Stochastic molecular modeling and reduction in reacting systems

Mathematical Biology Seminar
Wednesday, April 7, 2010 - 11:00am for 1 hour (actually 50 minutes)
Skiles 255
Martha Grover – School of Chemical & Biomolecular Engineering, Georgia Tech
Leonid Bunimovich
Individual chemical reactions between molecules are inherently stochastic, although for a large collection of molecules, the overall system behavior may appear to be deterministic. When deterministic chemical reaction models are sufficient to describe the behavior of interest, they are a compact way to describe chemical reactions. However, in other cases, these mass-action kinetics models are not applicable, such as when the number of molecules of a particular type is small, or when no closed-form expressions exist to describe the dynamic evolution of overall system properties. The former case is common in biological systems, such as intracellular reactions. The latter case may occur in either small or large systems, due to a lack of smoothness in the reaction rates. In both cases, kinetic Monte Carlo simulations are a useful tool to predict the evolution of overall system properties of interest. In this talk, an approach will be presented for generating approximate low-order dynamic models from kinetic Monte Carlo simulations. The low-order model describes the dynamic evolution of several expected properties of the system, and thus is not a stochastic model. The method is demonstrated using a kinetic Monte Carlo simulation of atomic cluster formation on a crystalline surface. The extremely high dimension of the molecular state is reduced using linear and nonlinear principal component analysis, and the state space is discretized using clustering, via a self-organizing map. The transitions between the discrete states are then computed using short simulations of the kinetic Monte Carlo simulations. These transitions may depend on external control inputs―in this application, we use dynamic programming to compute the optimal trajectory of gallium flux to achieve a desired surface structure.