Preprints

1. Adhesion differentials control the rheology of biomimetic emulsions
   Quentin Guigue, Marc Besse, Raphael Voituriez, Alexis M. Prevost, Elie Wandersman, Matthias Merkel, Lea-Laetitia Pontani
   arXiv: 2503.18782 (2025).
2. Epithelial-mesenchymal boundary guides cell shapes and axis elongation in embryonic explants
   Katia Barrett, Shalabh Anand, Virginie Thome, Pierre-François Lenne, Matthias Merkel
   bioRxiv: 10.1101/2024.08.20.608779 (2024).
3. Stabilization of active tissue deformation by a dynamic morphogen gradient
   Muhamet Ibrahimi, Matthias Merkel
   arXiv: 2412.15774 (2024).

Publications

1. Marangoni-like tissue flows enhance symmetry breaking of embryonic organoids
   Simon Gsell, Sham Tlili, Matthias Merkel, Pierre-François Lenne
   Nat. Phys. (2025). bioRxiv version.
2. Connecting Anomalous Elasticity and Sub-Arrhenius Structural Dynamics in a Cell-Based Model
   Chengling Li, Matthias Merkel, Daniel M. Sussman
   PRL 134 (4), p. 048203 (2025). arXiv version.
3. Generic Elasticity of Thermal, Underconstrained Systems
   Cheng-Tai Lee, Matthias Merkel
   PRL 133 (26), p. 268201 (2024). arXiv version.
4. Partition sum of thermal, underconstrained systems
   Cheng-Tai Lee, Matthias Merkel
   PRE 110 (6), p. 064147 (2024). arXiv version.
5. Soft matter roadmap
   Jean-Louis Barrat, Emanuela Del Gado, Stefan U Egelhaaf, Xiaoming Mao, Marjolein Dijkstra, David J Pine, Sanat K Kumar, Kyle Bishop, Oleg Gang, Allie Obermeyer, Christine M Papadakis, et al.
   J. Phys. Mater. 7 (1), p. 012501 (2023).
6. Curvature gradient drives polarized tissue flow in the Drosophila embryo
   Emily W. Gehrels, Bandan Chakrabortty, Marc-Eric Perrin, Matthias Merkel, Thomas Lecuit
   PNAS 120 (6), p. e2214205120 (2023).
7. Deforming polar active matter in a scalar field gradient
   Muhamet Ibrahimi, Matthias Merkel
   New J. Phys. 25 (1), p. 013022 (2023).
8. Structure and Rheology in Vertex Models under Cell-Shape-Dependent Active Stresses
   Shao-Zhen Lin, Matthias Merkel, Jean-François Rupprecht
   PRL 130 (5), p. 058202 (2023). HAL version.
9. Phase separation dynamics in deformable droplets
   Simon Gsell, Matthias Merkel
   Soft Matter 18 (13), p. 2672-2683 (2022).
10. Stiffening of under-constrained spring networks under isotropic strain
    Cheng-Tai Lee, Matthias Merkel
    Soft Matter 18 (29), p. 5410-5425 (2022).
11. Implementation of cellular bulk stresses in vertex models of biological tissues
    Shao-Zhen Lin, Matthias Merkel, Jean-francois Rupprecht
    EPJE 45 (1), p. 4 (2022). HAL version.
12. Cell and Nucleus Shape as an Indicator of Tissue Fluidity in Carcinoma
    Steffen Grosser, Jürgen Lippoldt, Linda Oswald, Matthias Merkel, Daniel M Sussman, Frédéric Renner, Pablo Gottheil, Erik W Morawetz, Thomas Fuhs, Xiaofan Xie, Steve Pawlizak, et al.
    PRX 11 (1), p. 011033 (2021).
13. Anisotropy links cell shapes to tissue flow during convergent extension
    Xun Wang, Matthias Merkel, Leo B. Sutter, Gonca Erdemci-Tandogan, M. Lisa Manning, Karen E. Kasza
    PNAS 117 (24), p. 13541-13551 (2020). arXiv version.
14. A minimal-length approach unifies rigidity in underconstrained materials
    Matthias Merkel, Karsten Baumgarten, Brian P Tighe, M Lisa Manning
