Simulation of flow through corrguated channels and calculation of bacterial adhesion rates for paper: 'Bacterial adhesion to curved surfaces in flow'

Authors: Edwina Yeo Date: 02/06/26

Dependencies: Versions used: Python 3.12.4, Matlab R2023b, Inkscape for combining figures and creating diagrams Packages and toolboxes: python: Matlotlib, numpy, os, argparse, Fenics legacy version 2019.1.0, GMSH Details of how to install: legacy fenics - https://fenicsproject.org/download/archive/, GMSH: https://gmsh.info.

To create stokes flow data bash processing script 'run.sh' should be run. An empty '/data' storage folder should be made.
Scripts:

1. stokes-flow.py: Python script which solves the stokes flow problem for input wall parameters lambda and A, saves wall shear rate, flow solutions and wall boundary in in .txt format
2. run.sh: runs stokes-flow.py for a variety of wall parameters.
3. plotting.m: uses stokes flow solutions and evaluates analytical adhesion rate to create figures.
4. fig1.svg and fig2.svg are paper figures/sketches combined in pdf form.