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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
Geometrie eines weißen Rauchers

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 data generated in William Orsi’s lab at LMU. Data will be translated into smoker topology to calculate flows through the smoker. You will learn Matlab, Image Analysis and the fluid physics of laminar flow in flow networks. Prerequisites: Statistical Physics and fascination for the marvels of nature.

suitable as
  • Bachelor’s Thesis Physics
Supervisor: Karen Alim
Source of energy for a gigantic cell

Where does the energy for the gigantic cell Physarum polycephalum come from? Physarum is a giant unicellular organism, that can grow up to centimeter-size. The organism behaves intelligently and makes decisions through peristaltic pumping, which drives efficient transport of signals and nutrients throughout Physarums body. To supply every part of its large cell body with energy, it needs a huge number of mitochondria (the powerhouse of the cell). You will develop an assay to clarify the appearance of these organelles using fluorescence microscopy and spectrometry. Moreover, you will get the chance to image the organism and find out where the mitochondria are hidden and how many are there. With that, you might be able to set the foundation for important assumptions about the energy the organism consumes. Prerequisities: Curiosity on how cell biology goes hand in hand with physics and a fascination for uncovering the beauty of nature under the microscope.

suitable as
  • Bachelor’s Thesis Physics
Supervisor: Karen Alim


Encoding memory in tube diameter hierarchy of living flow network
Mirna Kramar (author), Karen Alim (author)
journal article
Proceedings of the National Academy of Sciences
DOI: 10.1073/pnas.2007815118
Tissue-wide integration of mechanical cues promotes effective auxin patterning
João R. D. Ramos (author), Alexis Maizel (author), Karen Alim (author)
journal article
The European Physical Journal Plus
DOI: 10.1140/epjp/s13360-021-01204-6
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

further publications (total of 31).

See ORCID profile of Karen Alim as well.

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