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Prof. Dr. rer. nat. Karen Alim

Photo von Prof. Dr. rer. nat. Karen Alim.
Phone
+49 89 289-12192
Room
EG.036
E-Mail
k.alim@tum.de
frauenbeauftragte@ph.tum.de (Equal Opportunity Officer of the Physics Department)
Links
Homepage
Page in TUMonline
Group
Theory of Biological Networks
Job Titles

Courses and Dates

Title and Module Assignment
ArtSWSLecturer(s)Dates
Advanced Statistical Physics
eLearning course
Assigned to modules:
VO 4 Alim, K. singular or moved dates
Current Developments in Physics of Biological Networks
Assigned to modules:
HS 2 Alim, K. singular or moved dates
Exercise to Advanced Statistical Physics
Assigned to modules:
UE 2
Responsible/Coordination: Alim, K.
dates in groups
Journal Club Biological Physics and Morphogenesis
Assigned to modules:
SE 2 Alim, K. 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
Our gut moves, and it matters
Our gut is the center of food absorption. However, the gut is not just a still tube: its walls contract to produce fluid flows that propel the food onward and mix it. Indeed, our gut varies the contraction patterns during the day; the fluid characteristics like viscosity and rheological properties may also vary during the day due to the food content. However, it is not entirely clear yet how these different elements vary the food transport. Therefore, you will investigate how different contraction patterns and different fluid characteristics (Newtonian and non-newtonian fluids) change the flow. You will additionally study how this impacts the transport of nutrients. You will learn about fluid flows and transport, Comsol. Prerequisites: differential equations Task 1 Implement in Comsol contracting walls with specific contraction patterns with Comsol package “Deformed Geometry (dg)” Task 2 Calculate the corresponding fluid flow for different viscosities and fluid types Task 3 Calculate solute distribution with the “Transport of Diluted Species in Porous Media (tds)” package and compare it to previous work from the group and literature
suitable as
  • Bachelor’s Thesis Physics
Supervisor: Karen Alim

Publications

Changing Flows Balance Nutrient Absorption and Bacterial Growth along the Gut
Agnese Codutti (author), Jonas Cremer (author), Karen Alim (author)
2022-09-23
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)
2022-07-06
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)
2022-02-18
other
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)
2021-12-30
other
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)
2021-04-30
other
DOI: 10.1101/2021.04.29.441915
Encoding memory in tube diameter hierarchy of living flow network
Mirna Kramar (author), Karen Alim (author)
2021-03-09
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)
2021-02
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)
2020-09-08
other
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)
2020-03-05
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)
2019-11-26
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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