Professor Kim acknowledges the support of the National Science Foundation and of the Office of Naval Research to develop these rheological animations. Video Clips Huber, G. A. and S. Kim. Weighted-Ensemble Brownian Dynamics Simulations for Protein Association Reactions. Click on image to play MPEG clip . A point in configuration space with 2-D energy surface.
Stochastic simulation shows very low probability of crossing the energy barrier.
Many trajectories must be run to obtain accurate statistics to estimate reaction rate constant. Embarrasingly parallel algorithm helps, but not much. We see a few particles at higher energy levels, but crossing probability is still very low. In the WE method, the space is subdivided into bins. The particles in each bin are split or merged to keep an equal number in each bin.