Computational Modeling of Bacterial Dynamics and Biofilm Formation
AUTHOR: Kartik Jain1, Christoph Lohrmann1, and Christian Holm1
1Institute for Computational Physics, University of Stuttgart, Germany
BACKGROUND: Microorganisms like bacteria show interesting dynamics as they can propel, proliferate and aggregate in a number of mediums. In addition to being self-propelled, some bacteria can adhere to each other and to surfaces where they can create fast growing colonies, called biofilms. Studies have demonstrated that bacteria more commonly accumulate at surfaces and around obstacles that they encounter in their propulsion path. The initiation, growth, and decline of a biofilm depends largely on the flow field, surfaces and the obstacles bacteria encounter in their propulsion path. In this work, we developed a model to study the dynamics of Escherichia Coli (E. Coli) bacteria including their growth, replication, and adherence to surfaces.
METHODS: We represented the E. Coli as rod-shaped objects formed by molecular dynamics (MD) beads. The fluid flow was modeled using a lattice Boltzmann method (LBM). The MD and LBM were coupled using a friction point coupling scheme that ensures momentum conservation. The interactions between MD particles, and those between particles and obstacles were defined by a Lennard-Jones potential. The bacteria were self-propelled and moved under the influence of an external flow-field. Adherence to surfaces was modeled on the basis of residence time in an area, and replication was based on nutritional availability.
RESULTS: Transient dynamics of about 4000 bacteria in a confined geometry demonstrated 92% accuracy in bacterial accumulation in comparison to experiments. The bacteria ephemerally tend to stasis in flow recirculation regions, and this behaviour resulted in their adherence to surfaces, replication, and subsequent formation of a biofilm. The bacteria started replicating after adherence to surfaces thereby growing the mass of the biofilm, which in turn was deteriorated by flows of high shear rates.
DISCUSSION & CONCLUSIONS: The model reproduces the dynamics of E. Coli with a reasonable accuracy. The adherence of bacteria and their replication thereon has interest in many applications. The model is being extended to incorporate chemical reactions wherein we wish to include the deterioration of biofilm through motility of the bacteria. Ongoing work includes application of the model to study infections, and extension to other species like Pseudomonas aeruginosa and Vibrio cholerae.
ACKNOWLEDGEMENTS: The research performed in this work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project number 327154368 – SFB 1313 and the EXC SimTech.