Publications

Publications

This list contains selected recent publications from the group, including the group members located at Leiden University as well as the University of Bristol.


2024

Soft and Stiff Normal Modes in Floppy Colloidal Square Lattices

Julio Melio, Silke E. Henkes, and Daniela J. Kraft

Physical Review Letters - (2024) [arXiv]

Floppy microscale spring networks are widely studied in theory and simulations, but no well-controlled experimental system currently exists. Here, we show that square lattices consisting of colloid-supported lipid bilayers functionalized with DNA linkers act as microscale floppy spring networks. We extract their normal modes by inverting the particle displacement correlation matrix, showing the emergence of a spectrum of soft modes with low effective stiffness in addition to stiff modes that derive from linker interactions. Evaluation of the softest mode, a uniform shear mode, reveals that shear stiffness decreases with lattice size. Experiments match well with Brownian particle simulations, and we develop a theoretical description based on mapping interactions onto a linear response model to describe the modes. Our results reveal the importance of entropic steric effects and can be used for developing reconfigurable materials at the colloidal length scale.

Soft and Stiff Normal Modes in Floppy Colloidal Square Lattices

Julio Melio, Silke E. Henkes, and Daniela J. Kraft

Physical Review Letters - (2024) [arXiv]

Floppy microscale spring networks are widely studied in theory and simulations, but no well-controlled experimental system currently exists. Here, we show that square lattices consisting of colloid-supported lipid bilayers functionalized with DNA linkers act as microscale floppy spring networks. We extract their normal modes by inverting the particle displacement correlation matrix, showing the emergence of a spectrum of soft modes with low effective stiffness in addition to stiff modes that derive from linker interactions. Evaluation of the softest mode, a uniform shear mode, reveals that shear stiffness decreases with lattice size. Experiments match well with Brownian particle simulations, and we develop a theoretical description based on mapping interactions onto a linear response model to describe the modes. Our results reveal the importance of entropic steric effects and can be used for developing reconfigurable materials at the colloidal length scale.

Self-Aligning Polar Active Matter

Paul Baconnier, Olivier Dauchot, Vincent Démery, Gustavo Düring, Silke Henkes, Cristián Huepe, Amir Shee

arXiv preprint - (2024) [arXiv]

Self-alignment describes the property of a polar active unit to align or anti-align its orientation towards its velocity. In contrast to mutual alignment, where the headings of multiple active units tend to directly align to each other -- as in the celebrated Vicsek model --, self-alignment impacts the dynamics at the individual level by coupling the rotation and displacements of each active unit. This enriches the dynamics even without interactions or external forces, and allows, for example, a single self-propelled particle to orbit in a harmonic potential. At the collective level, self-alignment modifies the nature of the transition to collective motion already in the mean field description, and it can also lead to other forms of self-organization such as collective actuation in dense or solid elastic assemblies of active units. This has significant implications for the study of dense biological systems, metamaterials, and swarm robotics. Here, we review a number of models that were introduced independently to describe the previously overlooked property of self-alignment and identify some of its experimental realizations.

Self-Aligning Polar Active Matter

Paul Baconnier, Olivier Dauchot, Vincent Démery, Gustavo Düring, Silke Henkes, Cristián Huepe, Amir Shee

arXiv preprint - (2024) [arXiv]

Self-alignment describes the property of a polar active unit to align or anti-align its orientation towards its velocity. In contrast to mutual alignment, where the headings of multiple active units tend to directly align to each other -- as in the celebrated Vicsek model --, self-alignment impacts the dynamics at the individual level by coupling the rotation and displacements of each active unit. This enriches the dynamics even without interactions or external forces, and allows, for example, a single self-propelled particle to orbit in a harmonic potential. At the collective level, self-alignment modifies the nature of the transition to collective motion already in the mean field description, and it can also lead to other forms of self-organization such as collective actuation in dense or solid elastic assemblies of active units. This has significant implications for the study of dense biological systems, metamaterials, and swarm robotics. Here, we review a number of models that were introduced independently to describe the previously overlooked property of self-alignment and identify some of its experimental realizations.

