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Prof. Dr. rer. nat. Karen Alim

Photo von Prof. Dr. rer. nat. Karen Alim.
Phone
+49 89 289-12192
Room
CPA: 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

Offered Bachelor’s or Master’s Theses Topics

Höhlen für den Ursprung des Lebens

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. 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
  • Bachelor’s Thesis Physics
Supervisor: Karen Alim
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
Koordinierung von Informationen innerhalb eines nicht-neuralen Organismus
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
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
Strukturen für den Ursprung des Lebens

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 Condensed Matter Physics
Supervisor: Karen Alim
Wie Adern wachsen und sich anpassen
Unser Adernetzwerk ist wichtig um Sauerstoff und andere wichtige Ressourcen in unserem Körper zu transportieren. Dabei ist unser Adernetzwerk nicht statisch sonder passt sich in seiner Struktur, in der Dicke einzelner Adern fortwährend an. Welche Gesetzmäßigkeiten folgt die Dynamik einzelner Adern? Welche Rolle spielt dabei die Strömung in den Adern? Du wirst Daten von Adernetzwerken auf einem Mikrofluidik Chip analysieren, um die Dynamik der Adern quantitativ zu erfassen. Dazu entwickelst Du Bildanalyseverfahren weiter und passt sich auf unsere ganz neuen Daten von Adern an. Neben der Bildanalyse bekommst Du auch Einblick in in vitro Techniken und Mikrofluidiktechniken.
suitable as
  • Bachelor’s Thesis Physics
Supervisor: Karen Alim
Wie koordiniert man Verhalten ohne ein organisierendes Zentrum?
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
  • Bachelor’s Thesis Physics
Supervisor: Karen Alim

Publications

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
Tissue-wide integration of mechanical cues promotes efficient auxin patterning
João R. D. Ramos (author), Alexis Maizel (author), Karen Alim (author)
2019-10-28
other
DOI: 10.1101/820837
The emergent Yo-yo movement of nuclei driven by collective cytoskeletal remodeling in pseudo-synchronous mitotic cycles
2019-06-06
other
[]
URL: http://dx.doi.org/10.1101/662965
DOI: 10.1101/662965
Order parameter allows classification of planar graphs based on balanced fixed points in the Kuramoto model
2019-05-23
journal article
Physical Review E
URL: http://dx.doi.org/10.1103/physreve.99.052308
DOI: 10.1103/physreve.99.052308
ISSN: 2470-0045
ISSN: 2470-0053
Controlling effective dispersion within a channel with flow and active walls
2019-01-08
other
ARXIV: arXiv:1901.03697v1

further publications (total of 32).

See ORCID profile of Karen Alim as well.

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