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Open Access Methodology article

Constructing stochastic models from deterministic process equations by propensity adjustment

Jialiang Wu1, Brani Vidakovic2 and Eberhard O Voit23*

Author Affiliations

1 Deparment of Mathematics, Bioinformatics Program, Georgia Institute of Technology, Atlanta, GA30332, USA

2 The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA30332, USA

3 Integrative BioSystems Institute and The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA30332, USA

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BMC Systems Biology 2011, 5:187  doi:10.1186/1752-0509-5-187

Published: 8 November 2011

Abstract

Background

Gillespie's stochastic simulation algorithm (SSA) for chemical reactions admits three kinds of elementary processes, namely, mass action reactions of 0th, 1st or 2nd order. All other types of reaction processes, for instance those containing non-integer kinetic orders or following other types of kinetic laws, are assumed to be convertible to one of the three elementary kinds, so that SSA can validly be applied. However, the conversion to elementary reactions is often difficult, if not impossible. Within deterministic contexts, a strategy of model reduction is often used. Such a reduction simplifies the actual system of reactions by merging or approximating intermediate steps and omitting reactants such as transient complexes. It would be valuable to adopt a similar reduction strategy to stochastic modelling. Indeed, efforts have been devoted to manipulating the chemical master equation (CME) in order to achieve a proper propensity function for a reduced stochastic system. However, manipulations of CME are almost always complicated, and successes have been limited to relative simple cases.

Results

We propose a rather general strategy for converting a deterministic process model into a corresponding stochastic model and characterize the mathematical connections between the two. The deterministic framework is assumed to be a generalized mass action system and the stochastic analogue is in the format of the chemical master equation. The analysis identifies situations: where a direct conversion is valid; where internal noise affecting the system needs to be taken into account; and where the propensity function must be mathematically adjusted. The conversion from deterministic to stochastic models is illustrated with several representative examples, including reversible reactions with feedback controls, Michaelis-Menten enzyme kinetics, a genetic regulatory motif, and stochastic focusing.

Conclusions

The construction of a stochastic model for a biochemical network requires the utilization of information associated with an equation-based model. The conversion strategy proposed here guides a model design process that ensures a valid transition between deterministic and stochastic models.