Fig. 1: A detailed, holistic model of growth rate control has been incorporated into the E. coli Whole-Cell Modeling Project.

a A schematic representing biological functions and regulation that link the environment to growth. Black arrows represent mass flow, red arrows indicate regulatory inhibition and green arrows represent activation. b A schematic illustrating the integration of the biological functions in (a) in the context of the E. coli whole-cell model by including regulatory interactions and kinetic reaction rates. Such integration allows the growth rate to be determined by the simulation state, which is responsive to the simulated environment of interest. Dashed lines represent the link between the new mathematical representations and existing modeling processes that were modified. The resulting model includes more gene functions, accounts for the action of more small molecules, and can accommodate simulations in more environments.