From local defects to shear-organized biofilms in tonsillar crypts via computational simulations

Biofilms in human tonsillar crypts show long term persistence with episodic dispersal that current biochemical and microbiological descriptions do not fully explain, particularly with respect to spatial localization. We introduce a biophysical framework in which tonsillar biofilm dynamics arise from the interaction between two mechanical phenomena: a Kosterlitz Thouless type defect nucleation process and a Kelvin Helmholtz type shear driven interfacial instability. Crypt geometry is modeled as a confined, heterogeneous environment that promotes mechanically persistent surface defects generated by growth induced compression. Tangential shear associated with breathing and swallowing selectively amplifies these defects, producing organized surface deformations. Numerical simulations show that only the coexistence of both mechanisms yields localized, propagating, and persistent interface structures, whereas their absence leads to diffuse, unstructured dynamics.