Publications

Vein fate determined by flow-based but time-delayed integration of network architecture
Sophie Marbach, Noah Ziethen, Leonie Bastin, Felix Bäuerle & Karen Alim,
eLife 12:e78100 (2023), bioRxiv 2021.12.29.474405. dedicated Insight article.

Alkaline vents recreated in two dimensions to study pH gradients,
precipitation morphology and molecule accumulation
Maximilian Weingart, Siyu Chen , Clara Donat , Vanessa Helmbrecht,
William D. Orsi, Dieter Braun & Karen Alim,
arXiv 2303.10156 (2023). (PDF).

Vascular adaptation model from force balance:Physarum polycephalum as a case study.
Sophie Marbach, Noah Ziethen & Karen Alim,
arXiv:2303.01439 (2023). (PDF).

Flux driven control of pulse length in excitable media.
Adrian Misselwitz, Suzanne Lafon, Jean-Daniel Julien & Karen Alim,
Phys. Rev. E 107, 054218 (2023) arXiv:2212.03837. (PDF).

Network topology enables efficient response to environment in Physarum polycephalum.
Siyu Chen & Karen Alim,
Phys. Biol. 20, 046003 (2023). bioRxiv 2022.11.09.515897. (PDF).

Flow modes provide a quantification of Physarum network peristalsis.
R. Wilkinson, M. Koziol, Karen Alim & M. Roper
Available at SSRN: https://ssrn.com/abstract=4267724 (2022). (PDF).

Dispersive transport dynamics in porous media emerge from local correlations.
Felix Meigel, Thomas Darwent, Leonie Bastin, Lucas Goehring & Karen Alim,
Nat. Comm. 13, 5885 (2022). (PDF).

Changing flows balance nutrient absorption and bacterial growth along the gut.
Agnese Codutti, Jonas Cremer & Karen Alim,
Phys. Rev. Lett. 129, 138101 (2022). (PDF), (Physics Focus) ,  (Physics World) , (Press English) , (Press German) .

Memory capacity of adaptive flow networks.
Komal Bhattacharyya, David Zwicker & Karen Alim,
Phys. Rev. E 107, 034407 , arXiv:2208.11192 (2023). (PDF).

Memory Formation in Adaptive Networks.
Komal Bhattacharyya, David Zwicker & Karen Alim,
Phys. Rev. Lett. 129, 028101 (2022). (PDF) (Press English) , (Press German) .

Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium.
Tobias Gerber, Cristina Loureiro, Nico Schramma, Siyu Chen, Akanksha Jain, Anne Weber, Anne Weigert, Malgorzata Santel, Karen Alim, Barbara Treutlein & J Gray Camp
bioRxiv 2021.04.29.441915 (2021). eLife 11:e69745 (2022).

Emergence of behavior in a self-organized living matter network.
Philipp Fleig, Mirna Kramar, Michael Wilczek & Karen Alim,
bioRxiv 2020.09.06.285080 (2020). eLife 11:e62863 (2022). (PDF)

Gut microbiota-motility interregulation: insights from in vivo, ex vivo and in silico studies.
Barbora Waclawiková, Agnese Codutti, Karen Alim, Sahar El Aidy,
Gut Microbes, 14:1, 1997296 (2022). (PDF)

Avoiding air bubbles when filling microfluidic chips by use of an ultrasonic bath
Leonie Bastin & Karen Alim,
Lab on a Chip Blog (2021).

Encoding memory in tube diameter hierarchy of living flow network.
Mirna Kramar & Karen Alim,
Proc. Natl. Acad. Sci. U.S.A. 118 (10) e2007815118 (2021). (PDF),
(Press English) , (Press German) .

Living system adapts harmonics of peristaltic wave for cost-efficient optimization of pumping performance.
Felix K. Bäuerle, Stefan Karpitschka & Karen Alim,
Phys. Rev. Lett. 124,098102 (2020). (PDF), (Press English) , (Press German) .

