Project for Bachelor or Master thesis

Spatial analysis of cellular signaling dynamics with agent-based modeling

Cellular components move restricted by the actual shape of the cell, which in turn influences dynamic interactions. We are interested in the dynamics of cell signaling and specifically the dynamics of kinase networks. Based on results of a previous project, in this project we want to investigate the dynamics of prototypical signaling pathways such as the EGF signaling in space and time depending on the shape of the cell. To this end, agent-based modeling will be employed using the tool STEPs. You will learn the principles of both spatial modeling and agent-based modeling, will explore the effect of typical cell shapes and investigate general properties of signaling networks such as clustering at membranes, free diffusion, scaffold formation. Together with our cooperation partners from the Institute of Cancer Research (ICR) in London, we also plan to investigate the effect of real 3D cell shapes on EGF/MAPK signaling.

Requirements: Interest in mathematical modeling of cell processes, basic programming skills, interest in challenging biological questions. Given teaching content, biophysics students would have the required background.

Skills you will acquire: Learn how to formulate testable scientific questions. Improve your programming skills, especially in the field of agent-based modeling. Cooperation in an interdisciplinary and international environment.

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