Simulation software of biofilms based on our extension to the Immersed Boundary Method. To run simulations, use RunSimulation.m. Requires access to data file for initial bacteria coordinates.
Note: the Analyze_Data2D does not return the right results. Instead, use the following matlab commands:
[t,m]=max(fStrain); %or min
[t2,m2]=max(v0visc0/charLengthvShear-eShear); %or min
delta=(t-t2)wdt;
G1=m2/m*cos(delta);
G2=m2/m*sin(delta);