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.