Figure 1.
Types of interactions between processes. Reactions are indicated by arrows. The reaction rate for each reaction is denoted as di and parameterized by ki and k-i. A) Visualization of a graded interaction between the processes of L binding and D phosphorylation. The same scheme can be taken to demonstrate non-interacting processes. For non-interacting processes the parameter restrictions k1 = k3, k-1 = k-3, k2 = k4 and k-2 = k-4 hold. B) Visualization of an all-or-none interaction between the processes of binding site phosphorylation and E binding. E can only bind to phosphorylated sites, while the dephosphorylation of D is only possible in the absence of a bound effector. C) The cyclic reaction scheme degenerates to a reaction chain, as the species D[0, 0, E] does not exist. In this case, the notation can be simplified by describing binding site phosphorylation and E binding as modifications of the same site.