Agent-based Modeling and Simulation of Biomolecular Reactions
Vaishali Vallurupalli, Carla Purdy · 2001
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. 1.