Simulation code for modeling biofilm cell ejection driven by self-generated hydrogel.
This repository contains the numerical model used in the study:
Self-generated hydrogel locally ejects cells from a biofilm,
Chou et al. (2026)
The code simulates the coupled dynamics of:
- motile cells
- non-motile cells
- hydrogel
- nutrient field
- pressure-driven flow
and reproduces the mechanical ejection (dispersion) of cells from a growing biofilm.
Run Dispersion.ipynb to reproduce the simulations.
The simulation describes a growing biofilm as a compressible active mixture where:
- Cells grow depending on nutrient availability
- Motile cells produce hydrogel
- Hydrogel and growth generate pressure
- Pressure drives flows that advect cells and matrix
- These flows can eject cells from the colony
The model solves coupled PDEs for:
| Field | Meaning |
|---|---|
| ρₘ | motile cell density |
| ρₙ | non-motile cell density |
| h | γ-PGA hydrogel density |
| c | nutrient concentration |
| p | pressure field |
