Stochastic modeling of cytoplasmic reactions in complex biological systems

The use of "in silico" stochastic event based modeling can identify the dynamic interactions of different processes in a complex biological system. This requires the computation of the time taken by different events in the system based on their biological functions. One such important event is the reactions between the molecules inside the cytoplasm of a cell. We present a mathematical formulation for the estimation of the reaction time between two molecules within a cell based on the system state. We derive expressions for the average and second moment of the time for reaction to be used by our stochastic event-based simulation. Unlike rate equations, the proposed model does not require the assumption of concentration stability for multiple molecule reactions.