Model of the mechanisms of bacterial colonisation of the root tip
Bacterial colonisation of the moving root tip is achieved through mobility of bacterial cells towards root surfaces, and attachment, transportation and proliferation in pools of carbon exudates along the root. This is modelled using 3 coupled transport equations (paper submitted).
We have developped a simulation tools to explore the behaviour of the model. Simulations are performed following the principles of the Smoothed Particle Hydrodynamics methods (SPH). Bacteria colonies are represented as a ensemble of weighted particles, whose position and weight are determined to solve the set of transport equations. The program was implemented in python using the scientific library Numpy, and a graphical interface was constructed to operate the model interactively. Software and source code can be downloaded here