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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
Oscillatory fluid flow drives scaling of contraction wave with system size
Jean-Daniel Julien (author), Karen Alim (author)
2018-10-16
journal article
Proceedings of the National Academy of Sciences
DOI: 10.1073/pnas.1805981115
Flow rate of transport network controls uniform metabolite supply to tissue
Felix J. Meigel (author), Karen Alim (author)
2018-05-31
journal article
Journal of The Royal Society Interface
DOI: 10.1098/rsif.2018.0075
Fluid flows shaping organism morphology
Karen Alim (author)
2018-05-26
journal article
Philosophical Transactions of the Royal Society B: Biological Sciences
DOI: 10.1098/rstb.2017.0112
Mechanical Model of Nuclei Ordering in Drosophila Embryos Reveals Dilution of Stochastic Forces.
Kaiser F (author), Lv Z (author), Marques Rodrigues D (author), Rosenbaum J (author), Aspelmeier T (author), Großhans J (author), Alim K (author)
2018-04
journal article
Biophysical journal
URL: http://europepmc.org/abstract/med/29642041
PMID: 29642041
DOI: 10.1016/j.bpj.2018.02.018
Local Pore Size Correlations Determine Flow Distributions in Porous Media.
Alim K (author), Parsa S (author), Weitz DA (author), Brenner MP (author)
2017-10
journal article
Physical review letters
URL: http://europepmc.org/abstract/med/29053310
PMID: 29053310
DOI: 10.1103/physrevlett.119.144501
Spatial mapping reveals multi-step pattern of wound healing in Physarum polycephalum
Felix K Bäuerle (author), Mirna Kramar (author), Karen Alim (author)
2017-10
journal article
Journal of Physics D: Applied Physics
DOI: 10.1088/1361-6463/aa8a21
ISSN: 0022-3727
Mechanism of signal propagation in Physarum polycephalum.
Alim K (author), Andrew N (author), Pringle A (author), Brenner MP (author)
2017-05
journal article
Proceedings of the National Academy of Sciences of the United States of America
URL: http://europepmc.org/abstract/med/28465441
PMID: 28465441
PMC: PMC5441820
DOI: 10.1073/pnas.1618114114
Pruning to Increase Taylor Dispersion in Physarum polycephalum Networks.
Marbach S (author), Alim K (author), Andrew N (author), Pringle A (author), Brenner MP (author)
2016-10
journal article
Physical review letters
URL: http://europepmc.org/abstract/med/27824465
PMID: 27824465
DOI: 10.1103/physrevlett.117.178103
Leaf growth is conformal.
Alim K (author), Armon S (author), Shraiman BI (author), Boudaoud A (author)
2016-09
journal article
Physical biology
URL: http://europepmc.org/abstract/med/27597439
PMID: 27597439
DOI: 10.1088/1478-3975/13/5/05lt01
Matrix elasticity of void-forming hydrogels controls transplanted-stem-cell-mediated bone formation.
Huebsch N (author), Lippens E (author), Lee K (author), Mehta M (author), Koshy ST (author), Darnell MC (author), Desai RM (author), Madl CM (author), Xu M (author), Zhao X (author), Chaudhuri O (author), Verbeke C (author), Kim WS (author), Alim K (author), Mammoto A (author), Mooney DJ (author)
2015-09
journal article
Nature materials
URL: http://europepmc.org/abstract/med/26366848
PMID: 26366848
PMC: PMC4654683
DOI: 10.1038/nmat4407
Physarum
Karen Alim (author), Natalie Andrew (author), Anne Pringle (author)
2013
journal article
Current Biology
DOI: 10.1016/j.cub.2013.09.040
ISSN: 0960-9822
Being Squeezed into the Right Place within the Egg Shell
Karen Alim (author)
2013-10
journal article
Biophysical Journal
DOI: 10.1016/j.bpj.2013.09.016
ISSN: 0006-3495
Random network peristalsis in Physarum polycephalum organizes fluid flows across an individual.
Alim K (author), Amselem G (author), Peaudecerf F (author), Brenner MP (author), Pringle A (author)
2013-07
journal article
Proceedings of the National Academy of Sciences of the United States of America
URL: http://europepmc.org/abstract/med/23898203
PMID: 23898203
PMC: PMC3746869
DOI: 10.1073/pnas.1305049110
Regulatory role of cell division rules on tissue growth heterogeneity
Karen Alim (author)
2012
journal article
Frontiers in Plant Science
DOI: 10.3389/fpls.2012.00174
ISSN: 1664-462X
Mechanical stress acts via katanin to amplify differences in growth rate between adjacent cells in Arabidopsis.
Uyttewaal M (author), Burian A (author), Alim K (author), Landrein B (author), Borowska-Wykręt D (author), Dedieu A (author), Peaucelle A (author), Ludynia M (author), Traas J (author), Boudaoud A (author), Kwiatkowska D (author), Hamant O (author)
2012-04
journal article
Cell
URL: http://europepmc.org/abstract/med/22500806
PMID: 22500806
DOI: 10.1016/j.cell.2012.02.048
Quantitative Analysis of the Nanopore Translocation Dynamics of Simple Structured Polynucleotides
Severin Schink (author), Stephan Renner (author), Karen Alim (author), Vera Arnaut (author), Friedrich C. Simmel (author), Ulrich Gerland (author)
2012-01
journal article
Biophysical Journal
DOI: 10.1016/j.bpj.2011.11.4011
ISSN: 0006-3495
Confinement induces conformational transition of semiflexible polymer rings to figure eight form
Katja Ostermeir (author), Karen Alim (author), Erwin Frey (author)
2010
journal article
Soft Matter
DOI: 10.1039/c0sm00290a
ISSN: 1744-683X
Buckling of stiff polymer rings in weak spherical confinement
Katja Ostermeir (author), Karen Alim (author), Erwin Frey (author)
2010-06
journal article
Physical Review E
DOI: 10.1103/physreve.81.061802
ISSN: 1539-3755
Quantitative predictions on auxin-induced polar distribution of PIN proteins during vein formation in leaves.
Alim K (author), Frey E (author)
2010-06
journal article
The European physical journal. E, Soft matter
URL: http://europepmc.org/abstract/med/20571847
PMID: 20571847
DOI: 10.1140/epje/i2010-10604-5
Excluded Volume Effects on Semiflexible Ring Polymers
Fabian Drube (author), Karen Alim (author), Guillaume Witz (author), Giovanni Dietler (author), Erwin Frey (author)
2010-04
journal article
Nano Letters
DOI: 10.1021/nl1003575
ISSN: 1530-6984
Shapes of Semiflexible Polymer Rings
Karen Alim (author), Erwin Frey (author)
2007-11-07
journal article
Physical Review Letters
DOI: 10.1103/physrevlett.99.198102
ISSN: 0031-9007
Fluctuating semiflexible polymer ribbon constrained to a ring.
Alim K (author), Frey E (author)
2007-10
journal article
The European physical journal. E, Soft matter
URL: http://europepmc.org/abstract/med/17992469
PMID: 17992469
DOI: 10.1140/epje/i2007-10228-x

See ORCID profile of Karen Alim as well.

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