Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework

Table 1

Agents, behavioural rules, and interacting agents.

Agent	Rules	Interacts with
Enzyme (apoenzyme)	Moving and binding	Metabolite and cofactor
Metabolite	Moving, binding, and death	Enzyme-cofactor complex
Cofactor	Moving, binding, and reconverting	Enzyme and cell membrane
Enzyme-cofactor complex (holoenzyme)	Moving, reaction, and decoupling	Metabolite
Obstacle	Preventing movement	All agents in movement