Brownian Dynamics simulation of partially absorbing surfaces The Brownian Dynamics algorithm has an adaptive timestep [1]. Far from the partially absorbing surface, the first-passage-time technique [2] is used: the timestep is chosen based on the distance to the lower (trap-covered) and the upper (reflective) boundary. Next to the trap-covered surface the trapping probability is computed according to the exact one-dimensional propagators for the partially absorbing boundary [3]. |
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1. Batsilas et al., Biophys. J., 85, 3659 (2003). |