Model exploration.

(A) Spontaneous transients are observed in simulations of the particle-based and the Gillespie’s SSA model but not in the Mean Field model. (B) The three models display the same basal calcium level when μ, the calcium influx rate through open IP₃R channels, increases. The higher variability in the stochastic models reflects the integer value of basal calcium (either 49 or 50, depending on simulations). (C) Quantification of calcium transients in the stochastic models (calcium peak frequency and mean peak amplitude). No significant difference between the two models was observed. (D) Excitability of the Mean-Field model: increasing quantities of exogenous IP₃ molecules were injected at time t = 20Δt, after model equilibration. The amplitude of the resulting calcium response (D1) was quantified depending on the amount of IP₃ injected and the value of the binding rate constant to the first calcium IP₃R site, a₁ (D2). Parameter values for the particle-based model: D_Ca = D_IP3 = ∞ (perfect mixing) and η = 1, R_γ = 200, i.e. no IP₃R channels clustering, and no co-localization of IP₃R with IP₃R-independent Ca²⁺ sources. For SSA and particle-based models, the figure shows the average ± standard deviation over 20 simulations.