Theory of Complex Bio-Systems

Course with Participations of Group Members

Offers for Theses in the Group

Growing shapes: Kinetics of integrating cell wall material into the envelope of a growing cell

The aim of this Master thesis is to explore different modes of cell wall growth, which is locally controlled by enzymes but has a global effect on the shape of the cell. Which schemes of enzymatic action permit stably growing cell shapes? And which ones can mimick the observed growth behavior of different bacterial species? These fundamental questions are surpisingly largely open, partially due to the difficulty of experimentally determining which local properties of the cell wall affect the enzymatic activity. In light of this experimental barrier, conceptual theoretical models can classify different plausible schemes by their large-scale behavior, which is more easily observed experimentally. This thesis will combine simulations of stochastic models for growing shapes with simple analytical toy models to address some of the open questions.

suitable as

• Master’s Thesis Biophysics

Supervisor: Ulrich Gerland

Simulating the collective motion of encapsulated enzymes in external substrate gradients

Recent experiments revealed that the diffusion coefficients of enzymes can depend on the concentration of their corresponding substrates: the enzyme diffuses faster in the presence of more substrate. The aim of this thesis is to understand the consequences of this effect on the collective motion of enzymes. Imagine a vesicle immersed in a substrate gradient and loaded with thousands of units of a specific enzyme. What would happen to this vesicle? Would the non-uniform motion of the enzymes inside affect the shape of the vesicle? And what kind of deformations could be produced? Would it be possible to cause the movement of the vesicle along a preferred direction? To tackle these questions, you will be involved in the implementation of Brownian dynamics simulations combining a mesh description of the vesicle, the diffusion-dependent movement of enzymes and the interactions between the enzymes and the vesicle. With this work you can contribute to some of the latest developments in enzyme dynamics and active matter. Moreover, your results can be utilized to design and analyze experiments. Prerequisites: Interest in biophysical systems and in simulations of dynamical systems.

suitable as

• Master’s Thesis Biophysics

Supervisor: Ulrich Gerland

Studying the bacterial life cycle and morphology using flow cytometry

The flow cytometer is an optical device that can measure cell properties at a single cell level with a high throughput. The aim of this Master thesis is to explore the dynamics of bacterial populations using flow cytometry to address the following questions: How does a cell population change at the onset of growth arrest? What are the dynamics of cellular viability during starvation? Do bacteria uniformly die under starvation or are there growing subpopulations? Can one accurately infer morphological information from flow cytometry data? How can cell dynamics under starvation be modeled with the help of stochastic processes?

suitable as

• Master’s Thesis Biophysics

Supervisor: Ulrich Gerland

Current and Finished Theses in the Group