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Prof. Dr. rer. nat. Karen Alim

Photo von Prof. Dr. rer. nat. Karen Alim.
+49 89 289-12192
E-Mail (Equal Opportunity Officer of the Physics Department)
Page in TUMonline
Theory of Biological Networks
Job Titles

Courses and Dates

Title and Module Assignment
Advanced Statistical Physics
eLearning course
Assigned to modules:
VO 4 Alim, K. Tue, 08:00–10:00, PH 1121
Fri, 10:00–12:00, PH 1121
Current Developments in Physics of Biological Networks
Assigned to modules:
PS 2 Alim, K. Wed, 10:00–12:00, CPA EG.006B
Wed, 10:00–12:00, CPA EG.006B
and singular or moved dates
Exercise to Advanced Statistical Physics
Assigned to modules:
UE 2
Responsible/Coordination: Alim, K.
Journal Club Biological Physics and Morphogenesis
Assigned to modules:
SE 2 Alim, K. Thu, 13:00–15:00, CPA EG.006B
and singular or moved dates
Revision Course to Current Developments in Physics of Biological Networks
Assigned to modules:
RE 2
Responsible/Coordination: Alim, K.
Tag der Physikerinnen
current information
Assigned to modules:
KO 0.1 Alim, K. singular or moved dates
Seminar for Tutors in Advanced Statistical Physics
This course is not assigned to a module.
SE 2 Alim, K.

Offered Bachelor’s or Master’s Theses Topics

Active response by adaptation of mechanical properties?

The complex behavior of the giant cell Physarum polycephalum finds its origin in the versatile transformation of liquid cytoplasm to gel-like actin-myosin meshwork making up the tube walls and vice versa. These active mechanics allow the organism to recycle its’ gel-like tubes at its rear and move it in its fluid form to the front, where it grows. Also, responding to stimuli like food, touch, or light, a change in cytoplasm viscosity seems to initiate the response. Yet, what are the mechanical properties of the liquid cytoplasm, and how much do they change upon stimulation? Do the mechanical properties of the cytoplasm change with the location in the cell? The measure of the mechanical properties of cells is challenging, but one can probe their visco-elasticity by tracking injected micron-sized beads - a technique called microrheology. You will measure the mechanical properties of cytoplasm extracts and grown Physarum, and quantify how they change upon stimulation by passive and active microrheology. Task 1: Establish cytoplasm extraction following previous work in the literature. Task 2: Perform passive microrheology on cytoplasmic droplets without and with stimulation (light, food, drugs) and analyze your data quantitatively. Task 3: Establish active microrheology to extract cytoplasm viscosity in different parts of Physarum’s network.

suitable as
  • Bachelor’s Thesis Physics
Supervisor: Karen Alim
Mapping network theory to network function
Networks exist as our social network, the world wide web, traffic routes but also as flow networks making up the vasculature of animals, plants, fungi and slime moulds. While a lot of measures have been developed to describe networks in general it is not clear how these measures are predicting network function via network architecture. You will quantify physical networks of the slime mould and numerically generated model networks with network theoretic measures. Mapping to slime mould behaviour and model network flow and transport function will allow you to identify predictive network theoretic measures. You will learn network theory, Matlab. Prerequisites: statistical physics. Task 1 Collect network theoretic measures from the literature and Matlab packages Task 2 Apply network theoretic measures on slime mould and model data and map their property onto the network architecture Task 3 Correlate link by link network theoretic measure and flow/transport in the link under inspection to identify measures of predictive power.
suitable as
  • Bachelor’s Thesis Physics
Supervisor: Karen Alim


Changing Flows Balance Nutrient Absorption and Bacterial Growth along the Gut
Agnese Codutti (author), Jonas Cremer (author), Karen Alim (author)
journal article
Physical Review Letters
DOI: 10.1103/PhysRevLett.129.138101
Memory Formation in Adaptive Networks
Komal Bhattacharyya (author), David Zwicker (author), Karen Alim (author)
journal article
Physical Review Letters
DOI: 10.1103/PhysRevLett.129.028101
Changing flows balance nutrient absorption and bacterial growth along the gut
Agnese Codutti (author), Jonas Cremer (author), Karen Alim (author)
DOI: 10.1101/2022.02.16.480685
Network architecture determines vein fate during spontaneous reorganization, with a time delay
Sophie Marbach (author), Noah Ziethen (author), Leonie Bastin (author), Felix K. Bäuerle (author), Karen Alim (author)
DOI: 10.1101/2021.12.29.474405
Nuclei are mobile processors enabling specialization in a gigantic single-celled syncytium
Tobias Gerber (author), Cristina Loureiro (author), Nico Schramma (author), Siyu Chen (author), Akanksha Jain (author), Anne Weber (author), Anne Weigert (author), Malgorzata Santel (author), Karen Alim (author), Barbara Treutlein (author), J. Gray Camp (author)
DOI: 10.1101/2021.04.29.441915
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

further publications (total of 36).

See ORCID profile of Karen Alim as well.

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