FIGURE 1.

Multi-agent modeling can support the design of emergent collective functions in synthetic biology. (A) Key components of a multi-agent model. Populations of autonomous agents following user-prescribed rules are placed in a virtual environment that simulates relevant physical processes (e.g., physical collisions, chemical diffusion, movement, and fluid flows). Simulations of multi-agent models can be used to derive design principles that capture the basic ingredients (e.g., specific patterns of interactions) needed for a particular emergent behavior. (B) Potential applications of multi-agent modeling within synthetic biology and the underlying agents (bottom, dashed boxes) used to generate specific emergent collective behaviors: (top left) exploring how to create life-like behaviors from basic chemical components with sender protocells (blue) able to spatially propagate a signal to receiver protocells and bacteria (gray when inactive, red when active) using a small diffusive chemical (small blue dots); (top middle) understanding the developmental programs used during morphogenesis as a step toward the creation of synthetic multi-cellular life; (top right) improving scale-up of microbial fermentations by accounting for heterogeneity across a bioreactor and designing engineered microbes able to robustly function under these conditions.