Robust increase in supply by vessel dilation in globally coupled microvasculature.
Felix Meigel, Peter Cha, Michael P. Brenner & Karen Alim,
Phys. Rev. Lett. 123, 228103 (2019). (PDF), (Physics Synopsis) , (Physics World Research Synopsis), (Press English) , (Press German) .

Tissue-wide integration of mechanical cues promotes efficient auxin patterning.
João R. D. Ramos, Alexis Maizel & Karen Alim,
Eur. Phys. J. Plus 136, 250 (2021). (PDF), bioRxiv, 820837.

Feedback from tissue mechanics self-organizes efficient outgrowth of plant organ.
Jason Khadka, Jean-Daniel Julien & Karen Alim,
Biophys. J., 117, 1995-2004. (PDF), arxiv 2004.12220 .

Controlling effective dispersion within a channel with flow and active
walls.
Sophie Marbach & Karen Alim,
Phys. Rev. Fluids, 4, 114202 (2019)
arxiv 1901.03697. (PDF)

The emergent yo-yo movement of nuclei driven by cytoskeletal remodeling in pseudo-synchronous mitotic cycles.
Zhiyi Lv, Jan Rosenbaum, Stephan Mohr, Xiaozhu Zhang, Helen Preiß, Sebastian Kruss, Karen Alim, Timo Aspelmeier, Jörg Großhans,
bioRxiv 662965 (2019). (PDF) Curr. Biol. 30 (13), 2564-2573 (2020)

Order parameter allows classification of planar graphs based on balanced fixed points in the Kuramoto model.
Franz Kaiser & Karen Alim,
Phys. Rev. E 99, 052308 (2019) arxiv 1809.100000. (PDF)

Oscillatory fluid flow drives scaling of contraction wave with system size.
Jean-Daniel Julien & Karen Alim,
Proc. Natl. Acad. Sci. U.S.A., 115, 10612–10617 (2018). (PDF)

Flow rate of transport network controls uniform metabolite supply to tissue.
Felix J. Meigel & Karen Alim,
Roy. Soc. Interface, 15, 20180075 (2018). (PDF)

Mechanical model of nuclei ordering in Drosophila embryos reveals dilution of stochastic forces.
Franz Kaiser, Zhiyi Lv, Daniel Marques Rodrigues, Jan Rosenbaum, Timo Aspelmeier, Jörg Großhans, Karen Alim,
Biophys. J., 114(7), 1730-1740 (2018). (PDF)

Fluid flows shaping organism morphology.
Karen Alim,
Philos. Trans. Royal Soc. B, 373, 20170112 (2018). (PDF)

Spatial mapping reveals multi-step pattern of wound healing in Physarum polycephalum.
Felix Bäuerle, Mirna Kramar & Karen Alim,
J. Phys. D: Appl. Phys., 50, 434005 (2017). (PDF)

Local pore size correlations determine flow distributions in porous media.
Karen Alim, Shima Parsa, David A. Weitz, & Michael P. Brenner,
Phys. Rev. Lett., 119, 144501 (2017). (PDF)

Mechanism of signal propagation in Physarum polycephalum.
Karen Alim, Natalie Andrew, Anne Pringle & Michael P. Brenner,
Proc. Natl. Acad. Sci. U.S.A.,114(20), 5236-5141 (2017). (PDF) (Press German) (Press English)

Pruning to increase Taylor dispersion in Physarum polycephalum networks.
Sophie Marbach, Karen Alim, Natalie Andrew, Anne Pringle & Michael P. Brenner ,
Phys. Rev. Lett., 117, 178103 (2016). (PDF)

Leaf growth is conformal.
Karen Alim, Shahaf Armon, Boris I. Shraiman & Arezki Boudaoud ,
Phys. Biol., 13(5), 05LT01 (2016). (PDF)

