Bronstein-1

Numerical comparison of moment closure methods for chemical kinetics

Description

The dynamics in cells are routinely described within the continuous-time Markov chain framework. Unfortunately, numerical methods for dealing with these models are infeasible for many realistic settings. A common approach to deal with this are moment equations. These in turn require the use of moment closure techniques, of which several have been proposed in the literature.

The goal of this thesis project is to implement the various existing methods and perform a systematic numerical evaluation of their approximation accuracy. This will involve selecting a representative set of example models, choosing comparison criteria and planning the numerical experiments.

Experience with MATLAB advantageous.

Literature

Gillespie, Colin S. „Moment-closure approximations for mass-action models.“ IET systems biology 3.1 (2009): 52-58.

Ale, Angelique, Paul Kirk, and Michael PH Stumpf. „A general moment expansion method for stochastic kinetic models.“ The Journal of chemical physics 138.17 (2013): 174101.

Barzel, Baruch, and Ofer Biham. „Binomial moment equations for stochastic reaction systems.“ Physical review letters 106.15 (2011): 150602.

Contact

Leo Bronstein