by means of short molecular dynamics simulations

Maddalena Venturoli

Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Many relevant phenomena, such as allosteric transitions in biomolecules, chemical reactions, nucleation events during phase transformation, etc., are activated processes, involving time-scales which span several orders of mag- nitude. To study these processes by molecular simulation it is often nec- essary to use multiscale algorithms. In this talk I will describe one such algorithm, called milestoning, which allows to efficiently compute the ki- netic properties of rare events. Milestoning is a procedure to reduce the dynamics of a molecular dynamics (MD) trajectory to a continuous-time Markov chain describing the succession of transitions between hypersurfaces (the milestones). The main issue is then the estimation of the rate matrix specifying this chain. In this talk I will discuss a new milestoning procedure in which the edges of Voronoi cells define the milestones, and the rate matrix is calculated by running MD simulations restricted to these cells. I will then illustrate an extension of this method to compute the rate of activated processes arising in systems at nonequilibrium steady state.