Figure 6
From: Rule-based spatial modeling with diffusing, geometrically constrained molecules
Effect of Scaffold Proteins: Each line corresponds to the number of phosphorylated particles of species A in a different simulation. Simulation in SRSim and BioNetGen enabled and disabled the binding of molecules A to scaffold molecules S through a change in the k s rate. "w-Scf" means a high k s rate whereas "wo-Scf" means a zero k s rate. The angular forces were excluded for the simulations plotted in the left panel. When the scaffold proteins are active and thus bind to molecules A, a higher concentration of phosphorylated A is only measured in the spatial simulation (red line).