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].

1. Batsilas et al., Biophys. J., 85, 3659 (2003).
2. Torquato et al., Appl. Phys. Lett., 55, 1847 (1989).
3. Lamm & Schulten., J. Chem. Phys. 78, 2713 (1983).