Specification and Simulation of Synthetic Multicelled Behaviors

• DOI: 10.1021/sb300034m
• Publication Date: 2012-07-23T19:42:05Z
• Authors: Seunghee S. Jang; Kevin T. Oishi; Robert G. Egbert; Eric Klavins
• Keywords: 0303 health sciences; 03 medical and health sciences; Escherichia coli; Computer Simulation; Gene Regulatory Networks; Synthetic Biology; Models, Biological; Algorithms; Software; Signal Transduction; 3. Good health

Recent advances in the design and construction of synthetic multicelled systems in E. coli and S. cerevisiae suggest that it may be possible to implement sophisticated distributed algorithms with these relatively simple organisms. However, existing design frameworks for synthetic biology do not account for the unique morphologies of growing microcolonies, the interaction of gene circuits with the spatial diffusion of molecular signals, or the relationship between multicelled systems and parallel algorithms. Here, we introduce a framework for the specification and simulation of multicelled behaviors that combines a simple simulation of microcolony growth and molecular signaling with a new specification language called gro. The framework allows the researcher to explore the collective behaviors induced by high level descriptions of individual cell behaviors. We describe example specifications of previously published systems and introduce two novel specifications: microcolony edge detection and programmed microcolony morphogenesis. Finally, we illustrate through example how specifications written in gro can be refined to include increasing levels of detail about their bimolecular implementations.