Preprints

1. Models of 3D confluent tissue as under-constrained glasses
   Chengling Li, Matthias Merkel, Daniel M. Sussman
   arXiv: 2603.24438 (2026).
2. Non-linear visco-elasto-plastic rheology of a viscous vertex model
   Shalabh Kumar Anand, Matthias Merkel
   arXiv: 2602.22855 (2026).

Publications

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
   Biophysical Journal 125 (7), p. 1686-1700 (2026), arXiv, HAL.
2. Shape-transitions of a morphing illusory contour can be decoded during multiple-object tracking from the ongoing EEG
   Christian Merkel, Matthias Merkel, Jens-Max Hopf, Mircea Ariel Schoenfeld
   Commun Psychol 4 (1), p. 48 (2026), HAL.
3. Biophysics of organoids
   Vanessa Weichselberger, Gareth Moore, Sham Tlili, Matthias Merkel, Pierre-François Lenne, Vikas Trivedi
   Developmental Cell 61 (1), p. 24-41 (2026), HAL.
4. Stabilization of Active Tissue Deformation by a Dynamic Signaling Gradient
   Muhamet Ibrahimi, Matthias Merkel
   PRX Life 3 (4), p. 043013 (2025), arXiv, HAL.
5. Epithelial-mesenchymal interface guides cell shapes and axis elongation in embryonic explants
   Katia Barrett, Shalabh Anand, Virginie Thome, Laurent Kodjabachian, Matthias Merkel, Pierre-François Lenne
   Development 152 (14), p. dev204344 (2025), HAL.
6. Marangoni-like tissue flows enhance symmetry breaking of embryonic organoids
   Simon Gsell, Sham Tlili, Matthias Merkel, Pierre-François Lenne
   Nat. Phys. 21 (4), p. 644-653 (2025), bioRxiv, HAL.
7. 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, HAL.
8. Generic Elasticity of Thermal, Underconstrained Systems
   Cheng-Tai Lee, Matthias Merkel
   PRL 133 (26), p. 268201 (2024), arXiv, HAL.
9. Partition sum of thermal, underconstrained systems
   Cheng-Tai Lee, Matthias Merkel
   PRE 110 (6), p. 064147 (2024), arXiv, HAL.
10. 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), HAL.
11. 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), HAL.
12. 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.
13. Deforming polar active matter in a scalar field gradient
    Muhamet Ibrahimi, Matthias Merkel
    New J. Phys. 25 (1), p. 013022 (2023), arXiv, HAL.
14. Stiffening of under-constrained spring networks under isotropic strain
    Cheng-Tai Lee, Matthias Merkel
    Soft Matter 18 (29), p. 5410-5425 (2022), arXiv, HAL.
15. 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.
16. Phase separation dynamics in deformable droplets
    Simon Gsell, Matthias Merkel
    Soft Matter 18 (13), p. 2672-2683 (2022), arXiv, HAL.
17. 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), HAL.
18. 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, HAL.
19. 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, HAL.
20. 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).
21. 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), arXiv.
22. 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).
23. No unjamming transition in a Voronoi model of biological tissue
    Daniel M. Sussman, Matthias Merkel
    Soft Matter 14 (17), p. 3397-3403 (2018), arXiv.
24. 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), arXiv.
25. 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), PMC.
26. 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.
27. 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).
28. 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), HAL.
29. 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).
30. 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).
31. 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).
32. From cells to tissues: tissue remodeling and polarity reorientation in shearing epithelia
    Matthias Merkel
    PhD thesis, Technische Universität Dresden (2014).
33. 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).
34. Synaptic filtering of rate-coded information
    Matthias Merkel, Benjamin Lindner
    PRE 81 (4), p. 41921 (2010).