Abstract:

There are principally two conceptual frameworks in which to model and/or simulate biochemical reaction networks (pathways): a) stochastic simulation of the chemical master equation, derived from the Chapman-Kolmogorov equation and b) mass action type models, employing nonlinear differential equations. I am going to compare these two conceptual frameworks with respect to their mathematical roots and their application to dynamic modeling of signal transduction pathways. Towards this end I am going to derive Gillespie’s stochastic reaction constant.