2023

Mechanochemical Active Feedback Generates Convergence Extension in Epithelial Tissue

Aondoyima Ioratim-Uba, Tanniemola B. Liverpool, and Silke Henkes

Physical Review Letters - (2023) [arXiv]

Convergence extension, the simultaneous elongation of tissue along one axis while narrowing along a perpendicular axis, occurs during embryonic development. A fundamental process that contributes to shaping the organism, it happens in many different species and tissue types. Here, we present a minimal continuum model, that can be directly linked to the controlling microscopic biochemistry, which shows spontaneous convergence extension. It is comprised of a 2D viscoelastic active material with a mechanochemical active feedback mechanism coupled to a substrate via friction. Robust convergent extension behavior emerges beyond a critical value of the activity parameter and is controlled by the boundary conditions and the coupling to the substrate. Oscillations and spatial patterns emerge in this model when internal dissipation dominates over friction, as well as in the active elastic limit.

Mechanochemical Active Feedback Generates Convergence Extension in Epithelial Tissue

Aondoyima Ioratim-Uba, Tanniemola B. Liverpool, and Silke Henkes

Physical Review Letters - (2023) [arXiv]

Convergence extension, the simultaneous elongation of tissue along one axis while narrowing along a perpendicular axis, occurs during embryonic development. A fundamental process that contributes to shaping the organism, it happens in many different species and tissue types. Here, we present a minimal continuum model, that can be directly linked to the controlling microscopic biochemistry, which shows spontaneous convergence extension. It is comprised of a 2D viscoelastic active material with a mechanochemical active feedback mechanism coupled to a substrate via friction. Robust convergent extension behavior emerges beyond a critical value of the activity parameter and is controlled by the boundary conditions and the coupling to the substrate. Oscillations and spatial patterns emerge in this model when internal dissipation dominates over friction, as well as in the active elastic limit.

Generating active T1 transitions through mechanochemical feedback

Rastko Sknepnek, Ilyas Djafer-Cherif, Manli Chuai, Cornelis Weijer and Silke Henkes

eLife - (2023) [arXiv]

Convergence–extension in embryos is controlled by chemical and mechanical signalling. A key cellular process is the exchange of neighbours via T1 transitions. We propose and analyse a model with positive feedback between recruitment of myosin motors and mechanical tension in cell junctions. The model produces active T1 events, which act to elongate the tissue perpendicular to the main direction of tissue stress. Using an idealised tissue patch comprising several active cells embedded in a matrix of passive hexagonal cells, we identified an optimal range of mechanical stresses to trigger an active T1 event. We show that directed stresses also generate tension chains in a realistic patch made entirely of active cells of random shapes and leads to convergence–extension over a range of parameters. Our findings show that active intercalations can generate stress that activates T1 events in neighbouring cells, resulting in tension-dependent tissue reorganisation, in qualitative agreement with experiments on gastrulation in chick embryos.

Generating active T1 transitions through mechanochemical feedback

Rastko Sknepnek, Ilyas Djafer-Cherif, Manli Chuai, Cornelis Weijer and Silke Henkes

eLife - (2023) [arXiv]

Convergence–extension in embryos is controlled by chemical and mechanical signalling. A key cellular process is the exchange of neighbours via T1 transitions. We propose and analyse a model with positive feedback between recruitment of myosin motors and mechanical tension in cell junctions. The model produces active T1 events, which act to elongate the tissue perpendicular to the main direction of tissue stress. Using an idealised tissue patch comprising several active cells embedded in a matrix of passive hexagonal cells, we identified an optimal range of mechanical stresses to trigger an active T1 event. We show that directed stresses also generate tension chains in a realistic patch made entirely of active cells of random shapes and leads to convergence–extension over a range of parameters. Our findings show that active intercalations can generate stress that activates T1 events in neighbouring cells, resulting in tension-dependent tissue reorganisation, in qualitative agreement with experiments on gastrulation in chick embryos.

2022

The nonlinear motion of cells subject to external forces

Aondoyima Ioratim-Uba, Aurore Loisy, Silke Henkes and Tanniemola B Liverpool

Soft Matter - (2022) [arXiv] [pdf]

To develop a minimal model for a cell moving in a crowded environment such as in tissue, we investigate the response of a liquid drop of active matter moving on a flat rigid substrate to forces applied at its boundaries. We consider two different self-propulsion mechanisms, active stresses and treadmilling polymerisation, and we investigate how the active drop motion is altered by these surface forces. We find a highly non-linear response to forces that we characterise using drop velocity, drop shape, and the traction between the drop and the substrate.

