TinkerCell is a Computer-Aided Design software tool for Synthetic Biology that promotes collaboration through its plugin interface. This blog is used to keep notes on updates to the project.
Friday, September 2, 2011
Same network, different behaviors
Since TinkerCell decouples the notion of a "biological network", or system, from the actual mathematical model, it is possible to generate multiple models of the same system. The screenshot below is of an enzyme with two states, enz1 and enz2. Both states are auto-catalytic. Because of this dual positive feedback, one would guess that the system would become bistable. However, this system is bistable only for certain model implementations. If steady state assumptions are used in the model, then the system is bistable. If mass-action kinetics is used, we see that the intermediate states of the enzyme catalysis process are not really in steady state, and in such models, the bistability also disappears.