E. coli Colony Simulation

This simulation places a whole-cell E. coli model — with 55 biological processes including metabolism, transcription, translation, DNA replication, and chromosome segregation — inside a 2D colony alongside simpler surrogate cells.

Each whole-cell E. coli is implemented as an EcoliWCM process — a process-bigraph Process that holds an internal Composite connected via a bridge. The bridge maps external colony ports (mass, length, volume) to internal whole-cell stores. The whole-cell model (v2ecoli) runs the full mechanistic simulation of intracellular biology, while the colony framework (pymunk-process) handles spatial physics: cell body collisions, growth-driven elongation, and division mechanics.

The green cell is the whole-cell E. coli — its length and mass are driven by the internal biological simulation. The grey cells are surrogate cells using a simple adder growth model. When the whole-cell model reaches its division threshold (~702 fg dry mass, ~42 min), the bridge removes the mother cell and adds two daughter cells, each with a fresh copy of the whole-cell model. Daughters are shown with color-shifted variants of the mother’s green.