Abstract

We present a position-based dynamics model for microcolony growth. In addition to achieving fast and stable simulation of thousands of cells, this model allows for the computation of cell interaction with the environment without sacrificing robustness and predictability. We introduce state-of-the-art principles of synthetic biology into our framework to enable biologically-informed microcolony pattern formation. We give detailed implementation of growth, communication, and external influences within the system and demonstrate our method for several scenarios which are experimentally verified. Finally, we provide a use case for rapid simulations enabled through our method including parameter search for tuning spoke-based pattern formation utilizing predefined and formulated biological primitives.

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