Articles
Since 2020
Mechanotransduction in Lateral Root Initiation: A Model Integrating Growth Mechanics and Auxin Signaling.
Joao R. D. Ramos, Blanca Jazmin Reyes-Hernandez, Karen Alim, and Alexis Maizel,
[bioRxiv 2023] [PDF]
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, and Karen Alim,
[Sci. Adv. 2023] [in press]
Flow modes provide a quantification of Physarum network peristalsis.
Ryan Wilkinson, Matthieu Koziol, Karen Alim, and Marcus Roper,
[Fungal Ecol. 2023] [PDF]
Physarum polycephalum: Smart network adaptation.
Mathieu Le Verge-Serandour and Karen Alim,
[arXiv 2023] [PDF]
Vein fate determined by flow-based but time-delayed integration of network architecture.
Sophie Marbach, Noah Ziethen, Leonie Bastin, Felix Bäuerle, and Karen Alim,
[eLife 2023] [bioRxiv 2023] [PDF] [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, and Karen Alim,
[arXiv 2023] [PDF]
Vascular adaptation model from force balance: Physarum polycephalum as a case study.
Sophie Marbach, Noah Ziethen, and Karen Alim,
[arXiv 2023] [PDF]
Flux driven control of pulse length in excitable media.
Adrian Misselwitz, Suzanne Lafon, Jean-Daniel Julien, and Karen Alim,
[Phys. Rev. E 2023] [arXiv 2023] [PDF]
Network topology enables efficient response to environment in Physarum polycephalum.
Siyu Chen and Karen Alim,
[Phys. Biol. 2023] [bioRxiv 2022] [PDF]
Dispersive transport dynamics in porous media emerge from local correlations.
Felix Meigel, Thomas Darwent, Leonie Bastin, Lucas Goehring, and Karen Alim,
[Nat. Comm. 2022] [PDF]
Changing flows balance nutrient absorption and bacterial growth along the gut.
Agnese Codutti, Jonas Cremer, and Karen Alim,
[Phys. Rev. Lett. 2022] [PDF] [Physics Focus] [Physics World] [Press English] [Press German]
Memory capacity of adaptive flow networks.
Komal Bhattacharyya, David Zwicker, and Karen Alim,
[Phys. Rev. E 2022] [arXiv 2023] [PDF]
Memory Formation in Adaptive Networks.
Komal Bhattacharyya, David Zwicker, and Karen Alim,
[Phys. Rev. Lett. 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, and J Gray Camp
[bioRxiv 2021] [eLife 2022] [PDF]
Emergence of behavior in a self-organized living matter network.
Philipp Fleig, Mirna Kramar, Michael Wilczek, and Karen Alim,
[bioRxiv 2020] [eLife 2022] [PDF]
Gut microbiota-motility interregulation: insights from in vivo, ex vivo and in silico studies.
Barbora Waclawiková, Agnese Codutti, Karen Alim, and Sahar El Aidy,
[Gut Microbes 2022] [PDF]
Avoiding air bubbles when filling microfluidic chips by use of an ultrasonic bath
Leonie Bastin and Karen Alim,
[Lab on a Chip Blog 2021]
Encoding memory in tube diameter hierarchy of living flow network.
Mirna Kramar and Karen Alim,
[Proc. Natl. Acad. Sci. 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, and Karen Alim,
[Phys. Rev. Lett. 2020] [PDF] [Press English] [Press German]
Robust increase in supply by vessel dilation in globally coupled microvasculature.
Felix Meigel, Peter Cha, Michael P. Brenner, and Karen Alim,
[Phys. Rev. Lett. 2019] [PDF] [Physics Synopsis] [Physics World] [Press English] [Press German]
Tissue-wide integration of mechanical cues promotes efficient auxin patterning.
João R. D. Ramos, Alexis Maizel, and Karen Alim,
[Eur. Phys. J. Plus 2021] [bioRxiv 2021] [PDF]
2015 – 2019
Feedback from tissue mechanics self-organizes efficient outgrowth of plant organ.
