Mechano-genetic interactions in stem cell aggregates
Most animals display one or more body axes, such as the head-to-tail axis, which usually form during early embryogenesis. Such axis formation can be studied in vitro, in stem cell aggregates called gastruloids. While initially isotropic, gastruloids break rotational symmetry over the course of roughly a day, reflected in an asymmetric distribution of cell fates.
We want to understand how cell fate dynamics interacts with cell motion and tissue dynamics.
On this project, we work together with the theory group of Simon Gsell and the experimental groups of Pierre-François Lenne (Marseille), Vikas Trivedi (Barcelona), and Verena Ruprecht (Innsbruck).
Recent publications:
- Biophysics of organoids, Vanessa Weichselberger, Gareth Moore, Sham Tlili, Matthias Merkel, Pierre-François Lenne, Vikas Trivedi
- Marangoni-like tissue flows enhance symmetry breaking of embryonic organoids, Simon Gsell, Sham Tlili, Matthias Merkel, Pierre-François Lenne
- Phase separation dynamics in deformable droplets, Simon Gsell, Matthias Merkel

Dynamics of anisotropic tissues
A key process during animal development is the anisotropic deformation of tissues. Often, such deformation is driven by tissue-internal active processes, which are controlled by some kind of orientational information present in the tissue (for instance cell polarity or cell shape anisotropy). Yet, generic theories for such active materials with orientational information predict inherent instabilities. How could such instabilities be prevented to during animal development? To address this question, we study the interplay between orientational information and tissue mechanics using both cell-based and hydrodynamic models for biological tissues.
Recent publications:
- Stabilization of Active Tissue Deformation by a Dynamic Signaling Gradient, Muhamet Ibrahimi, Matthias Merkel
- 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
- Deforming polar active matter in a scalar field gradient, Muhamet Ibrahimi, Matthias Merkel
- Structure and Rheology in Vertex Models under Cell-Shape-Dependent Active Stresses, Shao-Zhen Lin, Matthias Merkel, Jean-François Rupprecht
- Implementation of cellular bulk stresses in vertex models of biological tissues, Shao-Zhen Lin, Matthias Merkel, Jean-Francois Rupprecht
Dynamics of curved tissues
Sheet-like biological tissues, called epithelia, are often curved during animal development. How does curvature affect the tissue dynamics? For instance, when tissues change their Gaussian curvature, then they need to deform tangentially. What are the consequences of this for tissue flow?
On this project, we work together with the experimental group of Thomas Lecuit (Marseille).
Recent publications:
- Curvature gradient drives polarized tissue flow in the Drosophila embryo, Emily W. Gehrels, Bandan Chakrabortty, Marc-Eric Perrin, Matthias Merkel, Thomas Lecuit
Mechanics of under-constrained materials
How do large-scale properties of disordered systems arise from the complex interplay of their microscopic constituents? This question is important to understand a large class of materials both living and non-living. Recently, we have shown analytically that the elastic properties of the broad class of under-constrained materials can be predicted by very generic relations. This is relevant to understand systems as diverse as semi-flexible polymer networks like collagen, cell-based vertex models for biological tissue, colloidal gels, and membranes.
On this project, we work together with the theory group of Daniel Sussman (Atlanta).
Recent publications:
- Models of 3D confluent tissue as under-constrained glasses, Chengling Li, Matthias Merkel, Daniel M. Sussman
- Connecting Anomalous Elasticity and Sub-Arrhenius Structural Dynamics in a Cell-Based Model, Chengling Li, Matthias Merkel, Daniel M. Sussman
- Generic Elasticity of Thermal, Underconstrained Systems, Cheng-Tai Lee, Matthias Merkel
- Partition sum of thermal, underconstrained systems, Cheng-Tai Lee, Matthias Merkel
- Stiffening of under-constrained spring networks under isotropic strain, Cheng-Tai Lee, Matthias Merkel

Yielding in cellular materials
How does the rheology of cellular materials - like biological tissues, emulsions, and foams - arise from their cellular structure? Combining microscopic simulations, the development of mesoscopic models, and experimental collaborations, we systematically dissect the relation between structure and non-linear visco-elasto-plastic material rheology.
On this project, we work together with the theory group of Simon Gsell (Marseille) and the experimental group of Léa-Laëtitia Pontani (Paris).
Recent publications:
- Non-linear visco-elasto-plastic rheology of a viscous vertex model, Shalabh Kumar Anand, Matthias Merkel
- Adhesion differentials control the rheology of biomimetic emulsions, Quentin Guigue, Marc Besse, Raphael Voituriez, Alexis M. Prevost, Elie Wandersman, Matthias Merkel, Lea-Laetitia Pontani
