Deterministic and stochastic dynamics in bacterial systems
Microorganisms form an essential part of our biosphere and represent roughly 14 percent of the biomass on earth. In spite of this abundance, the majority of chemical and physical processes governing the live of microorganisms remain poorly understood. In this work, we focus on three different phe...
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|Summary:||Microorganisms form an essential part of our biosphere and represent roughly 14 percent of the biomass on earth. In spite of this abundance, the majority of chemical and physical processes governing the live of microorganisms remain poorly understood. In this work, we focus on three different phenomena from the realm of microorganisms and aim to explain the physical processes behind them. We examine how the bacterium Shewanella Putrefaciens exploits a mechanical instability to wrap its flagellum around its cell body, effectively forming a screw that allows the bacterium to escape from traps. Based on a numerical model we study the onset of screw formation in dependence of the flagellar geometry and the existence of multiple equilibrium configurations of the flagellum. Furthermore, we study the effects of actively swimming microorganisms on the diffusion of passive tracer particles. By means of a numerical simulation we examine a single swimmer-tracer interaction and use the results to develop a model based on continuous time random walks that captures a series of swimmer-tracer interactions. We derive an analytical expression for the one dimensional probability density function of the tracer displacements and use numerical simulations to approximate the two- and three-dimensional distributions. We then extend the model to include periods of free tracer diffusion between the tracerswimmer interactions and fit this extended model to a number of experimentally observed tracer distributions. In the third part of this work we examine how the cylindrical shape of a bacterium affects the isotropic trajectories of membrane proteins when observed with a microscope. We derive an analytical expression for the anisotropic distribution of the particle displacements when projected in the observation plane and use this result to calculate the mean squared displacement curves. Finally, we use numerical simulations to study the effects of a limited focus depth and to understand the resulting challenges for the estimation of the diffusion coefficients.|
|Physical Description:||102 Pages|