Jason Khadka, Jean-Daniel Julien, and Karen Alim,
[Biophys. J. 2019] [arXiv 2020] [PDF]
Controlling effective dispersion within a channel with flow and active walls.
Sophie Marbach and Karen Alim,
[Phys. Rev. Fluids 2019] [arXiv 2019] [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, and Jörg Großhans,
[bioRxiv 2019] [Curr. Biol. 2020] [PDF]
Order parameter allows classification of planar graphs based on balanced fixed points in the Kuramoto model.
Franz Kaiser and Karen Alim,
[Phys. Rev. E 2019] [arXiv 2019] [PDF]
Oscillatory fluid flow drives scaling of contraction wave with system size.
Jean-Daniel Julien and Karen Alim,
[Proc. Natl. Acad. Sci. 2018] [PDF]
Flow rate of transport network controls uniform metabolite supply to tissue.
Felix J. Meigel and Karen Alim,
[Roy. Soc. Interface 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, and Karen Alim,
[Biophys. J. 2018] [PDF]
Fluid flows shaping organism morphology.
Karen Alim,
[Philos. Trans. Royal Soc. B 2018] [PDF]
Spatial mapping reveals multi-step pattern of wound healing in Physarum polycephalum.
Felix Bäuerle, Mirna Kramar, and Karen Alim,
[J. Phys. D 2017] [PDF]
Local pore size correlations determine flow distributions in porous media.
Karen Alim, Shima Parsa, David A. Weitz, and Michael P. Brenner,
[Phys. Rev. Lett. 2017] [PDF]
Mechanism of signal propagation in Physarum polycephalum.
Karen Alim, Natalie Andrew, Anne Pringle, and Michael P. Brenner,
[Proc. Natl. Acad. Sci. 2017] [PDF] [Press German] [Press English]
Pruning to increase Taylor dispersion in Physarum polycephalum networks.
Sophie Marbach, Karen Alim, Natalie Andrew, Anne Pringle, and Michael P. Brenner ,
[Phys. Rev. Lett. 2016] [PDF]
Leaf growth is conformal.
Karen Alim, Shahaf Armon, Boris I. Shraiman, and Arezki Boudaoud ,
[Phys. Biol. 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, and David J. Mooney,
[Nat. Mat. 2015] [PDF]
2010 – 2014
Quickguide: Physarum.
Karen Alim, Natalie Andrew, and Anne Pringle,
[Curr. Biol. 2013] [PDF]
Being squeezed into the right place within the egg shell.
Karen Alim,
[Biophys. J. 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. 2013] [PDF]
Regulatory role of cell division rules on tissue growth heterogeneity.
Karen Alim, Olivier Hamant, and Arezki Boudaoud,
[Front. Plant Sci. 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 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. 2012] [PDF]
Confinement induces conformational transition of semiflexible polymer rings to figure eight form.
Katja Ostermeir*, Karen Alim*, and Erwin Frey,
[Soft Matter 2010] [arXiv 2010] [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 2010] [arXiv 2010] [PDF]
Buckling of stiff polymer rings in weak spherical confinement.
Katja Ostermeir, Karen Alim, and Erwin Frey,
[Phys. Rev. E 2010] [arXiv 2010] [PDF]
Excluded volume effects on semiflexible ring polymers.
Fabian Drube, Karen Alim, Guillaume Witz, Giovanni Dietler, and Erwin Frey,
[Nano Letters 2010] [arXiv 2010] [PDF]
Before 2010
Fluctuating semiflexible polymer ribbon constrained to a ring.
Karen Alim and Erwin Frey,
[Eur. Phys. J. E 2007] [arXiv 2007] [PDF]
Shapes of semiflexible polymer rings.
Karen Alim and Erwin Frey,
[Phys. Rev. Lett. 2007] [arXiv 2007] [PDF]
Drowsy cheetah hunting antelopes: A diffusing predator seeking fleeing prey.
Karen Winkler and Alan J. Bray,
[J. Stat. Mech 2005] [arXiv 2005] [PDF]
Vicious walkers in a potential.
Alan J. Bray and Karen Winkler,
[J. Phys. A 2004] [arXiv 2004] [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]