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From 2010.igem.org

Open Issues

Debating Questions

Why would stochastic simulation (on the molecular level) be good:
• It sounds more cool than ODE – based models;
• It generally gives (or at least it should give) a more realistic view of the biological process studied;
• Individual complexes could be traced all through the simulation (not sure if we’d ever need that; probably not).

Why would stochastic simulation (on the molecular level) not be of interest:
• In terms of the results, the predicted values of the CheY concentration levels fluctuate around the deterministically obtained ones, with amplitude of fluctuations indirectly proportional to population size (number of molecules).

Existing Stochastic Models

Introduction

StochSim

General

StochSim (Morton-Firth & Bray 1998) is a stochastic program for modeling the intracellular signaling pathway responsible for chemotaxis behavior. Molecules are represented as individual software objects and their interactions are probability - governed (based on empirically - derived distributions of concentrations and kinetic rates).

Algorithm

Molecules are discretely represented, as number of particles and reactions happen probabilistically. At each time step, two molecules are randomly selected and, after this, another random number is generated (used to see if a reaction between the two molecules will occur). The random number is compared to the probability of that particular reaction occurring (value retrieved from a look – up table). If the probability exceeds the random number, the particles don’t react, otherwise, they do and the system is updated accordingly. Both unimolecular and bimolecular reactions are permitted. In the case of the former, a dummy variable, pseudo – molecule, is created. The probabilities for unimolecular and bimolecular reactions happening have fixed formulae, dependent on the rate of unimolecular/bimolecular reactions, the total number of molecules in the system, the time – slice duration, the volume of the system.