Theory of Complex Bio-Systems

Course with Participations of Group Members

Offers for Theses in the Group

Pattern formation and regeneration in cell layers

Pattern formation in cell layers is experimentally studied in both biological and synthetic systems. For instance, in developmental biology, the correct relative positioning of different cell types is essential to ensure that the organism functions correctly. This project will explore some of the underlying physical concepts with a theoretical approach. Whilst many models for pattern formation exist, the focus here is on cellularized systems with interactions only between neighboring cells. This form of communication has previously received less attention from theoretical research than e.g. long-range diffusible signals as a means of communication. Our goal is to explore fundamental limits and patterning concepts with a simple top-down model based on cellular automata. Building on previous work, the project will concentrate on exploring mechanisms of pattern formation with the goal of investigating how cell division and cell death can influence pattern formation in tissues and how tissue regeneration following damage can be achieved. Successful work on this project requires some background in the concepts and methods of statistical physics, as well as skills in computational problem solving.

suitable as

• Bachelor’s Thesis Physics

Supervisor: Ulrich Gerland

Interplay of mechanics and information processing in cell tissues

A common theme in developmental biology and useful feature for synthetic systems is the coupling of patterning processes (cell differentiation) with mechanical processes and cell growth and death. Understanding the interplay of these different processes is crucial to be able to explain development, as well as to manipulate pattern formation processes in  synthetic systems. In this thesis, a well-known model of tissue dynamics will be implemented and coupled to intercellular signaling dynamics in order to answer questions about the stability and robustness of the pattern creation process and the role of initial and boundary conditions. Of particular interest will be the study of feedbacks between the ‘mechanics’ and the ‘information processing’ in these systems.

suitable as

• Master’s Thesis Biophysics
• Master’s Thesis Applied and Engineering Physics
• Master’s Thesis Theoretical and Mathematical Physics

Supervisor: Ulrich Gerland

Pattern formation based on short-range communication between cells

Pattern formation in cell layers is experimentally studied in both biological and synthetic systems. For instance, in developmental biology, the correct relative positioning of different cell types is essential to ensure that the organism functions correctly. This project will explore some of the underlying physical concepts with a theoretical approach. Whilst many models for pattern formation exist, the focus here is on cellularized systems with interactions only between neighboring cells. This form of communication has previously received less attention from theoretical research than e.g. long-range diffusible signals as a means of communication. Our goal is to explore fundamental limits and patterning concepts with a simple top-down model based on cellular automata. Building on previous work, the project will concentrate on investigating how the interaction range between cells can influence the ability to realiably create typical biological patterns such as a heterogeneous stripe-pattern. Successful work on this project requires some background in the concepts and methods of statistical physics, as well as skills in computational problem solving.

suitable as

• Bachelor’s Thesis Physics

Supervisor: Ulrich Gerland

Current and Finished Theses in the Group