Figure 1.

Reaction kinetics at two levels of modeling detail. (A) The first steps of the photoactivation cascade consist of the following activation reactions: M1/${\text{R}}^{\ast }$ equilibrium (1); G-activation reactions, comprising formation of ${\text{R}}^{\ast }$G complex, subsequent nucleotide exchange in G, and ${\text{R}}^{\ast }$${\text{G}}^{\ast }$-complex dissociation (2); and dissociation of ${\text{G}}^{\ast }$ from the membrane (3). A nonproductive RG-complex formation (4) is added for the precomplex case. These reactions are used for the ODE model of the cascade. (B) Using particle-based reaction-diffusion (ReaDDy), bimolecular association reactions have to be split into the explicitly simulated diffusional encounter and the first-order transition from encounter complex to stable complex. This affects the ${\text{R}}^{\ast }$G- and RG complex formation in (2.2) and (4.2) (red and blue). (C) Graphical representation of the microscopic diffusion and reaction components, illustrating space exclusions, molecular shape, and crowding. To see this figure in color, go online.