Agent-based Modeling and Simulation of Biomolecular Reactions

Abstract

We present an agent-based, three-dimensional model of phage lambda, a virus infecting E. coli which exhibits two phases, lysogenic and lytic. This process is useful for bio-based sensors or switches and is a widely studied gene regulatory system. We model system constituents as software agents. Complex system behavior emerges from local agent interactions. Agent-based modeling lets us study how individual parameters affect overall system behavior. This bottom-up approach is an alternative to top-down approaches using differential equations and stochastic simulation. It can model any system of biomolecular reactions, with applications in physiology, pharmacology, medicine, environmental monitoring, and homeland security.