Verification of Biochemical Processes Using Stochastic Hybrid Systems

Abstract

Modeling and analysis of biochemical systems are critical problems because they can provide new insights into systems which can not be easily tested with real experiments. One such biochemical process is the formation of sugar cataracts in the lens of an eye. Analyzing the sugar cataract development process is a challenging problem due to the highly-coupled chemical reactions that are involved. In this paper we model sugar cataract development as a stochastic hybrid system. Based on this model, we present a probabilistic verification method for computing the probability of sugar cataract formation for different chemical concentrations. Our analysis can potentially provide useful insights into the complicated dynamics of the process and assist in focusing experiments on specific regions of concentrations. The verification method employs dynamic programming based on a discretization of the state space and therefore suffers from the curse of dimensionality. To verify the sugar cataract development process we have developed a parallel dynamic programming implementation that can handle large systems. Although scalability is a limiting factor, this work demonstrates that the technique is feasible for realistic biochemical systems.