Matrix elasticity of void-forming hydrogels controls transplanted-stem-cell-mediated bone formation.
Nathaniel Huebsch, Evi Lippens, Kangwon Lee, Manav Mehta, Sandeep T. Koshy, Max C. Darnell, Rajiv M. Desai, Christopher M. Madl, Maria Xu, Xuanhe Zhao, Ovijit Chaudhuri, Catia Verbeke, Woo Seob Kim, Karen Alim, Akiko Mammoto, Donald E. Ingber, Georg N. Duda & David J. Mooney ,
Nat. Mat., 14(12), 1269-1277 (2015). (PDF)

Quickguide: Physarum.
Karen Alim, Natalie Andrew and Anne Pringle,
Curr. Biol., 23(24), R1082-R1083 (2013). (PDF)

Being squeezed into the right place within the egg shell.
Karen Alim,
Biophys. J., 105(8), 1735-1736 (2013). (PDF)

Random network peristalsis in Physarum polycephalums organizes fluid flows across an individual.
Karen Alim*, Gabriel Amselem*, François Peaudecerf, Michael P. Brenner and Anne Pringle,
Proc. Natl. Acad. Sci. U.S.A., 110(33), 13306-13311 (2013). (PDF)

Regulatory role of cell division rules on tissue growth heterogeneity.
Karen Alim, Olivier Hamant and Arezki Boudaoud,
Front. Plant Sci. 3, 00174 (2012). (PDF)

Mechanical stress acts via katanin to amplify differences in growth rate between adjacent cells in Arabidopsis.
Magalie Uyttewaal*, Agata Burian*, Karen Alim*, Benoît Landrein, Dorota Borowska-Wykręt, Annick Dedieu, Alexis Peaucelle, Michał Ludynia, Jan Traas, Arezki Boudaoud**, Dorota Kwiatkowska** and Olivier Hamant**,
Cell 149, 439-451 (2012). (PDF)

Quantitative analysis of the nanopore translocation dynamics of simple structured polynucleotides.
Severin Schink, Stephan Renner, Karen Alim, Vera Arnaut, Friedrich C. Simmel and Ulrich Gerland,
Biophys. J. 102, 85-95 (2012). (PDF)

Confinement induces conformational transition of semiflexible polymer rings to figure eight form.
Katja Ostermeir*, Karen Alim* and Erwin Frey,
Soft Matter 6, 3467-3471 (2010). arXiv:1004.4574. (PDF)

Quantitative predictions on auxin-induced polar distribution of PIN proteins during vein formation in leaves.
Karen Alim and Erwin Frey,
Eur. Phys. J. E 33, 165 (2010). arXiv:1005.3768. (PDF)

Buckling of stiff polymer rings in weak spherical confinement.
Katja Ostermeir, Karen Alim and Erwin Frey,
Phys. Rev. E 81, 061802 (2010). arXiv:1003.4267. (PDF)

Excluded volume effects on semiflexible ring polymers.
Fabian Drube, Karen Alim, Guillaume Witz, Giovanni Dietler and Erwin Frey,
Nano Letters 10, 1445-1449 (2010). arXiv:0906.3991. (PDF)

Fluctuating semiflexible polymer ribbon constrained to a ring.
Karen Alim and Erwin Frey,
Eur. Phys. J. E 24, 185-191 (2007). arXiv:0708.0111. (PDF)

Shapes of semiflexible polymer rings.
Karen Alim and Erwin Frey,
Phys. Rev. Lett. 99, 198102 (2007). arXiv:q-bio/0703049. (PDF)

Drowsy cheetah hunting antelopes: A diffusing predator seeking fleeing prey.
Karen Winkler and Alan J. Bray,
J. Stat. Mech P02005 (2005). arXiv:cond-mat/0410449. (PDF)

Vicious walkers in a potential.
Alan J. Bray and Karen Winkler,
J. Phys. A 37, 5493 (2004). arXiv:cond-mat/0403220. (PDF)

Theses:

Shape and structure in biological systems.
PhD Thesis, Ludwig-Maximilians-Universität München (2010). (PDF)

Statistical mechanics of fluctuating polymer rings.
Diploma Thesis, Ludwig-Maximilians-Universität München (2006). (PDF)

Vicious walkers in one-body potentials.
Master Thesis, University of Manchester (2004). (PDF)