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Prof. Dr. rer. nat. Karen Alim

Photo von Prof. Dr. rer. nat. Karen Alim.
+49 89 289-12192
PH: 3027
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Theory of Biological Networks
Job Title
Professorship on Theory of Biological Networks

Courses and Dates

Offered Bachelor’s or Master’s Theses Topics

Biophysik der Nahrungsaufnahme im Darm

The gut microbiota has a direct impact on health, influencing how the gut digests nutrients. The microbiota itself and the nutrients are influenced by the gut contractions and the fluid flow produced by them. How do different contractions influence the dispersal of bacteria and nutrients? You will simulate the fluid flows and particle dispersal in a contracting tube (possible methodologies: COMSOL, Matlab, C, etc.). The aim is to quantify which type of contraction mixes the nutrients and the bacteria better, helping to understand the basic principle behind gut functioning.

suitable as
  • Master’s Thesis Condensed Matter Physics
  • Master’s Thesis Biophysics
  • Master’s Thesis Applied and Engineering Physics
  • Master’s Thesis Biomedical Engineering and Medical Physics
  • Master’s Thesis Matter to Life
  • Master’s Thesis Theoretical and Mathematical Physics
Supervisor: Karen Alim
Ordnung im lebendigen Strömungsnetzwerken

Der intelligente Schleimpilz Physarum polycephalum ist dafür bekannt, dass er seinen netzförmigen Körper anpasst, um komplexe Probleme zu lösen, wie z.B. den kürzesten Weg durch ein Labyrinth zu finden oder das Problem des Handlungsreisenden zu lösen. Wie kann ein hirnloses Lebewesen solch komplexe Aufgaben bewältigen? Unsere Antwort: mit Hilfe der Physik von Strömungsnetzen. Finde heraus, wie Physarum sein Netzwerk anpasst, indem Du seine Netzwerkarchitektur quantifizierst und nach Skalierungsgesetzen suchst. Vorraussetzung: Statistische Physik. Zu verwendende und zu erlernende Werkzeuge: Matlab-Programmierung, Physik von laminaren Strömungen in Netzwerken, möglicherweise auch Zellkultur- und Hellfeldmikroskopie.

The smart slime mould Physarum polycephalum is renowned for adapting its network-shaped body to solve complex problems like finding the shortest path through a maze or solving the traveling salesman problem. How can a brainless critter accomplish such complex tasks? Our answer: by using the physics of flow networks. Find out how Physarum adapts its network by quantifying its network architecture searching for scaling laws in flow networks. Prerequisite: Statistical Physics. Tools to be used and learned: Matlab programming, physics of laminar flows in networks, potentially also cell culture and brightfieqld microscopy.

suitable as
  • Bachelor’s Thesis Physics
Supervisor: Karen Alim
Smoke in a white smoker

White smokers are likely the cradle of life. Their pores and tunnels allow for pockets of catalytic sites that fuel reactions at the very origin of life. How do these catalytic sites form and grow with the smoker? You will map out the structure of two-dimensional smoker models generated in William Orsi’s lab at LMU. You will then use your maps to simulate the flow and transport of reactants with the flow through the smoker. Methods: Matlab, Image Analysis, Statistical Physics, Stochastic Processes, Fluid Physics. Prerequisites: Statistical Physics and fascination for the marvels of nature.

suitable as
  • Master’s Thesis Condensed Matter Physics
  • Master’s Thesis Biophysics
  • Master’s Thesis Applied and Engineering Physics
  • Master’s Thesis Matter to Life
  • Master’s Thesis Theoretical and Mathematical Physics
Supervisor: Karen Alim


Emergence of behavior in a self-organized living matter network
Philipp Fleig (author), Mirna Kramar (author), Michael Wilczek (author), Karen Alim (author)
DOI: 10.1101/2020.09.06.285080
Living System Adapts Harmonics of Peristaltic Wave for Cost-Efficient Optimization of Pumping Performance
Felix K. Bäuerle (author), Stefan Karpitschka (author), Karen Alim (author)
journal article
Physical Review Letters
DOI: 10.1103/PhysRevLett.124.098102
Robust Increase in Supply by Vessel Dilation in Globally Coupled Microvasculature
Felix J. Meigel (author), Peter Cha (author), Michael P. Brenner (author), Karen Alim (author)
journal article
Physical Review Letters
DOI: 10.1103/PhysRevLett.123.228103
Tissue-wide integration of mechanical cues promotes efficient auxin patterning
João R. D. Ramos (author), Alexis Maizel (author), Karen Alim (author)
DOI: 10.1101/820837
The emergent Yo-yo movement of nuclei driven by collective cytoskeletal remodeling in pseudo-synchronous mitotic cycles
DOI: 10.1101/662965
Order parameter allows classification of planar graphs based on balanced fixed points in the Kuramoto model
journal article
Physical Review E
DOI: 10.1103/physreve.99.052308
ISSN: 2470-0045
ISSN: 2470-0053
Controlling effective dispersion within a channel with flow and active walls
ARXIV: arXiv:1901.03697v1
Oscillatory fluid flow drives scaling of contraction wave with system size
Jean-Daniel Julien (author), Karen Alim (author)
journal article
Proceedings of the National Academy of Sciences
DOI: 10.1073/pnas.1805981115
Flow rate of transport network controls uniform metabolite supply to tissue
Felix J. Meigel (author), Karen Alim (author)
journal article
Journal of The Royal Society Interface
DOI: 10.1098/rsif.2018.0075
Fluid flows shaping organism morphology
Karen Alim (author)
journal article
Philosophical Transactions of the Royal Society B: Biological Sciences
DOI: 10.1098/rstb.2017.0112

further publications (total of 29).

See ORCID profile of Karen Alim as well.

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