arXiv subjects

Silke Henkes

Publications and source records attributed to Silke Henkes.

At least 19 recordsLinked to original sources

arXiv2026

Active elastic theory of self-aligning solids

Active disordered solids including dense human crowds and epithelial cells under confinement exhibit striking system-scale oscillatory spatiotemporal patterns. These are linked to a local feedback mechanism, self-alignment, that aligns the direction of a particle's motility vector to the total force. Simulations and experiments of solids made of such agents show these spontaneous oscillation patterns. Theoretically, they have been linked to both a nonlinear bifurcation and to selection of long-wavelength normal modes. Here we derive a closed nonlinear equation for the displacement field of active self-aligning 2d solids subject to angular noise. Along the normal modes of the solid, the dynamics of the mode amplitudes correspond to nonlinearly damped and stochastically driven harmonic oscillators. To linear order, we show that the system transitions from Active Brownian type correlated motion to oscillatory motion that increasingly condenses onto the lowest modes of the solid. We compare the analytical predictions for the mode spectra with simulations, finding excellent agreement approaching the transition from the disordered side. Strong nonlinearities manifest deep in the oscillating phase at strong alignment and small noise, consistent with the previous observations. At the continuum level, we derive a closed-form nonlinear wave equation for self-aligning solids. The transition to undamped oscillations is a second order dynamical phase transition driven by the competition between noise and alignment. At the linear level, we predict travelling acto-elastic waves, together with the emergence of system-scale oscillations for confined systems, consistent with observations in tissues and crowds. Our framework extends the understanding of self-aligning solids, which are pervasive among artificial and biological systems across multiple scales.

cond-mat.soft↗

arXiv2026

Exotic rheology of materials with active rearrangements

The flow of biological tissues during development is controlled through the active stresses generated by cells interacting with their mechanical environment in the tissue. Many developmental processes are driven by convergence-extension flows where the tissue has an emergent negative shear modulus and viscosity. This exotic rheology is generated through active T1 transitions where rearrangements are opposite the applied stress direction. Here, we introduce a mean-field elasto-plastic model which shows convergence-extension, based on the Hebraud-Lequeux model, that includes both passive and active elastic elements with opposite stress responses. We find that the introduction of active elements profoundly changes the rheology. Beyond a threshold fraction of active elements, it gives rise to non-monotonic flow curves and negative stresses at positive strain rates. Controlled by the active fraction and the stress diffusion rate, we find both yield stress materials and fluids, with either a positive or negative yield stress or viscosity. Furthermore, allowing for residual active stresses generates rheological curves with an asymmetry in strain rate dependence, resembling hysteresis. These features are characteristic of metamaterials, and highlight how biology uses disordered, active materials with exotic rheology.

cond-mat.soft↗

arXiv2025

Correlated cell movements drive epithelial finger formation

Epithelia form protective barriers in multicellular organisms. To maintain homeostasis, they must be able to regenerate and heal damaged areas. This occurs through collective cell migration, during which finger-like protrusions commonly appear. Whether these protrusions are driven by specialised leader cells, biochemical cues, or generic physical interactions remains unclear. Integrating in vitro imaging, agent-based simulations, and continuum modelling, we show that correlated active cell motion alone suffices to produce fingers. Leader cells, signalling, and proliferation modulate, but do not trigger, this pattern. Our results show that the key mechanism underlying a complex biological process can be understood using a general framework of the physics of dense active matter.

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arXiv2025

Long-range order in two-dimensional systems with fluctuating active stresses

In two-dimensional tissues, such as developing germ layers, pair-wise forces (or active stresses) arise from the contractile activity of the cytoskeleton, with dissipation provided by the three-dimensional surroundings. We show analytically how these pair-wise stochastic forces, unlike the particle-wise independent fluctuating forces usually considered in active matter systems, produce conserved centre-of-mass dynamics and so are able to damp large-wavelength displacement fluctuations in elastic systems. A consequence of this is the stabilisation of long-range translational order in two dimensions, in clear violation of the celebrated Mermin-Wagner theorem, and the emergence of hyperuniformity with a structure factor $S(q) \sim q^2$ in the $q \to 0$ limit. We then introduce two numerical cell tissue models which feature these pair-wise active forces. First a vertex model, in which the cell tissue is represented by a tiling of polygons where the edges represent cell junctions and with activity provided by stochastic junctional contractions. Second an active disk model, derived from active Brownian particles, but with pairs of equal and opposite stochastic forces between particles. We study the melting transition of these models and find a first-order phase transition between an ordered and a disordered phase in the disk model with active stresses. We confirm our analytical prediction of long-range order in both numerical models and show that hyperuniformity survives in the disordered phase, thus constituting a hidden order in our model tissue. Owing to the generality of this mechanism, we expect our results to be testable in living organisms, and to also apply to artificial systems with the same symmetry.

