Analysis of Goldbeter-Koshland Switch Using the Chemical Master Equation

The chemical master equation is considered as an accurate description of general chemical systems, and especially so for modeling gene regulatory networks and protein-protein interaction networks. This paper examines some “off-the-shelf” numerical approaches to solve the chemical master equation for the Goldbeter-Koshland switch on both sequential and parallel machines. The numerical results show that for moderate sized problems, some numerical approaches perform better than MonteCarlo algorithms. However, to solve even larger models more efficiently, special approximation techniques at the model/numerical level may be required. Numerical methods for the steady state solutions are also discussed here.