Eukaryo is a 3D, interactive simulation of a eukaryotic cell. In comparison to existing cell simulations, our model illustrates the structures and processes within a biological cell with increased fidelity and a higher degree of real-time interactivity using a virtual reality environment. Implemented in a game engine, Eukaryo is a hybrid model that combines agent-based and mathematical modelling. Through the use of visual scripting, Eukaryo incorporates both agent-based modelling and mathematical representations to describe gene expression, energy production and waste removal within the cell in a highly visual, interactive simulation environment. With the help of virtual reality displays, users can be immersed in the crowded spaces of biomolecular worlds and observe metabolic reactions at a high level of detail. Compared to traditional media, such as illustrations and videos, Eukaryo offers superior representations of cellular architecture, its components and dynamics of the machineries of life.

We present an interactive, agent-based, multi-scale 3D model of a colony of E. coli bacteria. We simulate chemical diffusion on an agar plate which is inhabited by a colony of bacterial cells. The cells interact with a discrete grid that models diffusion of attractants and repellents, to which the cells react. For each bacterium, we simulate its chemotactic behaviour, making a cell either follow a gradient or tumble. Cell propulsion is determined by the spinning direction of the motors that drive its flagella. In an agent-based model, we have implemented the molecular elements that comprise the two key chemotactic pathways of excitation and adaptation, which, in turn, regulate the motors and influence a cells movement through the agar medium. We show four interconnected model layers that capture the biological processes from the colony layer down to the level of interacting molecules.