cond-mat.soft↗

arXiv2024

Emergent Mesoscale Correlations in Active Solids with Noisy Chiral Dynamics

We present the linear response theory for an elastic solid composed of active Brownian particles with intrinsic individual chirality, deriving both a normal mode formulation and a continuum elastic formulation. Using this theory, we compute analytically the velocity correlations and energy spectra under different conditions, showing an excellent agreement with simulations. We generate the corresponding phase diagram, identifying chiral and achiral disordered regimes (for high chirality or noise levels), as well as chiral and achiral states with mesoscopic-range order (for low chirality and noise). The chiral ordered states display mesoscopic spatial correlations and oscillating time correlations, but no wave propagation. In the high chirality regime, we find a peak in the elastic energy spectrum that leads to a non-monotonic behavior with increasing noise strength that is consistent with the emergence of the `hammering' state recently identified in chiral glasses. Finally, we show numerically that our theory, despite its linear response nature, can be applied beyond the idealized homogeneous solid assumed in our derivations. Indeed, by increasing the level of activity, we show that it remains a good approximation of the system dynamics until just below the melting transition. In addition, we show that there is still an excellent agreement between our analytical results and simulations when we extend our results to heterogeneous solids composed of mixtures of active particles with different intrinsic chirality and noise levels. Our work provides a thorough analytical and numerical description of the emergent states in a densely packed system of chiral self-propelled Brownian disks, thus allowing a detailed understanding of the phases and dynamics identified in a minimal chiral active systems.

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arXiv2024

Traveling strings of active dipolar colloids

We study an intriguing new type of self-assembled active colloidal polymer system in 3D. It is obtained from a suspension of Janus particles in an electric field that induces parallel dipoles in the particles as well as self-propulsion in the plane perpendicular to the field. At low packing fractions, in experiment, the particles self-assemble into 3D columns that are self-propelled in 2D. Explicit numerical simulations combining dipolar interactions and active self-propulsion find an activity dependent transition to a string phase by increasing dipole strength. We classify the collective dynamics of strings as a function of rotational and translational diffusion. Using an anisotropic version of the Rouse model of polymers with active driving, we analytically compute the strings' collective dynamics and centre of mass motion, which matches simulations and is consistent with experimental data. We also discover long range correlations of the fluctuations along the string contour that grow with the active persistence time, a purely active effect that disappears in the thermal limit.

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arXiv2024

Self-Aligning Polar Active Matter

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. Our aim is three-fold: (i)~underline the importance of self-alignment in active systems, especially in the context of dense populations of active units and active solids; (ii)~provide a unified mathematical and conceptual framework for the description of self-aligning systems; (iii)~discuss the common features and specific differences of the existing models of self-alignment. We conclude by discussing promising research avenues in which the concept of self-alignment could play a significant role.

cond-mat.soft↗

arXiv2023

Ductile-to-brittle transition and yielding in soft amorphous materials: perspectives and open questions

Soft amorphous materials are viscoelastic solids ubiquitously found around us, from clays and cementitious pastes to emulsions and physical gels encountered in food or biomedical engineering. Under an external deformation, these materials undergo a noteworthy transition from a solid to a liquid state that reshapes the material microstructure. This yielding transition was the main theme of a workshop held from January 9 to 13, 2023 at the Lorentz Center in Leiden. The manuscript presented here offers a critical perspective on the subject, synthesizing insights from the various brainstorming sessions and informal discussions that unfolded during this week of vibrant exchange of ideas. The result of these exchanges takes the form of a series of open questions that represent outstanding experimental, numerical, and theoretical challenges to be tackled in the near future.

cond-mat.soft↗

arXiv2023

Discriminating between individual-based models of collective cell motion in a benchmark flow geometry using standardised spatiotemporal patterns

Collectively coordinated cell migration plays a role in tissue embryogenesis, cancer, homeostasis and healing. To study these processes, different cell-based modelling approaches have been developed, ranging from lattice-based cellular automata to lattice-free models that treat cells as point-like particles or extended detailed cell shape contours. In the spirit of what Osborne et al. [PLOS Computational Biology, (2017) 13, 1-34] did for cellular tissue structure simulation models, we here compare five simulation models of collective cell migration, chosen to be representative in increasing order of included detail. They are Vicsek-Grégoire particles, Szabó-like particles, self-propelled Voronoi model, cellular Potts model, and multiparticle cells, where each model includes cell motility. We examine how these models compare when applied to the same biological problem, and what differences in behaviour are due to different model assumptions and abstractions. For that purpose, we use a benchmark that discriminates between complex material flow models, and that can be experimentally approached using cell cultures: the flow within a channel around a circular obstacle, that is, the geometry Stokes used in his historical 1851 experiment. For each model we explain how to best implement it; vary cell density, attraction force and alignment interaction; draw the resulting maps of velocity, density and deformation fields; and eventually discuss its respective advantages and limitations. We thus provide a recommendation on how to select a model to answer a given question, and we examine whether models of motile particles and motile cells display similar collective effects.

