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First published July 1 2016

Eukaryo: An Agent-based, Interactive Simulation of a Eukaryotic Cell

Douglas Yuen and Christian Jacob

Abstract (Excerpt)

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.