Discrete modeling


What: Predict the behavior of cells based on the pathways investigated. EGFR and FAS-apoptotic pathways have been simulated.

Why: The simulation of biochemical interactions within a living cell is itself not a new idea. The literature is rife with various simulators and models, focusing often on small sets of local sub-cellular processes. While these simulations are intriguing, there is a necessity for large scale whole cell simulation. Accounts may vary, but scientists generally put the number of possible interactions in the hundreds of thousands. So, the question remains: how can one feasibly simulate the biochemical evolution of an entire cell?
Simulated reaction Employing systems of ordinary differential equations (ODEs) to model biological phenomena leaves much to be desired, since these techniques are inherently deterministic and continuous - i.e., based on concentrations instead of multiplicities of molecules. Because of this, they fail to capture the discrete nature of actual biological situations. In contrast to ODEs, Gillespie developed the Direct Method (DM) and the First Reaction Method (FRM) in the late seventies.
We have chosen to explore an alternative method to biochemical modeling. Our approach draws upon the emerging field of membrane systems computing. Simply stated, we are further developing/refining an algorithm which is (a) faster than the Gillespie approach, and yet is (b) discrete and nondeterministic, which we argue is more sensitive to biological situations than deterministic ordinary differential equations. With (a) and (b), our algorithm is somewhere between the standard ODE and Gillespie techniques.