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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
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
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 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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