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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
Links
Homepage
Page in TUMonline
Group
Theory of Biological Networks
Job Title
Professorship on Theory of Biological Networks

Courses and Dates

Offered Bachelor’s or Master’s Theses Topics

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
Stabile Muster die der Strömung widerstehen

Der intelligente Schleimpilz Physarum polycephalum ist dafür bekannt, dass er komplexe Probleme löst, wie z.B. den kürzesten Weg durch ein Labyrinth zu finden. Dabei ist noch nicht einmal klar, wie der Organismus ‘vorne’ und ‘hinten’ in seinem netzwerkförmigen Körper unterscheidet. Kann in dem flüssigen Inneren des Netzwerks trotz starker Strömung ein chemischer Gradient bestehen, der vorne und hinten markiert? In Deinem Projekt untersuchst Du, ob Zellkerne, die chemische Botenstoffe ausschütten, durch ihren Wechsel zwischen festhalten und mitschwimmen in dem Netzwerk einen stabilen chemischen Gradienten erzeugen können. Dazu löst Du die Bewegungsgleichungen der Zellkerne und der Botenstoffe numerisch und quantifizierst unter welchen Bedingungen sich ein Gradient an Botenstoffen einstellen kann. Deine theoretischen Vorhersagen stehen dabei im engen Austausch mit experimentellen Beobachtungen in unserer Arbeitsgruppe.

The intelligent slime mould Physarum polycephalum is known for solving complex problems, such as finding the shortest path through a maze. Yet it’s not even clear how the organism distinguishes ‘front’ and ‘back’ in its network-like body. Can a chemical gradient exist in the fluid interior of the network that marks front and back, despite strong flow pervading the network? In your project, you will investigate whether cell nuclei that secrete chemical messengers can create a stable chemical gradient in the network by alternating between staying fixed and floating along with the flow. To do this, you will solve the equations of motion of the cell nuclei and the chemical messengers numerically and quantify under which conditions a gradient of chemical messengers can occur. Your theoretical predictions are in close exchange with experimental observations in our group.


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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