BROWNIAN DYNAMICS SIMULATIONS OF DIFFUSION-INFLUENCED REACTIONS - INCLUSION OF INTRINSIC REACTIVITY AND GATING

The Brownian dynamics algorithm for calculating steady-state bimolecular rate constants of diffusion-influenced reactions is applied to a number of simple model systems that are not fully diffusion controlled because of finite intrinsic reactivity and/or gating of the active site. Finite reactivity is dealt with by using procedures originally developed by Lamm and Schulten (J. Chem. Phys. 1983, 78, 2713) and extended by Northrup et al. (J. Chem. Phys. 1986, 84, 2196). According to Northrup et al., rate constants are derived from survival probabilities averaged over many independent Brownian dynamics trajectories. For the systems studied in this work, simulated rate constants are in very good agreement with analytic values. This is true even for extremely low intrinsic reactivities, where the reactions are far from diffusion controlled. © 1990 American Chemical Society.