Self-Organizing Mechanics
Plant Development
During plant development, tissues morph into shapes or aquire patterns due to the feedback of tissues-wide mechanical stresses and ensuing biochemical patterns or plant cell growth.
- 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] - 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] - 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] - Leaf growth is conformal.
Karen Alim, Shahaf Armon, Boris I. Shraiman, and Arezki Boudaoud ,
[Phys. Biol. 2016] [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 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]
Gut Mechanics
Mechanical contractions along the small intestine, driving food transport along the longest route through our digestive tract, self-organize in response to signals transported within the flow.
- 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] - 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]
Self-Sustained Contractions
Cross-sectional contractions of fluid filled tubes form self-sustained travelling waves, where flow-transported molecules feed back onto contractions.
- 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] - Oscillatory fluid flow drives scaling of contraction wave with system size.
Jean-Daniel Julien and Karen Alim,
[Proc. Natl. Acad. Sci. 2018] [PDF]
Nuclei Order
Nuclei on the surface of the fruit fly embryo form ordered patterns and division dynamics due to active mechanics of nuclei embedding.
- 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] - 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]