Model parameters.

For reactions, the values listed are for microscopic rate constants. For second-order reactions, the corresponding λ values can be calculated from Eqs 2 or 26, depending on the type of reaction. The parameters kh, khd, kc and kcd used in spatial Gillespie simulations are computed from Eqs 8, 13, 16 and 19, respectively. The parameters for the 3D model correspond with the 2D parameters, except when they have been scaled to account for dimensionality (Methods). Both 2D and 3D particle-based simulations were performed using Smoldyn [22,23] specifying reaction probabilities for second-order interactions. Such probabilities are computed from the rate constants presented here as described in the Methods.