This repository contains code tutorials that describe the algorithms used in my PhD Thesis "Data-driven modelling of robust Turing patterns in synthetic biofilms". This work was produced under the supervision of Prof. Robert Endres and Prof. Mark Isalan at Imperial College London.
The full thesis document can be found in PhD_thesis.pdf.
The tutorials can be found in different directories:
- Algorithms to find steady states
- Linear stability analysis to study reaction-diffusion PDE systems
- PDE Numerical solvers in 1D (Crank-Nicolson) and 2D (Alternating implicit direction method)
- Cellular automata model for bacterial colony growth
- Sampling of parameters using latin hypercube sampling
- Code parallelisation
- High Performance Computing Cluster access