Simulation results for different antibiotic entry conditions.

(A) Untreated microscopy x-slices selected using the quantification algorithm (Sect 4.6 ) to identify protected regions. (B) Initial conditions using (A) as source data. Note that in order for the cells to respond to antibiotic influx an extended vertical domain is required, since the stress distance () is 15 . Therefore, we added an extra 2 layers of uniformly distributed cells with a non-stressed carrying capacity above the complex structures as is seen in microscopy images. (C) Simulation results for scenario 1 (no reaction or diffusion barrier). (D) Simulation results for scenario 2 (diffusion barrier but no reaction barrier). (E) Simulation results for scenario 3 (diffusion and reaction barrier. (F) Post-treatment biofilms exposed to erythromycin for one hour. Note that the initial- and post-treatment biofilms are not the same samples. Scale bar has length 10 . For videos of simulations see supporting information S1 and S2 Video .