    PNAS 116 (14), p. 6560-6568 (2019). arXiv version.
15. Inferring statistical properties of 3D cell geometry from 2D slices
    Tristan A. Sharp, Matthias Merkel, M. Lisa Manning, Andrea J. Liu
    PLOS ONE 14 (2), p. e0209892 (2019).
16. Cell volume changes contribute to epithelial morphogenesis in zebrafish Kupffer’s vesicle
    Agnik Dasgupta, Matthias Merkel, Madeline J Clark, Andrew E Jacob, Jonathan Edward Dawson, M Lisa Manning, Jeffrey D Amack
    eLife 7 (5), p. 710-722 (2018).
17. A geometrically controlled rigidity transition in a model for confluent 3D tissues
    Matthias Merkel, M Lisa Manning
    New J. Phys. 20 (2), p. 022002 (2018).
18. No unjamming transition in a Voronoi model of biological tissue
    Daniel M. Sussman, Matthias Merkel
    Soft Matter 14 (17), p. 3397-3403 (2018). arXiv version.
19. Quantitative methods to study epithelial morphogenesis and polarity
    B. Aigouy, C. Collinet, M. Merkel, A. Sagner
    Methods in Cell Biology 139, p. 121-152 (2017).
20. Triangles bridge the scales: Quantifying cellular contributions to tissue deformation
    Matthias Merkel, Raphaël Etournay, Marko Popović, Guillaume Salbreux, Suzanne Eaton, Frank Jülicher
    PRE 95 (3), p. 032401 (2017). arXiv version.
21. Using cell deformation and motion to predict forces and collective behavior in morphogenesis
    Matthias Merkel, M. Lisa Manning
    Seminars in Cell & Developmental Biology 67, p. 161-169 (2017).
22. Active dynamics of tissue shear flow
    Marko Popović, Amitabha Nandi, Matthias Merkel, Raphaël Etournay, Suzanne Eaton, Frank Jülicher, Guillaume Salbreux
    New J. Phys. 19 (3), p. 033006 (2017).
23. Correlating Cell Shape and Cellular Stress in Motile Confluent Tissues
    Xingbo Yang, Dapeng Bi, Michael Czajkowski, Matthias Merkel, M. Lisa Manning, M. Cristina Marchetti
    PNAS 114 (48), p. 12663-12668 (2017).
24. TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics
    Raphaël Etournay, Matthias Merkel, Marko Popović, Holger Brandl, Natalie A. Dye, Benoît Aigouy, Guillaume Salbreux, Suzanne Eaton, Frank Jülicher
    eLife 5, p. e14334 (2016).
25. Interplay of cell dynamics and epithelial tension during morphogenesis of the Drosophila pupal wing
    Raphaël Etournay, Marko Popović, Matthias Merkel, Amitabha Nandi, Corinna Blasse, Benoît Aigouy, Holger Brandl, Gene Myers, Guillaume Salbreux, Frank Jülicher, Suzanne Eaton
    eLife 4, p. e07090 (2015).
26. The balance of prickle/spiny-legs isoforms controls the amount of coupling between core and fat PCP systems
    Matthias Merkel, Andreas Sagner, Franz Sebastian Gruber, Raphael Etournay, Corinna Blasse, Eugene Myers, Suzanne Eaton, Frank Jülicher
    Current Biology 24 (18), p. 2111-2123 (2014).
27. From cells to tissues: tissue remodeling and polarity reorientation in shearing epithelia
    Matthias Merkel
    PhD thesis, Technische Universität Dresden (2014).
28. Establishment of global patterns of planar polarity during growth of the drosophila wing epithelium
    Andreas Sagner, Matthias Merkel, Benoit Aigouy, Julia Gaebel, Marko Brankatschk, Frank Jülicher, Suzanne Eaton
    Current Biology 22 (14), p. 1296-1301 (2012).
29. Synaptic filtering of rate-coded information
    Matthias Merkel, Benjamin Lindner
    PRE 81 (4), p. 41921 (2010).