Optimal Reaction Coordinates and Kinetic Rates from the Projected Dynamics of Transition Paths

Findingoptimal reaction coordinates and predicting accurate kineticrates for activated processes are two of the foremost challenges ofmolecular simulations. We introduce an algorithm that tackles thetwo problems at once: starting from a limited number of reactive moleculardynamics trajectories (transition paths), we automatically generatewith a Monte Carlo approach a sequence of different reaction coordinatesthat progressively reduce the kinetic rate of their projected effectivedynamics. Based on a variational principle, the minimal rate accuratelyapproximates the exact one, and it corresponds to the optimal reactioncoordinate. After benchmarking the method on an analytic double-wellsystem, we apply it to complex atomistic systems: the interactionof carbon nanoparticles of different sizes in water.

Automated summary

This paper presents an algorithm that addresses the challenges of finding optimal reaction coordinates and predicting accurate kinetic rates through a Monte Carlo approach. The algorithm generates a sequence of reaction coordinates from a limited number of reactive molecular dynamics trajectories, progressively reducing the kinetic rate. The method is benchmarked on an analytic double-well system and applied to complex atomistic systems, demonstrating its feasibility and accuracy.