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Theory of Biological Networks

Prof. Karen Alim

Research Field

Life is mesmerizing. How does shape and structure emerge when organism grow? We want to identify the physics that are underlying the morphing of life. Physical forces are eminent for pushing and squeezing living matter as it morphs into life. Observing the physical forces that arise from cell mechanics or fluid flows is key to understand how these physical forces generate and transport information - information that is read out by living matter and feeds back onto its dynamics but also its physical properties itself, thus morphing structures, organs and organisms. To succeed we combine quantitative observation of life with theoretical models to finally capture the key processes in simple mathematical terms. Here, it is important to choose experimental model systems that are particularly good for observation and quantification but also provide an accessible level of abstraction for theory. That is why we work with the slime mould Physarum polycephalum and at the same time built in vitro model systems in the lab. Theoretical models developed both with pen and paper and simulations in the group both inspire experiments and explain observations. Life still hides many fundamental processes that once uncovered can revolutionize our designs, engineering or medical treatment.


James-Franck-Str. 1/I
85748 Garching b. München

Members of the Research Group





Other Staff


Course with Participations of Group Members

Offers for Theses in the Group

In vitro and in silico assessment of the microvascular network under fluid flow
Blood vessels deliver oxygen and necessary nutrients to all tissues in the body. During embryonic development, formation of the first primitive vascular labyrinth though vasculogenesis is followed by vascular network expansion and maturation through angiogenesis. The latter comprises formation of new blood vessels out of pre-existing ones and the subsequent vascular remodeling in order to adapt the vascular network to the specific metabolic demands of the surrounding tissue. Onset of blood flow into the primary vascular network is known for having major impacts on vascular remodeling ensuring the network’s efficiency through structural normalization and hierarchy. Owing to the fact that vessel remodeling is often found impaired in pathological angiogenesis, many therapeutic methods have been developed to interfere with the vessel growth and normalization strictly affecting vascular morphology. However, the exact correlation between vessel morphological variations and alterations in blood flow dynamics has not been fully elucidated. Moreover, while many animal models have been developed to assess the effect of blood fluid flow on vascular morphology, translating their outcomes to human vascular system is often challenging. Employing the recent state-of-the-art microfluidic techniques for human organ-on-a-chip developments, one can grow perfusable human capillaries on polymeric chips for direct investigation of vascular structural development under flow through real time observations. Taking advantage of our in-house established human microvasculature on PDMS chip models, this project is aimed to assess the impact of fluid flow on the microvascular network architecture and vessel caliber. You will be working with 2D network image datasets analysing the microvascular structural remodeling in response to the fluid flow.
suitable as
  • Master’s Thesis Biomedical Engineering and Medical Physics
Supervisor: Karen Alim
Coordinating information within a non-neural organism
The smart slime mould Physarum polycephalum is renowned for its ability to solve complex problems - lacking any brain nor organising center. Instead the giant cell that makes up the entire organism houses thousands of nuclei that altogether control the organisms behaviour. How do nuclei interact to mount behaviour? Do they compete, cooperate or happily ignore each other? You will follow nuclei dynamics with fluorescence microscopy during the organism’s response to an environmental challenge. Quantification of individual nuclei trajectories will inform you if nuclei act individually or cooperatively during behavioural response. You will have the opportunity to discuss your findings with biologists and applied mathematicians throughout your project.
suitable as
  • Master’s Thesis Biophysics
Supervisor: Karen Alim
Structures for the Origin of Life

Weiße Raucher sind wahrscheinlich die Wiege des Lebens. Ihre Höhlen und Tunnel ermöglichen es Reaktanten an katalytischen Stellen anzusammeln, um damit die Reaktionen am Ursprung des Lebens in Gang setzen. Wie entstehen und wachsen diese katalytischen Stellen mit dem Smoker? Sie werden zweidimensionalen Smoker auf einem Mikrofluidik-Chip wachsen lassen und aus Ihren Daten die Rauchergeometrie vermessen und damit Strömung und Transport im Netzwerk berechnen und mit Ihren Daten vergleichen. Sie lernen Mikrofluidik, Mikroskopie, Matlab, Bildanalyse und die Strömungsphysik der laminaren Strömung in Strömungsnetzen kennen. Voraussetzungen: Statistische Physik und Faszination für die Wunder der Natur.

suitable as
  • Master’s Thesis Applied and Engineering Physics
Supervisor: Karen Alim

Current and Finished Theses in the Group

Principles of Optimal Heat Transport in Snakes
Abschlussarbeit im Masterstudiengang Physics (Applied and Engineering Physics)
Themensteller(in): Karen Alim
Controlling Physarum Polycephalum Using Pattern Illumination
Abschlussarbeit im Bachelorstudiengang Physik
Themensteller(in): Karen Alim
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