TABLE 2:

Programs used for the simulations.

Simulation type	Folder	Description
No vesicle simulations	reaction_diffusion\	Runs the reaction-diffusion model for a while and then bleaches a FRAP circle, diameter determined automatically, and 1% of the cytoplasm.
Vesicle simulations	reaction_diffusion_vesicle\
	FZ = frozen internal compartment
	ACC = accessible internal compartment
	C = Cdc42 concentrated
	BT = Cdc42 bulk traffic
	D = Cdc42 depleted
Quasi–steady-state simulations	FZ_C\FZ_C_peak	Takes reaction-diffusion steady state as initial condition and runs the reaction diffusion + vesicle traffic model.
	FZ_BT\FZ_BT_peak
	FZ_D\FZ_D_peak
	ACC_C\ACC_C_peak'
	ACC_BT\ACC_BT_peak
	ACC_D\ACC_D_peak
FRAP simulations	FZ_C\FZ_C_FRAP	Takes reaction diffusion + vesicle traffic quasi–steady state and either runs for a while before FRAP or FRAPs straight away. FRAP circle diameter determined automatically.
	FZ_BT\FZ_BT_FRAP
	FZ_D\FZ_D_FRAP
	ACC_C\ACC_C_FRAP
	ACC_BT\ACC_BT_FRAP
	ACC_D\ACC_D_FRAP
Traffic speed simulations	FZ_C\FZ_C_TS	Takes reaction-diffusion steady state as initial condition and runs the reaction diffusion + vesicle traffic model. Endocytic patches move in response to vesicle fusion/fission.
	FZ_BT\FZ_BT_TS
	FZ_D\FZ_D_TS
	ACC_C\ACC_C_TS
	ACC_BT\ACC_BT_TS
	ACC_D\ACC_D_TS

All programs (Matlab) available on request.