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arXiv2023

Graph-informed simulation-based inference for models of active matter

Many collective systems exist in nature far from equilibrium, ranging from cellular sheets up to flocks of birds. These systems reflect a form of active matter, whereby individual material components have internal energy. Under specific parameter regimes, these active systems undergo phase transitions whereby small fluctuations of single components can lead to global changes to the rheology of the system. Simulations and methods from statistical physics are typically used to understand and predict these phase transitions for real-world observations. In this work, we demonstrate that simulation-based inference can be used to robustly infer active matter parameters from system observations. Moreover, we demonstrate that a small number (from one to three) snapshots of the system can be used for parameter inference and that this graph-informed approach outperforms typical metrics such as the average velocity or mean square displacement of the system. Our work highlights that high-level system information is contained within the relational structure of a collective system and that this can be exploited to better couple models to data.

cond-mat.soft↗

arXiv2023

Mechano-chemical active feedback generates convergence extension in epithelial tissue

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 mechano-chemical active feedback mechanism coupled to a substrate via friction. Robust convergent extension behaviour 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.

cond-mat.soft↗

arXiv2022

The nonlinear motion of cells subject to external forces

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. Each self-propulsion mechanism gives rise to two main modes of motion: a long thin drop with zero traction in the bulk, mostly occurring under strong stretching forces, and a parabolic drop with finite traction in the bulk, mostly occurring under strong squeezing forces. In each case there is a sharp transition between parabolic, and long thin drops as a function of the applied forces and indications of drop break-up where large forces stretch the drop.

cond-mat.soft↗

arXiv2022

Generating active T1 transitions through mechanochemical feedback

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 external pulling. Using an idealized tissue patch comprising several active cells embedded in a matrix of passive hexagonal cells we identified an optimal range of pulling forces to trigger an active T1 event. We show that pulling also generates 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 re-organisation, in qualitative agreement with experiments on gastrulation in chick embryos.

physics.bio-ph↗

arXiv2021

Coordinated tractions increase the size of a collectively moving pack in a cell monolayer

Cells in an epithelial monolayer coordinate motion with their neighbors giving rise to collectively moving packs of sizes spanning multiple cell diameters. The physical mechanism controlling the pack size, however, remains unclear. A potential mechanism comes from assuming that cell-substrate traction forces persist over some time scale: with large enough persistence time, collective cell packs emerge. To test this hypothesis, we measured the velocity and net traction of each cell. The data showed that in addition to having some temporal persistence, tractions were spatially correlated, suggesting that cells coordinate with their neighbors to apply tractions in the same direction. Chemical inhibitors and activators of actomyosin contraction were used to determine effects of altering the traction persistence and alignment. Numerical simulations based on the self-propelled Voronoi model, augmented to include both traction persistence and alignment and calibrated against the experimental data, matched the experimentally measured pack size. The model identified that if there were no alignment of traction between neighboring cells, the size of the collective pack would be substantially smaller than observed in the experiments. Hence, combining experiments and a simple mechanical model, this study confirms the long-standing assumption of traction persistence and adds the notion of traction alignment between neighbors. Together, persistence and alignment are two factors controlling the size of a collectively moving cell pack.

physics.bio-ph↗

arXiv2020

Sponge-like rigid structures in frictional granular packings

We show how rigidity emerges in experiments of sheared 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 contact number of $z=2.4\pm 0.1$, a rigid backbone interspersed with floppy, particle-filled holes of a broad range of sizes emerges, creating a sponge-like morphology. We also find that the pressure within rigid structures always exceeds the pressure outside the rigid structures, i.e. that the backbone is load-bearing. These findings shows that it is necessary to go beyond mean-field theory to capture the physics of frictional jamming and also suggests that mechanical stability arises through arch structures and hinges at the mesoscale.

cond-mat.soft↗

arXiv2020

Dense active matter model of motion patterns in confluent cell monolayers

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.

cond-mat.soft↗

arXiv2018

Comment on "Field Theory for Amorphous Solids" by Eric DeGiuli

In a recent pair of papers, Eric DeGiuli has developed a field theory of glasses and granular materials based on the Edwards ensemble, extending our earlier theoretical framework. In this comment, we address a misconception regarding the relation between equiprobability of microstates and a flat measure in a field theory, which appears in the DeGiuli papers, and has often plagued discussions surrounding the Edwards ensemble. We point out that modeling this measure is the challenge addressed in both our earlier work and the recent DeGiuli work. Contrary to what is stated in the the DeGiuli papers, we did not assume a flat measure in our earlier work.

cond-mat.soft↗

arXiv2017

Dynamically Generated Patterns in Dense Suspensions of Active Filaments

We use Langevin dynamics simulations to study dynamical behaviour of a dense planar layer of active semi-flexible filaments. Using the strength of active force and the thermal persistence length as parameters, we map a detailed phase diagram and identify several non-equilibrium phases in this system. In addition to a slowly flowing melt phase, we observe that for sufficiently high activity, collective flow accompanied by signatures of local polar and nematic order appears in the system. This state is also characterised by strong density fluctuations. Furthermore, we identify an activity-driven cross-over from this state of coherently flowing bundles of filaments to a phase with no global flow, formed by individual filaments coiled into rotating spirals. This suggests a mechanism where the system responds to activity by changing the shape of active agents, an effect with no analogue in systems of active particles without internal degrees of freedom.

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