Modeling and simulation of bacterial biofilms

Zusammenfassung

The present thesis focus its efforts on developing a mathematical and experimental modelization of bacterial biofilms: bacterial colonies embedded into a polysaccharid matrix with a high resistance against removal processes, which result in a recurrent source of problems in other disciplines (medicine, engineering, etc). The behaviour of these organisms is highly dependant of the physical system in which they are present. So different case studies are faced here to show their complexity. First the dynamics of biofilms in straight ducts is studied. Experiments are performed to obtain statistics about spreading patterns, and a hybrid model (combining a discrete approach for bacterial population with stochastical behaviour rules and a continuum description of outer fields ruling those probabilities) is presented to simulate the biofilm dynamics, obtaining a successfully prediction of the different patterns observed in real experiments (at layers, ripples, streamers, mounds). This part is completed by providing an alternative continuum description of the biofilm dynamics (by deducing a lubrication equation) and extending the scope of the model to the formation of biofilm streamers inside a corner flow, where biomass adhesion mechanism become relevant. Streamers cross the channel joining both corners as observed experimentally. Additionally this thesis also includes a description of more complex dynamics observed in biofilms. An experimental description of biofilm dynamics under pulsatile flows at low Reynolds numbers show spiral patterns not reported yet, supported by a theoretical mechanism of formation based on the competence between flow dynamics and nutrient gradients. Quorum Sensing and differentiation mechanisms are also incorporated in a hybrid model to describe other kind of biofilms developed onto an agar-air interface, allowing similar geometries and cell distributions as in experiments reported previously. ---------------------------------------------------------------------------------------------------------------------------------------