A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement
Fig 4
kh and kc are benchmarked against particle-based simulations by looking at polarization dynamics and equilibrium.
(A) Time evolution of the clustering of total active Cdc42 from simulations of the polarity model in Fig 3A with parameters in Table 1. We contrast results from particle-based simulations and the spatial Gillespie approach using either kh or kc and a grid element size h = 5ρ. Clustering at a particular timepoint is quantified as the mean of H(r = 1.1μm) over 30 simulations. Uncertainty intervals are computed as mean ± standard deviation and presented as a shaded region enveloping the mean. (B) Clustering at equilibrium from simulations in (A) for different values of the total amount of GEF. The clustering at equilibrium is computed as the mean of H(r = 1.1μm) between 250s and 300s. The box plots were generated with the clustering at equilibrium from 30 simulations. (C) and (D) are corresponding figures to (A) and (B) respectively, the only difference is that the spatial Gillespie simulations are run with h = 2.5ρ and using only kc as kh cannot be computed for such h in this model (see Methods).