An agent-based model of the lac operon

The lactose (lac) operon is a prototypical gene regulatory system. This thesis describes a three-dimensional, agent-based, visual computer model of the lac operon. The reader is provided with relevant background knowledge from the fields of molecular biology, agent-based systems, and computer graphics, followed by a description of the model construction. The model simulates important structures and events of the lactose operon in a cell environment. Cellular elements, such as RNA polymerase, messenger RNA, synthesized proteins, etc., are represented by independent, situated agents with physical properties, acting in a decentralized fashion. From interactions of the agents emerge observable and measurable, complex real-time dynamics of the modelled system. A running simulation can be viewed in 3-D on a computer screen or stereoscopic 3-D in the CAVERTM virtual immersive environment, potentially serving as a valuable teaching and experimental tool.