The nonlinear motion of cells subject to external forces

Aondoyima Ioratim-Uba, Aurore Loisy, Silke Henkes and Tanniemola B Liverpool

Soft Matter - (2022) [arXiv] [pdf]

To develop a minimal model for a cell moving in a crowded environment such as in tissue, we investigate the response of a liquid drop of active matter moving on a flat rigid substrate to forces applied at its boundaries. We consider two different self-propulsion mechanisms, active stresses and treadmilling polymerisation, and we investigate how the active drop motion is altered by these surface forces. We find a highly non-linear response to forces that we characterise using drop velocity, drop shape, and the traction between the drop and the substrate.

2021

Spongelike Rigid Structures in Frictional Granular Packings

Kuang Liu, Jonathan E. Kollmer, Karen E. Daniels, J. M. Schwarz, and Silke Henkes

Phys. Rev. Lett. 126, 088002 - (2021) [arXiv]

We show how rigidity emerges in experiments on sheared two-dimensional frictional granular materials by using generalizations of two methods for identifying rigid structures. Both approaches, the force-based dynamical matrix and the topology-based rigidity percolation, agree with each other and identify similar rigid structures. As the system becomes jammed, at a critical contact number 2.4, a rigid backbone interspersed with floppy, particle-filled holes of a broad range of sizes emerges, creating a spongelike morphology. While the pressure within rigid structures always exceeds the pressure outside the rigid structures, they are not identified with the force chains of shear jamming. These findings highlight the need to focus on mechanical stability arising through arch structures and hinges at the mesoscale.

Spongelike Rigid Structures in Frictional Granular Packings

Kuang Liu, Jonathan E. Kollmer, Karen E. Daniels, J. M. Schwarz, and Silke Henkes

Phys. Rev. Lett. 126, 088002 - (2021) [arXiv]

We show how rigidity emerges in experiments on sheared two-dimensional frictional granular materials by using generalizations of two methods for identifying rigid structures. Both approaches, the force-based dynamical matrix and the topology-based rigidity percolation, agree with each other and identify similar rigid structures. As the system becomes jammed, at a critical contact number 2.4, a rigid backbone interspersed with floppy, particle-filled holes of a broad range of sizes emerges, creating a spongelike morphology. While the pressure within rigid structures always exceeds the pressure outside the rigid structures, they are not identified with the force chains of shear jamming. These findings highlight the need to focus on mechanical stability arising through arch structures and hinges at the mesoscale.

2020

Dense active matter model of motion patterns in confluent cell monolayers

Silke Henkes, Kaja Kostanjevec, J. Martin Collinson, Rastko Sknepnek & Eric Bertin

Nature Communications - (2020) [arXiv]

Epithelial cell monolayers show remarkable displacement and velocity correlations over distances of ten or more cell sizes that are reminiscent of supercooled liquids and active nematics. We show that many observed features can be described within the framework of dense active matter, and argue that persistent uncoordinated cell motility coupled to the collective elastic modes of the cell sheet is sufficient to produce swirl-like correlations. We obtain this result using both continuum active linear elasticity and a normal modes formalism, and validate analytical predictions with numerical simulations of two agent-based cell models, soft elastic particles and the self-propelled Voronoi model together with in-vitro experiments of confluent corneal epithelial cell sheets. Simulations and normal mode analysis perfectly match when tissue-level reorganisation occurs on times longer than the persistence time of cell motility. Our analytical model quantitatively matches measured velocity correlation functions over more than a decade with a single fitting parameter.

Dense active matter model of motion patterns in confluent cell monolayers

Silke Henkes, Kaja Kostanjevec, J. Martin Collinson, Rastko Sknepnek & Eric Bertin

Nature Communications - (2020) [arXiv]

Epithelial cell monolayers show remarkable displacement and velocity correlations over distances of ten or more cell sizes that are reminiscent of supercooled liquids and active nematics. We show that many observed features can be described within the framework of dense active matter, and argue that persistent uncoordinated cell motility coupled to the collective elastic modes of the cell sheet is sufficient to produce swirl-like correlations. We obtain this result using both continuum active linear elasticity and a normal modes formalism, and validate analytical predictions with numerical simulations of two agent-based cell models, soft elastic particles and the self-propelled Voronoi model together with in-vitro experiments of confluent corneal epithelial cell sheets. Simulations and normal mode analysis perfectly match when tissue-level reorganisation occurs on times longer than the persistence time of cell motility. Our analytical model quantitatively matches measured velocity correlation functions over more than a decade with a single fitting parameter.